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Sample records for alphaproteobacteria

  1. Genome sequences of eight morphologically diverse Alphaproteobacteria.

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    Brown, Pamela J B; Kysela, David T; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-09-01

    The Alphaproteobacteria comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  2. Global Regulatory Pathways in the Alphaproteobacteria

    Energy Technology Data Exchange (ETDEWEB)

    none

    2007-04-27

    A major goal for microbiologists in the twenty-first century is to develop an understanding of the microbial cell in all its complexity. In addition to understanding the function of individual gene products we need to focus on how the cell regulates gene expression at a global level to respond to different environmental parameters. Development of genomic technologies such as complete genome sequencing, proteomics, and global comparisons of mRNA expression patterns allows us to begin to address this issue. This proposal focuses on a number of phylogenetically related bacteria that are involved in environmentally important processes such as carbon sequestration and bioremediation. Genome sequencing projects of a number of these bacteria have revealed the presence of a small family of regulatory genes found thus far only in the alpha-proteobacteria. These genes encode proteins that are related to the global regulatory protein RosR in Rhizobium etli, which is involved in determining nodulation competitiveness in this bacterium. Our goal is to examine the function of the proteins encoded by this gene family in several of the bacteria containing homologs to RosR. We will construct gene disruption mutations in a number of these bacteria and characterize the resulting mutant strains using two-dimensional gel electrophoresis and genetic and biochemical techniques. We will thus determine if the other proteins also function as global regulators of gene expression. Using proteomics methods we will identify the specific proteins whose expression varies depending on the presence or absence of the RosR homolog. Over fifty loci regulated by RosR have been identified in R. etli using transposon mutagenesis; this will serve as out benchmark to which we will compare the other regulons. We expect to identify genes regulated by RosR homologs in several bacterial species, including, but not limited to Rhodopseudomonas palustris and Sphingomonas aromaticivorans. In this way we will

  3. Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms

    OpenAIRE

    Gruber-Vodicka, Harald Ronald; Dirks, Ulrich; Leisch, Nikolaus; Baranyi, Christian; Stoecker, Kilian; Bulgheresi, Silvia; Heindl, Niels Robert; Horn, Matthias; Lott, Christian; Loy, Alexander; Wagner, Michael; Ott, Jörg

    2011-01-01

    Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria—the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria...

  4. Paracatenula, an ancient symbiosis between thiotrophic Alphaproteobacteria and catenulid flatworms.

    Science.gov (United States)

    Gruber-Vodicka, Harald Ronald; Dirks, Ulrich; Leisch, Nikolaus; Baranyi, Christian; Stoecker, Kilian; Bulgheresi, Silvia; Heindl, Niels Robert; Horn, Matthias; Lott, Christian; Loy, Alexander; Wagner, Michael; Ott, Jörg

    2011-07-19

    Harnessing chemosynthetic symbionts is a recurring evolutionary strategy. Eukaryotes from six phyla as well as one archaeon have acquired chemoautotrophic sulfur-oxidizing bacteria. In contrast to this broad host diversity, known bacterial partners apparently belong to two classes of bacteria--the Gamma- and Epsilonproteobacteria. Here, we characterize the intracellular endosymbionts of the mouthless catenulid flatworm genus Paracatenula as chemoautotrophic sulfur-oxidizing Alphaproteobacteria. The symbionts of Paracatenula galateia are provisionally classified as "Candidatus Riegeria galateiae" based on 16S ribosomal RNA sequencing confirmed by fluorescence in situ hybridization together with functional gene and sulfur metabolite evidence. 16S rRNA gene phylogenetic analysis shows that all 16 Paracatenula species examined harbor host species-specific intracellular Candidatus Riegeria bacteria that form a monophyletic group within the order Rhodospirillales. Comparing host and symbiont phylogenies reveals strict cocladogenesis and points to vertical transmission of the symbionts. Between 33% and 50% of the body volume of the various worm species is composed of bacterial symbionts, by far the highest proportion among all known endosymbiotic associations between bacteria and metazoans. This symbiosis, which likely originated more than 500 Mya during the early evolution of flatworms, is the oldest known animal-chemoautotrophic bacteria association. The distant phylogenetic position of the symbionts compared with other mutualistic or parasitic Alphaproteobacteria promises to illuminate the common genetic predispositions that have allowed several members of this class to successfully colonize eukaryote cells.

  5. Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

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    Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

    2012-01-01

    Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial

  6. Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria.

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    Lukasz Dziewit

    Full Text Available Several trap plasmids (enabling positive selection of transposition events were used to identify a pool of functional transposable elements (TEs residing in bacteria of the genus Paracoccus (Alphaproteobacteria. Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i 37 insertion sequences (ISs representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634, (ii a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv a transposable genomic island TnPpa1 (45 kb. Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1 and (ii structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family. We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value by horizontal gene transfer, which is considered the driving force of

  7. Phylogenetic analysis of HpnP reveals the origin of 2-methylhopanoid production in Alphaproteobacteria.

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    Ricci, J N; Michel, A J; Newman, D K

    2015-05-01

    Hopanoids are bacterial steroid-like lipids that can be preserved in the rock record on billion-year timescales. 2-Methylhopanoids are of particular interest to geobiologists because methylation is one of the few chemical modifications that remain after diagenesis and catagenesis. 2-Methylhopanes, the molecular fossils of 2-methylhopanoids, are episodically enriched in the rock record, but we do not have a robust interpretation for their abundance patterns. Here, we exploit the evolutionary record found in molecular sequences from extant organisms to reconstruct the biosynthetic history of 2-methylhopanoids using the C-2 hopanoid methylase, HpnP. Based on HpnP phylogenetic analysis, we find that 2-methylhopanoids originated in a subset of the Alphaproteobacteria. This conclusion is statistically robust and reproducible in multiple trials varying the outgroup, trimming stringency, and ingroup dataset used to infer the evolution of this protein family. The capacity for 2-methylhopanoid production was likely horizontally transferred from the Alphaproteobacteria into the Cyanobacteria after the Cyanobacteria's major divergences. Together, these results suggest that the ancestral function of 2-methylhopanoids was not related to oxygenic photosynthesis but instead to a trait already present in the Alphaproteobacteria. Moreover, given that early 2-methylhopane deposits could have been made solely by Alphaproteobacteria before the acquisition of hpnP by Cyanobacteria, and that the Alphaproteobacteria are thought to be ancestrally aerobic, we infer that 2-methylhopanoids likely arose after the oxygenation of the atmosphere. This finding is consistent with the geologic record-the oldest syngenetic 2-methylhopanes occur after the rise of oxygen, in middle Proterozoic strata of the Barney Creek Formation.

  8. The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis

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    Mengoni Alessio

    2010-04-01

    Full Text Available Abstract Background In the bacterium Caulobacter crescentus, CtrA coordinates DNA replication, cell division, and polar morphogenesis and is considered the cell cycle master regulator. CtrA activity varies during cell cycle progression and is modulated by phosphorylation, proteolysis and transcriptional control. In a phosphorylated state, CtrA binds specific DNA sequences, regulates the expression of genes involved in cell cycle progression and silences the origin of replication. Although the circuitry regulating CtrA is known in molecular detail in Caulobacter, its conservation and functionality in the other alpha-proteobacteria are still poorly understood. Results Orthologs of Caulobacter factors involved in the regulation of CtrA were systematically scanned in genomes of alpha-proteobacteria. In particular, orthologous genes of the divL-cckA-chpT-ctrA phosphorelay, the divJ-pleC-divK two-component system, the cpdR-rcdA-clpPX proteolysis system, the methyltransferase ccrM and transcriptional regulators dnaA and gcrA were identified in representative genomes of alpha-proteobacteria. CtrA, DnaA and GcrA binding sites and CcrM putative methylation sites were predicted in promoter regions of all these factors and functions controlled by CtrA in all alphas were predicted. Conclusions The regulatory cell cycle architecture was identified in all representative alpha-proteobacteria, revealing a high diversification of circuits but also a conservation of logical features. An evolutionary model was proposed where ancient alphas already possessed all modules found in Caulobacter arranged in a variety of connections. Two schemes appeared to evolve: a complex circuit in Caulobacterales and Rhizobiales and a simpler one found in Rhodobacterales.

  9. Similar diversity of Alphaproteobacteria and nitrogenase gene amplicons on two related Sphagnum mosses

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    Anastasia eBragina

    2012-01-01

    Full Text Available Sphagnum mosses represent a main component in ombrotrophic wetlands. They harbor a specific and diverse microbial community with essential functions for the host. To understand extend and degree of host specificity, Sphagnum fallax and S. angustifolium, two phylogenetically closely related species, which show distinct habitat preference with respect to the nutrient level, were analyzed by a multifaceted approach. Microbial fingerprints obtained by PCR-SSCP (single-strand conformation polymorphism using universal, group-specific and functional primers were highly similar. Similarity was confirmed for colonization patterns obtained by fluorescence in situ hybridization (FISH coupled with confocal laser scanning microscopy (CLSM: Alphaproteobacteria were the main colonizers inside the hyaline cells of Sphagnum leaves. A deeper survey of Alphaproteobacteria by 16S rRNA gene amplicon sequencing reveals a high diversity with Acidocella, Acidisphaera, Rhodopila and Phenylobacterium as major genera for both mosses. Pathogen defense and nitrogen fixation are important functions of Sphagnum-associated bacteria, which are fulfilled by microbial communities of both Sphagna in a similar way. NifH libraries of Sphagnum-associated microbial communities were characterized by high diversity and abundance of Alphaproteobacteria but contained also diverse amplicons of other taxa, e.g. Cyanobacteria, Geobacter and Spirochaeta. Statistically significant differences between the microbial communities of both Sphagnum species could not be discovered in any of the experimental approach. Our results show that the same close relationship, which exists between the physical, morphological and chemical characteristics of Sphagnum mosses and the ecology and function of bog ecosystems, also connects moss plantlets with their associated bacterial communities.

  10. Plasmids of Carotenoid-Producing Paracoccus spp. (Alphaproteobacteria) - Structure, Diversity and Evolution

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    Maj, Anna; Dziewit, Lukasz; Czarnecki, Jakub; Wlodarczyk, Miroslawa; Baj, Jadwiga; Skrzypczyk, Grazyna; Giersz, Dorota; Bartosik, Dariusz

    2013-01-01

    Plasmids are components of many bacterial genomes. They enable the spread of a large pool of genetic information via lateral gene transfer. Many bacterial strains contain mega-sized replicons and these are particularly common in Alphaproteobacteria. Considerably less is known about smaller alphaproteobacterial plasmids. We analyzed the genomes of 14 such plasmids residing in 4 multireplicon carotenoid-producing strains of the genus Paracoccus (Alphaproteobacteria): P. aestuarii DSM 19484, P. haeundaensis LG P-21903, P. marcusii DSM 11574 and P. marcusii OS22. Comparative analyses revealed mosaic structures of the plasmids and recombinational shuffling of diverse genetic modules involved in (i) plasmid replication, (ii) stabilization (including toxin-antitoxin systems of the relBE/parDE, tad-ata, higBA, mazEF and toxBA families) and (iii) mobilization for conjugal transfer (encoding relaxases of the MobQ, MobP or MobV families). A common feature of the majority of the plasmids is the presence of AT-rich sequence islets (located downstream of exc1-like genes) containing genes, whose homologs are conserved in the chromosomes of many bacteria (encoding e.g. RelA/SpoT, SMC-like proteins and a retron-type reverse transcriptase). The results of this study have provided insight into the diversity and plasticity of plasmids of Paracoccus spp., and of the entire Alphaproteobacteria. Some of the identified plasmids contain replication systems not described previously in this class of bacteria. The composition of the plasmid genomes revealed frequent transfer of chromosomal genes into plasmids, which significantly enriches the pool of mobile DNA that can participate in lateral transfer. Many strains of Paracoccus spp. have great biotechnological potential, and the plasmid vectors constructed in this study will facilitate genetic studies of these bacteria. PMID:24260361

  11. Nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in Alphaproteobacteria

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    Olga V Tsoy

    2016-08-01

    Full Text Available Biological nitrogen fixation plays a crucial role in the nitrogen cycle. An ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of Bacteria and Archaea. Being a complex and sensitive process, nitrogen fixation requires a complicated regulatory system, also, on the level of transcription. The transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class Alphaproteobacteria. This regulatory network includes the activator of nitrogen fixation NifA, working in tandem with the alternative sigma-factor RpoN as well as oxygen-responsive regulatory systems, one-component regulators FnrN/FixK and two-component system FixLJ. Here we used a comparative genomics analysis for in silico study of the transcriptional regulatory network in 50 genomes of Alphaproteobacteria. We extended the known regulons and proposed the scenario for the evolution of the nitrogen fixation transcriptional network. The reconstructed network substantially expands the existing knowledge of transcriptional regulation in nitrogen-fixing microorganisms and can be used for genetic experiments, metabolic reconstruction, and evolutionary analysis.

  12. Whole-Proteome Analysis of Twelve Species of Alphaproteobacteria Links Four Pathogens

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    Yunyun Zhou

    2013-11-01

    Full Text Available Thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and sequences of millions more organisms will become available in the coming years. This wealth of genetic information will provide numerous opportunities to enhance our understanding of these organisms including a greater understanding of relationships among species. Researchers have used 16S rRNA and other gene sequences to study the evolutionary origins of bacteria, but these strategies do not provide insight into the sharing of genes among bacteria via horizontal transfer. In this work we use an open source software program called pClust to cluster proteins from the complete proteomes of twelve species of Alphaproteobacteria and generate a dendrogram from the resulting orthologous protein clusters. We compare the results with dendrograms constructed using the 16S rRNA gene and multiple sequence alignment of seven housekeeping genes. Analysis of the whole proteomes of these pathogens grouped Rickettsia typhi with three other animal pathogens whereas conventional sequence analysis failed to group these pathogens together. We conclude that whole-proteome analysis can give insight into relationships among species beyond their phylogeny, perhaps reflecting the effects of horizontal gene transfer and potentially providing insight into the functions of shared genes by means of shared phenotypes.

  13. Identification of bacteria from clinical samples using Bartonella alpha-Proteobacteria growth medium.

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    Cadenas, Maria B; Maggi, Ricardo G; Diniz, Pedro P V P; Breitschwerdt, Kyle T; Sontakke, Sushama; Breithschwerdt, Edward B

    2007-11-01

    In an effort to overcome historical problems associated with the isolation of Bartonella species from animal and human blood samples, our laboratory developed a novel, chemically modified, insect-based, liquid culture medium (Bartonella alpha-Proteobacteria growth medium, BAPGM). In this study, we describe the isolation of non-Bartonella bacteria from aseptically obtained human blood and tissue samples that were inoculated into BAPGM pre-enrichment culture medium, and were obtained during attempts to define each individuals Bartonella infection status. After incubation for at least 7 days in liquid BAPGM, pre-enriched inoculums were sub-cultured onto a BAPGM/blood agar plate. Bacterial DNA was extracted from pooled plated colonies and amplified using conventional PCR targeting the 16S rRNA gene. Subsequently, amplicons were cloned, sequenced and compared to GenBank database sequences using the BLAST program. Regardless of the patient's Bartonella status, seventeen samples generated only one 16S rDNA sequence, representing the following genera: Arthrobacter, Bacillus, Bartonella, Dermabacter, Methylobacterium, Propionibacterium, Pseudomonas, Staphylococcus and bacteria listed as "non-cultured" in the GenBank database. Alkalibacterium, Arthrobacter, Erwinia, Kineococcus, Methylobacterium, Propionibacterium, Sphingomonas, and Staphylococcus were isolated from nine Bartonella-infected individuals. Co-isolation of Acinetobacter, Sphingomonas, Staphylococcus spp. and bacteria listed as "non-cultured" in the GenBank database was achieved for four samples in which Bartonella spp. were not detected. Despite the phylogenetic limitations of using partial 16S rRNA gene sequencing for species and strain identification, the investigational methodology described in this study may provide a complementary approach for the isolation and identification of bacteria from patient samples.

  14. Description of Hyalodiscus flabellus sp. nov. (Vampyrellida, Rhizaria) and Identification of its Bacterial Endosymbiont, "Candidatus Megaira polyxenophila" (Rickettsiales, Alphaproteobacteria).

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    Hess, Sebastian

    2017-02-01

    The genus Hyalodiscus Hertwig and Lesser, 1874 comprises naked freshwater amoebae with a unique set of characters, namely a vibrant orange-red colour, a discoid or fan-shaped morphology, and a characteristic rolling locomotion. Some species feed on the chloroplasts of green algae and were regarded as relatives of Vampyrella Cienkowski, 1865. However, because of striking morphological differences and the lack of molecular data, the exact relationship of Hyalodiscus to vampyrellids is still obscure. Here, I describe Hyalodiscus flabellus sp. nov., a bright orange, fan-shaped amoeba feeding on Oedogonium (Chlorophyceae), which likely is a close relative of the type species H. rubicundus Hertwig and Lesser, 1874. Sequence comparisons of the SSU rRNA gene revealed that H. flabellus belongs to a deep-branching, so far uncharacterised lineage of the order Vampyrellida (Rhizaria), here defined as family Hyalodiscidae POCHE, 1913. Based on these results, the systematic position of the genus Hyalodiscus could be finally clarified, accompanied by the revision of relevant diagnoses and a taxonomic summary. Furthermore, the work reports on endosymbiotic bacteria inhabiting the cytoplasm of H. flabellus, which were identified as "Candidatus Megaira polyxenophila" (Rickettsiales, Alphaproteobacteria) using the full cycle rRNA approach with newly designed FISH probes for this widespread endosymbiotic bacterium.

  15. DNA binding of the cell cycle transcriptional regulator GcrA depends on N6-adenosine methylation in Caulobacter crescentus and other Alphaproteobacteria.

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    Fioravanti, Antonella; Fumeaux, Coralie; Mohapatra, Saswat S; Bompard, Coralie; Brilli, Matteo; Frandi, Antonio; Castric, Vincent; Villeret, Vincent; Viollier, Patrick H; Biondi, Emanuele G

    2013-05-01

    Several regulators are involved in the control of cell cycle progression in the bacterial model system Caulobacter crescentus, which divides asymmetrically into a vegetative G1-phase (swarmer) cell and a replicative S-phase (stalked) cell. Here we report a novel functional interaction between the enigmatic cell cycle regulator GcrA and the N6-adenosine methyltransferase CcrM, both highly conserved proteins among Alphaproteobacteria, that are activated early and at the end of S-phase, respectively. As no direct biochemical and regulatory relationship between GcrA and CcrM were known, we used a combination of ChIP (chromatin-immunoprecipitation), biochemical and biophysical experimentation, and genetics to show that GcrA is a dimeric DNA-binding protein that preferentially targets promoters harbouring CcrM methylation sites. After tracing CcrM-dependent N6-methyl-adenosine promoter marks at a genome-wide scale, we show that these marks recruit GcrA in vitro and in vivo. Moreover, we found that, in the presence of a methylated target, GcrA recruits the RNA polymerase to the promoter, consistent with its role in transcriptional activation. Since methylation-dependent DNA binding is also observed with GcrA orthologs from other Alphaproteobacteria, we conclude that GcrA is the founding member of a new and conserved class of transcriptional regulators that function as molecular effectors of a methylation-dependent (non-heritable) epigenetic switch that regulates gene expression during the cell cycle.

  16. DNA binding of the cell cycle transcriptional regulator GcrA depends on N6-adenosine methylation in Caulobacter crescentus and other Alphaproteobacteria.

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    Antonella Fioravanti

    2013-05-01

    Full Text Available Several regulators are involved in the control of cell cycle progression in the bacterial model system Caulobacter crescentus, which divides asymmetrically into a vegetative G1-phase (swarmer cell and a replicative S-phase (stalked cell. Here we report a novel functional interaction between the enigmatic cell cycle regulator GcrA and the N6-adenosine methyltransferase CcrM, both highly conserved proteins among Alphaproteobacteria, that are activated early and at the end of S-phase, respectively. As no direct biochemical and regulatory relationship between GcrA and CcrM were known, we used a combination of ChIP (chromatin-immunoprecipitation, biochemical and biophysical experimentation, and genetics to show that GcrA is a dimeric DNA-binding protein that preferentially targets promoters harbouring CcrM methylation sites. After tracing CcrM-dependent N6-methyl-adenosine promoter marks at a genome-wide scale, we show that these marks recruit GcrA in vitro and in vivo. Moreover, we found that, in the presence of a methylated target, GcrA recruits the RNA polymerase to the promoter, consistent with its role in transcriptional activation. Since methylation-dependent DNA binding is also observed with GcrA orthologs from other Alphaproteobacteria, we conclude that GcrA is the founding member of a new and conserved class of transcriptional regulators that function as molecular effectors of a methylation-dependent (non-heritable epigenetic switch that regulates gene expression during the cell cycle.

  17. Genome and metabolic network of Candidatus Phaeomarinobacter ectocarpi Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

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    Simon M Dittami

    2014-07-01

    Full Text Available Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of Candidatus Phaeomarinobacter ectocarpi Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The Ca. P. ectocarpi genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, Ca. P. ectocarpi has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥ 97% identity have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus Phaeomarinobacter may comprise several species, which may colonize different niches.

  18. Isolation, cultivation and genomic analysis of magnetosome biomineralization genes of a new genus of South-seeking magnetotactic cocci within the Alphaproteobacteria

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    Morillo, Viviana [Universidade Federal do Rio de Janeiro; Abreu, Fernanda [Universidade Federal do Rio de Janeiro; Araujo, Ana C [Universidade Federal do Rio de Janeiro; de Almeida, Luiz G [Laboratorio Nacional de Computacao Cientifica; Enrich-Prast, Alex [Universidade Federal do Rio de Janeiro; Farina, Marcos [Universidade Federal do Rio de Janeiro; de Vasconcelos, Ana T [Laboratorio Nacional de Computacao Cientifica; Bazylinski, Dennis A [Ames Laboratory; Lins, Ulysses [Universidade Federal do Rio de Janeiro

    2014-01-01

    Although magnetotactic bacteria (MTB) are ubiquitous in aquatic habitats, they are still considered fastidious microorganisms with regard to growth and cultivation with only a relatively low number of axenic cultures available to date. Here, we report the first axenic culture of an MTB isolated in the Southern Hemisphere (Itaipu Lagoon in Rio de Janeiro, Brazil). Cells of this new isolate are coccoid to ovoid in morphology and grow microaerophilically in semi-solid medium containing an oxygen concentration ([O2]) gradient either under chemoorganoheterotrophic or chemolithoautotrophic conditions. Each cell contains a single chain of approximately 10 elongated cuboctahedral magnetite (Fe3O4) magnetosomes. Phylogenetic analysis based on the 16S rRNA gene sequence shows that the coccoid MTB isolated in this study represents a new genus in the Alphaproteobacteria; the name Magnetofaba australis strain IT-1 is proposed. Preliminary genomic data obtained by pyrosequencing shows that M. australis strain IT-1 contains a genomic region with genes involved in biomineralization similar to those found in the most closely related magnetotactic cocci Magnetococcus marinus strain MC-1. However, organization of the magnetosome genes differs from M. marinus.

  19. Serial testing from a 3-day collection period by use of the Bartonella Alphaproteobacteria growth medium platform may enhance the sensitivity of Bartonella species detection in bacteremic human patients.

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    Pultorak, Elizabeth L; Maggi, Ricardo G; Mascarelli, Patricia E; Breitschwerdt, Edward B

    2013-06-01

    Patients with infection from bacteremic Bartonella spp., tested using Bartonella Alphaproteobacteria growth medium (BAPGM), were retrospectively categorized into one of two groups that included those whose blood was collected once (group 1; n = 55) or three times (group 2; n = 36) within a 1-week period. Overall, 19 patients (20.8%) were PCR positive for one or more Bartonella spp. using the BAPGM platform. Seven patients (12.7%) in group 1 tested positive, and 12 patients (33.3%) in group 2 tested positive. Detection was improved when the patients were tested three times within a 1-week period (odds ratio, 3.4 [95% confidence interval, 1.2 to 9.8]; P = 0.02). Obtaining three sequential blood samples during a 1-week period should be considered a diagnostic approach when bartonellosis is suspected.

  20. Bartonella apis sp. nov., a honey bee gut symbiont of the class Alphaproteobacteria.

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    Kešnerová, Lucie; Moritz, Roxane; Engel, Philipp

    2016-01-01

    Here, we report the culture and characterization of an alphaproteobacterium of the order Rhizobiales, isolated from the gut of the honey bee Apis mellifera. Strain PEB0122T shares >95 % 16S rRNA gene sequence similarity with species of the genus Bartonella, a group of mammalian pathogens transmitted by bloodsucking arthropods. Phylogenetic analyses showed that PEB0122T and related strains from the honey bee gut form a sister clade of the genus Bartonella. Optimal growth of strain PEB0122T was obtained on solid media supplemented with defibrinated sheep blood under microaerophilic conditions at 35-37 °C, which is consistent with the cultural characteristics of other species of the genus Bartonella. Reduced growth of strain PEB0122T also occurred under aerobic conditions. The rod-shaped cells of strain PEB0122T had a mean length of 1.2-1.8 μm and revealed hairy surface structures. Strain PEB0122T was positive for catalase, cytochrome c oxidase, urease and nitrate reductase. The fatty acid composition was comparable to those of other species of the genus Bartonella, with palmitic acid (C16 : 0) and isomers of 18- and 19-carbon chains being the most abundant. The genomic DNA G+C content of PEB0122T was determined to be about 45.5 mol%. The high 16S rRNA gene sequence similarity with species of Bartonella and its close phylogenetic position suggest that strain PEB0122T represents a novel species within the genus Bartonella, for which we propose the name Bartonella apis sp. nov. The type strain is PEB0122T ( = NCIMB 14961T = DSM 29779T).

  1. Asaia krungthepensis sp. nov., an acetic acid bacterium in the alpha-Proteobacteria.

    Science.gov (United States)

    Yukphan, Pattaraporn; Potacharoen, Wanchern; Tanasupawat, Somboon; Tanticharoen, Morakot; Yamada, Yuzo

    2004-03-01

    Three bacterial strains were isolated from flowers collected in Bangkok, Thailand, by an enrichment-culture approach for acetic acid bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were located in the lineage of the genus Asaia but constituted a cluster separate from the type strains of Asaia bogorensis and Asaia siamensis. The DNA base composition of the isolates was 60.2-60.5 mol% G+C, with a range of 0.3 mol%. The isolates constituted a taxon separate from Asaia bogorensis and Asaia siamensis on the basis of DNA-DNA relatedness. The isolates had morphological, physiological, biochemical and chemotaxonomic characteristics similar to those of the type strains of Asaia bogorensis and Asaia siamensis, but the isolates grew on maltose. The major ubiquinone was Q(10). On the basis of the results obtained, the name Asaia krungthepensis sp. nov. is proposed for the isolates. The type strain is isolate AA08(T) (=BCC 12978(T)=TISTR 1524(T)=NBRC 100057(T)=NRIC 0535(T)), which had a DNA G+C content of 60.3 mol% and was isolated from a heliconia flower ('paksaasawan' in Thai; Heliconia sp.) collected in Bangkok, Thailand.

  2. Detection of Wolbachia (Alphaproteobacteria: rickettsiales in three species of terrestrial isopods (crustacea: isopoda: oniscidea in Brazil

    Directory of Open Access Journals (Sweden)

    Bianca Laís Zimmermann

    2012-06-01

    Full Text Available Terrestrial isopods are widely infected with Wolbachia. However, little is known about the presence of bacteria in the Neotropical species. The objective of this study was to test the hypothesis of presence of Wolbachia infection in the native species of terrestrial isopods, Atlantoscia floridana and Circoniscus bezzii, and in the introduced species Burmoniscus meeusei.

  3. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    OpenAIRE

    Brown, Pamela J.B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  4. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    Science.gov (United States)

    Brown, Pamela J. B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V.

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium. PMID:21705585

  5. Isolation and characterization of Reyranella massiliensis gen. nov., sp. nov. from freshwater samples by using an amoeba co-culture procedure.

    Science.gov (United States)

    Pagnier, Isabelle; Raoult, Didier; La Scola, Bernard

    2011-09-01

    The analysis of three water samples from two cooling towers and one river allowed us to isolate three strains of a novel species of the class Alphaproteobacteria which is phylogenetically related to uncultured alphaproteobacteria. Based upon 16S rRNA gene sequence analysis and phenotypic characterization, we propose to name this novel species Reyranella massiliensis gen. nov., sp. nov., type strain 521(T) ( = CSUR P115(T)  = DSM 23428(T)). The most closely related cultivable micro-organism to this novel bacterium is a member of the genus Magnetospirillum.

  6. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion.

    Directory of Open Access Journals (Sweden)

    Kalliopi Georgiades

    Full Text Available BACKGROUND: The evolution of the Alphaproteobacteria and origin of the mitochondria are topics of considerable debate. Most studies have placed the mitochondria ancestor within the Rickettsiales order. Ten years ago, the bacterium Odyssella thessalonicensis was isolated from Acanthamoeba spp., and the 16S rDNA phylogeny placed it within the Rickettsiales. Recently, the whole genome of O. thessalonicensis has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins. METHODOLOGY/PRINCIPAL FINDINGS: The results suggested that the O. thessalonicensis emerged between the Rickettsiales and other Alphaproteobacteria. The mitochondrial proteins of the Reclinomonas americana have been used to locate the phylogenetic position of the mitochondrion ancestor within the Alphaproteobacteria tree. Using the K tree score method, nine mitochondrion-encoded proteins, whose phylogenies were congruent with the Alphaproteobacteria phylogenomic tree, have been selected and concatenated for Bayesian and Maximum Likelihood phylogenies. The Reclinomonas americana mitochondrion is a sister taxon to the free-living bacteria Candidatus Pelagibacter ubique, and together, they form a clade that is deeply rooted in the Rickettsiales clade. CONCLUSIONS/SIGNIFICANCE: The Reclinomonas americana mitochondrion phylogenomic study confirmed that mitochondria emerged deeply in the Rickettsiales clade and that they are closely related to Candidatus Pelagibacter ubique.

  7. [Sexual reproduction of insects is regulated by cytoplasmic bacteria].

    Science.gov (United States)

    Markov, A V; Zakharov, I A

    2005-01-01

    The effects have been considered that the intracellular symbiotic alpha-proteobacteria Wolbachia pipientis induces in its hosts, such as insects and other arthropods: cytoplasmic incompatibility upon mating, feminization, parthenogenesis, and androcide. Specific features of the bacterium genome and possible mechanisms of its action on hosts are discussed.

  8. In-Situ Incubation of Iron-Sulfide Mineral in Seawater Reveals Colonization by Iron-Oxidizing Gammaproteobacteria and Zetaproteobacteria.

    Science.gov (United States)

    Barco, R. A.; Ramírez, G. A.; Sylvan, J. B.; Edwards, K. J.

    2015-12-01

    Sulfide mineral precipitation occurs at mid-ocean ridge (MOR) spreading centers, both in the form of plume particles and massive sulfide structures. A common constituent of MOR sulfide mineral is pyrrhotite (Fe1-xS). This mineral was chosen as a substrate for in-situ incubation studies in the shallow waters of Catalina Islands, CA to investigate the colonization of iron-oxidizing bacteria. Gammaproteobacteria and Alphaproteobacteria largely dominated the bacterial community on pyrrhotite samples incubated in the water column. Pyrrhotite samples incubated at the sediment/water column interface showed more even dominance by Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria and Bacteroidetes. Cultivations that originated from these pyrrhotite samples resulted in the enrichment of Zetaproteobacteria with either twisted-stalks (Mariprofundus) or sheath structures. Additionally, a candidate novel Gammaproteobacterium was isolated and shown to grow autotrophically via the oxidation of iron.

  9. Effects of prokaryotic diversity changes on hydrocarbon degradation rates and metal partitioning during bioremediation of contaminated anoxic marine sediments.

    Science.gov (United States)

    Rocchetti, Laura; Beolchini, Francesca; Hallberg, Kevin B; Johnson, D Barrie; Dell'Anno, Antonio

    2012-08-01

    We investigated changes of prokaryotic diversity during bioremediation experiments carried out on anoxic marine sediments characterized by high hydrocarbon and metal content. Microcosms containing contaminated sediments were amended with lactose and acetate and incubated in anaerobic conditions up to 60 d at 20 or 35 °C. Microcosms displaying higher degradation efficiency of hydrocarbons were characterized by the dominance of Alphaproteobacteria and Methanosarcinales and the lack of gene sequences belonging to known hydrocarbonoclastic bacteria. Multivariate analyses support the hypothesis that Alphaproteobacteria are important for hydrocarbon degradation and highlight a potential synergistic effect of archaea and bacteria in changes of metal partitioning. Overall, these results point out that the identification of changes in the prokaryotic diversity during bioremediation of contaminated marine sediments is not only important for the improvement of bio-treatment performance towards hydrocarbons, but also for a better comprehension of changes occurring in metal partitioning which affect their mobility and toxicity.

  10. Genome Analysis of a Novel Broad Host Range Proteobacteria Phage Isolated from a Bioreactor Treating Industrial Wastewater

    Science.gov (United States)

    de Leeuw, Marina; Baron, Maayan; Brenner, Asher; Kushmaro, Ariel

    2017-01-01

    Bacteriophages are viruses that infect bacteria, and consequently they have a major impact on the development of a microbial population. In this study, the genome of a novel broad host range bacteriophage, Aquamicrobium phage P14, isolated from a wastewater treatment plant, was analyzed. The Aquamicrobium phage P14 was found to infect members of different Proteobacteria classes (Alphaproteobacteria and Betaproteobacteria). This phage contains a 40,551 bp long genome and 60% of its genes had blastx hits. Furthermore, the bacteriophage was found to share more than 50% of its genes with several podoviruses and has the same gene order as other polyvalent bacteriophages. The results obtained in this study led to the conclusion that indeed general features of the genome of the Aquamicrobium phage P14 are shared with other broad host range bacteriophages, however further analysis of the genome is needed in order to identify the specific mechanisms which enable the bacteriophage to infect both Alphaproteobacteria and Betaproteobacteria. PMID:28106814

  11. Autoregulation of Nodulation Interferes with Impacts of Nitrogen Fertilization Levels on the Leaf-Associated Bacterial Community in Soybeans ▿ †

    OpenAIRE

    2011-01-01

    The diversities leaf-associated bacteria on nonnodulated (Nod−), wild-type nodulated (Nod+), and hypernodulated (Nod++) soybeans were evaluated by clone library analyses of the 16S rRNA gene. To analyze the impact of nitrogen fertilization on the bacterial leaf community, soybeans were treated with standard nitrogen (SN) (15 kg N ha−1) or heavy nitrogen (HN) (615 kg N ha−1) fertilization. Under SN fertilization, the relative abundance of Alphaproteobacteria was significantly higher in Nod− an...

  12. A clinical Acanthamoeba isolate harboring two distinct bacterial endosymbionts.

    Science.gov (United States)

    Müller, Anneliese; Walochnik, Julia; Wagner, Martin; Schmitz-Esser, Stephan

    2016-10-01

    Acanthamoebae feed on bacteria but are also frequent hosts of bacterial symbionts. Here, we describe the stable co-occurrence of two symbionts, one affiliated to the genus Parachlamydia and the other to the candidate genus Paracaedibacter (Alphaproteobacteria), within a clinical isolate of Acanthamoeba hatchetti genotype T4. We performed fluorescence in situ hybridization (FISH) and transmission electron microscopy (TEM) to describe this symbiosis. Our study adds to other reports of simultaneous co-occurrence of two symbionts within one Acanthamoeba cell.

  13. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade

    OpenAIRE

    Beyersmann, Paul G.; Chertkov, Olga; Petersen, Jörn; Fiebig, Anne; Chen, Amy; Pati, Amrita; Ivanova, Natalia; Lapidus, Alla; Lynne A Goodwin; Chain, Patrick; Detter, John C.; Rohde, Manfred; Gronow, Sabine; Kyrpides, Nikos C; Woyke, Tanja

    2013-01-01

    In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. ...

  14. Autoregulation of nodulation interferes with impacts of nitrogen fertilization levels on the leaf-associated bacterial community in soybeans.

    Science.gov (United States)

    Ikeda, Seishi; Anda, Mizue; Inaba, Shoko; Eda, Shima; Sato, Shusei; Sasaki, Kazuhiro; Tabata, Satoshi; Mitsui, Hisayuki; Sato, Tadashi; Shinano, Takuro; Minamisawa, Kiwamu

    2011-03-01

    The diversities leaf-associated bacteria on nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans were evaluated by clone library analyses of the 16S rRNA gene. To analyze the impact of nitrogen fertilization on the bacterial leaf community, soybeans were treated with standard nitrogen (SN) (15 kg N ha(-1)) or heavy nitrogen (HN) (615 kg N ha(-1)) fertilization. Under SN fertilization, the relative abundance of Alphaproteobacteria was significantly higher in Nod(-) and Nod(++) soybeans (82% to 96%) than in Nod(+) soybeans (54%). The community structure of leaf-associated bacteria in Nod(+) soybeans was almost unaffected by the levels of nitrogen fertilization. However, differences were visible in Nod(-) and Nod(++) soybeans. HN fertilization drastically decreased the relative abundance of Alphaproteobacteria in Nod(-) and Nod(++) soybeans (46% to 76%) and, conversely, increased those of Gammaproteobacteria and Firmicutes in these mutant soybeans. In the Alphaproteobacteria, cluster analyses identified two operational taxonomic units (OTUs) (Aurantimonas sp. and Methylobacterium sp.) that were especially sensitive to nodulation phenotypes under SN fertilization and to nitrogen fertilization levels. Arbuscular mycorrhizal infection was not observed on the root tissues examined, presumably due to the rotation of paddy and upland fields. These results suggest that a subpopulation of leaf-associated bacteria in wild-type Nod(+) soybeans is controlled in similar ways through the systemic regulation of autoregulation of nodulation, which interferes with the impacts of N levels on the bacterial community of soybean leaves.

  15. Bacterial communities of surface mixed layer in the Pacific sector of the western Arctic Ocean during sea-ice melting.

    Directory of Open Access Journals (Sweden)

    Dukki Han

    Full Text Available From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1 surface seawater, (2 ice core, and (3 melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting.

  16. Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation.

    Science.gov (United States)

    Yang, Gang; Xu, Zhenjiang; Tian, Xiangli; Dong, Shuanglin; Peng, Mo

    2015-02-27

    β-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal microbiota. High-throughput sequencing techniques provide an opportunity for the identification and characterization of microbes. In this study, we investigated the intestinal microbial community composition, interaction among species, and intestinal immune genes in sea cucumber fed with diet supplemented with or without β-glucan supplementation. The results show that the intestinal dominant classes in the control group are Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, whereas Alphaproteobacteria, Flavobacteriia, and Verrucomicrobiae are enriched in the β-glucan group. Dietary β-glucan supplementation promoted the proliferation of the family Rhodobacteraceae of the Alphaproteobacteria class and the family Verrucomicrobiaceae of the Verrucomicrobiae class and reduced the relative abundance of the family Flavobacteriaceae of Flavobacteria class. The ecological network analysis suggests that dietary β-glucan supplementation can alter the network interactions among different microbial functional groups by changing the microbial community composition and topological roles of the OTUs in the ecological network. Dietary β-glucan supplementation has a positive impact on immune responses of the intestine of sea cucumber by activating NF-κB signaling pathway, probably through modulating the balance of intestinal microbiota.

  17. Different Bacterial Communities Involved in Peptide Decomposition between Normoxic and Hypoxic Coastal Waters

    Science.gov (United States)

    Liu, Shuting; Wawrik, Boris; Liu, Zhanfei

    2017-01-01

    Proteins and peptides are key components of the labile dissolved organic matter pool in marine environments. Knowing which types of bacteria metabolize peptides can inform the factors that govern peptide decomposition and further carbon and nitrogen remineralization in marine environments. A 13C-labeled tetrapeptide, alanine-valine-phenylalanine-alanine (AVFA), was added to both surface (normoxic) and bottom (hypoxic) seawater from a coastal station in the northern Gulf of Mexico for a 2-day incubation experiment, and bacteria that incorporated the peptide were identified using DNA stable isotope probing (SIP). The decomposition rate of AVFA in the bottom hypoxic seawater (0.018–0.035 μM h-1) was twice as fast as that in the surface normoxic seawater (0.011–0.017 μM h-1). SIP experiments indicated that incorporation of 13C was highest among the Flavobacteria, Sphingobacteria, Alphaproteobacteria, Acidimicrobiia, Verrucomicrobiae, Cyanobacteria, and Actinobacteria in surface waters. In contrast, highest 13C-enrichment was mainly observed in several Alphaproteobacteria (Thalassococcus, Rhodobacteraceae, Ruegeria) and Gammaproteobacteria genera (Colwellia, Balneatrix, Thalassomonas) in the bottom water. These data suggest that a more diverse group of both oligotrophic and copiotrophic bacteria may be involved in metabolizing labile organic matter such as peptides in normoxic coastal waters, and several copiotrophic genera belonging to Alphaproteobacteria and Gammaproteobacteria and known to be widely distributed may contribute to faster peptide decomposition in the hypoxic waters. PMID:28326069

  18. Bacterial communities of surface mixed layer in the Pacific sector of the western Arctic Ocean during sea-ice melting.

    Science.gov (United States)

    Han, Dukki; Kang, Ilnam; Ha, Ho Kyung; Kim, Hyun Cheol; Kim, Ok-Sun; Lee, Bang Yong; Cho, Jang-Cheon; Hur, Hor-Gil; Lee, Yoo Kyung

    2014-01-01

    From July to August 2010, the IBRV ARAON journeyed to the Pacific sector of the Arctic Ocean to monitor bacterial variation in Arctic summer surface-waters, and temperature, salinity, fluorescence, and nutrient concentrations were determined during the ice-melting season. Among the measured physicochemical parameters, we observed a strong negative correlation between temperature and salinity, and consequently hypothesized that the melting ice decreased water salinity. The bacterial community compositions of 15 samples, includicng seawater, sea-ice, and melting pond water, were determined using a pyrosequencing approach and were categorized into three habitats: (1) surface seawater, (2) ice core, and (3) melting pond. Analysis of these samples indicated the presence of local bacterial communities; a deduction that was further corroborated by the discovery of seawater- and ice-specific bacterial phylotypes. In all samples, the Alphaproteobacteria, Flavobacteria, and Gammaproteobacteria taxa composed the majority of the bacterial communities. Among these, Alphaproteobacteria was the most abundant and present in all samples, and its variation differed among the habitats studied. Linear regression analysis suggested that changes in salinity could affect the relative proportion of Alphaproteobacteria in the surface water. In addition, the species-sorting model was applied to evaluate the population dynamics and environmental heterogeneity in the bacterial communities of surface mixed layer in the Arctic Ocean during sea-ice melting.

  19. Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Gang [The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China (China); Xu, Zhenjiang [Biofrontiers Institute, University of Colorado, Boulder, CO (United States); Tian, Xiangli, E-mail: xianglitian@ouc.edu.cn [The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China (China); Dong, Shuanglin [The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China (China); Peng, Mo [School of Animal Science and Technology, Jiangxi Agricultural University (China)

    2015-02-27

    β-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal microbiota. High-throughput sequencing techniques provide an opportunity for the identification and characterization of microbes. In this study, we investigated the intestinal microbial community composition, interaction among species, and intestinal immune genes in sea cucumber fed with diet supplemented with or without β-glucan supplementation. The results show that the intestinal dominant classes in the control group are Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, whereas Alphaproteobacteria, Flavobacteriia, and Verrucomicrobiae are enriched in the β-glucan group. Dietary β-glucan supplementation promoted the proliferation of the family Rhodobacteraceae of the Alphaproteobacteria class and the family Verrucomicrobiaceae of the Verrucomicrobiae class and reduced the relative abundance of the family Flavobacteriaceae of Flavobacteria class. The ecological network analysis suggests that dietary β-glucan supplementation can alter the network interactions among different microbial functional groups by changing the microbial community composition and topological roles of the OTUs in the ecological network. Dietary β-glucan supplementation has a positive impact on immune responses of the intestine of sea cucumber by activating NF-κB signaling pathway, probably through modulating the balance of intestinal microbiota. - Highlights: • Dietary β-glucan supplementation increases the abundance of Rhodobacteraceae and Verrucomicrobiaceae in the intestine. • Dietary β-glucan supplementation changes the topological roles of OTUs in the ecological network. • Dietary β-glucan supplementation has a positive impact on the immune response of intestine of sea cucumber.

  20. Comparison of soil bacterial communities of Pinus patula of Nilgiris, western ghats with other biogeographically distant pine forest clone libraries.

    Science.gov (United States)

    Rohini-Kumar, M; Osborne, Jabez W; Saravanan, V S

    2013-07-01

    The bacterial community structure of the rhizosphere and non-rhizosphere soil of Pinus patula, found in the Nilgiris region of Western Ghats, was studied by constructing 16S rRNA gene clone libraries. In the rhizosphere and non-rhizosphere soil clone libraries constructed, 13 and 15 bacterial phyla were identified, respectively. The clone libraries showed the predominance of members of culturally underrepresented phyla like Acidobacteria and Verrucomicrobia. The Alphaproteobacteria and Acidobacteria clones were predominant in rhizosphere and non-rhizosphere soil samples, respectively. In rhizosphere, amongst Alphaproteobacteria members, Bradyrhizobium formed the significant proportion, whereas in non-rhizosphere, members of subdivision-6 of phylum Acidobacteria were abundant. The diversity analysis of P. patula soil libraries showed that the phylotypes (16S rRNA gene similarity cutoff, ≥97 %) of Acidobacteria and Bacteroidetes were relatively predominant and diverse followed by Alphaproteobacteria and Verrucomicrobia. The diversity indices estimated higher richness and abundance of bacteria in P. patula soil clone libraries than the pine forest clone libraries retrieved from previous studies. The tools like principal co-ordinate analysis and Jackknife cluster analysis, which were under UniFrac analysis indicated that variations in soil bacterial communities were attributed to their respective geographical locations due to the phylogenetic divergence amongst the clone libraries. Overall, the P. patula rhizosphere and non-rhizosphere clone libraries were found significantly unique in composition, evenly distributed and highly rich in phylotypes, amongst the biogeographically distant clone libraries. It was finally hypothesised that the phylogenetic divergence amongst the bacterial phylotypes and natural selection plays a pivotal role in the variations of bacterial communities across the geographical distance.

  1. Potential DMSP-degrading Roseobacter clade dominates endosymbiotic microflora of Pyrodinium bahamense var. compressum (Dinophyceae) in vitro.

    Science.gov (United States)

    Onda, Deo Florence L; Azanza, Rhodora V; Lluisma, Arturo O

    2015-09-01

    Many aspects of the biology and ecology of the toxic dinoflagellate Pyrodinium bahamense var. compressum are still poorly understood. In this brief note, we present identification of its associated intracellular bacteria or endosymbionts via PCR cloning and 16s rRNA gene sequencing and their localization by confocal microscopy, a first for Pyrodinium. The most frequently observed species in the endosymbiotic microflora were from Roseobacter clade (Alphaproteobacteria, 68%) and Gilvibacter sediminis (Flavobacteriaceae, 20%). Roseobacter lineage, the most abundant taxa in this study, is known to be involved in dimethylsulfoniopropionate metabolism which is highly produced in dinoflagellates-a possible strong factor shaping the structure of the associated bacterial community.

  2. Exploring the plant-associated bacterial communities in Medicago sativa L

    Directory of Open Access Journals (Sweden)

    Pini Francesco

    2012-05-01

    Full Text Available Abstract Background Plant-associated bacterial communities caught the attention of several investigators which study the relationships between plants and soil and the potential application of selected bacterial species in crop improvement and protection. Medicago sativa L. is a legume crop of high economic importance as forage in temperate areas and one of the most popular model plants for investigations on the symbiosis with nitrogen fixing rhizobia (mainly belonging to the alphaproteobacterial species Sinorhizobium meliloti. However, despite its importance, no studies have been carried out looking at the total bacterial community associated with the plant. In this work we explored for the first time the total bacterial community associated with M. sativa plants grown in mesocosms conditions, looking at a wide taxonomic spectrum, from the class to the single species (S. meliloti level. Results Results, obtained by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP analysis, quantitative PCR and sequencing of 16 S rRNA gene libraries, showed a high taxonomic diversity as well as a dominance by members of the class Alphaproteobacteria in plant tissues. Within Alphaproteobacteria the families Sphingomonadaceae and Methylobacteriaceae were abundant inside plant tissues, while soil Alphaproteobacteria were represented by the families of Hyphomicrobiaceae, Methylocystaceae, Bradyirhizobiaceae and Caulobacteraceae. At the single species level, we were able to detect the presence of S. meliloti populations in aerial tissues, nodules and soil. An analysis of population diversity on nodules and soil showed a relatively low sharing of haplotypes (30-40% between the two environments and between replicate mesocosms, suggesting drift as main force shaping S. meliloti population at least in this system. Conclusions In this work we shed some light on the bacterial communities associated with M. sativa plants, showing that Alphaproteobacteria may

  3. Dual Control of Sinorhizobium meliloti RpoE2 Sigma Factor Activity by Two PhyR-Type Two-Component Response Regulators▿ †

    OpenAIRE

    Bastiat, Bénédicte; Sauviac, Laurent; Bruand, Claude

    2010-01-01

    RpoE2 is an extracytoplasmic function (ECF) sigma factor involved in the general stress response of Sinorhizobium meliloti, the nitrogen-fixing symbiont of the legume plant alfalfa. RpoE2 orthologues are widely found among alphaproteobacteria, where they play various roles in stress resistance and/or host colonization. In this paper, we report a genetic and biochemical investigation of the mechanisms of signal transduction leading to S. meliloti RpoE2 activation in response to stress. We show...

  4. Complete genome sequences of Brucella melitensis strains M28 and M5-90, with different virulence backgrounds.

    Science.gov (United States)

    Wang, Fangkun; Hu, Sen; Gao, Yuzhe; Qiao, Zujian; Liu, Wenxing; Bu, Zhigao

    2011-06-01

    Brucella melitensis is a Gram-negative coccobacillus bacteria belonging to the Alphaproteobacteria subclass. It is an important zoonotic pathogen that causes brucellosis, a disease affecting sheep, cattle, and sometimes humans. The B. melitensis strain M5-90, a live attenuated vaccine cultured from the B. melitensis virulent strain M28, has been an effective tool to control brucellosis in goats and sheep in China. Here we report the complete genome sequences of B. melitensis M28 and M5-90, strains with different virulence backgrounds, which will serve as a valuable reference for future studies.

  5. Characterization and transcriptional analysis of two gene clusters for type IV secretion machinery in Wolbachia of Armadillidium vulgare

    DEFF Research Database (Denmark)

    Félix, Christine; Pichon, Samuel; Braquart-Varnier, Christine;

    2008-01-01

    Wolbachia are maternally inherited alpha-proteobacteria that induce feminization of genetic males in most terrestrial crustacean isopods. Two clusters of vir genes for a type IV secretion machinery have been identified at two separate loci and characterized for the first time in a feminizing...... Wolbachia. Furthermore, we demonstrated that these operons are transcriptionally active in ovaries and in all other tissues tested, suggesting that T4SS has a significant role in Wolbachia biology. These observations and the identification of homologous vir genes in Wolbachia strains infecting insects...... or nematodes show that vir genes are conserved among Wolbachia strains whatever the phenotype induced by the bacteria....

  6. Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels.

    Science.gov (United States)

    Ikeda, Seishi; Okubo, Takashi; Kaneko, Takakazu; Inaba, Shoko; Maekawa, Tomiya; Eda, Shima; Sato, Shusei; Tabata, Satoshi; Mitsui, Hisayuki; Minamisawa, Kiwamu

    2010-03-01

    The diversity of stem-associated bacteria of non-nodulated (Nod(-)), wild-type nodulated (Nod(+)) and hypernodulated (Nod(++)) soybeans were evaluated by clone library analyses of the 16S ribosomal RNA gene. Soybeans were dressed with standard nitrogen (SN) fertilization (15 kg N ha(-1)) and heavy nitrogen (HN) fertilization (615 kg N ha(-1)). The relative abundance of Alphaproteobacteria in Nod(+) soybeans (66%) was smaller than that in Nod(-) and Nod(++) soybeans (75-76%) under SN fertilization, whereas that of Gammaproteobacteria showed the opposite pattern (23% in Nod(+) and 12-16% in Nod(-) and Nod(++) soybeans). Principal coordinate analysis showed that the bacterial communities of Nod(-) and Nod(++) soybeans were more similar to each other than to that of Nod(+) soybeans under SN fertilization. HN fertilization increased the relative abundance of Gammaproteobacteria in all nodulation phenotypes (33-57%) and caused drastic shifts of the bacterial community. The clustering analyses identified a subset of operational taxonomic units (OTUs) at the species level in Alpha- and Gammaproteobacteria responding to both the nodulation phenotypes and nitrogen fertilization levels. Meanwhile, the abundance of Betaproteobacteria was relatively constant in all libraries constructed under these environmental conditions. The relative abundances of two OTUs in Alphaproteobacteria (Aurantimonas sp. and Methylobacterium sp.) were especially sensitive to nodulation phenotype and were drastically decreased under HN fertilization. These results suggested that a subpopulation of proteobacteria in soybeans is controlled in a similar manner through both the regulation systems of plant-rhizobia symbiosis and the nitrogen signaling pathway in plants.

  7. The microbiome of North Sea copepods

    Science.gov (United States)

    Gerdts, G.; Brandt, P.; Kreisel, K.; Boersma, M.; Schoo, K. L.; Wichels, A.

    2013-12-01

    Copepods can be associated with different kinds and different numbers of bacteria. This was already shown in the past with culture-dependent microbial methods or microscopy and more recently by using molecular tools. In our present study, we investigated the bacterial community of four frequently occurring copepod species, Acartia sp., Temora longicornis, Centropages sp. and Calanus helgolandicus from Helgoland Roads (North Sea) over a period of 2 years using DGGE (denaturing gradient gel electrophoresis) and subsequent sequencing of 16S-rDNA fragments. To complement the PCR-DGGE analyses, clone libraries of copepod samples from June 2007 to 208 were generated. Based on the DGGE banding patterns of the two years survey, we found no significant differences between the communities of distinct copepod species, nor did we find any seasonality. Overall, we identified 67 phylotypes (>97 % similarity) falling into the bacterial phyla of Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The most abundant phylotypes were affiliated to the Alphaproteobacteria. In comparison with PCR-DGGE and clone libraries, phylotypes of the Gammaproteobacteria dominated the clone libraries, whereas Alphaproteobacteria were most abundant in the PCR-DGGE analyses.

  8. Identification of chromosomal alpha-proteobacterial small RNAs by comparative genome analysis and detection in Sinorhizobium meliloti strain 1021

    Directory of Open Access Journals (Sweden)

    Barloy-Hubler Frédérique

    2007-12-01

    Full Text Available Abstract Background Small untranslated RNAs (sRNAs seem to be far more abundant than previously believed. The number of sRNAs confirmed in E. coli through various approaches is above 70, with several hundred more sRNA candidate genes under biological validation. Although the total number of sRNAs in any one species is still unclear, their importance in cellular processes has been established. However, unlike protein genes, no simple feature enables the prediction of the location of the corresponding sequences in genomes. Several approaches, of variable usefulness, to identify genomic sequences encoding sRNA have been described in recent years. Results We used a combination of in silico comparative genomics and microarray-based transcriptional profiling. This approach to screening identified ~60 intergenic regions conserved between Sinorhizobium meliloti and related members of the alpha-proteobacteria sub-group 2. Of these, 14 appear to correspond to novel non-coding sRNAs and three are putative peptide-coding or 5' UTR RNAs (ORF smaller than 100 aa. The expression of each of these new small RNA genes was confirmed by Northern blot hybridization. Conclusion Small non coding RNA (sra genes can be found in the intergenic regions of alpha-proteobacteria genomes. Some of these sra genes are only present in S. meliloti, sometimes in genomic islands; homologues of others are present in related genomes including those of the pathogens Brucella and Agrobacterium.

  9. Clone-based comparative sequence analysis of 16S rRNA genes retrieved from biodeteriorating brick buildings of the former Auschwitz II-Birkenau concentration and extermination camp.

    Science.gov (United States)

    Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

    2015-02-01

    The aim of this work was to analyze the bacterial communities in four samples of historical materials (plaster, brick, and wood) derived from buildings located in the former Auschwitz II-Birkenau concentration and extermination camp in Brzezinka, Poland. For this purpose a molecular strategy based on the construction of 16S rRNA clone libraries was used. In total, 138 partial 16S rRNA gene sequences (∼600bp) were obtained and compared. The clones belonged to phyla Proteobacteria (classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes. The plaster samples predominantly contained clones closely related to Actinobacteria and Alphaproteobacteria, brick samples contained Gammaproteobacteria, while wood samples had Actinobacteria clones. Interestingly, the historic plaster and brick samples contained the following bacteria with known and described biodeterioration potential: chemoorganotrophic Streptomyces sp. and Pseudonocardia sp., halotolerant or halophilic Rubrobacter sp., Salinisphaera sp. and Halomonas sp. Principal component analysis (PCA) showed that amongst the bacterial species detected and identified none occurred on all the tested historical materials. The 16S rRNA clone library construction method was successfully used for the detection and diversity determination of bacterial communities inhabiting brick barracks located in the former Auschwitz II-Birkenau concentration and extermination camp in Brzezinka.

  10. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics.

    Science.gov (United States)

    Duan, Yongping; Zhou, Lijuan; Hall, David G; Li, Wenbin; Doddapaneni, Harshavardhan; Lin, Hong; Liu, Li; Vahling, Cheryl M; Gabriel, Dean W; Williams, Kelly P; Dickerman, Allan; Sun, Yijun; Gottwald, Tim

    2009-08-01

    Citrus huanglongbing is the most destructive disease of citrus worldwide. It is spread by citrus psyllids and is associated with a low-titer, phloem-limited infection by any of three uncultured species of alpha-Proteobacteria, 'Candidatus Liberibacter asiaticus', 'Ca. L. americanus', and 'Ca. L. africanus'. A complete circular 'Ca. L. asiaticus' genome has been obtained by metagenomics, using the DNA extracted from a single 'Ca. L. asiaticus'-infected psyllid. The 1.23-Mb genome has an average 36.5% GC content. Annotation revealed a high percentage of genes involved in both cell motility (4.5%) and active transport in general (8.0%), which may contribute to its virulence. 'Ca. L. asiaticus' appears to have a limited ability for aerobic respiration and is likely auxotrophic for at least five amino acids. Consistent with its intracellular nature, 'Ca. L. asiaticus' lacks type III and type IV secretion systems as well as typical free-living or plant-colonizing extracellular degradative enzymes. 'Ca. L. asiaticus' appears to have all type I secretion system genes needed for both multidrug efflux and toxin effector secretion. Multi-protein phylogenetic analysis confirmed 'Ca. L. asiaticus' as an early-branching and highly divergent member of the family Rhizobiaceae. This is the first genome sequence of an uncultured alpha-proteobacteria that is both an intracellular plant pathogen and insect symbiont.

  11. Azospirillum brasilense does not affect population structure of specific rhizobacterial communities of inoculated maize (Zea mays).

    Science.gov (United States)

    Herschkovitz, Yoav; Lerner, Anat; Davidov, Yaacov; Okon, Yaacov; Jurkevitch, Edouard

    2005-11-01

    Positive response of plant species to plant growth-promoting rhizobacteria have led to an increased interest in their use as bacterial inoculants. However, the introduction of exogenous bacteria into natural ecosystems may perturb bacterial populations within the microbial community and lead to the disruption of indigenous populations performing key functional roles. In this study the effect of Azospirillum brasilense inoculation on maize (Zea mays) rhizosphere Actinobacteria, Bacteroidetes, alpha-Proteobacteria, Pseudomonas and Bdellovibrio spp. was assessed using a polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) approach in conjunction with group-specific primers. The DGGE fingerprints analysis revealed that the introduction of A. brasilense did not alter or disrupt the microbial system at the group-specific level. However, some communities such as the alpha-Proteobacteria and Bdellovibrio were influenced by plant age while the other bacterial groups remained unaffected. Based on these as well as previous data, it can be inferred that inoculation with A. brasilense does not perturb the natural bacterial populations investigated.

  12. The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.

    Science.gov (United States)

    Gonzalez, Diego; Kozdon, Jennifer B; McAdams, Harley H; Shapiro, Lucy; Collier, Justine

    2014-04-01

    DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the initiation of chromosome replication or for DNA mismatch repair. By contrast, our transcriptome analysis shows that >10% of the genes are misexpressed in cells lacking or constitutively over-expressing CcrM. Strikingly, GANTC methylation is needed for the efficient transcription of dozens of genes that are essential for cell cycle progression, in particular for DNA metabolism and cell division. Many of them are controlled by promoters methylated by CcrM and co-regulated by other global cell cycle regulators, demonstrating an extensive cross talk between DNA methylation and the complex regulatory network that controls the cell cycle of C. crescentus and, presumably, of many other Alphaproteobacteria.

  13. DNA methylation by CcrM activates the transcription of two genes required for the division of Caulobacter crescentus.

    Science.gov (United States)

    Gonzalez, Diego; Collier, Justine

    2013-04-01

    DNA methylation regulates many processes, including gene expression, by superimposing secondary information on DNA sequences. The conserved CcrM enzyme, which methylates adenines in GANTC sequences, is essential to the viability of several Alphaproteobacteria. In this study, we find that Caulobacter crescentus cells lacking the CcrM enzyme accumulate low levels of the two conserved FtsZ and MipZ proteins, leading to a severe defect in cell division. This defect can be compensated by the expression of the ftsZ gene from an inducible promoter or by spontaneous suppressor mutations that promote FtsZ accumulation. We show that CcrM promotes the transcription of the ftsZ and mipZ genes and that the ftsZ and mipZ promoter regions contain a conserved CGACTC motif that is critical to their activities and to their regulation by CcrM. In addition, our results suggest that the ftsZ promoter has the lowest activity when the CGACTC motif is non-methylated, an intermediate activity when it is hemi-methylated and the highest activity when it is fully methylated. The regulation of ftsZ expression by DNA methylation may explain why CcrM is essential in a subset of Alphaproteobacteria.

  14. Variation in the diets of hydrothermal vent gastropods

    Science.gov (United States)

    Govenar, Breea; Fisher, Charles R.; Shank, Timothy M.

    2015-11-01

    A prevailing paradigm of hydrothermal vent ecology is that primary consumers feed on chemoautotrophic bacteria. However, for the purposes of reconstructing vent food webs and for tracking energy flow from the generation of rock and fluid chemistry through primary/ secondary productivity and consumption to the overlying water column, it remains unclear which consumers feed on which bacteria. In paired analyses of carbon and nitrogen tissue stable isotope values with unique 16S rRNA sequences from the stomach contents, we determined that two species of gastropod grazers appear to feed on epsilon-proteobacteria, while two other species have more diverse diets, including one species that consumes alpha-proteobacteria, planctomycetes, and non-green sulfur bacteria. Different carbon fixation pathways used by epsilon- and alpha-proteobacteria may account for the variation in the carbon stable isotope values among the consumers. Furthermore, our results indicate that trophic specialization and niche partitioning may contribute to the distribution and abundance of vent-endemic gastropods and support the hypothesis that consumers in the warmer habitats commonly feed on epsilon-proteobacteria that use the rTCA cycle, while in the cooler habitats they feed on additional bacteria that use the CBB cycle. These results suggest that the phylogenetic and metabolic diversity of free-living bacteria may play an important and previously overlooked role in facilitating species coexistence among primary consumers at hydrothermal vents and other chemosynthesis-based ecosystems.

  15. Phylogenetic analysis of a microbialite-forming microbial mat from a hypersaline lake of the Kiritimati atoll, Central Pacific.

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    Dominik Schneider

    Full Text Available On the Kiritimati atoll, several lakes exhibit microbial mat-formation under different hydrochemical conditions. Some of these lakes trigger microbialite formation such as Lake 21, which is an evaporitic, hypersaline lake (salinity of approximately 170‰. Lake 21 is completely covered with a thick multilayered microbial mat. This mat is associated with the formation of decimeter-thick highly porous microbialites, which are composed of aragonite and gypsum crystals. We assessed the bacterial and archaeal community composition and its alteration along the vertical stratification by large-scale analysis of 16S rRNA gene sequences of the nine different mat layers. The surface layers are dominated by aerobic, phototrophic, and halotolerant microbes. The bacterial community of these layers harbored Cyanobacteria (Halothece cluster, which were accompanied with known phototrophic members of the Bacteroidetes and Alphaproteobacteria. In deeper anaerobic layers more diverse communities than in the upper layers were present. The deeper layers were dominated by Spirochaetes, sulfate-reducing bacteria (Deltaproteobacteria, Chloroflexi (Anaerolineae and Caldilineae, purple non-sulfur bacteria (Alphaproteobacteria, purple sulfur bacteria (Chromatiales, anaerobic Bacteroidetes (Marinilabiacae, Nitrospirae (OPB95, Planctomycetes and several candidate divisions. The archaeal community, including numerous uncultured taxonomic lineages, generally changed from Euryarchaeota (mainly Halobacteria and Thermoplasmata to uncultured members of the Thaumarchaeota (mainly Marine Benthic Group B with increasing depth.

  16. Community structure of microbial biofilms associated with membrane-based water purification processes as revealed using a polyphasic approach

    Energy Technology Data Exchange (ETDEWEB)

    Chen, C.L.; Chong, M.L.; Wong, M.T.; Ong, S.L.; Ng, W.J. [Dept. of Civil Engineering, National Univ. of Singapore (Singapore); Liu, W.T. [Dept. of Civil Engineering, National Univ. of Singapore (Singapore); Nanoscience and Nanotechnology Initiative, National Univ. of Singapore (Singapore); Seah, H. [Public Utilities Board (Singapore)

    2004-07-01

    The microbial communities of membrane biofilms occurring in two full-scale water purification processes employing microfiltration (MF) and reverse osmosis (RO) membranes were characterized using a polyphasic approach that employed bacterial cultivation, 16S rDNA clone library and fluorescence in situ hybridization techniques. All methods showed that the {alpha}-proteobacteria was the largest microbial fraction in the samples, followed by the {gamma}-proteobacteria. This suggested that members of these two groups could be responsible for the biofouling on the membranes studied. Furthermore, the microbial community structures between the MF and RO samples were considerably different in composition of the most predominant 16S rDNA clones and bacterial isolates from the {alpha}-proteobacteria and only shared two common groups (Bradyrhizobium, Bosea) out of more than 17 different bacterial groups observed. The MF and RO samples further contained Planctomycetes and Fibroacter/Acidobacteria as the second predominant bacterial clones, respectively, and differed in minor bacterial clones and isolates. The community structure differences were mainly attributed to differences in feed water, process configurations and operating environments, such as the pressure and hydrodynamic conditions present in the water purification systems. (orig.)

  17. Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures.

    Science.gov (United States)

    Zhou, Guixiang; Zhang, Jiabao; Zhang, Congzhi; Feng, Youzhi; Chen, Lin; Yu, Zhenghong; Xin, Xiuli; Zhao, Bingzi

    2016-02-26

    Differences in the composition of a bacterial community engaged in decomposing wheat straw in a fluvo-aquic soil at 15 °C, 25 °C, and 35 °C were identified using barcode pyrosequencing. Functional carbon groups in the decomposing wheat straw were evaluated by (13)C-NMR (nuclear magnetic resonance). Actinobacteria and Firmicutes were more abundant, whereas Alphaproteobacteria and Bacteroidetes were less abundant, at higher temperatures during the later stages of decomposition. Differences in the chemical properties of straw accounted for 19.3% of the variation in the community composition, whereas soil properties accounted for more (24.0%) and temperature, for less (7.4%). Carbon content of the soil microbial biomass and nitrogen content of straw were significantly correlated with the abundance of Alphaproteobacteria, Actinobacteria, and Bacteroidetes. The chemical properties of straw, especially the NCH/OCH3, alkyl O-C-O, and O-alkyl functional groups, exercised a significant effect on the composition of the bacterial community at different temperatures during decomposition-results that extend our understanding of bacterial communities associated with the decomposition of straw in agro-ecosystems and of the effects of temperature and chemical properties of the decomposing straw and soil on such communities.

  18. Phototrophic Biofilm Assembly in Microbial-Mat-Derived Unicyanobacterial Consortia: Model Systems for the Study of Autotroph-Heterotroph Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Cole, Jessica K.; Hutchison, Janine R.; Renslow, Ryan S.; Kim, Young-Mo; Chrisler, William B.; Engelmann, Heather E.; Dohnalkova, Alice; Hu, Dehong; Metz, Thomas O.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2014-04-07

    Though microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, the diversity and complexity of natural systems and their intractability to in situ environmental manipulation makes elucidation of the principles governing these interactions challenging. Examination of primary succession during phototrophic biofilm assembly provides a robust means by which to elucidate the dynamics of such interactions and determine their influence upon recruitment and maintenance of phylogenetic and functional diversity in microbial communities. We isolated and characterized two unicyanobacterial consortia from the Hot Lake phototrophic mat, quantifying the structural and community composition of their assembling biofilms. The same heterotrophs were retained in both consortia and included members of Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes, taxa frequently reported as consorts of microbial photoautotrophs. Cyanobacteria led biofilm assembly, eventually giving way to a late heterotrophic bloom. The consortial biofilms exhibited similar patterns of assembly, with the relative abundances of members of Bacteroidetes and Alphaproteobacteria increasing and members of Gammaproteobacteria decreasing as colonization progressed. Despite similar trends in assembly at higher taxa, the consortia exhibited substantial differences in community structure at the species level. These similar patterns of assembly with divergent community structures suggest that, while similar niches are created by the metabolism of the cyanobacteria, the resultant webs of autotroph-heterotroph and heterotroph-heterotroph interactions driving metabolic exchange are specific to each primary producer. Altogether, our data support these Hot Lake unicyanobacterial consortia as generalizable model systems whose simplicity and tractability permit the deciphering of community assembly principles relevant to natural microbial communities.

  19. Bacterial diversity in surface water of the Yellow Sea duringand after a green alga tide in 2008

    Institute of Scientific and Technical Information of China (English)

    GUO Cong; LI Fuchao; JIANG Peng; LIU Zhaopu; QIN Song

    2011-01-01

    From May to August 2008,a large "green tide",consisting of the alga Ulva (Enteromorpha) prolifera,occurred in the Yellow Sea,China,affecting the local marine ecosystem and human activities.We investigated the influence of the green tide on the microbial community in the surface seawater,at four sites from July to August 2008,using bacterial 16S rRNA gene clone libraries.We sequenced 228clones of unique patterns identified by restriction fragment length polymorphism (RFLP) techniques.The results show that 228 sequenced clones fell into six bacterial phyla:Proteobacteria,Bacteroidetes,Cyanobacteria,Verrucomicrobia,Actinobacteria,and Planctomycetes.Alphaproteobacteria (33%),Gammaproteobacteria (25%),Bacteroidetes (23%) and Cyanobacteria (9%) dominated the assemblage.Comparison between samples collected in July (during the tide) and those collected in August (after the tide) showed that,in the microbial community,diversities of Alphaproteobacteria and Cyanobacteria increased after the tide,while those of Gammaproteobacteria and Bacteroidetes decreased.These results indicate that the green tide influenced the growth of some bacteria,and provide information for further studies on the interactions and relationships between U.prolifera and the bacterial community.This study suggests that microbial community analysis is a good approach to monitoring green tides.

  20. Diversity of the aerobic anoxygenic phototrophy genepufM in Arctic and Antarctic coastal seawaters

    Institute of Scientific and Technical Information of China (English)

    ZENG Yinxin; DONG Peiyan; QIAO Zongyun; ZHENG Tianling

    2016-01-01

    Aerobic anoxygenic phototrophic (AAP) bacteria serve important functions in marine carbon and energy cycling because of their capability to utilize dissolved organic substrates and harvest light energy. AAP bacteria are widely distributed in marine environments, and their diversity has been examined in marine habitats. However, information about AAP bacteria at high latitudes remains insufficient to date. Therefore, this study determined the summer AAP bacterial diversity in Arctic Kongsfjorden and in the Antarctic coastal seawater of King George Island on the basis ofpufM, a gene that encodes a pigment-binding protein subunit of the reaction center complex. FourpufM clone libraries were constructed, and 674 positive clones were obtained from four investigated stations (two in Kongsfjorden and two in the Antarctic Maxwell Bay). Arctic clones were clustered within theAlphaproteobacteria, whereas Antarctic clones were classified into theAlphaproteobacteria and Betaproteobacteria classes.Rhodobacteraceae-likepufM genes dominated in all samples. In addition, sequences closely related topufM encoded on a plasmid inSulfitobacter guttiformis were predominant in both Arctic and Antarctic samples. This result indicates the transpolar or even global distribution ofpufM genes in marine environments. Meanwhile, differences between the Arctic and Antarctic sequences may prove polar endemism. These results indicate the important role ofRhodobacteraceae as AAP bacteria in bipolar coastal waters.

  1. The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis

    Science.gov (United States)

    Tamas, Ivica; Smirnova, Angela V; He, Zhiguo; Dunfield, Peter F

    2014-01-01

    The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. This was supported by a compositional analysis suggesting that all MMOs in Alphaproteobacteria methanotrophs are foreign in origin. Some members of the Beijerinckiaceae subsequently lost methanotrophic functions and regained the ability to grow on multicarbon energy substrates. We conclude that B. indica is a recidivist multitroph, the only known example of a bacterium having completely abandoned an evolved lifestyle of specialized methanotrophy. PMID:23985741

  2. Effect of Natural Sunlight on Bacterial Activity and Differential Sensitivity of Natural Bacterioplankton Groups in Northwestern Mediterranean Coastal Waters

    Science.gov (United States)

    Alonso-Sáez, Laura; Gasol, Josep M.; Lefort, Thomas; Hofer, Julia; Sommaruga, Ruben

    2006-01-01

    We studied the effects of natural sunlight on heterotrophic marine bacterioplankton in short-term experiments. We used a single-cell level approach involving flow cytometry combined with physiological probes and microautoradiography to determine sunlight effects on the activity and integrity of the cells. After 4 h of sunlight exposure, most bacterial cells maintained membrane integrity and viability as assessed by the simultaneous staining with propidium iodide and SYBR green I. In contrast, a significant inhibition of heterotrophic bacterial activity was detected, measured by 5-cyano-2,3 ditolyl tetrazolium chloride reduction and leucine incorporation. We applied microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization to test the sensitivity of the different bacterial groups naturally occurring in the Northwestern Mediterranean to sunlight. Members of the Gammaproteobacteria and Bacteroidetes groups appeared to be highly resistant to solar radiation, with small changes in activity after exposure. On the contrary, Alphaproteobacteria bacteria were more sensitive to radiation as measured by the cell-specific incorporation of labeled amino acids, leucine, and ATP. Within Alphaproteobacteria, bacteria belonging to the Roseobacter group showed higher resistance than members of the SAR11 cluster. The activity of Roseobacter was stimulated by exposure to photosynthetic available radiation compared to the dark treatment. Our results suggest that UV radiation can significantly affect the in situ single-cell activity of bacterioplankton and that naturally dominating phylogenetic bacterial groups have different sensitivity to natural levels of incident solar radiation. PMID:16957198

  3. Long-term forest soil warming alters microbial communities in temperate forest soils

    Directory of Open Access Journals (Sweden)

    Kristen M DeAngelis

    2015-02-01

    Full Text Available Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER site (Petersham, MA have warmed soils 5oC above ambient temperatures for 5, 8 and 20 years. We used this chronosequence to examine soil microbial communities in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences. Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 10% to 2% relative abundance with warming. We also observed a significant decrease in mean bacterial ribosomal RNA gene copy number in warming plots compared to controls, a trait linked to maximum growth rate or trophic strategy among bacteria. Increased bacterial alpha diversity, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria suggest that more or alternative niche space is being created over the course of long-term warming.

  4. Uncultivated Magnetotactic Cocci from Yuandadu Park in Beijing, China▿

    Science.gov (United States)

    Lin, Wei; Pan, Yongxin

    2009-01-01

    In the present study, we investigated a group of uncultivated magnetotactic cocci, which was magnetically isolated from a freshwater pond in Beijing, China. Light and transmission electron microscopy showed that these cocci ranged from 1.5 to 2.5 μm and contained two to four chains of magnetite magnetosomes, which sometimes were partially disorganized. Overall, the size of the disorganized magnetosomes was significantly smaller than that arranged in chains. All characterized magnetosome crystals were elongated (shape factor = 0.64) and fall into the single-domain size range (30 to 115 nm). Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization showed that the enriched bacteria were a virtually homogeneous population and represented a novel lineage in the Alphaproteobacteria. The closest cultivated relative was magnetotactic coccoid strain MC-1 (88% sequence identity). First-order reversal curve diagrams revealed that these cocci had relatively strong magnetic interactions compared to the single-chain magnetotactic bacteria. Low-temperature magnetic measurements showed that the Verwey transition of them was ∼108 K, confirming magnetite magnetosomes, and the delta ratio δFC/δZFC was >2. Based on the structure, phylogenetic position and magnetic properties, the enriched magnetotactic cocci of Alphaproteobacteria are provisionally named as “Candidatus Magnetococcus yuandaducum.” PMID:19376904

  5. Fluorescence in situ hybridization and sequential catalysed reporter deposition (2C-FISH for the flow cytometric sorting of freshwater ultramicrobacteria

    Directory of Open Access Journals (Sweden)

    Stefan M Neuenschwander

    2015-03-01

    Full Text Available Flow cytometric sorting is a powerful tool to physically separate cells within mixed microbial communities. If combined with phylogenetic staining (fluorescence in situ hybridization, FISH it allows to specifically sort defined genotypic microbial populations from complex natural samples. However, the targeted enrichment of freshwater ultramicrobacteria, such as members of the LD12 clade of Alphaproteobacteria (SAR11-IIIb, is still challenging. Current FISH protocols, even in combination with signal amplification by catalysed reporter deposition (CARD, are not sufficiently sensitive for the distinction of these bacteria from background noise by flow cytometry, presumably due to their low ribosome content and small cell sizes. We, therefore, modified a CARD based flow sorting protocol with the aim of increasing its sensitivity to a level sufficient for ultramicrobacteria. This was achieved by a second signal amplification step mediated by horseradish peroxidase labelled antibodies targeted to the fluorophores that were previously deposited by CARD-FISH staining. The protocol was tested on samples from an oligo-mesotrophic lake. Ultramicrobacteria affiliated with LD12 Alphaproteobacteria could be successfully sorted to high purity by flow cytometry. The ratios of median fluorescence signal to background ranged around 20, and hybridization rates determined by flow cytometry were comparable to those obtained by fluorescence microscopy. Potential downstream applications of our modified cell staining approach range from the analysis of microdiversity within 16S rRNA-defined populations to that of functional properties, such as the taxon-specific incorporation rates of organic substrates.

  6. Subcuticular bacteria associated with two common New Zealand echinoderms: Characterization using 16S rRNA sequence analysis and fluorescence in situ hybridization.

    Science.gov (United States)

    Lawrence, Scott A; O'Toole, Ronan; Taylor, Michael W; Davy, Simon K

    2010-02-01

    Many echinoderms contain subcuticular bacteria (SCB), symbionts which reside in the lumen between the host's epidermal cells and outer cuticle. This relationship is common, existing in about 60% of echinoderms studied so far, yet the function of SCB remains largely unknown. In this study, phylogenetic analysis was carried out on 16S rRNA sequences obtained from echinoderm-associated bacteria, resulting in the identification of four species of putative SCB. All four bacteria were identified from the holothurian Stichopus mollis, and two of the four were also found in the asteroid Patiriella sp. Two of these bacteria belong to the Alphaproteobacteria, and two to the Gammaproteobacteria. In addition to phylogenetic analysis, fluorescence in situ hybridization (FISH) assays were carried out on Patiriella sp., S. mollis, and the asteroid Astrostole scabra. Results showed that Patiriella sp. and S. mollis contain SCB, in agreement with the phylogenetic analysis, while SCB were not detected in A. scabra. Of the bacteria detected using FISH, more than 80% were recognized as belonging to the Alphaproteobacteria in both host species. However, in S. mollis about 20% of the detected SCB successfully hybridized with the Gammaproteobacteria-specific probe, whereas bacteria belonging to this class were never observed in Patiriella sp. This is only the second study to characterize SCB by molecular means, and is the first to identify SCB in situ using FISH.

  7. Biodiversity and physiological characteristics of Antarctic and Arctic lichens-associated bacteria.

    Science.gov (United States)

    Lee, Yung Mi; Kim, Eun Hye; Lee, Hong Kum; Hong, Soon Gyu

    2014-10-01

    The diversity and physiological characteristics of culturable bacteria associated with lichens from different habitats of the Arctic and Antarctica were investigated. The 68 retrieved isolates could be grouped on the basis of their 16S rRNA gene sequences into 26 phylotypes affiliated with the phyla Actinobacteria, Bacteroidetes, Deinococcus-Thermus, and Firmicutes and with the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Isolates belonging to the Alphaproteobacteria were the most abundant, followed by those belonging to Actinobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, and Deinococcus-Thermus. Phylogenetic analysis showed that approximately 21 % of the total isolates represented a potentially novel species or genus (≤97 % sequence similarity). Strains belonging to the genera Sphingomonas, Frondihabitans, Hymenobacter, and Burkholderia were recovered from lichen samples from both geographic locations, implying common and important bacterial functions within lichens. Extracellular protease activities were detected in six isolates, affiliated with Burkholderia, Frondihabitans, Hymenobacter, Pseudomonas, and Rhodanobacter. Extracellular lipase activities were detected in 37 isolates of the genera Burkholderia, Deinococcus, Frondihabitans, Pseudomonas, Rhodanobacter, Sphingomonas, and Subtercola. This is the first report on the culturable bacterial diversity present within lichens from Arctic and Antarctica and the isolates described herein are valuable resources to decode the functional and ecological roles of bacteria within lichens. In addition, the low similarity (≤97 %) of the recovered isolates to known species and their production of cold-active enzymes together suggest that lichens are noteworthy sources of novel bacterial strains for use in biotechnological applications.

  8. Microbial communities in flowback water impoundments from hydraulic fracturing for recovery of shale gas

    Energy Technology Data Exchange (ETDEWEB)

    Mohan, Arvind Murali; Hartsock, Angela; Hammack, Richard W; Vidic, Radisav D; Gregory, Kelvin B

    2013-12-01

    Hydraulic fracturing for natural gas extraction from shale produces waste brine known as flowback that is impounded at the surface prior to reuse and/or disposal. During impoundment, microbial activity can alter the fate of metals including radionuclides, give rise to odorous compounds, and result in biocorrosion that complicates water and waste management and increases production costs. Here, we describe the microbial ecology at multiple depths of three flowback impoundments from the Marcellus shale that were managed differently. 16S rRNA gene clone libraries revealed that bacterial communities in the untreated and biocide-amended impoundments were depth dependent, diverse, and most similar to species within the taxa [gamma]-proteobacteria, [alpha]-proteobacteria, δ-proteobacteria, Clostridia, Synergistetes, Thermotogae, Spirochetes, and Bacteroidetes. The bacterial community in the pretreated and aerated impoundment was uniform with depth, less diverse, and most similar to known iodide-oxidizing bacteria in the [alpha]-proteobacteria. Archaea were identified only in the untreated and biocide-amended impoundments and were affiliated to the Methanomicrobia class. This is the first study of microbial communities in flowback water impoundments from hydraulic fracturing. The findings expand our knowledge of microbial diversity of an emergent and unexplored environment and may guide the management of flowback impoundments.

  9. Microbial quality and phylogenetic diversity of fresh rainwater and tropical freshwater reservoir.

    Science.gov (United States)

    Kaushik, Rajni; Balasubramanian, Rajasekhar; Dunstan, Hugh

    2014-01-01

    The impact of rainwater on the microbial quality of a tropical freshwater reservoir through atmospheric wet deposition of microorganisms was studied for the first time. Reservoir water samples were collected at four different sampling points and rainwater samples were collected in the immediate vicinity of the reservoir sites for a period of four months (January to April, 2012) during the Northeast monsoon period. Microbial quality of all fresh rainwater and reservoir water samples was assessed based on the counts for the microbial indicators: Escherichia coli (E. coli), total coliforms, and Enterococci along with total heterotrophic plate counts (HPC). The taxonomic richness and phylogenetic relationship of the freshwater reservoir with those of the fresh rainwater were also assessed using 16 S rRNA gene clone library construction. The levels of E. coli were found to be in the range of 0 CFU/100 mL-75 CFU/100 mL for the rainwater, and were 10-94 CFU/100 mL for the reservoir water. The sampling sites that were influenced by highway traffic emissions showed the maximum counts for all the bacterial indicators assessed. There was no significant increase in the bacterial abundances observed in the reservoir water immediately following rainfall. However, the composite fresh rainwater and reservoir water samples exhibited broad phylogenetic diversity, including sequences representing Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Lentisphaerae and Bacteriodetes. Members of the Betaproteobacteria group were the most dominant in both fresh rainwater and reservoir water, followed by Alphaproteobacteria, Sphingobacteria, Actinobacteria and Gammaproteobacteria.

  10. Seasonal Dynamics of Marine Microbial Community in the South Sea of Korea.

    Directory of Open Access Journals (Sweden)

    Sung-Suk Suh

    Full Text Available High-resolution 16S rRNA tag pyrosequencing was used to obtain seasonal snapshots of the bacterial diversity and community structure at two locations in Gosung Bay (South Sea, Korea over a one year period. Seasonal sampling from the water column at each site revealed highly diverse bacterial communities containing up to 900 estimated Operational Taxonomic Units (OTUs. The Alphaproteobacteria and Gammaproteobacteria were the most abundant groups, and the most frequently recorded OTUs were members of Pelagibacter and Glaciecola. In particular, it was observed that Arcobacter, a genus of the Epsilonproteobacteria, dominated during summer. In addition, Psedoalteromonadaceae, Vibrionaceae and SAR11-1 were predominant members of the OTUs found in all sampling seasons. Environmental factors significantly influenced the bacterial community structure among season, with the phosphate and nitrate concentrations contributing strongly to the spatial distribution of the Alphaproteobacteria; the Gammaproteobacteria, Flavobacteria, and Actinobacteria all showed marked negative correlations with all measured nutrients, particularly silicon dioxide and chlorophyll-a. The results suggest that seasonal changes in environmental variables contribute to the dynamic structure of the bacterial community in the study area.

  11. Diversity of bacteria producing pigmented colonies in aerosol, snow and soil samples from remote glacial areas (Antarctica, Alps and Andes

    Directory of Open Access Journals (Sweden)

    E. González-Toril

    2008-04-01

    Full Text Available Four different communities and one culture of pigmented microbial assemblages were obtained by incubation in mineral medium of samples collected from high elevation snow in the Alps (Mt. Blanc area and the Andes (Nevado Illimani summit, Bolivia, from Antarctic aerosol (French station Dumont d'Urville and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. The phylogenetic comparison with the currently available rDNA database allowed the identification of sequences belonging to Proteobacteria (Alpha-, Beta- and Gamma-proteobacteria, Actinobacteria and Bacteroidetes phyla. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified and the maritime Antarctic soil the poorest (only one. Snow samples from Col du midi (Alps and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones. These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteria clone. The only microorganism identified in the maritime Antarctica soil (Brevundimonas sp. was also detected in the Antarctic aerosol. The two snow samples from the Alps only shared one common microorganism. Most of the identified microorganisms have been detected previously in cold environments (Dietzia kujamenisi, Pseudonocardia Antarctica, Hydrogenophaga palleronii and Brebundimonas sp., marine sediments (Aquiflexus balticus, Pseudomonas pseudoalkaligenes, Pseudomonas sp. and one uncultured Alphaproteobacteria, and soils and rocks (Pseudonocardia sp.,

  12. Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer.

    Science.gov (United States)

    Schnarrenberger, Claus; Martin, William

    2002-02-01

    The citric acid or tricarboxylic acid cycle is a central element of higher-plant carbon metabolism which provides, among other things, electrons for oxidative phosphorylation in the inner mitochondrial membrane, intermediates for amino-acid biosynthesis, and oxaloacetate for gluconeogenesis from succinate derived from fatty acids via the glyoxylate cycle in glyoxysomes. The tricarboxylic acid cycle is a typical mitochondrial pathway and is widespread among alpha-proteobacteria, the group of eubacteria as defined under rRNA systematics from which mitochondria arose. Most of the enzymes of the tricarboxylic acid cycle are encoded in the nucleus in higher eukaryotes, and several have been previously shown to branch with their homologues from alpha-proteobacteria, indicating that the eukaryotic nuclear genes were acquired from the mitochondrial genome during the course of evolution. Here, we investigate the individual evolutionary histories of all of the enzymes of the tricarboxylic acid cycle and the glyoxylate cycle using protein maximum likelihood phylogenies, focusing on the evolutionary origin of the nuclear-encoded proteins in higher plants. The results indicate that about half of the proteins involved in this eukaryotic pathway are most similar to their alpha-proteobacterial homologues, whereas the remainder are most similar to eubacterial, but not specifically alpha-proteobacterial, homologues. A consideration of (a) the process of lateral gene transfer among free-living prokaryotes and (b) the mechanistics of endosymbiotic (symbiont-to-host) gene transfer reveals that it is unrealistic to expect all nuclear genes that were acquired from the alpha-proteobacterial ancestor of mitochondria to branch specifically with their homologues encoded in the genomes of contemporary alpha-proteobacteria. Rather, even if molecular phylogenetics were to work perfectly (which it does not), then some nuclear-encoded proteins that were acquired from the alpha

  13. Marine bacterioplankton community turnover within seasonally hypoxic waters of a subtropical sound

    DEFF Research Database (Denmark)

    Parsons, Rachel J.; Nelson, Craig E.; Carlson, Craig A.

    2015-01-01

    changes, including both direct counts and rRNA gene sequencing. During stratification, the surface waters were dominated by the SAR11 clade of Alphaproteobacteria and the cyanobacterium Synechococcus. In the suboxic bottom waters, cells from the order Chlorobiales prevailed, with gene sequences indicating......, Bermuda during the 6-week annual transition from a strongly stratified water column with suboxic and high-pCO2 bottom waters to a fully mixed and ventilated state during 2008. A suite of culture-independent methods provided a quantitative spatiotemporal characterization of bacterioplankton community...... members of the genera Chlorobium and Prosthecochloris – anoxygenic photoautotrophs that utilize sulfide as a source of electrons for photosynthesis. Transitional zones of hypoxia also exhibited elevated levels of methane- and sulfur-oxidizing bacteria relative to the overlying waters. The abundance...

  14. Ultrastructural and molecular identification of a Wolbachia endosymbiont in a spider, Nephila clavata.

    Science.gov (United States)

    Oh, H W; Kim, M G; Shin, S W; Bae, K S; Ahn, Y J; Park, H Y

    2000-10-01

    Wolbachia-like bacteria were observed in the egg cells of golden orb-weaving spider, Nephila clavata, by means of transmission electron microscopy. The bacteria exhibited the typical morphology of Wolbachia, including three enveloping membranes. Based on the amplification and sequencing of partial 16S rDNA and ftsZ gene, the bacteria were identified as Wolbachia, intracellular, transovarially inherited alpha-proteobacteria in invertebrates. Phylogenetic analysis based on 16S rDNA and ftsZ gene sequences invariably indicated that the intracellular bacteria from N. clavata belonged to group A Wolbachia, which were found only from insects. Clustering of Wolbachia from N. clavata with group A Wolbachia indicates that the bacteria were probably transferred horizontally between insects and the spider.

  15. New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria

    DEFF Research Database (Denmark)

    Ioannidis, Panagiotis; Dunning Hotopp, Julie C; Sapountzis, Panagiotis;

    2007-01-01

    , the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori...... bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the ori regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes......BACKGROUND: The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori). Identifying the ori of these bacteria and related alpha-Proteobacteria as well...

  16. Biofilm comprising phototrophic, diazotrophic, and hydrocarbon-utilizing bacteria: a promising consortium in the bioremediation of aquatic hydrocarbon pollutants.

    Science.gov (United States)

    Al-Bader, Dhia; Kansour, Mayada K; Rayan, Rehab; Radwan, Samir S

    2013-05-01

    Biofilms harboring simultaneously anoxygenic and oxygenic phototrophic bacteria, diazotrophic bacteria, and hydrocarbon-utilizing bacteria were established on glass slides suspended in pristine and oily seawater. Via denaturing gradient gel electrophoresis analysis on PCR-amplified rRNA gene sequence fragments from the extracted DNA from biofilms, followed by band amplification, biofilm composition was determined. The biofilms contained anoxygenic phototrophs belonging to alphaproteobacteria; pico- and filamentous cyanobacteria (oxygenic phototrophs); two species of the diazotroph Azospirillum; and two hydrocarbon-utilizing gammaproteobacterial genera, Cycloclasticus and Oleibacter. The coexistence of all these microbial taxa with different physiologies in the biofilm makes the whole community nutritionally self-sufficient and adequately aerated, a condition quite suitable for the microbial biodegradation of aquatic pollutant hydrocarbons.

  17. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

    Science.gov (United States)

    Breider, Sven; Scheuner, Carmen; Schumann, Peter; Fiebig, Anne; Petersen, Jörn; Pradella, Silke; Klenk, Hans-Peter; Brinkhoff, Thorsten; Göker, Markus

    2014-01-01

    Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

  18. GLOBAL MOLECULAR ANALYSES OF METHANE METABOLISM IN METHANOTROPHIC ALPHAPROTEOBACTERIUM, METHYLOSINUS TRICHOSPORIUM OB3B.PART II. METABOLOMICS AND 13C-LABELING STUDY

    Directory of Open Access Journals (Sweden)

    Marina G. Kalyuzhanaya

    2013-04-01

    Full Text Available In this work we use metabolomics and 13C-labeling data to refine central metabolic pathways for methane utilization in Methylosinus trichosporium OB3b, a model alphaproteobacterial methanotrophic bacterium. We demonstrate here that similar to non-methane utilizing methylotrophic alphaproteobacteria the core metabolism of the microbe is represented by several tightly connected metabolic cycles, such as the serine pathway, the ethylmalonyl-CoA (EMC pathway, and the citric acid (TCA cycle. Both in silico estimations and stable isotope labeling experiments combined with single cell (NanoSIMS and bulk biomass analyses indicate that a significantly larger portion of the cell carbon (over 60% is derived from CO2 in this methanotroph. Our 13C-labeling studies revealed an unusual topology of the assimilatory network in which phosph(enolpyruvate/pyruvate interconversions are key metabolic switches. A set of additional pathways for carbon fixation are identified and discussed.

  19. Themes and Variations: Regulation of RpoN-Dependent Flagellar Genes across Diverse Bacterial Species

    Directory of Open Access Journals (Sweden)

    Jennifer Tsang

    2014-01-01

    Full Text Available Flagellar biogenesis in bacteria is a complex process in which the transcription of dozens of structural and regulatory genes is coordinated with the assembly of the flagellum. Although the overall process of flagellar biogenesis is conserved among bacteria, the mechanisms used to regulate flagellar gene expression vary greatly among different bacterial species. Many bacteria use the alternative sigma factor σ54 (also known as RpoN to transcribe specific sets of flagellar genes. These bacteria include members of the Epsilonproteobacteria (e.g., Helicobacter pylori and Campylobacter jejuni, Gammaproteobacteria (e.g., Vibrio and Pseudomonas species, and Alphaproteobacteria (e.g., Caulobacter crescentus. This review characterizes the flagellar transcriptional hierarchies in these bacteria and examines what is known about how flagellar gene regulation is linked with other processes including growth phase, quorum sensing, and host colonization.

  20. Removal performance and microbial communities in a sequencing batch reactor treating hypersaline phenol-laden wastewater.

    Science.gov (United States)

    Jiang, Yu; Wei, Li; Zhang, Huining; Yang, Kai; Wang, Hongyu

    2016-10-01

    Hypersaline phenol-rich wastewater is hard to be treated by traditional biological systems. In this work, a sequencing batch reactor was used to remove phenol from hypersaline wastewater. The removal performance was evaluated in response to the variations of operating parameters and the microbial diversity was investigated by 454 pyrosequencing. The results showed that the bioreactor had high removal efficiency of phenol and was able to keep stable with the increase of initial phenol concentration. DO, pH, and salinity also affected the phenol removal rate. The most abundant bacterial group was phylum Proteobacteria in the two working conditions, and class Gammaproteobacteria as well as Alphaproteobacteria was predominant subgroup. The abundance of bacterial clusters was notably different along with the variation of operation conditions, resulting in changes of phenol degradation rates. The high removal efficiency of phenol suggested that the reactor might be promising in treating phenol-laden industrial wastewater in high-salt condition.

  1. [The new eubacterium Roseomonas baikalica sp. nov. isolated from core samples collected by deep-hole drilling of the bottom of Lake Baĭkal].

    Science.gov (United States)

    Andreeva, I S; Pechurkina, N I; Morozova, O V; Riabchikova, E I; Belikov, S I; Puchkova, L I; Emel'ianova, E K; Torok, T; Repin, V E

    2007-01-01

    Microbiological analysis of samples of sedimentary rocks from various eras of the geological history of the Baikal rift has enabled us to isolate a large number of microorganisms that can be classified into new, previously undescribed species. The present work deals with the identification and study of the morphological, biochemical, and physiological properties of one such strain, Che 82, isolated from sample C-29 of 3.4-3.5 Ma-old sedimentary rocks taken at a drilling depth of 146.74 m. As a result of our investigations, strain Che 82 is described as a new bacterial species, Roseomonas baikalica sp. nov., belonging to the genus Roseomonas within the family Methylobacteriaceae, class Alphaproteobacteria.

  2. Deterioration of an Etruscan tomb by bacteria from the order Rhizobiales

    Science.gov (United States)

    Diaz-Herraiz, Marta; Jurado, Valme; Cuezva, Soledad; Laiz, Leonila; Pallecchi, Pasquino; Tiano, Piero; Sanchez-Moral, Sergio; Saiz-Jimenez, Cesareo

    2014-01-01

    The Etruscan civilisation originated in the Villanovan Iron Age in the ninth century BC and was absorbed by Rome in the first century BC. Etruscan tombs, many of which are subterranean, are one of the best representations of this culture. The principal importance of these tombs, however, lies in the wall paintings and in the tradition of rich burial, which was unique in the Mediterranean Basin, with the exception of Egypt. Relatively little information is available concerning the biodeterioration of Etruscan tombs, which is caused by a colonisation that covers the paintings with white, circular to irregular aggregates of bacteria or biofilms that tend to connect each other. Thus, these colonisations sometimes cover extensive surfaces. Here we show that the colonisation of paintings in Tomba del Colle is primarily due to bacteria of the order Rhizobiales (Alphaproteobacteria), which were likely influenced by the neighbouring rhizosphere community and the availability of nutrients from root exudates. PMID:24402302

  3. Comparative analysis of the bacterial diversity in a lab-scale moving bed biofilm reactor (MBBR) applied to treat urban wastewater under different operational conditions.

    Science.gov (United States)

    Calderón, Kadiya; Martín-Pascual, Jaime; Poyatos, José Manuel; Rodelas, Belén; González-Martínez, Alejandro; González-López, Jesús

    2012-10-01

    Different types of carriers were tested as support material in a lab-scale moving bed biofilm reactor (MBBR) used to treat urban wastewater under three different conditions of hydraulic retention time (HRT) and carrier filling ratios (FR). The bacterial diversity developed on the biofilms responsible of the treatment was studied using a cultivation-independent approach based on the polymerase chain reaction-temperature gradient gel electrophoresis technique (PCR-TGGE). Cluster analysis of TGGE fingerprints showed significant differences of community structure dependent upon the different operational conditions applied. Redundancy analysis (RDA) was used to determine the relationship between the operational conditions (type of carrier, HRT, FR) and bacterial biofilm diversity, demonstrating a significant effect of FR=50%. Phylogenetic analysis of PCR-reamplified and sequenced TGGE bands revealed that the prevalent Bacteria populations in the biofilm were related to Betaproteobacteria (46%), Firmicutes (34%),Alphaproteobacteria (14%) and Gammaproteobacteria (9%).

  4. Molecular phylogenetic diversity of bacteria associated with soil of the savanna-like Cerrado vegetation.

    Science.gov (United States)

    Quirino, Betania F; Pappas, Georgios J; Tagliaferro, Andrea C; Collevatti, Rosane G; Neto, Eduardo Leonardecz; da Silva, Maria Regina S S; Bustamante, Mercedes M C; Krüger, Ricardo H

    2009-01-01

    The Brazilian savanna-like vegetation of Cerrado is rapidly being converted to pasture and agricultural fields. A 16S rDNA-based approach was taken to study the bacterial community associated with the soil of a native cerrado area (sensu stricto) and an area that has been converted to pasture. The bacterial group most abundantly identified in cerrado sensu stricto soil was the alpha-Proteobacteria while in cerrado converted to pasture the Actinobacteria were the most abundant. Rarefaction curves indicate that the species richness of cerrado sensu stricto is greater than that of cerrado converted to pasture. Furthermore, lineage-through-time plots show that the expected richness of species present in cerrado sensu stricto soil is approximately 10 times greater than that of cerrado converted to pasture.

  5. Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers

    Science.gov (United States)

    Newman, Dianne K.; Neubauer, Cajetan; Ricci, Jessica N.; Wu, Chia-Hung; Pearson, Ann

    2016-06-01

    Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record.

  6. Perception and Homeostatic Control of Iron in the Rhizobia and Related Bacteria.

    Science.gov (United States)

    O'Brian, Mark R

    2015-01-01

    Iron is an essential nutrient, but it can also be toxic. Therefore, iron homeostasis must be strictly regulated. Transcriptional control of iron-dependent gene expression in the rhizobia and other taxa of the Alphaproteobacteria is fundamentally different from the Fur paradigm in Escherichia coli and other model systems. Rather than sense iron directly, the rhizobia employ the iron response regulator (Irr) to monitor and respond to the status of an iron-dependent process, namely, heme biosynthesis. This novel control mechanism allows iron homeostasis to be integrated with other cellular processes, and it permits differential control of iron regulon genes in a manner not readily achieved by Fur. Moreover, studies of Irr have defined a role for heme in conditional protein stability that has been subsequently described in eukaryotes. Finally, Irr-mediated control of iron metabolism may reflect a cellular strategy that accommodates a greater reliance on manganese.

  7. Temporal controls of the asymmetric cell division cycle in Caulobacter crescentus.

    Directory of Open Access Journals (Sweden)

    Shenghua Li

    2009-08-01

    Full Text Available The asymmetric cell division cycle of Caulobacter crescentus is orchestrated by an elaborate gene-protein regulatory network, centered on three major control proteins, DnaA, GcrA and CtrA. The regulatory network is cast into a quantitative computational model to investigate in a systematic fashion how these three proteins control the relevant genetic, biochemical and physiological properties of proliferating bacteria. Different controls for both swarmer and stalked cell cycles are represented in the mathematical scheme. The model is validated against observed phenotypes of wild-type cells and relevant mutants, and it predicts the phenotypes of novel mutants and of known mutants under novel experimental conditions. Because the cell cycle control proteins of Caulobacter are conserved across many species of alpha-proteobacteria, the model we are proposing here may be applicable to other genera of importance to agriculture and medicine (e.g., Rhizobium, Brucella.

  8. BrucellaBase: Genome information resource.

    Science.gov (United States)

    Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Khader, L K M Abdul; Sridhar, Jayavel; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

    2016-09-01

    Brucella sp. causes a major zoonotic disease, brucellosis. Brucella belongs to the family Brucellaceae under the order Rhizobiales of Alphaproteobacteria. We present BrucellaBase, a web-based platform, providing features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) (Whatmore et al., 2007) and phylogenetic analysis of Brucella spp. BrucellaBase currently contains genome data of 510 Brucella strains along with the user interfaces for BLAST, VFDB, CARD, pairwise genome alignment and MLST typing. Availability of these tools will enable the researchers interested in Brucella to get meaningful information from Brucella genome sequences. BrucellaBase will regularly be updated with new genome sequences, new features along with improvements in genome annotations. BrucellaBase is available online at http://www.dbtbrucellosis.in/brucellabase.html or http://59.99.226.203/brucellabase/homepage.html.

  9. Dynamics of seawater bacterial communities in a shellfish hatchery.

    Science.gov (United States)

    Powell, S M; Chapman, C C; Bermudes, M; Tamplin, M L

    2013-08-01

    Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.

  10. Molecular characterization of an endolithic microbial community in dolomite rock in the central Alps (Switzerland).

    Science.gov (United States)

    Horath, Thomas; Bachofen, Reinhard

    2009-08-01

    Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1-8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the eukaryotic diversity was outside the scope of the study, an amoeba (39 clones), and several green algae (51 clones) have been observed. We conclude that the bacterial diversity in this endolithic habitat, especially of chemotrophic, nonpigmented organisms, is considerable and that Archaea are present as well.

  11. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade.

    Science.gov (United States)

    Beyersmann, Paul G; Chertkov, Olga; Petersen, Jörn; Fiebig, Anne; Chen, Amy; Pati, Amrita; Ivanova, Natalia; Lapidus, Alla; Goodwin, Lynne A; Chain, Patrick; Detter, John C; Rohde, Manfred; Gronow, Sabine; Kyrpides, Nikos C; Woyke, Tanja; Simon, Meinhard; Göker, Markus; Klenk, Hans-Peter; Brinkhoff, Thorsten

    2013-07-30

    In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564(T) was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.

  12. The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

    Science.gov (United States)

    Mohan, Arvind Murali; Bibby, Kyle J; Lipus, Daniel; Hammack, Richard W; Gregory, Kelvin B

    2014-01-01

    Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

  13. Spatial variability of particle-attached and free-living bacterial diversity in surface waters from the Mackenzie River to the Beaufort Sea (Canadian Arctic)

    Science.gov (United States)

    Ortega-Retuerta, E.; Joux, F.; Jeffrey, W. H.; Ghiglione, J. F.

    2013-04-01

    We explored the patterns of total and active bacterial community structure in a gradient covering surface waters from the Mackenzie River to the coastal Beaufort Sea in the Canadian Arctic Ocean, with a particular focus on free-living (FL) vs. particle-attached (PA) communities. Capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) showed significant differences when comparing river, coast and open sea bacterial community structures. In contrast to the river and coastal waters, total (16S rDNA-based) and active (16S rRNA-based) communities in the open sea samples were not significantly different, suggesting that most present bacterial groups were equally active in this area. Additionally, we observed significant differences between PA and FL bacterial community structure in the open sea, but similar structure in the two fractions for coastal and river samples. Direct multivariate statistical analyses showed that total community structure was mainly driven by salinity (a proxy of dissolved organic carbon and chromophoric dissolved organic matter), suspended particles, amino acids and chlorophyll a. Pyrosequencing of 16S rRNA genes from selected samples confirmed significant differences between river, coastal and sea samples. The PA fraction was only different (15.7% similarity) from the FL one in the open sea sample. Furthermore, PA samples generally showed higher diversity (Shannon, Simpson and Chao indices) than FL samples. At the class level, Opitutae was most abundant in the PA fraction of the sea sample, followed by Flavobacteria and Gammaproteobacteria, while the FL sea sample was dominated by Alphaproteobacteria. Finally, for the coast and river samples and both PA and FL fractions, Betaproteobacteria, Alphaproteobacteria and Actinobacteria were dominant. These results highlight the coexistence of particle specialists and generalists and the role of particle quality in structuring bacterial communities in the area. These results may also

  14. Long-term forest soil warming alters microbial communities in temperate forest soils.

    Science.gov (United States)

    DeAngelis, Kristen M; Pold, Grace; Topçuoğlu, Begüm D; van Diepen, Linda T A; Varney, Rebecca M; Blanchard, Jeffrey L; Melillo, Jerry; Frey, Serita D

    2015-01-01

    Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.

  15. Profile of the culturable microbiome capable of producing acyl-homoserine lactone in the tobacco phyllosphere

    Institute of Scientific and Technical Information of China (English)

    Di Lv; Anzhou Ma; Xuanming Tang; Zhihui Bai; Hongyan Qi; Guoqiang Zhuang

    2013-01-01

    Bacterial populations coexisting in the phyllosphere niche have important effects on plant health.Quorum sensing (QS) allows bacteria to communicate via diffusible signal molecules,but QS-dependent behaviors in phyllosphere bacterial populations are poorly understood.We investigate the dense and diverse N-acyl-homoserine lactone (AHL)-producing phyllosphere bacteria living on tobacco leaf surfaces via a culture-dependent method and 16S rRNA gene sequencing.Our results indicated that approximately 7.9%-11.7%of the culturable leaf-associated bacteria have the ability to produce AHL based on the assays using whole-cell biosensors.Sequencing of the 16S rRNA gene assigned the AHL-producing strains to two phylogenetic groups,with Gammaproteobacteria (93%) as the predominant group,followed by Alphaproteobacteria.All of the AHL-producing Alphaproteobacteria were affiliated with the genus Rhizobium,whereas the AHL-producing bacteria belonging to the Gammaproteobacteria mainly fell within the genera Pseudomonas,Acinetobacter,Citrobacter,Enterobacter,Pantoea and Serratia.The bioassays of supernatant extracts revealed that a portion of the strains have a remarkable AHL profile for AHL induction activity using the two different biosensors,and one compound in the active extract of a representative isolate,NTL223,corresponded to 3-oxo-hexanoyl-homoserine lactone.A large population size and diversity of bacteria capable of AHL-driven QS were found to cohabit on leaves,implying that cross-communication based AHL-type QS may be common in the phyllosphere.Furthermore,this study provides a general snapshot of a potential valuable application of AHL-producing bacteria inhabiting leaves for their presumable ecological roles in the phyllosphere.

  16. An abundance of Epsilonproteobacteria revealed in the gut microbiome of the laboratory cultured sea urchin, Lytechinus variegatus

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    Joseph Antoine Hakim

    2015-10-01

    Full Text Available In this study, we have examined the bacterial community composition in the laboratory cultured sea urchin Lytechinus variegatus gut microbiome and its culture environment using NextGen amplicon sequencing of the V4 segment of the 16S rRNA gene, and downstream bioinformatics tools. Overall, the gut and tank water was dominated by Proteobacteria, whereas the feed consisted of a co-occurrence of Proteobacteria and Firmicutes at a high abundance. The gut tissue represented Epsilonproteobacteria as dominant, with order Campylobacterales at the highest relative abundance (>95%. However, the pharynx tissue was dominated by class Alphaproteobacteria. The gut digesta and egested fecal pellets had a high abundance of class Gammaproteobacteria, from which Vibrio was found to be the primary genus, and Epsilonproteobacteria, with genus Arcobacter occurring at a moderate level. At the class level, the tank water was dominated by Gammaproteobacteria, and the feed by Alphaproteobacteria. Multi-Dimensional Scaling analysis showed that the microbial community of the gut tissue clustered together, as did the pharynx tissue to the feed. The gut digesta and egested fecal pellets showed a similar relationship to the tank water. Further analysis of Campylobacterales at a lower taxonomic level using the oligotyping method revealed 37 unique types across the ten samples, where Oligotype 1 was primarily represented in the gut tissue. BLAST analysis identified Oligotype 1 to be Arcobacter sp., Sulfuricurvum sp., and Arcobacter bivalviorum at an identity level >90%. This study showed that although distinct microbial communities were evident across multiple components of the sea urchin gut ecosystem, there is a noticeable correlation between the overall microbial communities of the gut with the sea urchin L. variegatus culture environment.

  17. Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types.

    Energy Technology Data Exchange (ETDEWEB)

    Gottel, Neil R [ORNL; Castro Gonzalez, Hector F [ORNL; Kerley, Marilyn K [ORNL; Yang, Zamin [ORNL; Pelletier, Dale A [ORNL; Podar, Mircea [ORNL; Karpinets, Tatiana V [ORNL; Uberbacher, Edward C [ORNL; Tuskan, Gerald A [ORNL; Vilgalys, Rytas [Duke University; Doktycz, Mitchel John [ORNL; Schadt, Christopher Warren [ORNL

    2011-01-01

    The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.

  18. Genetic and computational identification of a conserved bacterial metabolic module.

    Directory of Open Access Journals (Sweden)

    Cara C Boutte

    2008-12-01

    Full Text Available We have experimentally and computationally defined a set of genes that form a conserved metabolic module in the alpha-proteobacterium Caulobacter crescentus and used this module to illustrate a schema for the propagation of pathway-level annotation across bacterial genera. Applying comprehensive forward and reverse genetic methods and genome-wide transcriptional analysis, we (1 confirmed the presence of genes involved in catabolism of the abundant environmental sugar myo-inositol, (2 defined an operon encoding an ABC-family myo-inositol transmembrane transporter, and (3 identified a novel myo-inositol regulator protein and cis-acting regulatory motif that control expression of genes in this metabolic module. Despite being encoded from non-contiguous loci on the C. crescentus chromosome, these myo-inositol catabolic enzymes and transporter proteins form a tightly linked functional group in a computationally inferred network of protein associations. Primary sequence comparison was not sufficient to confidently extend annotation of all components of this novel metabolic module to related bacterial genera. Consequently, we implemented the Graemlin multiple-network alignment algorithm to generate cross-species predictions of genes involved in myo-inositol transport and catabolism in other alpha-proteobacteria. Although the chromosomal organization of genes in this functional module varied between species, the upstream regions of genes in this aligned network were enriched for the same palindromic cis-regulatory motif identified experimentally in C. crescentus. Transposon disruption of the operon encoding the computationally predicted ABC myo-inositol transporter of Sinorhizobium meliloti abolished growth on myo-inositol as the sole carbon source, confirming our cross-genera functional prediction. Thus, we have defined regulatory, transport, and catabolic genes and a cis-acting regulatory sequence that form a conserved module required for myo

  19. The Arsenite Oxidation Potential of Native Microbial Communities from Arsenic-Rich Freshwaters.

    Science.gov (United States)

    Fazi, Stefano; Crognale, Simona; Casentini, Barbara; Amalfitano, Stefano; Lotti, Francesca; Rossetti, Simona

    2016-07-01

    Microorganisms play an important role in speciation and mobility of arsenic in the environment, by mediating redox transformations of both inorganic and organic species. Since arsenite [As(III)] is more toxic than arsenate [As(V)] to the biota, the microbial driven processes of As(V) reduction and As(III) oxidation may play a prominent role in mediating the environmental impact of arsenic contamination. However, little is known about the ecology and dynamics of As(III)-oxidizing populations within native microbial communities exposed to natural high levels of As. In this study, two techniques for single cell quantification (i.e., flow cytometry, CARD-FISH) were used to analyze the structure of aquatic microbial communities across a gradient of arsenic (As) contamination in different freshwater environments (i.e., groundwaters, surface and thermal waters). Moreover, we followed the structural evolution of these communities and their capacity to oxidize arsenite, when experimentally exposed to high As(III) concentrations in experimental microcosms. Betaproteobacteria and Deltaproteobacteria were the main groups retrieved in groundwaters and surface waters, while Beta and Gammaproteobacteria dominated the bacteria community in thermal waters. At the end of microcosm incubations, the communities were able to oxidize up to 95 % of arsenite, with an increase of Alphaproteobacteria in most of the experimental conditions. Finally, heterotrophic As(III)-oxidizing strains (one Alphaproteobacteria and two Gammaproteobacteria) were isolated from As rich waters. Our findings underlined that native microbial communities from different arsenic-contaminated freshwaters can efficiently perform arsenite oxidation, thus contributing to reduce the overall As toxicity to the aquatic biota.

  20. Ubiquitous dissolved inorganic carbon assimilation by marine bacteria in the Pacific Northwest coastal ocean as determined by stable isotope probing.

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    Suzanne DeLorenzo

    Full Text Available In order to identify bacteria that assimilate dissolved inorganic carbon (DIC in the northeast Pacific Ocean, stable isotope probing (SIP experiments were conducted on water collected from 3 different sites off the Oregon and Washington coasts in May 2010, and one site off the Oregon Coast in September 2008 and March 2009. Samples were incubated in the dark with 2 mM (13C-NaHCO(3, doubling the average concentration of DIC typically found in the ocean. Our results revealed a surprising diversity of marine bacteria actively assimilating DIC in the dark within the Pacific Northwest coastal waters, indicating that DIC fixation is relevant for the metabolism of different marine bacterial lineages, including putatively heterotrophic taxa. Furthermore, dark DIC-assimilating assemblages were widespread among diverse bacterial classes. Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes dominated the active DIC-assimilating communities across the samples. Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia were also implicated in DIC assimilation. Alteromonadales and Oceanospirillales contributed significantly to the DIC-assimilating Gammaproteobacteria within May 2010 clone libraries. 16S rRNA gene sequences related to the sulfur-oxidizing symbionts Arctic96BD-19 were observed in all active DIC assimilating clone libraries. Among the Alphaproteobacteria, clones related to the ubiquitous SAR11 clade were found actively assimilating DIC in all samples. Although not a dominant contributor to our active clone libraries, Betaproteobacteria, when identified, were predominantly comprised of Burkholderia. DIC-assimilating bacteria among Deltaproteobacteria included members of the SAR324 cluster. Our research suggests that DIC assimilation is ubiquitous among many bacterial groups in the coastal waters of the Pacific Northwest marine environment and may represent a significant metabolic process.

  1. Bacterial diversity of autotrophic enriched cultures from remote, glacial Antarctic, Alpine and Andean aerosol, snow and soil samples

    Directory of Open Access Journals (Sweden)

    E. González-Toril

    2009-01-01

    Full Text Available Four different communities and one culture of autotrophic microbial assemblages were obtained by incubation of samples collected from high elevation snow in the Alps (Mt. Blanc area and the Andes (Nevado Illimani summit, Bolivia, from Antarctic aerosol (French station Dumont d'Urville and a maritime Antarctic soil (King George Island, South Shetlands, Uruguay Station Artigas, in a minimal mineral (oligotrophic media. Molecular analysis of more than 200 16S rRNA gene sequences showed that all cultured cells belong to the Bacteria domain. Phylogenetic comparison with the currently available rDNA database allowed sequences belonging to Proteobacteria Alpha-, Beta- and Gamma-proteobacteria, Actinobacteria and Bacteroidetes phyla to be identified. The Andes snow culture was the richest in bacterial diversity (eight microorganisms identified and the marine Antarctic soil the poorest (only one. Snow samples from Col du Midi (Alps and the Andes shared the highest number of identified microorganisms (Agrobacterium, Limnobacter, Aquiflexus and two uncultured Alphaproteobacteria clones. These two sampling sites also shared four sequences with the Antarctic aerosol sample (Limnobacter, Pseudonocardia and an uncultured Alphaproteobacteriaclone. The only microorganism identified in the Antarctica soil (Brevundimonas sp. was also detected in the Antarctic aerosol. Most of the identified microorganisms had been detected previously in cold environments, marine sediments soils and rocks. Air current dispersal is the best model to explain the presence of very specific microorganisms, like those identified in this work, in environments very distant and very different from each other.

  2. Culturing marine bacteria - an essential prerequisite for biodiscovery.

    Science.gov (United States)

    Joint, Ian; Mühling, Martin; Querellou, Joël

    2010-09-01

    The potential for using marine microbes for biodiscovery is severely limited by the lack of laboratory cultures. It is a long-standing observation that standard microbiological techniques only isolate a very small proportion of the wide diversity of microbes that are known in natural environments from DNA sequences. A number of explanations are reviewed. The process of establishing laboratory cultures may destroy any cell-to-cell communication that occurs between organisms in the natural environment and that are vital for growth. Bacteria probably grow as consortia in the sea and reliance on other bacteria for essential nutrients and substrates is not possible with standard microbiological approaches. Such interactions should be considered when designing programmes for the isolation of marine microbes. The benefits of novel technologies for manipulating cells are reviewed, including single cell encapsulation in gel micro-droplets. Although novel technologies offer benefits for bringing previously uncultured microbes into laboratory culture, many useful bacteria can still be isolated using variations of plating techniques. Results are summarized for a study to culture bacteria from a long-term observatory station in the English Channel. Bacterial biodiversity in this assemblage has recently been characterized using high-throughput sequencing techniques. Although Alphaproteobacteria dominated the natural bacterial assemblage throughout the year, Gammaproteobacteria were the most frequent group isolated by plating techniques. The use of different gelling agents and the addition of ammonium to seawater-based agar did lead to the isolation of a higher proportion of Alphaproteobacteria. Variation in medium composition was also able to increase the recovery of other groups of particular interest for biodiscovery, such as Actinobacteria.

  3. Marine microbial community response to inorganic and organic sediment amendments in laboratory mesocosms.

    Science.gov (United States)

    Kan, Jinjun; Wang, Yanbing; Obraztsova, Anna; Rosen, Gunther; Leather, James; Scheckel, Kirk G; Nealson, Kenneth H; Arias-Thode, Y Meriah

    2011-10-01

    Sediment amendments provide promising strategies of enhancing sequestration of heavy metals and degradation of organic contaminants. The impacts of sediment amendments for metal and organic remediation including apatite, organoclay (and apatite and organoclay in geotextile mats), acetate, and chitin on environmental microbial communities in overlying water and sediment profiles are reported here. These experiments were performed concurrent with an ecotoxicity evaluation (data submitted in companion paper) and X-ray absorption spectroscopy of zinc speciation post apatite amendments. X-ray absorption spectra showed that a modest modification of zinc speciation occurred in amended treatments. Significant changes in both bacterial cell densities and populations were observed in response to amendments of apatite+organoclay, chitin, and acetate. The enriched bacteria and breakdown of these amendments were likely attributed to water quality degradation (e.g. ammonia and dissolved oxygen). Molecular fingerprints of bacterial communities by denaturant gradient gel electrophoresis (DGGE) showed that distinct bacterial populations occurred in overlying waters from different amendments: apatite+organoclay led to the dominance of Gammaproteobacteria, acetate enriched Alphaproteobacteria, and chitin treatment led to a dominance of Bacteroidetes and Alphaproteobacteria. In amended sediments, Firmicutes, Bacteroidetes, and Deltaproteobacteria (Desulfovibrio) were commonly found with chitin and apatite+chitin treatments. Finally, sulfate-reducing bacteria (e.g. Desulfovibrio) and metal-reducing bacteria were also recovered with most probable number (MPN) analyses in treatments with acetate, chitin, and apatite+chitin. These geochemically important bacteria were stimulated by amendments and may play critical functional roles in the metal and organic contaminant remediation process for future investigations of contaminated sediments.

  4. Isolation of novel pelagic bacteria from the German bight and their seasonal contributions to surface picoplankton.

    Science.gov (United States)

    Eilers, H; Pernthaler, J; Peplies, J; Glöckner, F O; Gerdts, G; Amann, R

    2001-11-01

    We tested new strategies for the isolation of abundant bacteria from coastal North Sea surface waters, which included reducing by several orders of magnitude the concentrations of inorganic N and P compounds in a synthetic seawater medium. Agar plates were resampled over 37 days, and slowly growing colonies were allowed to develop by repeatedly removing all newly formed colonies. A fivefold increase of colonies was observed on plates with reduced nutrient levels, and the phylogenetic composition of the culture collection changed over time, towards members of the Roseobacter lineage and other alpha-proteobacteria. Novel gamma-proteobacteria from a previously uncultured but cosmopolitan lineage (NOR5) formed colonies only after 12 days of plate incubation. A time series of German Bight surface waters (January to December 1998) was screened by fluorescence in situ hybridization (FISH) with isolate-specific and general probes. During spring and early summer, a prominent fraction of FISH-detectable bacteria (mean, 51%) were affiliated with the Cytophaga-Flavobacterium group (CF) of the Bacteroidetes. One Cytophaga sp. lineage with cultured representatives formed almost 20% of the CF group. Members of the Roseobacter cluster constituted approximately 50% of alpha-proteobacteria, but none of the Roseobacter-related isolates formed populations of >1% in the environment. Thus, the readily culturable members of this clade are probably not representative of Roseobacter species that are common in the water column. In contrast, members of NOR5 were found at high abundances (>10(5) cells ml(-1)) in the summer plankton. Some abundant pelagic bacteria are apparently able to form colonies on solid media, but appropriate isolation techniques for different species need to be developed.

  5. Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

    Directory of Open Access Journals (Sweden)

    Jessica K Cole

    2014-04-01

    Full Text Available Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling phototrophic biofilm communities provides a robust means to identify such interactions and evaluate their contributions to the recruitment and maintenance of phylogenetic and functional diversity over time. To examine primary succession in phototrophic communities, we isolated two unicyanobacterial consortia from the microbial mat in Hot Lake, Washington, characterizing the membership and metabolic function of each consortium. We then analyzed the spatial structures and quantified the community compositions of their assembling biofilms. The consortia retained the same suite of heterotrophic species, identified as abundant members of the mat and assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Autotroph growth rates dominated early in assembly, yielding to increasing heterotroph growth rates late in succession. The two consortia exhibited similar assembly patterns, with increasing relative abundances of members from Bacteroidetes and Alphaproteobacteria concurrent with decreasing relative abundances of those from Gammaproteobacteria. Despite these similarities at higher taxonomic levels, the relative abundances of individual heterotrophic species were substantially different in the developing consortial biofilms. This suggests that, although similar niches are created by the cyanobacterial metabolisms, the resulting webs of autotroph-heterotroph and heterotroph-heterotroph interactions are specific to each primary producer. The relative simplicity and tractability of the Hot Lake unicyanobacterial consortia make them useful model systems for deciphering interspecies interactions and assembly principles relevant to natural

  6. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types.

    Science.gov (United States)

    Gottel, Neil R; Castro, Hector F; Kerley, Marilyn; Yang, Zamin; Pelletier, Dale A; Podar, Mircea; Karpinets, Tatiana; Uberbacher, Ed; Tuskan, Gerald A; Vilgalys, Rytas; Doktycz, Mitchel J; Schadt, Christopher W

    2011-09-01

    The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.

  7. The differential interaction of Brucella and ochrobactrum with innate immunity reveals traits related to the evolution of stealthy pathogens.

    Directory of Open Access Journals (Sweden)

    Elías Barquero-Calvo

    Full Text Available BACKGROUND: During evolution, innate immunity has been tuned to recognize pathogen-associated molecular patterns. However, some alpha-Proteobacteria are stealthy intracellular pathogens not readily detected by this system. Brucella members follow this strategy and are highly virulent, but other Brucellaceae like Ochrobactrum are rhizosphere inhabitants and only opportunistic pathogens. To gain insight into the emergence of the stealthy strategy, we compared these two phylogenetically close but biologically divergent bacteria. METHODOLOGY/PRINCIPAL FINDINGS: In contrast to Brucella abortus, Ochrobactrum anthropi did not replicate within professional and non-professional phagocytes and, whereas neutrophils had a limited action on B. abortus, they were essential to control O. anthropi infections. O. anthropi triggered proinflammatory responses markedly lower than Salmonella enterica but higher than B. abortus. In macrophages and dendritic cells, the corresponding lipopolysaccharides reproduced these grades of activation, and binding of O. anthropi lipopolysaccharide to the TLR4 co-receptor MD-2 and NF-kappaB induction laid between those of B. abortus and enteric bacteria lipopolysaccharides. These differences correlate with reported variations in lipopolysaccharide core sugars, sensitivity to bactericidal peptides and outer membrane permeability. CONCLUSIONS/SIGNIFICANCE: The results suggest that Brucellaceae ancestors carried molecules not readily recognized by innate immunity, so that non-drastic variations led to the emergence of stealthy intracellular parasites. They also suggest that some critical envelope properties, like selective permeability, are profoundly altered upon modification of pathogen-associated molecular patterns, and that this represents a further adaptation to the host. It is proposed that this adaptive trend is relevant in other intracellular alpha-Proteobacteria like Bartonella, Rickettsia, Anaplasma, Ehrlichia and Wolbachia.

  8. Effects of seawater ozonation on biofilm development in aquaculture tanks.

    Science.gov (United States)

    Wietz, Matthias; Hall, Michael R; Høj, Lone

    2009-07-01

    Microbial biofilms developing in aquaculture tanks represent a reservoir for opportunistic bacterial pathogens, and procedures to control formation and bacterial composition of biofilms are important for the development of commercially viable aquaculture industries. This study investigated the effects of seawater ozonation on biofilm development on microscope glass slides placed in small-scale aquaculture tanks containing the live feed organism Artemia. Fluorescence in situ hybridization (FISH) demonstrated that ozonation accelerated the biofilm formation cycle, while it delayed the establishment of filamentous bacteria. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial groups in the biofilm for both water types, but ozonation influenced their dynamics. With ozonation, the bacterial community structure was relatively stable and dominated by Gammaproteobacteria throughout the experiment (21-66% of total bacteria). Without ozonation, the community showed larger fluctuations, and Alphaproteobacteria emerged as dominant after 18 days (up to 54% of total bacteria). Ozonation of seawater also affected the dynamics of less abundant populations in the biofilm such as Betaproteobacteria, Planctomycetales and the Cytophaga/Flavobacterium branch of phylum Bacteroidetes. The abundance of Thiothrix, a bacterial genus capable of filamentous growth and fouling of larvae, increased with time for both water types, while no temporal trend could be detected for the genus Vibrio. Denaturing gradient gel electrophoresis (DGGE) demonstrated temporal changes in the dominant bacterial populations for both water types. Sequencing of DGGE bands confirmed the FISH data, and sequences were related to bacterial groups commonly found in biofilms of aquaculture systems. Several populations were closely related to organisms involved in sulfur cycling. Improved Artemia survival rates in tanks receiving ozonated water suggested a positive effect of ozonation on animal

  9. The Bartonella quintana Extracytoplasmic Function Sigma Factor RpoE Has a Role in Bacterial Adaptation to the Arthropod Vector Environment

    Science.gov (United States)

    Abromaitis, Stephanie

    2013-01-01

    Bartonella quintana is a vector-borne bacterial pathogen that causes fatal disease in humans. During the infectious cycle, B. quintana transitions from the hemin-restricted human bloodstream to the hemin-rich body louse vector. Because extracytoplasmic function (ECF) sigma factors often regulate adaptation to environmental changes, we hypothesized that a previously unstudied B. quintana ECF sigma factor, RpoE, is involved in the transition from the human host to the body louse vector. The genomic context of B. quintana rpoE identified it as a member of the ECF15 family of sigma factors found only in alphaproteobacteria. ECF15 sigma factors are believed to be the master regulators of the general stress response in alphaproteobacteria. In this study, we examined the B. quintana RpoE response to two stressors that are encountered in the body louse vector environment, a decreased temperature and an increased hemin concentration. We determined that the expression of rpoE is significantly upregulated at the body louse (28°C) versus the human host (37°C) temperature. rpoE expression also was upregulated when B. quintana was exposed to high hemin concentrations. In vitro and in vivo analyses demonstrated that RpoE function is regulated by a mechanism involving the anti-sigma factor NepR and the response regulator PhyR. The ΔrpoE ΔnepR mutant strain of B. quintana established that RpoE-mediated transcription is important in mediating the tolerance of B. quintana to high hemin concentrations. We present the first analysis of an ECF15 sigma factor in a vector-borne human pathogen and conclude that RpoE has a role in the adaptation of B. quintana to the hemin-rich arthropod vector environment. PMID:23564167

  10. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

    Science.gov (United States)

    Ding, Tao; Melcher, Ulrich

    2016-01-01

    Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

  11. Microbiome change by symbiotic invasion in lichens

    Science.gov (United States)

    Maier, Stefanie; Wedin, Mats; Fernandez-Brime, Samantha; Cronholm, Bodil; Westberg, Martin; Weber, Bettina; Grube, Martin

    2016-04-01

    Biological soil crusts (BSC) seal the soil surface from erosive forces in many habitats where plants cannot compete. Lichens symbioses of fungi and algae often form significant fraction of these microbial assemblages. In addition to the fungal symbiont, many species of other fungi can inhabit the lichenic structures and interact with their hosts in different ways, ranging from commensalism to parasitism. More than 1800 species of lichenicolous (lichen-inhabiting) fungi are known to science. One example is Diploschistes muscorum, a common species in lichen-dominated BSC that infects lichens of the genus Cladonia. D. muscorum starts as a lichenicolous fungus, invading the lichen Cladonia symphycarpa and gradually develops an independent Diploschistes lichen thallus. Furthermore, bacterial groups, such as Alphaproteobacteria and Acidobacteria, have been consistently recovered from lichen thalli and evidence is rapidly accumulating that these microbes may generally play integral roles in the lichen symbiosis. Here we describe lichen microbiome dynamics as the parasitic lichen D. muscorum takes over C. symphycarpa. We used high-throughput 16S rRNA gene and photobiont-specific ITS rDNA sequencing to track bacterial and algal transitions during the infection process, and employed fluorescence in situ hybridization to localize bacteria in the Cladonia and Diploschistes lichen thalli. We sampled four transitional stages, at sites in Sweden and Germany: A) Cladonia with no visible infection, B) early infection stage defined by the first visible Diploschistes thallus, C) late-stage infection with parts of the Cladonia thallus still identifiable, and D) final stage with a fully developed Diploschistes thallus, A gradual microbiome shift occurred during the transition, but fractions of Cladonia-associated bacteria were retained during the process of symbiotic reorganization. Consistent changes observed across sites included a notable decrease in the relative abundance of

  12. Analysis of bacterial community during the fermentation of pulque, a traditional Mexican alcoholic beverage, using a polyphasic approach.

    Science.gov (United States)

    Escalante, Adelfo; Giles-Gómez, Martha; Hernández, Georgina; Córdova-Aguilar, María Soledad; López-Munguía, Agustín; Gosset, Guillermo; Bolívar, Francisco

    2008-05-31

    In this study, the characterization of the bacterial community present during the fermentation of pulque, a traditional Mexican alcoholic beverage from maguey (Agave), was determined for the first time by a polyphasic approach in which both culture and non-culture dependent methods were utilized. The work included the isolation of lactic acid bacteria (LAB), aerobic mesophiles, and 16S rDNA clone libraries from total DNA extracted from the maguey sap (aguamiel) used as substrate, after inoculation with a sample of previously produced pulque and followed by 6-h fermentation. Microbiological diversity results were correlated with fermentation process parameters such as sucrose, glucose, fructose and fermentation product concentrations. In addition, medium rheological behavior analysis and scanning electron microscopy in aguamiel and during pulque fermentation were also performed. Our results showed that both culture and non-culture dependent approaches allowed the detection of several new and previously reported species within the alpha-, gamma-Proteobacteria and Firmicutes. Bacteria diversity in aguamiel was composed by the heterofermentative Leuconostoc citreum, L. mesenteroides, L. kimchi, the gamma-Proteobacteria Erwinia rhapontici, Enterobacter spp. and Acinetobacter radioresistens. Inoculation with previously fermented pulque incorporated to the system microbiota, homofermentative lactobacilli related to Lactobacillus acidophilus, several alpha-Proteobacteria such as Zymomonas mobilis and Acetobacter malorum, other gamma-Proteobacteria and an important amount of yeasts, creating a starting metabolic diversity composed by homofermentative and heterofermentative LAB, acetic and ethanol producing microorganisms. At the end of the fermentation process, the bacterial diversity was mainly composed by the homofermentative Lactobacillus acidophilus, the heterofermentative L. mesenteroides, Lactococcus lactis subsp. lactis and the alpha-Proteobacteria A. malorum. After

  13. Influence of Vegetation on the In Situ Bacterial Community and Polycyclic Aromatic Hydrocarbon (PAH) Degraders in Aged PAH-Contaminated or Thermal-Desorption-Treated Soil▿ †

    Science.gov (United States)

    Cébron, Aurélie; Beguiristain, Thierry; Faure, Pierre; Norini, Marie-Paule; Masfaraud, Jean-François; Leyval, Corinne

    2009-01-01

    The polycyclic aromatic hydrocarbon (PAH) contamination, bacterial community, and PAH-degrading bacteria were monitored in aged PAH-contaminated soil (Neuves-Maisons [NM] soil; with a mean of 1,915 mg of 16 PAHs·kg−1 of soil dry weight) and in the same soil previously treated by thermal desorption (TD soil; with a mean of 106 mg of 16 PAHs·kg−1 of soil dry weight). This study was conducted in situ for 2 years using experimental plots of the two soils. NM soil was colonized by spontaneous vegetation (NM-SV), planted with Medicago sativa (NM-Ms), or left as bare soil (NM-BS), and the TD soil was planted with Medicago sativa (TD-Ms). The bacterial community density, structure, and diversity were estimated by real-time PCR quantification of the 16S rRNA gene copy number, temporal thermal gradient gel electrophoresis fingerprinting, and band sequencing, respectively. The density of the bacterial community increased the first year during stabilization of the system and stayed constant in the NM soil, while it continued to increase in the TD soil during the second year. The bacterial community structure diverged among all the plot types after 2 years on site. In the NM-BS plots, the bacterial community was represented mainly by Betaproteobacteria and Gammaproteobacteria. The presence of vegetation (NM-SV and NM-Ms) in the NM soil favored the development of a wider range of bacterial phyla (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi) that, for the most part, were not closely related to known bacterial representatives. Moreover, under the influence of the same plant, the bacterial community that developed in the TD-Ms was represented by different bacterial species (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Actinobacteria) than that in the NM-Ms. During the 2 years of monitoring, the PAH concentration did not evolve significantly. The abundance of gram-negative (GN

  14. Microbial Communities and a Novel Symbiotic Interaction in Extremely Acidic Mine Drainage at Iron Mountain, California

    Science.gov (United States)

    Baker, B. J.; Banfield, J. F.

    2002-12-01

    Culture-independent studies of microbial communities in the acid mine drainage (AMD) system associated with the Richmond ore body at Iron Mountain, CA, demonstrated that the total number of prokaryote lineages is small compared to other environments. Phylogenetic analyses of 232 small subunit ribosomal RNA (rRNA) genes from six clone libraries revealed some novel lines of descent. Many of the novel clones were from libraries constructed from subaerial biofilms associated with fine grained pyrite. The clones form several distinct groups within the order Thermoplasmatales and are most closely related to Ferroplasma spp. and Thermoplasma spp. Another novel group detected in a pH 1.4 pool and a pH 0.8 biofilm falls within the Rickettsiales (alpha-proteobacteria and related to mitochondria) and is most closely related to a-proteobacterial endosymbionts of Acanthamoeba spp. An oligonucleotide rRNA probe designed to target alpha-proteobacteria revealed that these are protist endosymbionts, and that they are associated with a small percentage (2%) of the total eukaryotes in samples from the Richmond mine. Measurements of the internal pH of these protists show that their cytosol is close to neutral. Thus, protists provide a habitat within the AMD system that is at least 5 pH units less acidic than the surroundings. The uncultured AMD endosymbionts have a conserved 273 nucleotide intervening sequence (IVS) in the variable V1 region of their 16S rRNA gene. The IVS does not match any sequence in current databases, but predicted secondary structure form well defined stem loops. The discovery of inserts within a highly conserved gene is extremely rare. At present we have not identified the protist host. However, it is interesting to note that protists previously shown to have a-proteobacterial endosymbionts possess 18S rRNA genes that contain both IVSs and group I introns. The possibility that the IVS in the AMD bacteria is a result of extensive genetic exchange between a

  15. Exceptional preservation of Mn-oxidizing microbes in cave stromatolites (El Soplao, Spain)

    Science.gov (United States)

    Lozano, Rafael P.; Rossi, Carlos

    2012-05-01

    Many ferromanganese stromatolites of El Soplao Cave (N Spain) are characterized for the exceptional preservation and high diversity of microbial fossils, probably representing the best example of microbial preservation described in ferromanganese deposits so far. The El Soplao stromatolites are mainly formed by polymetallic Mn-rich oxides with subordinate and variable amounts of detrital material, and consist of both dendritic and laminar microfacies. In both microfacies, microbial forms are abundant in the relatively pure Mn-oxide rich material, whereas they are scarce in areas with significant detrital material. Microbial forms are observed either in cross section, completely embedded in the Mn-oxide-rich matrix, or in three dimensions lining the walls of pores. Based on their morphology, we have separated the most abundant microbial forms into six main morphotypes and six additional submorphotypes, most of which can be assigned to bacteria. Most morphotypes consist of coccoid, coccobacilus, or filamentous forms. Therefore they are not diagnostic of any particular bacterial group. However, the ovoid cells of morphotype B show cylindrical polar protuberances typical of prosthecate alpha-Proteobacteria. On the basis of characteristic morphological features, three submorphotypes of morphotype B can be assigned to three alpha-Proteobacteria genera: Hyphomicrobium, Pedomicrobium, and Caulobacter. This ascription is supported by the well known Mn-oxidizing behavior of both Pedomicrobium and Caulobacter, and by the common presence of Hyphomicrobium in ferromanganese deposits elsewhere. The excellent microbial preservation is partly related to the origin of the ferromanganese oxides, i.e. extracellular precipitation induced by microbial metabolism. Other factors contributing to the good microbial preservation are the relatively low degree of diagenetic alteration, and the relatively high accretion rates of stromatolites compared to other ferromanganese deposits. The

  16. [Effect of long-term application of nitrogen fertilizer on the diversity of nitrifying genes (amoA and hao) in paddy soil].

    Science.gov (United States)

    Chen, Chun-lan; Wu, Min-na; Wei, Wen-xue

    2011-05-01

    The aim of this study was to determine the effect of long-term (16 years) application of nitrogen fertilizer on the diversity of nitrifying genes (amoA and hao) in paddy soil on the basis of long-term paddy field experimental station (started in 1990) located in Taoyuan, with the molecular approaches of PCR, constructing libraries and sequencing. The fertilizer was urea and no fertilizer was as control. The Shannon index showed that long-term application of nitrogen fertilizer made the diversity of amoA gene descend while no effect on the diversity of hao gene. The LIBSHUFF statistical analyses demonstrated that both amoA and hao libraries of CK and N treatments were significantly different from each other and the rarefaction curves of libraries failed to meet the plateaus indicating that there were lots kinds of genes haven't been detected. The results of blasting with GenBank and the phylogenetic tree showed that the amoA genes detected in our study had a similarity with the uncultured gene of amoA, which showed some similar to Nitrosospira. Otherwise, the hao genes cloned showed a relationship to the genes of cultured bacteria such as Silicibacteria, Nitrosospira and Methylococcus, and the hao genes found in the N treatment dominated in alpha-Proteobacteria. These results suggest that long-term fertilization of nitrogen had significant impacts on the diversity or community of amoA and hao genes.

  17. A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean

    Institute of Scientific and Technical Information of China (English)

    WANG Jing; KAN Jinjun; BORECKI Laura; ZHANG Xiaodong; WANG Dongxiao; SUN Jun

    2016-01-01

    Besides being critical components of marine food web, microorganisms play vital roles in biogeochemical cycling of nutrients and elements in the ocean. Currently little is known about microbial population structure and their distributions in the eastern Indian Ocean. In this study, we applied molecular approaches including polymerase chain reaction-denaturant gradient gel electrophoresis (PCR-DGGE) and High-Throughput next generation sequencing to investigate bacterial 16S rRNA genes from the equatorial regions and the adjacent Bay of Bengal in the eastern Indian Ocean. In general,Bacteroidetes,Proteobacteria (mainlyAlpha, andGamma),Actinobacteria, Cyanobacteria andPlanctomycetes dominated the microbial communities. Horizontally distinct spatial distribution of major microbial groups was observed from PCR-DGGE gel image analyses. However, further detailed characterization of community structures by pyrosequencing suggested a more pronounced stratified distribution pattern:Cyanobacteria andActinobacteria were more predominant at surface water (25 m);Bacteroidetes dominated at 25 m and 150 m whileProteobacteria (mainlyAlphaproteobacteria) occurred more frequently at 75 m water depth. With increasing water depth, the bacterial communities from different locations tended to share high similarity, indicating a niche partitioning for minor groups of bacteria recovered with high throughput sequencing approaches. This study provided the first “snapshot” on biodiversity and spatial distribution ofBacteria in water columns in the eastern Indian Ocean, and the findings further emphasized the potential functional roles of these microbes in energy and resource cycling in the eastern Indian Ocean.

  18. Genomic differentiation among two strains of the PS1 clade isolated from geographically separated marine habitats

    KAUST Repository

    Jimenez Infante, Francy M.

    2014-05-22

    Using dilution-to-extinction cultivation, we isolated a strain affiliated with the PS1 clade from surface waters of the Red Sea. Strain RS24 represents the second isolate of this group of marine Alphaproteobacteria after IMCC14465 that was isolated from the East (Japan) Sea. The PS1 clade is a sister group to the OCS116 clade, together forming a putatively novel order closely related to Rhizobiales. While most genomic features and most of the genetic content are conserved between RS24 and IMCC14465, their average nucleotide identity (ANI) is < 81%, suggesting two distinct species of the PS1 clade. Next to encoding two different variants of proteorhodopsin genes, they also harbor several unique genomic islands that contain genes related to degradation of aromatic compounds in IMCC14465 and in polymer degradation in RS24, possibly reflecting the physicochemical differences in the environment they were isolated from. No clear differences in abundance of the genomic content of either strain could be found in fragment recruitment analyses using different metagenomic datasets, in which both genomes were detectable albeit as minor part of the communities. The comparative genomic analysis of both isolates of the PS1 clade and the fragment recruitment analysis provide first insights into the ecology of this group. © 2014 Federation of European Microbiological Societies.

  19. Live Probiotic Cultures and the Gastrointestinal Tract: Symbiotic Preservation of Tolerance Whilst Attenuating Pathogenicity.

    Directory of Open Access Journals (Sweden)

    Luis eVitetta

    2014-10-01

    Full Text Available Bacteria comprise the earliest form of independent life on this planet. Bacterial development has included co–operative symbiosis with plants (e.g., Leguminosae family and nitrogen fixing bacteria in soil and animals (e.g., the gut microbiome. A fusion event of two prokaryotes evolutionarily gave rise to the eukaryote cell in which mitochondria may be envisaged as a genetically functional mosaic, a relic from one of the prokaryote cells. The discovery of bacterial inhibitors such chloramphenicol and others has been exploited to highlight mitochondria as arising from a bacterial progenitor. As such the evolution of human life has been complexly connected to bacterial activity. This is embodied, by the appearance of mitochondria in eukaryotes (alphaproteobacteria contribution, a significant endosymbiotic evolutionary event. During the twentieth century there was an increasing dependency on anti–microbials as mainline therapy against bacterial infections. It is only comparatively recently that the essential roles played by the gastrointestinal tract (GIT microbiome in animal health and development has been recognized as opposed to the GIT microbiome being a toxic collection of micro–organisms. It is now well documented that t

  20. Brucella β 1,2 cyclic glucan is an activator of human and mouse dendritic cells.

    Directory of Open Access Journals (Sweden)

    Anna Martirosyan

    Full Text Available Bacterial cyclic glucans are glucose polymers that concentrate within the periplasm of alpha-proteobacteria. These molecules are necessary to maintain the homeostasis of the cell envelope by contributing to the osmolarity of Gram negative bacteria. Here, we demonstrate that Brucella β 1,2 cyclic glucans are potent activators of human and mouse dendritic cells. Dendritic cells activation by Brucella β 1,2 cyclic glucans requires TLR4, MyD88 and TRIF, but not CD14. The Brucella cyclic glucans showed neither toxicity nor immunogenicity compared to LPS and triggered antigen-specific CD8(+ T cell responses in vivo. These cyclic glucans also enhanced antigen-specific CD4(+ and CD8(+ T cell responses including cross-presentation by different human DC subsets. Brucella β 1,2 cyclic glucans increased the memory CD4(+ T cell responses of blood mononuclear cells exposed to recombinant fusion proteins composed of anti-CD40 antibody and antigens from both hepatitis C virus and Mycobacterium tuberculosis. Thus cyclic glucans represent a new class of adjuvants, which might contribute to the development of effective antimicrobial therapies.

  1. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident

    Energy Technology Data Exchange (ETDEWEB)

    Kasai, Y.; Kishira, H.; Syutsubo, K.; Harayama, S.

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, {alpha}-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10{sup 5} to 1.6 x 10{sup 6} bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation. (Author)

  2. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident.

    Science.gov (United States)

    Kasai, Y; Kishira, H; Syutsubo, K; Harayama, S

    2001-04-01

    In January 1997, the tanker Nakhodka sank in the Japan Sea, and more than 5000 tons of heavy oil leaked. The released oil contaminated more than 500 km of the coastline, and some still remained even by June 1999. To investigate the long-term influence of the Nakhodka oil spill on marine bacterial populations, sea water and residual oil were sampled from the oil-contaminated zones 10, 18, 22 and 29 months after the accident, and the bacterial populations in these samples were analysed by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. The dominant DGGE bands were sequenced, and the sequences were compared with those in DNA sequence libraries. Most of the bacteria in the sea water samples were classified as the Cytophaga-Flavobacterium-Bacteroides phylum, alpha-Proteobacteria or cyanobacteria. The bacteria detected in the oil paste samples were different from those detected in the sea water samples; they were types related to hydrocarbon degraders, exemplified by strains closely related to Sphingomonas subarctica and Alcanivorax borkumensis. The sizes of the major bacterial populations in the oil paste samples ranged from 3.4 x 10(5) to 1.6 x 10(6) bacteria per gram of oil paste, these low numbers explaining the slow rate of natural attenuation.

  3. Culturable bacterial diversity in rhizosphere of Bashania fangiana%冷箭竹根际土壤中可培养细菌的多样性

    Institute of Scientific and Technical Information of China (English)

    刘敏; 李潞滨; 杨凯; 韩继刚; 朱宝成; 彭镇华

    2008-01-01

    为了解冷箭竹(Bashania fangiana)根际土壤中可培养细菌的多样性,2006年5月从四川卧龙自然保护区冷箭竹根际土壤中共分离出50株具不同菌落形态的细菌.16S rDNA序列分析结果表明:50株菌分属于10个属26个种.27株属于变形菌门γ亚群(Gammaproteobaeteria)(42.3%)、9株属于厚壁菌门(Firmicutes)(26.9%)、4株属于放线菌门(Actinobacteria)(15.4%)、6株属于变形菌门β亚群(Betaproteobacteria)(7.7%)、3株属于变形菌门α亚群(Alphaproteobacteria)(3.9%),1株与土地杆菌属(Pedobacter)关系密切.假单胞菌属(Pseudomonas)和芽孢杆菌属(Bacillus)为优势菌属.2株菌为可能的新种或属.研究表明冷箭竹根际土壤中含有较为丰富的微生物多样性.

  4. Simultaneous selection of soil electroactive bacterial communities associated to anode and cathode in a two-chamber Microbial Fuel Cell

    Science.gov (United States)

    Chiellini, Carolina; Bacci, Giovanni; Fani, Renato; Mocali, Stefano

    2016-04-01

    Different bacteria have evolved strategies to transfer electrons over their cell surface to (or from) their extracellular environment. This electron transfer enables the use of these bacteria in bioelectrochemical systems (BES) such as Microbial Fuel Cells (MFCs). In MFC research the biological reactions at the cathode have long been a secondary point of interest. However, bacterial biocathodes in MFCs represent a potential advantage compared to traditional cathodes, for both their low costs and their low impact on the environment. The main challenge in biocathode set-up is represented by the selection of a bacterial community able to efficiently accept electrons from the electrode, starting from an environmental matrix. In this work, a constant voltage was supplied on a two-chamber MFC filled up with soil over three weeks in order to simultaneously select an electron donor bacterial biomass on the anode and an electron acceptor biomass on the cathode, starting from the same soil. Next Generation Sequencing (NGS) analysis was performed to characterize the bacterial community of the initial soil, in the anode, in the cathode and in the control chamber not supplied with any voltage. Results highlighted that both the MFC conditions and the voltage supply affected the soil bacterial communities, providing a selection of different bacterial groups preferentially associated to the anode (Betaproteobacteria, Bacilli and Clostridia) and to the cathode (Actinobacteria and Alphaproteobacteria). These results confirmed that several electroactive bacteria are naturally present within a top soil and, moreover, different soil bacterial genera could provide different electrical properties.

  5. Genome-engineered Sinorhizobium meliloti for the production of poly(lactic-co-3-hydroxybutyric) acid copolymer.

    Science.gov (United States)

    Tran, Tam T; Charles, Trevor C

    2016-02-01

    Economically competitive commercial production of biodegradable bioplastics with desirable properties is an important goal. In this study, we demonstrate the use of chromosome engineering of an alternative bacterial host, Sinorhizobium meliloti, for production of the copolymer, poly(lactate-co-3-hydroxybutyrate). Codon-optimized genes for 2 previously engineered enzymes, Clostridium propionicum propionate CoA transferase (Pct532Cp) and Pseudomonas sp. strain MBEL 6-19 polyhydroxyalkanoate (PHA) synthase 1 (PhaC1400Ps6-19), were introduced into S. meliloti Rm1021 by chromosome integration, replacing the native phbC gene. On the basis of phenotypic analysis and detection of polymer product by gas chromatography analysis, synthesis and accumulation of the copolymer was confirmed. The chromosome integrant strain, with the introduced genes under the control of the native phbC promoter, is able to produce over 15% cell dry mass of poly(lactate-co-3-hydroxybutyrate), containing 30 mol% lactate, from growth on mannitol. We were also able to purify the polymer from the culture and confirm the structure by NMR and GC-MS. To our knowledge, this is the first demonstration of production of this copolymer in the Alphaproteobacteria. Further optimization of this system may eventually yield strains that are able to produce economically viable commercial product.

  6. Sinorhizobium meliloti CpdR1 is critical for co-ordinating cell cycle progression and the symbiotic chronic infection.

    Science.gov (United States)

    Kobayashi, Hajime; De Nisco, Nicole J; Chien, Peter; Simmons, Lyle A; Walker, Graham C

    2009-08-01

    ATP-driven proteolysis plays a major role in regulating the bacterial cell cycle, development and stress responses. In the nitro -fixing symbiosis with host plants, Sinorhizobium meliloti undergoes a profound cellular differentiation, including endoreduplication of the ome. The regulatory mechanisms governing the alterations of the S. meliloti cell cycle in planta are largely unknown. Here, we report the characterization of two cpdR homologues, cpdR1 and cpdR2, of S. meliloti that encode single-domain response regulators. In Caulobacter crescentus, CpdR controls the polar localization of the ClpXP protease, thereby mediating the regulated proteolysis of key protein(s), such as CtrA, involved in cell cycle progression. The S. meliloti cpdR1-null mutant can invade the host cytoplasm, however, the intracellular bacteria are unable to differentiate into bacteroids. We show that S. meliloti CpdR1 has a polar localization pattern and a role in ClpX positioning similar to C. crescentus CpdR, suggesting a conserved function of CpdR proteins among alpha-proteobacteria. However, in S. meliloti, free-living cells of the cpdR1-null mutant show a striking morphology of irregular coccoids and aberrant DNA replication. Thus, we demonstrate that CpdR1 mediates the co-ordination of cell cycle events, which are critical for both the free-living cell division and the differentiation required for the chronic intracellular infection.

  7. The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti.

    Science.gov (United States)

    Pini, Francesco; Frage, Benjamin; Ferri, Lorenzo; De Nisco, Nicole J; Mohapatra, Saswat S; Taddei, Lucilla; Fioravanti, Antonella; Dewitte, Frederique; Galardini, Marco; Brilli, Matteo; Villeret, Vincent; Bazzicalupo, Marco; Mengoni, Alessio; Walker, Graham C; Becker, Anke; Biondi, Emanuele G

    2013-10-01

    Sinorhizobium meliloti is a soil bacterium that invades the root nodules it induces on Medicago sativa, whereupon it undergoes an alteration of its cell cycle and differentiates into nitrogen-fixing, elongated and polyploid bacteroid with higher membrane permeability. In Caulobacter crescentus, a related alphaproteobacterium, the principal cell cycle regulator, CtrA, is inhibited by the phosphorylated response regulator DivK. The phosphorylation of DivK depends on the histidine kinase DivJ, while PleC is the principal phosphatase for DivK. Despite the importance of the DivJ in C. crescentus, the mechanistic role of this kinase has never been elucidated in other Alphaproteobacteria. We show here that the histidine kinases DivJ together with CbrA and PleC participate in a complex phosphorylation system of the essential response regulator DivK in S. meliloti. In particular, DivJ and CbrA are involved in DivK phosphorylation and in turn CtrA inactivation, thereby controlling correct cell cycle progression and the integrity of the cell envelope. In contrast, the essential PleC presumably acts as a phosphatase of DivK. Interestingly, we found that a DivJ mutant is able to elicit nodules and enter plant cells, but fails to establish an effective symbiosis suggesting that proper envelope and/or low CtrA levels are required for symbiosis.

  8. Dual control of Sinorhizobium meliloti RpoE2 sigma factor activity by two PhyR-type two-component response regulators.

    Science.gov (United States)

    Bastiat, Bénédicte; Sauviac, Laurent; Bruand, Claude

    2010-04-01

    RpoE2 is an extracytoplasmic function (ECF) sigma factor involved in the general stress response of Sinorhizobium meliloti, the nitrogen-fixing symbiont of the legume plant alfalfa. RpoE2 orthologues are widely found among alphaproteobacteria, where they play various roles in stress resistance and/or host colonization. In this paper, we report a genetic and biochemical investigation of the mechanisms of signal transduction leading to S. meliloti RpoE2 activation in response to stress. We showed that RpoE2 activity is negatively controlled by two paralogous anti-sigma factors, RsiA1 (SMc01505) and RsiA2 (SMc04884), and that RpoE2 activation by stress requires two redundant paralogous PhyR-type response regulators, RsiB1 (SMc01504) and RsiB2 (SMc00794). RsiB1 and RsiB2 do not act at the level of rpoE2 transcription but instead interact with the anti-sigma factors, and we therefore propose that they act as anti-anti-sigma factors to relieve RpoE2 inhibition in response to stress. This model closely resembles a recently proposed model of activation of RpoE2-like sigma factors in Methylobacterium extorquens and Bradyrhizobium japonicum, but the existence of two pairs of anti- and anti-anti-sigma factors in S. meliloti adds an unexpected level of complexity, which may allow the regulatory system to integrate multiple stimuli.

  9. Microbial Community Changes in Hydraulic Fracturing Fluids and Produced Water from Shale Gas Extraction

    Energy Technology Data Exchange (ETDEWEB)

    Mohan, Arvind Murali; Hartsock, Angela; Bibby, Kyle J; Hammack, Richard W; Vidic, Radisav D; Gregory, Kelvin B

    2013-11-19

    Microbial communities associated with produced water from hydraulic fracturing are not well understood, and their deleterious activity can lead to significant increases in production costs and adverse environmental impacts. In this study, we compared the microbial ecology in prefracturing fluids (fracturing source water and fracturing fluid) and produced water at multiple time points from a natural gas well in southwestern Pennsylvania using 16S rRNA gene-based clone libraries, pyrosequencing, and quantitative PCR. The majority of the bacterial community in prefracturing fluids constituted aerobic species affiliated with the class Alphaproteobacteria. However, their relative abundance decreased in produced water with an increase in halotolerant, anaerobic/facultative anaerobic species affiliated with the classes Clostridia, Bacilli, Gammaproteobacteria, Epsilonproteobacteria, Bacteroidia, and Fusobacteria. Produced water collected at the last time point (day 187) consisted almost entirely of sequences similar to Clostridia and showed a decrease in bacterial abundance by 3 orders of magnitude compared to the prefracturing fluids and produced water samplesfrom earlier time points. Geochemical analysis showed that produced water contained higher concentrations of salts and total radioactivity compared to prefracturing fluids. This study provides evidence of long-term subsurface selection of the microbial community introduced through hydraulic fracturing, which may include significant implications for disinfection as well as reuse of produced water in future fracturing operations.

  10. Intrinsic rates of petroleum hydrocarbon biodegradation in Gulf of Mexico intertidal sandy sediments and its enhancement by organic substrates

    Energy Technology Data Exchange (ETDEWEB)

    Mortazavi, Behzad, E-mail: bmortazavi@ua.edu [University of Alabama, Department of Biological Sciences, Box 870344, University of Alabama, Tuscaloosa, AL 35487 (United States); Dauphin Island Sea Lab, 101 Bienville Boulevard, Dauphin Island, AL, 36528 (United States); Horel, Agota [University of Alabama, Department of Biological Sciences, Box 870344, University of Alabama, Tuscaloosa, AL 35487 (United States); Dauphin Island Sea Lab, 101 Bienville Boulevard, Dauphin Island, AL, 36528 (United States); Beazley, Melanie J.; Sobecky, Patricia A. [University of Alabama, Department of Biological Sciences, Box 870344, University of Alabama, Tuscaloosa, AL 35487 (United States)

    2013-01-15

    The rates of crude oil degradation by the extant microorganisms in intertidal sediments from a northern Gulf of Mexico beach were determined. The enhancement in crude oil degradation by amending the microbial communities with marine organic matter was also examined. Replicate mesocosm treatments consisted of: (i) controls (intertidal sand), (ii) sand contaminated with crude oil, (iii) sand plus organic matter, and (iv) sand plus crude oil and organic matter. Carbon dioxide (CO{sub 2}) production was measured daily for 42 days and the carbon isotopic ratio of CO{sub 2} (δ{sup 13}CO{sub 2}) was used to determine the fraction of CO{sub 2} derived from microbial respiration of crude oil. Bacterial 16S rRNA clone library analyses indicated members of Actinobacteria, Bacteroidetes, and Chloroflexi occurred exclusively in control sediments whereas Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Firmicutes occurred in both control and oil contaminated sediments. Members of the hydrocarbon-degrading genera Hydrocarboniphaga, Pseudomonas, and Pseudoxanthomonas were found primarily in oil contaminated treatments. Hydrocarbon mineralization was 76% higher in the crude oil amended with organic matter treatment compared to the rate in the crude oil only treatment indicating that biodegradation of crude oil in the intertidal zone by an extant microbial community is enhanced by input of organic matter.

  11. Persistence of bacterial and archaeal communities in sea ice through an Arctic winter.

    Science.gov (United States)

    Collins, R Eric; Rocap, Gabrielle; Deming, Jody W

    2010-07-01

    The structure of bacterial communities in first-year spring and summer sea ice differs from that in source seawaters, suggesting selection during ice formation in autumn or taxon-specific mortality in the ice during winter. We tested these hypotheses by weekly sampling (January-March 2004) of first-year winter sea ice (Franklin Bay, Western Arctic) that experienced temperatures from -9 degrees C to -26 degrees C, generating community fingerprints and clone libraries for Bacteria and Archaea. Despite severe conditions and significant decreases in microbial abundance, no significant changes in richness or community structure were detected in the ice. Communities of Bacteria and Archaea in the ice, as in under-ice seawater, were dominated by SAR11 clade Alphaproteobacteria and Marine Group I Crenarchaeota, neither of which is known from later season sea ice. The bacterial ice library contained clones of Gammaproteobacteria from oligotrophic seawater clades (e.g. OM60, OM182) but no clones from gammaproteobacterial genera commonly detected in later season sea ice by similar methods (e.g. Colwellia, Psychrobacter). The only common sea ice bacterial genus detected in winter ice was Polaribacter. Overall, selection during ice formation and mortality during winter appear to play minor roles in the process of microbial succession that leads to distinctive spring and summer sea ice communities.

  12. Inoculum selection is crucial to ensure operational stability in anaerobic digestion.

    Science.gov (United States)

    De Vrieze, Jo; Gildemyn, Sylvia; Vilchez-Vargas, Ramiro; Jáuregui, Ruy; Pieper, Dietmar H; Verstraete, Willy; Boon, Nico

    2015-01-01

    Anaerobic digestion is considered a key technology for the future bio-based economy. The microbial consortium carrying out the anaerobic digestion process is quite complex, and its exact role in terms of "elasticity", i.e., the ability to rapidly adapt to changing conditions, is still unknown. In this study, the role of the initial microbial community in terms of operational stability and stress tolerance was evaluated during a 175-day experiment. Five different inocula from stable industrial anaerobic digesters were fed a mixture of waste activated sludge and glycerol. Increasing ammonium pulses were applied to evaluate stability and stress tolerance. A different response in terms of start-up and ammonium tolerance was observed among the different inocula. Methanosaetaceae were the dominant acetoclastic methanogens, yet, Methanosarcinaceae increased in abundance at elevated ammonium concentrations. A shift from a Firmicutes to a Proteobacteria dominated bacterial community was observed in failing digesters. Methane production was strongly positively correlated with Methanosaetaceae, but also with Bacteria related to Anaerolinaceae, Clostridiales, and Alphaproteobacteria. Volatile fatty acids were strongly positively correlated with Betaproteobacteria and Bacteroidetes, yet ammonium concentration only with Bacteroidetes. Overall, these results indicate the importance of inoculum selection to ensure stable operation and stress tolerance in anaerobic digestion.

  13. A novel bacterial disease of the European shore crab, Carcinus maenas molecular pathology and epidemiology.

    Science.gov (United States)

    Eddy, Fiona; Powell, Adam; Gregory, Simon; Nunan, Linda M; Lightner, Donald V; Dyson, Paul J; Rowley, Andrew F; Shields, Robin J

    2007-09-01

    Several rickettsia-like diseases have been reported in arthropods (insects and crustaceans), some of which result in significant losses of economically important species such as shrimp and crabs. This study reports on the molecular pathology of a recently emerged disease of the European shore crab, Carcinus maenas, termed milky disease - named as a result of the unusual milky appearance of the haemolymph (blood). This disease was more prevalent (>26 %) during summer months when the water temperature in a pilot crab farm was approximately 19 degrees C. The putative causative agent of the disease was a Gram-negative bacterium that could not be cultured on a range of agar-based growth media. Diseased crabs showed significant reductions in free blood cell numbers and total serum protein. Such animals also displayed raised levels of glucose and ammonium in blood. Ultrastructural and in situ hybridization studies revealed that the causative agent associated with milky disease multiplied in the fixed phagocytes of the hepatopancreas (digestive gland), ultimately to be released into the haemolymph, where the circulating blood cells showed little response to the presence of these agents. Attempts to induce the infection by short-term temperature stress failed, as did transmission experiments where healthy crabs were fed infected tissues from milky disease affected individuals. Sequence analysis of the 16S rRNA gene from the milky disease bacteria indicated that they are a previously undescribed species of alpha-proteobacteria with little phylogenetic similarity to members of the order Rickettsiales.

  14. Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.

    Science.gov (United States)

    Baron, Julianne L; Vikram, Amit; Duda, Scott; Stout, Janet E; Bibby, Kyle

    2014-01-01

    Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.

  15. Oil sheen weathering post Deepwater Horizon

    Science.gov (United States)

    Kellermann, M. Y.; Redmond, M. C.; Reddy, C. M.; Aeppli, C.; Nelson, R. K.; Valentine, D. L.

    2013-12-01

    A recently published study identified the source of the reoccurred oil sheens close to the Deepwater Horizon (DWH) disaster site as a finite contamination most likely derived from tanks and pits on the DWH wreckage itself. Here we use geochemical fingerprinting and microbial community analysis to better understand the fate and weathering processes affecting these surface oils. Both, alkanes and polycyclic aromatic hydrocarbons (PAHs) are shown to reflect a linear decrease of hydrocarbon compounds with increasing distance to the DWH wreckage site (equivalent to exposure time on the sea surface). These results indicate that in the early stage of weathering the combined effects of dissolution and evaporation dominate the degradation of these surface oils. Sheen microbial communities were dominated by Cyanobacteria, Planctomycetes, Verrucomicrobia, Flavobacteria, Alphaproteobacteria, and Deltaproteobacteria, with low relative abundances of Gammaproteobacteria likely to be hydrocarbon degraders (no more than 15% of sequences in each sample). However, some of these Gammaproteobacteria were closely related to putative hydrocarbon degraders observed in abundance in deep water plumes during the primary Deepwater Horizon spill, suggesting that very low levels of biodegradation may be also occurring. This in situ weathering experiment provides new insights in hydrocarbon weathering dynamics and shows how chemical and biological changes can potentially be masked by large evaporative losses of compounds smaller than C18 n-alkanes.

  16. Metaproteomics provides functional insight into activated sludge wastewater treatment.

    Directory of Open Access Journals (Sweden)

    Paul Wilmes

    Full Text Available BACKGROUND: Through identification of highly expressed proteins from a mixed culture activated sludge system this study provides functional evidence of microbial transformations important for enhanced biological phosphorus removal (EBPR. METHODOLOGY/PRINCIPAL FINDINGS: A laboratory-scale sequencing batch reactor was successfully operated for different levels of EBPR, removing around 25, 40 and 55 mg/l P. The microbial communities were dominated by the uncultured polyphosphate-accumulating organism "Candidatus Accumulibacter phosphatis". When EBPR failed, the sludge was dominated by tetrad-forming alpha-Proteobacteria. Representative and reproducible 2D gel protein separations were obtained for all sludge samples. 638 protein spots were matched across gels generated from the phosphate removing sludges. 111 of these were excised and 46 proteins were identified using recently available sludge metagenomic sequences. Many of these closely match proteins from "Candidatus Accumulibacter phosphatis" and could be directly linked to the EBPR process. They included enzymes involved in energy generation, polyhydroxyalkanoate synthesis, glycolysis, gluconeogenesis, glycogen synthesis, glyoxylate/TCA cycle, fatty acid beta oxidation, fatty acid synthesis and phosphate transport. Several proteins involved in cellular stress response were detected. CONCLUSIONS/SIGNIFICANCE: Importantly, this study provides direct evidence linking the metabolic activities of "Accumulibacter" to the chemical transformations observed in EBPR. Finally, the results are discussed in relation to current EBPR metabolic models.

  17. Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

    KAUST Repository

    Bougouffa, Salim

    2013-03-29

    Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

  18. Dust Rains Deliver Diverse Assemblages of Microorganisms to the Eastern Mediterranean

    Science.gov (United States)

    Itani, Ghida Nouhad; Smith, Colin Andrew

    2016-03-01

    Dust rains may be particularly effective at delivering microorganisms, yet their biodiversities have been seldom examined. During 2011 and 2012 in Beirut, Lebanon, 16 of 21 collected rainfalls appeared dusty. Trajectory modelling of air mass origins was consistent with North African sources and at least one Southwest Asian source. As much as ~4 g particulate matter, ~20 μg DNA, and 50 million colony forming units were found deposited per square meter during rainfalls each lasting less than one day. Sequencing of 93 bacteria and 25 fungi cultured from rain samples revealed diverse bacterial phyla, both Gram positive and negative, and Ascomycota fungi. Denaturing Gradient Gel Electrophoresis of amplified 16S rDNA of 13 rains revealed distinct and diverse assemblages of bacteria. Dust rain 16S libraries yielded 131 sequences matching, in decreasing order of abundance, Betaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria, Epsilonproteobacteria, Gammaproteobacteria, and Deltaproteobacteria. Clean rain 16S libraries yielded 33 sequences matching only Betaproteobacteria family Oxalobacteraceae. Microbial composition varied between dust rains, and more diverse and different microbes were found in dust rains than clean rains. These results show that dust rains deliver diverse communities of microorganisms that may be complex products of revived desert soil species and fertilized cloud species.

  19. Ocean currents shape the microbiome of Arctic marine sediments.

    Science.gov (United States)

    Hamdan, Leila J; Coffin, Richard B; Sikaroodi, Masoumeh; Greinert, Jens; Treude, Tina; Gillevet, Patrick M

    2013-04-01

    Prokaryote communities were investigated on the seasonally stratified Alaska Beaufort Shelf (ABS). Water and sediment directly underlying water with origin in the Arctic, Pacific or Atlantic oceans were analyzed by pyrosequencing and length heterogeneity-PCR in conjunction with physicochemical and geographic distance data to determine what features structure ABS microbiomes. Distinct bacterial communities were evident in all water masses. Alphaproteobacteria explained similarity in Arctic surface water and Pacific derived water. Deltaproteobacteria were abundant in Atlantic origin water and drove similarity among samples. Most archaeal sequences in water were related to unclassified marine Euryarchaeota. Sediment communities influenced by Pacific and Atlantic water were distinct from each other and pelagic communities. Firmicutes and Chloroflexi were abundant in sediment, although their distribution varied in Atlantic and Pacific influenced sites. Thermoprotei dominated archaea in Pacific influenced sediments and Methanomicrobia dominated in methane-containing Atlantic influenced sediments. Length heterogeneity-PCR data from this study were analyzed with data from methane-containing sediments in other regions. Pacific influenced ABS sediments clustered with Pacific sites from New Zealand and Chilean coastal margins. Atlantic influenced ABS sediments formed another distinct cluster. Density and salinity were significant structuring features on pelagic communities. Porosity co-varied with benthic community structure across sites and methane did not. This study indicates that the origin of water overlying sediments shapes benthic communities locally and globally and that hydrography exerts greater influence on microbial community structure than the availability of methane.

  20. Hydrography shapes bacterial biogeography of the deep Arctic Ocean.

    Science.gov (United States)

    Galand, Pierre E; Potvin, Marianne; Casamayor, Emilio O; Lovejoy, Connie

    2010-04-01

    It has been long debated as to whether marine microorganisms have a ubiquitous distribution or patterns of biogeography, but recently a consensus for the existence of microbial biogeography is emerging. However, the factors controlling the distribution of marine bacteria remain poorly understood. In this study, we combine pyrosequencing and traditional Sanger sequencing of the 16S rRNA gene to describe in detail bacterial communities from the deep Arctic Ocean. We targeted three separate water masses, from three oceanic basins and show that bacteria in the Arctic Ocean have a biogeography. The biogeographical distribution of bacteria was explained by the hydrography of the Arctic Ocean and subsequent circulation of its water masses. Overall, this first taxonomic description of deep Arctic bacteria communities revealed an abundant presence of SAR11 (Alphaproteobacteria), SAR406, SAR202 (Chloroflexi) and SAR324 (Deltaproteobacteria) clusters. Within each cluster, the abundance of specific phylotypes significantly varied among water masses. Water masses probably act as physical barriers limiting the dispersal and controlling the diversity of bacteria in the ocean. Consequently, marine microbial biogeography involves more than geographical distances, as it is also dynamically associated with oceanic processes. Our ocean scale study suggests that it is essential to consider the coupling between microbial and physical oceanography to fully understand the diversity and function of marine microbes.

  1. Changes in microbial communities, photosynthesis and calcification of the coral Acropora gemmifera in response to ocean acidification

    Science.gov (United States)

    Zhou, Guowei; Yuan, Tao; Cai, Lin; Zhang, Weipeng; Tian, Renmao; Tong, Haoya; Jiang, Lei; Yuan, Xiangcheng; Liu, Sheng; Qian, Peiyuan; Huang, Hui

    2016-10-01

    With the increasing anthropogenic CO2 concentration, ocean acidification (OA) can have dramatic effects on coral reefs. However, the effects of OA on coral physiology and the associated microbes remain largely unknown. In the present study, reef-building coral Acropora gemmifera collected from a reef flat with highly fluctuating environmental condition in the South China Sea were exposed to three levels of partial pressure of carbon dioxide (pCO2) (i.e., 421, 923, and 2070 μatm) for four weeks. The microbial community structures associated with A. gemmifera under these treatments were analyzed using 16S rRNA gene barcode sequencing. The results revealed that the microbial community associated with A. gemmifera was highly diverse at the genus level and dominated by Alphaproteobacteria. More importantly, the microbial community structure remained rather stable under different pCO2 treatments. Photosynthesis and calcification in A. gemmifera, as indicated by enrichment of δ18O and increased depletion of δ13C in the coral skeleton, were significantly impaired only at the high pCO2 (2070 μatm). These results suggest that A. gemmifera can maintain a high degree of stable microbial communities despite of significant physiological changes in response to extremely high pCO2.

  2. Microbiote shift in the Medicago sativa rhizosphere in response to cyanotoxins extract exposure.

    Science.gov (United States)

    El Khalloufi, Fatima; Oufdou, Khalid; Bertrand, Marie; Lahrouni, Majida; Oudra, Brahim; Ortet, Philippe; Barakat, Mohamed; Heulin, Thierry; Achouak, Wafa

    2016-01-01

    The bloom-containing water bodies may have an impact due to cyanotoxins production on other microorganisms and aquatic plants. Where such water is being used for crops irrigation, the presence of cyanotoxins may also have a toxic impact on terrestrial plants and their rhizosphere microbiota. For that purpose, PCR-based 454 pyrosequencing was applied to phylogenetically characterize the bacterial community of Medicago sativa rhizosphere in response to cyanotoxins extract. This analysis revealed a wide diversity at species level, which decreased from unplanted soil to root tissues indicating that only some populations were able to compete for nutrients and niches in this selective habitat. Gemmatimonas, Actinobacteria, Deltaproteobacteria and Opitutae mainly inhabited the bulk soil, whereas, the root-adhering soil and the root tissues were inhabited by Gammaproteobacteria and Alphaproteobacteria. The proportion of these populations fluctuated in response to cyanotoxins extract exposure. Betaproteobacteria proportion increased in the three studied compartments, whereas Gammaproteobacteria proportion decreased except in the bulk soil. This study revealed the potential toxicity of cyanotoxins extract towards Actinobacteria, Gemmatimonas, Deltaproteobacteria, and Gammaproteobacteria, however Clostridia, Opitutae and bacteria related with Betaproteobacteria, were stimulated denoting their tolerance. Altogether, these data indicate that crop irrigation using cyanotoxins containing water might alter the rhizosphere functioning.

  3. Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

    Science.gov (United States)

    Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

    2015-02-01

    Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

  4. Microbial cargo: do bacteria on symbiotic propagules reinforce the microbiome of lichens?

    Science.gov (United States)

    Aschenbrenner, Ines Aline; Cardinale, Massimiliano; Berg, Gabriele; Grube, Martin

    2014-12-01

    According to recent research, bacteria contribute as recurrent associates to the lichen symbiosis. Yet, the variation of the microbiomes within species and across geographically separated populations remained largely elusive. As a quite common dispersal mode, lichens evolved vertical transmission of both fungal and algal partners in specifically designed mitotic propagules. Bacteria, if co-transmitted with these symbiotic propagules, could contribute to a geographical structure of lichen-associated microbiomes. The lung lichen was sampled from three localities in eastern Austria to analyse their associated bacterial communities by bar-coded pyrosequencing, network analysis and fluorescence in situ hybridization. For the first time, bacteria were documented to colonize symbiotic propagules of lichens developed for short-distance transmission of the symbionts. The propagules share the overall bacterial community structure with the thalli at class level, except for filamentous Cyanobacteria (Nostocophycideae), and with Alphaproteobacteria as predominant group. All three sampling sites share a core fraction of the microbiome. Bacterial communities of lichen thalli from the same sampling site showed higher similarity than those of distant populations. This variation and the potential co-dispersal of a microbiome fraction with structures of the host organism contribute new aspects to the 'everything is everywhere' hypothesis.

  5. Picoplankton Community Composition by CARD-FISH and Flow Cytometric Techniques: A Preliminary Study in Central Adriatic Sea Water

    Directory of Open Access Journals (Sweden)

    Anita Manti

    2012-01-01

    Full Text Available Data concerning picoplanktonic community composition and abundance in the Central Adriatic Sea are presented in an effort to improve the knowledge of bacterioplankton and autotrophic picoplankton and their seasonal changes. Flow cytometry analyses revealed the presence of two distinct bacteria populations: HNA and LNA cells. HNA cells showed an explicit correlation with viable and actively respiring cells. The study of viability and activity may increase our knowledge of the part that contributes really to the remineralization and bacterial biomass production. Authotrophic picoplankton abundance, especially picocyanobacteria, was strongly influenced by seasonality, indicating that light availability and water temperature are very important regulating factors. In terms of total carbon biomass, the main contribution came from heterotrophic bacteria with a lower contribution from autotrophic picoplankton. CARD-FISH evidenced, within the Eubacteria domain, the dominance of members of the phyla Alphaproteobacteria, with a strong contribution from SAR11clade, followed by Cytophaga-Flavobacterium and Gammaproteobacteria. The bacterial groups detected contributed differently depending when the sample was taken, suggesting possible seasonal patterns. This study documents for the first time picoplankton community composition in the Central Adriatic Sea using two different approaches, FCM and CARD-FISH, and could provide preliminary data for future studies.

  6. High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula

    Science.gov (United States)

    Franco, Diego C.; Signori, Camila N.; Duarte, Rubens T. D.; Nakayama, Cristina R.; Campos, Lúcia S.; Pellizari, Vivian H.

    2017-01-01

    Microorganisms dominate most Antarctic marine ecosystems, in terms of biomass and taxonomic diversity, and play crucial role in ecosystem functioning due to their high metabolic plasticity. Admiralty Bay is the largest bay on King George Island (South Shetland Islands, Antarctic Peninsula) and a combination of hydro-oceanographic characteristics (bathymetry, sea ice and glacier melting, seasonal entrance of water masses, turbidity, vertical fluxes) create conditions favoring organic carbon deposition on the seafloor and microbial activities. We sampled surface sediments from 15 sites across Admiralty Bay (100–502 m total depth) and the adjacent North Bransfield Basin (693–1147 m), and used the amplicon 454-sequencing of 16S rRNA gene tags to compare the bacterial composition, diversity, and microbial community structure across environmental parameters (sediment grain size, pigments and organic nutrients) between the two areas. Marine sediments had a high abundance of heterotrophic Gammaproteobacteria (92.4% and 83.8% inside and outside the bay, respectively), followed by Alphaproteobacteria (2.5 and 5.5%), Firmicutes (1.5 and 1.6%), Bacteroidetes (1.1 and 1.7%), Deltaproteobacteria (0.8 and 2.5%) and Actinobacteria (0.7 and 1.3%). Differences in alpha-diversity and bacterial community structure were found between the two areas, reflecting the physical and chemical differences in the sediments, and the organic matter input. PMID:28210255

  7. Opportunistic pathogens and elements of the resistome that are common in bottled mineral water support the need for continuous surveillance.

    Science.gov (United States)

    Falcone-Dias, Maria Fernanda; Centrón, Daniela; Pavan, Fernando; Moura, Adriana Candido da Silva; Naveca, Felipe Gomes; de Souza, Victor Costa; Farache Filho, Adalberto; Leite, Clarice Queico Fujimura

    2015-01-01

    Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc). A total of one hundred and six isolates were recovered from four of these bottled mineral water brands. Betaproteobacteria was predominant followed by Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Ninety percent of the bacteria isolated demonstrated resistance to seventeen of the nineteen antimicrobials tested. These antimicrobials included eight different classes, including 3rd and 4th generation cephalosporins, carbapenems and fluoroquinolones. Multidrug resistant bacteria were detected for fifty-nine percent of isolates in three water brands at counts up to 103 CFU/ml. Of major concern, the two bottled mineral water harboring opportunistic pathogens were also source of elements of the resistome that could be directly transferred to humans. All these differences found among brands highlight the need for continuous bacteriological surveillance of bottled mineral water.

  8. A Genomic Encyclopedia of the Root Nodule Bacteria: assessing genetic diversity through a systematic biogeographic survey.

    Science.gov (United States)

    Reeve, Wayne; Ardley, Julie; Tian, Rui; Eshragi, Leila; Yoon, Je Won; Ngamwisetkun, Pinyaruk; Seshadri, Rekha; Ivanova, Natalia N; Kyrpides, Nikos C

    2015-01-01

    Root nodule bacteria are free-living soil bacteria, belonging to diverse genera within the Alphaproteobacteria and Betaproteobacteria, that have the capacity to form nitrogen-fixing symbioses with legumes. The symbiosis is specific and is governed by signaling molecules produced from both host and bacteria. Sequencing of several model RNB genomes has provided valuable insights into the genetic basis of symbiosis. However, the small number of sequenced RNB genomes available does not currently reflect the phylogenetic diversity of RNB, or the variety of mechanisms that lead to symbiosis in different legume hosts. This prevents a broad understanding of symbiotic interactions and the factors that govern the biogeography of host-microbe symbioses. Here, we outline a proposal to expand the number of sequenced RNB strains, which aims to capture this phylogenetic and biogeographic diversity. Through the Vavilov centers of diversity (Proposal ID: 231) and GEBA-RNB (Proposal ID: 882) projects we will sequence 107 RNB strains, isolated from diverse legume hosts in various geographic locations around the world. The nominated strains belong to nine of the 16 currently validly described RNB genera. They include 13 type strains, as well as elite inoculant strains of high commercial importance. These projects will strongly support systematic sequence-based studies of RNB and contribute to our understanding of the effects of biogeography on the evolution of different species of RNB, as well as the mechanisms that determine the specificity and effectiveness of nodulation and symbiotic nitrogen fixation by RNB with diverse legume hosts.

  9. Integrated metagenomic and physiochemical analyses to evaluate the potential role of microbes in the sand filter of a drinking water treatment system.

    Directory of Open Access Journals (Sweden)

    Yaohui Bai

    Full Text Available While sand filters are widely used to treat drinking water, the role of sand filter associated microorganisms in water purification has not been extensively studied. In the current investigation, we integrated molecular (based on metagenomic and physicochemical analyses to elucidate microbial community composition and function in a common sand filter used to treat groundwater for potable consumption. The results revealed that the biofilm developed rapidly within 2 days (reaching ≈ 10(11 prokaryotes per gram in the sand filter along with abiotic and biotic particulates accumulated in the interstitial spaces. Bacteria (up to 90% dominated the biofilm microbial community, with Alphaproteobacteria being the most common class. Thaumarchaeota was the sole phylum of Archaea, which might be involved in ammonia oxidation. Function annotation of metagenomic datasets revealed a number of aromatic degradation pathway genes, such as aromatic oxygenase and dehydrogenase genes, in the biofilm, suggesting a significant role for microbes in the breakdown of aromatic compounds in groundwater. Simultaneous nitrification and denitrification pathways were confirmed as the primary routes of nitrogen removal. Dissolved heavy metals in groundwater, e.g. Mn(2+ and As(3+, might be biologically oxidized to insoluble or easily adsorbed compounds and deposited in the sand filter. Our study demonstrated that the role of the microbial community in the sand filter treatment system are critical to effective water purification in drinking water.

  10. Effects of Transgenic DREB Toybean Dongnong50 on Diversity of Soil Nitrogen-ifxing Bacteria

    Institute of Scientific and Technical Information of China (English)

    Zhang Chun-miao; Dong Lei; Jin Yu; Qu Juan-juan

    2015-01-01

    Drought is a bottleneck for worldwide soybean production which is getting more serious as the climate continues to worsen. Dehydration responsive element binding (DREB) is a kind of transcription factor that regulates the expression of stress tolerance-related genes in response to drought, high salinity and cold stress in plant. Soybean withDREB gene possesses the drought resisting capability which is helpful to increase the yield. However, the potential risk of genetically modified plants (GMPs) on soil microbial community is still in debate. In order to understand the effects of transgenic DREB soybean on the nitrogen-fixing bacteria, the diversity ofnifH gene in pot experiments planted transgenic soybean and near-isogenic nontransgenic soybean under normal water condition and drought stress condition was analyzed by PCR-DGGE and sequence analysis. The results showed that transgenic soybean under normal water condition decrease the diversity of the nitrogen-fixing bacteria in the seeding stage and flowering stage, but had no notable effect in other stages. Under drought stress, transgenic soybean reduced the diversity of the nitrogen-fixing bacteria in the flowering stage, but had no notable effects on other stages. Phylogenic analysis revealed that g7, g13, g15 and g19 had a close relationship withAlphaproteobacteria, g12 had a close relationship withAzonexus, others were related toBetaproteobacteria and Burkholderia.

  11. Bioremediation of polychlorinated-p-dioxins/dibenzofurans contaminated soil using simulated compost-amended landfill reactors under hypoxic conditions.

    Science.gov (United States)

    Chen, Wei-Yu; Wu, Jer-Horng; Lin, Shih-Chiang; Chang, Juu-En

    2016-07-15

    Compost-amended landfill reactors were developed to reduce polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) in contaminated soils. By periodically recirculating leachate and suppling oxygen, the online monitoring of the oxidation reduction potential confirmed that the reactors were maintained under hypoxic conditions, with redox levels constantly fluctuating between -400 and +80mV. The subsequent reactor operation demonstrated that PCDD/F degradation in soil could be facilitated by amending compost originating from the cow manure and waste sludge and that the degradation might be affected by the availability of easily degradable substrates in the soil and compost. The pyrosequencing analysis of V4/V5 regions of bacterial 16S rRNA genes suggested that species richness of the soil microbial community was increased by a factor of 1.37-1.61. Although the bacterial community varied with the compost origin and changed markedly during reactor operation, it was dominated by Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Firmicutes. The aerotolerant anaerobic Sedimentibacter and Propionibacterium spp., and the uncultured Chloroflexi group could be temporarily induced to a high abundance by amending the cow manure compost; the bacterial growths were associated with the rapid degradation of PCDD/Fs. Overall, the novel bioremediation method for PCDD/F-contaminated soils using hypoxic conditions was effective, simple, energy saving, and thus easily practicable.

  12. Bacterial Diversity and Bioprospecting for Cold-Active Hydrolytic Enzymes from Culturable Bacteria Associated with Sediment from Nella Fjord, Eastern Antarctica

    Directory of Open Access Journals (Sweden)

    Bo Chen

    2011-01-01

    Full Text Available The diversity and cold-active hydrolytic enzymes of culturable bacteria associated with sandy sediment from Nella Fjord, Eastern Antarctica (69°22′6″ S, 76°21′45″ E was investigated. A total of 33 aerobic heterotrophic bacterial strains were isolated at 4 °C. These bacterial isolates could be sorted into 18 phylotypes based on the 16S rRNA gene sequence belonging to four phyla, namely Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Only seven isolates were psychrophilic, 15 isolates were moderately psychrophilic, and 11 isolates were psychrotolerant. More than 72% of the isolates required sodium chloride to grow. Esterase, b-glucosidase and proteases activities at 4 °C were detected in more than 45% of the strains while approximately 21%, 15% and 12% of the strains possessed lipase, amylase and chitinase, respectively. These results indicate that a relatively high culturable bacterial diversity is present within marine sediment of Nella Fjord and it could serve as an ideal candidate region for bioprospecting.

  13. Bacterial diversity and bioprospecting for cold-active hydrolytic enzymes from culturable bacteria associated with sediment from Nella Fjord, Eastern Antarctica.

    Science.gov (United States)

    Yu, Yong; Li, Hui-Rong; Zeng, Yin-Xin; Chen, Bo

    2011-01-31

    The diversity and cold-active hydrolytic enzymes of culturable bacteria associated with sandy sediment from Nella Fjord, Eastern Antarctica (69°22'6″ S, 76°21'45″ E) was investigated. A total of 33 aerobic heterotrophic bacterial strains were isolated at 4 °C. These bacterial isolates could be sorted into 18 phylotypes based on the 16S rRNA gene sequence belonging to four phyla, namely Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Only seven isolates were psychrophilic, 15 isolates were moderately psychrophilic, and 11 isolates were psychrotolerant. More than 72% of the isolates required sodium chloride to grow. Esterase, β-glucosidase and proteases activities at 4 °C were detected in more than 45% of the strains while approximately 21%, 15% and 12% of the strains possessed lipase, amylase and chitinase, respectively. These results indicate that a relatively high culturable bacterial diversity is present within marine sediment of Nella Fjord and it could serve as an ideal candidate region for bioprospecting.

  14. Metagenomics as a preliminary screen for antimicrobial bioprospecting.

    Science.gov (United States)

    Al-Amoudi, Soha; Razali, Rozaimi; Essack, Magbubah; Amini, Mohammad Shoaib; Bougouffa, Salim; Archer, John A C; Lafi, Feras F; Bajic, Vladimir B

    2016-12-15

    Since the composition of soil directs the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies has been focused on sediment types with unique features characteristic of extreme environments. However, not much is known about the potential of microbiomes that inhabit the highly saline and hot Red Sea lagoons. This case study explores mangrove mud and the microbial mat of sediments collected from the Rabigh harbor lagoon and Al Kharrar lagoon for antimicrobial bioprospecting. Rabigh harbor lagoon appears the better location, and the best sediment type for this purpose is mangrove mud. On the other hand, Al Kharrar lagoon displayed increased anaerobic hydrocarbon degradation and an abundance of bacterial DNA associated with antibiotic resistance. Moreover, our findings show an identical shift in phyla associated with historic hydrocarbon contamination exposure reported in previous studies (that is, enrichment of Gamma- and Delta-proteobacteria), but we also report that bacterial DNA sequences associated with antibiotic synthesis enzymes are derived from Gamma-, Delta- and Alpha-proteobacteria. This suggests that selection pressure associated with hydrocarbon contamination tend to enrich the bacterial classes DNA associated with antibiotic synthesis enzymes. Although Actinobacteria tends to be the common target for research when it comes to antimicrobial bioprospecting, our study suggests that Firmicutes (Bacilli and Clostridia), Bacteroidetes, Cyanobacteria, and Proteobacteria should be antimicrobial bioprospecting targets as well. To the best of our knowledge, this is the first metagenomic study that analyzed the microbiomes in Red Sea lagoons for antimicrobial bioprospecting.

  15. Bacteria associated with an encrusting sponge (Terpios hoshinota) and the corals partially covered by the sponge.

    Science.gov (United States)

    Tang, Sen-Lin; Hong, Mei-Jhu; Liao, Ming-Hui; Jane, Wann-Neng; Chiang, Pei-Wen; Chen, Chung-Bin; Chen, Chaolun A

    2011-05-01

    Terpios hoshinota, a dark encrusting sponge, is known to be a competitor for space in coral reef environments, and facilitates the death of corals. Although numerous cyanobacteria have been detected in the sponge, little is known of the sponge-associated bacterial community. This study examined the sponge-associated bacterial community and the difference between the bacterial communities in the sponge and the coral partially covered by the sponge by analysis of 16S rRNA gene sequences of samples isolated from the sponge covering the corals Favia complanata, Isopora palifera, Millepora sp., Montipora efflorescens and Porites lutea. The sponge-associated bacterial community was mainly (61-98%) composed of cyanobacteria, with approximately 15% of these alphaproteobacteria and gammaproteobacteria, although the proportions varied in different sponge samples. The dominant cyanobacteria group was an isolated group closely related to Prochloron sp. The comparison of the bacterial communities isolated from sponge-free and the sponge-covered P. lutea showed that covering by the sponge caused changes in the coral-associated bacterial communities, with the presence of bacteria similar to those detected in black-band disease, suggesting the sponge might benefit from the presence of bacteria associated with unhealthy coral, particularly in the parts of the coral closest to the margin of the sponge.

  16. Microbiological investigations on the water of a thermal bath at Budapest.

    Science.gov (United States)

    Szuróczki, Sára; Kéki, Zsuzsa; Káli, Szandra; Lippai, Anett; Márialigeti, Károly; Tóth, Erika

    2016-06-01

    Thermal baths are unique aquatic environments combining a wide variety of natural and anthropogenic ecological factors, which also appear in their microbiological state. There is limited information on the microbiology of thermal baths in their complexity, tracking community shifts from the thermal wells to the pools. In the present study, the natural microbial community of well and pool waters in Gellért bath was studied in detail by cultivation-based techniques. To isolate bacteria, 10% R2A and minimal synthetic media (with "bath water") with agar-agar and gellan gum were used after prolonged incubation time; moreover, polyurethane blocks covered with media were also applied. Strains were identified by sequencing their 16S rRNA gene after grouping them by amplified rDNA restriction analysis. From each sample, the dominance of Alphaproteobacteria was characteristic though their diversity differed among samples. Members of Actinobacteria, Firmicutes, Beta- and Gamma-proteobacteria, Deinococcus-Thermus, and Bacteroidetes were also identified. Representatives of Deinococcus-Thermus phylum appeared only in the pool water. The largest groups in the pool water belonged to the Tistrella and Chelatococcus genera. The most dominant member in the well water was a new taxon, its similarity to Hartmannibacter diazotrophicus as closest relative was 93.93%.

  17. Biodiversity patterns of plankton assemblages at the extremes of the Red Sea

    KAUST Repository

    Pearman, John K.

    2016-01-07

    The diversity of microbial plankton has received limited attention in the main basin of the Red Sea. This study investigates changes in the community composition and structure of prokaryotes and eukaryotes at the extremes of the Red Sea along cross-shelf gradients and between the surface and deep chlorophyll maximum. Using molecular methods to target both the 16S and 18S rRNA genes, it was observed that the dominant prokaryotic classes were Acidimicrobiia, Alphaproteobacteria and Cyanobacteria, regardless of the region and depth. The eukaryotes Syndiniophyceae and Dinophyceae between them dominated in the north, with Bacillariophyceae and Mamiellophyceae more prominent in the southern region. Significant differences were observed for prokaryotes and eukaryotes for region, depth and distance from shore. Similarly, it was noticed that communities became less similar with increasing distance from the shore. Canonical correspondence analysis at the class level showed that Mamiellophyceae and Bacillariophyceae correlated with increased nutrients and chlorophyll a found in the southern region, which is influenced by the input of Gulf of Aden Intermediate Water.

  18. Molecular analysis of bacterial communities in biofilms of a drinking water clearwell.

    Science.gov (United States)

    Zhang, Minglu; Liu, Wenjun; Nie, Xuebiao; Li, Cuiping; Gu, Junnong; Zhang, Can

    2012-01-01

    Microbial community structures in biofilms of a clearwell in a drinking water supply system in Beijing, China were examined by clone library, terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing of the amplified 16S rRNA gene. Six biofilm samples (designated R1-R6) collected from six locations (upper and lower sites of the inlet, middle and outlet) of the clearwell revealed similar bacterial patterns by T-RFLP analysis. With respect to the dominant groups, the phylotypes detected by clone library and T-RFLP generally matched each other. A total of 9,543 reads were obtained from samples located at the lower inlet and the lower outlet sites by pyrosequencing. The bacterial diversity of the two samples was compared at phylum and genus levels. Alphaproteobacteria dominated the communities in both samples and the genus of Sphingomonas constituted 75.1%-99.6% of this phylum. A high level of Sphingomonas sp. was first observed in the drinking water biofilms with 0.6-1.0 mg L(-1) of chlorine residual. Disinfectant-resistant microorganisms deserve special attention in drinking water management. This study provides novel insights into the microbial populations in drinking water systems and highlights the important role of Sphingomonas species in biofilm formation.

  19. A bacterial enrichment study and overview of the extractable lipids from paleosols in the Dry Valleys, Antarctica: implications for future Mars reconnaissance.

    Science.gov (United States)

    Hart, Kris M; Szpak, Michal T; Mahaney, William C; Dohm, James M; Jordan, Sean F; Frazer, Andrew R; Allen, Christopher C R; Kelleher, Brian P

    2011-05-01

    The Dry Valleys of Antarctica are one of the coldest and driest environments on Earth with paleosols in selected areas that date to the emplacement of tills by warm-based ice during the Early Miocene. Cited as an analogue to the martian surface, the ability of the Antarctic environment to support microbial life-forms is a matter of special interest, particularly with the upcoming NASA/ESA 2018 ExoMars mission. Lipid biomarkers were extracted and analyzed by gas chromatography--mass spectrometry to assess sources of organic carbon and evaluate the contribution of microbial species to the organic matter of the paleosols. Paleosol samples from the ice-free Dry Valleys were also subsampled and cultivated in a growth medium from which DNA was extracted with the explicit purpose of the positive identification of bacteria. Several species of bacteria were grown in solution and the genus identified. A similar match of the data to sequenced DNA showed that Alphaproteobacteria, Gammaproteobacteria, Bacteriodetes, and Actinobacteridae species were cultivated. The results confirm the presence of bacteria within some paleosols, but no assumptions have been made with regard to in situ activity at present. These results underscore the need not only to further investigate Dry Valley cryosols but also to develop reconnaissance strategies to determine whether such likely Earth-like environments on the Red Planet also contain life.

  20. 浙江镇海潮间带沉积物中可培养微生物初步研究%A preliminary study of the culturable microorganisms in tidal flat sediment from Zhenhai, Zhejiang Province

    Institute of Scientific and Technical Information of China (English)

    郑莹; 霍颖异

    2012-01-01

    Marine microorganisms in the tidal flat sediment from Zhenhai were isolated with pure culture method and bacterial community and diversity were analyzed. The tidal flat sediment sample was collected from Zhenhai, Zhejiang Province of China in June, 2008. The diluted sediment was plated on modified ZoBell medium agar plates. After incubation aerobically at 25 °C and 37 °C, strains were selected and purified. The 16S rRNA genes were amplified with primers 27F (5 '-AGAGTTTGATCCTGGCTCAG 3') and 1492R (5'-GGTTACCTTGTTACGACTT-3') and sequenced. The sequences obtained were compared with closely related sequences of described bacteria from the EzTaxon-c online service. Sequence data were aligned with Clustal W and phylogenetic tree were constructed by the neighbor-joining method with the MEGA 5 program package. Totally, 39 bacterial strains were isolated. Analysis of the 16S rRNA gene sequences show that the isolates were closely related to described bacteria and fell into four lineages: Firmicutes (20 strains, 51. 3%) ,Proteobacteria (12 strains, 30.8%), Bacteroidetes (6 strains, 15.4%) and Actinobacteria (1 strain, 2.6%). Firmicutes strains belong to genera Bacillus, Ornithinibacillus and Thalassobacillus; Proteobacteria strains belong to genera Roseicyclus, Rhodobacter, Erythrobacter, Jannaschia and Ruegeria of Alphaproteobacteria and genera Acinetobacter and Pseudomonas of Gammaproteobacteria; Bacteroidetes strains belong to genus Algoriphagus and family Flavobacteriaceae; and Actinobacteria strains belong to genus Gordonia. Bacilli and Alphaproteobacteria were the largest group in Firmicutes and Proteobacteria, respectively. They might play an important role in biogeochemical cycles in the coastal sediment ecosystem. Bacilli strains are heterotrophic bacteria, and their occurrence indicates that the tidal flat environment is rich in organic nutrition. 15 out of 20 (75%) of the isolated Bacilli strains showed closer phylogenetic relationship with the bacteria of land

  1. Ultrastructural and molecular characterization of a bacterial symbiosis in the ecologically important scale insect family Coelostomidiidae.

    Science.gov (United States)

    Dhami, Manpreet K; Turner, Adrian P; Deines, Peter; Beggs, Jacqueline R; Taylor, Michael W

    2012-09-01

    Scale insects are important ecologically and as agricultural pests. The majority of scale insect taxa feed exclusively on plant phloem sap, which is carbon rich but deficient in essential amino acids. This suggests that, as seen in the related aphids and psyllids, scale insect nutrition might also depend upon bacterial symbionts, yet very little is known about scale insect-bacteria symbioses. We report here the first identification and molecular characterization of symbiotic bacteria associated with the New Zealand giant scale Coelostomidia wairoensis, using fluorescence in situ hybridization (FISH), transmission electron microscopy (TEM) and 16S rRNA gene-based analysis. Dissection and FISH confirmed the location of the bacteria in large, paired, multilobate organs in the abdominal region of the insect. TEM indicated that the dominant pleomorphic bacteria were confined to bacteriocytes in the sheath-enclosed bacteriome. Phylogenetic analysis revealed the presence of three distinct bacterial types, the bacteriome-associated B-symbiont (Bacteroidetes), an Erwinia-related symbiont (Gammaproteobacteria) and Wolbachia sp. (Alphaproteobacteria). This study extends the current knowledge of scale insect symbionts and is the first microbiological investigation of the ecologically important coelostomidiid scales.

  2. Short-term dynamics of culturable bacteria in a soil amended with biotransformed dry olive residue.

    Science.gov (United States)

    Siles, J A; Pascual, J; González-Menéndez, V; Sampedro, I; García-Romera, I; Bills, G F

    2014-03-01

    Dry olive residue (DOR) transformation by wood decomposing basidiomycetes (e.g. Coriolopsis floccosa) is a possible strategy for eliminating the liabilities related to the use of olive oil industry waste as an organic soil amendment. The effects of organic fertilization with DOR on the culturable soil microbiota are largely unknown. Therefore, the objectives of this study were to measure the short-term effects of DOR and C. floccosa-transformed DOR on the culturable bacterial soil community, while at the same time documenting the bacterial diversity of an agronomic soil in the southeastern Iberian Peninsula. The control soil was compared with the same soil treated with DOR and with C. floccosa-transformed DOR for 0, 30 and 60 days. Impact was measured from total viable cells and CFU counts, as well as the isolation and characterization of 900 strains by fatty acid methyl ester profiles and 16S rRNA partial sequencing. The bacterial diversity was distributed between Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, Betaproteobacteria, Bacilli, Sphingobacteria and Cytophagia. Analysis of the treatments and controls demonstrated that soil amendment with untransformed DOR produced important changes in bacterial density and diversity. However, when C. floccosa-transformed DOR was applied, bacterial proliferation was observed but bacterial diversity was less affected, and the distribution of microorganisms was more similar to the unamended soil.

  3. Quantitative role of shrimp fecal bacteria in organic matter fluxes in a recirculating shrimp aquaculture system.

    Science.gov (United States)

    Beardsley, Christine; Moss, Shaun; Malfatti, Francesca; Azam, Farooq

    2011-07-01

    Microorganisms play integral roles in the cycling of carbon (C) and nitrogen (N) in recirculating aquaculture systems (RAS) for fish and shellfish production. We quantified the pathways of shrimp fecal bacterial activities and their role in C- and N-flux partitioning relevant to culturing Pacific white shrimp, Penaeus (Litopenaeus) vannamei, in RAS. Freshly produced feces from P. vannamei contained 0.6-7 × 10(10) bacteria g(-1) dry wt belonging to Bacteroidetes (7%), Alphaproteobacteria (4%), and, within the Gammaproteobacteria, almost exclusively to the genus Vibrio (61%). Because of partial disintegration of the feces (up to 27% within 12 h), the experimental seawater became inoculated with fecal bacteria. Bacteria grew rapidly in the feces and in the seawater, and exhibited high levels of aminopeptidase, chitinase, chitobiase, alkaline phosphatase, α- and β-glucosidase, and lipase activities. Moreover, fecal bacteria enriched the protein content of the feces within 12 h, potentially enriching the feces for the coprophagous shrimp. The bacterial turnover time was much faster in feces (1-10 h) than in mature RAS water (350 h). Thus, shrimp fecal bacteria not only inoculate RAS water but also contribute to bacterial abundance and productivity, and regulate system processes important for shrimp health.

  4. Bacterial quorum sensing and nitrogen cycling in rhizosphere soil

    Energy Technology Data Exchange (ETDEWEB)

    DeAngelis, K.M.; Lindow, S.E.; Firestone, M.K.

    2008-10-01

    Plant photosynthate fuels carbon-limited microbial growth and activity, resulting in increased rhizosphere nitrogen (N)-mineralization. Most soil organic N is macromolecular (chitin, protein, nucleotides); enzymatic depolymerization is likely rate-limiting for plant N accumulation. Analyzing Avena (wild oat) planted in microcosms containing sieved field soil, we observed increased rhizosphere chitinase and protease specific activities, bacterial cell densities, and dissolved organic nitrogen (DON) compared to bulk soil. Low-molecular weight DON (<3000 Da) was undetectable in bulk soil but comprised 15% of rhizosphere DON. Extracellular enzyme production in many bacteria requires quorum sensing (QS), cell-density dependent group behavior. Because proteobacteria are considered major rhizosphere colonizers, we assayed the proteobacterial QS signals acyl-homoserine lactones (AHLs), which were significantly increased in the rhizosphere. To investigate the linkage between soil signaling and N cycling, we characterized 533 bacterial isolates from Avena rhizosphere: 24% had chitinase or protease activity and AHL production; disruption of QS in 7 of 8 eight isolates disrupted enzyme activity. Many {alpha}-Proteobacteria were newly found with QS-controlled extracellular enzyme activity. Enhanced specific activities of N-cycling enzymes accompanied by bacterial density-dependent behaviors in rhizosphere soil gives rise to the hypothesis that QS could be a control point in the complex process of rhizosphere N-mineralization.

  5. Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too.

    Science.gov (United States)

    Tripathi, Binu M; Kim, Mincheol; Singh, Dharmesh; Lee-Cruz, Larisa; Lai-Hoe, Ang; Ainuddin, A N; Go, Rusea; Rahim, Raha Abdul; Husni, M H A; Chun, Jongsik; Adams, Jonathan M

    2012-08-01

    The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.

  6. Thermal and sedimentation stress are unlikely causes of brown spot syndrome in the coral reef sponge, Ianthella basta.

    Directory of Open Access Journals (Sweden)

    Heidi M Luter

    Full Text Available BACKGROUND: Marine diseases are being increasingly linked to anthropogenic factors including global and local stressors. On the Great Barrier Reef, up to 66% of the Ianthella basta population was recently found to be afflicted by a syndrome characterized by brown spot lesions and necrotic tissue. METHODOLOGY/PRINCIPAL FINDINGS: Manipulative experiments were undertaken to ascertain the role of environmental stressors in this syndrome. Specifically, the effects of elevated temperature and sedimentation on sponge health and symbiont stability in I. basta were examined. Neither elevated temperature nor increased sedimentation were responsible for the brown spot lesions, but sponges exposed to 32°C developed substantial discoloration and deterioration of their tissues, resulting in death after eight days and a higher microbial diversity in those samples. No shifts in the microbial community of I. basta were observed across a latitudinal gradient or with increased sedimentation, with three previously described symbionts dominating the community of all sponges (Alphaproteobacteria, Gammaproteobacteria and Thaumarchaea. CONCLUSIONS/SIGNIFICANCE: Results from this study highlight the stable microbial community of I. basta and indicate that thermal and sedimentation stress are not responsible for the brown spot lesions currently affecting this abundant and ecologically important sponge species.

  7. Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan

    Science.gov (United States)

    Hirose, Setsuko; Matsuura, Katsumi; Haruta, Shin

    2016-01-01

    The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms. PMID:27453124

  8. [Genome Rearrangements in Azospirillum brasilense Sp7 with the Involvement of the Plasmid pRhico and the Prophage phiAb-Cd].

    Science.gov (United States)

    Katsy, E I; Petrova, L P

    2015-12-01

    Alphaproteobacteria of the species Azospirillum brasilense have a multicomponent genome that undergoes frequent spontaneous rearrangements, yielding changes in the plasmid profiles of strains. Specifically, variants (Cd, Sp7.K2, Sp7.1, Sp7.4, Sp7.8, etc.) of the type strainA. brasilense Sp7 that had lost a 115-MDa plasmid were previously selected. In many of them, the molecular weight of a 90-MDa plasmid (p90 or pRhico), which is a kind of "depot" for glycopolymer biosynthesis genes, increased. In this study, a collection of primers was designed to the plasmid pRhico and to the DNA of prophage phiAb-Cd integrated in it. The use ofthese primers in polymerase chain reactions allowed the detection of the probable excision of phiAb-Cd phage from the DNA of A. brasilense variants Sp7.4 and Sp7.8 and other alterations of the pRhico structure in A. brasilense strains Cd, Sp7.K2, and Sp7.8. The developed primers and PCR conditions may be recoin mended for primary analysis of spontaneous plasmid rearrangements in A. brasilense Sp7 and related strains.

  9. RpoH2 sigma factor controls the photooxidative stress response in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7.

    Science.gov (United States)

    Kumar, Santosh; Rai, Ashutosh Kumar; Mishra, Mukti Nath; Shukla, Mansi; Singh, Pradhyumna Kumar; Tripathi, Anil Kumar

    2012-12-01

    Bacteria belonging to the Alphaproteobacteria normally harbour multiple copies of the heat shock sigma factor (known as σ(32), σ(H) or RpoH). Azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours five copies of rpoH genes, one of which is an rpoH2 homologue. The genes around the rpoH2 locus in A. brasilense show synteny with that found in rhizobia. The rpoH2 of A. brasilense was able to complement the temperature-sensitive phenotype of the Escherichia coli rpoH mutant. Inactivation of rpoH2 in A. brasilense results in increased sensitivity to methylene blue and to triphenyl tetrazolium chloride (TTC). Exposure of A. brasilense to TTC and the singlet oxygen-generating agent methylene blue induced several-fold higher expression of rpoH2. Comparison of the proteome of A. brasilense with its rpoH2 deletion mutant and with an A. brasilense strain overexpressing rpoH2 revealed chaperone GroEL, elongation factors (Ef-Tu and EF-G), peptidyl prolyl isomerase, and peptide methionine sulfoxide reductase as the major proteins whose expression was controlled by RpoH2. Here, we show that the RpoH2 sigma factor-controlled photooxidative stress response in A. brasilense is similar to that in the photosynthetic bacterium Rhodobacter sphaeroides, but that RpoH2 is not involved in the detoxification of methylglyoxal in A. brasilense.

  10. Hydrocarbon biodegradation by Arctic sea-ice and sub-ice microbial communities during microcosm experiments, Northwest Passage (Nunavut, Canada).

    Science.gov (United States)

    Garneau, Marie-Ève; Michel, Christine; Meisterhans, Guillaume; Fortin, Nathalie; King, Thomas L; Greer, Charles W; Lee, Kenneth

    2016-10-01

    The increasing accessibility to navigation and offshore oil exploration brings risks of hydrocarbon releases in Arctic waters. Bioremediation of hydrocarbons is a promising mitigation strategy but challenges remain, particularly due to low microbial metabolic rates in cold, ice-covered seas. Hydrocarbon degradation potential of ice-associated microbes collected from the Northwest Passage was investigated. Microcosm incubations were run for 15 days at -1.7°C with and without oil to determine the effects of hydrocarbon exposure on microbial abundance, diversity and activity, and to estimate component-specific hydrocarbon loss. Diversity was assessed with automated ribosomal intergenic spacer analysis and Ion Torrent 16S rRNA gene sequencing. Bacterial activity was measured by (3)H-leucine uptake rates. After incubation, sub-ice and sea-ice communities degraded 94% and 48% of the initial hydrocarbons, respectively. Hydrocarbon exposure changed the composition of sea-ice and sub-ice communities; in sea-ice microcosms, Bacteroidetes (mainly Polaribacter) dominated whereas in sub-ice microcosms, the contribution of Epsilonproteobacteria increased, and that of Alphaproteobacteria and Bacteroidetes decreased. Sequencing data revealed a decline in diversity and increases in Colwellia and Moritella in oil-treated microcosms. Low concentration of dissolved organic matter (DOM) in sub-ice seawater may explain higher hydrocarbon degradation when compared to sea ice, where DOM was abundant and composed of labile exopolysaccharides.

  11. So close, so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites.

    Science.gov (United States)

    Gagliano, A L; Tagliavia, M; D'Alessandro, W; Franzetti, A; Parello, F; Quatrini, P

    2016-03-01

    This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH4 consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH4 consumption. Next-Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia-oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo-acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH4(+) concentration. At the same time, abundant availability of NH4(+) and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non-nitrogen-limited soils.

  12. Sinorhizobium meliloti mutants lacking phosphotransferase system enzyme HPr or EIIA are altered in diverse processes, including carbon metabolism, cobalt requirements, and succinoglycan production.

    Science.gov (United States)

    Pinedo, Catalina Arango; Bringhurst, Ryan M; Gage, Daniel J

    2008-04-01

    Sinorhizobium meliloti is a member of the Alphaproteobacteria that fixes nitrogen when it is in a symbiotic relationship. Genes for an incomplete phosphotransferase system (PTS) have been found in the genome of S. meliloti. The genes present code for Hpr and ManX (an EIIA(Man)-type enzyme). HPr and EIIA regulate carbon utilization in other bacteria. hpr and manX in-frame deletion mutants exhibited altered carbon metabolism and other phenotypes. Loss of HPr resulted in partial relief of succinate-mediated catabolite repression, extreme sensitivity to cobalt limitation, rapid die-off during stationary phase, and altered succinoglycan production. Loss of ManX decreased expression of melA-agp and lac, the operons needed for utilization of alpha- and beta-galactosides, slowed growth on diverse carbon sources, and enhanced accumulation of high-molecular-weight succinoglycan. A strain with both hpr and manX deletions exhibited phenotypes similar to those of the strain with a single hpr deletion. Despite these strong phenotypes, deletion mutants exhibited wild-type nodulation and nitrogen fixation when they were inoculated onto Medicago sativa. The results show that HPr and ManX (EIIA(Man)) are involved in more than carbon regulation in S. meliloti and suggest that the phenotypes observed occur due to activity of HPr or one of its phosphorylated forms.

  13. Microbial Diversity of Chromium-Contaminated Soils and Characterization of Six Chromium-Removing Bacteria

    Science.gov (United States)

    He, Zhiguo; Hu, Yuting; Yin, Zhen; Hu, Yuehua; Zhong, Hui

    2016-06-01

    Three soil samples obtained from different sites adjacent to a chromium slag heap in a steel alloy factory were taken to examine the effect of chromium contamination on soil bacterial diversity as determined by construction of 16S rDNA clone libraries and sequencing of selected clones based on restriction fragment length polymorphism (RFLP) analysis. Results revealed that Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Alphaproteobacteria occurred in all three soil samples, although the three samples differed in their total diversity. Sample 1 had the highest microbial diversity covering 12 different classes, while Sample 3 had the lowest microbial diversity. Strains of six different species were successfully isolated, one of which was identified as Zobellella denitrificans. To our knowledge, this is the first report of a strain belonging to the genus Zobellella able to resist and reduce chromium. Among all isolates studied, Bacillus odysseyi YH2 exhibited the highest Cr(VI)-reducing capability, with a total removal of 23.5 % of an initial Cr(VI) concentration of 350 mg L-1.

  14. Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5'-phosphosulfate reductase genes from gamma- and alphaproteobacterial symbionts in gutless marine worms (oligochaeta) from Bermuda and the Bahamas.

    Science.gov (United States)

    Blazejak, Anna; Kuever, Jan; Erséus, Christer; Amann, Rudolf; Dubilier, Nicole

    2006-08-01

    Gutless oligochaetes are small marine worms that live in obligate associations with bacterial endosymbionts. While symbionts from several host species belonging to the genus Olavius have been described, little is known of the symbionts from the host genus Inanidrilus. In this study, the diversity of bacterial endosymbionts in Inanidrilus leukodermatus from Bermuda and Inanidrilus makropetalos from the Bahamas was investigated using comparative sequence analysis of the 16S rRNA gene and fluorescence in situ hybridization. As in all other gutless oligochaetes examined to date, I. leukodermatus and I. makropetalos harbor large, oval bacteria identified as Gamma 1 symbionts. The presence of genes coding for ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) and adenosine 5'-phosphosulfate reductase (aprA) supports earlier studies indicating that these symbionts are chemoautotrophic sulfur oxidizers. Alphaproteobacteria, previously identified only in the gutless oligochaete Olavius loisae from the southwest Pacific Ocean, coexist with the Gamma 1 symbionts in both I. leukodermatus and I. makropetalos, with the former harboring four and the latter two alphaproteobacterial phylotypes. The presence of these symbionts in hosts from such geographically distant oceans as the Atlantic and Pacific suggests that symbioses with alphaproteobacterial symbionts may be widespread in gutless oligochaetes. The high phylogenetic diversity of bacterial endosymbionts in two species of the genus Inanidrilus, previously known only from members of the genus Olavius, shows that the stable coexistence of multiple symbionts is a common feature in gutless oligochaetes.

  15. Phylogeny of 16S rRNA, Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase, and Adenosine 5′-Phosphosulfate Reductase Genes from Gamma- and Alphaproteobacterial Symbionts in Gutless Marine Worms (Oligochaeta) from Bermuda and the Bahamas

    Science.gov (United States)

    Blazejak, Anna; Kuever, Jan; Erséus, Christer; Amann, Rudolf; Dubilier, Nicole

    2006-01-01

    Gutless oligochaetes are small marine worms that live in obligate associations with bacterial endosymbionts. While symbionts from several host species belonging to the genus Olavius have been described, little is known of the symbionts from the host genus Inanidrilus. In this study, the diversity of bacterial endosymbionts in Inanidrilus leukodermatus from Bermuda and Inanidrilus makropetalos from the Bahamas was investigated using comparative sequence analysis of the 16S rRNA gene and fluorescence in situ hybridization. As in all other gutless oligochaetes examined to date, I. leukodermatus and I. makropetalos harbor large, oval bacteria identified as Gamma 1 symbionts. The presence of genes coding for ribulose-1,5-bisphosphate carboxylase/oxygenase form I (cbbL) and adenosine 5′-phosphosulfate reductase (aprA) supports earlier studies indicating that these symbionts are chemoautotrophic sulfur oxidizers. Alphaproteobacteria, previously identified only in the gutless oligochaete Olavius loisae from the southwest Pacific Ocean, coexist with the Gamma 1 symbionts in both I. leukodermatus and I. makropetalos, with the former harboring four and the latter two alphaproteobacterial phylotypes. The presence of these symbionts in hosts from such geographically distant oceans as the Atlantic and Pacific suggests that symbioses with alphaproteobacterial symbionts may be widespread in gutless oligochaetes. The high phylogenetic diversity of bacterial endosymbionts in two species of the genus Inanidrilus, previously known only from members of the genus Olavius, shows that the stable coexistence of multiple symbionts is a common feature in gutless oligochaetes. PMID:16885306

  16. Assessing environmental drivers of microbial communities in estuarine soils of the Aconcagua River in Central Chile.

    Science.gov (United States)

    Fuentes, Sebastián; Ding, Guo-Chun; Cárdenas, Franco; Smalla, Kornelia; Seeger, Michael

    2015-10-01

    Aconcagua River basin (Central Chile) harbors diverse economic activities such as agriculture, mining and a crude oil refinery. The aim of this study was to assess environmental drivers of microbial communities in Aconcagua River estuarine soils, which may be influenced by anthropogenic activities taking place upstream and by natural processes such as tides and flood runoffs. Physicochemical parameters were measured in floodplain soils along the estuary. Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Pseudomonas, Bacillus and Fungi were studied by DGGE fingerprinting of 16S rRNA gene and ribosomal ITS-1 amplified from community DNA. Correlations between environment and communities were assessed by distance-based redundancy analysis. Mainly hydrocarbons, pH and the composed variable copper/arsenic/calcium but in less extent nitrogen and organic matter/phosphorous/magnesium correlated with community structures at different taxonomic levels. Aromatic hydrocarbons degradation potential by bacterial community was studied. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases genes were detected only at upstream sites. Naphthalene dioxygenase ndo genes were heterogeneously distributed along estuary, and related to Pseudomonas, Delftia, Comamonas and Ralstonia. IncP-1 plasmids were mainly present at downstream sites, whereas IncP-7 and IncP-9 plasmids showed a heterogeneous distribution. This study strongly suggests that pH, copper, arsenic and hydrocarbons are main drivers of microbial communities in Aconcagua River estuarine soils.

  17. mdRNA-Seq analysis of marine microbial communities from the northern Red Sea

    Science.gov (United States)

    Hou, Shengwei; Pfreundt, Ulrike; Miller, Dan; Berman-Frank, Ilana; Hess, Wolfgang R.

    2016-01-01

    Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5′ ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities. 16S rDNA quantification revealed that 24% of the analyzed community were group II marine Euryarchaeota in which we identified a highly abundant non-coding RNA, Tan1, and detected very high expression of genes encoding intrinsically disordered proteins, as well as enzymes for the synthesis of specific B vitamins, extracellular peptidases, carbohydrate-active enzymes, and transport systems. These results highlight previously unknown functions of Euryarchaeota with community-wide relevance. The complementation of metatranscriptomic studies with mdRNA-Seq provides substantial additional information regarding transcriptional start sites, promoter activities, and the identification of non-coding RNAs. PMID:27759035

  18. Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential.

    Science.gov (United States)

    White, Richard Allen; Power, Ian M; Dipple, Gregory M; Southam, Gordon; Suttle, Curtis A

    2015-01-01

    Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid, and chlorophyll biosynthesis) and carbon fixation (e.g., CO dehydrogenase). The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R (2) Mexico, but are more similar to polar Arctic mats (R (2) > 0.900). These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

  19. Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential

    Directory of Open Access Journals (Sweden)

    Richard Allen White III

    2015-09-01

    Full Text Available Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid and chlorophyll biosynthesis and carbon fixation (e.g., CO dehydrogenase. The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R2 0.900. These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

  20. Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu.

    Science.gov (United States)

    Xia, Kai; Li, Yudong; Sun, Jing; Liang, Xinle

    2016-01-01

    Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes.

  1. Quorum sensing in marine snow and its possible influence on production of extracellular hydrolytic enzymes in marine snow bacterium Pantoea ananatis B9.

    Science.gov (United States)

    Jatt, Abdul Nabi; Tang, Kaihao; Liu, Jiwen; Zhang, Zenghu; Zhang, Xiao-Hua

    2015-02-01

    Marine snow is a continuous shower of organic and inorganic detritus, and plays a crucial role in transporting materials from the sea surface to the deep ocean. The aims of the current study were to identify N-acyl homoserine lactone (AHL)-based quorum sensing (QS) signaling molecules directly from marine snow particles and to investigate the possible regulatory link between QS signals and extracellular hydrolytic enzymes produced by marine snow bacteria. The marine snow samples were collected from the surface water of China marginal seas. Two AHLs, i.e. 3OC6-HSL and C8-HSL, were identified directly from marine snow particles, while six different AHL signals, i.e. C4-HSL, 3OC6-HSL, C6-HSL, C10-HSL, C12-HSL and C14-HSL were produced by Pantoea ananatis B9 inhabiting natural marine snow particles. Of the extracellular hydrolytic enzymes produced by P. ananatis B9, alkaline phosphatase activity was highly enhanced in growth medium supplemented with exogenous AHL (C10-HSL), while quorum quenching enzyme (AiiA) drastically reduced the enzyme activity. To our knowledge, this is the first report revealing six different AHL signals produced by P. ananatis B9 and AHL-based QS system enhanced the extracellular hydrolytic enzyme in P. ananatis B9. Furthermore, this study first time revealing 3OC6-HSL production by Paracoccus carotinifaciens affiliated with Alphaproteobacteria.

  2. Magnetotactic bacteria in microcosms originating from the French Mediterranean Coast subjected to oil industry activities.

    Science.gov (United States)

    Postec, Anne; Tapia, Nicolas; Bernadac, Alain; Joseph, Manon; Davidson, Sylvain; Wu, Long-Fei; Ollivier, Bernard; Pradel, Nathalie

    2012-01-01

    Magnetotactic bacteria (MTB) mineralize nanosized magnetite or greigite crystals within cells and thus play an important role in the biogeochemical process. Despite decades of research, knowledge of MTB distribution and ecology, notably in areas subjected to oil industry activities, is still limited. In the present study, we investigated the presence of MTB in the Gulf of Fos, French Mediterranean coast, which is subjected to intensive oil industry activities. Microcosms containing sediments/water (1:2, v/v) from several sampling sites were monitored over several weeks. The presence of MTB was revealed in five of eight sites. Diverse and numerous MTB were revealed particularly from one site (named CAR), whilst temporal variations of a homogenous magnetotactic cocci population was shown within the LAV site microcosm over a 4-month period. Phylogenetic analysis revealed that they belonged to Alphaproteobacteria, and a novel genus from the LAV site was evidenced. Among the physicochemical parameters measured, a correlation was shown between the variation of MTB abundance in microcosms and the redox state of sulphur compounds.

  3. Posttranslational modification of a vanadium nitrogenase.

    Science.gov (United States)

    Heiniger, Erin K; Harwood, Caroline S

    2015-08-01

    In microbes that fix nitrogen, nitrogenase catalyzes the conversion of N2 to ammonia in an ATP-demanding reaction. To help conserve energy some bacteria inhibit nitrogenase activity upon exposure to ammonium. The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 can synthesize three functional nitrogenase isoenzymes: a molybdenum nitrogenase, a vanadium nitrogenase, and an iron nitrogenase. Previous studies showed that in some alphaproteobacteria, including R. palustris, molybdenum nitrogenase activity is inhibited by ADP-ribosylation when cells are exposed to ammonium. Some iron nitrogenases are also posttranslationally modified. However, the posttranslational modification of vanadium nitrogenase has not been reported. Here, we investigated the regulation of the alternative nitrogenases of R. palustris and determined that both its vanadium nitrogenase and its iron nitrogenase activities were inhibited and posttranslationally modified when cells are exposed to ammonium. Vanadium nitrogenase is not found in all strains of R. palustris, suggesting that it may have been acquired by horizontal gene transfer. Also, phylogenetic analyses of the three nitrogenases suggest that VnfH, the target of ADP-ribosylation, may be the product of a gene duplication of nifH, the molybdenum nitrogenase homolog.

  4. Nitrogen fertilization has a stronger effect on soil nitrogen-fixing bacterial communities than elevated atmospheric CO2.

    Science.gov (United States)

    Berthrong, Sean T; Yeager, Chris M; Gallegos-Graves, Laverne; Steven, Blaire; Eichorst, Stephanie A; Jackson, Robert B; Kuske, Cheryl R

    2014-05-01

    Biological nitrogen fixation is the primary supply of N to most ecosystems, yet there is considerable uncertainty about how N-fixing bacteria will respond to global change factors such as increasing atmospheric CO2 and N deposition. Using the nifH gene as a molecular marker, we studied how the community structure of N-fixing soil bacteria from temperate pine, aspen, and sweet gum stands and a brackish tidal marsh responded to multiyear elevated CO2 conditions. We also examined how N availability, specifically, N fertilization, interacted with elevated CO2 to affect these communities in the temperate pine forest. Based on data from Sanger sequencing and quantitative PCR, the soil nifH composition in the three forest systems was dominated by species in the Geobacteraceae and, to a lesser extent, Alphaproteobacteria. The N-fixing-bacterial-community structure was subtly altered after 10 or more years of elevated atmospheric CO2, and the observed shifts differed in each biome. In the pine forest, N fertilization had a stronger effect on nifH community structure than elevated CO2 and suppressed the diversity and abundance of N-fixing bacteria under elevated atmospheric CO2 conditions. These results indicate that N-fixing bacteria have complex, interacting responses that will be important for understanding ecosystem productivity in a changing climate.

  5. Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats.

    Science.gov (United States)

    Ali, Nidaa; Dashti, Narjes; Salamah, Samar; Sorkhoh, Naser; Al-Awadhi, Husain; Radwan, Samir

    2016-03-01

    This study describes a bench-scale attempt to bioremediate Kuwaiti, oily water and soil samples through bioaugmentation with coastal microbial mats rich in hydrocarbonoclastic bacterioflora. Seawater and desert soil samples were artificially polluted with 1% weathered oil, and bioaugmented with microbial mat suspensions. Oil removal and microbial community dynamics were monitored. In batch cultures, oil removal was more effective in soil than in seawater. Hydrocarbonoclastic bacteria associated with mat samples colonized soil more readily than seawater. The predominant oil degrading bacterium in seawater batches was the autochthonous seawater species Marinobacter hydrocarbonoclasticus. The main oil degraders in the inoculated soil samples, on the other hand, were a mixture of the autochthonous mat and desert soil bacteria; Xanthobacter tagetidis, Pseudomonas geniculata, Olivibacter ginsengisoli and others. More bacterial diversity prevailed in seawater during continuous than batch bioremediation. Out of seven hydrocarbonoclastic bacterial species isolated from those cultures, only one, Mycobacterium chlorophenolicum, was of mat origin. This result too confirms that most of the autochthonous mat bacteria failed to colonize seawater. Also culture-independent analysis of seawater from continuous cultures revealed high-bacterial diversity. Many of the bacteria belonged to the Alphaproteobacteria, Flavobacteria and Gammaproteobacteria, and were hydrocarbonoclastic. Optimal biostimulation practices for continuous culture bioremediation of seawater via mat bioaugmentation were adding the highest possible oil concentration as one lot in the beginning of bioremediation, addition of vitamins, and slowing down the seawater flow rate.

  6. Characterization of a cryptic plasmid from an alpha-proteobacterial endosymbiont of Amoeba proteus.

    Science.gov (United States)

    Park, Miey; Kim, Min-Soo; Lee, Kyung-Min; Hwang, Sue-Yun; Ahn, Tae In

    2009-01-01

    A new cryptic plasmid pAP3.9 was discovered in symbiotic alpha-proteobacteria present in the cytoplasm of Amoeba proteus. The plasmid is 3869bp with a GC content of 34.66% and contains replication origins for both double-strand (dso) and single-strand (sso). It has three putative ORFs encoding Mob, Rep and phosphoglycolate phosphatase (PGPase). The pAP3.9 plasmid appears to propagate by the conjugative rolling-circle replication (RCR), since it contains all required factors such as Rep, sso and dso. Mob and Rep showed highest similarities to those of the cryptic plasmid pBMYdx in Bacillus mycoides. The PGPase was homologous to that of Bacillus cereus and formed a clade with those of Bacillus sp. in molecular phylogeny. These results imply that the pAP3.9 plasmid evolved by the passage through Bacillus species. We hypothesize that the plasmid-encoded PGPase may have contributed to the establishment of bacterial symbiosis within the hostile environment of amoeba cytoplasm.

  7. Acetic acid bacteria: A group of bacteria with versatile biotechnological applications.

    Science.gov (United States)

    Saichana, Natsaran; Matsushita, Kazunobu; Adachi, Osao; Frébort, Ivo; Frebortova, Jitka

    2015-11-01

    Acetic acid bacteria are gram-negative obligate aerobic bacteria assigned to the family Acetobacteraceae of Alphaproteobacteria. They are members of the genera Acetobacter, Gluconobacter, Gluconacetobacter, Acidomonas, Asaia, Kozakia, Swaminathania, Saccharibacter, Neoasaia, Granulibacter, Tanticharoenia, Ameyamaea, Neokomagataea, and Komagataeibacter. Many strains of Acetobacter and Komagataeibacter have been known to possess high acetic acid fermentation ability as well as the acetic acid and ethanol resistance, which are considered to be useful features for industrial production of acetic acid and vinegar, the commercial product. On the other hand, Gluconobacter strains have the ability to perform oxidative fermentation of various sugars, sugar alcohols, and sugar acids leading to the formation of several valuable products. Thermotolerant strains of acetic acid bacteria were isolated in order to serve as the new strains of choice for industrial fermentations, in which the cooling costs for maintaining optimum growth and production temperature in the fermentation vessels could be significantly reduced. Genetic modifications by adaptation and genetic engineering were also applied to improve their properties, such as productivity and heat resistance.

  8. Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time.

    Science.gov (United States)

    Sheik, Cody S; Stevenson, Emily I; Den Uyl, Paul A; Arendt, Carli A; Aciego, Sarah M; Dick, Gregory J

    2015-01-01

    Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical, and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG) in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream, and the glacier's terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria, and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

  9. Relationships among bulk soil physicochemical, biochemical, and microbiological parameters in an organic alfalfa-rice rotation system.

    Science.gov (United States)

    Lopes, Ana R; Bello, Diana; Prieto-Fernández, Ángeles; Trasar-Cepeda, Carmen; Manaia, Célia M; Nunes, Olga C

    2015-08-01

    The microbial communities of bulk soil of rice paddy fields under an ancient organic agriculture regimen, consisting on an alfalfa-rice rotation system, were characterized. The drained soil of two adjacent paddies at different stages of the rotation was compared before rice seeding and after harvesting. The relationships among the soil microbial, physicochemical, and biochemical parameters were investigated using multivariate analyses. In the first year of rice cropping, aerobic cultivable heterotrophic populations correlated with lineages of presumably aerobic bacteria (e.g., Sphingobacteriales, Sphingomonadales). In the second year of rice cropping, the total C content correlated with presumable anaerobic bacteria (e.g., Anaerolineae). Independently of the year of rice cropping, before rice seeding, proteolytic activity correlated positively with the cultivable aerobic heterotrophic and ammonifier populations, the soil catabolic profile and with presumable aerobes (e.g., Sphingobacteriales, Rhizobiales) and anaerobes (e.g., Bacteroidales, Anaerolineae). After harvesting, strongest correlations were observed between cultivable diazotrophic populations and bacterial groups described as comprising N2 fixing members (e.g., Chloroflexi-Ellin6529, Betaproteobacteria, Alphaproteobacteria). It was demonstrated that chemical parameters and microbial functions were correlated with variations on the total bacterial community composition and structure occurring during rice cropping. A better understanding of these correlations and of their implications on soil productivity may be valid contributors for sustainable agriculture practices, based on ancient processes.

  10. Biodegradation of low-ethoxylated nonylphenols in a bioreactor packed with a new ceramic support (Vukopor ® S10).

    Science.gov (United States)

    Sciubba, Luigi; Bertin, Lorenzo; Todaro, Daniela; Bettini, Cristina; Fava, Fabio; Di Gioia, Diana

    2014-03-01

    This work was aimed at studying the possibility of biodegrading 4-nonylphenol and low ethoxylated nonylphenol mixtures, which are particularly recalcitrant to microbial degradation, by employing a biofilm reactor packed with a ceramic support (Vukopor® S10). A selected microbial consortium (Consortium A) was used to colonize the support. 4-Nonylphenol and ethoxylated nonylphenol degradation and mineralization capabilities were studied both in batch and continuous mode. The results showed that Vukopor® S10 was able to be colonized by an active biofilm for the degradation of the target pollutants with the reactor operating both in batch and continuous mode. On the other hand, pollutant adsorption on the support was negligible. FISH showed equal proportion of Alphaproteobacteria and Gammaproteobacteria in the Igepal CO-520 degrading reactor. A shift towards high proportion of Gammaproteobacteria was observed by supplying Igepal CO-210. PCR-density gradient gel electrophoresis (DGGE) analyses also evidenced that the biofilm evolved with time by changing the mixture applied and that Proteobacteria were the most represented phylum in the biofilm. Taken together, the data obtained provide a strong indication that the biofilm reactor packed with Vukopor® S10 and inoculated with Consortium A could potentially be used to develop a technology for the decontamination of 4-nonylphenol and low ethoxylated nonylphenol polluted effluents.

  11. Bacterial communities associated with the lichen symbiosis.

    Science.gov (United States)

    Bates, Scott T; Cropsey, Garrett W G; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2011-02-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N(2) fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N(2) fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.

  12. Metagenome of microorganisms associated with the toxic Cyanobacteria Microcystis aeruginosa analyzed using the 454 sequencing platform

    Institute of Scientific and Technical Information of China (English)

    LI Nan; ZHANG Lei; LI Fuchao; WANG Yuezhu; ZHU Yongqiang; KANG Hui; WANG Shengyue; QIN Song

    2011-01-01

    In this study, the 454 pyrosequencing technology was used to analyze the DNA of the Microcystis aeruginosa symbiosis system from cyanobacterial algal blooms in Taihu Lake, China. We generated 183 228 reads with an average length of 248 bp. Running the 454 assembly algorithm over our sequences yielded 22 239 significant contigs. After excluding the M. aeruginosa sequences, we obtained 1 322 assembled contigs longer than 1 000 bp. Taxonomic analysis indicated that four kingdoms were represented in the community: Archaea (n=9; 0.01%), Bacteria (n=98 921; 99.6%), Eukaryota (n=373;3.7%), and Viruses (n=18; 0.02%). The bacterial sequences were predominantly Alphaproteobacteria(n=41 805; 83.3%), Betaproteobacteria (n=5 254; 10.5%) and Gammaproteobacteria (n= 1 180; 2.4%).Gene annotations and assignment of COG (clusters of orthologous groups) functional categories indicate that a large number of the predicted genes are involved in metabolic, genetic, and environmental information processes. Our results demonstrate the extraordinary diversity of a microbial community in an ectosymbiotic system and further establish the tremendous utility of pyrosequencing.

  13. The role of lipids in activated sludge floc formation

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    Anna Liza Kretzschmar

    2015-03-01

    Full Text Available Activated sludge is widely used to treat municipal and industrial wastewater globally and the formation of activated sludge flocculates (flocs underpins the ability to separate sludge from treated water. Despite the importance of activated sludge flocs to human civilization there have been precious few attempts to rationally design fit for purpose flocs using a bottom-up approach based on a solid scientific foundation. Recently we have been developing experimental models for activated sludge floc formation based on the colonization and consumption of particulate organic matter (chitin and cellulose. In this study we lay the foundation for investigation of activated sludge floc formation based on biofilm formation around spheres of the lipid glycerol trioleate (GT that form spontaneously when GT is introduced into activated sludge incubations. Sludge biomass was observed to associate tightly with the lipid spheres. An increase in extracellular lipase activity was associated with a decrease in size of the colonized lipid spheres over a 25 day incubation. Bacterial community composition shifted from predominantly Betaproteobacteria to Alphaproteobacteria in GT treated sludge. Four activated sludge bacteria were isolated from lipid spheres and two of them were shown to produce AHL like quorum sensing signal activity, suggesting quorum sensing may play a role in lipid spheres colonization and biodegradation in activated sludge. The development of this experimental model of activated sludge floc formation lays the foundation for rational production of flocs for wastewater treatment using lipids as floc nuclei and further development of the flocculate life-cycle concept.

  14. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain through Culture-Dependent and Independent Approaches.

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    Javier Pascual

    Full Text Available Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria, Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.

  15. Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches.

    Science.gov (United States)

    Pascual, Javier; Blanco, Silvia; García-López, Marina; García-Salamanca, Adela; Bursakov, Sergey A; Genilloud, Olga; Bills, Gerald F; Ramos, Juan L; van Dillewijn, Pieter

    2016-01-01

    Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit.

  16. The CckA-ChpT-CtrA phosphorelay system is regulated by quorum sensing and controls flagellar motility in the marine sponge symbiont Ruegeria sp. KLH11.

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    Jindong Zan

    Full Text Available Bacteria respond to their environment via signal transduction pathways, often two-component type systems that function through phosphotransfer to control expression of specific genes. Phosphorelays are derived from two-component systems but are comprised of additional components. The essential cckA-chpT-ctrA phosphorelay in Caulobacter crescentus has been well studied and is important in orchestrating the cell cycle, polar development and flagellar biogenesis. Although cckA, chpT and ctrA homologues are widespread among the Alphaproteobacteria, relatively few is known about their function in the large and ecologically significant Roseobacter clade of the Rhodobacterales. In this study the cckA-chpT-ctrA system of the marine sponge symbiont Ruegeria sp. KLH11 was investigated. Our results reveal that the cckA, chpT and ctrA genes positively control flagellar biosynthesis. In contrast to C. crescentus, the cckA, chpT and ctrA genes in Ruegeria sp. KLH11 are non-essential and do not affect bacterial growth. Gene fusion and transcript analyses provide evidence for ctrA autoregulation and the control of motility-related genes. In KLH11, flagellar motility is controlled by the SsaRI system and acylhomoserine lactone (AHL quorum sensing. SsaR and long chain AHLs are required for cckA, chpT and ctrA gene expression, providing a regulatory link between flagellar locomotion and population density in KLH11.

  17. A quantitative study of the division cycle of Caulobacter crescentus stalked cells.

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    Shenghua Li

    2008-01-01

    Full Text Available Progression of a cell through the division cycle is tightly controlled at different steps to ensure the integrity of genome replication and partitioning to daughter cells. From published experimental evidence, we propose a molecular mechanism for control of the cell division cycle in Caulobacter crescentus. The mechanism, which is based on the synthesis and degradation of three "master regulator" proteins (CtrA, GcrA, and DnaA, is converted into a quantitative model, in order to study the temporal dynamics of these and other cell cycle proteins. The model accounts for important details of the physiology, biochemistry, and genetics of cell cycle control in stalked C. crescentus cell. It reproduces protein time courses in wild-type cells, mimics correctly the phenotypes of many mutant strains, and predicts the phenotypes of currently uncharacterized mutants. Since many of the proteins involved in regulating the cell cycle of C. crescentus are conserved among many genera of alpha-proteobacteria, the proposed mechanism may be applicable to other species of importance in agriculture and medicine.

  18. Computational and genetic reduction of a cell cycle to its simplest, primordial components.

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    Seán M Murray

    2013-12-01

    Full Text Available What are the minimal requirements to sustain an asymmetric cell cycle? Here we use mathematical modelling and forward genetics to reduce an asymmetric cell cycle to its simplest, primordial components. In the Alphaproteobacterium Caulobacter crescentus, cell cycle progression is believed to be controlled by a cyclical genetic circuit comprising four essential master regulators. Unexpectedly, our in silico modelling predicted that one of these regulators, GcrA, is in fact dispensable. We confirmed this experimentally, finding that ΔgcrA cells are viable, but slow-growing and elongated, with the latter mostly due to an insufficiency of a key cell division protein. Furthermore, suppressor analysis showed that another cell cycle regulator, the methyltransferase CcrM, is similarly dispensable with simultaneous gcrA/ccrM disruption ameliorating the cytokinetic and growth defect of ΔgcrA cells. Within the Alphaproteobacteria, gcrA and ccrM are consistently present or absent together, rather than either gene being present alone, suggesting that gcrA/ccrM constitutes an independent, dispensable genetic module. Together our approaches unveil the essential elements of a primordial asymmetric cell cycle that should help illuminate more complex cell cycles.

  19. Viscera-associated bacterial diversity among intertidal gastropods from Northern-Atlantic coast of Portugal.

    Science.gov (United States)

    Pratheepa, Vijaya K; Silva, Marisa; Vasconcelos, Vitor

    2014-02-01

    Culture-dependent evaluation of the bacteria was carried out on gastropods, such as Monodonta lineata, Gibbula umbilicalis, Nucella lapillus and Patella intermedia, and the environmental samples (biofilm and surrounding sea water) collected from six different locations of Northern Portugal coastal area to investigate the interactions between the microbes in the viscera of gastropods and in the environment. A total of 141 isolates and 39 operational taxonomic units were identified. Phylogenetic analysis based on the 16S rRNA gene showed that bacterial isolates are highly diverse and most of them were found in other marine environment. The observed bacterial diversity was distributed over five different classes (Gammaproteobacteria, Alphaproteobacteria, Flavobacteria, Bacilli and Actinobacteria) with the greatest number of 16S rRNA gene sequence derived from the Gammaproteobacteria (77 %). Vibrio is found to be the dominant one among the different bacterial species isolated. The results suggest that the microorganisms in the environment are maintained in the viscera of the gastropods which may have a key role in the metabolic functions.

  20. Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments.

    Science.gov (United States)

    Jorquera, Milko A; Maruyama, Fumito; Ogram, Andrew V; Navarrete, Oscar U; Lagos, Lorena M; Inostroza, Nitza G; Acuña, Jacquelinne J; Rilling, Joaquín I; de La Luz Mora, María

    2016-10-01

    Chile is topographically and climatically diverse, with a wide array of diverse undisturbed ecosystems that include native plants that are highly adapted to local conditions. However, our understanding of the diversity, activity, and role of rhizobacteria associated with natural vegetation in undisturbed Chilean extreme ecosystems is very poor. In the present study, the combination of denaturing gradient gel electrophoresis and 454-pyrosequencing approaches was used to describe the rhizobacterial community structures of native plants grown in three representative Chilean extreme environments: Atacama Desert (ATA), Andes Mountains (AND), and Antarctic (ANT). Both molecular approaches revealed the presence of Proteobacteria, Bacteroidetes, and Actinobacteria as the dominant phyla in the rhizospheres of native plants. Lower numbers of operational taxonomic units (OTUs) were observed in rhizosphere soils from ATA compared with AND and ANT. Both approaches also showed differences in rhizobacterial community structures between extreme environments and between plant species. The differences among plant species grown in the same environment were attributed to the higher relative abundance of classes Gammaproteobacteria and Alphaproteobacteria. However, further studies are needed to determine which environmental factors regulate the structures of rhizobacterial communities, and how (or if) specific bacterial groups may contribute to the growth and survival of native plants in each Chilean extreme environments.

  1. Molecular characterization of natural biofilms from household taps with different materials: PVC, stainless steel, and cast iron in drinking water distribution system.

    Science.gov (United States)

    Lin, Wenfang; Yu, Zhisheng; Chen, Xi; Liu, Ruyin; Zhang, Hongxun

    2013-09-01

    Microorganism in drinking water distribution system may colonize in biofilms. Bacterial 16S rRNA gene diversities were analyzed in both water and biofilms grown on taps with three different materials (polyvinyl chloride (PVC), stainless steel, and cast iron) from a local drinking water distribution system. In total, five clone libraries (440 sequences) were obtained. The taxonomic composition of the microbial communities was found to be dominated by members of Proteobacteria (65.9-98.9 %), broadly distributed among the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Other bacterial groups included Firmicutes, Acidobacteria, Bacteroidetes, Cyanobacteria, and Deinococcus-Thermus. Moreover, a small proportion of unclassified bacteria (3.5-10.6 %) were also found. This investigation revealed that the bacterial communities in biofilms appeared much more diversified than expected and more care should be taken to the taps with high bacterial diversity. Also, regular monitor of outflow water would be useful as potentially pathogenic bacteria were detected. In addition, microbial richness and diversity in taps ranked in the order as: PVC steel iron. All the results interpreted that PVC would be a potentially suitable material for use as tap component in drinking water distribution system.

  2. Heme degrading protein HemS is involved in oxidative stress response of Bartonella henselae.

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    MaFeng Liu

    Full Text Available Bartonellae are hemotropic bacteria, agents of emerging zoonoses. These bacteria are heme auxotroph Alphaproteobacteria which must import heme for supporting their growth, as they cannot synthesize it. Therefore, Bartonella genome encodes for a complete heme uptake system allowing the transportation of this compound across the outer membrane, the periplasm and the inner membranes. Heme has been proposed to be used as an iron source for Bartonella since these bacteria do not synthesize a complete system required for iron Fe³⁺ uptake. Similarly to other bacteria which use heme as an iron source, Bartonellae must transport this compound into the cytoplasm and degrade it to allow the release of iron from the tetrapyrrole ring. For Bartonella, the gene cluster devoted to the synthesis of the complete heme uptake system also contains a gene encoding for a polypeptide that shares homologies with heme trafficking or degrading enzymes. Using complementation of an E. coli mutant strain impaired in heme degradation, we demonstrated that HemS from Bartonella henselae expressed in E. coli allows the release of iron from heme. Purified HemS from B. henselae binds heme and can degrade it in the presence of a suitable electron donor, ascorbate or NADPH-cytochrome P450 reductase. Knocking down the expression of HemS in B. henselae reduces its ability to face H₂O₂ induced oxidative stress.

  3. Deciphering bartonella diversity, recombination, and host specificity in a rodent community.

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    Jean-Philippe Buffet

    Full Text Available Host-specificity is an intrinsic feature of many bacterial pathogens, resulting from a long history of co-adaptation between bacteria and their hosts. Alpha-proteobacteria belonging to the genus Bartonella infect the erythrocytes of a wide range of mammal orders, including rodents. In this study, we performed genetic analysis of Bartonella colonizing a rodent community dominated by bank voles (Myodes glareolus and wood mice (Apodemus sylvaticus in a French suburban forest to evaluate their diversity, their capacity to recombine and their level of host specificity. Following the analysis of 550 rodents, we detected 63 distinct genotypes related to B. taylorii, B. grahamii, B. doshiae and a new B. rochalimae-like species. Investigating the most highly represented species, we showed that B. taylorii strain diversity was markedly higher than that of B. grahamii, suggesting a possible severe bottleneck for the latter species. The majority of recovered genotypes presented a strong association with either bank voles or wood mice, with the exception of three B. taylorii genotypes which had a broader host range. Despite the physical barriers created by host specificity, we observed lateral gene transfer between Bartonella genotypes associated with wood mice and Bartonella adapted to bank voles, suggesting that those genotypes might co-habit during their life cycle.

  4. Deciphering bartonella diversity, recombination, and host specificity in a rodent community.

    Science.gov (United States)

    Buffet, Jean-Philippe; Pisanu, Benoît; Brisse, Sylvain; Roussel, Sophie; Félix, Benjamin; Halos, Lénaïg; Chapuis, Jean-Louis; Vayssier-Taussat, Muriel

    2013-01-01

    Host-specificity is an intrinsic feature of many bacterial pathogens, resulting from a long history of co-adaptation between bacteria and their hosts. Alpha-proteobacteria belonging to the genus Bartonella infect the erythrocytes of a wide range of mammal orders, including rodents. In this study, we performed genetic analysis of Bartonella colonizing a rodent community dominated by bank voles (Myodes glareolus) and wood mice (Apodemus sylvaticus) in a French suburban forest to evaluate their diversity, their capacity to recombine and their level of host specificity. Following the analysis of 550 rodents, we detected 63 distinct genotypes related to B. taylorii, B. grahamii, B. doshiae and a new B. rochalimae-like species. Investigating the most highly represented species, we showed that B. taylorii strain diversity was markedly higher than that of B. grahamii, suggesting a possible severe bottleneck for the latter species. The majority of recovered genotypes presented a strong association with either bank voles or wood mice, with the exception of three B. taylorii genotypes which had a broader host range. Despite the physical barriers created by host specificity, we observed lateral gene transfer between Bartonella genotypes associated with wood mice and Bartonella adapted to bank voles, suggesting that those genotypes might co-habit during their life cycle.

  5. Tellurium as a valuable tool for studying the prokaryotic origins of mitochondria.

    Science.gov (United States)

    Pontieri, Paola; De Stefano, Mario; Massardo, Domenica Rita; Gunge, Norio; Miyakawa, Isamu; Sando, Nobundo; Pignone, Domenico; Pizzolante, Graziano; Romano, Roberta; Alifano, Pietro; Del Giudice, Luigi

    2015-04-01

    Mitochondria are eukaryotic organelles which contain the own genetic material and evolved from free-living Eubacteria, namely hydrogen-producing Alphaproteobacteria. Since 1965, biologists provided, by research at molecular level, evidence for the prokaryotic origins of mitochondria. However, determining the precise origins of mitochondria is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. The use of new tools to evidence the prokaryotic origin of mitochondria could be useful to gain an insight into the bacterial endosymbiotic event that resulted in the permanent acquisition of bacteria, from the ancestral cell, that through time were transformed into mitochondria. Electron microscopy has shown that both proteobacterial and yeast cells during their growth in the presence of increasing amount of tellurite resulted in dose-dependent blackening of the culture due to elemental tellurium (Te(0)) that formed large deposits either along the proteobacterial membrane or along the yeast cell wall and mitochondria. Since the mitochondrial inner membrane composition is similar to that of proteobacterial membrane, in the present work we evidenced the black tellurium deposits on both, cell wall and mitochondria of ρ(+) and respiratory deficient ρ(-) mutants of yeast. A possible role of tellurite in studying the evolutionary origins of mitochondria will be discussed.

  6. Bioremediation using Novosphingobium strain DY4 for 2,4-dichlorophenoxyacetic acid-contaminated soil and impact on microbial community structure.

    Science.gov (United States)

    Dai, Yu; Li, Ningning; Zhao, Qun; Xie, Shuguang

    2015-04-01

    The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is commonly used for weed control. The ubiquity of 2,4-D has gained increasing environmental concerns. Biodegradation is an attractive way to clean up 2,4-D in contaminated soil. However, information on the bioaugmentation trial for remediating contaminated soil is still very limited. The impact of bioaugmentation using 2,4-D-degraders on soil microbial community remains unknown. The present study investigated the bioremediation potential of a novel degrader (strain DY4) for heavily 2,4-D-polluted soil and its bioaugmentation impact on microbial community structure. The strain DY4 was classified as a Novosphingobium species within class Alphaproteobacteria and harbored 2,4-D-degrading TfdAα gene. More than 50 and 95 % of the herbicide could be dissipated in bioaugmented soil (amended with 200 mg/kg 2,4-D) respectively in 3-4 and 5-7 days after inoculation of Novosphingobium strain DY4. A significant growth of the strain DY4 was observed in bioaugmented soil with the biodegradation of 2,4-D. Moreover, herbicide application significantly altered soil bacterial community structure but bioaumentation using the strain DY4 showed a relatively weak impact.

  7. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov.

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    Sven eBreider

    2014-08-01

    Full Text Available Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov. and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.

  8. Determinants of bacterial communities in Canadian agroforestry systems.

    Science.gov (United States)

    Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

    2016-06-01

    Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems.

  9. Cannibalism and predation as paths for horizontal passage of Wolbachia between terrestrial isopods.

    Science.gov (United States)

    Le Clec'h, Winka; Chevalier, Frédéric D; Genty, Lise; Bertaux, Joanne; Bouchon, Didier; Sicard, Mathieu

    2013-01-01

    The alpha-proteobacteria Wolbachia are the most widespread endosymbionts in arthropods and nematodes. Mainly maternally inherited, these so-called sex parasites have selected several strategies that increase their vertical dispersion in host populations. However, the lack of congruence between the Wolbachia and their host phylogenies suggests frequent horizontal transfers. One way that could be used for horizontal Wolbachia transfers between individuals is predation. The aim of this study was to test whether horizontal passage of Wolbachia is possible when an uninfected terrestrial isopod eats an infected one. After having eaten Armadillidium vulgare harbouring Wolbachia, the predator-recipients (the two woodlice A. vulgare and Porcellio dilatatus dilatatus) that were initially Wolbachia-free were tested positive for the presence of Wolbachia both by quantitative PCR and Fluorescence in situ Hybridization (FISH). Even if the titers were low compared to vertically infected individuals, this constitutes the first demonstration of Wolbachia occurrence in various organs of an initially uninfected host after eating an infected one.

  10. Global proteomic analysis of two tick-borne emerging zoonotic agents: Anaplasma phagocytophilum and Ehrlichia chaffeensis

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Mingqun ..; Kikuchi, Takane; Brewer, Heather M.; Norbeck, Angela D.; Rikihisa, Yasuko

    2011-02-17

    Anaplasma phagocytophilum and Ehrlichia chaffeensis are obligatory intracellular {alpha}-proteobacteria that infect human leukocytes and cause potentially fatal emerging zoonoses. In the present study, we determined global protein expression profiles of these bacteria cultured in the human promyelocytic leukemia cell line, HL-60. Mass spectrometric (MS) analyses identified a total of 1,212 A. phagocytophilum and 1,021 E. chaffeensis proteins, representing 89.3 and 92.3% of the predicted bacterial proteomes, respectively. Nearly all bacterial proteins ({approx}99%) with known functions were expressed, whereas only approximately 80% of hypothetical proteins were detected in infected human cells. Quantitative MS/MS analyses indicated that highly expressed proteins in both bacteria included chaperones, enzymes involved in biosynthesis and metabolism, and outer membrane proteins, such as A. phagocytophilum P44 and E. chaffeensis P28/OMP-1. Among 113 A. phagocytophilum p44 paralogous genes, 110 of them were expressed and 88 of them were encoded by pseudogenes. In addition, bacterial infection of HL-60 cells up-regulated the expression of human proteins involved mostly in cytoskeleton components, vesicular trafficking, cell signaling, and energy metabolism, but down regulated some pattern recognition receptors involved in innate immunity. Our proteomics data represent a comprehensive analysis of A. phagocytophilum and E. chaffeensis proteomes, and provide a quantitative view of human host protein expression profiles regulated by bacterial infection. The availability of these proteomic data will provide new insights into biology and pathogenesis of these obligatory intracellular pathogens.

  11. Crustose coralline algal species host distinct bacterial assemblages on their surfaces.

    Science.gov (United States)

    Sneed, Jennifer M; Ritson-Williams, Raphael; Paul, Valerie J

    2015-11-01

    Crustose coralline algae (CCA) are important components of many marine ecosystems. They aid in reef accretion and stabilization, create habitat for other organisms, contribute to carbon sequestration and are important settlement substrata for a number of marine invertebrates. Despite their ecological importance, little is known about the bacterial communities associated with CCA or whether differences in bacterial assemblages may have ecological implications. This study examined the bacterial communities on four different species of CCA collected in Belize using bacterial tag-encoded FLX amplicon pyrosequencing of the V1-V3 region of the 16S rDNA. CCA were dominated by Alphaproteobacteria, Gammaproteobacteria and Actinomycetes. At the operational taxonomic unit (OTU) level, each CCA species had a unique bacterial community that was significantly different from all other CCA species. Hydrolithon boergesenii and Titanoderma prototypum, CCA species that facilitate larval settlement in multiple corals, had higher abundances of OTUs related to bacteria that inhibit the growth and/or biofilm formation of coral pathogens. Fewer coral larvae settle on the surfaces of Paragoniolithon solubile and Porolithon pachydermum. These CCA species had higher abundances of OTUs related to known coral pathogens and cyanobacteria. Coral larvae may be able to use the observed differences in bacterial community composition on CCA species to assess the suitability of these substrata for settlement and selectively settle on CCA species that contain beneficial bacteria.

  12. Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome.

    Science.gov (United States)

    Lemaire, Benny; Van Cauwenberghe, Jannick; Chimphango, Samson; Stirton, Charles; Honnay, Olivier; Smets, Erik; Muasya, A Muthama

    2015-11-01

    The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.

  13. Biodiversity of amoebae and amoeba-resisting bacteria in a hospital water network.

    Science.gov (United States)

    Thomas, Vincent; Herrera-Rimann, Katia; Blanc, Dominique S; Greub, Gilbert

    2006-04-01

    Free-living amoebae (FLA) are ubiquitous organisms that have been isolated from various domestic water systems, such as cooling towers and hospital water networks. In addition to their own pathogenicity, FLA can also act as Trojan horses and be naturally infected with amoeba-resisting bacteria (ARB) that may be involved in human infections, such as pneumonia. We investigated the biodiversity of bacteria and their amoebal hosts in a hospital water network. Using amoebal enrichment on nonnutrient agar, we isolated 15 protist strains from 200 (7.5%) samples. One thermotolerant Hartmannella vermiformis isolate harbored both Legionella pneumophila and Bradyrhizobium japonicum. By using amoebal coculture with axenic Acanthamoeba castellanii as the cellular background, we recovered at least one ARB from 45.5% of the samples. Four new ARB isolates were recovered by culture, and one of these isolates was widely present in the water network. Alphaproteobacteria (such as Rhodoplanes, Methylobacterium, Bradyrhizobium, Afipia, and Bosea) were recovered from 30.5% of the samples, mycobacteria (Mycobacterium gordonae, Mycobacterium kansasii, and Mycobacterium xenopi) were recovered from 20.5% of the samples, and Gammaproteobacteria (Legionella) were recovered from 5.5% of the samples. No Chlamydia or Chlamydia-like organisms were recovered by amoebal coculture or detected by PCR. The observed strong association between the presence of amoebae and the presence of Legionella (P amoebae when water control measures are designed.

  14. Culturable bacterial diversity from a feed water of a reverse osmosis system, evaluation of biofilm formation and biocontrol using phages.

    Science.gov (United States)

    Belgini, D R B; Dias, R S; Siqueira, V M; Valadares, L A B; Albanese, J M; Souza, R S; Torres, A P R; Sousa, M P; Silva, C C; De Paula, S O; Oliveira, V M

    2014-10-01

    Biofilm formation on reverse osmosis (RO) systems represents a drawback in the application of this technology by different industries, including oil refineries. In RO systems the feed water maybe a source of microbial contamination and thus contributes for the formation of biofilm and consequent biofouling. In this study the planktonic culturable bacterial community was characterized from a feed water of a RO system and their capacities were evaluated to form biofilm in vitro. Bacterial motility and biofilm control were also analysed using phages. As results, diverse Protobacteria, Actinobacteria and Bacteroidetes were identified. Alphaproteobacteria was the predominant group and Brevundimonas, Pseudomonas and Mycobacterium the most abundant genera. Among the 30 isolates, 11 showed at least one type of motility and 11 were classified as good biofilm formers. Additionally, the influence of non-specific bacteriophage in the bacterial biofilms formed in vitro was investigated by action of phages enzymes or phage infection. The vB_AspP-UFV1 (Podoviridae) interfered in biofilm formation of most tested bacteria and may represent a good alternative in biofilm control. These findings provide important information about the bacterial community from the feed water of a RO system that may be used for the development of strategies for biofilm prevention and control in such systems.

  15. 'Candidatus Megaira polyxenophila' gen. nov., sp. nov.: considerations on evolutionary history, host range and shift of early divergent rickettsiae.

    Directory of Open Access Journals (Sweden)

    Martina Schrallhammer

    Full Text Available "Neglected Rickettsiaceae" (i.e. those harboured by non-hematophagous eukaryotic hosts display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure of a novel rickettsial bacterium, herewith proposed as 'Candidatus Megaira polyxenophila' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora; furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta. Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that 'Candidatus Megaira polyxenophila' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria.

  16. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    Science.gov (United States)

    Mou, Xiaozhen; Lu, Xinxin; Jacob, Jisha; Sun, Shulei; Heath, Robert

    2013-01-01

    Cyanobacterial harmful blooms (CyanoHABs) that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera) and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax) of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr) were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

  17. Pathogenomic inference of virulence-associated genes in Leptospira interrogans.

    Directory of Open Access Journals (Sweden)

    Jason S Lehmann

    Full Text Available Leptospirosis is a globally important, neglected zoonotic infection caused by spirochetes of the genus Leptospira. Since genetic transformation remains technically limited for pathogenic Leptospira, a systems biology pathogenomic approach was used to infer leptospiral virulence genes by whole genome comparison of culture-attenuated Leptospira interrogans serovar Lai with its virulent, isogenic parent. Among the 11 pathogen-specific protein-coding genes in which non-synonymous mutations were found, a putative soluble adenylate cyclase with host cell cAMP-elevating activity, and two members of a previously unstudied ∼15 member paralogous gene family of unknown function were identified. This gene family was also uniquely found in the alpha-proteobacteria Bartonella bacilliformis and Bartonella australis that are geographically restricted to the Andes and Australia, respectively. How the pathogenic Leptospira and these two Bartonella species came to share this expanded gene family remains an evolutionary mystery. In vivo expression analyses demonstrated up-regulation of 10/11 Leptospira genes identified in the attenuation screen, and profound in vivo, tissue-specific up-regulation by members of the paralogous gene family, suggesting a direct role in virulence and host-pathogen interactions. The pathogenomic experimental design here is generalizable as a functional systems biology approach to studying bacterial pathogenesis and virulence and should encourage similar experimental studies of other pathogens.

  18. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

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    Lee F Stanish

    Full Text Available The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria, MLE1-12 (phylum Cyanobacteria, Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.

  19. Microbial community structure of Arctic seawater as revealed by pyrosequencing

    Institute of Scientific and Technical Information of China (English)

    LI Yang; WANG Zhen; LIN Xuezheng

    2016-01-01

    This study aimed to determine the microbial community structure of seawater in (ICE-1) and out (FUBIAO) of the pack ice zone in the Arctic region. Approximate 10 L seawater was filtrated by 0.2 μm Whatman nuclepore filters and the environmental genomic DNA was extracted. We conducted a detailed census of microbial communities by pyrosequencing. Analysis of the microbial community structures indicated that these two samples had high bacterial, archaeal and eukaryotic diversity. Proteobacteria and Bacteroidetes were the two dominant members of the bacterioplankton community in both samples, and their relative abundance were 51.29% and 35.39%, 72.95%and 23.21%, respectively. Euryarchaeota was the most abundant archaeal phylum, and the relative abundance was nearly up to 100% in FUBIAO and 60% in ICE-1. As for the eukaryotes, no_rank_Eukaryota, Arthropoda and no_rank_Metazoa were the most abundant groups in Sample FUBIAO, accounting for 85.29% of the total reads. The relative abundance of the most abundant phylum in Sample ICE-1, no_rank_Eukaryota and no_rank_Metazoa, was up to 90.69% of the total reads. Alphaproteobacteria, Flavobacteria and Gammaproteobacteria were the top three abundant classes in the two samples at the bacterial class level. There were also differences in the top ten abundant bacterial, archaeal and eukaryotic OTUs at the level of 97% similarity between the two samples.

  20. Molecular Analysis of the Bacterial Communities in Crude Oil Samples from Two Brazilian Offshore Petroleum Platforms

    Directory of Open Access Journals (Sweden)

    Elisa Korenblum

    2012-01-01

    Full Text Available Crude oil samples with high- and low-water content from two offshore platforms (PA and PB in Campos Basin, Brazil, were assessed for bacterial communities by 16S rRNA gene-based clone libraries. RDP Classifier was used to analyze a total of 156 clones within four libraries obtained from two platforms. The clone sequences were mainly affiliated with Gammaproteobacteria (78.2% of the total clones; however, clones associated with Betaproteobacteria (10.9%, Alphaproteobacteria (9%, and Firmicutes (1.9% were also identified. Pseudomonadaceae was the most common family affiliated with these clone sequences. The sequences were further analyzed by MOTHUR, yielding 81 operational taxonomic units (OTUs grouped at 97% stringency. Richness estimators also calculated by MOTHUR indicated that oil samples with high-water content were the most diverse. Comparison of bacterial communities present in these four samples using LIBSHUFF and Principal Component Analysis (PCA indicated that the water content significantly influenced the community structure only of crude oil obtained from PA. Differences between PA and PB libraries were observed, suggesting the importance of the oil field as a driver of community composition in this habitat.

  1. Characterization of heterotrophic prokaryote subgroups in the Sfax coastal solar salterns by combining flow cytometry cell sorting and phylogenetic analysis.

    Science.gov (United States)

    Trigui, Hana; Masmoudi, Salma; Brochier-Armanet, Céline; Barani, Aude; Grégori, Gérald; Denis, Michel; Dukan, Sam; Maalej, Sami

    2011-05-01

    Here, we combined flow cytometry (FCM) and phylogenetic analyses after cell sorting to characterize the dominant groups of the prokaryotic assemblages inhabiting two ponds of increasing salinity: a crystallizer pond (TS) with a salinity of 390 g/L, and the non-crystallizer pond (M1) with a salinity of 200 g/L retrieved from the solar saltern of Sfax in Tunisia. As expected, FCM analysis enabled the resolution of high nucleic acid content (HNA) and low nucleic acid content (LNA) prokaryotes. Next, we performed a taxonomic analysis of the bacterial and archaeal communities comprising the two most populated clusters by phylogenetic analyses of 16S rRNA gene clone library. We show for the first time that the presence of HNA and LNA content cells could also be extended to the archaeal populations. Archaea were detected in all M1 and TS samples, whereas representatives of Bacteria were detected only in LNA for M1 and HNA for TS. Although most of the archaeal sequences remained undetermined, other clones were most frequently affiliated to Haloquadratum and Halorubrum. In contrast, most bacterial clones belonged to the Alphaproteobacteria class (Phyllobacterium genus) in M1 samples and to the Bacteroidetes phylum (Sphingobacteria and Salinibacter genus) in TS samples.

  2. Olive mill wastewater treatment in single-chamber air-cathode microbial fuel cells.

    Science.gov (United States)

    Bermek, Hakan; Catal, Tunc; Akan, S Süha; Ulutaş, Mehmet Sefa; Kumru, Mert; Özgüven, Mine; Liu, Hong; Özçelik, Beraat; Akarsubaşı, Alper Tunga

    2014-04-01

    Olive mill wastewaters create significant environmental issues in olive-processing countries. One of the most hazardous groups of pollutants in these wastewaters is phenolic compounds. Here, olive mill wastewater was used as substrate and treated in single-chamber air-cathode microbial fuel cells. Olive mill wastewater yielded a maximum voltage of 381 mV on an external resistance of 1 kΩ. Notable decreases in the contents of 3,4-dihydroxybenzoic acid, tyrosol, gallic acid and p-coumaric acid were detected. Chemical oxygen demand removal rates were 65 % while removal of total phenolics by the process was lower (49 %). Microbial community analysis during the olive mill wastewater treating MFC has shown that both exoelectrogenic and phenol-degrading microorganisms have been enriched during the operation. Brevundimonas-, Sphingomonas- and Novosphingobium-related phylotypes were enriched on the anode biofilm, while Alphaproteobacteria and Bacteriodetes dominated the cathode biofilm. As one of the novel studies, it has been demonstrated that recalcitrant olive mill wastewaters could be treated and utilized for power generation in microbial fuel cells.

  3. Spatial variations of prokaryotic communities in surface water from India Ocean to Chinese marginal seas and their underlining environmental determinants

    Directory of Open Access Journals (Sweden)

    Xiaowei eZheng

    2016-02-01

    Full Text Available To illustrate the biogeographic patterns of prokaryotic communities in surface sea water, 24 samples were systematically collected across a large distance from Indian Ocean to Chinese marginal seas, with an average distance of 453 km between two adjacent stations. A total of 841,364 quality reads was produced by the high throughput DNA sequencing of the 16S rRNA genes. Phylogenetic analysis showed that Proteobacteria were predominant in all samples, with Alphaproteobacteria and Gammaproteobacteria being the two most abundant components. Cyanobacteria represented the second largest fraction of the total quality reads, and mainly included Prochlorococcus and Synechococcus. The semi-closed marginal seas, including South China Sea (SCS and nearby regions, exhibited a transition in community composition between oceanic and coastal seas, based on the distribution patterns of Prochlorococcus and Synechococcus as well as a non-metric multidimensional scaling (NMDS analysis. Distinct clusters of prokaryotes from coastal and open seas, and from different water masses in Indian Ocean were obtained by Bray-Curtis dissimilarity analysis at the OTU level, revealing a clear spatial heterogeneity. The major environmental factors correlated with the community variation in this broad scale were identified as salinity, temperature and geographic distance. Community comparison among regions shows that anthropogenic contamination is another dominant factor in shaping the biogeographic patterns of the microorganisms. These results suggest that environmental factors involved in complex interactions between land and sea act synergistically in driving spatial variations in coastal areas.

  4. Integrated Metagenomic and Metatranscriptomic Analyses of Microbial Communities in the Meso- and Bathypelagic Realm of North Pacific Ocean

    Directory of Open Access Journals (Sweden)

    Deirdre R. Meldrum

    2013-10-01

    Full Text Available Although emerging evidence indicates that deep-sea water contains an untapped reservoir of high metabolic and genetic diversity, this realm has not been studied well compared with surface sea water. The study provided the first integrated meta-genomic and -transcriptomic analysis of the microbial communities in deep-sea water of North Pacific Ocean. DNA/RNA amplifications and simultaneous metagenomic and metatranscriptomic analyses were employed to discover information concerning deep-sea microbial communities from four different deep-sea sites ranging from the mesopelagic to pelagic ocean. Within the prokaryotic community, bacteria is absolutely dominant (~90% over archaea in both metagenomic and metatranscriptomic data pools. The emergence of archaeal phyla Crenarchaeota, Euryarchaeota, Thaumarchaeota, bacterial phyla Actinobacteria, Firmicutes, sub-phyla Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria, and the decrease of bacterial phyla Bacteroidetes and Alphaproteobacteria are the main composition changes of prokaryotic communities in the deep-sea water, when compared with the reference Global Ocean Sampling Expedition (GOS surface water. Photosynthetic Cyanobacteria exist in all four metagenomic libraries and two metatranscriptomic libraries. In Eukaryota community, decreased abundance of fungi and algae in deep sea was observed. RNA/DNA ratio was employed as an index to show metabolic activity strength of microbes in deep sea. Functional analysis indicated that deep-sea microbes are leading a defensive lifestyle.

  5. Water quality and microbial diversity in cisterns from semiarid areas in Brazil.

    Science.gov (United States)

    Alves, Fellipe; Köchling, Thorsten; Luz, Julio; Santos, Sylvana Melo; Gavazza, Savia

    2014-09-01

    Harvesting rainwater is a common practice worldwide, particularly in areas with no access to a public water supply or insufficient groundwater reserves. More than two million people living in semiarid regions of Brazil consume rainwater stored in cisterns, and little information is available regarding the water quality. Despite the initial good quality of the rainwater, its harvest and storage can introduce contaminants that must be eliminated before consumption. To evaluate the influence of handling, cistern age and precipitation on the quality of harvested rainwater, we monitored seven cisterns in the semiarid Brazilian Northeast over 4 years. Microbial and physicochemical parameters were monitored once a month, and denaturant gradient gel electrophoresis (DGGE) was performed at the end of the monitoring period. Coliform bacteria were detected in 100% of samples, while Escherichia coli were observed in 73.8%. The alkalinity and conductivity were the highest for the recently built cisterns due to the dissolution of construction materials. The DGGE of the 16S r DNA did not reveal the presence of E. coli. Instead, DGGE bands sequencing indicated that species primarily affiliated with Alphaproteobacteria were present in all cisterns, indicating the presence of microbial ecosystems capable of purifying and stabilizing the stored rainwater.

  6. Pilot-scale study on nitrogen and aromatic compounds removal in printing and dyeing wastewater by reinforced hydrolysis-denitrification coupling process and its microbial community analysis.

    Science.gov (United States)

    Li, Chao; Ren, Hongqiang; Yin, Erqin; Tang, Siyuan; Li, Yi; Cao, Jiashun

    2015-06-01

    Aiming to efficiently dispose printing and dyeing wastewater with "high organic nitrogen and aromatic compounds, but low carbon source quality", the reinforced anaerobic hydrolysis-denitrification coupling process, based on improved UASB reactors and segregated collection-disposition strategy, was designed and applied at the pilot scale. Results showed that the coupling process displayed efficient removal for these two kinds of pollutants (nitrogen and aromatics), since the concentration of NH3-N (shortened as ρ (NH3-N)) aromatics reduced greatly by UASBs according to GC-MS. Microbial community analysis by PCR-DGGE showed that Bacteroidetes and Alphaproteobacteria were the dominant communities in the bioreactors and some kinds of VFAs-producing, denitrifying and aromatic ring opening microorganisms were discovered. Further, the nirK and bcrA genes quantification also indicated the coupling process owned outstanding denitrification and aromatic compound-degrading potential, which demonstrates that the coupling process owns admirable applicability for this kind of wastewater treatment.

  7. Structural and Functional Characterization of a Novel Family of Cyclophilins, the AquaCyps

    Science.gov (United States)

    Jakob, Roman P.; Schmidpeter, Philipp A. M.; Koch, Johanna R.; Schmid, Franz X.; Maier, Timm

    2016-01-01

    Cyclophilins are ubiquitous cis-trans-prolyl isomerases (PPIases) found in all kingdoms of life. Here, we identify a novel family of cyclophilins, termed AquaCyps, which specifically occurs in marine Alphaproteobacteria, but not in related terrestric species. In addition to a canonical PPIase domain, AquaCyps contain large extensions and insertions. The crystal structures of two representatives from Hirschia baltica, AquaCyp293 and AquaCyp300, reveal the formation of a compact domain, the NIC domain, by the N- and C-terminal extensions together with a central insertion. The NIC domain adopts a novel mixed alpha-helical, beta-sheet fold that is linked to the cyclophilin domain via a conserved disulfide bond. In its overall fold, AquaCyp293 resembles AquaCyp300, but the two proteins utilize distinct sets of active site residues, consistent with differences in their PPIase catalytic properties. While AquaCyp293 is a highly active general PPIase, AquaCyp300 is specific for hydrophobic substrate peptides and exhibits lower overall activity. PMID:27276069

  8. Metagenomic identification of bacterioplankton taxa and pathways involved in microcystin degradation in lake erie.

    Directory of Open Access Journals (Sweden)

    Xiaozhen Mou

    Full Text Available Cyanobacterial harmful blooms (CyanoHABs that produce microcystins are appearing in an increasing number of freshwater ecosystems worldwide, damaging quality of water for use by human and aquatic life. Heterotrophic bacteria assemblages are thought to be important in transforming and detoxifying microcystins in natural environments. However, little is known about their taxonomic composition or pathways involved in the process. To address this knowledge gap, we compared the metagenomes of Lake Erie free-living bacterioplankton assemblages in laboratory microcosms amended with microcystins relative to unamended controls. A diverse array of bacterial phyla were responsive to elevated supply of microcystins, including Acidobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria of the alpha, beta, gamma, delta and epsilon subdivisions and Verrucomicrobia. At more detailed taxonomic levels, Methylophilales (mainly in genus Methylotenera and Burkholderiales (mainly in genera Bordetella, Burkholderia, Cupriavidus, Polaromonas, Ralstonia, Polynucleobacter and Variovorax of Betaproteobacteria were suggested to be more important in microcystin degradation than Sphingomonadales of Alphaproteobacteria. The latter taxa were previously thought to be major microcystin degraders. Homologs to known microcystin-degrading genes (mlr were not overrepresented in microcystin-amended metagenomes, indicating that Lake Erie bacterioplankton might employ alternative genes and/or pathways in microcystin degradation. Genes for xenobiotic metabolism were overrepresented in microcystin-amended microcosms, suggesting they are important in bacterial degradation of microcystin, a phenomenon that has been identified previously only in eukaryotic systems.

  9. Persistent Infection by Wolbachia wAlbB Has No Effect on Composition of the Gut Microbiota in Adult Female Anopheles stephensi

    Science.gov (United States)

    Chen, Shicheng; Zhao, Jiangchao; Joshi, Deepak; Xi, Zhiyong; Norman, Beth; Walker, Edward D.

    2016-01-01

    The bacteria in the midgut of Anopheles stephensi adult females from laboratory colonies were studied by sequencing the V4 region of 16S rRNA genes, with respect to three experimental factors: stable or cured Wolbachia infection; sugar or blood diet; and age. Proteobacteria and Bacteroidetes dominated the community [>90% of operational taxonomic units (OTUs)]; most taxa were in the classes Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, and were assigned to Elizabethkingia (46.9%), Asaia (6.4%) and Pseudomonas (6.0%), or unclassified Enterobacteriaceae (37.2%). Bacterial communities were similar between Wolbachia-cured and Wolbachia-infected mosquito lines, indicating that the gut microbiota were not dysregulated in the presence of Wolbachia. The proportion of Enterobacteriaceae was higher in mosquitoes fed a blood meal compared to those provided a sugar meal. Collectively, the bacterial community had a similar structure in older Wolbachia-infected mosquitoes 8 days after the blood meal, as in younger Wolbachia-infected mosquitoes before a blood meal, except that older mosquitoes had a higher proportion of Enterobacteriaceae and lower proportion of Elizabethkingia. Consistent presence of certain predominant bacteria (Elizabethkingia, Asaia, Pseudomonas, and Enterobacteriaceae) suggests they would be useful for paratransgenesis to control malaria infection, particularly when coupled to a Wolbachia-based intervention strategy. PMID:27708633

  10. Seasonal Variations in the Contributions of Different Bacterial Groups to the Uptake of Low-Molecular-Weight Compounds in Northwestern Mediterranean Coastal Waters▿

    Science.gov (United States)

    Alonso-Sáez, Laura; Gasol, Josep M.

    2007-01-01

    We analyzed the contributions of different heterotrophic bacterial groups to the uptake of several low-molecular weight compounds during a seasonal cycle on the northwestern Mediterranean coast (Blanes Bay Microbial Observatory). The bacterial assemblage structure had been shown to change substantially year-round for this site, but whether changes in the activities of the different bacterial groups also occurred on the seasonal scale was unknown. Microautoradiography combined with catalyzed reporter deposition fluorescence in situ hybridization was used to analyze the patterns of glucose, amino acid, and ATP uptake by different bacterial groups. Gammaproteobacteria and Bacteroidetes were not very active in the uptake of glucose at any time of the year (20% of cells were active). Dissolved free amino acids were taken up considerably by Alphaproteobacteria and Gammaproteobacteria but not by Bacteroidetes. Relatively high percentages of cells of the three broad phylogenetic groups actively took up ATP, which could be related to the important phosphorous limitation of bacterial production during most of the year in Blanes Bay. The contribution of SAR11 to the uptake of the monomers was variable year-round, generally with fewer than 30% of the cells being active. By contrast, Roseobacter were highly overrepresented in the uptake of all the substrates throughout all the year, with more than 50% of cells being active in all the samples and for all substrates. Our results suggest that substantial changes in the activity of some phylogenetic groups of bacteria occur throughout the year. PMID:17400772

  11. Hydrogeology, water quality, and microbial assessment of a coastal alluvial aquifer in western Saudi Arabia: potential use of coastal wadi aquifers for desalination water supplies [Hydrogéologie, qualité de l’eau et évaluation microbienne d’un aquifère côtier alluvial dans l’Ouest de l’Arabie Saoudite: utilisation potentielle des aquifères côtiers des oueds pour l’alimentation en eau après désalinisation] [Hidrogeologia, qualidade da água e avaliação microbiológica de um aquífero costeiro no oeste da Arábia Saudita: uso potencial de aquíferos de wadi costeiros para dessalinização de águas destinadas a abastecimento] [Hidrogeología, calidad de agua y evaluación microbiana de un acuífero costero aluvial en Arabia Saudita occidental: uso potencial de acuíferos costeros uadis para la desalinización de los abastecimientos de agua

    KAUST Repository

    Missimer, Thomas M.

    2014-07-20

    Wadi alluvial aquifers located along coastal areas of the Middle East have been assumed to be suitable sources of feed water for seawater reverse osmosis facilities based on high productivity, connectedness to the sea for recharge, and the occurrence of seawater with chemistry similar to that in the adjacent Red Sea. An investigation of the intersection of Wadi Wasimi with the Red Sea in western Saudi Arabia has revealed that the associated predominantly unconfined alluvial aquifer divides into two sand-and-gravel aquifers at the coast, each with high productivity (transmissivity = 42,000 m2/day). This aquifer system becomes confined near the coast and contains hypersaline water. The hydrogeology of Wadi Wasimi shows that two of the assumptions are incorrect in that the aquifer is not well connected to the sea because of confinement by very low hydraulic conductivity terrigenous and marine muds and the aquifer contains hypersaline water as a result of a hydraulic connection to a coastal sabkha. A supplemental study shows that the aquifer system contains a diverse microbial community composed of predominantly of Proteobacteria with accompanying high percentages of Gammaproteobacteria, Alphaproteobacteria and Deltaproteobacteria.

  12. Opportunistic pathogens and elements of the resistome that are common in bottled mineral water support the need for continuous surveillance.

    Directory of Open Access Journals (Sweden)

    Maria Fernanda Falcone-Dias

    Full Text Available Several differences concerning bacterial species, opportunistic pathogens, elements of the resistome as well as variations concerning the CFU/mL counts were identified in some of the five most marketed bottled mineral water from Araraquara city, São Paulo, Brazil. Two out of five brands tested were confirmed as potential source of opportunistic pathogens, including Mycobacterium gordonae, Ralstonia picketti and Burkholderia cepacia complex (Bcc. A total of one hundred and six isolates were recovered from four of these bottled mineral water brands. Betaproteobacteria was predominant followed by Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Ninety percent of the bacteria isolated demonstrated resistance to seventeen of the nineteen antimicrobials tested. These antimicrobials included eight different classes, including 3rd and 4th generation cephalosporins, carbapenems and fluoroquinolones. Multidrug resistant bacteria were detected for fifty-nine percent of isolates in three water brands at counts up to 103 CFU/ml. Of major concern, the two bottled mineral water harboring opportunistic pathogens were also source of elements of the resistome that could be directly transferred to humans. All these differences found among brands highlight the need for continuous bacteriological surveillance of bottled mineral water.

  13. XoxF encoding an alternative methanol dehydrogenase is widespread in coastal marine environments.

    Science.gov (United States)

    Taubert, Martin; Grob, Carolina; Howat, Alexandra M; Burns, Oliver J; Dixon, Joanna L; Chen, Yin; Murrell, J Colin

    2015-10-01

    The xoxF gene, encoding a pyrroloquinoline quinone-dependent methanol dehydrogenase, is found in all known proteobacterial methylotrophs. In several newly discovered methylotrophs, XoxF is the active methanol dehydrogenase, catalysing the oxidation of methanol to formaldehyde. Apart from that, its potential role in methylotrophy and carbon cycling is unknown. So far, the diversity of xoxF in the environment has received little attention. We designed PCR primer sets targeting clades of the xoxF gene, and used 454 pyrosequencing of PCR amplicons obtained from the DNA of four coastal marine environments for a unique assessment of the diversity of xoxF in these habitats. Phylogenetic analysis of the data obtained revealed a high diversity of xoxF genes from two of the investigated clades, and substantial differences in sequence composition between environments. Sequences were classified as being related to a wide range of both methylotrophs and non-methylotrophs from Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. The most prominent sequences detected were related to the family Rhodobacteraceae, the genus Methylotenera and the OM43 clade of Methylophilales, and are thus related to organisms that employ XoxF for methanol oxidation. Furthermore, our analyses revealed a high degree of so far undescribed sequences, suggesting a high number of unknown bacterial species in these habitats.

  14. Reproducing stone monument photosynthetic-based colonization under laboratory conditions.

    Science.gov (United States)

    Miller, Ana Zélia; Laiz, Leonila; Gonzalez, Juan Miguel; Dionísio, Amélia; Macedo, Maria Filomena; Saiz-Jimenez, Cesareo

    2008-11-01

    In order to understand the biodeterioration process occurring on stone monuments, we analyzed the microbial communities involved in these processes and studied their ability to colonize stones under controlled laboratory experiments. In this study, a natural green biofilm from a limestone monument was cultivated, inoculated on stone probes of the same lithotype and incubated in a laboratory chamber. This incubation system, which exposes stone samples to intermittently sprinkling water, allowed the development of photosynthetic biofilms similar to those occurring on stone monuments. Denaturing gradient gel electrophoresis (DGGE) analysis was used to evaluate the major microbial components of the laboratory biofilms. Cyanobacteria, green microalgae, bacteria and fungi were identified by DNA-based molecular analysis targeting the 16S and 18S ribosomal RNA genes. The natural green biofilm was mainly composed by the Chlorophyta Chlorella, Stichococcus, and Trebouxia, and by Cyanobacteria belonging to the genera Leptolyngbya and Pleurocapsa. A number of bacteria belonging to Alphaproteobacteria, Bacteroidetes and Verrucomicrobia were identified, as well as fungi from the Ascomycota. The laboratory colonization experiment on stone probes showed a colonization pattern similar to that occurring on stone monuments. The methodology described in this paper allowed to reproduce a colonization equivalent to the natural biodeteriorating process.

  15. Major similarities in the bacterial communities associated with lesioned and healthy Fungiidae corals

    KAUST Repository

    Apprill, Amy

    2013-03-21

    Cultivation-based studies have demonstrated that yellow-band disease (YBD), a lesion-producing ailment affecting diverse species of coral, is caused by a consortium of Vibrio spp. This study takes the first cultivation-independent approach to examine the whole bacterial community associated with YBD-like lesioned corals. Two species of Fungiidae corals, Ctenactis crassa and Herpolitha limax, displaying YBD-like lesions were examined across diverse reefs throughout the Red Sea. Using a pyrosequencing approach targeting the V1-V3 regions of the SSU rRNA gene, no major differences in bacterial community composition or diversity were identified between healthy and lesioned corals of either species. Indicator species analysis did not find Vibrio significantly associated with the lesioned corals. However, operational taxonomic units belonging to the Ruegeria genus of Alphaproteobacteria and NS9 marine group of Flavobacteria were significantly associated with the lesioned corals. The most striking trend of this dataset was that reef location was found to be the most significant influence on the coral-bacterial community. It is possible that more pronounced lesion-specific bacterial signatures might have been concealed by the strong influence of environmental conditions on coral-bacteria. Overall, this study demonstrates inconsistencies between cultivation-independent and cultivation-based studies regarding the role of specific bacteria in coral diseases. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

  16. Design and application of oligonucleotide probes for fluorescent in situ identification of the filamentous bacterial morphotype Nostocoida limicola in activated sludge.

    Science.gov (United States)

    Liu, J R; Seviour, R J

    2001-09-01

    16S rRNA targeted probes, designed using sequence data from pure cultures of the three morphotypes of the filamentous bulking bacteria Nostocoida limicola I, II and III and their successful application to the in situ identification of these bacteria in activated sludge biomass samples are described here. Two probes were required to detect all the sequenced N. limicola II isolates. Results from fluorescent in situ hybridization suggest that the morphotypes N. limicola I and II contain at least two phylogenetically unrelated bacteria. The N. limicola II filaments that did not respond to the probes designed in this study fluoresced instead with the probes previously designed for the alpha-Proteobacteria. The data also suggest that both N. limicola I and III can exist in activated sludge as single, paired or clumped cells and thus in a form not recognizable microscopically as this morphotype. Some N. limicola II filaments which responded to the probes designed here were much thinner than the filaments conventionally 'identified' as this morphotype and better fitted the descriptions often used in the literature for N. limicola I.

  17. Molecular analyses of the diversity in marine bacterioplankton assemblages along the coastline of the northeastern Gulf of Mexico.

    Science.gov (United States)

    Olapade, Ola A

    2010-10-01

    Bacterial community diversity in marine bacterioplankton assemblages were examined in 3 coastal locations along the northeastern Gulf of Mexico (GOM) using 16S rRNA gene libraries and fluorescence in situ hybridization approaches. The majority of the sequences (30%-60%) were similar to the 16S rRNA gene sequences of unknown bacteria; however, the operational taxonomic units from members of the Cyanobacteria, Proteobacteria, and Bacteroidetes were also present at the 3 GOM sites. Overall, sequence diversity was more similar between the Gulf sites of Carrabelle and Ochlockonee than between either of the Gulf sites and Apalachicola Bay. Fluorescence in situ hybridization analyses revealed the quantitative predominance of members of the Alphaproteobacteria subclass and the Cytophaga-Flavobacterium cluster within the bacterioplankton assemblages. In general, the study further reveals the presence of many bacterial taxa that have been previously found to be dominant in coastal marine environments. Differences observed in the representation of the various bacterial phylogenetic groups among the GOM coastal sites could be partly attributed to dynamic variations in several site-specific conditions, including intermittent tidal events, nutrient availability, and anthropogenic influences.

  18. New biosynthetic pathway for pink pigments from uncultured oceanic viruses.

    Science.gov (United States)

    Ledermann, Benjamin; Béjà, Oded; Frankenberg-Dinkel, Nicole

    2016-12-01

    The pink open-chain tetrapyrrole pigment phycoerythrobilin (PEB) is employed by marine cyanobacteria, red algae and cryptophytes as a light-harvesting chromophore in phycobiliproteins. Genes encoding biosynthesis proteins for PEB have also been discovered in cyanophages, viruses that infect cyanobacteria, and mimic host pigment biosynthesis with the exception of PebS which combines the enzymatic activities of two host enzymes. In this study, we have identified novel members of the PEB biosynthetic enzyme families, heme oxygenases and ferredoxin-dependent bilin reductases. Encoding genes were found in metagenomic datasets and could be traced back to bacteriophage but not cyanophage origin. While the heme oxygenase exhibited standard activity, a new bilin reductase with highest homology to the teal pigment producing enzyme PcyA revealed PEB biosynthetic activity. Although PcyX possesses PebS-like activity both enzymes share only 9% sequence identity and likely catalyze the reaction via two independent mechanisms. Our data point towards the presence of phycobilin biosynthetic genes in phages that probably infect alphaproteobacteria and, therefore, further support a role of phycobilins outside oxygenic phototrophs.

  19. GES-5 among the β-lactamases detected in ubiquitous bacteria isolated from aquatic environment samples.

    Science.gov (United States)

    Manageiro, Vera; Ferreira, Eugénia; Caniça, Manuela; Manaia, Célia M

    2014-02-01

    In this study, we investigated the β-lactamase-encoding genes responsible for β-lactam resistance phenotypes detected among 56 Gram-negative isolates (Gamma- and Alpha-proteobacteria) recovered from wastewater, urban streams, and drinking water. The β-lactam resistance mechanisms detected in 36 isolates comprised the presence of class A (blaTEM-1 , blaSHV-1 , blaSHV-11 , blaGES-5 ), class B (ImiS, L1), class C (blaCMY-2 , blaCMY-34 , blaCMY-65 , blaCMY-89 , blaCMY-90 , blaACC-5 , blaACT-13 ), and class D (blaOXA-309)β-lactamase-encoding genes, some variants described for the first time here. Notably, the results showed antimicrobial resistance genes related not only to commonly used antibiotics, but also to carbapenems, providing the first description of a GES-5-producing Enterobacteriaceae. The importance of ubiquitous bacteria thriving in aquatic environments as reservoirs or carriers of clinically relevant resistance determinants was confirmed, and the need to monitor water habitats as potential sources for the emergence and/or spread of antibiotic resistance in the environment was highlighted.

  20. Quorum Sensing in Some Representative Species of Halomonadaceae

    Directory of Open Access Journals (Sweden)

    Inmaculada Llamas

    2013-03-01

    Full Text Available Cell-to-cell communication, or quorum-sensing (QS, systems are employed by bacteria for promoting collective behaviour within a population. An analysis to detect QS signal molecules in 43 species of the Halomonadaceae family revealed that they produced N-acyl homoserine lactones (AHLs, which suggests that the QS system is widespread throughout this group of bacteria. Thin-layer chromatography (TLC analysis of crude AHL extracts, using Agrobacterium tumefaciens NTL4 (pZLR4 as biosensor strain, resulted in different profiles, which were not related to the various habitats of the species in question. To confirm AHL production in the Halomonadaceae species, PCR and DNA sequencing approaches were used to study the distribution of the luxI-type synthase gene. Phylogenetic analysis using sequence data revealed that 29 of the species studied contained a LuxI homolog. Phylogenetic analysis showed that sequences from Halomonadaceae species grouped together and were distinct from other members of the Gammaproteobacteria and also from species belonging to the Alphaproteobacteria and Betaproteobacteria.

  1. Spatial Distribution of Bacterial Communities Driven by Multiple Environmental Factors in a Beach Wetland of the Largest Freshwater Lake in China

    Directory of Open Access Journals (Sweden)

    Xia eDing

    2015-02-01

    Full Text Available The spatial distributions of bacterial communities may be driven by multiple environmental factors. Thus, understanding the relationships between bacterial distribution and environmental factors is critical for understanding wetland stability and the functioning of freshwater lakes. However, little research on the bacterial communities in deep sediment layers exists. In this study, thirty clone libraries of 16S rRNA were constructed from a beach wetland of the Poyang Lake along both horizontal (distance to the water-land junction and vertical (sediment depth gradients to assess the effects of sediment properties on bacterial community structure and diversity. Our results showed that bacterial diversity increased along the horizontal gradient and decreased along the vertical gradient. The heterogeneous sediment properties along gradients substantially affected the dominant bacterial groups at the phylum and species levels. For example, the NH4+ concentration decreased with increasing depth, which was positively correlated with the relative abundance of Alphaproteobacteria. The changes in bacterial diversity and dominant bacterial groups showed that the top layer had a different bacterial community structure than the deeper layers. Principal component analysis revealed that both gradients, not each gradient independently, contributed to the shift in the bacterial community structure. A multiple linear regression model explained the changes in bacterial diversity and richness along the depth and distance gradients. Overall, our results suggest that spatial gradients associated with sediment properties shaped the bacterial communities in the Poyang Lake beach wetland.

  2. Endo-and exoglucanase activities in bacteria from mangrove sediment

    Directory of Open Access Journals (Sweden)

    Fábio Lino Soares Júnior

    2013-09-01

    Full Text Available The mangrove ecosystem is an unexplored source for biotechnological applications. In this unique environment, endemic bacteria have the ability to thrive in the harsh environmental conditions (salinity and anaerobiosis, and act in the degradation of organic matter, promoting nutrient cycles. Thus, this study aimed to assess the cellulolytic activities of bacterial groups present in the sediment from a mangrove located in Ilha do Cardoso (SP, Brazil. To optimize the isolation of cellulolytic bacteria, enrichments in two types of culture media (tryptone broth and minimum salt medium, both supplemented with 5% NaCl and 1% of cellulose, were performed. Tests conducted with the obtained colonies showed a higher occurrence of endoglycolytic activity (33 isolates than exoglycolytic (19 isolates, and the degradation activity was shown to be modulated by the presence of NaCl. The isolated bacteria were clustered by BOX-PCR and further classified on the basis of partial 16S rRNA sequences as Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes or Bacteroidetes. Therefore, this study highlights the importance of studies focusing on the endemic species found in mangroves to exploit them as novel biotechnological tools for the degradation of cellulose.

  3. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

    Science.gov (United States)

    Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

  4. A pyrosequencing insight into sprawling bacterial diversity and community dynamics in decaying deadwood logs of Fagus sylvatica and Picea abies.

    Science.gov (United States)

    Hoppe, Björn; Krger, Krüger; Kahl, Tiemo; Arnstadt, Tobias; Buscot, François; Bauhus, Jürgen; Wubet, Tesfaye

    2015-04-08

    Deadwood is an important biodiversity hotspot in forest ecosystems. While saproxylic insects and wood-inhabiting fungi have been studied extensively, little is known about deadwood-inhabiting bacteria. The study we present is among the first to compare bacterial diversity and community structure of deadwood under field conditions. We therefore compared deadwood logs of two temperate forest tree species Fagus sylvatica and Picea abies using 16S rDNA pyrosequencing to identify changes in bacterial diversity and community structure at different stages of decay in forest plots under different management regimes. Alphaproteobacteria, Acidobacteria and Actinobacteria were the dominant taxonomic groups in both tree species. There were no differences in bacterial OTU richness between deadwood of Fagus sylvatica and Picea abies. Bacteria from the order Rhizobiales became more abundant during the intermediate and advanced stages of decay, accounting for up to 25% of the entire bacterial community in such logs. The most dominant OTU was taxonomically assigned to the genus Methylovirgula, which was recently described in a woodblock experiment of Fagus sylvatica. Besides tree species we were able to demonstrate that deadwood physico-chemical properties, in particular remaining mass, relative wood moisture, pH, and C/N ratio serve as drivers of community composition of deadwood-inhabiting bacteria.

  5. Phylogenetic diversity and specificity of bacteria associated with Microcystis aeruginosa and other cyanobacteria

    Institute of Scientific and Technical Information of China (English)

    SHI Limei; CAI Yuanfeng; YANG Hualin; XING Peng; LI Pengfu; KONG Lingdong; KONG Fanxiang

    2009-01-01

    Interactions between bacteria and cyanobacteria have been suggested to have a potential to influence harmful algal bloom dynamics,however,little information on these interactions is reported.In this study,the bacterial communities associated with five strains of Microcystis aeruginosa,three species of other Microcystis spp.,and four representative species of non-Microcystis cyanobacteria were compared.Bacterial 16S rDNA fragments were amplified and separated by denaturing gradient gel electrophoresis (DGGE) followed DNA sequence analysis.The similarities among bacterial communities associated with these cyanobacteria were compared to the digitized DGGE profiles using the cluster analyses technique.The bacterial community structure of all cyanobacterial cultures differed.Cluster analysis showed that the similarity values among M.aeruginosa cultures were higher than those of other cyanobacterial cultures.Sequence analysis of DGGE fragments indicated the presence of bacteria including Alphaproteobacteria,Betaproteobacteria,Gammaproteobacteria,Bacteroidetes and Actinobacteria in the cyanobacterial cultures.Members of the Sphingobacteriales were the prevalent group among the Microcystis-associated bacteria.The results provided further evidence for species-specific associations between cyanoabcteria and heterotrophic bacteria,which are useful for understanding interactions between Microcystis and their associated bacteria.

  6. Evaluating bacterial community structures in oil collected from the sea surface and sediment in the northern Gulf of Mexico after the Deepwater Horizon oil spill.

    Science.gov (United States)

    Liu, Zhanfei; Liu, Jiqing

    2013-06-01

    Bacterial community structures were evaluated in oil samples using culture-independent pyrosequencing, including oil mousses collected on sea surface and salt marshes during the Deepwater Horizon oil spill, and oil deposited in sediments adjacent to the wellhead 1 year after the spill. Phylogenetic analysis suggested that Erythrobacter, Rhodovulum, Stappia, and Thalassospira of Alphaproteobacteria were the prevailing groups in the oil mousses, which may relate to high temperatures and strong irradiance in surface Gulf waters. In the mousse collected from the leaves of Spartina alterniflora, Vibrio of Gammaproteobacteria represented 57% of the total operational taxonomic units, suggesting that this indigenous genus is particularly responsive to the oil contamination in salt marshes. The bacterial communities in oil-contaminated sediments were highly diversified. The relatively high abundance of the Methylococcus, Methylobacter, Actinobacteria, Firmicutes, and Chlorofexi bacteria resembles those found in certain cold-seep sediments with gas hydrates. Bacterial communities in the overlying water of the oil-contaminated sediment were dominated by Ralstonia of Betaproteobacteria, which can degrade small aromatics, and Saccharophagus degradans of Gammaproteobacteria, a cellulose degrader, suggesting that overlying water was affected by the oil-contaminated sediments, possibly due to the dissolution of small aromatics and biosurfactants produced during biodegradation. Overall, these results provided key information needed to evaluate oil degradation in the region and develop future bioremediation strategies.

  7. Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland.

    Science.gov (United States)

    Eldridge, David J; Woodhouse, Jason N; Curlevski, Nathalie J A; Hayward, Matthew; Brown, Mark V; Neilan, Brett A

    2015-12-01

    Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance.

  8. The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jing; Todd, Jonathan D.; Thrash, J. Cameron; Qian, Yanping; Qian, Michael C.; Temperton, Ben; Guo, Jiazhen; Fowler, Emily K.; Aldrich, Joshua T.; Nicora, Carrie D.; Lipton, Mary S.; Smith, Richard D.; De Leenheer, Patrick; Payne, Samuel H.; Johnston, Andrew W. B.; Davie-Martin, Cleo L.; Halsey, Kimberly H.; Giovannoni, Stephen J.

    2016-05-16

    Marine phytoplankton produce ~109 tons of dimethylsulfoniopropionate (DMSP) per year1,2, an estimated 10% of which is catabolized by bacteria through the DMSP cleavage pathway to the climatically active gas dimethyl sulfide (DMS)3,4. SAR11 Alphaproteobacteria (order Pelagibacterales), the most abundant chemoorganotrophic bacteria in the oceans, have been shown to assimilate DMSP into biomass, thereby supplying this cell’s unusual requirement for reduced sulfur5,6. Here we report that Pelagibacter HTCC1062 produces the gas methanethiol (MeSH) and that simultaneously a second DMSP catabolic pathway, mediated by a DMSP lyase, shunts as much as 59% of DMSP uptake to DMS production. We propose a model in which the allocation of DMSP between these pathways is kinetically controlled to release increasing amounts of DMS as the supply of DMSP exceeds cellular sulfur demands for biosynthesis. These findings suggest that DMSP supply and demand relationships in Pelagibacter metabolism are important to determining rates of oceanic DMS production.

  9. Characterization of Bacterial Community Structure and Diversity in Rhizosphere Soils of Three Plants in Rapidly Changing Salt Marshes Using 16S rDNA

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The structure and diversity of the bacterial communities in rhizosphere soils of native Phragmites australis and Scirpus mariqueter and alien Spartina alterniflora in the Yangtze River Estuary were investigated by constructing 16S ribosomal DNA (rDNA) clone libraries. The bacterial diversity was quantified by placing the clones into operational taxonomic unit (OTU) groups at the level of sequence similarity of > 97%. Phylogenetic analysis of the resulting 398 clone sequences indicated a high diversity of bacteria in the rhizosphere soils of these plants. The members of Alphaproteobacteria,Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria of the phylum Proteobacteria were the most abundant in rhizobacteria. Chao 1 nonparametric diversity estimator coupled with the reciprocal of Simpson's index (1/D) was applied to sequence data obtained from each library to evaluate total sequence diversity and quantitatively compare the level of dominance. The results showed that Phragmites, Scirpus, and Spartina rhizosphere soils contained 200, 668, and 382 OTUs, respectively. The bacterial communities in the Spartina and Phragmites rhizosphere soils displayed species dominance revealed by 1/D, whereas the bacterial community in Scirpus rhizosphere soil had uniform distributions of species abundance. Overall, analysis of 16S rDNA clone libraries from the rhizosphere soils indicates that the changes in bacterial composition may occur concomitantly with the shift of species composition in plant communities.

  10. PHA production by mixed cultures: a way to valorize wastes from pulp industry.

    Science.gov (United States)

    Queirós, Diogo; Rossetti, Simona; Serafim, Luísa S

    2014-04-01

    In this work, hardwood spent sulfite liquor (HSSL), a complex feedstock originating from the pulp industry, was tested for the first time as a substrate for polyhydroxyalkanoate (PHA) production by a mixed microbial culture (MMC) under aerobic dynamic feeding (ADF) conditions. A sequencing batch reactor (SBR) fed with HSSL was operated for 67days and the selected MMC reached a maximum PHA content of 67.6%. The MMC demonstrated a differential utilization of the carbon sources present in HSSL. Acetic acid was fully consumed, while xylose and lignosulphonates were partially consumed (30% and 14%, respectively). The selected culture was characterized by Fluorescence in Situ Hybridization (FISH). Bacteria belonging to the three main classes were identified: Alpha- (72.7±4.0%), Beta- (11.1±0.37%) and Gammaproteobacteria (10.3±0.3%). Within Alphaproteobacteria, a small amount of Paracoccus (4.2±0.51%) and Defluvicoccus related to Tetrad Forming Organisms (9.0±0.28%) were detected.

  11. Geobacter, Anaeromyxobacter and Anaerolineae populations are enriched on anodes of root exudate-driven microbial fuel cells in rice field soil.

    Science.gov (United States)

    Cabezas, Angela; Pommerenke, Bianca; Boon, Nico; Friedrich, Michael W

    2015-06-01

    Plant-based sediment microbial fuel cells (PMFCs) couple the oxidation of root exudates in living rice plants to current production. We analysed the composition of the microbial community on anodes from PMFC with natural rice field soil as substratum for rice by analysing 16S rRNA as an indicator of microbial activity and diversity. Terminal restriction fragment length polymorphism (TRFLP) analysis indicated that the active bacterial community on anodes from PMFCs differed strongly compared with controls. Moreover, clones related to Deltaproteobacteria and Chloroflexi were highly abundant (49% and 21%, respectively) on PMFCs anodes. Geobacter (19%), Anaeromyxobacter (15%) and Anaerolineae (17%) populations were predominant on anodes with natural rice field soil and differed strongly from those previously detected with potting soil. In open circuit (OC) control PMFCs, not allowing electron transfer, Deltaproteobacteria (33%), Betaproteobacteria (20%), Chloroflexi (12%), Alphaproteobacteria (10%) and Firmicutes (10%) were detected. The presence of an electron accepting anode also had a strong influence on methanogenic archaea. Hydrogenotrophic methanogens were more active on PMFC (21%) than on OC controls (10%), whereas acetoclastic Methanosaetaceae were more active on OC controls (31%) compared with PMFCs (9%). In conclusion, electron accepting anodes and rice root exudates selected for distinct potential anode-reducing microbial populations in rice soil inoculated PMFC.

  12. Comparison of two radio-frequency plasma sterilization processes using microspot evaluation of microbial inactivation.

    Science.gov (United States)

    Lassen, Klaus S; Johansen, Jens E; Grün, Reinar

    2006-07-01

    In this study, we evaluated gas plasma surface sterilization methods in a specific sterilizer. We have introduced a new monitoring method using 0.4 microm pore size membranes, which in this study gave the information corresponding to 3000 exposed biological indicators per treatment cycle. This enabled us to compare the fraction of inoculates that showed no growth after exposure for 30 different locations in the chamber, and hereby identify weak and strong spots in the chamber with regard to sporicidal effect. Membranes were also used to expose a broad spectrum of soil bacteria for plasma treatment at four different conditions. The organisms were identified using PCR and sequencing. The test showed that Bacillus stearothermophilus spores were inactivated at the slowest rate among the tested microorganisms. Further alpha-proteobacteria (Gram negative) seemed more sensitive than the rest of the tested organisms. The microspot evaluation approach has been a most useful tool in the assessment of sterilization performance in sterilizers that do not have clear measurable parameters related to the sterilization.

  13. Dynamic bacterial communities on reverse-osmosis membranes in a full-scale desalination plant.

    Science.gov (United States)

    Manes, C-L de O; West, N; Rapenne, S; Lebaron, P

    2011-01-01

    To better understand biofouling of seawater reverse osmosis (SWRO) membranes, bacterial diversity was characterized in the intake water, in subsequently pretreated water and on SWRO membranes from a full-scale desalination plant (FSDP) during a 9 month period. 16S rRNA gene fingerprinting and sequencing revealed that bacterial communities in the water samples and on the SWRO membranes were very different. For the different sampling dates, the bacterial diversity of the active and the total bacterial fractions of the water samples remained relatively stable over the sampling period whereas the bacterial community structure on the four SWRO membrane samples was significantly different. The richness and evenness of the SWRO membrane bacterial communities increased with usage time with an increase in the Shannon diversity index of 2.2 to 3.7. In the oldest SWRO membrane (330 days), no single operational taxonomic unit (OTU) dominated and the majority of the OTUs fell into the Alphaproteobacteria or the Planctomycetes. In striking contrast, a Betaproteobacteria OTU affiliated to the genus Ideonella was dominant and exclusively found in the membrane used for the shortest time (10 days). This suggests that bacteria belonging to this genus could be one of the primary colonizers of the SWRO membrane. Knowledge of the dominant bacterial species on SWRO membranes and their dynamics should help guide culture studies for physiological characterization of biofilm forming species.

  14. Composition and variability of biofouling organisms in seawater reverse osmosis desalination plants.

    Science.gov (United States)

    Zhang, Minglu; Jiang, Sunny; Tanuwidjaja, Dian; Voutchkov, Nikolay; Hoek, Eric M V; Cai, Baoli

    2011-07-01

    Seawater reverse osmosis (SWRO) membrane biofouling remains a common challenge in the desalination industry, but the marine bacterial community that causes membrane fouling is poorly understood. Microbial communities at different stages of treatment processes (intake, cartridge filtration, and SWRO) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. Bacterial isolates were identified to match the genera Shewanella, Alteromonas, Vibrio, and Cellulophaga based on 16S rRNA gene sequencing analysis. The 16S rRNA gene clone library of the SWRO membrane biofilm showed that a filamentous bacterium, Leucothrix mucor, which belongs to the gammaproteobacteria, accounted for nearly 30% of the clone library, while the rest of the microorganisms (61.2% of the total clones) were related to the alphaproteobacteria. 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that bacteria colonizing the SWRO membrane represented a subportion of microbes in the source seawater; however, they were quite different from those colonizing the cartridge filter. The examination of five SWRO membranes from desalination plants located in different parts of the world showed that although the bacterial communities from the membranes were not identical to each other, some dominant bacteria were commonly observed. In contrast, bacterial communities in source seawater were significantly different based on location and season. Microbial profiles from 14 cartridge filters collected from different plants also revealed spatial trends.

  15. Composition and Variability of Biofouling Organisms in Seawater Reverse Osmosis Desalination Plants ▿ †

    Science.gov (United States)

    Zhang, Minglu; Jiang, Sunny; Tanuwidjaja, Dian; Voutchkov, Nikolay; Hoek, Eric M. V.; Cai, Baoli

    2011-01-01

    Seawater reverse osmosis (SWRO) membrane biofouling remains a common challenge in the desalination industry, but the marine bacterial community that causes membrane fouling is poorly understood. Microbial communities at different stages of treatment processes (intake, cartridge filtration, and SWRO) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. Bacterial isolates were identified to match the genera Shewanella, Alteromonas, Vibrio, and Cellulophaga based on 16S rRNA gene sequencing analysis. The 16S rRNA gene clone library of the SWRO membrane biofilm showed that a filamentous bacterium, Leucothrix mucor, which belongs to the gammaproteobacteria, accounted for nearly 30% of the clone library, while the rest of the microorganisms (61.2% of the total clones) were related to the alphaproteobacteria. 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that bacteria colonizing the SWRO membrane represented a subportion of microbes in the source seawater; however, they were quite different from those colonizing the cartridge filter. The examination of five SWRO membranes from desalination plants located in different parts of the world showed that although the bacterial communities from the membranes were not identical to each other, some dominant bacteria were commonly observed. In contrast, bacterial communities in source seawater were significantly different based on location and season. Microbial profiles from 14 cartridge filters collected from different plants also revealed spatial trends. PMID:21551282

  16. Functional diversity and dynamics of bacterial communities in a membrane bioreactor for the treatment of metal-working fluid wastewater.

    Science.gov (United States)

    Grijalbo, Lucía; Garbisu, Carlos; Martín, Iker; Etxebarria, Javier; Gutierrez-Mañero, F Javier; Lucas Garcia, Jose Antonio

    2015-12-01

    An extensive microbiological study has been carried out in a membrane bioreactor fed with activated sludge and metal-working fluids. Functional diversity and dynamics of bacterial communities were studied with different approaches. Functional diversity of culturable bacterial communities was studied with different Biolog™ plates. Structure and dynamics of bacterial communities were studied in culturable and in non-culturable fractions using a 16S rRNA analysis. Among the culturable bacteria, Alphaproteobacteria and Gammaproteobacteria were the predominant classes. However, changes in microbial community structure were detected over time. Culture-independent analysis showed that Betaproteobacteria was the most frequently detected class in the membrane bioreactor (MBR) community with Zoogloea and Acidovorax as dominant genera. Also, among non-culturable bacteria, a process of succession was observed. Longitudinal structural shifts observed were more marked for non-culturable than for culturable bacteria, pointing towards an important role in the MBR performance. Microbial community metabolic abilities assessed with Biolog™ Gram negative, Gram positive and anaerobic plates also showed differences over time for Shannon's diversity index, kinetics of average well colour development, and the intensely used substrates by bacterial community in each plate.

  17. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers.

    Science.gov (United States)

    Heylen, Kim; Gevers, Dirk; Vanparys, Bram; Wittebolle, Lieven; Geets, Joke; Boon, Nico; De Vos, Paul

    2006-11-01

    Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.

  18. A prevalent alpha-proteobacterium Paracoccus sp. in a population of the Cayenne ticks (Amblyomma cajennense from Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    Erik Machado-Ferreira

    2012-01-01

    Full Text Available As Rocky Mountain Spotted Fever is the most common tick-borne disease in South America, the presence of Rickettsia sp. in Amblyomma ticks is a possible indication of its endemicity in certain geographic regions. In the present work, bacterial DNA sequences related to Rickettsia amblyommii genes in A. dubitatum ticks, collected in the Brazilian state of Mato Grosso, were discovered. Simultaneously, Paracoccus sp. was detected in aproximately 77% of A. cajennense specimens collected in Rio de Janeiro, Brazil. This is the first report of Paracoccus sp. infection in a specific tick population, and raises the possibility of these bacteria being maintained and/or transmitted by ticks. Whether Paracoccus sp. represents another group of pathogenic Rhodobacteraceae or simply plays a role in A. cajennense physiology, is unknown. The data also demonstrate that the rickettsial 16S rRNA specific primers used forRickettsia spp. screening can also detect Paracoccus alpha-proteobacteria infection in biological samples. Hence, a PCRRFLP strategy is presented to distinguish between these two groups of bacteria.

  19. A prevalent alpha-proteobacterium Paracoccus sp. in a population of the Cayenne ticks (Amblyomma cajennense) from Rio de Janeiro, Brazil.

    Science.gov (United States)

    Machado-Ferreira, Erik; Piesman, Joseph; Zeidner, Nordin S; Soares, Carlos A G

    2012-12-01

    As Rocky Mountain Spotted Fever is the most common tick-borne disease in South America, the presence of Rickettsia sp. in Amblyomma ticks is a possible indication of its endemicity in certain geographic regions. In the present work, bacterial DNA sequences related to Rickettsia amblyommii genes in A. dubitatum ticks, collected in the Brazilian state of Mato Grosso, were discovered. Simultaneously, Paracoccus sp. was detected in aproximately 77% of A. cajennense specimens collected in Rio de Janeiro, Brazil. This is the first report of Paracoccus sp. infection in a specific tick population, and raises the possibility of these bacteria being maintained and/or transmitted by ticks. Whether Paracoccus sp. represents another group of pathogenic Rhodobacteraceae or simply plays a role in A. cajennense physiology, is unknown. The data also demonstrate that the rickettsial 16S rRNA specific primers used forRickettsia spp. screening can also detect Paracoccus alpha-proteobacteria infection in biological samples. Hence, a PCR-RFLP strategy is presented to distinguish between these two groups of bacteria.

  20. "Candidatus Mesochlamydia elodeae" (Chlamydiae: Parachlamydiaceae), a novel chlamydia parasite of free-living amoebae.

    Science.gov (United States)

    Corsaro, Daniele; Müller, Karl-Dieter; Wingender, Jost; Michel, Rolf

    2013-02-01

    Vannella sp. isolated from waterweed Elodea sp. was found infected by a chlamydia-like organism. This organism behaves like a parasite, causing the death through burst of its host. Once the vannellae degenerated, the parasite was successfully kept in laboratory within a Saccamoeba sp. isolated from the same waterweed sample, which revealed in fine through electron microscopy to harbor two bacterial endosymbionts: the chlamydial parasite we introduce and another endosymbiont initially and naturally present in the host. Herein, we provide molecular-based identification of both the amoeba host and its two endosymbionts, with special focus on the chlamydia parasite. High sequence similarity values of the 18S rDNA permitted to assign the amoeba to the species Saccamoeba lacustris (Amoebozoa, Tubulinea). The bacterial endosymbiont naturally harbored by the host belonged to Sphingomonas koreensis (Alpha-Proteobacteria). The chlamydial parasite showed a strict specificity for Saccamoeba spp., being unable to infect a variety of other amoebae, including Acanthamoeba, and it was itself infected by a bacteriophage. Sequence similarity values of the 16S rDNA and phylogenetic analysis indicated that this strain is a new member of the family Parachlamydiaceae, for which we propose the name "Candidatus Mesochlamydia elodeae."

  1. The shifts of diazotrophic communities in spring and summer associated with coral Galaxea astreata, Pavona decussata and Porites lutea

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    Yanying Zhang

    2016-11-01

    Full Text Available The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata and Porites lutea, were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata, both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11% to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were species-specific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris- and Gluconacetobacter diazotrophicus-affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea. The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont.

  2. A multicopper oxidase is essential for manganese oxidation and laccase-like activity in Pedomicrobium sp. ACM 3067.

    Science.gov (United States)

    Ridge, Justin P; Lin, Marianne; Larsen, Eloise I; Fegan, Mark; McEwan, Alastair G; Sly, Lindsay I

    2007-04-01

    Pedomicrobium sp. ACM 3067 is a budding-hyphal bacterium belonging to the alpha-Proteobacteria which is able to oxidize soluble Mn2+ to insoluble manganese oxide. A cosmid, from a whole-genome library, containing the putative genes responsible for manganese oxidation was identified and a primer-walking approach yielded 4350 bp of novel sequence. Analysis of this sequence showed the presence of a predicted three-gene operon, moxCBA. The moxA gene product showed homology to multicopper oxidases (MCOs) and contained the characteristic four copper-binding motifs (A, B, C and D) common to MCOs. An insertion mutation of moxA showed that this gene was essential for both manganese oxidation and laccase-like activity. The moxB gene product showed homology to a family of outer membrane proteins which are essential for Type I secretion in Gram-negative bacteria. moxBA has not been observed in other manganese-oxidizing bacteria but homologues were identified in the genomes of several bacteria including Sinorhizobium meliloti 1021 and Agrobacterium tumefaciens C58. These results suggest that moxBA and its homologues constitute a family of genes encoding an MCO and a predicted component of the Type I secretion system.

  3. Unexpected Diversity of Magnetococci in Intertidal Sediments of Xiaoshi Island in the North Yellow Sea

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    Haitao Chen

    2015-01-01

    Full Text Available Magnetotactic bacteria (MTB are a group of prokaryotes that, despite their high morphological, phylogenetic, and ecological diversity, share a common capability of forming intracellular nanocrystals of magnetite (Fe3O4 or greigite (Fe3S4, called magnetosomes, and swimming along geomagnetic field lines in a process called magnetotaxis. In this study, we investigated the MTB diversity within the intertidal sediments near Xiaoshi Island (Weihai in the North Yellow Sea using a combination of molecular ecology techniques and transmission electron microscopy (TEM. The combination of restriction fragment length polymorphism (RFLP analysis and 16S rRNA gene sequencing revealed seven new MTB genera affiliated with the Alphaproteobacteria class. Fluorescence in situ hybridization (FISH analyses suggested that one magnetotactic coccus (designated as WHI-2 is the dominant species. TEM observations and energy dispersive X-ray analyses revealed that MTB cells mainly form magnetite magnetosomes that are organized into two chains of magnetosomes composed of e-prismatic magnetite crystals. This finding suggests the adaptation of a magnetotactic bacterial population to the marine tide. This is the first report of magnetotactic bacteria near Xiaoshi Island, which should be useful for studies of biogeochemical cycling and the geohistory of this area.

  4. Growth of Dunaliella tertiolecta and associated bacteria in photobioreactors.

    Science.gov (United States)

    Lakaniemi, Aino-Maija; Intihar, Veera M; Tuovinen, Olli H; Puhakka, Jaakko A

    2012-09-01

    The aim of this study was to test three flat-plate photobioreactor configurations for cultivation of marine green alga Dunaliella tertiolecta under non-axenic growth conditions and to characterize and quantify the associated bacteria. The photobioreactor cultivations were conducted using tap water-based media. Static mixers intended to enhance mixing and light utilization did not generally increase algal growth at the low light intensities used. The maximum biomass concentration (measured as volatile suspended solids) and maximum specific growth rate achieved in the flat plate with no mixer were 2.9 g l⁻¹ and 1.3 day⁻¹, respectively. Based on quantitative polymerase chain reaction, bacterial growth followed the growth of D. tertiolecta. Based on 16S rDNA amplification and denaturing gradient gel electrophoresis profiling, heterotrophic bacteria in the D. tertiolecta cultures mainly originated from the non-axenic algal inocula, and tap water heterotrophs were not enriched in high chloride media (3 % salinity). Bacterial communities were relatively stable and reproducible in all flat-plate cultivations and were dominated by Gammaproteobacteria, Flavobacteria, and Alphaproteobacteria.

  5. Growth of Chlorella vulgaris and associated bacteria in photobioreactors.

    Science.gov (United States)

    Lakaniemi, Aino-Maija; Intihar, Veera M; Tuovinen, Olli H; Puhakka, Jaakko A

    2012-01-01

    The aim of this study was to test three flat plate photobioreactor configurations for growth of Chlorella vulgaris under non-axenic conditions and to characterize and quantify associated bacterial communities. The photobioreactor cultivations were conducted using tap water-based media to introduce background bacterial population. Growth of algae was monitored over time with three independent methods. Additionally, the quantity and quality of eukaryotes and bacteria were analysed using culture-independent molecular tools based on denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative polymerase chain reaction (QPCR). Static mixers used in the flat plate photobioreactors did not generally enhance the growth at the low light intensities used. The maximum biomass concentration and maximum specific growth rate were 1.0 g l(-1) and 2.0 day(-1) respectively. Bacterial growth as determined by QPCR was associated with the growth of C. vulgaris. Based on PCR-DGGE, bacteria in the cultures mainly originated from the tap water. Bacterial community profiles were diverse but reproducible in all flat plate cultures. Most prominent bacteria in the C. vulgaris cultures belonged to the class Alphaproteobacteria and especially to the genus Sphingomonas. Analysis of the diversity of non-photosynthetic microorganisms in algal mass cultures can provide useful information on the public health aspects and unravel community interactions.

  6. Resilience of SAR11 bacteria to rapid acidification in the high-latitude open ocean.

    Science.gov (United States)

    Hartmann, Manuela; Hill, Polly G; Tynan, Eithne; Achterberg, Eric P; Leakey, Raymond J G; Zubkov, Mikhail V

    2016-02-01

    Ubiquitous SAR11 Alphaproteobacteria numerically dominate marine planktonic communities. Because they are excruciatingly difficult to cultivate, there is comparatively little known about their physiology and metabolic responses to long- and short-term environmental changes. As surface oceans take up anthropogenic, atmospheric CO2, the consequential process of ocean acidification could affect the global biogeochemical significance of SAR11. Shipping accidents or inadvertent release of chemicals from industrial plants can have strong short-term local effects on oceanic SAR11. This study investigated the effect of 2.5-fold acidification of seawater on the metabolism of SAR11 and other heterotrophic bacterioplankton along a natural temperature gradient crossing the North Atlantic Ocean, Norwegian and Greenland Seas. Uptake rates of the amino acid leucine by SAR11 cells as well as other bacterioplankton remained similar to controls despite an instant ∼50% increase in leucine bioavailability upon acidification. This high physiological resilience to acidification even without acclimation, suggests that open ocean dominant bacterioplankton are able to cope even with sudden and therefore more likely with long-term acidification effects.

  7. Leisingera sp. JC1, a Bacterial Isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios.

    Science.gov (United States)

    Gromek, Samantha M; Suria, Andrea M; Fullmer, Matthew S; Garcia, Jillian L; Gogarten, Johann Peter; Nyholm, Spencer V; Balunas, Marcy J

    2016-01-01

    Female members of many cephalopod species house a bacterial consortium in the accessory nidamental gland (ANG), part of the reproductive system. These bacteria are deposited into eggs that are then laid in the environment where they must develop unprotected from predation, pathogens, and fouling. In this study, we characterized the genome and secondary metabolite production of Leisingera sp. JC1, a member of the roseobacter clade (Rhodobacteraceae) of Alphaproteobacteria isolated from the jelly coat of eggs from the Hawaiian bobtail squid, Euprymna scolopes. Whole genome sequencing and MLSA analysis revealed that Leisingera sp. JC1 falls within a group of roseobacters associated with squid ANGs. Genome and biochemical analyses revealed the potential for and production of a number of secondary metabolites, including siderophores and acyl-homoserine lactones involved with quorum sensing. The complete biosynthetic gene cluster for the pigment indigoidine was detected in the genome and mass spectrometry confirmed the production of this compound. Furthermore, we investigated the production of indigoidine under co-culture conditions with Vibrio fischeri, the light organ symbiont of E. scolopes, and with other vibrios. Finally, both Leisingera sp. JC1 and secondary metabolite extracts of this strain had differential antimicrobial activity against a number of marine vibrios, suggesting that Leisingera sp. JC1 may play a role in host defense against other marine bacteria either in the eggs and/or ANG. These data also suggest that indigoidine may be partially, but not wholly, responsible for the antimicrobial activity of this squid-associated bacterium.

  8. A comparative genomics approach to the evolution of eukaryotes and their mitochondria.

    Science.gov (United States)

    Lang, B F; Seif, E; Gray, M W; O'Kelly, C J; Burger, G

    1999-01-01

    The Organelle Genome Megasequencing Program (OGMP) investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. Some of the most interesting protists include the jakobid flagellates Reclinomonas americana, Malawimonas jakobiformis, and Jakoba libera, which share ultrastructural similarities with amitochondriate retortamonads, and harbor mitochondrial genes not seen before in mtDNAs of other organisms. In R. americana and J. libera, gene clusters are found that resemble, to an unprecedented degree, the contiguous ribosomal protein operons str, S10, spc, and alpha of eubacteria. In addition, their mtDNAs code for an RNase P RNA that displays all the elements of a bacterial minimum consensus structure. This structure has been instrumental in detecting the rnpB gene in additional protists. Gene repertoire and gene order comparisons as well as multiple-gene phylogenies support the view of a single endosymbiotic origin of mitochondria, whose closest extant relatives are Rickettsia-type alpha-Proteobacteria.

  9. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA

    Science.gov (United States)

    Stanish, Lee F.; Hull, Natalie M.; Robertson, Charles E.; Harris, J. Kirk; Stevens, Mark J.; Spear, John R.; Pace, Norman R.

    2016-01-01

    The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources. PMID:27362708

  10. [Analysis on Diversity of Denitrifying Microorganisms in Sequential Batch Bioreactor Landfill].

    Science.gov (United States)

    Li, Wei-Hua; Sun, Ying-Jie; Liu, Zi-Liang; Ma, Qiang; Yang, Qiang

    2016-01-15

    A denitrification functional microorganism gene clone library (amoA, nosZ) and the PCR-RFLP technology was constructed to investigate the microbial diversity of denitrifying microorganisms in the late period of stabilization of sequential batch bioreactor landfill. The results indicated that: the bacterial diversity of ammonia oxidizing bacteria in the aged refuse reactor was very high, and most of them were unknown groups, also, all bacteria were unculturable or had not been isolated. The phylogenetic analysis suggested that the dominant ammonia oxidizing bacteria were presumably Nitrosomonas of 6-Proteobacteria. The diversity of denitrifying bacteria in fresh refuse reactor was abundant, which mainly included Thauera and Thiobacillus of 6-Proteobacteria. As Thauera sp. has the denitrification characteristics under the condition of aerobic while Thiobacillus denitrificans has the autotrophic denitrification characteristics, it was speculated that aerobic denitrification and autotrophic denitrification might be the main pathways for nitrogen removal in the fresh refuse reactor at the late period of stabilization. Additionally, another group in the gene clone library of denitrifying bacteria may be classified as Bradyrhizobiaceae of alpha-Proteobacteria.

  11. Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation.

    Science.gov (United States)

    Kuppusamy, Saranya; Thavamani, Palanisami; Megharaj, Mallavarapu; Venkateswarlu, Kadiyala; Lee, Yong Bok; Naidu, Ravi

    2016-11-05

    Diversity, distribution and composition of bacterial community of soils contaminated long-term with both polycyclic aromatic hydrocarbons (PAHs) and heavy metals were explored for the first time following 454 pyrosequencing. Strikingly, the complete picture of the Gram positive (+ve) and Gram negative (-ve) bacterial profile obtained in our study illustrates novel postulates that include: (1) Metal-tolerant and PAH-degrading Gram -ves belonging to the class Alphaproteobacteria persist relatively more in the real contaminated sites compared to Gram +ves, (2) Gram +ves are not always resistant to heavy metal toxicity, (3) Stenotrophomonas followed by Burkholderia and Pseudomonas are the dominant genera of PAH degraders with high metabolic activity in long-term contaminated soils, (4) Actinobacteria is the predominant group among the Gram +ves in soils contaminated with high molecular weight PAHs that co-exist with toxic heavy metals like Pb, Cu and Zn, (5) Microbial communities are nutrient-driven in natural environments and (6) Catabolically potential Gram +/-ves with diverse applicability to remediate the real contaminated sites evolve eventually in the historically-polluted soils. Thus, the most promising indigenous Gram +/-ve strains from the long-term contaminated sites with increased catabolic potential, enzymatic activity and metal tolerance need to be harnessed for mixed contaminant cleanups.

  12. Novel bacteria associated with Arctic seashore lichens have potential roles in nutrient scavenging.

    Science.gov (United States)

    Sigurbjörnsdóttir, Margrét Auður; Heiðmarsson, Starri; Jónsdóttir, Anna Rut; Vilhelmsson, Oddur

    2014-05-01

    While generally described as a bipartite mutualistic association between fungi and algae or cyanobacteria, lichens also host diverse and heretofore little explored communities of nonphototrophic endolichenic bacteria. The composition and possible roles of these bacterial communities in the lichen symbiotic association constitute an emerging field of research. Saxicolous (rock-dwelling) seashore lichens present an unusual environment, characterized by rapid fluctuations in temperature, salinity, exposure to solar radiation, etc. The present study focuses on the bacterial biota associated with 4 species of crustose, halophilic, saxicolous seashore lichens found in northern Iceland. A denaturing gradient gel electrophoresis based characterization of the composition of the lichen-associated microbiotas indicated that they are markedly lichen-species-specific and clearly distinguishable from the environmental microbiota represented by control sampling. A collection of bacterial strains was investigated and partially identified by 16S rDNA sequencing. The strains were found to belong to 7 classes: Alphaproteobacteria, Bacilli, Actinobacteria, Flavobacteria, Cytophagia, Sphingobacteria, and Gammaproteobacteria. Several isolates display only a modest level of similarity to their nearest relatives found in GenBank, suggesting that they comprise previously undescribed taxa. Selected strains were tested for inorganic phosphate solubilization and biodegradation of several biopolymers, such as barley β-glucan, xylan, chitosan, and lignin. The results support a nutrient-scavenging role of the associate microbiota in the seashore lichen symbiotic association.

  13. Rickettsial ompB promoter regulated expression of GFPuv in transformed Rickettsia montanensis.

    Directory of Open Access Journals (Sweden)

    Gerald D Baldridge

    Full Text Available Rickettsia spp. (Rickettsiales: Rickettsiaceae are Gram-negative, obligate intracellular, alpha-proteobacteria that have historically been associated with blood-feeding arthropods. Certain species cause typhus and spotted fevers in humans, but others are of uncertain pathogenicity or may be strict arthropod endosymbionts. Genetic manipulation of rickettsiae should facilitate a better understanding of their interactions with hosts.We transformed a species never associated with human disease, Rickettsia montanensis, by electroporation with a TN5 transposon (pMOD700 containing green fluorescent protein (GFPuv and chloramphenicol acetyltransferase (CAT genes under regulation of promoters cloned from the Rickettsia rickettsii ompB gene, and isolated a Chloramphenicol-resistant GFP-fluorescent rickettsiae population (Rmontanensis700. The Rmontanensis700 rickettsiae contained a single transposon integrated near an acetyl-CoA acetyltransferase gene in the rickettsial chromosome. Northern blots showed that GFPuv and CAT mRNAs were both expressed as two transcripts of larger and smaller than predicted length. Western immunoblots showed that Rmontanensis700 and E. coli transformed with a plasmid containing the pMOD700 transposon both expressed GFPuv proteins of the predicted molecular weight.Long-standing barriers to transformation of rickettsiae have been overcome by development of transposon-based rickettsial transformation vectors. The ompB promoter may be the most problematic of the four promoters so far employed in those vectors.

  14. The microbiology of olive mill wastes.

    Science.gov (United States)

    Ntougias, Spyridon; Bourtzis, Kostas; Tsiamis, George

    2013-01-01

    Olive mill wastes (OMWs) are high-strength organic effluents, which upon disposal can degrade soil and water quality, negatively affecting aquatic and terrestrial ecosystems. The main purpose of this review paper is to provide an up-to-date knowledge concerning the microbial communities identified over the past 20 years in olive mill wastes using both culture-dependent and independent approaches. A database survey of 16S rRNA gene sequences (585 records in total) obtained from olive mill waste environments revealed the dominance of members of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. Independent studies confirmed that OMW microbial communities' structure is cultivar dependent. On the other hand, the detection of fecal bacteria and other potential human pathogens in OMWs is of major concern and deserves further examination. Despite the fact that the degradation and detoxification of the olive mill wastes have been mostly investigated through the application of known bacterial and fungal species originated from other environmental sources, the biotechnological potential of indigenous microbiota should be further exploited in respect to olive mill waste bioremediation and inactivation of plant and human pathogens. The implementation of omic and metagenomic approaches will further elucidate disposal issues of olive mill wastes.

  15. Endo- and exoglucanase activities in bacteria from mangrove sediment

    Science.gov (United States)

    Júnior, Fábio Lino Soares; Dias, Armando Cavalcante Franco; Fasanella, Cristiane Cipola; Taketani, Rodrigo Gouvêa; de Souza Lima, André Oliveira; Melo, Itamar Soares; Andreote, Fernando Dini

    2013-01-01

    The mangrove ecosystem is an unexplored source for biotechnological applications. In this unique environment, endemic bacteria have the ability to thrive in the harsh environmental conditions (salinity and anaerobiosis), and act in the degradation of organic matter, promoting nutrient cycles. Thus, this study aimed to assess the cellulolytic activities of bacterial groups present in the sediment from a mangrove located in Ilha do Cardoso (SP, Brazil). To optimize the isolation of cellulolytic bacteria, enrichments in two types of culture media (tryptone broth and minimum salt medium), both supplemented with 5% NaCl and 1% of cellulose, were performed. Tests conducted with the obtained colonies showed a higher occurrence of endoglycolytic activity (33 isolates) than exoglycolytic (19 isolates), and the degradation activity was shown to be modulated by the presence of NaCl. The isolated bacteria were clustered by BOX-PCR and further classified on the basis of partial 16S rRNA sequences as Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes or Bacteroidetes. Therefore, this study highlights the importance of studies focusing on the endemic species found in mangroves to exploit them as novel biotechnological tools for the degradation of cellulose. PMID:24516466

  16. Responses of Bacterial Communities to Simulated Climate Changes in Alpine Meadow Soil of the Qinghai-Tibet Plateau.

    Science.gov (United States)

    Rui, Junpeng; Li, Jiabao; Wang, Shiping; An, Jiaxing; Liu, Wen-tso; Lin, Qiaoyan; Yang, Yunfeng; He, Zhili; Li, Xiangzhen

    2015-09-01

    The soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, microbial responses to climate warming or cooling remain poorly understood, limiting our ability to predict the consequences of future climate changes. To address this issue, it is critical to identify microbes sensitive to climate change and key driving factors shifting microbial communities. In this study, alpine soil transplant experiments were conducted downward or upward along an elevation gradient between 3,200 and 3,800 m in the Qinghai-Tibet plateau to simulate climate warming or cooling. After a 2-year soil transplant experiment, soil bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. The results showed that the transplanted soil bacterial communities became more similar to those in their destination sites and more different from those in their "home" sites. Warming led to increases in the relative abundances in Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria and decreases in Acidobacteria, Betaproteobacteria, and Deltaproteobacteria, while cooling had opposite effects on bacterial communities (symmetric response). Soil temperature and plant biomass contributed significantly to shaping the bacterial community structure. Overall, climate warming or cooling shifted the soil bacterial community structure mainly through species sorting, and such a shift might correlate to important biogeochemical processes such as greenhouse gas emissions. This study provides new insights into our understanding of soil bacterial community responses to climate warming and cooling.

  17. Selective growth promotion of bloom-forming raphidophyte Heterosigma akashiwo by a marine bacterial strain.

    Science.gov (United States)

    Higashi, Aiko; Fujitani, Yoshiko; Nakayama, Natsuko; Tani, Akio; Ueki, Shoko

    2016-12-01

    Algal bloom is typically caused by aberrant propagation of a single species, resulting in its predomination in the local population. While environmental factors including temperature and eutrophication are linked to bloom, the precise mechanism of its formation process is still obscure. Here, we isolated a bacterial strain that promotes growth of Heterosigma akashiwo, a Raphidophyceae that causes harmful algal blooms. Based on 16S rRNA gene sequence, the strain was identified as Altererythrobacter ishigakiensis, a member of the class Alphaproteobacteria. When added to culture, this strain facilitated growth of H. akashiwo and increased its cell culture yield significantly. Importantly, this strain did not affect the growth of other raphidophytes, Chattonella ovate and C. antiqua, indicating that it promotes growth of H. akashiwo in a species-specific manner. We also found that, in co-culture, H. akashiwo suppressed the growth of C. ovate. When A. ishigakiensis was added to the mixed culture, H. akashiwo growth was facilitated while C. ovate propagation was markedly suppressed, indicating that the presence of the bacterium enhances the dominance of H. akashiwo over C. ovate. This is the first example of selective growth promotion of H. akashiwo by a marine bacterium, and may exemplify importance of symbiotic bacterium on algal bloom forming process in general.

  18. Diversity of prokaryotes at a shallow submarine vent of Panarea Island (Italy by high-throughput sequencing

    Directory of Open Access Journals (Sweden)

    Teresa L. Maugeri

    2013-09-01

    Full Text Available To determine microbial community composition and possible key microbial processes in the shallow-sea hydrothermal vent system off Panarea Island (Italy, we examined bacterial and archaeal communities of sediment and fluid samples from a hot vent by 16S rDNA Illumina sequencing technique. Both high abundant (>1% of total sequences, low abundant (from 0.1 to <1% and rare (< 0.1% phylogenetic groups were responsible for the distinct prokaryotic communities characterizing the heated sediment and fluid. The bacterial and archaeal communities from sediment were dominated by sequences affiliated with Rhodovulum genus (Alphaproteobacteria, including phototrophic ferrous-iron-oxidizing purple bacteria, Thiohalospira and Thiomicrospira (Gammaproteobacteria, typically involved in the sulphur cycle, and Methanococcus (Euryarchaeota. Fluid communities were dominated by anoxygenic phototrophic members of Chlorobium, followed by Thiomicrospira (Gammaproteobacteria, Sulfurimonas, Arcobacter and Sulfurospirillum (Epsilonproteobacteria, and Methanosarcina (Euryarchaeota. Obtained sequences were affiliated with prokaryotes taking a key part in the carbon, iron and sulphur cycling at the shallow hydrothermal system off Panarea Island. Despite the huge sequencing efforts, a great number of Bacteria and Archaea still remains unaffiliated at genus level, indicating that Black Point vent represents a hotspot of prokaryotic diversity.

  19. Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders

    Directory of Open Access Journals (Sweden)

    Guo-Chun eDing

    2012-08-01

    Full Text Available Considering their key role for ecosystem processes, it is important to understand the response of microbial communities in unpolluted soils to pollution with polycyclic aromatic hydrocarbons (PAH. Phenanthrene, a model compound for PAH, was spiked to a Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and control soils collected on days 0, 21 and 63 were analyzed based on PCR-amplified 16S rRNA genefragments. Denaturing gradient gel electrophoresis (DGGE fingerprints of bacterial communities increasingly deviated with time between spiked and control soils. In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacteria became only detectable after 63 days, while significant effects on Betaproteobacteria were detectable in both soils after 21 days. Comparison of the taxonomic distribution of bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta- or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils. Despite the significant differences in the bacterial community structure between both soils on day 0, similar genera increased in relative abundance after PAH spiking, especially Sphingomonas and Polaromonas. However, this did not result in an increased overall similarity of the bacterial communities in both soils.

  20. Microbial community compositional shifts in bleached colonies of the Brazilian reef-building coral Siderastrea stellata.

    Science.gov (United States)

    Lins-de-Barros, Monica M; Cardoso, Alexander M; Silveira, Cynthia B; Lima, Joyce L; Clementino, Maysa M; Martins, Orlando B; Albano, Rodolpho M; Vieira, Ricardo P

    2013-01-01

    The association of metazoan, protist, and microbial communities with Scleractinian corals forms the basis of the coral holobiont. Coral bleaching events have been occurring around the world, introducing changes in the delicate balance of the holobiont symbiotic interactions. In this study, Archaea, bacteria, and eukaryotic phototrophic plastids of bleached colonies of the Brazilian coral Siderastrea stellata were analyzed for the first time, using 16S rRNA gene libraries. Prokaryotic communities were slightly more diverse in healthy than in bleached corals. However, the eukaryotic phototrophic plastids community was more diverse in bleached corals. Archaea phylogenetic analyses revealed a high percentage of Crenarchaeota sequences, mainly related to Nitrosopumilus maritimus and Cenarchaeum symbiosum. Dramatic changes in bacterial community composition were observed in this bleaching episode. The dominant bacterial group was Alphaproteobacteria followed by Gammaproteobacteria in bleached and Betaproteobacteria in healthy samples. Plastid operational taxonomic units (OTUs) from both coral samples were mainly related to red algae chloroplasts (Florideophycea), but we also observed some OTUs related to green algae chloroplasts (Chlorophyta). There seems to be a strong relationship between the Bacillariophyta phylum and our bleached coral samples as clones related to members of the diatom genera Amphora and Nitzschia were detected. The present study reveals information from a poorly investigated coral species and improves the knowledge of coral microbial community shifts that could occur during bleaching episodes.

  1. Bacterial communities involved in soil formation and plant establishment triggered by pyrite bioweathering on arctic moraines.

    Science.gov (United States)

    Mapelli, Francesca; Marasco, Ramona; Rizzi, Agostino; Baldi, Franco; Ventura, Stefano; Daffonchio, Daniele; Borin, Sara

    2011-02-01

    In arctic glacier moraines, bioweathering primed by microbial iron oxidizers creates fertility gradients that accelerate soil development and plant establishment. With the aim of investigating the change of bacterial diversity in a pyrite-weathered gradient, we analyzed the composition of the bacterial communities involved in the process by sequencing 16S rRNA gene libraries from different biological soil crusts (BSC). Bacterial communities in three BSC of different morphology, located within 1 m distance downstream a pyritic conglomerate rock, were significantly diverse. The glacier moraine surrounding the weathered site showed wide phylogenetic diversity and high evenness with 15 represented bacterial classes, dominated by Alphaproteobacteria and pioneer Cyanobacteria colonizers. The bioweathered area showed the lowest diversity indexes and only nine bacterial families, largely dominated by Acidobacteriaceae and Acetobacteraceae typical of acidic environments, in accordance with the low pH of the BSC. In the weathered BSC, iron-oxidizing bacteria were cultivated, with counts decreasing along with the increase of distance from the rock, and nutrient release from the rock was revealed by environmental scanning electron microscopy-energy dispersive X-ray analyses. The vegetated area showed the presence of Actinomycetales, Verrucomicrobiales, Gemmatimonadales, Burkholderiales, and Rhizobiales, denoting a bacterial community typical of developed soils and indicating that the lithoid substrate of the bare moraine was here subjected to an accelerated colonization, driven by iron-oxidizing activity.

  2. Characterization of a newly discovered symbiont of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Bing, Xiao-Li; Yang, Jiao; Zchori-Fein, Einat; Wang, Xiao-Wei; Liu, Shu-Sheng

    2013-01-01

    Bemisia tabaci (Hemiptera: Aleyrodidae) is a species complex containing >28 cryptic species, some of which are important crop pests worldwide. Like many other sap-sucking insects, whiteflies harbor an obligatory symbiont, "Candidatus Portiera aleyrodidarum," and a number of secondary symbionts. So far, six genera of secondary symbionts have been identified in B. tabaci. In this study, we report and describe the finding of an additional bacterium in the indigenous B. tabaci cryptic species China 1 (formerly known as B. tabaci biotype ZHJ3). Phylogenetic analysis based on the 16S rRNA and gltA genes showed that the bacterium belongs to the Alphaproteobacteria subdivision of the Proteobacteria and has a close relationship with human pathogens of the genus Orientia. Consequently, we temporarily named it Orientia-like organism (OLO). OLO was found in six of eight wild populations of B. tabaci China 1, with the infection rate ranging from 46.2% to 76.8%. Fluorescence in situ hybridization (FISH) of B. tabaci China 1 in nymphs and adults revealed that OLOs are confined to the bacteriome and co-occur with "Ca. Portiera aleyrodidarum." The vertical transmission of OLO was demonstrated by detection of OLO at the anterior pole end of the oocytes through FISH. Quantitative PCR analysis of population dynamics suggested a complex interaction between "Ca. Portiera aleyrodidarum" and OLO. Based on these results, we propose "Candidatus Hemipteriphilus asiaticus" for the classification of this symbiont from B. tabaci.

  3. [Petroleum pollution and the microbial community structure in the soil of Shengli Oilfield].

    Science.gov (United States)

    Liu, Jian; Song, Xue-Ying; Sun, Rui-Lian; Xie, Fu-Ju; Wang, Ren-Qing; Wang, Wen-Xing

    2014-03-01

    Soils around a new oil well (2011- ) and an old oil well (1966-2003) were sampled to investigate the characteristics of petroleum pollution in the oilfield. The structure of soil microbial community was analyzed by PCR-DGGE and clone sequencing techniques. Results showed that the soils around the two oil wells were generally contaminated with petroleum, and the concentrations of total petroleum hydrocarbons mostly exceeded the threshold of the environmental quality standards of soil (500 mg x kg(-1)). The total petroleum hydrocarbons concentration of the polluted soil was significantly positively correlated with the contents of organic carbon, total nitrogen and available potassium, respectively. The microbial diversity index in the soil around the old oil well decreased with the increasing total petroleum hydrocarbons concentration, however, it was reversed for the soil around the new oil well. Sequence analysis of the prominent bands in DGGE profiles showed that some dominant species existed in the petroleum-contaminated soils around the oil wells and mostly were oil-associated and hydrocarbon degrading bacteria, including Microbacterium, Streptomyces, Dietzia, Flavobacterium, alpha-Proteobacteria, and gamma-Proteobacteria.

  4. Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

    Science.gov (United States)

    Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

    2014-08-01

    The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska.

  5. Diversity and antimicrobial potential of bacterial isolates associated with the soft coral Alcyonium digitatum from the Baltic Sea.

    Science.gov (United States)

    Pham, Thi Mien; Wiese, Jutta; Wenzel-Storjohann, Arlette; Imhoff, Johannes F

    2016-01-01

    It is well recognized that microorganisms associated with marine invertebrates, in particular sponges and hard corals, are an excellent source of new natural products. Therefore, the diversity of bacteria associated with marine invertebrates and their potential to produce bioactive compounds have received much attention in recent years. We report here for the first time on the biodiversity of bacteria associated with the soft coral Alcyonium digitatum, which is abundant in the Baltic Sea. In order to increase the cultured diversity, bacteria were isolated using four different media, identified with support of 16S rRNA gene sequences and screened for antimicrobial activity using two different media. Activity of crude extracts was tested against Bacillus subtilis, Staphylococcus epidermidis, Escherichia coli, and the yeast Candida albicans. A total of 251 coral-associated bacterial isolates were classified and found to belong to 41 species in 14 genera of the Firmicutes, Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria. The genus Bacillus was most abundant and diverse with 17 recognized species. Forty-eight percent of all 251 isolates exhibited antimicrobial activity. All isolates of Bacillus methylotrophicus and Bacillus amyloliquefaciens displayed inhibition of at least three out of the four tested microorganisms. It became obvious during this study that the production of antibiotic substances not only is strain-specific, but in many cases also depends on the media composition and growth conditions. In addition, the antimicrobial potential of bacteria associated with A. digitatum may represent a promising source for antimicrobial substances.

  6. DIVERSITY AND MAGNETISM OF MAGNETOTACTIC BACTERIA IN LAKE WEIYANG NEAR XI'AN CITY%西安未央湖趋磁细菌多样性与磁学研究

    Institute of Scientific and Technical Information of China (English)

    陈海涛; 林巍; 王寅炤; 李金华; 陈冠军; 潘永信

    2013-01-01

    对西安郊区未央湖趋磁细菌的生物多样性和磁学性质进行了系统研究.光学和透射电子显微镜分析发现,未央湖趋磁细菌主要为杆菌,它们的磁小体多为子弹头形状并呈链状排列;磁学分析表明这些磁小体颗粒以单畴磁铁矿为主;并发现一类同时含有磁铁矿和胶黄铁矿磁小体的趋磁杆菌.基于16S rRNA基因的系统发育分析发现,未央湖趋磁细菌主要分布在变形菌门的δ-变形菌纲(75%)和α-变形菌纲(25%).本研究结果还有助于为利用趋磁细菌群落指示环境变化提供依据.%Magnetotactic bacteria are a group of morphologically and phylogenetically heterogenous prokaryotes which synthesize intracellular nano-sized magnetic crystals of magnetite ( Fe3O4) and/or greigite ( Fe3S4). Magnetotactic bacteria are ubiquitous in freshwater and marine environments. Most observed magnetotactic bacteria are affiliated with the Alphaproteobacteria, while bacteria in the Deltaproteobacteria, Gammaproteobacteria, phylum Nitrospira, and the candidate division OP3 are also discovered. In this study,the diversity and magnetic properties of magnetotactic bacteria collected from Lake Weiyang in Xi'an city (34°24′23. 96"N, 108°58′55. 51"E) , Shaanxi Province, were analyzed and characterized. Surface sediments ( 5cm to 10cm) were collected, and magnetotactic bacteria were magnetically enriched using the capillary racetrack method. Transmission electron microscopy analyses have revealed that rod-shaped bacteria containing bullet-shaped magnetsomes were the dominant group of magnetotactic bacteria in Lake Weiyang. Other kinds of magnetotactic bacteria,such as cocci and spirilla,were also observed. Interestingly, the energy dispersive x-rayspectrometer of transmission electron microscopy showed some rod-shaped bacteria were able to simultaneously biomineralize magnetite and greigite magnetosomes in a single cell, which is unusual in magnetotactic bacteria. The

  7. 凡纳滨对虾土塘养殖与循环养殖系统细菌群落结构比较研究%Comparison of bacterial communities in the earthen pond and the recirculating aquaculture system for Litopenaeus vannamei cultivation

    Institute of Scientific and Technical Information of China (English)

    裘钱玲琳; 徐如卫; 朱建林; 杨福生; 俞奇力; 张德民

    2015-01-01

    Recirculating aquaculture system ( RAS) has gradually replaced the traditional earthen pond ( Earth) for shrimp cultivation because of its less pollution and higher economical benefit. A comprehensive knowledge on bacterial community structure is necessary for disease control and process improvement. In this paper amplicon pyrosequencing of 16S rRNA gene was used to compare the bacte-rial community structure among recirculating aquaculture system (water and biofilm) and earthen pond (water). The results showed that the bacterial communities were distinct among Earth water, RAS water and biofilm, with the highest alpha-diversity in RAS water. Cyanobacteria and Actinobacteria were the predominant phyla in earthen pond. In contrast, Alphaproteobacteria was the highest in the RAS water, while Betaproteobacteria and Bacteroidetes were the dominant phyla in the RAS biofilm. Similarity percentage ( SIMPER) analysis identified 11 OTUs that cumulatively contributed to 35. 14% dissimilarity of the bacterial community. These taxa were affilia-ted with Saprospiraceae, Rhodobacteraceae, ACK-M1 and Synechococcaceae, Caldilineaceae, Betaproteobacteria, Sphingomonadales, Flavobacteria. At a finer resolution, the members of family Nitrosomonadaceae and Nitrospiraceae, which contribute to denitrification and nitrification, were dramatically higher in RAS biofilm than in waters. Overall, this work provides microbial ecological evidences for the advantages of recirculating aquaculture system over earthen pond.%对虾循环水养殖因污染排放少、经济效益高而正在逐步取代土塘养殖,成为高效养殖模式发展的方向,了解养殖系统的细菌群落结构特征对于病害控制和养殖工艺改进具有重要意义. 采用细菌16S rRNA基因扩增子焦磷酸测序,比较了循环养殖水体、生物膜与土塘养殖水环境中的细菌群落结构差异. 结果表明,循环养殖水体、生物膜与土塘水体的细菌群落结构差异明显,且循环

  8. Microbiological fingerprint of African dust deposition in alpine snow pack, Mont Blanc summit

    Science.gov (United States)

    Chuvochina, Maria; Alekhina, Irina; Normand, Philippe; Petit, Jean-Robert; Bulat, Sergey

    2010-05-01

    The biogeochemical effect of African dust transport has been reported mostly with respect to nutrient budget change in both terrestrial and aquatic ecosystems and global transport of microorganisms, including pathogens. However, its potential to seed or colonize the remote environments by transported microorganisms is poorly understood. This study has focused on bacterial content and diversity of Saharan dust deposition from 2006, 2008 and 2009 in snow pack of Mont Blanc (MtBl) glacier as well as recognition of bacteria which could be involved in establishing microbiota in this icy environment. Four snow samples recorded Saharan dust events from June 2006 (SDm06/2006 - 3,5 months aged), May and June 2008 (SDm05/2008 and SDm06/2008 - 1 month in between and 1 week aged each) and May 2009 (SDm05/2009 - 1 week aged) were collected at Col du Dome area (4250m a.s.l.). Bacterial community structure was assessed by ribotyping and subsequent sequencing of bacterial 16S rRNA genes. To exclude human-associated and laboratory contamination several controls were run in parallel updating our contaminant library. The obtained phylotypes were tested against this library keeping only those which successfully passed through this exam. Of 176 selected clones from four clone libraries 29.8% were met in our contaminant library. The ‘true' sequences were assigned to 57 phylotypes (>97.5% sequence similarity) originating mostly from soil. The prevalent phylotypes recovered were belonging to different bacterial divisions: Deinococcus-Thermus, Alpha-proteobacteria and CFB groups for SDm06/2006; Actinobacteria, Alpha-proteobacteria and CFB for SDm05/2008 and SDm06/2008; Actinobacteria and chloroplasts/plastids for SDm05/2009. Phylogenetic analysis of all phylotypes showed no shared species amongst all 4 dust layers in MtBl snow pack in 2006, 2008 and 2009. However, two phylotypes (Blastococcus saxobsidens sp. - 99%, Geodermatophilus obscurus sp. - 99%) were shared between 2008 and 2009

  9. High diversity of methanotrophic bacteria in geothermal soils affected by high methane fluxes

    Science.gov (United States)

    D'Alessandro, Walter; Gagliano, Antonina Lisa; Quatrini, Paola; Parello, Francesco

    2014-05-01

    Volcanic and geothermal systems emit endogenous gases by widespread degassing from soils, including CH4, a greenhouse gas 25 times as potent as CO2. Recently, it has been demonstrated that volcanic/geothermal soils act as source, but also as biological filter for methane release to the atmosphere. For long time, volcanic/geothermal soils has been considered inhospitable for methanotrophic microorganisms, but new extremophile methanotrophs belonging to Verrucomicrobia were identified in three different areas (Pozzuoli, Italy; Hell's Gate, New Zealand; Kamchatka, Russia), explaining anomalous behaviours in methane leakages of several geothermal/volcanic sites. Our aim was to increase the knowledge of the relationship between methane emissions from volcanic/geothermal areas and biological methane oxidation, by investigating a geothermal site of Pantelleria island (Italy). Pantelleria Island hosts a high enthalpy geothermal system characterized by high temperature, high CH4 and very low H2S fluxes. Such characteristics are reflected in potentially great supply of methane for methanotrophs and scarce presence of inhibitors of their activity (H2S and NH3) in the Pantelleria soils. Potential methanotrophic activity within these soils was already evidenced by the CH4/CO2 ratio of the flux measurements which was lower than that of the respective fumarolic manifestations indicating a loss of CH4 during the gas travel towards the earth's surface. In this study laboratory incubation experiments using soils sampled at Favara Grande, the main hydrothermal area of Pantelleria, showed very high methane consumption rates (up to 9500 ng CH4 h-1 g-1). Furthermore, microbiological and culture-independent molecular analyses allowed to detect the presence of methanotrophs affiliated to Gamma- and Alpha-Proteobacteria and to the newly discovered acidothermophilic methanotrophs Verrucomicrobia. Culturable methanotrophic Alpha-proteobacteria of the genus Methylocystis were isolated by

  10. Effects of selected pharmaceuticals on riverine biofilm communities.

    Science.gov (United States)

    Lawrence, John R; Swerhone, George D W; Wassenaar, Leonard I; Neu, Thomas R

    2005-08-01

    Although pharmaceutical and therapeutic products are widely found in the natural environment, there is limited understanding of their ecological effects. Here we used rotating annular bioreactors to assess the impact of 10 microg.L(-1) of the selected pharmaceuticals ibuprofen, carbamazepine, furosemide, and caffeine on riverine biofilms. After 8 weeks of development, community structure was assessed using in situ microscopic analyses, fluor-conjugated lectin binding, standard plate counts, fluorescent in situ hybridization, carbon utilization spectra, and stable carbon isotope analyses. The biofilm communities varied markedly in architecture although only caffeine treated biofilms were significantly thicker. Cyanobacteria were suppressed by all 4 compounds, whereas the nitrogen containing caffeine, furosemide, and carbamazepine increased algal biomass. Ibuprofen and carbamazepine reduced bacterial biomass, while caffeine and furosemide increased it. Exopolymer content and composition of the biofilms was also influenced. Significant positive and negative effects were observed in carbon utilization spectra. In situ hybridization analyses indicated all treatments significantly decreased the gamma-proteobacterial populations and increased beta-proteobacteria. Ibuprofen in particular increased the alpha-proteobacteria, beta-proteobacteria, cytophaga-flavobacteria, and SRB385 probe positive populations. Caffeine and carbamazepine additions resulted in significant increases in the high GC354c and low GC69a probe positive cells. Live-dead analyses of the biofilms indicated that all treatments influenced the ratio of live-to-dead cells with controls having a ratio of 2.4, carbamazepine and ibuprofen being 3.2 and 3.5, respectively, and furosemide and caffeine being 1.9 and 1.7, respectively. Stable isotope analyses of the biofilms indicated delta 13C values shifted to more negative values relative to control biofilms. This shift may be consistent with proportional loss of

  11. Abundance of Two Pelagibacter ubique Bacteriophage Genotypes along a Latitudinal Transect in the North and South Atlantic Oceans

    Science.gov (United States)

    Eggleston, Erin M.; Hewson, Ian

    2016-01-01

    This study characterizes viral and bacterial dynamics along a latitudinal transect in the Atlantic Ocean from approximately 10 N–40 S. Overall viral abundance decreased with depth, on average there were 1.64 ± 0.71 × 107 virus like particles (VLPs) in surface waters, decreasing to an average of 6.50 ± 2.26 × 105 VLPs in Antarctic Bottom Water. This decrease was highly correlated to bacterial abundance. There are six major water masses in the Southern Tropical Atlantic Ocean, and inclusion of water mass, temperature and salinity variables explained a majority of the variation in total viral abundance. Recent discovery of phages infecting bacteria of the SAR11 clade of Alphaproteobacteria (i.e., pelagiphages) leads to intriguing questions about the roles they play in shaping epipelagic communities. Viral-size fraction DNA from epipelagic water was used to quantify the abundance of two pelagiphages, using pelagiphage-specific quantitative PCR primers and probes along the transect. We found that HTVC010P, a member of a podoviridae sub-family, was most abundant in surface waters. Copy numbers ranged from an average of 1.03 ± 2.38 × 105 copies ml−1 in surface waters, to 5.79 ± 2.86 × 103 in the deep chlorophyll maximum. HTVC008M, a T4-like myovirus, was present in the deep chlorophyll maximum (5.42 ± 2.8 × 103 copies ml−1 on average), although it was not as highly abundant as HTVC010P in surface waters (6.05 ± 3.01 × 103 copies ml−1 on average). Interestingly, HTVC008M was only present at a few of the most southern stations, suggesting latitudinal biogeography of SAR11 phages. PMID:27733846

  12. Occurrence of novel verrucomicrobial species, endosymbiotic and associated with parthenogenesis in Xiphinema americanum-group species (Nematoda, Longidoridae).

    Science.gov (United States)

    Vandekerckhove, T T; Willems, A; Gillis, M; Coomans, A

    2000-11-01

    Numerous micro-organisms have been described as cytoplasmic symbionts of eukaryotes. Many so-called obligate endosymbionts rely exclusively on maternal (vertical or transovarial) transmission to maintain themselves, rendering them dependent on the host sex ratio, which they would tend to manipulate to their own advantage. The latter phenomenon is often associated with the presence of Wolbachia pipientis (alpha-Proteobacteria) in arthropods and nematodes. A potentially similar situation was discovered involving members of a new clade of Verrucomicrobia, another main line of descent in the Bacteria. Nematode species of the Xiphinema americanum group (Nematoda, Longidoridae), viz. Xiphinema americanum, Xiphinema rivesi and Xiphinema brevicollum, each harbour their own specific verrucomicrobial endosymbionts. They are exclusively maternally inherited and their hosts reproduce by thelytokous (mother-to-daughter) parthenogenesis, males being extremely rare. A new genus, 'Candidatus Xiphinematobacter' gen. nov., along with three new candidate verrucomicrobial species, 'Candidatus Xiphinematobacter americani' sp. nov., 'Candidatus Xiphinematobacter rivesi' sp. nov. and 'Candidatus Xiphinematobacter brevicolli' sp. nov., are described on the basis of transmission electron microscopy, scanning electron microscopy, DAPI (4',6-diamidino-2-phenylindole) epifluorescence microscopy and 16S rDNA sequence analysis. These are the first endosymbiotic species described among the Verrucomicrobia. They share a mean 16S rDNA similarity of about 93%, whereas similarity to their closest relative, clone WCHD3-88, is less than 87%. Thus, the endosymbionts form a homogeneous clade for which the new candidate genus 'Candidatus Xiphinematobacter' gen. nov. is proposed. The type species is 'Candidatus Xiphinematobacter brevicolli' sp. nov.

  13. Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil

    Directory of Open Access Journals (Sweden)

    Gaidi eRen

    2015-01-01

    Full Text Available Understanding the potential for PAH degradation by indigenous microbiota and the influence of PAHs on native microbial communities is of great importance for bioremediation and ecological evaluation. Various studies have focused on the bacterial communities in the environment where obvious PAH degradation was observed, little is known about the microbiota in the soil where poor degradation was observed. Soil microcosms were constructed with a red soil by supplementation with a high-molecular-weight PAH (pyrene at three dosages (5, 30, and 70 mg.kg-1. Real-time PCR was used to evaluate the changes in bacterial abundance and pyrene dioxygenase gene (nidA quantity. Illumina sequencing was used to investigate changes in diversity, structure, and composition of bacterial communities. After 42 days of incubation, no evident degradation was observed. The poor degradation ability was associated with the stability or significant decrease of abundance of the nidA gene. Although the abundance of the bacterial 16S rRNA gene was not affected by pyrene, the bacterial richness and diversity were decreased with increasing dosage of pyrene and the community structure was changed. Phylotypes affected by pyrene were comprehensively surveyed: (1 at the high taxonomic level, seven of the abundant phyla/classes (relative abundance >1.0% including Chloroflexi, AD3, WPS-2, GAL5, Alphaproteobacteria, Actinobacteria, and Deltaproteobacteria and one rare phylum Crenarchaeota were significantly decreased by at least one dosage of pyrene, while 3 phyla/classes (Acidobacteria, Betaproteobacteria, and Gammaproteobacteria were significantly increased; and (2 at the lower taxonomic level, the relative abundances of twelve orders were significantly depressed, whereas those of nine orders were significantly increased. This work enhanced our understanding of the biodegradation potential of pyrene in red soil and the effect of pyrene on soil ecosystems at the microbial community

  14. Next-generation sequencing reveals significant bacterial diversity of botrytized wine.

    Directory of Open Access Journals (Sweden)

    Nicholas A Bokulich

    Full Text Available While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5. This study was designed to serve two goals: 1 to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP of LAB communities; and 2 to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the

  15. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community.

    Science.gov (United States)

    Zoccarato, Luca; Celussi, Mauro; Pallavicini, Alberto; Fonda Umani, Serena

    2016-01-01

    Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of

  16. Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome.

    Science.gov (United States)

    Babujia, Letícia Carlos; Silva, Adriana Pereira; Nakatani, André Shigueyoshi; Cantão, Mauricio Egidio; Vasconcelos, Ana Tereza Ribeiro; Visentainer, Jesuí Vergilio; Hungria, Mariangela

    2016-08-01

    The transgenic soybean [Glycine max (L.) Merrill] occupies about 80 % of the global area cropped with this legume, the majority comprising the glyphosate-resistant trait (Roundup Ready(®), GR or RR). However, concerns about possible impacts of transgenic crops on soil microbial communities are often raised. We investigated soil chemical, physical and microbiological properties, and grain yields in long-term field trials involving conventional and nearly isogenic RR transgenic genotypes. The trials were performed at two locations in Brazil, with different edaphoclimatic conditions. Large differences in physical, chemical and classic microbiological parameters (microbial biomass of C and N, basal respiration), as well as in grain production were observed between the sites. Some phyla (Proteobacteria, Actinobacteria, Acidobacteria), classes (Alphaproteobacteria, Actinomycetales, Solibacteres) and orders (Rhizobiales, Burkholderiales, Myxococcales, Pseudomonadales), as well as some functional subsystems (clustering-based subsystems, carbohydrates, amino acids and protein metabolism) were, in general, abundant in all treatments. However, bioindicators related to superior soil fertility and physical properties at Londrina were identified, among them a higher ratio of Proteobacteria:Acidobacteria. Regarding the transgene, the metagenomics showed differences in microbial taxonomic and functional abundances, but lower in magnitude than differences observed between the sites. Besides the site-specific differences, Proteobacteria, Firmicutes and Chlorophyta were higher in the transgenic treatment, as well as sequences related to protein metabolism, cell division and cycle. Although confirming effects of the transgenic trait on soil microbiome, no differences were recorded in grain yields, probably due to the buffering capacity associated with the high taxonomic and functional microbial diversity observed in all treatments.

  17. Genotyping of Brucella species using clade specific SNPs

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    Foster Jeffrey T

    2012-06-01

    Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

  18. Microbial community evolution during simulated managed aquifer recharge in response to different biodegradable dissolved organic carbon (BDOC) concentrations

    KAUST Repository

    Li, Dong

    2013-05-01

    This study investigates the evolution of the microbial community in laboratory-scale soil columns simulating the infiltration zone of managed aquifer recharge (MAR) systems and analogous natural aquifer sediment ecosystems. Parallel systems were supplemented with either moderate (1.1 mg/L) or low (0.5 mg/L) biodegradable dissolved organic carbon (BDOC) for a period of six months during which time, spatial (1 cm, 30 cm, 60 cm, 90 cm, and 120 cm) and temporal (monthly) analyses of sediment-associated microbial community structure were analyzed. Total microbial biomass associated with sediments was positively correlated with BDOC concentration where a significant decline in BDOC was observed along the column length. Analysis of 16S rRNA genes indicated dominance by Bacteria with Archaea comprising less than 1 percent of the total community. Proteobacteria was found to be the major phylum in samples from all column depths with contributions from Betaproteobacteria, Alphaproteobacteria and Gammaproteobacteria. Microbial community structure at all the phylum, class and genus levels differed significantly at 1 cm between columns receiving moderate and low BDOC concentrations; in contrast strong similarities were observed both between parallel column systems and across samples from 30 to 120 cm depths. Samples from 1 cm depth of the low BDOC columns exhibited higher microbial diversity (expressed as Shannon Index) than those at 1 cm of moderate BDOC columns, and both increased from 5.4 to 5.9 at 1 cm depth to 6.7-8.3 at 30-120 cm depths. The microbial community structure reached steady state after 3-4 months since the initiation of the experiment, which also resulted in an improved DOC removal during the same time period. This study suggested that BDOC could significantly influence microbial community structure regarding both composition and diversity of artificial MAR systems and analogous natural aquifer sediment ecosystems. © 2013 Elsevier Ltd.

  19. Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation.

    Science.gov (United States)

    Nadalig, Thierry; Greule, Markus; Bringel, Françoise; Keppler, Frank; Vuilleumier, Stéphane

    2014-01-01

    Chloromethane (CH3Cl) is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH3Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH3Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial, and phyllospheric environments. Improving our knowledge of these degradation processes and their magnitude is thus highly relevant for a better understanding of the global budget of CH3Cl. The cmu pathway, for chloromethane utilisation, is the only microbial pathway for CH3Cl degradation elucidated so far, and was characterized in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH3Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment. Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH3Cl contain part or all of the complement of cmu genes required for CH3Cl degradation. These organisms, unlike bacteria shown to grow with CH3Cl using the cmu pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium Leisingera methylohalidivorans MB2 showed that this bacterium does not contain cmu genes. Isotope fractionation experiments with L. methylohalidivorans MB2 suggest that the unknown pathway used by this bacterium for growth with CH3Cl can be differentiated from the cmu pathway. This result opens the prospect that contributions from bacteria with the cmu and Leisingera-type pathways to the atmospheric CH3Cl budget may be teased apart in the future.

  20. Probing the diversity of chloromethane-degrading bacteria by comparative genomics and isotopic fractionation

    Directory of Open Access Journals (Sweden)

    Thierry eNADALIG

    2014-10-01

    Full Text Available Chloromethane (CH3Cl is produced on earth by a variety of abiotic and biological processes. It is the most important halogenated trace gas in the atmosphere, where it contributes to ozone destruction. Current estimates of the global CH3Cl budget are uncertain and suggest that microorganisms might play a more important role in degrading atmospheric CH3Cl than previously thought. Its degradation by bacteria has been demonstrated in marine, terrestrial and phyllospheric environments. Improving our knowledge of these degradation processes and its magnitude is thus highly relevant for a better understanding of the global budget of CH3Cl.The cmu pathway, for chloromethane utilisation, is the only microbial pathway for CH3Cl degradation elucidated so far, and was characterised in detail in aerobic methylotrophic Alphaproteobacteria. Here, we reveal the potential of using a two-pronged approach involving a combination of comparative genomics and isotopic fractionation during CH3Cl degradation to newly address the question of the diversity of chloromethane-degrading bacteria in the environment.Analysis of available bacterial genome sequences reveals that several bacteria not yet known to degrade CH3Cl contain part or all of the complement of cmu genes required for CH3Cl degradation. These organisms, unlike bacteria shown to grow with CH3Cl using the cmu pathway, are obligate anaerobes. On the other hand, analysis of the complete genome of the chloromethane-degrading bacterium Leisingera methylohalidivorans showed that this bacterium does not contain cmu genes. Isotope fractionation experiments with L. methylohalidivorans suggest that the unknown pathway used by this bacterium for growth with CH3Cl can be differentiated from the cmu pathway. This result opens the prospect that contributions from bacteria with the cmu and Leisingera-type pathways to the atmospheric CH3Cl budget may be teased apart in the future.

  1. Response of Deep Subsurface Microbial Community to Different Carbon Sources and Electron Acceptors during ∼2 months Incubation in Microcosms

    Science.gov (United States)

    Purkamo, Lotta; Bomberg, Malin; Nyyssönen, Mari; Ahonen, Lasse; Kukkonen, Ilmo; Itävaara, Merja

    2017-01-01

    Acetate plays a key role as electron donor and acceptor and serves as carbon source in oligotrophic deep subsurface environments. It can be produced from inorganic carbon by acetogenic microbes or through breakdown of more complex organic matter. Acetate is an important molecule for sulfate reducers that are substantially present in several deep bedrock environments. Aceticlastic methanogens use acetate as an electron donor and/or a carbon source. The goal of this study was to shed light on carbon cycling and competition in microbial communities in fracture fluids of Finnish crystalline bedrock groundwater system. Fracture fluid was anaerobically collected from a fracture zone at 967 m depth of the Outokumpu Deep Drill Hole and amended with acetate, acetate + sulfate, sulfate only or left unamended as a control and incubated up to 68 days. The headspace atmosphere of microcosms consisted of 80% hydrogen and 20% CO2. We studied the changes in the microbial communities with community fingerprinting technique as well as high-throughput 16S rRNA gene amplicon sequencing. The amended microcosms hosted more diverse bacterial communities compared to the intrinsic fracture zone community and the control treatment without amendments. The majority of the bacterial populations enriched with acetate belonged to clostridial hydrogenotrophic thiosulfate reducers and Alphaproteobacteria affiliating with groups earlier found from subsurface and groundwater environments. We detected a slight increase in the number of sulfate reducers after the 68 days of incubation. The microbial community changed significantly during the experiment, but increase in specifically acetate-cycling microbial groups was not observed. PMID:28265265

  2. Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture.

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    Paul A Den Uyl

    Full Text Available Black band disease (BBD is a cyanobacterial-dominated polymicrobial mat that propagates on and migrates across coral surfaces, necrotizing coral tissue. Culture-based laboratory studies have investigated cyanobacteria and heterotrophic bacteria isolated from BBD, but the metabolic potential of various BBD microbial community members and interactions between them remain poorly understood. Here we report genomic insights into the physiological and metabolic potential of the BBD-associated cyanobacterium Geitlerinema sp. BBD 1991 and six associated bacteria that were also present in the non-axenic culture. The essentially complete genome of Geitlerinema sp. BBD 1991 contains a sulfide quinone oxidoreductase gene for oxidation of sulfide, suggesting a mechanism for tolerating the sulfidic conditions of BBD mats. Although the operon for biosynthesis of the cyanotoxin microcystin was surprisingly absent, potential relics were identified. Genomic evidence for mixed-acid fermentation indicates a strategy for energy metabolism under the anaerobic conditions present in BBD during darkness. Fermentation products may supply carbon to BBD heterotrophic bacteria. Among the six associated bacteria in the culture, two are closely related to organisms found in culture-independent studies of diseased corals. Their metabolic pathways for carbon and sulfur cycling, energy metabolism, and mechanisms for resisting coral defenses suggest adaptations to the coral surface environment and biogeochemical roles within the BBD mat. Polysulfide reductases were identified in a Flammeovirgaceae genome (Bacteroidetes and the sox pathway for sulfur oxidation was found in the genome of a Rhodospirillales bacterium (Alphaproteobacteria, revealing mechanisms for sulfur cycling, which influences virulence of BBD. Each genomic bin possessed a pathway for conserving energy from glycerol degradation, reflecting adaptations to the glycerol-rich coral environment. The presence of genes

  3. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing.

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    Özgül Inceoğlu

    Full Text Available BACKGROUND: Plants selectively attract particular soil microorganisms, in particular consumers of root-excreted compounds. It is unclear to what extent cultivar type and/or growth stage affect this process. METHODOLOGY/PRINCIPAL FINDINGS: DNA-based pyrosequencing was used to characterize the structure of bacterial communities in a field cropped with potato. The rhizospheres of six cultivars denoted Aveka, Aventra, Karnico, Modena, Premiere and Desiree, at three growth stages (young, flowering and senescence were examined, in addition to corresponding bulk soils. Around 350,000 sequences were obtained (5,700 to 38,000 per sample. Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species. Grouping of the sequences showed that members of the Actinobacteria, Alphaproteobacteria, next to as-yet-unclassified bacteria, dominated. Other groups that were consistently found, albeit at lower abundance, were Beta-, Gamma- and Deltaproteobacteria and Acidobacteria. Principal components analyses revealed that rhizosphere samples were significantly different from corresponding bulk soil in each growth stage. Furthermore, cultivar effects were found in the young plant stage, whereas these became insignificant in the flowering and senescence stages. Besides, an effect of time of season was observed for both rhizosphere and bulk soils. The analyzed rhizosphere samples of the potato cultivars were grouped into two groups, in accordance with the allocation of carbon to starch in their tubers, i.e. Aveka, Aventra and Karnico (high versus Premiere and Desiree (low and thus replicates per group were established. CONCLUSIONS: Across all potato cultivars, the young plant stages revealed cultivar-dependent bacterial community structures, which disappeared in the flowering and senescence stages. Furthermore, Pseudomonas, Beta-, Alpha- and

  4. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti

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    Jänicke Sebastian

    2010-04-01

    Full Text Available Abstract Background Small untranslated RNAs (sRNAs are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti applying deep sequencing of cDNAs and microarray hybridizations. Results A total of 1,125 sRNA candidates that were classified as trans-encoded sRNAs (173, cis-encoded antisense sRNAs (117, mRNA leader transcripts (379, and sense sRNAs overlapping coding regions (456 were identified in a size range of 50 to 348 nucleotides. Among these were transcripts corresponding to 82 previously reported sRNA candidates. Enrichment for RNAs with primary 5'-ends prior to sequencing of cDNAs suggested transcriptional start sites corresponding to 466 predicted sRNA regions. The consensus σ70 promoter motif CTTGAC-N17-CTATAT was found upstream of 101 sRNA candidates. Expression patterns derived from microarray hybridizations provided further information on conditions of expression of a number of sRNA candidates. Furthermore, GenBank, EMBL, DDBJ, PDB, and Rfam databases were searched for homologs of the sRNA candidates identified in this study. Searching Rfam family models with over 1,000 sRNA candidates, re-discovered only those sequences from S. meliloti already known and stored in Rfam, whereas BLAST searches suggested a number of homologs in related alpha-proteobacteria. Conclusions The screening data suggests that in S. meliloti about 3% of the genes encode trans-encoded sRNAs and about 2% antisense transcripts. Thus, this first comprehensive screen for sRNAs applying deep sequencing in an alpha-proteobacterium shows that sRNAs also occur in high number in this group of bacteria.

  5. The tRNAarg gene and engA are essential genes on the 1.7-Mb pSymB megaplasmid of Sinorhizobium meliloti and were translocated together from the chromosome in an ancestral strain.

    Science.gov (United States)

    diCenzo, George; Milunovic, Branislava; Cheng, Jiujun; Finan, Turlough M

    2013-01-01

    Bacterial genomes with two (or more) chromosome-like replicons are known, and these appear to be particularly frequent in alphaproteobacteria. The genome of the N(2)-fixing alfalfa symbiont Sinorhizobium meliloti 1021 contains a 3.7-Mb chromosome and 1.4-Mb (pSymA) and 1.7-Mb (pSymB) megaplasmids. In this study, the tRNA(arg) and engA genes, located on the pSymB megaplasmid, are shown to be essential for growth. These genes could be deleted from pSymB when copies were previously integrated into the chromosome. However, in the closely related strain Sinorhizobium fredii NGR234, the tRNA(arg) and engA genes are located on the chromosome, in a 69-kb region designated the engA-tRNA(arg)-rmlC region. This region includes bacA, a gene that is important for intracellular survival during host-bacterium interactions for S. meliloti and the related alphaproteobacterium Brucella abortus. The engA-tRNA(arg)-rmlC region lies between the kdgK and dppF2 (NGR_c24410) genes on the S. fredii chromosome. Synteny analysis showed that kdgK and dppF2 orthologues are adjacent to each other on the chromosomes of 15 sequenced strains of S. meliloti and Sinorhizobium medicae, whereas the 69-kb engA-tRNA(arg)-rmlC region is present on the pSymB-equivalent megaplasmids. This and other evidence strongly suggests that the engA-tRNA(arg)-rmlC region translocated from the chromosome to the progenitor of pSymB in an ancestor common to S. meliloti and S. medicae. To our knowledge, this work represents one of the first experimental demonstrations that essential genes are present on a megaplasmid.

  6. Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255

    Energy Technology Data Exchange (ETDEWEB)

    Hauser, Loren John [ORNL; Land, Miriam L [ORNL; Larimer, Frank W [ORNL; Arp, D J [Oregon State University; Hickey, W J [University of Wisconsin, Madison

    2006-03-01

    The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.

  7. Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales.

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    Mary Ellen Heavner

    Full Text Available Both bacterial symbionts and pathogens rely on their host-sensing mechanisms to activate the biosynthetic pathways necessary for their invasion into host cells. The Gram-negative bacterium Sinorhizobium meliloti relies on its RSI (ExoR-ExoS-ChvI Invasion Switch to turn on the production of succinoglycan, an exopolysaccharide required for its host invasion. Recent whole-genome sequencing efforts have uncovered putative components of RSI-like invasion switches in many other symbiotic and pathogenic bacteria. To explore the possibility of the existence of a common invasion switch, we have conducted a phylogenomic survey of orthologous ExoR, ExoS, and ChvI tripartite sets in more than ninety proteobacterial genomes. Our analyses suggest that functional orthologs of the RSI invasion switch co-exist in Rhizobiales, an order characterized by numerous invasive species, but not in the order's close relatives. Phylogenomic analyses and reconstruction of orthologous sets of the three proteins in Alphaproteobacteria confirm Rhizobiales-specific gene synteny and congruent RSI evolutionary histories. Evolutionary analyses further revealed site-specific substitutions correlated specifically to either animal-bacteria or plant-bacteria associations. Lineage restricted conservation of any one specialized gene is in itself an indication of species adaptation. However, the orthologous phylogenetic co-occurrence of all interacting partners within this single signaling pathway strongly suggests that the development of the RSI switch was a key adaptive mechanism. The RSI invasion switch, originally found in S. meliloti, is a characteristic of the Rhizobiales, and potentially a conserved crucial activation step that may be targeted to control host invasion by pathogenic bacterial species.

  8. The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington. Community Structural Responses to Seasonal Cycling

    Energy Technology Data Exchange (ETDEWEB)

    Lindemann, Stephen R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Moran, James J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Stegen, James C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Renslow, Ryan S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Cole, Jessica K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dohnalkova, Alice [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Tremblay, Julien [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Singh, Kanwar [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Malfatti, Stephanie [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chen, Feng [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Beyenal, Haluk [Washington State Univ., Pullman, WA (United States); Fredrickson, Jim K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-11-13

    Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring, disassembles each fall, and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO2-4) and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by amplicon sequencing of the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya), and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus). Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium) and Deltaproteobacteria (e.g., Desulfofustis) that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.

  9. Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia

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    Dominik eSchneider

    2015-12-01

    Full Text Available Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use system comprised rubber agroforests (jungle rubber, rubber plantation and oil plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 20,494 bacterial and 1,762 archaeal Operational Taxonomic Units at species level (97% genetic identity. Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to

  10. Metagenomics as a preliminary screen for antimicrobial bioprospecting

    KAUST Repository

    Al Amoudi, Soha

    2016-09-16

    Since the composition of soil directs the diversity of the contained microbiome and its potential to produce bioactive compounds, many studies has been focused on sediment types with unique features characteristic of extreme environments. However, not much is known about the potential of microbiomes that inhabit the highly saline and hot Red Sea lagoons. This case study explores mangrove mud and the microbial mat of sediments collected from the Rabigh harbor lagoon and Al Kharrar lagoon for antimicrobial bioprospecting. Rabigh harbor lagoon appears the better location, and the best sediment type for this purpose is mangrove mud. On the other hand, Al Kharrar lagoon displayed increased anaerobic hydrocarbon degradation and an abundance of bacterial DNA associated with antibiotic resistance. Moreover, our findings show an identical shift in phyla associated with historic hydrocarbon contamination exposure reported in previous studies (that is, enrichment of Gamma-and Delta-proteobacteria), but we also report that bacterial DNA sequences associated with antibiotic synthesis enzymes are derived from Gamma-, Delta-and Alpha-proteobacteria. This suggests that selection pressure associated with hydrocarbon contamination tend to enrich the bacterial classes DNA associated with antibiotic synthesis enzymes. Although Actinobacteria tends to be the common target for research when it comes to antimicrobial bioprospecting, our study suggests that Firmicutes (Bacilli and Clostridia), Bacteroidetes, Cyanobacteria, and Proteobacteria should be antimicrobial bioprospecting targets as well. To the best of our knowledge, this is the first metagenomic study that analyzed the microbiomes in Red Sea lagoons for antimicrobial bioprospecting. (C) 2016 The Authors. Published by Elsevier B.V.

  11. Prospect, isolation, and characterization of microorganisms for potential use in cases of oil bioremediation along the coast of Trindade Island, Brazil.

    Science.gov (United States)

    Rodrigues, Edmo M; Kalks, Karlos H M; Tótola, Marcos R

    2015-06-01

    In the present study, acrylic coupons with a thin layer of oil on the surface were incubated in the coastal water of Trindade Island, Brazil, for 60 days. The microorganisms adhered to the coupons were isolated using enrichment medium with hexadecane and naphthalene as the sole carbon and energy source. A total of 15 bacterial isolates were obtained, and the ability of these isolates to use different hydrocarbons as the source of carbon and energy was investigated. None of the isolates produced biosurfactants under our experimental conditions. Subsequently, identification methods such as partial sequencing of the 16S rRNA gene and analysis of fatty acids (MIDI) profile were employed. Among the 15 isolates, representatives of Actinobacteria, Firmicutes, and Alphaproteobacteria were detected. The isolates Rhodococcus rhodochrous TRN7 and Nocardia farcinica TRH1 were able to use all the hydrocarbons added to the culture medium (toluene, octane, xylene, naphthalene, phenanthrene, pyrene, hexadecane, anthracene, eicosane, tetracosane, triacontane, and pentacontane). Polymerase chain reaction amplification of the DNA isolated by employing primers for catechol 2,3-dioxygenase, alkane dehydrogenase and the alpha subunit of hydroxylating dioxygenases polycyclic aromatic hydrocarbon rings genes demonstrated that various isolates capable of utilizing hydrocarbons do not exhibit genes of known routes of catabolism, suggesting the existence of unknown catabolic pathways in these microorganisms. Our findings suggest that the microbiota associated to the coast of tropical oceanic islands has the ability to assist in environmental regeneration in cases of accidents involving oil spills in its shore. Thus, it motivates studies to map bioremediation strategies using the autochthonous microbiota from these environments.

  12. Spatial and temporal dynamics of microbial communities in a human-perturbed estuary of China

    Science.gov (United States)

    Hu, A.; Yu, C. P.; Hou, L.

    2015-12-01

    Estuaries are responsible for the transport and transformation of nutrients and organic matters from the continent to the adjacent coastal zone, and therefore play critical roles in global biogeochemical cycles. They are under increasing stress from human activities, especially in China, yet we still know little about the responses of microbial communities that mediate biogeochemical processes. Here, we investigated planktonic and benthic microbial communities in the human-perturbed Jiulong River estuary (JRE), southern China by using Illumina 16S ribosomal RNA amplicon sequencing. The results of taxonomic assignments indicated that Beta- (23.32%), Alpha- (22.21%), Gammaproteobacteria (14.83%), Actinobacteria (8.67%), and Flavobacteria (7.56%) were the five most abundant classes in estuarine surface waters, while benthic microbial communities were dominated by Gamma- (20.09%), Delta- (14.68%), Beta- (9.82%), Alphaproteobacteria (7.63%), and Anaerolineae (7.25%). The results of Adnois and ANOSIM tests confirmed that the compositions of microbial communities from waters and sediments of the JRE were significantly different from each other, and then salinity may be the primary factor controlling spatial distributions of planktonic and benthic microbial communities in this estuary. At the temporal scale, planktonic communities showed a more clear variation pattern. Remarkably, the ratios of Thaumarchaeota (putative ammonia-oxidizing archaea) to Nitrosomonadales (ammonia-oxidizing bacteria) either in water or sediments of the JRE increased from freshwater to marine end, suggesting that bacterial and archaeal nitrifiers occupy low-salinity and high-salinity niches, respectively. The nutrient concentrations and salinity might be the most important factors which are responsible for this niche diversification. Overall, this study shed light on our understanding of the biogeographic patterns and its ecological drivers of estuarine microbial communities.

  13. HISH-SIMS analysis of bacterial uptake of algal-derived carbon in the Río de la Plata estuary.

    Science.gov (United States)

    Alonso, Cecilia; Musat, Niculina; Adam, Birgit; Kuypers, Marcel; Amann, Rudolf

    2012-12-01

    One of the main goals of microbial ecologists is to assess the contribution of distinct bacterial groups to biogeochemical processes, e.g. carbon cycling. Until very recently, it was not possible to quantify the uptake of a given compound at single cell level. The advent of nano-scale secondary-ion mass spectrometry (nanoSIMS), and its combination with halogen in situ hybridization (HISH) opened up this possibility. Despite its power, difficulties in cell identification during analysis of environmental samples might render this approach challenging for certain applications. A pilot study, designed to quantify the incorporation of phytoplankton-derived carbon by the main clades of heterotrophic aquatic bacteria (i.e. Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes), is used to exemplify and suggest potential solutions to these technical difficulties. The results obtained indicate that the main aquatic bacterial clades quantitatively differ in the incorporation of algae-derived organic matter. From the methodological point of view, they highlight the importance of the concentration of the target cells, which needs to be sufficient to allow for a rapid mapping under the nanoSIMS. Moreover, when working with highly productive waters, organic and inorganic particles pose a serious problem for cell recognition based on HISH-SIMS. In this work several technical suggestions are presented to minimize the above mentioned difficulties, including alternatives to improve the halogen labeling of the cells and proposing the use of a combination of FISH and HISH along with a mapping system. This approach considerably enhances the reliability of cell identification and the speed of the subsequent nanoSIMS analysis in such complex samples.

  14. Characterization of geographically distinct bacterial communities associated with coral mucus produced by Acropora spp. and Porites spp.

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    McKew, B A; Dumbrell, A J; Daud, S D; Hepburn, L; Thorpe, E; Mogensen, L; Whitby, C

    2012-08-01

    Acropora and Porites corals are important reef builders in the Indo-Pacific and Caribbean. Bacteria associated with mucus produced by Porites spp. and Acropora spp. from Caribbean (Punta Maroma, Mexico) and Indo-Pacific (Hoga and Sampela, Indonesia) reefs were determined. Analysis of pyrosequencing libraries showed that bacterial communities from Caribbean corals were significantly more diverse (H', 3.18 to 4.25) than their Indonesian counterparts (H', 2.54 to 3.25). Dominant taxa were Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Cyanobacteria, which varied in relative abundance between coral genera and region. Distinct coral host-specific communities were also found; for example, Clostridiales were dominant on Acropora spp. (at Hoga and the Mexican Caribbean) compared to Porites spp. and seawater. Within the Gammproteobacteria, Halomonas spp. dominated sequence libraries from Porites spp. (49%) and Acropora spp. (5.6%) from the Mexican Caribbean, compared to the corresponding Indonesian coral libraries (<2%). Interestingly, with the exception of Porites spp. from the Mexican Caribbean, there was also a ubiquity of Psychrobacter spp., which dominated Acropora and Porites libraries from Indonesia and Acropora libraries from the Caribbean. In conclusion, there was a dominance of Halomonas spp. (associated with Acropora and Porites [Mexican Caribbean]), Firmicutes (associated with Acropora [Mexican Caribbean] and with Acropora and Porites [Hoga]), and Cyanobacteria (associated with Acropora and Porites [Hoga] and Porites [Sampela]). This is also the first report describing geographically distinct Psychrobacter spp. associated with coral mucus. In addition, the predominance of Clostridiales associated with Acropora spp. provided additional evidence for coral host-specific microorganisms.

  15. Abundance and single-cell activity of heterotrophic bacterial groups in the western Arctic Ocean in summer and winter.

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    Nikrad, Mrinalini P; Cottrell, M T; Kirchman, D L

    2012-04-01

    Environmental conditions in the western Arctic Ocean range from constant light and nutrient depletion in summer to complete darkness and sea ice cover in winter. This seasonal environmental variation is likely to have an effect on the use of dissolved organic matter (DOM) by heterotrophic bacteria in surface water. However, this effect is not well studied and we know little about the activity of specific bacterial clades in the surface oceans. The use of DOM by three bacterial subgroups in both winter and summer was examined by microautoradiography combined with fluorescence in situ hybridization. We found selective use of substrates by these groups, although the abundances of Ant4D3 (Antarctic Gammaproteobacteria), Polaribacter (Bacteroidetes), and SAR11 (Alphaproteobacteria) were not different between summer and winter in the Beaufort and Chukchi Seas. The number of cells taking up glucose within all three bacterial groups decreased significantly from summer to winter, while the percentage of cells using leucine did not show a clear pattern between seasons. The uptake of the amino acid mix increased substantially from summer to winter by the Ant4D3 group, although such a large increase in uptake was not seen for the other two groups. Use of glucose by bacteria, but not use of leucine or the amino acid mix, related strongly to inorganic nutrients, chlorophyll a, and other environmental factors. Our results suggest a switch in use of dissolved organic substrates from summer to winter and that the three phylogenetic subgroups examined fill different niches in DOM use in the two seasons.

  16. Going deeper: metagenome of a hadopelagic microbial community.

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    Emiley A Eloe

    Full Text Available The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT. A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional

  17. Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.

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    Julianne L Baron

    Full Text Available Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms.

  18. Phenylobacterium muchangponense sp. nov., isolated from beach soil, and emended description of the genus Phenylobacterium.

    Science.gov (United States)

    Oh, Yong-Sik; Roh, Dong-Hyun

    2012-04-01

    A Gram-staining-negative, non-motile, aerobic bacterium, designated strain A8T, was isolated from the beach soil of Muchangpo, Korea. Cells were rod-shaped (0.5-0.6×0.7-1.3 µm) and colonies were colourless, circular with entire edges and had a glistening surface. The isolate grew optimally at 25-35 °C and did not require NaCl for growth. Strain A8T could not assimilate acetate, DL-lactate, succinate, antipyrine or chloridazon, but weakly assimilated L-phenylalanine. Major fatty acids were summed feature 7 (comprising C18:1ω7c/ω9t/ω12t), C16:0 and summed feature 4 (comprising C16:1ω7c/ iso-C15:0 2-OH). The major isoprenoid quinone was ubiquinone-10 and the DNA G+C content was 72.3 mol%. Comparative 16S rRNA gene sequence studies showed that strain A8T belonged to the family Caulobacteraceae, class Alphaproteobacteria and was most closely related to type strains of members of the genus Phenylobacterium (95.7-97.1 % similarity). Signature nucleotides and phylogenetic analysis of the 16S rRNA gene sequence also suggested that strain A8T was affiliated with the genus Phenylobacterium. Low DNA-DNA relatedness values (3.0±1.8-11.5±3.2 %) indicated that strain A8T represented a distinct species that was separated from other type strains in the genus Phenylobacterium. On the basis of evidence from a polyphasic study, it is proposed that strain A8T (=KACC 15042T=LMG 25973T) represents the type strain of a novel species, Phenylobacterium muchangponense sp. nov. An emended description of the genus Phenylobacterium is also presented.

  19. Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.

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    James R White

    Full Text Available BACKGROUND: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge "holobiont" system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown. METHODOLOGY/PRINCIPAL FINDINGS: We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs. Approximately 65,550 rRNA sequences (24% could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa, and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described. CONCLUSIONS/SIGNIFICANCE: Slight shifts in several bacterial taxa

  20. Effect of biostimulation using sewage sludge, soybean meal and wheat straw on oil degradation and bacterial community composition in a contaminated desert soil

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    Sumaiya eAl-Kindi

    2016-03-01

    Full Text Available Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO2 and by using gas chromatography-mass spectrometry (GC-MS, shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities more than the addition of soybean meal. GC-MS analysis revealed that the addition of addition of sewage sludge and wheat straw resulted in 1.7 to 1.8 fold increase in the degraded C14 to C30 alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥ 90% of the C14 to C30 alkanes were measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5-86.4% of total sequences of acquired sequences from the original soil belonged to Alphaproteobacteria, Gammaproteobacteria and Firmicutes. Multivariate analysis of operational taxonomic units (OTUs placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R=0.66, P=0.0001. The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95-98% of the total sequences belonging to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils.

  1. Genomic and functional characterization of the modular broad-host-range RA3 plasmid, the archetype of the IncU group.

    Science.gov (United States)

    Kulinska, Anna; Czeredys, Magdalena; Hayes, Finbarr; Jagura-Burdzy, Grazyna

    2008-07-01

    IncU plasmids are a distinctive group of mobile elements with highly conserved backbone functions and variable antibiotic resistance gene cassettes. The IncU archetype is conjugative plasmid RA3, whose sequence (45,909 bp) shows it to be a mosaic, modular replicon with a class I integron different from that of other IncU replicons. Functional analysis demonstrated that RA3 possesses a broad host range and can efficiently self-transfer, replicate, and be maintained stably in alpha-, beta-, and gammaproteobacteria. RA3 contains 50 open reading frames clustered in distinct functional modules. The replication module encompasses the repA and repB genes embedded in long repetitive sequences. RepA, which is homologous to antitoxin proteins from alpha- and gammaproteobacteria, contains a Cro/cI-type DNA-binding domain present in the XRE family of transcriptional regulators. The repA promoter is repressed by RepA and RepB. The minireplicon encompasses repB and the downstream repetitive sequence r1/r2. RepB shows up to 80% similarity to putative replication initiation proteins from environmental plasmids of beta- and gammaproteobacteria, as well as similarity to replication proteins from alphaproteobacteria and Firmicutes. Stable maintenance functions of RA3 are most like those of IncP-1 broad-host-range plasmids and comprise the active partitioning apparatus formed by IncC (ParA) and KorB (ParB), the antirestriction protein KlcA, and accessory stability components KfrA and KfrC. The RA3 origin of transfer was localized experimentally between the maintenance and conjugative-transfer operons. The putative conjugative-transfer module is highly similar in organization and in its products to transfer regions of certain broad-host-range environmental plasmids.

  2. Bacterial communities associated with biofouling materials used in bench-scale hydrocarbon bioremediation.

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    Al-Mailem, Dina; Kansour, Mayada; Radwan, Samir

    2015-03-01

    Biofouling material samples from the Arabian (Persian) Gulf, used as inocula in batch cultures, brought about crude oil and pure-hydrocarbon removal in a mineral medium. Without any added nitrogen fertilizers, the hydrocarbon-removal values were between about 10 and 50 %. Fertilization with NaNO3 alone or together with a mixture of the vitamins thiamine, pyridoxine, vitamin B12, biotin, riboflavin, and folic acid increased the hydrocarbon-removal values, to reach 90 %. Biofouling material samples harbored total bacteria in the magnitude of 10(7) cells g(-1), about 25 % of which were hydrocarbonoclastic. These numbers were enhanced by NaNO3 and vitamin amendment. The culture-independent analysis of the total bacterioflora revealed the predominance of the gammaproteobacterial genera Marinobacter, Acinetobacter, and Alcanivorax, the Flavobacteriia, Flavobacterium, Gaetbulibacter, and Owenweeksia, and the Alphaproteobacteria Tistrella, Zavarzinia, and others. Most of those bacteria are hydrocarbonoclastic. Culture-dependent analysis of hydrocarbonoclastic bacteria revealed that Marinobacter hydrocarbonoclasticus, Dietzia maris, and Gordonia bronchialis predominated in the fouling materials. In addition, each material had several more-specific hydrocarbonoclastic species, whose frequencies were enhanced by NaNO3 and vitamin fertilization. The same samples of fouling materials were used in four successive crude-oil-removal cycles without any dramatic loss of their hydrocarbon-removal potential nor of their associated hydrocarbonoclastic bacteria. In the fifth cycle, the oil-removal value was reduced by about 50 % in only one of the studied samples. This highlights how firmly biofouling materials were immobilizing the hydrocarbonoclastic bacteria.

  3. Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils.

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    Etienne Yergeau

    Full Text Available As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0 and one month after the start of the bioremediation treatment (t = 1m, when degradation rates were at their highest, but decreased after one year (t = 1y, when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons.

  4. Spatial distribution of microbial communities associated with dune landform in the Gurbantunggut Desert, China.

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    Liu, Ruyin; Li, Ke; Zhang, Hongxun; Zhu, Junge; Joshi, DevRaj

    2014-11-01

    The microbial community compositions and potential ammonia oxidation in the topsoil at different positions of sand dune (stoss slope, crest, lee slope, and interdune) from the Gurbantunggut Desert, the largest semi-fixed desert in China, were investigated using several molecular methods. Actinobacteria and Proteobacteria (especially Alphaproteobacteria) were commonly the dominant taxa across all soil samples. Bacterial communities were similar in soils collected from the stoss slopes and interdunes (HC-BSCs, biological soil crusts with a high abundance of cyanobacteria), containing more abundant cyanobacterial populations (16.9-24.5%) than those (0.2-0.7% of Cyanobacteria) in the crests and lee slopes (LC-BSCs, biological soil crusts with a low abundance of cyanobacteria). The Cyanobacteria were mainly composed of Microcoleus spp., and quantitative PCR analysis revealed that 16S rRNA gene copy numbers of Cyanobacteria (especially genus Microcoleus) were at least two orders of magnitude higher in HC-BSCs than in LC-BSCs. Heterotrophic Geodermatophilus spp. frequently occurred in HC-BSCs (2.5-8.0%), whereas genera Arthrobacter, Bacillus, and Segetibacter were significantly abundant in LC-BSC communities. By comparison, the desert archaeal communities were less complex, and were dominated by Nitrososphaera spp. The amoA gene abundance of ammonia-oxidizing archaea (AOA) was higher than that of ammonia-oxidizing bacteria (AOB) in all soil samples, particularly in the interdunal soils (10(6)-10(8) archaeal amoA gene copies per gram dry soil), indicating that AOA possibly dominate the ammonia oxidation at the interdunes.

  5. Identification of Brucella melitensis 16M genes required for bacterial survival in the caprine host.

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    Zygmunt, Michel S; Hagius, Sue D; Walker, Joel V; Elzer, Philip H

    2006-01-01

    Brucella species are gram-negative bacteria which belong to alpha-Proteobacteria family. These organisms are zoonotic pathogens that induce abortion and sterility in domestic mammals and chronic infections in humans known as Malta fever. The virulence of Brucella is dependent upon its ability to enter and colonize the cells in which it multiplies. The genetic basis of this aspect is poorly understood. Signature-tagged mutagenesis (STM) was used to identify potential Brucella virulence factors. PCR amplification has been used in place of DNA hybridization to identify the STM-generated attenuated mutants. A library of 288 Brucella melitensis 16M tagged mini-Tn5 Km2 mutants, in 24 pools, was screened for its ability to colonize spleen, lymph nodes and liver of goats at three weeks post-i.v. infection. This comparative screening identified 7 mutants (approximately 5%) which were not recovered from the output pool in goats. Some genes were known virulence genes involved in biosynthesis of LPS (lpsA gene) or in intracellular survival (the virB operon). Other mutants included ones which had a disrupted gene homologous to flgF, a gene coding for the basal-body rod of the flagellar apparatus, and another with a disruption in a gene homologous to ppk which is involved in the biosynthesis of inorganic polyphosphate (PolyP) from ATP. Other genes identified encoded factors involved in DNA metabolism and oxidoreduction metabolism. Using STM and the caprine host for screening, potential virulence determinants in B. melitensis have been identified.

  6. Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development.

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    Andreote, Fernando D; Mendes, Rodrigo; Dini-Andreote, Francisco; Rossetto, Priscilla B; Labate, Carlos A; Pizzirani-Kleiner, Aline A; van Elsas, Jan Dirck; Azevedo, João L; Araújo, Welington L

    2008-05-01

    The rhizosphere constitutes a complex niche that may be exploited by a wide variety of bacteria. Bacterium-plant interactions in this niche can be influenced by factors such as the expression of heterologous genes in the plant. The objective of this work was to describe the bacterial communities associated with the rhizosphere and rhizoplane regions of tobacco plants, and to compare communities from transgenic tobacco lines (CAB1, CAB2 and TRP) with those found in wild-type (WT) plants. Samples were collected at two stages of plant development, the vegetative and flowering stages (1 and 3 months after germination). The diversity of the culturable microbial community was assessed by isolation and further characterization of isolates by amplified ribosomal RNA gene restriction analysis (ARDRA) and 16S rRNA sequencing. These analyses revealed the presence of fairly common rhizosphere organisms with the main groups Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacilli. Analysis of the total bacterial communities using PCR-DGGE (denaturing gradient gel electrophoresis) revealed that shifts in bacterial communities occurred during early plant development, but the reestablishment of original community structure was observed over time. The effects were smaller in rhizosphere than in rhizoplane samples, where selection of specific bacterial groups by the different plant lines was demonstrated. Clustering patterns and principal components analysis (PCA) were used to distinguish the plant lines according to the fingerprint of their associated bacterial communities. Bands differentially detected in plant lines were found to be affiliated with the genera Pantoea, Bacillus and Burkholderia in WT, CAB and TRP plants, respectively. The data revealed that, although rhizosphere/rhizoplane microbial communities can be affected by the cultivation of transgenic plants, soil resilience may be able to restore the original bacterial diversity after one cycle of plant

  7. Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.

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    Johannes Asplund-Samuelsson

    Full Text Available Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18% were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota. Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  8. Diazotrophic bacterial community variability in a subtropical deep reservoir is correlated with seasonal changes in nitrogen.

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    Wang, Lina; Yu, Zheng; Yang, Jun; Zhou, Jing

    2015-12-01

    Nitrogen-fixing microorganisms (diazotrophs) play important roles in aquatic biogeochemistry and ecosystem functioning. However, little is known about the spatiotemporal variation of diazotrophic microbial communities in deep subtropical reservoirs. In this study, denaturing gradient gel electrophoresis (DGGE), clone libraries, quantitative PCR, and quantitative reverse transcription (RT)-PCR were used together to examine the vertical and seasonal patterns of diazotrophic microbial communities based on nitrogenase (nifH) gene sequences in the Dongzhen Reservoir, China, across time (every 3 months for 1 year) and space (five different water depths). In general, the numbers of DGGE bands increased with water depth during the stratification seasons (spring, summer, and autumn), with the clone-library-based operational taxonomic unit (OTU) number and nifH gene diversity being highest in autumn (6 OTUs at depth 0 m; 15 OTUs at 33 m) and winter (12 OTUs at 0 m, 13 OTUs at 33 m) but decreasing drastically in spring (2 OTUs at 0 m, 3 OTUs at 33 m) and summer (3 OTUs at 0 m, 2 OTUs at 33 m). The nifH gene abundance was lowest in the water mixing season (winter average, 5.17 × 10(7) copies/L) but increased in the three other seasons (9.03 × 10(9) copies/L). Cyanobacteria (dominated by filamentous thermophilic cyanobacteria and Cylindrospermopsis raciborskii) were the most dominant diazotrophic group at all depths and seasons, while both alphaproteobacteria and gammaproteobacteria were co-dominant in the bottom waters in autumn and winter. The distinct seasonal and spatial patterns in diazotrophic communities were significantly related to total nitrogen (TN) and ammonium nitrogen (NH4-N) in the reservoir (P cyanobacteria blooms.

  9. 16S rRNA gene survey of microbial communities in Winogradsky columns.

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    Ethan A Rundell

    Full Text Available A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities.

  10. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

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    Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

    2013-06-01

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

  11. Analysis of virus genomes from glacial environments reveals novel virus groups with unusual host interactions

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    Bellas, Christopher M.; Anesio, Alexandre M.; Barker, Gary

    2015-01-01

    Microbial communities in glacial ecosystems are diverse, active, and subjected to strong viral pressures and infection rates. In this study we analyse putative virus genomes assembled from three dsDNA viromes from cryoconite hole ecosystems of Svalbard and the Greenland Ice Sheet to assess the potential hosts and functional role viruses play in these habitats. We assembled 208 million reads from the virus-size fraction and developed a procedure to select genuine virus scaffolds from cellular contamination. Our curated virus library contained 546 scaffolds up to 230 Kb in length, 54 of which were circular virus consensus genomes. Analysis of virus marker genes revealed a wide range of viruses had been assembled, including bacteriophages, cyanophages, nucleocytoplasmic large DNA viruses and a virophage, with putative hosts identified as Cyanobacteria, Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, eukaryotic algae and amoebae. Whole genome comparisons revealed the majority of circular genome scaffolds (CGS) formed 12 novel groups, two of which contained multiple phage members with plasmid-like properties, including a group of phage-plasmids possessing plasmid-like partition genes and toxin-antitoxin addiction modules to ensure their replication and a satellite phage-plasmid group. Surprisingly we also assembled a phage that not only encoded plasmid partition genes, but a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas adaptive bacterial immune system. One of the spacers was an exact match for another phage in our virome, indicating that in a novel use of the system, the lysogen was potentially capable of conferring immunity on its bacterial host against other phage. Together these results suggest that highly novel and diverse groups of viruses are present in glacial environments, some of which utilize very unusual life strategies and genes to control their replication and maintain a long-term relationship with their hosts

  12. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.

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    Martin Wu

    2004-03-01

    Full Text Available The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for

  13. Microencapsulation by spray drying of nitrogen-fixing bacteria associated with lupin nodules.

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    Campos, Daniela C; Acevedo, Francisca; Morales, Eduardo; Aravena, Javiera; Amiard, Véronique; Jorquera, Milko A; Inostroza, Nitza G; Rubilar, Mónica

    2014-09-01

    Plant growth promoting bacteria and nitrogen-fixing bacteria (NFB) used for crop inoculation have important biotechnological potential as a sustainable fertilization tool. However, the main limitation of this technology is the low inoculum survival rate under field conditions. Microencapsulation of bacterial cells in polymer matrices provides a controlled release and greater protection against environmental conditions. In this context, the aim of this study was to isolate and characterize putative NFB associated with lupin nodules and to evaluate their microencapsulation by spray drying. For this purpose, 21 putative NFB were isolated from lupin nodules and characterized (16S rRNA genes). Microencapsulation of bacterial cells by spray drying was studied using a mixture of sodium alginate:maltodextrin at different ratios (0:15, 1:14, 2:13) and concentrations (15 and 30% solids) as the wall material. The microcapsules were observed under scanning electron microscopy to verify their suitable morphology. Results showed the association between lupin nodules of diverse known NFB and nodule-forming bacteria belonging to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Bacteroidetes. In microencapsulation assays, the 1:14 ratio of sodium alginate:maltodextrin (15% solids) showed the highest cell survival rate (79%), with a microcapsule yield of 27% and spherical microcapsules of 5-50 µm in diameter. In conclusion, diverse putative NFB genera and nodule-forming bacteria are associated with the nodules of lupine plants grown in soils in southern Chile, and their microencapsulation by spray drying using sodium alginate:maltodextrin represents a scalable process to generate a biofertilizer as an alternative to traditional nitrogen fertilization.

  14. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site.

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    Stingl, Ulrich; Tripp, Harry James; Giovannoni, Stephen J

    2007-08-01

    The introduction of high-throughput dilution-to-extinction culturing (HTC) of marine bacterioplankton using sterilized natural sea water as media yielded isolates of many abundant but previously uncultured marine bacterial clades. In early experiments, bacteria from the SAR11 cluster (class Alphaproteobacteria), which are presumed to be the most abundant prokaryotes on earth, were cultured. Although many additional attempts were made, no further strains of the SAR11 clade were obtained. Here, we describe improvements to the HTC technique, which led to the isolation of 17 new SAR11 strains from the Oregon coast and the Sargasso Sea, accounting for 28% and 31% of all isolates in these experiments. Phylogenetic analysis of the internal transcribed spacer (ITS) region showed that the isolates from the Oregon coast represent three different subclusters of SAR11, while isolates from the Sargasso Sea were more uniform and represented a single ITS cluster. A PCR assay proved the presence of proteorhodopsin (PR) in nearly all SAR11 isolates. Analysis of PR amino-acid sequences indicated that isolates from the Oregon coast were tuned to either green or blue light, while PRs from strains obtained from the Sargasso Sea were exclusively tuned to maximum absorbance in the blue. Interestingly, phylogenies based on PR and ITS did not correlate, suggesting lateral gene transfer. In addition to the new SAR11 strains, many novel strains belonging to clusters of previously uncultured or undescribed species of different bacterial phyla, including the first strain of the highly abundant alphaproteobacterial SAR116 clade, were isolated using the modified methods.

  15. Dilution-to-extinction culturing of psychrotolerant planktonic bacteria from permanently ice-covered lakes in the McMurdo Dry Valleys, Antarctica.

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    Stingl, U; Cho, J-C; Foo, W; Vergin, K L; Lanoil, B; Giovannoni, S J

    2008-04-01

    Lakes in the McMurdo Dry Valleys of Antarctica are characterized by a permanent ice cover and little or no anthropogenic influence. Although bacterial cultures have been obtained from these habitats, recent culture-independent studies indicate that the most abundant microbes in these systems are not yet cultivated. By using dilution-to-extinction cultivation methods with sterilized and nutrient-amended lake water as media, we isolated 148 chemotrophic psychrotolerant bacterial cultures from fresh surface water of Lake Fryxell and the east lobe of Lake Bonney and the hypersaline, suboxic bottom water from the west lobes of Lake Bonney. Screening of the 16S ribosomal ribonucleic acid (rRNA) genes of the cultures by restriction fragment length polymorphism (RFLP) yielded 57 putatively pure psychrotolerant, slow growing cultures grouped into 18 clusters. The sequencing of 16S rRNA genes of randomly selected representatives of each RFLP cluster revealed that the corresponding isolates belong to the Alphaproteobacteria (six RFLP patterns), Betaproteobacteria (six RFLP patterns), Bacteroidetes (four RFLP patterns), and Actinobacteria (two RFLP patterns). Phylogenetic analysis of the sequences showed that the vast majority of the isolates were not closely related to previously described species. Thirteen of 18 RFLP patterns shared a 16S ribosomal deoxyribonucleic acid sequence similarity of 97% or less with the closest described species, and four isolates had a sequence similarity of 93% or less with the nearest described species. Phylogenetic analysis showed that these sequences were representatives of deeply branching organisms in the respective phylum. A comparison of the isolates with 16S rRNA clone libraries prepared from the same environments showed substantial overlap, indicating that dilution-to-extinction culturing in natural lake water media can help isolate some of the most abundant organisms in these perennially ice-covered lakes.

  16. The Epsomitic Phototrophic Microbial Mat of Hot Lake, Washington: Community Structural Responses to Seasonal Cycling

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    Stephen R Lindemann

    2013-11-01

    Full Text Available Phototrophic microbial mats are compact ecosystems composed of highly interactive organisms in which energy and element cycling take place over millimeter-to-centimeter-scale distances. Although microbial mats are common in hypersaline environments, they have not been extensively characterized in systems dominated by divalent ions. Hot Lake is a meromictic, epsomitic lake that occupies a small, endorheic basin in north-central Washington. The lake harbors a benthic, phototrophic mat that assembles each spring and disassembles each fall and is subject to greater than tenfold variation in salinity (primarily Mg2+ and SO42- and irradiation over the annual cycle. We examined spatiotemporal variation in the mat community at five time points throughout the annual cycle with respect to prevailing physicochemical parameters by sequencing the V4 region of the 16S rRNA gene coupled to near-full-length 16S RNA clone sequences. The composition of these microbial communities was relatively stable over the seasonal cycle and included dominant populations of Cyanobacteria, primarily a group IV cyanobacterium (Leptolyngbya, and Alphaproteobacteria (specifically, members of Rhodobacteraceae and Geminicoccus. Members of Gammaproteobacteria (e.g., Thioalkalivibrio and Halochromatium and Deltaproteobacteria (e.g., Desulfofustis that are likely to be involved in sulfur cycling peaked in summer and declined significantly by mid-fall, mirroring larger trends in mat community richness and evenness. Phylogenetic turnover analysis of abundant phylotypes employing environmental metadata suggests that seasonal shifts in light variability exert a dominant influence on the composition of Hot Lake microbial mat communities. The seasonal development and organization of these structured microbial mats provide opportunities for analysis of the temporal and physical dynamics that feed back to community function.

  17. A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

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    Axmann Ilka M

    2007-10-01

    Full Text Available Abstract Background Non-coding RNAs (ncRNA are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the Prochlorococcus/Synechococcus group of marine cyanobacteria. Results Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of Prochlorococcus, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'. Conclusion Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of E. coli and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.

  18. Forest strata drive spatial structure of bacterial and archaeal communities and microbial methane cycling in neotropical bromeliad wetlands

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    Martinson, Guntars; Brandt, Franziska; Conrad, Ralf

    2016-04-01

    Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that harbors diverse communities of archaea and bacteria and emit substantial amounts of methane. We studied spatial distribution of archaeal and bacterial communities, microbial methane cycling and their environmental drivers in tank bromeliad wetlands. We selected tank bromeliads of different species and functional types (terrestrial and canopy bromeliads) in a neotropical montane forest of Southern Ecuador and sampled the organic tank slurry. Archaeal and bacterial communities were characterized using terminal-restriction fragment length polymorphism (T-RFLP) and Illumina MiSeq sequencing, respectively, and linked with physico-chemical tank-slurry properties. Additionally, we performed tank-slurry incubations to measure methane production potential, stable carbon isotope fractionation and pathway of methane formation. Archaeal and bacterial community composition in bromeliad wetlands was dominated by methanogens and by Alphaproteobacteria, respectively, and did not differ between species but between functional types. Hydrogenotrophic Methanomicrobiales were the dominant methanogens among all bromeliads but the relative abundance of aceticlastic Methanosaetaceae increased in terrestrial bromeliads. Complementary, hydrogenotrophic methanogenesis was the dominant pathway of methane formation but the relative contribution of aceticlastic methanogenesis increased in terrestrial bromeliads and led to a concomitant increase in total methane production. Rhodospirillales were characteristic for canopy bromeliads, Planctomycetales and Actinomycetalis for terrestrial bromeliads. While nitrogen concentration and pH explained 32% of the archaeal community variability, 29% of the bacterial community variability was explained by nitrogen, acetate and propionate concentrations. Our study demonstrates that bromeliad functional types, associated with different forest strata

  19. Microbial community analysis in the roots of aquatic plants and isolation of novel microbes including an organism of the candidate phylum OP10.

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    Tanaka, Yasuhiro; Tamaki, Hideyuki; Matsuzawa, Hiroaki; Nigaya, Masahiro; Mori, Kazuhiro; Kamagata, Yoichi

    2012-01-01

    A number of molecular ecological studies have revealed complex and unique microbial communities in various terrestrial plant roots; however, little is known about the microbial communities of aquatic plant roots in spite of their potential use for water quality improvement in aquatic environments (e.g. floating treatment wetland system). Here, we report the microbial communities inhabiting the roots of emerged plants, reed (Phragmites australis) and Japanese loosestrife (Lythrum anceps), collected from a floating treatment wetland in a pond by both culture-independent and culture-dependent approaches. Culture-independent analysis based on 16S rRNA gene sequences revealed that the microbial compositions between the two aquatic plant roots were clearly different (e.g. the predominant microbe was Betaproteobacteria for reed and Alphaproteobacteria for Japanese loosestrife). In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40-4.26 Shannon-Weiner index) were higher than that of pond water (e.g. 3.15 Shannon-Weiner index). Furthermore, the plant roots harbored 2.5-3.5 times more phylogenetically novel clone phylotypes than pond water. The culture-dependent approach also revealed differences in the microbial composition and diversity among the two plant roots and pond water. More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes) from the plant roots. These findings suggest that aquatic plants roots are significant sources for a variety of novel organisms.

  20. An extracytoplasmic function sigma factor cotranscribed with its cognate anti-sigma factor confers tolerance to NaCl, ethanol and methylene blue in Azospirillum brasilense Sp7.

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    Mishra, Mukti Nath; Kumar, Santosh; Gupta, Namrata; Kaur, Simarjot; Gupta, Ankush; Tripathi, Anil K

    2011-04-01

    Azospirillum brasilense, a plant-growth-promoting rhizobacterium, is exposed to changes in its abiotic environment, including fluctuations in temperature, salinity, osmolarity, oxygen concentration and nutrient concentration, in the rhizosphere and in the soil. Since extra-cytoplasmic function (ECF) sigma factors play an important role in stress adaptation, we analysed the role of ECF sigma factor (also known as RpoE or σ(E)) in abiotic stress tolerance in A. brasilense. An in-frame rpoE deletion mutant of A. brasilense Sp7 was carotenoidless and slow-growing, and was sensitive to salt, ethanol and methylene blue stress. Expression of rpoE in the rpoE deletion mutant complemented the defects in growth, carotenoid biosynthesis and sensitivity to different stresses. Based on data from reverse transcriptase-PCR, a two-hybrid assay and a pull-down assay, we present evidence that rpoE is cotranscribed with chrR and the proteins synthesized from these two overlapping genes interact with each other. Identification of the transcription start site by 5' rapid amplification of cDNA ends showed that the rpoE-chrR operon was transcribed by two promoters. The proximal promoter was less active than the distal promoter, whose consensus sequence was characteristic of RpoE-dependent promoters found in alphaproteobacteria. Whereas the proximal promoter was RpoE-independent and constitutively expressed, the distal promoter was RpoE-dependent and strongly induced in response to stationary phase and elevated levels of ethanol, salt, heat and methylene blue. This study shows the involvement of RpoE in controlling carotenoid synthesis as well as in tolerance to some abiotic stresses in A. brasilense, which might be critical in the adaptation, survival and proliferation of this rhizobacterium in the soil and rhizosphere under stressful conditions.

  1. Contrasting activity patterns determined by BrdU incorporation in bacterial ribotypes from the Arctic Ocean in winter

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    Pierre E Galand

    2013-05-01

    Full Text Available The winter Arctic Ocean is one of the most unexplored marine environments from a microbiological perspective. Heterotrophic bacteria maintain their activity at a baseline level during the extremely low energy conditions of the winter, but little is known about the specific phylotypes that have the potential to survive and grow in such harsh environment. In this study, we aimed at identifying actively growing ribotypes in winter Arctic Ocean seawater cultures by experimental incubations with the thymidine analogue bromodeoxyuridine (BrdU, followed by immunocapturing, terminal restriction fragment length polymorphism (TRFLP fingerprinting, cloning and sequencing the 16S rRNA gene. We incubated water collected at different months over the Arctic winter and showed that the actively growing bacterial fraction, taking up BrdU, represented only a subset of the total community. Among the BrdU-labeled bacterial taxa we identified the Flavobacteria Polaribacter, the Alphaproteobacteria SAR11, the Gammaproteobacteria Arctic 96B-16 cluster and, predominately, members of Colwellia spp. Interestingly, Colwellia sequences formed three clusters (93 and 97% pairwise 16S rRNA identity that contributed in contrasting ways to the active communities in the incubations. Polaribacter, Arctic 96B-16 and one cluster of Colwellia were more abundant in the active community represented by the BrdU labelled DNA. In contrast, SAR11 and two other Colwellia clusters were underrepresented in the BrdU labelled community compared to total communities. Despite the limitation of the long incubations needed to label slow growing arctic communities, the BrdU approach revealed the potential for active growth in low-energy conditions in some relevant groups of polar bacteria, including Polaribacter and Arctic 96B-16. Moreover, under similar incubation conditions, the growth of different Colwellia ribotypes varied, suggesting that related clusters of Colwellia may have distinct

  2. Reconstruction of the core and extended regulons of global transcription factors.

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    Yann S Dufour

    2010-07-01

    Full Text Available The processes underlying the evolution of regulatory networks are unclear. To address this question, we used a comparative genomics approach that takes advantage of the large number of sequenced bacterial genomes to predict conserved and variable members of transcriptional regulatory networks across phylogenetically related organisms. Specifically, we developed a computational method to predict the conserved regulons of transcription factors across alpha-proteobacteria. We focused on the CRP/FNR super-family of transcription factors because it contains several well-characterized members, such as FNR, FixK, and DNR. While FNR, FixK, and DNR are each proposed to regulate different aspects of anaerobic metabolism, they are predicted to recognize very similar DNA target sequences, and they occur in various combinations among individual alpha-proteobacterial species. In this study, the composition of the respective FNR, FixK, or DNR conserved regulons across 87 alpha-proteobacterial species was predicted by comparing the phylogenetic profiles of the regulators with the profiles of putative target genes. The utility of our predictions was evaluated by experimentally characterizing the FnrL regulon (a FNR-type regulator in the alpha-proteobacterium Rhodobacter sphaeroides. Our results show that this approach correctly predicted many regulon members, provided new insights into the biological functions of the respective regulons for these regulators, and suggested models for the evolution of the corresponding transcriptional networks. Our findings also predict that, at least for the FNR-type regulators, there is a core set of target genes conserved across many species. In addition, the members of the so-called extended regulons for the FNR-type regulators vary even among closely related species, possibly reflecting species-specific adaptation to environmental and other factors. The comparative genomics approach we developed is readily applicable to other

  3. Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

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    Lilibeth N Miranda

    Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

  4. Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery

    Science.gov (United States)

    Califano, Gianmaria; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Cox, Cymon J.; Mata, Leonardo; Costa, Rodrigo

    2017-01-01

    As wild fish stocks decline worldwide, land-based fish rearing is likely to be of increasing relevance to feeding future human generations. Little is known about the structure and role of microbial communities in fish aquaculture, particularly at larval developmental stages where the fish microbiome develops and host animals are most susceptible to disease. We employed next-generation sequencing (NGS) of 16S rRNA gene reads amplified from total community DNA to reveal the structure of bacterial communities in a gilthead seabream (Sparus aurata) larviculture system. Early- (2 days after hatching) and late-stage (34 days after hatching) fish larvae presented remarkably divergent bacterial consortia, with the genera Pseudoalteromonas, Marinomonas, Acinetobacter, and Acidocella (besides several unclassified Alphaproteobacteria) dominating the former, and Actinobacillus, Streptococcus, Massilia, Paracoccus, and Pseudomonas being prevalent in the latter. A significant reduction in rearing-water bacterial diversity was observed during the larviculture trial, characterized by higher abundance of the Cryomorphaceae family (Bacteroidetes), known to populate microniches with high organic load, in late-stage rearing water in comparison with early-stage rearing-water. Furthermore, we observed the recruitment, into host tissues, of several bacterial phylotypes—including putative pathogens as well as mutualists—that were detected at negligible densities in rearing-water or in the live feed (i.e., rotifers and artemia). These results suggest that, besides host-driven selective forces, both the live feed and the surrounding rearing environment contribute to shaping the microbiome of farmed gilthead sea-bream larvae, and that a differential establishment of host-associated bacteria takes place during larval development. PMID:28261166

  5. Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil

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    Ana Paula B. Moreira

    2015-10-01

    Full Text Available The aim of this study was to investigate the planktonic and the holobiont Madracis decactis (Scleractinia microbial diversity along a turbulence-driven upwelling event, in the world´s most isolated tropical island, St Peter and St Paul Archipelago (SPSPA, Brazil. Twenty one metagenomes were obtained for seawater (N=12, healthy and bleached holobionts (N=9 before, during and after the episode of high seawater turbulence and upwelling. Microbial assemblages differed between low turbulence-low nutrient (LLR and high-turbulence-high nutrient (HHR regimes in seawater. During LLR there was a balance between autotrophy and heterotrophy in the bacterioplankton and the ratio cyanobacteria:heterotrophs ~1 (C:H. Prochlorales, unclassified Alphaproteobacteria and Euryarchaeota were the dominant bacteria and archaea, respectively. Basic metabolisms and cyanobacterial phages characterized the LLR. During HHR C:H << 0.05 and Gammaproteobacteria approximated 50% of the most abundant organisms in seawater. Alteromonadales, Oceanospirillales and Thaumarchaeota were the dominant bacteria and archaea. Prevailing metabolisms were related to membrane transport, virulence, disease and defense. Phages targeting heterotrophs and virulence factor genes characterized HHR. Shifts were also observed in coral microbiomes, according to both annotation–indepent and -dependent methods. HHR bleached corals metagenomes were the most dissimilar and could be distinguished by their di- and tetranucleotides frequencies, Iron Acquision metabolism and virulence genes, such as V. cholerae-related virulence factors. The healthy coral holobiont was shown to be less sensitive to transient seawater-related perturbations than the diseased animals. A conceptual model for the turbulence-induced shifts is put forward.

  6. Microbial Community Structure of Activated Sludge for Biosolubilization of Two Different Rock Phosphates.

    Science.gov (United States)

    Xiao, Chunqiao; Wu, Xiaoyan; Liu, Tingting; Xu, Guang; Chi, Ruan

    2016-12-16

    A microbial consortium was directly taken from activated sludge and was used to solubilize rock phosphates (RPs) in a lab-scale bioreactor in this study. Results showed that the microbial consortium could efficiently release soluble phosphorus (P) from the RPs, and during 30-day incubation, it grew well in the bioreactor and reduced the pH of the solutions. The biosolubilization process was also illustrated by the observation of scanning electron microscopy combined with an energy dispersive X-ray spectroscopy (SEM-EDX), which showed an obvious corrosion on the ore surfaces, and most elements were removed from the ore samples. The analysis of microbial community structure by Illumina 16S ribosomal RNA (rRNA) gene and 18S rRNA gene MiSeq sequencing reflected different microbial diversity and richness in the solutions added with different ore samples. A lower richness and diversity of bacteria but a higher richness and diversity of fungi occurred in the solution added with ore sample 1 compared to that of in the solution added with ore sample 2. Alphaproteobacteria and Saccharomycetes were the dominating bacterial and fungal group, respectively, both in the solutions added with ore samples 1 and 2 at the class level. However, their abundances in the solution added with ore sample 1 were obviously lower than that in the solution added with ore sample 2. This study provides new insights into our understanding of the microbial community structure in the biosolubilization of RPs by a microbial consortium directly taken from activated sludge.

  7. One carbon metabolism in SAR11 pelagic marine bacteria.

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    Jing Sun

    Full Text Available The SAR11 Alphaproteobacteria are the most abundant heterotrophs in the oceans and are believed to play a major role in mineralizing marine dissolved organic carbon. Their genomes are among the smallest known for free-living heterotrophic cells, raising questions about how they successfully utilize complex organic matter with a limited metabolic repertoire. Here we show that conserved genes in SAR11 subgroup Ia (Candidatus Pelagibacter ubique genomes encode pathways for the oxidation of a variety of one-carbon compounds and methyl functional groups from methylated compounds. These pathways were predicted to produce energy by tetrahydrofolate (THF-mediated oxidation, but not to support the net assimilation of biomass from C1 compounds. Measurements of cellular ATP content and the oxidation of (14C-labeled compounds to (14CO(2 indicated that methanol, formaldehyde, methylamine, and methyl groups from glycine betaine (GBT, trimethylamine (TMA, trimethylamine N-oxide (TMAO, and dimethylsulfoniopropionate (DMSP were oxidized by axenic cultures of the SAR11 strain Ca. P. ubique HTCC1062. Analyses of metagenomic data showed that genes for C1 metabolism occur at a high frequency in natural SAR11 populations. In short term incubations, natural communities of Sargasso Sea microbial plankton expressed a potential for the oxidation of (14C-labeled formate, formaldehyde, methanol and TMAO that was similar to cultured SAR11 cells and, like cultured SAR11 cells, incorporated a much larger percentage of pyruvate and glucose (27-35% than of C1 compounds (2-6% into biomass. Collectively, these genomic, cellular and environmental data show a surprising capacity for demethylation and C1 oxidation in SAR11 cultures and in natural microbial communities dominated by SAR11, and support the conclusion that C1 oxidation might be a significant conduit by which dissolved organic carbon is recycled to CO(2 in the upper ocean.

  8. Diversity of bacteria contaminating paper machines.

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    Lahtinen, Tomi; Kosonen, Mirva; Tiirola, Marja; Vuento, Matti; Oker-Blom, Christian

    2006-09-01

    Formation of microbial biofilms and slimes is a general and serious problem in the operation of paper machines. Studies of microbial populations in paper machine-derived biofilms have been conducted using standard microbiological procedures; however, the bacterial genera present in this type of samples as well as their diversity are quite poorly known. Here, the bacterial diversity of 38 process water and 22 biofilm samples from four different Finnish paper machines were analyzed by length heterogeneity analysis of PCR-amplified 16S ribosomal DNA (LH-PCR). In addition, sequencing of the amplified 16S rRNA gene from 69 clones was conducted for characterization of the bacterial genera present in biofilm and slime samples. The LH-PCR profiles of both the free-living (process waters) and immobilized (biofilms) bacteria were diverse at all stages of the papermaking process. Out of the 69 sequenced clones, 44 belonged to alpha-Proteobacteria, most of which were close to the nitrogen-fixing root nodule genera Sinorhizobium, Rhizobium and Azorhizobium. Other clones were assigned to beta- and gamma-Proteobacteria and the phylum Bacteroidetes. In addition, eight of the clones were assigned to a yet uncultivated phylum, TM7. Finally, epifluorescence microscopy revealed that Gram-negative bacteria were predominant in both the biofilm (65%) and process water (54%) samples and a small coccoid cell morphology was most common in all samples. Together, our results show that the analysis of microbial samples from paper machines using modern molecular biology techniques adds valuable information and should, therefore, be useful as a more specific and sensitive microbiological method for the paper industry. This information could further be applied, e.g., in the development of more specific and environmental friendly antimicrobial agents for paper mills.

  9. Bacterial indicator of agricultural management for soil under no-till crop production.

    Directory of Open Access Journals (Sweden)

    Eva L M Figuerola

    Full Text Available The rise in the world demand for food poses a challenge to our ability to sustain soil fertility and sustainability. The increasing use of no-till agriculture, adopted in many areas of the world as an alternative to conventional farming, may contribute to reduce the erosion of soils and the increase in the soil carbon pool. However, the advantages of no-till agriculture are jeopardized when its use is linked to the expansion of crop monoculture. The aim of this study was to survey bacterial communities to find indicators of soil quality related to contrasting agriculture management in soils under no-till farming. Four sites in production agriculture, with different soil properties, situated across a west-east transect in the most productive region in the Argentinean pampas, were taken as the basis for replication. Working definitions of Good no-till Agricultural Practices (GAP and Poor no-till Agricultural Practices (PAP were adopted for two distinct scenarios in terms of crop rotation, fertilization, agrochemicals use and pest control. Non-cultivated soils nearby the agricultural sites were taken as additional control treatments. Tag-encoded pyrosequencing was used to deeply sample the 16S rRNA gene from bacteria residing in soils corresponding to the three treatments at the four locations. Although bacterial communities as a whole appeared to be structured chiefly by a marked biogeographic provincialism, the distribution of a few taxa was shaped as well by environmental conditions related to agricultural management practices. A statistically supported approach was used to define candidates for management-indicator organisms, subsequently validated using quantitative PCR. We suggest that the ratio between the normalized abundance of a selected group of bacteria within the GP1 group of the phylum Acidobacteria and the genus Rubellimicrobium of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between

  10. Longitudinal Analysis of Microbiota in Microalga Nannochloropsis salina Cultures.

    Science.gov (United States)

    Geng, Haifeng; Sale, Kenneth L; Tran-Gyamfi, Mary Bao; Lane, Todd W; Yu, Eizadora T

    2016-07-01

    Large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded with the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.

  11. Jellyfish modulate bacterial dynamic and community structure.

    Science.gov (United States)

    Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

    2012-01-01

    Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in

  12. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  13. Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Kazakov, Alexey E.; Rodionov, Dmitry A.; Arkin, Adam Paul; Dubchak, Inna; Gelfand, Mikhail S.; Alm, Eric

    2008-10-31

    Bacteria can use branched-chain amino acids (ILV, i.e. isoleucine, leucine, valine) and fatty acids (FA) as sole carbon and energy sources convering ILV into acetyl-CoA, propanoyl-CoA and propionyl-CoA, respectively. In this work, we used the comparative genomic approach to identify candidate transcriptional factors and DNA motifs that control ILV and FA utilization pathways in proteobacteria. The metabolic regulons were characterized based on the identification and comparison of candidate transcription factor binding sites in groups of phylogenetically related genomes. The reconstructed ILV/FA regulatory network demonstrates considerable variability and involves six transcriptional factors from the MerR, TetR and GntR families binding to eleven distinct DNA motifs. The ILV degradation genes in gamma- and beta-proteobacteria are mainly regulated by anovel regulator from the MerR family (e.g., LiuR in Pseudomonas aeruginosa) (40 species), in addition, the TetR-type regulator LiuQ was identified in some beta-proteobacteria (8 species). Besides the core set of ILV utilization genes, the LiuR regulon in some lineages is expanded to include genes from other metabolic pathways, such as the glyoxylate shunt and glutamate synthase in the Shewanella species. The FA degradation genes are controlled by four regulators including FadR in gamma-proteobacteria (34 species), PsrA in gamma- and beta-proteobacteria (45 species), FadP in beta-proteobacteria (14 species), and LiuR orthologs in alpha-proteobacteria (22 species). The remarkable variability of the regulatory systems associated with the FA degradation pathway is discussed from the functional and evolutionary points of view.

  14. Biodegradation of geosmin by a novel Gram-negative bacterium; isolation, phylogenetic characterisation and degradation rate determination.

    Science.gov (United States)

    Hoefel, Daniel; Ho, Lionel; Monis, Paul T; Newcombe, Gayle; Saint, Christopher P

    2009-06-01

    Biologically active sand filters within water treatment plants (WTPs) are now recognised as an effective barrier for the removal of geosmin. However, little is known regarding the actual microbiological processes occurring or the bacteria capable of degrading geosmin. This study reports the enrichment and isolation of a Gram-negative bacterium, Geo48, from the biofilm of a WTP sand filter where the isolate was shown to effectively degrade geosmin individually. Experiments revealed that Geo48 degraded geosmin in a planktonic state by a pseudo-first-order mechanism. Initial geosmin concentrations ranging from 100 to 1000ng/l were shown to directly influence geosmin degradation in reservoir water by Geo48, with rate constants increasing from 0.010h(-1) (R(2)=0.93) to 0.029h(-1) (R(2)=0.97) respectively. Water temperature also influenced degradation of geosmin by Geo48 where temperatures of 11, 22 and 30 degrees C resulted in rate constants of 0.017h(-1) (R(2)=0.98), 0.023h(-1) (R(2)=0.91) and 0.019h(-1) (R(2)=0.85) respectively. Phylogenetic analysis using the 16S rRNA gene of Geo48 revealed it was a member of the Alphaproteobacteria and clustered with 99% bootstrap support with an isolate designated Geo24, a Sphingopyxis sp. previously described as degrading geosmin but only as a member of a bacterial consortium. Of the previously described bacteria, Geo48 was most similar to Sphingopyxis alaskensis (97.2% sequence similarity to a 1454bp fragment of the 16S rRNA gene). To date, this is the only study to report the isolation and characterisation of a Gram-negative bacterium from a biologically active sand filter capable of the sole degradation of geosmin.

  15. Dominance of sphingomonads in a copper-exposed biofilm community for groundwater treatment.

    Science.gov (United States)

    Vílchez, R; Pozo, C; Gómez, M A; Rodelas, B; González-López, J

    2007-02-01

    The structure, biological activity and microbial biodiversity of a biofilm used for the removal of copper from groundwater were studied and compared with those of a biofilm grown under copper-free conditions. A laboratory-scale submerged fixed biofilter was fed with groundwater (2.3 l h(-1)) artificially polluted with Cu(II) (15 mg l(-1)) and amended with sucrose (150 mg l(-1)) as carbon source. Between 73 and 90 % of the Cu(II) was removed from water during long-term operation (over 200 days). The biofilm was a complex ecosystem, consisting of eukaryotic and prokaryotic micro-organisms. Scanning electron microscopy revealed marked structural changes in the biofilm induced by Cu(II), compared to the biofilm grown in absence of the heavy metal. Analysis of cell-bound extracellular polymeric substances (EPS) demonstrated a significant modification of the composition of cell envelopes in response to Cu(II). Transmission electron microscopy and energy-dispersive X-ray microanalysis (EDX) showed that copper bioaccumulated in the EPS matrix by becoming bound to phosphates and/or silicates, whereas copper accumulated only intracytoplasmically in cells of eukaryotic microbes. Cu(II) also decreased sucrose consumption, ATP content and alkaline phosphatase activity of the biofilm. A detailed study of the bacterial community composition was conducted by 16S rRNA-based temperature gradient gel electrophoresis (TGGE) profiling, which showed spatial and temporal stability of the species diversity of copper-exposed biofilms during biofilter operation. PCR reamplification and sequencing of 14 TGGE bands showed the prevalence of alphaproteobacteria, with most sequences (78 %) affiliated to the Sphingomonadaceae. The major cultivable colony type in plate counts of the copper-exposed biofilm was also identified as that of Sphingomonas sp. These data confirm a major role of these organisms in the composition of the Cu(II)-removing community.

  16. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community

    Science.gov (United States)

    Zoccarato, Luca; Celussi, Mauro; Pallavicini, Alberto; Fonda Umani, Serena

    2016-01-01

    Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of

  17. Deciphering the prokaryotic community and metabolisms in South African deep-mine biofilms through antibody microarrays and graph theory.

    Directory of Open Access Journals (Sweden)

    Yolanda Blanco

    Full Text Available In the South African deep mines, a variety of biofilms growing in mine corridor walls as water seeps from intersections or from fractures represents excellent proxies for deep-subsurface environments. However, they may be greatly affected by the oxygen inputs through the galleries of mining activities. As a consequence, the interaction between the anaerobic water coming out from the walls with the oxygen inputs creates new conditions that support rich microbial communities. The inherent difficulties for sampling these delicate habitats, together with transport and storage conditions may alter the community features and composition. Therefore, the development of in situ monitoring methods would be desirable for quick evaluation of the microbial community. In this work, we report the usefulness of an antibody-microarray (EMChip66 immunoassay for a quick check of the microbial diversity of biofilms located at 1.3 km below surface within the Beatrix deep gold mine (South Africa. In addition, a deconvolution method, previously described and used for environmental monitoring, based on graph theory and applied on antibody cross-reactivity was used to interpret the immunoassay results. The results were corroborated and further expanded by 16S rRNA gene sequencing analysis. Both culture-independent techniques coincided in detecting features related to aerobic sulfur-oxidizers, aerobic chemoorganotrophic Alphaproteobacteria and metanotrophic Gammaproteobacteria. 16S rRNA gene sequencing detected phylotypes related to nitrate-reducers and anaerobic sulfur-oxidizers, whereas the EMChip66 detected immunological features from methanogens and sulfate-reducers. The results reveal a diverse microbial community with syntrophic metabolisms both anaerobic (fermentation, methanogenesis, sulphate and nitrate reduction and aerobic (methanotrophy, sulphur oxidation. The presence of oxygen-scavenging microbes might indicate that the system is modified by the artificial

  18. Insights into the Structure and Metabolic Function of Microbes That Shape Pelagic Iron-Rich Aggregates ( Iron Snow )

    Energy Technology Data Exchange (ETDEWEB)

    Lu, S [Friedrich Schiller University Jena, Jena Germany; Chourey, Karuna [ORNL; REICHE, M [Friedrich Schiller University Jena, Jena Germany; Nietzsche, S [Friedrich Schiller University Jena, Jena Germany; Shah, Manesh B [ORNL; Hettich, Robert {Bob} L [ORNL; Kusel, K [Friedrich Schiller University Jena, Jena Germany

    2013-01-01

    Metaproteomics combined with total nucleic acid-based methods aided in deciphering the roles of microorganisms in the formation and transformation of iron-rich macroscopic aggregates (iron snow) formed in the redoxcline of an acidic lignite mine lake. Iron snow had high total bacterial 16S rRNA gene copies, with 2 x 109 copies g (dry wt)-1 in the acidic (pH 3.5) central lake basin and 4 x 1010 copies g (dry wt)-1 in the less acidic (pH 5.5) northern lake basin. Active microbial communities in the central basin were dominated by Alphaproteobacteria (36.6%) and Actinobacteria (21.4%), and by Betaproteobacteria (36.2%) in the northern basin. Microbial Fe-cycling appeared to be the dominant metabolism in the schwertmannite-rich iron snow, because cloning and qPCR assigned up to 61% of active bacteria as Fe-cycling bacteria (FeB). Metaproteomics revealed 70 unique proteins from central basin iron snow and 283 unique proteins from 43 genera from northern basin. Protein identification provided a glimpse into in situ processes, such as primary production, motility, metabolism of acidophilic FeB, and survival strategies of neutrophilic FeB. Expression of carboxysome shell proteins and RubisCO indicated active CO2 fixation by Fe(II) oxidizers. Flagellar proteins from heterotrophs indicated their activity to reach and attach surfaces. Gas vesicle proteins related to CO2-fixing Chlorobium suggested that microbes could influence iron snow sinking. We suggest that iron snow formed by autotrophs in the redoxcline acts as a microbial parachute, since it is colonized by motile heterotrophs during sinking which start to dissolve schwertmannite.

  19. Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways

    Directory of Open Access Journals (Sweden)

    Wagner-Döbler Irene

    2004-09-01

    Full Text Available Abstract Background Quorum sensing is a process of bacterial cell-to-cell communication involving the production and detection of extracellular signaling molecules called autoinducers. Recently, it has been proposed that autoinducer-2 (AI-2, a furanosyl borate diester derived from the recycling of S-adenosyl-homocysteine (SAH to homocysteine, serves as a universal signal for interspecies communication. Results In this study, 138 completed genomes were examined for the genes involved in the synthesis and detection of AI-2. Except for some symbionts and parasites, all organisms have a pathway to recycle SAH, either using a two-step enzymatic conversion by the Pfs and LuxS enzymes or a one-step conversion using SAH-hydrolase (SahH. 51 organisms including most Gamma-, Beta-, and Epsilonproteobacteria, and Firmicutes possess the Pfs-LuxS pathway, while Archaea, Eukarya, Alphaproteobacteria, Actinobacteria and Cyanobacteria prefer the SahH pathway. In all 138 organisms, only the three Vibrio strains had strong, bidirectional matches to the periplasmic AI-2 binding protein LuxP and the central signal relay protein LuxU. The initial two-component sensor kinase protein LuxQ, and the terminal response regulator luxO are found in most Proteobacteria, as well as in some Firmicutes, often in several copies. Conclusions The genomic analysis indicates that the LuxS enzyme required for AI-2 synthesis is widespread in bacteria, while the periplasmic binding protein LuxP is only present in Vibrio strains. Thus, other organisms may either use components different from the AI-2 signal transduction system of Vibrio strains to sense the signal of AI-2, or they do not have such a quorum sensing system at all.

  20. New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria

    Directory of Open Access Journals (Sweden)

    Baldo Laura

    2007-06-01

    Full Text Available Abstract Background The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori. Identifying the ori of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria. Results Using features that have been previously experimentally verified in the alpha-Proteobacterium Caulobacter crescentus, the origin of DNA replication (ori regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori boundary genes were found to be hemE and COG1253 protein (CBS domain protein. Comparisons of the putative ori region among related Wolbachia strains showed higher conservation of bases within binding sites. Conclusion The sequences of the ori regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the ori regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the ori region in genome sequencing projects.

  1. A structural model of anti-anti-[sigma] inhibition by a two-component receiver domain: the PhyR stress response regulator

    Energy Technology Data Exchange (ETDEWEB)

    Herrou, Julien; Foreman, Robert; Fiebig, Aretha; Crosson, Sean (UC)

    2012-05-09

    PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Direct intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.

  2. A structural model of anti-anti-[sigma];#963; inhibition by a two-component receiver domain: the PhyR stress response regulator

    Energy Technology Data Exchange (ETDEWEB)

    Herrou, Julien; Foreman, Robert; Fiebig, Aretha; Crosson, Sean (UC)

    2012-03-30

    PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Direct intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.

  3. Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings.

    Science.gov (United States)

    Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng; Huang, Li-Nan

    2014-06-01

    Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions.

  4. Roseomonas aestuarii sp. nov., a bacteriochlorophyll-a containing alphaproteobacterium isolated from an estuarine habitat of India.

    Science.gov (United States)

    Venkata Ramana, V; Sasikala, Ch; Takaichi, S; Ramana, Ch V

    2010-06-01

    Two strains (JC17(T) and JC19a) of orange pigmented bacteria were isolated from an estuarine sample. Cells of both the strains were Gram-negative coccobacilli, non-motile, non-spore forming and strictly aerobic. Chemo-organoheterotrophy was the growth mode for both strains and was possible on a wide range of organic compounds. Strains were non-hemolytic and contained low levels of BChl-a and carotenoids. The fatty acids (>1.0%) comprised C(18:1)omega7c, C(16:1)omega7c/iso-C(15:0)2OH, C(16:0), C(16:0) 3-OH, C(18:1)2OH, C(16:1)omega5c, and C(19:0) cycloomega8c. The genomic DNA G+C content of strain JC17(T) was 66.2mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strains JC17(T) and JC19a had the highest similarity to members of the genus Roseomonas and were closely related to Roseomonas cervicalis CIP104027(T) (96.4%) and Roseomonas ludipueritiae CIP107418(T) (96.3%) of the family Acetobacteraceae within the class Alphaproteobacteria. Strains JC17(T) and JC19a shared 100% 16S rRNA gene sequence similarity, were phenotypically (morphological, physiological, biochemical characters) identical and had closely related genomes (85% DDH). Based on polyphasic taxonomic data, strain JC17(T) is classified as a novel species of the genus Roseomonas for which the name Roseomonas aestuarii sp. nov. is proposed. The type strain is JC17(T) (=CCUG 57456(T) =KCTC 22692(T) =NBRC105654(T)).

  5. Roseomonas pecuniae sp. nov., isolated from the surface of a copper-alloy coin.

    Science.gov (United States)

    Lopes, André; Esp Rito Santo, Christophe; Grass, Gregor; Chung, Ana Paula; Morais, Paula V

    2011-03-01

    Strain N75(T) was isolated from the surface of a copper-alloy 50 Euro cent coin collected from general circulation. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain N75(T) formed a distinct branch within the genus Roseomonas and placed it in the Alphaproteobacteria. Strain N75(T) showed 16S rRNA gene sequence similarities of 92.4-97.1  % to type strains of species of the genus Roseomonas. Strain N75(T) was a Gram-negative, non-spore-forming, non-motile coccoid, with an optimum growth temperature of about 30 °C; the strain did not grow at 5 or 37 °C. Strain N75(T) did not grow in medium containing NaCl. The major respiratory quinone was ubiquinone 10 (Q-10). The major fatty acids were unsaturated C₁₆:₁ω7c/C₁₆:₁ω6c and C₁₈:₁ω7c (around 70 % of the total fatty acids); the third most abundant fatty acid was the hydroxylated C₁₈:₁ 2-OH. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine and an unknown aminolipid. The DNA G+C content was 72.8 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, we conclude that strain N75(T) represents a novel species of the genus Roseomonas, for which we propose the name Roseomonas pecuniae sp. nov. (type strain N75(T) =LMG 25481(T) =CIP 110074(T)).

  6. 相似穿孔线虫伴生细菌群落多样性研究%Community Diversity of Associated Bacteria of Radopholus similis

    Institute of Scientific and Technical Information of China (English)

    郑芬; 符美英; 赵志祥; 陈绵才

    2012-01-01

    [Objective] The paper was to reveal the species abundance of associated bacterial community, and the diversity of its bacteria. [Method ] Through the construction of 16S rDNA cloning library of bacteria, the positive clone was carried out ARDRA analysis, and the phy-logenetic tree was constructed. [Result] OUT (Operational Taxonomic Units) was classified according to sequences similarity of 97% , the constructed 16S rDNA library of bacteria contained 130TUs, belonging to Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria, respectively. The dominant species were Betaproteobacteria, especially Burkholderia was the dominant bacterium. [Conclusion] The diversity of associated bacteria of R. similis was high, and these bacteria may have certain ecological significance to R. similis.%[目的]揭示相似穿孔线虫伴生细菌群落物种丰度及其细菌多样性.[方法]通过构建细菌16S rDNA克隆文库,对阳性克隆进行ARDRA分析和构建系统发育树[结果]依据97%序列相似性划分OTU,构建的细菌16S rDNA文库包含13个OTU,分别属于Alphaproteobacteria、Betaproteobacteria和Gammaproteobacteria,其中优势菌群为Betaproteobacteria,特别是Burkholderia为优势细菌.[结论]相似穿孔线虫的伴生细菌多样性较高,这些细菌可能对相似穿孔线虫具有一定的生态意义.

  7. Enrichment culture and molecular identification of diverse Bartonella species in stray dogs.

    Science.gov (United States)

    Bai, Ying; Kosoy, Michael Y; Boonmar, Sumalee; Sawatwong, Pongpun; Sangmaneedet, Somboon; Peruski, Leonard F

    2010-12-15

    Using pre-enrichment culture in Bartonella alpha-Proteobacteria growth medium (BAPGM) followed by PCR amplification and DNA sequence identification that targeted a fragment of the citrate synthase gene (gltA), we provide evidence of common bartonella infections and diverse Bartonella species in the blood of stray dogs from Bangkok and Khon Kaen, Thailand. The overall prevalence of all Bartonella species was 31.3% (60/192), with 27.9% (31/111) and 35.8% (29/81) in the stray dogs from Bangkok and Khon Kaen, respectively. Phylogenetic analyzes of gltA identified eight species/genotypes of Bartonella in the blood of stray dogs, including B. vinsonii subsp. arupensis, B. elizabethae, B. grahamii, B. quintana, B. taylorii, and three novel genotypes (BK1, KK1 and KK2) possibly representing unique species with ≤ 90.2% similarities to any of the known Bartonella species B. vinsonii subsp. arupensis was the only species detected in dogs from both sites, B. quintana and BK1 were found in the dogs from Bangkok, B. elizabethae, B. taylorii, KK1 and KK2 were found in the dogs from Khon Kaen. We conclude that stray dogs in Thailand are frequently infected with Bartonella species that vary with geographic region. As some Bartonella species detected in the present study are considered pathogenic for humans, stray dogs in Thailand may serve as possible reservoirs for Bartonella causing human illnesses. Further work is needed to determine the role of those newly discovered Bartonella genotypes/species in human and veterinary medicine.

  8. Candidatus Bartonella antechini: a novel Bartonella species detected in fleas and ticks from the yellow-footed antechinus (Antechinus flavipes), an Australian marsupial.

    Science.gov (United States)

    Kaewmongkol, Gunn; Kaewmongkol, Sarawan; Owen, Helen; Fleming, Patricia A; Adams, Peter J; Ryan, Una; Irwin, Peter J; Fenwick, Stanley G

    2011-05-05

    Bartonella are fastidious, Gram-negative, aerobic bacilli belonging to the Alphaproteobacteria group. In the last ten years, the discovery of new Bartonella species from a variety of mammalian hosts, arthropod vectors and geographical areas has increased. More than 20 species of Bartonella have been identified, of which approximately thirteen are associated with disease in humans and animals. Recently, four novel species of Bartonella were isolated from mammalian hosts in Australia: Bartonella australis from eastern grey kangaroos (Macropus giganteus) and Bartonella rattaustraliani, Bartonella queenslandensis and Bartonella coopersplainsensis from rodents. Bartonella-like organisms have also been detected from Ixodes tasmani ticks collected from koalas (Phascolarctos cinereus). However, very little is known about Bartonella spp. in other marsupials in Australia. We report the identification of a novel Bartonella species detected from fleas (Acanthopsylla jordani) and ticks (Ixodes antechini) collected from a small carnivorous marsupial, Antechinus flavipes (Mardos or Yellow-footed antechinus) in the southwest of Western Australia. New nested-PCRs targeting the gltA gene and the ribosomal ITS region were developed as part of the present study. DNA sequencing of the 16S rRNA, gltA, ftsZ and rpoB genes and the ribosomal ITS region revealed that this detection is a distinct Bartonella species and is related to B. australis isolated from kangaroos. This is the first report of two different possible arthropod vectors in Australia (ticks and fleas) being infected with the same species of Bartonella. We propose the name Candidatus Bartonella antechini n. sp. for the recently characterized organism.

  9. Low Diversity Bacterial Community and the Trapping Activity of Metabolites from Cultivable Bacteria Species in the Female Reproductive System of the Oriental Fruit Fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae

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    Hongyu Zhang

    2012-05-01

    Full Text Available Our goal was to identify the bacteria inhabiting the reproductive system of the female oriental fruit fly, Bactrocera dorsalis (Hendel, and evaluate the chemotaxis of B. dorsalis to the metabolites produced by the bacteria. Based on 16S rRNA-based polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE, 18 operational taxonomic units (OTUs were assigned to the five bacterial classes Betaproteobacteria, Alphaproteobacteria, Gammaproteobacteria, Bacilli and Actinobacteria. Nine OTUs were assigned to Gammaproteobacteria, which was the most highly represented class. Enterobacteriaceae constituted the dominant family, and within this family, three genera and five species were identified, including Enterobacter sakazakii, Klebsiella oxytoca, Klebsiella pneumoniae, Raoultella terrigena and Enterobacter amnigenus. In this set, the first two species were the dominant components, and the latter three species were the minor ones. Finally, we found that the metabolites produced by R. terrigena, K. oxytoca and K. pneumoniae were attractive to the B. dorsalis adults, and in field studies, B. dorsalis adults were most attracted to K. oxytoca. Collectively, our results suggest that the female reproductive system plays an important role in the transfer of enterobacteria from the gut to fruit. Our data may prompt the development of a female-targeted population control strategy for this fly.

  10. Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris

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    Pechter, Kieran B.; Gallagher, Larry; Pyles, Harley; Manoil, Colin S.

    2015-01-01

    ABSTRACT Rhodopseudomonas palustris is an alphaproteobacterium that has served as a model organism for studies of photophosphorylation, regulation of nitrogen fixation, production of hydrogen as a biofuel, and anaerobic degradation of aromatic compounds. This bacterium is able to transition between anaerobic photoautotrophic growth, anaerobic photoheterotrophic growth, and aerobic heterotrophic growth. As a starting point to explore the genetic basis for the metabolic versatility of R. palustris, we used transposon mutagenesis and Tn-seq to identify 552 genes as essential for viability in cells growing aerobically on semirich medium. Of these, 323 have essential gene homologs in the alphaproteobacterium Caulobacter crescentus, and 187 have essential gene homologs in Escherichia coli. There were 24 R. palustris genes that were essential for viability under aerobic growth conditions that have low sequence identity but are likely to be functionally homologous to essential E. coli genes. As expected, certain functional categories of essential genes were highly conserved among the three organisms, including translation, ribosome structure and biogenesis, secretion, and lipid metabolism. R. palustris cells divide by budding in which a sessile cell gives rise to a motile swarmer cell. Conserved cell cycle genes required for this developmental process were essential in both C. crescentus and R. palustris. Our results suggest that despite vast differences in lifestyles, members of the alphaproteobacteria have a common set of essential genes that is specific to this group and distinct from that of gammaproteobacteria like E. coli. IMPORTANCE Essential genes in bacteria and other organisms are those absolutely required for viability. Rhodopseudomonas palustris has served as a model organism for studies of anaerobic aromatic compound degradation, hydrogen gas production, nitrogen fixation, and photosynthesis. We used the technique of Tn-seq to determine the essential genes of

  11. Bacterial community characterization and biogeochemistry of sediments from a tropical upwelling system (Cabo Frio, Southeastern Brazil)

    Science.gov (United States)

    Castelo-Branco, R.; Barreiro, A.; Silva, F. S.; Carvalhal-Gomes, S. B. V.; Fontana, L. F.; Mendonça-Filho, J. G.; Vasconcelos, V.

    2016-11-01

    The Cabo Frio Upwelling System is one of the largest and most productive areas in southeastern Brazil. Although it is well-known that bacterial communities play a crucial role in the biogeochemical cycles and food chain of marine ecosystems, little is known regarding the microbial communities in the sediments of this upwelling region. In this research, we address the effect of different hydrological conditions on the biogeochemistry of sediments and the diversity of bacterial communities. Biogeochemistry profiles of sediments from four sampling stations along an inner-outer transect on the continental shelf were evaluated and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments was used to study the bacterial community composition in these sediments. Our sequencing analysis of excised bands identified Alpha- and Gammaproteobacteria, Bacteroidetes and bacteria belonging to the Firmicutes phyla as the phylogenetic groups, indicating the existence of great diversity in these marine sediments. In this multidisciplinary study, the use of multivariate analysis was crucial for understanding how biogeochemical profiles influence bacterial community distribution. A Principal Component Analysis (PCA) indicated that the biogeochemical variables exhibited a clear spatial pattern that is mainly related to hydrological conditions. A Correspondence Analysis (CA) revealed an important association between certain taxonomic groups and specific sampling locations. Canonical Correspondence Analysis (CCA) demonstrated that the biogeochemistry influences the structure of the bacterial community in sediments. Among the bacterial groups identified, the most taxonomically diverse classes (Alphaproteobacteria and Gammaproteobacteria) were found to be distributed regardless of any studied biogeochemical variables influences, whereas other groups responded to biogeochemical conditions which, in turn, were influenced by hydrological conditions. This finding

  12. Bacterial community composition and extracellular enzyme activity in temperate streambed sediment during drying and rewetting.

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    Elisabeth Pohlon

    Full Text Available Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany. Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes

  13. Multivariate and phylogenetic analyses assessing the response of bacterial mat communities from an ancient oligotrophic aquatic ecosystem to different scenarios of long-term environmental disturbance.

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    Pajares, Silvia; Souza, Valeria; Eguiarte, Luis E

    2015-01-01

    Understanding the response of bacterial communities to environmental change is extremely important in predicting the effect of biogeochemical modifications in ecosystem functioning. The Cuatro Cienegas Basin is an ancient oasis in the Mexican Chihuahuan desert that hosts a wide diversity of microbial mats and stromatolites that have survived in extremely oligotrophic pools with nearly constant conditions. However, thus far, the response of these unique microbial communities to long-term environmental disturbances remains unexplored. We therefore studied the compositional stability of these bacterial mat communities by using a replicated (3x) mesocosm experiment: a) Control; b) Fluct: fluctuating temperature; c) 40C: increase to 40 ºC; d) UVplus: artificial increase in UV radiation; and f) UVmin: UV radiation protection. In order to observe the changes in biodiversity, we obtained 16S rRNA gene clone libraries from microbial mats at the end of the experiment (eight months) and analyzed them using multivariate and phylogenetic tools. Sequences were assigned to 13 major lineages, among which Cyanobacteria (38.8%) and Alphaproteobacteria (25.5%) were the most abundant. The less extreme treatments (Control and UVmin) had a more similar composition and distribution of the phylogenetic groups with the natural pools than the most extreme treatments (Fluct, 40C, and UVplus), which showed drastic changes in the community composition and structure, indicating a different community response to each environmental disturbance. An increase in bacterial diversity was found in the UVmin treatment, suggesting that protected environments promote the establishment of complex bacterial communities, while stressful environments reduce diversity and increase the dominance of a few Cyanobacterial OTUs (mainly Leptolyngbya sp) through environmental filtering. Mesocosm experiments using complex bacterial communities, along with multivariate and phylogenetic analyses of molecular data, can

  14. Multivariate and phylogenetic analyses assessing the response of bacterial mat communities from an ancient oligotrophic aquatic ecosystem to different scenarios of long-term environmental disturbance.

    Directory of Open Access Journals (Sweden)

    Silvia Pajares

    Full Text Available Understanding the response of bacterial communities to environmental change is extremely important in predicting the effect of biogeochemical modifications in ecosystem functioning. The Cuatro Cienegas Basin is an ancient oasis in the Mexican Chihuahuan desert that hosts a wide diversity of microbial mats and stromatolites that have survived in extremely oligotrophic pools with nearly constant conditions. However, thus far, the response of these unique microbial communities to long-term environmental disturbances remains unexplored. We therefore studied the compositional stability of these bacterial mat communities by using a replicated (3x mesocosm experiment: a Control; b Fluct: fluctuating temperature; c 40C: increase to 40 ºC; d UVplus: artificial increase in UV radiation; and f UVmin: UV radiation protection. In order to observe the changes in biodiversity, we obtained 16S rRNA gene clone libraries from microbial mats at the end of the experiment (eight months and analyzed them using multivariate and phylogenetic tools. Sequences were assigned to 13 major lineages, among which Cyanobacteria (38.8% and Alphaproteobacteria (25.5% were the most abundant. The less extreme treatments (Control and UVmin had a more similar composition and distribution of the phylogenetic groups with the natural pools than the most extreme treatments (Fluct, 40C, and UVplus, which showed drastic changes in the community composition and structure, indicating a different community response to each environmental disturbance. An increase in bacterial diversity was found in the UVmin treatment, suggesting that protected environments promote the establishment of complex bacterial communities, while stressful environments reduce diversity and increase the dominance of a few Cyanobacterial OTUs (mainly Leptolyngbya sp through environmental filtering. Mesocosm experiments using complex bacterial communities, along with multivariate and phylogenetic analyses of molecular

  15. Phylogenetic diversity and community structure of the symbionts associated with the coralline sponge Astrosclera willeyana of the Great Barrier Reef.

    Science.gov (United States)

    Karlińska-Batres, Klementyna; Wörheide, Gert

    2013-04-01

    The coralline sponge Astrosclera willeyana, considered to be a living representative of the reef-building stromatoporoids of the Mesozoic and the Paleozoic periods, occurs widely throughout the Indo-Pacific oceans. We aimed to examine, for the first time, the phylogenetic diversity of the microbial symbionts associated with A. willeyana using molecular methods and to investigate the spatial variability in the sponge-derived microbial communities of A. willeyana from diverse sites along the Great Barrier Reef (GBR). Both denaturing gradient gel electrophoresis (DGGE) analyses of 12 Astrosclera specimens and sequencing of a 16S rRNA gene clone library, constructed using a specimen of A. willeyana from the Yonge Reef (380 clones), revealed the presence of a complex microbial community with high diversity. An assessment of the 16S rRNA gene sequences to the particular phylogenetic groups showed domination of the Chloroflexi (42 %), followed by the Gammaproteobacteria (14 %), Actinobacteria (11 %), Acidobacteria (8 %), and the Deferribacteres (7 %). Of the microbes that were identified, a further 15 % belonged to the Deltaproteobacteria, Alphaproteobacteria, and Nitrospirae genera. The minor phylogenetic groups Gemmatimonadetes, Spirochaetes, Cyanobacteria, Poribacteria, and the Archaea composed 3 % of the community. Over 94 % of the sequences obtained from A. willeyana grouped together with other sponge- or coral-derived sequences, and of these, 72 % formed, with nearest relatives, 46 sponge-specific or sponge-coral clusters, highlighting the uniqueness of the microbial consortia in sponges. The DGGE results showed clear divisions according to the geographical origin of the samples, indicating closer relationships between the microbial communities with respect to their geographic origin (northern vs. southern GBR).

  16. Elevated seawater temperature causes a microbial shift on crustose coralline algae with implications for the recruitment of coral larvae.

    Science.gov (United States)

    Webster, Nicole S; Soo, Rochelle; Cobb, Rose; Negri, Andrew P

    2011-04-01

    Crustose coralline algae (CCA) are key reef-building primary producers that are known to induce the metamorphosis and recruitment of many species of coral larvae. Reef biofilms (particularly microorganisms associated with CCA) are also important as settlement cues for a variety of marine invertebrates, including corals. If rising sea surface temperatures (SSTs) affect CCA and/or their associated biofilms, this may in turn affect recruitment on coral reefs. Herein, we report that the CCA Neogoniolithon fosliei, and its associated microbial communities do not tolerate SSTs of 32 °C, only 2-4 °C above the mean maximum annual SST. After 7 days at 32 °C, the CCA exhibited clear signs of stress, including bleaching, a reduction in maximum quantum yield (F(v)/F(m)) and a large shift in microbial community structure. This shift at 32 °C involved an increase in Bacteroidetes and a reduction in Alphaproteobacteria, including the loss of the primary strain (with high-sequence similarity to a described coral symbiont). A recovery in F(v)/F(m) was observed in CCA exposed to 31 °C following 7 days of recovery (at 27 °C); however, CCA exposed to 32 °C did not recover during this time as evidenced by the rapid growth of endolithic green algae. A 50% reduction in the ability of N. fosliei to induce coral larval metamorphosis at 32 °C accompanied the changes in microbiology, pigmentation and photophysiology of the CCA. This is the first experimental evidence to demonstrate how thermal stress influences microbial associations on CCA with subsequent downstream impacts on coral recruitment, which is critical for reef regeneration and recovery from climate-related mortality events.

  17. Microbial diversity in the coralline sponge Vaceletia crypta.

    Science.gov (United States)

    Karlińska-Batres, Klementyna; Wörheide, Gert

    2013-05-01

    Coralline sponges of the genus Vaceletia are regarded as 'living fossils', the only recent members of the so-called 'sphinctozoan-type' sponges that contributed to reef-building during the Palaeozoic and Mesozoic eras. Vaceletia species were thought to be extinct until the discovery of Vaceletia crypta in the 1970s. Here, we used molecular methods to provide first insights into the microbial diversity of these coralline sponges. Both denaturing gradient gel electrophoresis (DGGE) analyses of 19 Vaceletia specimens and the analysis of 427 clones from a bacterial 16S rRNA gene clone library of a specimen of V. crypta from the Great Barrier Reef (Australia) revealed high diversity and a complex composition with a relatively uniform phylogenetic distribution. Only a single archaeal 16S rRNA phylotype was recovered. The most abundant bacteria were the Chloroflexi (35 %). Of the microbial community, 58 % consisted of the Gammaproteobacteria, Gemmatimonadetes, Actinobacteria, Nitrospira, Deltaproteobacteria, Deferribacteres and Acidobacteria, with nearly equal representation. Less abundant members of the microbial community belonged to the Alphaproteobacteria (3 %), as well as to the Poribacteria, Betaproteobacteria, Cyanobacteria, Spirochaetes, Bacteroidetes, Deinococcus-Thermus and Archaea (all together 4 %). Of the established 96 OTUs, 88 % were closely related to other sponge-derived sequences and thereof 71 OTUs fell into sponge- or sponge-coral specific clusters, which underscores that the "living fossil" coralline sponge Vaceletia shares features of its microbial community with other sponges. The DGGE cluster analysis indicated distinct microbial communities in the different growth forms (solitary and colonial) of Vaceletia species.

  18. Two distinct microbial communities revealed in the sponge Cinachyrella

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    Marie Laure Cuvelier

    2014-11-01

    Full Text Available Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes, which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1 with low diversity (Shannon-Weiner index: 3.73 ± 0.22 and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25. Hosts’ 28S rDNA sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences present in low abundance or below detection limits (<0.07% in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5% and 22.4% of SG1 and SG2’s total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.

  19. Bacterial communities from shoreline environments (costa da morte, northwestern Spain) affected by the prestige oil spill.

    Science.gov (United States)

    Alonso-Gutiérrez, Jorge; Figueras, Antonio; Albaigés, Joan; Jiménez, Núria; Viñas, Marc; Solanas, Anna M; Novoa, Beatriz

    2009-06-01

    The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution

  20. Bacterial indicator of agricultural management for soil under no-till crop production.

    Science.gov (United States)

    Figuerola, Eva L M; Guerrero, Leandro D; Rosa, Silvina M; Simonetti, Leandro; Duval, Matías E; Galantini, Juan A; Bedano, José C; Wall, Luis G; Erijman, Leonardo

    2012-01-01

    The rise in the world demand for food poses a challenge to our ability to sustain soil fertility and sustainability. The increasing use of no-till agriculture, adopted in many areas of the world as an alternative to conventional farming, may contribute to reduce the erosion of soils and the increase in the soil carbon pool. However, the advantages of no-till agriculture are jeopardized when its use is linked to the expansion of crop monoculture. The aim of this study was to survey bacterial communities to find indicators of soil quality related to contrasting agriculture management in soils under no-till farming. Four sites in production agriculture, with different soil properties, situated across a west-east transect in the most productive region in the Argentinean pampas, were taken as the basis for replication. Working definitions of Good no-till Agricultural Practices (GAP) and Poor no-till Agricultural Practices (PAP) were adopted for two distinct scenarios in terms of crop rotation, fertilization, agrochemicals use and pest control. Non-cultivated soils nearby the agricultural sites were taken as additional control treatments. Tag-encoded pyrosequencing was used to deeply sample the 16S rRNA gene from bacteria residing in soils corresponding to the three treatments at the four locations. Although bacterial communities as a whole appeared to be structured chiefly by a marked biogeographic provincialism, the distribution of a few taxa was shaped as well by environmental conditions related to agricultural management practices. A statistically supported approach was used to define candidates for management-indicator organisms, subsequently validated using quantitative PCR. We suggest that the ratio between the normalized abundance of a selected group of bacteria within the GP1 group of the phylum Acidobacteria and the genus Rubellimicrobium of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between sustainable vs. non

  1. Changes in bacterial community metabolism and composition during the degradation of dissolved organic matter from the jellyfish Aurelia aurita in a Mediterranean coastal lagoon.

    Science.gov (United States)

    Blanchet, Marine; Pringault, Olivier; Bouvy, Marc; Catala, Philippe; Oriol, Louise; Caparros, Jocelyne; Ortega-Retuerta, Eva; Intertaglia, Laurent; West, Nyree; Agis, Martin; Got, Patrice; Joux, Fabien

    2015-09-01

    Spatial increases and temporal shifts in outbreaks of gelatinous plankton have been observed over the past several decades in many estuarine and coastal ecosystems. The effects of these blooms on marine ecosystem functioning and particularly on the dynamics of the heterotrophic bacteria are still unclear. The response of the bacterial community from a Mediterranean coastal lagoon to the addition of dissolved organic matter (DOM) from the jellyfish Aurelia aurita, corresponding to an enrichment of dissolved organic carbon (DOC) by 1.4, was assessed for 22 days in microcosms (8 l). The high bioavailability of this material led to (i) a rapid mineralization of the DOC and dissolved organic nitrogen from the jellyfish and (ii) the accumulation of high concentrations of ammonium and orthophosphate in the water column. DOM from jellyfish greatly stimulated heterotrophic prokaryotic production and respiration rates during the first 2 days; then, these activities showed a continuous decay until reaching those measured in the control microcosms (lagoon water only) at the end of the experiment. Bacterial growth efficiency remained below 20%, indicating that most of the DOM was respired and a minor part was channeled to biomass production. Changes in bacterial diversity were assessed by tag pyrosequencing of partial bacterial 16S rRNA genes, DNA fingerprints, and a cultivation approach. While bacterial diversity in control microcosms showed little changes during the experiment, the addition of DOM from the jellyfish induced a rapid growth of Pseudoalteromonas and Vibrio species that were isolated. After 9 days, the bacterial community was dominated by Bacteroidetes, which appeared more adapted to metabolize high-molecular-weight DOM. At the end of the experiment, the bacterial community shifted toward a higher proportion of Alphaproteobacteria. Resilience of the bacterial community after the addition of DOM from the jellyfish was higher for metabolic functions than diversity

  2. Metagenomics of the deep Mediterranean, a warm bathypelagic habitat.

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    Ana-Belen Martín-Cuadrado

    Full Text Available BACKGROUND: Metagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. Most marine metagenomic analyses have been nearly exclusively devoted to photic waters. METHODOLOGY/PRINCIPAL FINDINGS: We constructed a metagenomic fosmid library from 3,000 m-deep Mediterranean plankton, which is much warmer (approximately 14 degrees C than waters of similar depth in open oceans (approximately 2 degrees C. We analyzed the library both by phylogenetic screening based on 16S rRNA gene amplification from clone pools and by sequencing both insert extremities of ca. 5,000 fosmids. Genome recruitment strategies showed that the majority of high scoring pairs corresponded to genomes from Rhizobiales within the Alphaproteobacteria, Cenarchaeum symbiosum, Planctomycetes, Acidobacteria, Chloroflexi and Gammaproteobacteria. We have found a community structure similar to that found in the aphotic zone of the Pacific. However, the similarities were significantly higher to the mesopelagic (500-700 m deep in the Pacific than to the single 4000 m deep sample studied at this location. Metabolic genes were mostly related to catabolism, transport and degradation of complex organic molecules, in agreement with a prevalent heterotrophic lifestyle for deep-sea microbes. However, we observed a high percentage of genes encoding dehydrogenases and, among them, cox genes, suggesting that aerobic carbon monoxide oxidation may be important in the deep ocean as an additional energy source. CONCLUSIONS/SIGNIFICANCE: The comparison of metagenomic libraries from the deep Mediterranean and the Pacific ALOHA water column showed that bathypelagic Mediterranean communities resemble more mesopelagic communities in the Pacific, and suggests that, in the absence of light, temperature is a major stratifying factor in the oceanic water column, overriding

  3. Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

    KAUST Repository

    Thompson, Luke R

    2013-05-11

    Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. 2013 The

  4. The effect of surface colour on the formation of marine micro and macrofouling communities

    KAUST Repository

    Dobretsov, Sergey V.

    2013-07-01

    The effect of substratum colour on the formation of micro- and macro fouling communities was investigated. Acrylic tiles, painted either black or white were covered with transparent sheets in order to ensure similar surface properties. All substrata were exposed to biofouling at 1 m depth for 40 d in the Marina Bandar al Rowdha (Muscat, Sea of Oman). Studies were conducted in 2010 over a time course of 5, 10 and 20 d, and in 2012 samples were collected at 7, 14 and 21 d. The densities of bacteria on the black and white substrata were similar with the exception of day 10, when the black substrata had a higher abundance than white ones. Pyrosequencing via 454 of 16S rRNA genes of bacteria from white and black substrata revealed that Alphaproteobacteria and Firmicutes were the dominant groups. SIMPER analysis demonstrated that bacterial phylotypes (uncultured Gammaproteobacteria, Actibacter, Gaetbulicola, Thalassobius and Silicibacter) and the diatoms (Navicula directa, Navicula sp. and Nitzschia sp.) contributed to the dissimilarities between communities developed on white and black substrata. At day 20, the highest amount of chlorophyll a was recorded in biofilms developed on black substrata. SIMPER analysis showed that Folliculina sp., Ulva sp. and Balanus amphitrite were the major macro fouling species that contributed to the dissimilarities between the communities formed on white and black substrata. Higher densities of these species were observed on black tiles. The results emphasise the effect of substratum colour on the formation of micro and macro fouling communities; substratum colour should to be taken into account in future studies. © 2013 Copyright Taylor and Francis Group, LLC.

  5. Isotopically labeled sulfur compounds and synthetic selenium and tellurium analogues to study sulfur metabolism in marine bacteria

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    Nelson L. Brock

    2013-05-01

    Full Text Available Members of the marine Roseobacter clade can degrade dimethylsulfoniopropionate (DMSP via competing pathways releasing either methanethiol (MeSH or dimethyl sulfide (DMS. Deuterium-labeled [2H6]DMSP and the synthetic DMSP analogue dimethyltelluriopropionate (DMTeP were used in feeding experiments with the Roseobacter clade members Phaeobacter gallaeciensis DSM 17395 and Ruegeria pomeroyi DSS-3, and their volatile metabolites were analyzed by closed-loop stripping and solid-phase microextraction coupled to GC–MS. Feeding experiments with [2H6]DMSP resulted in the incorporation of a deuterium label into MeSH and DMS. Knockout of relevant genes from the known DMSP demethylation pathway to MeSH showed in both species a residual production of [2H3]MeSH, suggesting that a second demethylation pathway is active. The role of DMSP degradation pathways for MeSH and DMS formation was further investigated by using the synthetic analogue DMTeP as a probe in feeding experiments with the wild-type strain and knockout mutants. Feeding of DMTeP to the R. pomeroyi knockout mutant resulted in a diminished, but not abolished production of demethylation pathway products. These results further corroborated the proposed second demethylation activity in R. pomeroyi. Isotopically labeled [2H3]methionine and 34SO42−, synthesized from elemental 34S8, were tested to identify alternative sulfur sources besides DMSP for the MeSH production in P. gallaeciensis. Methionine proved to be a viable sulfur source for the MeSH volatiles, whereas incorporation of labeling from sulfate was not observed. Moreover, the utilization of selenite and selenate salts by marine alphaproteobacteria for the production of methylated selenium volatiles was explored and resulted in the production of numerous methaneselenol-derived volatiles via reduction and methylation. The pathway of selenate/selenite reduction, however, proved to be strictly separated from sulfate reduction.

  6. Diversity of Bacteria in the Marine Sponge Aplysina fulva in Brazilian Coastal Waters▿ †

    Science.gov (United States)

    Hardoim, C. C. P.; Costa, R.; Araújo, F. V.; Hajdu, E.; Peixoto, R.; Lins, U.; Rosado, A. S.; van Elsas, J. D.

    2009-01-01

    Microorganisms can account for up to 60% of the fresh weight of marine sponges. Marine sponges have been hypothesized to serve as accumulation spots of particular microbial communities, but it is unknown to what extent these communities are directed by the organism or the site or occur randomly. To address this question, we assessed the composition of specific bacterial communities associated with Aplysina fulva, one of the prevalent sponge species inhabiting Brazilian waters. Specimens of A. fulva and surrounding seawater were collected in triplicate in shallow water at two sites, Caboclo Island and Tartaruga beach, Búzios, Brazil. Total community DNA was extracted from the samples using “direct” and “indirect” approaches. 16S rRNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the total bacterial community and of specific bacterial groups—Pseudomonas and Actinobacteria—revealed that the structure of these assemblages in A. fulva differed drastically from that observed in seawater. The DNA extraction methodology and sampling site were determinative for the composition of actinobacterial communities in A. fulva. However, no such effects could be gleaned from total bacterial and Pseudomonas PCR-DGGE profiles. Bacterial 16S rRNA gene clone libraries constructed from directly and indirectly extracted DNA did not differ significantly with respect to diversity and composition. Altogether, the libraries encompassed 15 bacterial phyla and the candidate division TM7. Clone sequences affiliated with the Cyanobacteria, Chloroflexi, Gamma- and Alphaproteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were, in this order, most abundant. The bacterial communities associated with the A. fulva specimens were distinct and differed from those described in studies of sponge-associated microbiota performed with other sponge species. PMID:19304829

  7. Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators.

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    Cindy H Wu

    Full Text Available BACKGROUND: Microbial communities in aquatic environments are spatially and temporally dynamic due to environmental fluctuations and varied external input sources. A large percentage of the urban watersheds in the United States are affected by fecal pollution, including human pathogens, thus warranting comprehensive monitoring. METHODOLOGY/PRINCIPAL FINDINGS: Using a high-density microarray (PhyloChip, we examined water column bacterial community DNA extracted from two connecting urban watersheds, elucidating variable and stable bacterial subpopulations over a 3-day period and community composition profiles that were distinct to fecal and non-fecal sources. Two approaches were used for indication of fecal influence. The first approach utilized similarity of 503 operational taxonomic units (OTUs common to all fecal samples analyzed in this study with the watershed samples as an index of fecal pollution. A majority of the 503 OTUs were found in the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. The second approach incorporated relative richness of 4 bacterial classes (Bacilli, Bacteroidetes, Clostridia and alpha-proteobacteria found to have the highest variance in fecal and non-fecal samples. The ratio of these 4 classes (BBC:A from the watershed samples demonstrated a trend where bacterial communities from gut and sewage sources had higher ratios than from sources not impacted by fecal material. This trend was also observed in the 124 bacterial communities from previously published and unpublished sequencing or PhyloChip- analyzed studies. CONCLUSIONS/SIGNIFICANCE: This study provided a detailed characterization of bacterial community variability during dry weather across a 3-day period in two urban watersheds. The comparative analysis of watershed community composition resulted in alternative community-based indicators that could be useful for assessing ecosystem health.

  8. Fe-phyllosilicate redox cycling organisms from a redox transition zone in Hanford 300 Area sediments

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    Jason eBenzine

    2013-12-01

    Full Text Available Microorganisms capable of reducing or oxidizing structural iron (Fe in Fe-bearing phyllosilicate minerals were enriched and isolated from a subsurface redox transition zone at the Hanford 300 Area site in eastern Washington, USA. Both conventional and in situ i-chip enrichment strategies were employed. One Fe(III-reducing Geobacter (G. bremensis strain R1, Deltaproteobacteria and six Fe(II phyllosilicate-oxidizing isolates from the Alphaproteobacteria (Bradyrhizobium japonicum strains 22, is5, and in8p8, Betaproteobacteria (Cupriavidus necator strain A5-1, Dechloromonas agitata strain is5, and Actinobacteria (Nocardioides sp. strain in31 were recovered. The G. bremensis isolate grew by oxidizing acetate with the oxidized form of NAu-2 smectite as the electron acceptor. The Fe(II-oxidizers grew by oxidation of chemically reduced smectite as the energy source with nitrate as the electron acceptor. The Bradyrhizobium isolates could also carry out aerobic oxidation of biotite. This is the first report of the recovery of a Fe(II-oxidizing Nocardioides, and to date only one other Fe(II-oxidizing Bradyrhizobium is known. The 16S rRNA gene sequences of the isolates were similar to ones found in clone libraries from Hanford 300 sediments and groundwater, suggesting that such organisms may be present and active in situ. Whole genome sequencing of the isolates is underway, the results of which will enable comparative genomic analysis of mechanisms of extracellular phyllosilicate Fe redox metabolism, and facilitate development of techniques to detect the presence and expression of genes associated with microbial phyllosilicate Fe redox cycling in sediments.

  9. Effects of Elevated Atmospheric CO2 on Microbial Community Structure at the Plant-Soil Interface of Young Beech Trees (Fagus sylvatica L.) Grown at Two Sites with Contrasting Climatic Conditions.

    Science.gov (United States)

    Gschwendtner, Silvia; Leberecht, Martin; Engel, Marion; Kublik, Susanne; Dannenmann, Michael; Polle, Andrea; Schloter, Michael

    2015-05-01

    Soil microbial community responses to elevated atmospheric CO2 concentrations (eCO2) occur mainly indirectly via CO2-induced plant growth stimulation leading to quantitative as well as qualitative changes in rhizodeposition and plant litter. In order to gain insight into short-term, site-specific effects of eCO2 on the microbial community structure at the plant-soil interface, young beech trees (Fagus sylvatica L.) from two opposing mountainous slopes with contrasting climatic conditions were incubated under ambient (360 ppm) CO2 concentrations in a greenhouse. One week before harvest, half of the trees were incubated for 2 days under eCO2 (1,100 ppm) conditions. Shifts in the microbial community structure in the adhering soil as well as in the root rhizosphere complex (RRC) were investigated via TRFLP and 454 pyrosequencing based on 16S ribosomal RNA (rRNA) genes. Multivariate analysis of the community profiles showed clear changes of microbial community structure between plants grown under ambient and elevated CO2 mainly in RRC. Both TRFLP and 454 pyrosequencing showed a significant decrease in the microbial diversity and evenness as a response of CO2 enrichment. While Alphaproteobacteria dominated by Rhizobiales decreased at eCO2, Betaproteobacteria, mainly Burkholderiales, remained unaffected. In contrast, Gammaproteobacteria and Deltaproteobacteria, predominated by Pseudomonadales and Myxococcales, respectively, increased at eCO2. Members of the order Actinomycetales increased, whereas within the phylum Acidobacteria subgroup Gp1 decreased, and the subgroups Gp4 and Gp6 increased under atmospheric CO2 enrichment. Moreover, Planctomycetes and Firmicutes, mainly members of Bacilli, increased under eCO2. Overall, the effect intensity of eCO2 on soil microbial communities was dependent on the distance to the roots. This effect was consistent for all trees under investigation; a site-specific effect of eCO2 in response to the origin of the trees was not observed.

  10. The Prestige oil spill: bacterial community dynamics during a field biostimulation assay.

    Science.gov (United States)

    Jiménez, Núria; Viñas, Marc; Bayona, Josep M; Albaiges, Joan; Solanas, Anna M

    2007-12-01

    A field bioremediation assay using the oleophilic fertilizer S200 was carried out 12 months after the Prestige heavy fuel-oil spill on a beach on the Cantabrian coast (north Spain). This assay showed that S200-enhanced oil degradation, particularly of high-molecular-weight n-alkanes and alkylated PAHs, suggesting an increase in the microbial bioavailability of these compounds. The bacterial community structure was determined by cultivation-independent analysis of polymerase chain reaction-amplified 16S rDNA by denaturing gradient gel electrophoresis. Bacterial community was mainly composed of alpha-Proteobacteria (Rhodobacteriaceae and Sphingomonadaceae). Representatives of gamma-Proteobacteria (Chromatiales, Moraxellaceae, and Halomonadaceae), Bacteroidetes (Flavobacteriaceae), and Actinobacteria group (Nocardiaceae and Corynebacteriaceae) were also found. The addition of the fertilizer led to the appearance of the bacterium Mesonia algae in the early stages, with a narrow range of growth substrates, which has been associated with the common alga Achrosiphonia sonderi. The presence of Mesonia algae may be attributable to the response of the microbial community to the addition of N and P rather than indicating a role in the biodegradation process. The Rhodococcus group appeared in both assay plots, especially at the end of the experiment. It was also found at another site on the Galician coast that had been affected by the same spill. This genus has been associated with the degradation of n-alkanes up to C(36). Taking into account the high content of heavy alkanes in the Prestige fuel, these microorganisms could play a significant role in the degradation of such fuel. A similar bacterial community structure was observed at another site that showed a similar degree of fuel weathering.

  11. Chelatococcus thermostellatus sp. nov., a new thermophile for bioplastic synthesis: comparative phylogenetic and physiological study.

    Science.gov (United States)

    Ibrahim, Mohammad H A; Lebbe, Liesbeth; Willems, Anne; Steinbüchel, Alexander

    2016-12-01

    The poly(3-hydroxybutyrate), PHB, accumulating thermophilic strain MW9(T), isolated from an aerobic organic waste treatment plant, was characterized by detailed physiological and phylogenetic studies. The strain is a Gram-stain-negative, rod shaped, non-spore forming member of Alphaproteobacteria. It shows optimum growth at 50 °C. Based on 16S rRNA gene sequence similarity, the strain together with five very similar isolates, was affiliated to the genus Chelatococcus (Ibrahim et al. in J Appl Microbiol 109:1579-1590, 2010). Rep-PCR genomic fingerprints and partial dnaK gene sequence also revealed that these isolates are very similar, but differ from other Chelatococcus type strains. The major fatty acids were similar to those of other strains of the genus Chelatococcus. DNA-DNA hybridization of strain MW9(T) with Chelatococcus species type strains revealed 11.0-47.7 % relatedness. G+C content of DNA was 67.1 mol%, which is comparable with the other strains of Chelatococcus species. The physiological and phenotypic characteristics of the new strain MW9(T) are sufficient to differentiate it from previously described species in the genus Chelatococcus. Strain MW9(T) is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus thermostellatus is proposed. The type strain is MW9(T) (=LMG 27009(T) = DSM 28244(T)). Compared to known Chelatococcus strains, strain MW9(T) could be a potent candidate for bioplastic production at elevated temperature.

  12. EDTA addition enhances bacterial respiration activities and hydrocarbon degradation in bioaugmented and non-bioaugmented oil-contaminated desert soils.

    Science.gov (United States)

    Al Kharusi, Samiha; Abed, Raeid M M; Dobretsov, Sergey

    2016-03-01

    The low number and activity of hydrocarbon-degrading bacteria and the low solubility and availability of hydrocarbons hamper bioremediation of oil-contaminated soils in arid deserts, thus bioremediation treatments that circumvent these limitations are required. We tested the effect of Ethylenediaminetetraacetic acid (EDTA) addition, at different concentrations (i.e. 0.1, 1 and 10 mM), on bacterial respiration and biodegradation of Arabian light oil in bioaugmented (i.e. with the addition of exogenous alkane-degrading consortium) and non-bioaugmented oil-contaminated desert soils. Post-treatment shifts in the soils' bacterial community structure were monitored using MiSeq sequencing. Bacterial respiration, indicated by the amount of evolved CO2, was highest at 10 mM EDTA in bioaugmented and non-bioaugmented soils, reaching an amount of 2.2 ± 0.08 and 1.6 ± 0.02 mg-CO2 g(-1) after 14 days of incubation, respectively. GC-MS revealed that 91.5% of the C14-C30 alkanes were degraded after 42 days when 10 mM EDTA and the bacterial consortium were added together. MiSeq sequencing showed that 78-91% of retrieved sequences in the original soil belonged to Deinococci, Alphaproteobacteria, Gammaproteobacteia and Bacilli. The same bacterial classes were detected in the 10 mM EDTA-treated soils, however with slight differences in their relative abundances. In the bioaugmented soils, only Alcanivorax sp. MH3 and Parvibaculum sp. MH21 from the exogenous bacterial consortium could survive until the end of the experiment. We conclude that the addition of EDTA at appropriate concentrations could facilitate biodegradation processes by increasing hydrocarbon availability to microbes. The addition of exogenous oil-degrading bacteria along with EDTA could serve as an ideal solution for the decontamination of oil-contaminated desert soils.

  13. Carbon, metals and grain size correlate with bacterial community composition in sediments of a high arsenic aquifer

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    Teresa eLegg

    2012-03-01

    Full Text Available Bacterial communities can exert significant influence on the biogeochemical cycling of arsenic (As. This has globally important implications since As toxicity in drinking water affects the health of millions of people worldwide, including in the Ganges-Brahmaputra Delta region of Bangladesh where geogenic groundwater arsenic concentrations can be more than 10 times the World Health Organization’s limit. Thus, the goal of this research was to investigate patterns in bacterial community composition across environmental gradients in an aquifer with elevated groundwater As concentrations in Araihazar, Bangladesh. We characterized the bacterial community by pyrosequencing 16S rRNA genes from aquifer sediment samples collected at three locations along a groundwater flowpath, at a range of depths between 1.5 and 15 m. We identified significant shifts in bacterial community composition along the groundwater flowpath in the aquifer. In addition, we found that bacterial community structure was significantly related to sediment grain size, and sediment carbon (C, manganese (Mn, and iron (Fe concentrations. Deltaproteobacteria and Chloroflexi were more abundant in silty sediments with higher concentrations of C, Fe, and Mn. By contrast, Alphaproteobacteria and Betaproteobacteria were more abundant in sediments with higher concentrations of sand and Si, and lower concentrations of C and metals. Based on the phylogenetic affiliations of these taxa, these results may indicate a shift to more Fe-, Mn-, and humic substance- reducers in the high C and metal sediments. It is well-documented that C, Mn and Fe may influence the mobility of groundwater arsenic, and it is intriguing that these constituents may also structure the bacterial community.

  14. Bacterial gut symbionts contribute to seed digestion in an omnivorous beetle.

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    Jonathan G Lundgren

    Full Text Available BACKGROUND: Obligate bacterial symbionts alter the diets of host animals in numerous ways, but the ecological roles of facultative bacterial residents that colonize insect guts remain unclear. Carabid beetles are a common group of beneficial insects appreciated for their ability to consume insect prey and seeds, but the contributions of microbes to diet diversification in this and similar groups of facultative granivores are largely unknown. METHODOLOGY AND PRINCIPAL FINDINGS: Using 16S rRNA gene clone libraries and terminal restriction fragment (tRF length polymorphism analyses of these genes, we examined the bacterial communities within the guts of facultatively granivorous, adult Harpalus pensylvanicus (Carabidae, fed one of five dietary treatments: 1 an untreated Field population, 2 Seeds with antibiotics (seeds were from Chenopodium album, 3 Seeds without antibiotics, 4 Prey with antibiotics (prey were Acheta domesticus eggs, and 5 Prey without antibiotics. The number of seeds and prey consumed by each beetle were recorded following treatment. Harpalus pensylvanicus possessed a fairly simple gut community of approximately 3-4 bacterial operational taxonomic units (OTU per beetle that were affiliated with the Gammaproteobacteria, Bacilli, Alphaproteobacteria, and Mollicutes. Bacterial communities of the host varied among the diet and antibiotic treatments. The field population and beetles fed seeds without antibiotics had the closest matching bacterial communities, and the communities in the beetles fed antibiotics were more closely related to each other than to those of the beetles that did not receive antibiotics. Antibiotics reduced and altered the bacterial communities found in the beetle guts. Moreover, beetles fed antibiotics ate fewer seeds, and those beetles that harbored the bacterium Enterococcus faecalis consumed more seeds on average than those lacking this symbiont. CONCLUSIONS/SIGNIFICANCE: We conclude that the relationships

  15. The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs

    Science.gov (United States)

    Scholz, Holger C.; Mühldorfer, Kristin; Shilton, Cathy; Benedict, Suresh; Whatmore, Adrian M.; Blom, Jochen; Eisenberg, Tobias

    2016-01-01

    The genus Brucella comprises various species of both veterinary and human medical importance. All species are genetically highly related to each other, sharing intra-species average nucleotide identities (ANI) of > 99%. Infections occur among various warm-blooded animal species, marine mammals, and humans. Until recently, amphibians had not been recognized as a host for Brucella. In this study, however, we show that novel Brucella species are distributed among exotic frogs worldwide. Comparative recA gene analysis of 36 frog isolates from various continents and different frog species revealed an unexpected high genetic diversity, not observed among classical Brucella species. In phylogenetic reconstructions the isolates consequently formed various clusters and grouped together with atypical more distantly related brucellae, like B. inopinata, strain BO2, and Australian isolates from rodents, some of which were isolated as human pathogens. Of one frog isolate (10RB9215) the genome sequence was determined. Comparative genome analysis of this isolate and the classical Brucella species revealed additional genetic material, absent from classical Brucella species but present in Ochrobactrum, the closest genetic neighbor of Brucella, and in other soil associated genera of the Alphaproteobacteria. The presence of gene clusters encoding for additional metabolic functions, flanked by tRNAs and mobile genetic elements, as well as by bacteriophages is suggestive for a different ecology compared to classical Brucella species. Furthermore it suggests that amphibian isolates may represent a link between free living soil saprophytes and the pathogenic Brucella with a preferred intracellular habitat. We therefore assume that brucellae from frogs have a reservoir in soil and, in contrast to classical brucellae, undergo extensive horizontal gene transfer. PMID:28036367

  16. High Voltage Electrochemiluminescence (ECL) as a New Method for Detection of PAH During Screening for PAH-Degrading Microbial Consortia.

    Science.gov (United States)

    Staninska, Justyna; Szczepaniak, Zuzanna; Staninski, Krzysztof; Czarny, Jakub; Piotrowska-Cyplik, Agnieszka; Nowak, Jacek; Marecik, Roman; Chrzanowski, Łukasz; Cyplik, Paweł

    The search for new bacterial consortia capable of removing PAH from the environment is associated with the need to employ novel, simple, and economically efficient detection methods. A fluorimetric method (FL) as well as high voltage electrochemiluminescence (ECL) on a modified surface of an aluminum electrode were used in order to determine the changes in the concentrations of PAH in the studied aqueous solutions. The ECL signal (the spectrum and emission intensity for a given wavelength) was determined with the use of an apparatus operating in single photon counting mode. The dependency of ECL and FL intensity on the concentration of naphthalene, phenanthrene, and pyrene was linear in the studied concentration range. The biodegradation kinetics of the particular PAH compounds was determined on the basis of the obtained spectroscopic determinations. It has been established that the half-life of naphthalene, phenanthrene, and pyrene at initial concentrations of 50 mg/l (beyond the solubility limit) reached 41, 75, and 130 h, accordingly. Additionally, the possibility of using ECL for rapid determination of the soluble fraction of PAH directly in the aqueous medium has been confirmed. Metagenomic analysis of the gene encoding 16S rRNA was conducted on the basis of V4 hypervariable region of the 16S rRNA gene and allowed to identify 198 species of bacteria that create the S4consortium. The consortium was dominated by Gammaproteobacteria (78.82 %), Flavobacteria (9.25 %), Betaproteobacteria (7.68 %), Sphingobacteria (3.76 %), Alphaproteobacteria (0.42 %), Clostridia (0.04 %), and Bacilli (0.03 %).

  17. Effect of Biostimulation Using Sewage Sludge, Soybean Meal, and Wheat Straw on Oil Degradation and Bacterial Community Composition in a Contaminated Desert Soil

    Science.gov (United States)

    Al-Kindi, Sumaiya; Abed, Raeid M. M.

    2016-01-01

    Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal, and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO2 and by using gas chromatography–mass spectrometry (GC–MS), shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities to reach 3.2–3.4 times higher than in the untreated soil, whereas the addition of soybean meal resulted in an insignificant change in the produced CO2, given the high respiration activities of the soybean meal alone. GC–MS analysis revealed that the addition of sewage sludge and wheat straw resulted in 1.7–1.8 fold increase in the degraded C14 to C30 alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥90% of the C14 to C30 alkanes was measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5–86.4% of total sequences) of acquired sequences from the untreated soil belonged to Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. Multivariate analysis of operational taxonomic units placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R = 0.66, P = 0.0001). The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95–98% of the total sequences were affiliated to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils. PMID:26973618

  18. Metagenome survey of a multispecies and alga-associated biofilm revealed key elements of bacterial-algal interactions in photobioreactors.

    Science.gov (United States)

    Krohn-Molt, Ines; Wemheuer, Bernd; Alawi, Malik; Poehlein, Anja; Güllert, Simon; Schmeisser, Christel; Pommerening-Röser, Andreas; Grundhoff, Adam; Daniel, Rolf; Hanelt, Dieter; Streit, Wolfgang R

    2013-10-01

    Photobioreactors (PBRs) are very attractive for sunlight-driven production of biofuels and capturing of anthropogenic CO2. One major problem associated with PBRs however, is that the bacteria usually associated with microalgae in nonaxenic cultures can lead to biofouling and thereby affect algal productivity. Here, we report on a phylogenetic, metagenome, and functional analysis of a mixed-species bacterial biofilm associated with the microalgae Chlorella vulgaris and Scenedesmus obliquus in a PBR. The biofilm diversity and population dynamics were examined through 16S rRNA phylogeny. Overall, the diversity was rather limited, with approximately 30 bacterial species associated with the algae. The majority of the observed microorganisms were affiliated with Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes. A combined approach of sequencing via GS FLX Titanium from Roche and HiSeq 2000 from Illumina resulted in the overall production of 350 Mbp of sequenced DNA, 165 Mbp of which was assembled in larger contigs with a maximum size of 0.2 Mbp. A KEGG pathway analysis suggested high metabolic diversity with respect to the use of polymers and aromatic and nonaromatic compounds. Genes associated with the biosynthesis of essential B vitamins were highly redundant and functional. Moreover, a relatively high number of predicted and functional lipase and esterase genes indicated that the alga-associated bacteria are possibly a major sink for lipids and fatty acids produced by the microalgae. This is the first metagenome study of microalga- and PBR-associated biofilm bacteria, and it gives new clues for improved biofuel production in PBRs.

  19. Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

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    Cody Springer Sheik

    2015-05-01

    Full Text Available Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

  20. Microbial characterization of microbial ecosystems associated to evaporites domes of gypsum in Salar de Llamara in Atacama desert.

    Science.gov (United States)

    Rasuk, Maria Cecilia; Kurth, Daniel; Flores, Maria Regina; Contreras, Manuel; Novoa, Fernando; Poire, Daniel; Farias, Maria Eugenia

    2014-10-01

    The Central Andes in northern Chile contains a large number of closed basins whose central depression is occupied by saline lakes and salt crusts (salars). One of these basins is Salar de Llamara (850 m a.s.l.), where large domed structures of seemingly evaporitic origin forming domes can be found. In this work, we performed a detailed microbial characterization of these domes. Mineralogical studies revealed gypsum (CaSO(4)) as a major component. Microbial communities associated to these structures were analysed by 454 16S rDNA amplicon sequencing and compared between winter and summer seasons. Bacteroidetes Proteobacteria and Planctomycetes remained as the main phylogenetic groups, an increased diversity was found in winter. Comparison of the upper air-exposed part and the lower water-submerged part of the domes in both seasons showed little variation in the upper zone, showing a predominance of Chromatiales (Gammaproteobacteria), Rhodospirillales (Alphaproteobacteria), and Sphingobacteriales (Bacteroidetes). However, the submerged part showed marked differences between seasons, being dominated by Proteobacteria (Alpha and Gamma) and Verrucomicrobia in summer, but with more diverse phyla found in winter. Even though not abundant by sequence, Cyanobacteria were visually identified by scanning electron microscopy (SEM), which also revealed the presence of diatoms. Photosynthetic pigments were detected by high-performance liquid chromatography, being more diverse on the upper photosynthetic layer. Finally, the system was compared with other endoevaporite, mats microbialite and Stromatolites microbial ecosystems, showing higher similitude with evaporitic ecosystems from Atacama and Guerrero Negro. This environment is of special interest for extremophile studies because microbial life develops associated to minerals in the driest desert all over the world. Nevertheless, it is endangered by mining activity associated to copper and lithium extraction; thus, its

  1. Diversity of bacteria carried by pinewood nematode in USA and phylogenetic comparison with isolates from other countries.

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    Diogo Neves Proença

    Full Text Available Pine wilt disease (PWD is native to North America and has spread to Asia and Europe. Lately, mutualistic relationship has been suggested between the pinewood nematode (PWN, Bursaphelenchus xylophilus the causal nematode agent of PWD, and bacteria. In countries where PWN occurs, nematodes from diseased trees were reported to carry bacteria from several genera. However no data exists for the United States. The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. The bacteria carried by PWN belonged to Gammaproteobacteria (79.9%, Betaproteobacteria (11.7%, Bacilli (5.0%, Alphaproteobacteria (1.7% and Flavobacteriia (1.7%. Strains from the genera Chryseobacterium and Pigmentiphaga were found associated with the nematode for the first time. These results were compared to results from similar studies conducted from other countries of three continents in order to assess the diversity of bacteria with associated with PWN. The isolates from the United States, Portugal and China belonged to 25 different genera and only strains from the genus Pseudomonas were found in nematodes from all countries. The strains from China were closely related to P. fluorescens and the strains isolated from Portugal and USA were phylogenetically related to P. mohnii and P. lutea. Nematodes from the different countries are associated with bacteria of different species, not supporting a relationship between PWN with a particular bacterial species. Moreover, the diversity of the bacteria carried by the pinewood nematode seems to be related to the geographic area and the Pinus species. The roles these bacteria play within the pine trees or when associated with the nematodes, might be independent of the presence of the nematode in the tree and only related on the bacteria's relationship with the tree.

  2. Melatonin in plants and other phototrophs: advances and gaps concerning the diversity of functions.

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    Hardeland, Rüdiger

    2015-02-01

    Melatonin is synthesized in Alphaproteobacteria, Cyanobacteria, Dinoflagellata, Euglenoidea, Rhodophyta, Phae ophyta, and Viridiplantae. The biosynthetic pathways have been identified in dinoflagellates and plants. Other than in dinoflagellates and animals, tryptophan is not 5-hydroxylated in plants but is first decarboxylated. Serotonin is formed by 5-hydroxylation of tryptamine. Serotonin N-acetyltransferase is localized in plastids and lacks homology to the vertebrate aralkylamine N-acetyltransferase. Melatonin content varies considerably among species, from a few picograms to several micrograms per gram, a strong hint for different actions of this indoleamine. At elevated levels, the common and presumably ancient property as an antioxidant may prevail. Although melatonin exhibits nocturnal maxima in some phototrophs, it is not generally a mediator of the signal 'darkness'. In various plants, its formation is upregulated by visible and/or UV light. Increases are often induced by high or low temperature and several other stressors including drought, salinity, and chemical toxins. In Arabidopsis, melatonin induces cold- and stress-responsive genes. It has been shown to support cold resistance and to delay experimental leaf senescence. Transcriptome data from Arabidopsis indicate upregulation of genes related to ethylene, abscisic acid, jasmonic acid, and salicylic acid. Auxin-like actions have been reported concerning root growth and inhibition, and hypocotyl or coleoptile lengthening, but effects caused by melatonin and auxins can be dissected. Assumptions on roles in flower morphogenesis and fruit ripening are based mainly on concentration changes. Whether or not melatonin will find a place in the phytohormone network depends especially on the identification of molecular signals regulating its synthesis, high-affinity binding sites, and signal transduction pathways.

  3. Plant-Microbial Interactions Define Potential Mechanisms of Organic Matter Priming in the Rhizosphere

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    Zhalnina, K.; Cho, H. J.; Hao, Z.; Mansoori, N.; Karaoz, U.; Jenkins, S.; White, R. A., III; Lipton, M. S.; Deng, K.; Zhou, J.; Pett-Ridge, J.; Northen, T.; Firestone, M. K.; Brodie, E.

    2015-12-01

    In the rhizosphere, metabolic processes of plants and microorganisms are closely coupled, and together with soil minerals, their interactions regulate the turnover of soil organic C (SOC). Plants provide readily assimilable metabolites for microorganisms through exudation, and it has been hypothesized that increasing concentrations of exudate C may either stimulate or suppress rates of SOC mineralization (rhizosphere priming). Both positive and negative rhizosphere priming has been widely observed, however the underlying mechanisms remain poorly understood. To begin to identify the molecular mechanisms underlying rhizosphere priming, we isolated a broad range of soil bacteria from a Mediterranean grassland dominated by annual grass. Thirty-nine heterotrophic bacteria were selected for genome sequencing and both rRNA gene analysis and metagenome coverage suggest that these isolates represent naturally abundant strain variants. We analyzed their genomes for potential metabolic traits related to life in the rhizosphere and the decomposition of polymeric SOC. While the two dominant groups, Alphaproteobacteria and Actinobacteria, were enriched in polymer degrading enzymes, Alphaproteobacterial isolates contained greater gene copies of transporters related to amino acid, organic acid and auxin uptake or export, suggesting an enhanced metabolic potential for life in the root zone. To verify this metabolic potential, we determined the enzymatic activities of these isolates and revealed preferences of strains to degrade certain polymers (xylan, cellulose or lignin). Fourier Transform Infrared spectroscopy is being used to determine which polymeric components of plant roots are targeted by specific strains and how exudates may impact their degradation. To verify the potential of isolates to assimilate root exudates and export key metabolites we are using LC-MS/MS based exometabolomic profiling. The traits hypothesized and verified here (transporters, enzymes, exudate uptake

  4. Abundance of two Pelagibacter ubique bacteriophage genotypes along a latitudinal transect in the North and South Atlantic Oceans

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    Erin M Eggleston

    2016-09-01

    Full Text Available This study characterizes viral and bacterial dynamics along a latitudinal transect in the Atlantic Ocean from approximately 10N to 40S. Overall viral abundance decreased with depth, on average there were 1.64 ± 0.71 x107 virus like particles (VLPs in surface waters, decreasing to an average of 6.50 ± 2.26 x105 VLPs in Antarctic Bottom Water. This decrease was highly correlated to bacterial abundance. There are six major water masses in the Southern Tropical Atlantic Ocean, and inclusion of water mass, temperature and salinity variables explained a majority of the variation in total viral abundance. Recent discovery of phages infecting bacteria of the SAR11 clade of Alphaproteobacteria (i.e. pelagiphages leads to intriguing questions about the roles they play in shaping epipelagic communities. Viral-size fraction DNA from epipelagic water was used to quantify the abundance of two pelagiphages, using pelagiphage-specific quantitative PCR primers and probes along the transect. We found that HTVC010P, a member of a podoviridae sub-family, was most abundant in surface waters. Copy numbers ranged from an average of 1.03 ± 2.38 x 105 copies ml-1 in surface waters, to 5.79 ± 2.86 x103 in the deep chlorophyll maximum. HTVC008M, a T4-like myovirus, was present in the deep chlorophyll maximum (5.42±2.8x103 copies ml-1 on average, although it was not as highly abundant as HTVC010P in surface waters (6.05±3.01x103 copies ml-1 on average. Interestingly, HTVC008M was only present at a few of the most southern stations, suggesting latitudinal biogeography of SAR11 phages.

  5. Bacterial community shift in the coastal Gulf of Mexico salt-marsh sediment microcosm in vitro following exposure to the Mississippi Canyon Block 252 oil (MC252)

    KAUST Repository

    Koo, Hyunmin

    2014-07-10

    In this study, we examined the responses by the indigenous bacterial communities in salt-marsh sediment microcosms in vitro following treatment with Mississippi Canyon Block 252 oil (MC252). Microcosms were constructed of sediment and seawater collected from Bayou La Batre located in coastal Alabama on the Gulf of Mexico. We used an amplicon pyrosequencing approach on microcosm sediment metagenome targeting the V3–V5 region of the 16S rRNA gene. Overall, we identified a shift in the bacterial community in three distinct groups. The first group was the early responders (orders Pseudomonadales and Oceanospirillales within class Gammaproteobacteria), which increased their relative abundance within 2 weeks and were maintained 3 weeks after oil treatment. The second group was identified as early, but transient responders (order Rhodobacterales within class Alphaproteobacteria; class Epsilonproteobacteria), which increased their population by 2 weeks, but returned to the basal level 3 weeks after oil treatment. The third group was the late responders (order Clostridiales within phylum Firmicutes; order Methylococcales within class Gammaproteobacteria; and phylum Tenericutes), which only increased 3 weeks after oil treatment. Furthermore, we identified oil-sensitive bacterial taxa (order Chromatiales within class Gammaproteobacteria; order Syntrophobacterales within class Deltaproteobacteria), which decreased in their population after 2 weeks of oil treatment. Detection of alkane (alkB), catechol (C2,3DO) and biphenyl (bph) biodegradation genes by PCR, particularly in oil-treated sediment metacommunity DNA, delineates proliferation of the hydrocarbon degrading bacterial community. Overall, the indigenous bacterial communities in our salt-marsh sediment in vitro microcosm study responded rapidly and shifted towards members of the taxonomic groups that are capable of surviving in an MC252 oil-contaminated environment.

  6. Treatment with a Monoclonal Anti-IL-12p40 Antibody Induces Substantial Gut Microbiota Changes in an Experimental Colitis Model

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    Josué Castro-Mejía

    2016-01-01

    Full Text Available Background and Aim. Crohn’s disease is associated with gut microbiota (GM dysbiosis. Treatment with the anti-IL-12p40 monoclonal antibody (12p40-mAb has therapeutic effect in Crohn’s disease patients. This study addresses whether a 12p40-mAb treatment influences gut microbiota (GM composition in mice with adoptive transfer colitis (AdTr-colitis. Methods. AdTr-colitis mice were treated with 12p40-mAb or rat-IgG2a or NaCl from days 21 to 47. Disease was monitored by changes in body weight, stool, endoscopic and histopathology scores, immunohistochemistry, and colonic cytokine/chemokine profiles. GM was characterized through DGGE and 16S rRNA gene-amplicon high-throughput sequencing. Results. Following 12p40-mAb treatment, most clinical and pathological parameters associated with colitis were either reduced or absent. GM was shifted towards a higher Firmicutes-to-Bacteroidetes ratio compared to rat-IgG2a treated mice. Significant correlations between 17 bacterial genera and biological markers were found. The relative abundances of the RF32 order (Alphaproteobacteria and Akkermansia muciniphila were positively correlated with damaged histopathology and colonic inflammation. Conclusions. Shifts in GM distribution were observed with clinical response to 12p40-mAb treatment, whereas specific GM members correlated with colitis symptoms. Our study implicates that specific changes in GM may be connected with positive clinical outcomes and suggests preventing or correcting GM dysbiosis as a treatment goal in inflammatory bowel disease.

  7. Strength of the pathogenicity caused by feminizing Wolbachia after transfer in a new host: strain or dose effect?

    Science.gov (United States)

    Le Clec'h, Winka; Raimond, Maryline; Bouchon, Didier; Sicard, Mathieu

    2014-02-01

    The alphaproteobacteria Wolbachia pipientis are among the most common and widespread symbionts in the animal world. Their vertical transmission mode is predicted to favour genotypes with low virulence. On the contrary, horizontal transfers of Wolbachia from one host to another have been shown to possibly increase the symbiont virulence. This situation has been previously described when two feminizing Wolbachia strains, wVulC and wVulM, from the ovaries of the woodlouse Armadillidium vulgare were introduced into another woodlouse named Porcellio dilatatus. These two Wolbachia strains induced severe symptoms and eventually caused the death of the recipient host. However, symptoms and death appeared sooner with wVulC than with wVulM. To know whether this difference was due to variation in the dose of infection or a difference in virulence between the two Wolbachia strains, we performed controlled and gradual doses of injection with wVulC and wVulM in P. dilatatus. We showed that the two strains differed intrinsically in their virulence against P. dilatatus and that their virulence is related to the injection dose. Moreover, we showed that wVulC reached higher concentrations in the recipient host than wVulM suggesting a potential link between the bacterial titers and the levels of virulence. We also addressed the impact of the tissue source of the Wolbachia used for the transinfection and demonstrated that Wolbachia transinfected via hemolymph colonized the body of the recipient more quickly and caused accelerated symptoms compared to Wolbachia introduced via a crushed ovaries suspension.

  8. Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.

    Science.gov (United States)

    La Duc, Myron T; Vaishampayan, Parag; Nilsson, Henrik R; Torok, Tamas; Venkateswaran, Kasthuri

    2012-08-01

    Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.

  9. Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

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    Purificacion eLopez-Garcia

    2015-08-01

    Full Text Available Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes or other metabolisms (e.g. anoxygenic photosynthesis, sulfate reduction, may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W and Northern (AL-N shores of the lake and, at the latter site, along a depth gradient (1, 5, 10 and 15 m depth. The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria, Verrucomicrobia, Actinobacteria, Firmicutes and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at

  10. Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses

    Energy Technology Data Exchange (ETDEWEB)

    Schostag, Morten; Stibal, Marek; Jacobsen, Carsten S.; Baelum, Jacob; Tas, Neslihan; Elberling, Bo; Jansson, Janet K.; Semenchuk, Phillip; Prieme, Anders

    2015-04-30

    The active layer of soil overlaying permafrost in the Arctic is subjected to dramatic annual changes in temperature and soil chemistry, which likely affect bacterial activity and community structure. We studied seasonal variations in the bacterial community of active layer soil from Svalbard (78°N) by co-extracting DNA and RNA from 12 soil cores collected monthly over a year. PCR amplicons of 16S rRNA genes (DNA) and reverse transcribed transcripts (cDNA) were quantified and sequenced to test for the effect of low winter temperature and seasonal variation in concentration of easily degradable organic matter on the bacterial communities. The copy number of 16S rRNA genes and transcripts revealed no distinct seasonal changes indicating potential bacterial activity during winter despite soil temperatures well below -10°C. Multivariate statistical analysis of the bacterial diversity data (DNA and cDNA libraries) revealed a season-based clustering of the samples, and, e.g., the relative abundance of potentially active Cyanobacteria peaked in June and Alphaproteobacteria increased over the summer and then declined from October to November. The structure of the bulk (DNA-based) community was significantly correlated with pH and dissolved organic carbon, while the potentially active (RNA-based) community structure was not significantly correlated with any of the measured soil parameters. A large fraction of the 16S rRNA transcripts was assigned to nitrogen-fixing bacteria (up to 24% in June) and phototrophic organisms (up to 48% in June) illustrating the potential importance of nitrogen fixation in otherwise nitrogen poor Arctic ecosystems and of phototrophic bacterial activity on the soil surface.

  11. Precipitation of Phosphate Minerals by Microorganisms Isolated from a Fixed-Biofilm Reactor Used for the Treatment of Domestic Wastewater

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    Almudena Rivadeneyra

    2014-04-01

    Full Text Available The ability of bacteria isolated from a fixed-film bioreactor to precipitate phosphate crystals for the treatment of domestic wastewater in both artificial and natural media was studied. When this was demonstrated in artificial solid media for crystal formation, precipitation took place rapidly, and crystal formation began 3 days after inoculation. The percentage of phosphate-forming bacteria was slightly higher than 75%. Twelve major colonies with phosphate precipitation capacity were the dominant heterotrophic platable bacteria growing aerobically in artificial media. According to their taxonomic affiliations (based on partial sequencing of the 16S rRNA, the 12 strains belonged to the following genera of Gram-negative bacteria: Rhodobacter, Pseudoxanthobacter, Escherichia, Alcaligenes, Roseobacter, Ochrobactrum, Agromyce, Sphingomonas and Paracoccus. The phylogenetic tree shows that most of the identified populations were evolutionarily related to the Alphaproteobacteria (91.66% of sequences. The minerals formed were studied by X-ray diffraction, scanning electron microscopy (SEM, and energy dispersive X-ray microanalysis (EDX. All of these strains formed phosphate crystals and precipitated struvite (MgNH4PO4·6H2O, bobierrite [Mg3(PO42·8H2O] and baricite [(MgFe3(PO42·8H2O]. The results obtained in this study show that struvite and spherulite crystals did not show any cell marks. Moreover, phosphate precipitation was observed in the bacterial mass but also near the colonies. Our results suggest that the microbial population contributed to phosphate precipitation by changing the media as a consequence of their metabolic activity. Moreover, the results of this research suggest that bacteria play an active role in the mineral precipitation of soluble phosphate from urban wastewater in submerged fixed-film bioreactors.

  12. Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean.

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    Cynthia B Silveira

    Full Text Available BACKGROUND: Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore and three freshwater (water spring, river, and mangrove environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%, whereas Cyanobacteria (30.5%, Alphaproteobacteria (25.5%, and Gammaproteobacteria (26.3% dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. CONCLUSIONS/SIGNIFICANCE: Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical

  13. Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina.

    Science.gov (United States)

    Vega-Avila, A D; Gumiere, T; Andrade, P A M; Lima-Perim, J E; Durrer, A; Baigori, M; Vazquez, F; Andreote, F D

    2015-02-01

    Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.

  14. Prokaryotic and eukaryotic community structure in field and cultured microbialites from the alkaline Lake Alchichica (Mexico.

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    Estelle Couradeau

    Full Text Available The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both field samples collected along a depth gradient (0-14 m depth and long-term-maintained laboratory aquaria. Using small subunit (SSU rRNA gene libraries and fingerprinting methods, we detected a wide diversity of bacteria and protists contrasting with a minor fraction of archaea. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms. Cyanobacterial diversity varied with depth, Oscillatoriales dominating shallow and intermediate microbialites and Pleurocapsales the deepest samples. The early-branching Gloeobacterales represented significant proportions in aquaria microbialites. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated in biomass, heterotrophic lineages were more diverse. We detected members of up to 21 bacterial phyla or candidate divisions, including lineages possibly involved in microbialite formation, such as sulfate-reducing Deltaproteobacteria but also Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia. Heterotrophic eukaryotes were dominated by Fungi (including members of the basal Rozellida or Cryptomycota, Choanoflagellida, Nucleariida, Amoebozoa, Alveolata and Stramenopiles. The diversity and relative abundance of many eukaryotic lineages suggest an unforeseen role for protists in microbialite ecology. Many lineages from lake microbialites were successfully maintained in aquaria. Interestingly, the diversity detected in aquarium microbialites was higher than

  15. Role of Sphingomonas sp. Strain Fr1 PhyR-NepR-σEcfG Cascade in General Stress Response and Identification of a Negative Regulator of PhyR▿†

    Science.gov (United States)

    Kaczmarczyk, Andreas; Campagne, Sébastien; Danza, Francesco; Metzger, Lisa C.; Vorholt, Julia A.; Francez-Charlot, Anne

    2011-01-01

    The general stress response in Alphaproteobacteria was recently described to depend on the alternative sigma factor σEcfG, whose activity is regulated by its anti-sigma factor NepR. The response regulator PhyR, in turn, regulates NepR activity in a partner-switching mechanism according to which phosphorylation of PhyR triggers sequestration of NepR by the sigma factor-like effector domain of PhyR. Although genes encoding predicted histidine kinases can often be found associated with phyR, little is known about their role in modulation of PhyR phosphorylation status. We demonstrate here that the PhyR-NepR-σEcfG cascade is important for multiple stress resistance and competitiveness in the phyllosphere in a naturally abundant plant epiphyte, Sphingomonas sp. strain Fr1, and provide evidence that the partner switching mechanism is conserved. We furthermore identify a gene, designated phyP, encoding a predicted histidine kinase at the phyR locus as essential. Genetic epistasis experiments suggest that PhyP acts upstream of PhyR, keeping PhyR in an unphosphorylated, inactive state in nonstress conditions, strictly depending on the predicted phosphorylatable site of PhyP, His-341. In vitro experiments show that Escherichia coli inner membrane fractions containing PhyP disrupt the PhyR-P/NepR complex. Together with the fact that PhyP lacks an obvious ATPase domain, these results are in agreement with PhyP functioning as a phosphatase of PhyR, rather than a kinase. PMID:21949070

  16. Role of Sphingomonas sp. strain Fr1 PhyR-NepR-σEcfG cascade in general stress response and identification of a negative regulator of PhyR.

    Science.gov (United States)

    Kaczmarczyk, Andreas; Campagne, Sébastien; Danza, Francesco; Metzger, Lisa C; Vorholt, Julia A; Francez-Charlot, Anne

    2011-12-01

    The general stress response in Alphaproteobacteria was recently described to depend on the alternative sigma factor σ(EcfG), whose activity is regulated by its anti-sigma factor NepR. The response regulator PhyR, in turn, regulates NepR activity in a partner-switching mechanism according to which phosphorylation of PhyR triggers sequestration of NepR by the sigma factor-like effector domain of PhyR. Although genes encoding predicted histidine kinases can often be found associated with phyR, little is known about their role in modulation of PhyR phosphorylation status. We demonstrate here that the PhyR-NepR-σ(EcfG) cascade is important for multiple stress resistance and competitiveness in the phyllosphere in a naturally abundant plant epiphyte, Sphingomonas sp. strain Fr1, and provide evidence that the partner switching mechanism is conserved. We furthermore identify a gene, designated phyP, encoding a predicted histidine kinase at the phyR locus as essential. Genetic epistasis experiments suggest that PhyP acts upstream of PhyR, keeping PhyR in an unphosphorylated, inactive state in nonstress conditions, strictly depending on the predicted phosphorylatable site of PhyP, His-341. In vitro experiments show that Escherichia coli inner membrane fractions containing PhyP disrupt the PhyR-P/NepR complex. Together with the fact that PhyP lacks an obvious ATPase domain, these results are in agreement with PhyP functioning as a phosphatase of PhyR, rather than a kinase.

  17. Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world.

    Science.gov (United States)

    Clementino, M M; Vieira, R P; Cardoso, A M; Nascimento, A P A; Silveira, C B; Riva, T C; Gonzalez, A S M; Paranhos, R; Albano, R M; Ventosa, A; Martins, O B

    2008-07-01

    Araruama Lagoon is an environment characterized by high salt concentrations. The low raining and high evaporation rates in this region favored the development of many salty ponds around the lagoon. In order to reveal the microbial composition of this system, we performed a 16S rRNA gene survey. Among archaea, most clones were related to uncultured environmental Euryarchaeota. In lagoon water, we found some clones related to Methanomicrobia and Methanothermococcus groups, while in the saline pond water members related to the genus Haloarcula were detected. Bacterial community was dominated by clones related to Gamma-proteobacteria, Actinobacteria, and Synechococcus in lagoon water, while Salinibacter ruber relatives dominated in saline pond. We also detected the presence of Alpha-proteobacteria, Pseudomonas-like bacteria and Verrucomicrobia. Only representatives of the genus Ralstonia were cosmopolitan, being observed in both systems. The detection of a substantial number of clones related to uncultured archaea and bacteria suggest that the hypersaline waters of Araruama harbor a pool of novel prokaryotic phylotypes, distinct from those observed in other similar systems. We also observed clones related to halophilic genera of cyanobacteria that are specific for each habitat studied. Additionally, two bacterioplankton molecular markers with ecological relevance were analyzed, one is linked to nitrogen fixation (nifH) and the other is linked to carbon fixation by bacterial photosynthesis, the protochlorophyllide genes, revealing a specific genetic distribution in this ecosystem. This is the first study of the biogeography and community structure of microbial assemblages in Brazilian tropical hypersaline environments. This work is directed towards a better understanding of the free-living prokaryotic diversity adapted to life in hypersaline waters.

  18. Effect of Biostimulation Using Sewage Sludge, Soybean Meal, and Wheat Straw on Oil Degradation and Bacterial Community Composition in a Contaminated Desert Soil.

    Science.gov (United States)

    Al-Kindi, Sumaiya; Abed, Raeid M M

    2016-01-01

    Waste materials have a strong potential in the bioremediation of oil-contaminated sites, because of their richness in nutrients and their economical feasibility. We used sewage sludge, soybean meal, and wheat straw to biostimulate oil degradation in a heavily contaminated desert soil. While oil degradation was assessed by following the produced CO2 and by using gas chromatography-mass spectrometry (GC-MS), shifts in bacterial community composition were monitored using illumina MiSeq. The addition of sewage sludge and wheat straw to the desert soil stimulated the respiration activities to reach 3.2-3.4 times higher than in the untreated soil, whereas the addition of soybean meal resulted in an insignificant change in the produced CO2, given the high respiration activities of the soybean meal alone. GC-MS analysis revealed that the addition of sewage sludge and wheat straw resulted in 1.7-1.8 fold increase in the degraded C14 to C30 alkanes, compared to only 1.3 fold increase in the case of soybean meal addition. The degradation of ≥90% of the C14 to C30 alkanes was measured in the soils treated with sewage sludge and wheat straw. MiSeq sequencing revealed that the majority (76.5-86.4% of total sequences) of acquired sequences from the untreated soil belonged to Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. Multivariate analysis of operational taxonomic units placed the bacterial communities of the soils after the treatments in separate clusters (ANOSIM R = 0.66, P = 0.0001). The most remarkable shift in bacterial communities was in the wheat straw treatment, where 95-98% of the total sequences were affiliated to Bacilli. We conclude that sewage sludge and wheat straw are useful biostimulating agents for the cleanup of oil-contaminated desert soils.

  19. Bacteria contribute to sediment nutrient release and reflect progressed eutrophication-driven hypoxia in an organic-rich continental sea.

    Directory of Open Access Journals (Sweden)

    Hanna Sinkko

    Full Text Available In the sedimental organic matter of eutrophic continental seas, such as the largest dead zone in the world, the Baltic Sea, bacteria may directly participate in nutrient release by mineralizing organic matter or indirectly by altering the sediment's ability to retain nutrients. Here, we present a case study of a hypoxic sea, which receives riverine nutrient loading and in which microbe-mediated vicious cycles of nutrients prevail. We showed that bacterial communities changed along the horizontal loading and vertical mineralization gradients in the Gulf of Finland of the Baltic Sea, using multivariate statistics of terminal restriction fragments and sediment chemical, spatial and other properties of the sampling sites. The change was mainly explained by concentrations of organic carbon, nitrogen and phosphorus, which showed strong positive correlation with Flavobacteria, Sphingobacteria, Alphaproteobacteria and Gammaproteobacteria. These bacteria predominated in the most organic-rich coastal surface sediments overlain by oxic bottom water, whereas sulphate-reducing bacteria, particularly the genus Desulfobacula, prevailed in the reduced organic-rich surface sediments in the open sea. They correlated positively with organic nitrogen and phosphorus, as well as manganese oxides. These relationships suggest that the bacterial groups participated in the aerobic and anaerobic degradation of organic matter and contributed to nutrient cycling. The high abundance of sulphate reducers in the surficial sediment layers reflects the persistence of eutrophication-induced hypoxia causing ecosystem-level changes in the Baltic Sea. The sulphate reducers began to decrease below depths of 20 cm, where members of the family Anaerolineaceae (phylum Chloroflexi increased, possibly taking part in terminal mineralization processes. Our study provides valuable information on how organic loading affects sediment bacterial community compositions, which consequently may

  20. Aerobic biodegradation of trichloroethylene and phenol co-contaminants in groundwater by a bacterial community using hydrogen peroxide as the sole oxygen source.

    Science.gov (United States)

    Li, Hui; Zhang, Shi-yang; Wang, Xiao-li; Yang, Jie; Gu, Ji-dong; Zhu, Rui-li; Wang, Ping; Lin, Kuang-fei; Liu, Yong-di

    2015-01-01

    Trichloroethylene (TCE) and phenol were often found together as co-contaminants in the groundwater of industrial contaminated sites. An effective method to remove TCE was aerobic biodegradation by co-metabolism using phenol as growth substrates. However, the aerobic biodegradation process was easily limited by low concentration of dissolved oxygen (DO) in groundwater, and DO was improved by air blast technique with difficulty. This study enriched a bacterial community using hydrogen peroxide (H2O2) as the sole oxygen source to aerobically degrade TCE by co-metabolism with phenol in groundwater. The enriched cultures were acclimatized to 2-8 mM H2O2 which induced catalase, superoxide dismutase and peroxidase to decompose H2O2 to release O2 and reduce the toxicity. The bacterial community could degrade 120 mg/L TCE within 12 days by using 8 mM H2O2 as the optimum concentration, and the TCE degradation efficiency reached up to 80.6%. 16S rRNA gene cloning and sequencing showed that Bordetella, Stenotrophomonas sp., Sinorhizobium sp., Variovorax sp. and Sphingobium sp. were the dominant species in the enrichments, which were clustered in three phyla: Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. Polymerase chain reaction detection proved that phenol hydroxylase (Lph) gene was involved in the co-metabolic degradation of phenol and TCE, which indicated that hydroxylase might catalyse the epoxidation of TCE to form the unstable molecule TCE-epoxide. The findings are significant for understanding the mechanism of biodegradation of TCE and phenol co-contamination and helpful for the potential applications of an aerobic bioremediation in situ the contaminated sites.

  1. Magnetotaxis as a means for nanofabrication of bioelectronics

    Science.gov (United States)

    Macwan, Isaac

    Self-assembly plays an important role in the formation of different nanostructures either organic or inorganic. Controlled assembly of molecules into higher ordered hierarchical structures on the other hand require a thorough insight into the interactive forces that lie behind such an assembly. The interface between organic and inorganic materials is thus of primary significance when it comes to the tasks of selective deposition and assembly of inorganic molecules through organic agents. One of the bacterial species that belong to the class alpha-proteobacteria called Magnetospirillum magneticum (classified as AMB-1) is investigated in this study and it is found that this species is able to fulfill the requirements that are imposed by the complexity of the selective deposition and controlled assembly tasks. AMB-1 contain single-domain crystals of magnetite (Fe3O4) called magnetosomes that sense the external magnetic field that is further utilized for cellular displacement (magnetotaxis) through lash-like cellular appendages called flagella. The two flagella located at the proximal and distal ends of the cell consists of a protein monomer flagellin. Individual flagellin in turn that are located on the periphery of each of the flagellum's central channel consists of four sub-domains, two inner domains (D0, D1) made up of alpha-helices and two outer domains (D2, D3) made up of beta sheets. However, it is the domain D3 that is exposed to the surrounding micro-environment, thereby interacting with the components to be selectively deposited, in this case, carbon nanotubes (CNT). Based on the electromagnetic and molecular dynamics simulations and the real-time experimental analysis involving optical microscopy utilizing 50 micron diameter conductor (44AWG) magnetic coils as directional magnetic field generation centers to visualize the motion of free as well as loaded AMB-1 as well as electron microscopy (TEM & SEM) to analyze the interactive forces between CNT and AMB-1

  2. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems.

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    Acacio Aparecido Navarrete

    Full Text Available This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N, vinasse (V; a liquid waste from ethanol production, and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N and decreasing MB carbon (MB-C in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%, Planctomycetes (12.3%, Deltaproteobacteria (12.3%, Alphaproteobacteria (12.0% and Betaproteobacteria (11.1% were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

  3. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

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    C. Jeanthon

    2011-07-01

    Full Text Available Aerobic anoxygenic phototrophic (AAP bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-a (BChl-a, the light-harvesting pigment of AAP bacteria. BChl-a-containing colonies represented a low part of the cultivable fraction. In total, 54 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-a and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94 % was affiliated to the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies

  4. Bacterial diversity of a consortium degrading high-molecular-weight polycyclic aromatic hydrocarbons in a two-liquid phase biosystem.

    Science.gov (United States)

    Lafortune, Isabelle; Juteau, Pierre; Déziel, Eric; Lépine, François; Beaudet, Réjean; Villemur, Richard

    2009-04-01

    -five percent of clones and strains were affiliated to Alphaproteobacteria and Betaproteobacteria; among them, several were affiliated to bacterial species known for their PAH degradation activities such as those belonging to the Sphingomonadaceae. Finally, three genes involved in the degradation of aromatic molecules were detected in the consortium and two in IAFILS9. This study provides information on the bacterial composition of a HWM PAH-degrading consortium and its dynamics in a TLP biosystem during PAH degradation.

  5. Electricity generation and dynamics characteristics of microbial community of microbial fuel cells started up with mixture of aerobic/anaerobic sludge%好氧-厌氧混合污泥启动微生物燃料电池产电性能及微生物群落动态特征

    Institute of Scientific and Technical Information of China (English)

    尹亚琳; 高崇洋; 赵阳国; 王爱杰; 王敏; 闫凯丽

    2014-01-01

    [目的]为探讨好氧-厌氧混合污泥启动微生物燃料电池(Microbial fuel cell,MFC)产电性能以及MFC对微生物群落的选择作用,[方法]以乳酸为底物,应用不依赖于培养的微生物分子生物学技术解析单室MFC启动过程中微生物群落的组成和结构动态学特征.[结果]结果表明,MFC经过3个周期启动成功,最高输出电压230 mV.当MFC外电阻为1656 Ω时,最大功率密度11.15W/m3,电池运行稳定.混合污泥启动MFC以后,阳极生物膜微生物群落结构同种泥差异较大,且多样性降低.生物膜中微生物类群按丰度依次为β-变形菌纲(Betaproteobacteria) 24.90%、拟杆菌门(Bacteroidetes) 21.30%、厚壁菌门(Firmicutes)9.70%、γ-变形菌纲(Gammaproteobacteria) 8.50%、δ-变形菌纲(Deltaproteobacteria) 7.90%、绿弯菌门(Chloroflexi) 4.20%以及α-变形菌纲(Alphaproteobacteria)3.60%.有利于生物膜形成与稳定的动胶菌属(Zoogloea)和不动杆菌属(Acinetobacter)序列丰度分别占生物膜群落的5.00%和3.90%,与MFC产电能力直接相关的地杆菌属(Geobacter)序列由混合污泥中的0.60%上升至阳极生物膜中的2.60%.[结论]本研究表明,MFC阳极生物膜在驯化过程中对污泥中的微生物进行淘汰和选择,最终驯化形成了有利于生物膜形成与稳定、有机物厌氧发酵与产电的微生物菌群.

  6. Identifying active methane-oxidizers in thawed Arctic permafrost by proteomics

    Science.gov (United States)

    Lau, C. M.; Stackhouse, B. T.; Chourey, K.; Hettich, R. L.; Vishnivetskaya, T. A.; Pfiffner, S. M.; Layton, A. C.; Mykytczuk, N. C.; Whyte, L.; Onstott, T. C.

    2012-12-01

    The rate of CH4 release from thawing permafrost in the Arctic has been regarded as one of the determining factors on future global climate. It is uncertain how indigenous microorganisms would interact with such changing environmental conditions and hence their impact on the fate of carbon compounds that are sequestered in the cryosol. Multitudinous studies of pristine surface cryosol (top 5 cm) and microcosm experiments have provided growing evidence of effective methanotrophy. Cryosol samples corresponding to active layer were sampled from a sparsely vegetated, ice-wedge polygon at the McGill Arctic Research Station at Axel Heiberg Island, Nunavut, Canada (N79°24, W90°45) before the onset of annual thaw. Pyrosequencing of 16S rRNA gene indicated the occurrence of methanotroph-containing bacterial families as minor components (~5%) in pristine cryosol including Bradyrhizobiaceae, Methylobacteriaceae and Methylocystaceae within alpha-Proteobacteria, and Methylacidiphilaceae within Verrucomicrobia. The potential of methanotrophy is supported by preliminary analysis of metagenome data, which indicated putative methane monooxygenase gene sequences relating to Bradyrhizobium sp. and Pseudonocardia sp. are present. Proteome profiling in general yielded minute traces of proteins, which likely hints at dormant nature of the soil microbial consortia. The lack of specific protein database for permafrost posted additional challenge to protein identification. Only 35 proteins could be identified in the pristine cryosol and of which 60% belonged to Shewanella sp. Most of the identified proteins are known to be involved in energy metabolism or post-translational modification of proteins. Microcosms amended with sodium acetate exhibited a net methane consumption of ~65 ngC-CH4 per gram (fresh weight) of soil over 16 days of aerobic incubation at room temperature. The pH in microcosm materials remained acidic (decreased from initial 4.7 to 4.5). Protein extraction and

  7. Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti.

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    Francesco Pini

    2015-05-01

    Full Text Available In all domains of life, proper regulation of the cell cycle is critical to coordinate genome replication, segregation and cell division. In some groups of bacteria, e.g. Alphaproteobacteria, tight regulation of the cell cycle is also necessary for the morphological and functional differentiation of cells. Sinorhizobium meliloti is an alphaproteobacterium that forms an economically and ecologically important nitrogen-fixing symbiosis with specific legume hosts. During this symbiosis S. meliloti undergoes an elaborate cellular differentiation within host root cells. The differentiation of S. meliloti results in massive amplification of the genome, cell branching and/or elongation, and loss of reproductive capacity. In Caulobacter crescentus, cellular differentiation is tightly linked to the cell cycle via the activity of the master regulator CtrA, and recent research in S. meliloti suggests that CtrA might also be key to cellular differentiation during symbiosis. However, the regulatory circuit driving cell cycle progression in S. meliloti is not well characterized in both the free-living and symbiotic state. Here, we investigated the regulation and function of CtrA in S. meliloti. We demonstrated that depletion of CtrA cause cell elongation, branching and genome amplification, similar to that observed in nitrogen-fixing bacteroids. We also showed that the cell cycle regulated proteolytic degradation of CtrA is essential in S. meliloti, suggesting a possible mechanism of CtrA depletion in differentiated bacteroids. Using a combination of ChIP-Seq and gene expression microarray analysis we found that although S. meliloti CtrA regulates similar processes as C. crescentus CtrA, it does so through different target genes. For example, our data suggest that CtrA does not control the expression of the Fts complex to control the timing of cell division during the cell cycle, but instead it negatively regulates the septum-inhibiting Min system. Our

  8. Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti.

    Science.gov (United States)

    Pini, Francesco; De Nisco, Nicole J; Ferri, Lorenzo; Penterman, Jon; Fioravanti, Antonella; Brilli, Matteo; Mengoni, Alessio; Bazzicalupo, Marco; Viollier, Patrick H; Walker, Graham C; Biondi, Emanuele G

    2015-05-01

    In all domains of life, proper regulation of the cell cycle is critical to coordinate genome replication, segregation and cell division. In some groups of bacteria, e.g. Alphaproteobacteria, tight regulation of the cell cycle is also necessary for the morphological and functional differentiation of cells. Sinorhizobium meliloti is an alphaproteobacterium that forms an economically and ecologically important nitrogen-fixing symbiosis with specific legume hosts. During this symbiosis S. meliloti undergoes an elaborate cellular differentiation within host root cells. The differentiation of S. meliloti results in massive amplification of the genome, cell branching and/or elongation, and loss of reproductive capacity. In Caulobacter crescentus, cellular differentiation is tightly linked to the cell cycle via the activity of the master regulator CtrA, and recent research in S. meliloti suggests that CtrA might also be key to cellular differentiation during symbiosis. However, the regulatory circuit driving cell cycle progression in S. meliloti is not well characterized in both the free-living and symbiotic state. Here, we investigated the regulation and function of CtrA in S. meliloti. We demonstrated that depletion of CtrA cause cell elongation, branching and genome amplification, similar to that observed in nitrogen-fixing bacteroids. We also showed that the cell cycle regulated proteolytic degradation of CtrA is essential in S. meliloti, suggesting a possible mechanism of CtrA depletion in differentiated bacteroids. Using a combination of ChIP-Seq and gene expression microarray analysis we found that although S. meliloti CtrA regulates similar processes as C. crescentus CtrA, it does so through different target genes. For example, our data suggest that CtrA does not control the expression of the Fts complex to control the timing of cell division during the cell cycle, but instead it negatively regulates the septum-inhibiting Min system. Our findings provide valuable

  9. A putative bifunctional histidine kinase/phosphatase of the HWE family exerts positive and negative control on the Sinorhizobium meliloti general stress response.

    Science.gov (United States)

    Sauviac, Laurent; Bruand, Claude

    2014-07-01

    The EcfG-type sigma factor RpoE2 is the regulator of the general stress response in Sinorhizobium meliloti. RpoE2 activity is negatively regulated by two NepR-type anti-sigma factors (RsiA1/A2), themselves under the control of two anti-anti-sigma factors (RsiB1/B2) belonging to the PhyR family of response regulators. The current model of RpoE2 activation suggests that in response to stress, RsiB1/B2 are activated by phosphorylation of an aspartate residue in their receiver domain. Once activated, RsiB1/B2 become able to interact with the anti-sigma factors and release RpoE2, which can then associate with the RNA polymerase to transcribe its target genes. The purpose of this work was to identify and characterize proteins involved in controlling the phosphorylation status of RsiB1/B2. Using in vivo approaches, we show that the putative histidine kinase encoded by the rsiC gene (SMc01507), located downstream from rpoE2, is able to both positively and negatively regulate the general stress response. In addition, our data suggest that the negative action of RsiC results from inhibition of RsiB1/B2 phosphorylation. From these observations, we propose that RsiC is a bifunctional histidine kinase/phosphatase responsible for RsiB1/B2 phosphorylation or dephosphorylation in the presence or absence of stress, respectively. Two proteins were previously proposed to control PhyR phosphorylation in Caulobacter crescentus and Sphingomonas sp. strain FR1. However, these proteins contain a Pfam:HisKA_2 domain of dimerization and histidine phosphotransfer, whereas S. meliloti RsiC harbors a Pfam:HWE_HK domain instead. Therefore, this is the first report of an HWE_HK-containing protein controlling the general stress response in Alphaproteobacteria.

  10. Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

    Directory of Open Access Journals (Sweden)

    M.-C. Ciobanu

    2012-09-01

    Full Text Available An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion. Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG, within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG and Halobacteria within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence

  11. Rates of N2 production and diversity and abundance of functional genes associated with denitrification and anaerobic ammonium oxidation in the sediment of the Amundsen Sea Polynya, Antarctica

    Science.gov (United States)

    Choi, Ayeon; Cho, Hyeyoun; Kim, Sung-Han; Thamdrup, Bo; Lee, SangHoon; Hyun, Jung-Ho

    2016-01-01

    A combination of molecular microbiological analyses and metabolic rate measurements was conducted to elucidate the diversity and abundance of denitrifying and anaerobic ammonium oxidation (anammox) bacteria and the nitrogen gas (N2) production rates in sediment underlying the highly productive polynya (Stns. 10 and 17) and the sea-ice zone on the outer shelf (Stn. 83) of the Amundsen Sea, Antarctica. Despite the high water column productivity, the N2 production rates by denitrification (0.04-0.31 nmol N cm-3sed. h-1) and anammox (0.13-0.26 nmol N cm-3 sed. h-1) were lower than those measured in other polar regions. In contrast, gene copy number (106-107 copies cm-3 of nirS and nosZ genes targeting denitirifiers and 105-107 copies cm-3 of 16S rRNA genes related to anammox bacteria) of the two bacterial groups at Stn. 17 was similar compared to those of other organic-rich environments. The majority of the nirS sequences were affiliated with Gammaproteobacteria (54% and 61% of the total nirS gene at Stns. 17 and 83, respectively), which were closely related to Pseudomonas aeruginosa. Most nosZ sequences (92% and 72% of the total nosZ genes at Stns. 17 and 83, respectively) were related to the Alphaproteobacteria, which were closely related to Ruegeria pomeroyi and Roseobacter denitrificans. Most (98%) of the sequences related to anammox bacteria were affiliated with Candidatus Scalindua at Stn. 17. Consequently, despite the low metabolic activity, the abundance and composition of most denitrifying and anammox bacteria detected from the ASP were similar to those reported from a variety of marine environments. Our results further imply that increased labile organic matter production resulting from a shift of the phytoplankton community from Phaeocystis to diatoms in response to rapid melting of sea ice stimulates metabolic activities of the denitrifying and anammox bacteria, thereby enhancing the N removal process in the ASP.

  12. Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre

    Science.gov (United States)

    Bryant, Jessica A.; Clemente, Tara M.; Viviani, Donn A.; Fong, Allison A.; Thomas, Kimberley A.; Kemp, Paul; Karl, David M.; White, Angelicque E.

    2016-01-01

    ABSTRACT Marine plastic debris has become a significant concern in ocean ecosystems worldwide. Little is known, however, about its influence on microbial community structure and function. In 2008, we surveyed microbial communities and metabolic activities in seawater and on plastic on an oceanographic expedition through the “great Pacific garbage patch.” The concentration of plastic particles in surface seawater within different size classes (2 to 5 mm and >5 mm) ranged from 0.35 to 3.7 particles m−3 across sampling stations. These densities and the particle size distribution were consistent with previous values reported in the North Pacific Ocean. Net community oxygen production (NCP = gross primary production − community respiration) on plastic debris was positive and so net autotrophic, whereas NCP in bulk seawater was close to zero. Scanning electron microscopy and metagenomic sequencing of plastic-attached communities revealed the dominance of a few metazoan taxa and a diverse assemblage of photoautotrophic and heterotrophic protists and bacteria. Bryozoa, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes dominated all plastic particles, regardless of particle size. Bacteria inhabiting plastic were taxonomically distinct from the surrounding picoplankton and appeared well adapted to a surface-associated lifestyle. Genes with significantly higher abundances among plastic-attached bacteria included che genes, secretion system genes, and nifH genes, suggesting enrichment for chemotaxis, frequent cell-to-cell interactions, and nitrogen fixation. In aggregate, our findings suggest that plastic debris forms a habitat for complex microbial assemblages that have lifestyles, metabolic pathways, and biogeochemical activities that are distinct from those of free-living planktonic microbial communities. IMPORTANCE Marine plastic debris is a growing concern that has captured the general public’s attention. While the negative impacts of plastic debris on

  13. Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

    Science.gov (United States)

    Verastegui, Y; Cheng, J; Engel, K; Kolczynski, D; Mortimer, S; Lavigne, J; Montalibet, J; Romantsov, T; Hall, M; McConkey, B J; Rose, D R; Tomashek, J J; Scott, B R; Charles, T C; Neufeld, J D

    2014-07-15

    Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This

  14. Methanotrophic activity and diversity of methanotrophs in volcanic geothermal soils at Pantelleria (Italy)

    Science.gov (United States)

    Gagliano, A. L.; D'Alessandro, W.; Tagliavia, M.; Parello, F.; Quatrini, P.

    2014-10-01

    Volcanic and geothermal systems emit endogenous gases by widespread degassing from soils, including CH4, a greenhouse gas twenty-five times as potent as CO2. Recently, it has been demonstrated that volcanic or geothermal soils are not only a source of methane, but are also sites of methanotrophic activity. Methanotrophs are able to consume 10-40 Tg of CH4 a-1 and to trap more than 50% of the methane degassing through the soils. We report on methane microbial oxidation in the geothermally most active site of Pantelleria (Italy), Favara Grande, whose total methane emission was previously estimated at about 2.5 Mg a-1 (t a-1). Laboratory incubation experiments with three top-soil samples from Favara Grande indicated methane consumption values of up to 59.2 nmol g-1 soil d.w. h-1. One of the three sites, FAV2, where the highest oxidation rate was detected, was further analysed on a vertical soil profile, the maximum methane consumption was measured in the top-soil layer, and values greater than 6.23 nmol g-1 h-1 were still detected up to a depth of 13 cm. The highest consumption rate was measured at 37 °C, but a still detectable consumption at 80 °C (> 1.25 nmol g-1 h-1) was recorded. The soil total DNA extracted from the three samples was probed by Polymerase Chain Reaction (PCR) using standard proteobacterial primers and newly designed verrucomicrobial primers, targeting the unique methane monooxygenase gene pmoA; the presence of methanotrophs was detected at sites FAV2 and FAV3, but not at FAV1, where harsher chemical-physical conditions and negligible methane oxidation were detected. The pmoA gene libraries from the most active site (FAV2) pointed to a high diversity of gammaproteobacterial methanotrophs, distantly related to Methylocaldum-Metylococcus genera, and the presence of the newly discovered acido-thermophilic Verrucomicrobia methanotrophs. Alphaproteobacteria of the genus Methylocystis were isolated from enrichment cultures under a methane

  15. Methanotrophic activity and bacterial diversity in volcanic-geothermal soils at Pantelleria island (Italy)

    Science.gov (United States)

    Gagliano, A. L.; D'Alessandro, W.; Tagliavia, M.; Parello, F.; Quatrini, P.

    2014-04-01

    Verrucomicrobia. Alphaproteobacteria of the genus Methylocystis were isolated from enrichment cultures, under a methane containing atmosphere at 37 °C. The isolates grow at pH 3.5-8 and temperatures of 18-45 °C, and show a methane oxidation rate of ~ 450 μmol mol-1 h-1. Soils from Favara Grande showed the largest diversity of methanotrophic bacteria until now detected in a geothermal soil. While methanotrophic Verrucomicrobia are reported to dominate highly acidic geothermal sites, our results suggest that slightly acidic soils, in high enthalpy geothermal systems, host a more diverse group of both culturable and uncultivated methanotrophs.

  16. Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family Rhodobacteraceae isolated from deep-sea sediment in the Red Sea, Saudi Arabia

    KAUST Repository

    Lai, PokYui

    2012-06-08

    A slow-growing, strictly aerobic, Gram-negative, coccus bacterial strain, designated KAUST100406-0324T, was isolated from sea-floor sediment collected from the Red Sea, Saudi Arabia. The catalase- and oxidase-positive strain was non-sporulating and only slightly halophilic. Optimum growth occurred at 20-25 °C and at pH values ranging from 7.0 to 8.0. The major cellular fatty acids of the strain were unsaturated C18: 1ω6c and/or C18:1ω7c, C18:1ω7c 11-methyl and C16:1ω7c and/or C16:1ω6c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. Ubiquinone 10 was the predominant lipoquinone. The DNA G+C content of strain KAUST100406-0324T was 64.0 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that the novel strain belonged to the family Rhodobacteraceae of the class Alphaproteobacteria but formed a distinct evolutionary lineage from other bacterial species with validly published names. The 16S rRNA gene sequence of the novel strain was distantly related, but formed a monophyletic cluster with, those of bacteria from two moderately halophilic genera, Hwanghaeicola and Maribius. The similarity of the sequence between the novel strain KAUST100406-0324T and the type strains Hwanghaeicola aestuarii Y26T (accession number FJ230842), Maribius pelagius B5-6T (DQ514326) and Maribius salinus CL-SP27T (AY906863) were 94.5 %, 95.2 % and 95.3 %, respectively. Based on the physiological, phylogenetic and chemotaxonomic characteristics presented in this study, we propose that this strain represents a novel species of a new genus in the family Rhodobacteraceae, for which the name of Profundibacterium mesophilum gen. nov., sp. nov. was proposed, with KAUST100406-0324T (= JCM 17872T = NRRL B-59665T) as the type strain. © 2013 IUMS.

  17. Pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions.

    Directory of Open Access Journals (Sweden)

    Yulia M Serkebaeva

    Full Text Available Northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. Here, we compared the bacterial community composition in the surface (0-5 cm depth and subsurface (45-50 cm peat layers of an acidic (pH 4.0 Sphagnum-dominated wetland, using pyrosequencing of 16S rRNA genes. The denoised sequences (37,229 reads, average length ∼430 bp were affiliated with 27 bacterial phyla and corresponded to 1,269 operational taxonomic units (OTUs determined at 97% sequence identity. Abundant OTUs were affiliated with the Acidobacteria (35.5±2.4% and 39.2±1.2% of all classified sequences in surface and subsurface peat, respectively, Alphaproteobacteria (15.9±1.7% and 25.8±1.4%, Actinobacteria (9.5±2.0% and 10.7±0.5%, Verrucomicrobia (8.5±1.4% and 0.6±0.2%, Planctomycetes (5.8±0.4% and 9.7±0.6%, Deltaproteobacteria (7.1±0.4% and 4.4%±0.3%, and Gammaproteobacteria (6.6±0.4% and 2.1±0.1%. The taxonomic patterns of the abundant OTUs were uniform across all the subsamples taken from each peat layer. In contrast, the taxonomic patterns of rare OTUs were different from those of the abundant OTUs and varied greatly among subsamples, in both surface and subsurface peat. In addition to the bacterial taxa listed above, rare OTUs represented the following groups: Armatimonadetes, Bacteroidetes, Chlamydia, Chloroflexi, Cyanobacteria, Elusimicrobia, Fibrobacteres, Firmicutes, Gemmatimonadetes, Spirochaetes, AD3, WS1, WS4, WS5, WYO, OD1, OP3, BRC1, TM6, TM7, WPS-2, and FCPU426. OTU richness was notably higher in the surface layer (882 OTUs than in the anoxic subsurface peat (483 OTUs, with only 96 OTUs common to both data sets. Most members of poorly studied phyla, such as the Acidobacteria, Verrucomicrobia, Planctomycetes and the candidate division TM6, showed a clear preference for growth in either oxic or anoxic conditions. Apparently, the bacterial communities in surface and

  18. Diversity of bacteria isolated from cysts Heterodera glycines in Heilongjiang%黑龙江大豆胞囊线虫胞囊可培养细菌多样性

    Institute of Scientific and Technical Information of China (English)

    朱英波; 史凤玉; 王牛牛; 田建卿; 向梅春; 刘杏忠

    2012-01-01

    [Objective] To understand the bacterial diversity isolated from the cysts of Heterodera glycines in the soybean field in Heilongjiang Province. [Methods] Bacteria were isolated from cysts on nutrient agar plates using dilution plate method and further identified by phylogenetic analysis based on 16S rDNA gene sequences. [Results] Totally 90 bacteria strains with different colony morphology were selected on nutrient agar plate and their phylogenetic features were analyzed based on the partial 16S rDNA sequences. In total 7 genera and 22 species were identified, including 46 strains in Gammaproteobacteria (51.1%) , 32 in Firmicutes (35. 6%) , 10 in Betaproteobacteria (11.1%) , and 2 in Alphaproteobacteria (2.2%). The dominant bacteria species were Pseudomonas and Bacillus. [Conclusion] There was abundant species diversity of bacteria isolated from cysts Heterodera glycines in Heilongjiang, and these bacteria may play a physical and ecological roles in nematodes.%[目的]了解黑龙江省大豆田大豆胞囊线虫胞囊可培养细菌的多样性.[方法]运用稀释平板法和16S rDNA基因序列的系统发育分析对胞囊可培养细菌多样性进行研究.[结果]用NA培养基从胞囊上分离90株具有不同菌落形态的细菌.16S rDNA序列分析结果表明:90株菌株分属于7个属22个种.46株属于变形菌门γ亚群(Gammaproteobacteria),32株属于厚壁菌门(Firmicutes),10株属于变形菌门β亚群(Betaproteobacteria),2株属于变形菌门α亚群(Alphaproteobacteria).假单胞菌属(Pseudomonas)和芽孢杆菌属(Bacillus)为优势菌属.[结果]黑龙江省大豆胞囊线虫胞囊中存在丰富的细菌物种多样性,这些细菌对大豆胞囊线虫可能具有一定的生理生态作用.