Absence of genome reduction in diverse, facultative endohyphal bacteria

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Baltrus, David A. [Univ. of Arizona, Tucson, AZ (United States); Dougherty, Kevin [Univ. of Arizona, Tucson, AZ (United States); Arendt, Kayla R. [Univ. of Arizona, Tucson, AZ (United States); Huntemann, Marcel [Joint Genome Institute, Walnut Creek, CA (United States); Clum, Alicia [Joint Genome Institute, Walnut Creek, CA (United States); Pillay, Manoj [Joint Genome Institute, Walnut Creek, CA (United States); Palaniappan, Krishnaveni [Joint Genome Institute, Walnut Creek, CA (United States); Varghese, Neha [Joint Genome Institute, Walnut Creek, CA (United States); Mikhailova, Natalia [Joint Genome Institute, Walnut Creek, CA (United States); Stamatis, Dimitrios [Joint Genome Institute, Walnut Creek, CA (United States); Reddy, T. B. K. [Joint Genome Institute, Walnut Creek, CA (United States); Ngan, Chew Yee [Joint Genome Institute, Walnut Creek, CA (United States); Daum, Chris [Joint Genome Institute, Walnut Creek, CA (United States); Shapiro, Nicole [Joint Genome Institute, Walnut Creek, CA (United States); Markowitz, Victor [Joint Genome Institute, Walnut Creek, CA (United States); Ivanova, Natalia [Joint Genome Institute, Walnut Creek, CA (United States); Kyrpides, Nikos [Joint Genome Institute, Walnut Creek, CA (United States); Woyke, Tanja [Joint Genome Institute, Walnut Creek, CA (United States); Arnold, A. Elizabeth [Univ. of Arizona, Tucson, AZ (United States)

2017-02-28

Fungi interact closely with bacteria, both on the surfaces of the hyphae and within their living tissues (i.e. endohyphal bacteria, EHB). These EHB can be obligate or facultative symbionts and can mediate diverse phenotypic traits in their hosts. Although EHB have been observed in many lineages of fungi, it remains unclear how widespread and general these associations are, and whether there are unifying ecological and genomic features can be found across EHB strains as a whole. We cultured 11 bacterial strains after they emerged from the hyphae of diverse Ascomycota that were isolated as foliar endophytes of cupressaceous trees, and generated nearly complete genome sequences for all. Unlike the genomes of largely obligate EHB, the genomes of these facultative EHB resembled those of closely related strains isolated from environmental sources. Although all analysed genomes encoded structures that could be used to interact with eukaryotic hosts, pathways previously implicated in maintenance and establishment of EHB symbiosis were not universally present across all strains. Independent isolation of two nearly identical pairs of strains from different classes of fungi, coupled with recent experimental evidence, suggests horizontal transfer of EHB across endophytic hosts. Given the potential for EHB to influence fungal phenotypes, these genomes could shed light on the mechanisms of plant growth promotion or stress mitigation by fungal endophytes during the symbiotic phase, as well as degradation of plant material during the saprotrophic phase. As such, these findings contribute to the illumination of a new dimension of functional biodiversity in fungi.

Diversity of rumen bacteria in canadian cervids.

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Robert J Gruninger

Full Text Available Interest in the bacteria responsible for the breakdown of lignocellulosic feedstuffs within the rumen has increased due to their potential utility in industrial applications. To date, most studies have focused on bacteria from domesticated ruminants. We have expanded the knowledge of the microbial ecology of ruminants by examining the bacterial populations found in the rumen of non-domesticated ruminants found in Canada. Next-generation sequencing of 16S rDNA was employed to characterize the liquid and solid-associated bacterial communities in the rumen of elk (Cervus canadensis, and white tailed deer (Odocoileus virginianus. Despite variability in the microbial populations between animals, principle component and weighted UniFrac analysis indicated that bacterial communities in the rumen of elk and white tail deer are distinct. Populations clustered according to individual host animal and not the association with liquid or solid phase of the rumen contents. In all instances, Bacteroidetes and Firmicutes were the dominant bacterial phyla, although the relative abundance of these differed among ruminant species and between phases of rumen digesta, respectively. In the elk samples Bacteroidetes were more predominant in the liquid phase whereas Firmicutes was the most prevalent phyla in the solid digesta (P = 1×10(-5. There were also statistically significant differences in the abundance of OTUs classified as Fibrobacteres (P = 5×10(-3 and Spirochaetes (P = 3×10(-4 in the solid digesta of the elk samples. We identified a number of OTUs that were classified as phylotypes not previously observed in the rumen environment. Our results suggest that although the bacterial diversity in wild North American ruminants shows overall similarities to domesticated ruminants, we observed a number of OTUs not previously described. Previous studies primarily focusing on domesticated ruminants do not fully represent the microbial diversity of the

Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale.

Science.gov (United States)

Aminov, Rustam I; Walker, Alan W; Duncan, Sylvia H; Harmsen, Hermie J M; Welling, Gjalt W; Flint, Harry J

2006-09-01

Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eubacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 in feces from 10 healthy volunteers. Most of the diversity within this important group of butyrate-producing gut bacteria can apparently be retrieved through cultivation.

Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients.

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Noon, Jason B; Baum, Thomas J

2016-04-12

Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria. Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar

Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria.

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Delamuta, Jakeline Renata Marçon; Ribeiro, Renan Augusto; Menna, Pâmela; Bangel, Eliane Villamil; Hungria, Mariangela

2012-04-01

Symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family Leguminosae (=Fabaceae) results in the process of biological nitrogen fixation, playing a key role in global N cycling, and also bringing relevant contributions to the agriculture. Bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. The genus encompasses a variety of diverse bacteria, but the diversity captured in the analysis of the 16S rRNA is often low. In this study, we analyzed twelve Bradyrhizobium strains selected from previous studies performed by our group for showing high genetic diversity in relation to the described species. In addition to the 16S rRNA, five housekeeping genes (recA, atpD, glnII, gyrB and rpoB) were analyzed in the MLSA (multilocus sequence analysis) approach. Analysis of each gene and of the concatenated housekeeping genes captured a considerably higher level of genetic diversity, with indication of putative new species. The results highlight the high genetic variability associated with Bradyrhizobium microsymbionts of a variety of legumes. In addition, the MLSA approach has proved to represent a rapid and reliable method to be employed in phylogenetic and taxonomic studies, speeding the identification of the still poorly known diversity of nitrogen-fixing rhizobia in the tropics.

Culturable diversity of halophilic bacteria in foreshore soils.

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Irshad, Aarzoo; Ahmad, Irshad; Kim, Seung Bum

2014-01-01

Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%), Proteobacteria (31%), Bacteriodetes (5%) and Actinobacteria (4%). Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12%) and Shewanella (12%) were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity.

Culturable diversity of halophilic bacteria in foreshore soils

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Aarzoo Irshad

2014-06-01

Full Text Available Halophilic bacteria are commonly found in natural environments containing significant concentration of NaCl such as inland salt lakes and evaporated sea-shore pools, as well as environments such as curing brines, salted food products and saline soils. Dependence on salt is an important phenotypic characteristic of halophilic bacteria, which can be used in the polyphasic characterization of newly discovered microorganisms. In this study the diversity of halophilic bacteria in foreshore soils of Daecheon, Chungnam, and Saemangeum, Jeonbuk, was investigated. Two types of media, namely NA and R2A supplemented with 3%, 5%, 9%, 15%, 20% and 30% NaCl were used. More than 200 halophilic bacteria were isolated and BOX-PCR fingerprinting analysis was done for the typing of the isolates. The BLAST identification results showed that isolated strains were composed of 4 phyla, Firmicutes (60%, Proteobacteria (31%, Bacteriodetes (5% and Actinobacteria (4%. Isolates were affiliated with 16 genera and 36 species. Bacillus was the dominant genus in the phylum Firmicutes, comprising 24% of the total isolates. Halomonas (12% and Shewanella (12% were also found as the main genera. These findings show that the foreshore soil of Daecheon Beach and Saemangeum Sea of Korea represents an untapped source of bacterial biodiversity.

Diversity of purple nonsulfur bacteria in shrimp ponds with varying mercury levels

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Kanokwan Mukkata

2016-07-01

Full Text Available This research aimed to study the diversity of purple nonsulfur bacteria (PNSB and to investigate the effect of Hg concentrations in shrimp ponds on PNSB diversity. Amplification of the pufM gene was detected in 13 and 10 samples of water and sediment collected from 16 shrimp ponds in Southern Thailand. In addition to PNSB, other anoxygenic phototrophic bacteria (APB were also observed; purple sulfur bacteria (PSB and aerobic anoxygenic phototrophic bacteria (AAPB although most of them could not be identified. Among identified groups; AAPB, PSB and PNSB in the samples of water and sediment were 25.71, 11.43 and 8.57%; and 27.78, 11.11 and 22.22%, respectively. In both sample types, Roseobacter denitrificans (AAPB was the most dominant species followed by Halorhodospira halophila (PSB. In addition two genera, observed most frequently in the sediment samples were a group of PNSB (Rhodovulum kholense, Rhodospirillum centenum and Rhodobium marinum. The UPGMA dendrograms showed 7 and 6 clustered groups in the water and sediment samples, respectively. There was no relationship between the clustered groups and the total Hg (HgT concentrations in the water and sediment samples used (<0.002–0.03 μg/L and 35.40–391.60 μg/kg dry weight for studying the biodiversity. It can be concluded that there was no effect of the various Hg levels on the diversity of detected APB species; particularly the PNSB in the shrimp ponds.

Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture-dependent and PCR-DGGE methods.

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Lin, Xiao-Li; Pan, Qin-Jian; Tian, Hong-Gang; Douglas, Angela E; Liu, Tong-Xian

2015-03-01

Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture-dependent method and PCR-DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty-five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella. © 2013 Institute of Zoology, Chinese Academy of Sciences.

Rainforest Conversion to Rubber Plantation May Not Result in Lower Soil Diversity of Bacteria, Fungi, and Nematodes.

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Kerfahi, Dorsaf; Tripathi, Binu M; Dong, Ke; Go, Rusea; Adams, Jonathan M

2016-08-01

Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function.

[Community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan salt lake on Qinghai-Tibet Plateau].

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Shen, Shuo

2017-04-04

I studied the community structure and diversity of culturable moderate halophilic bacteria isolated from Qrhan Salt Lake. I isolated and cultured the moderate halophilic bacteria on different selective media. After the 16S rRNA gene sequences was amplified and measured, I constructed the phylogenic tree, analyzed the community structure and calculated the diversity indexes according to the 16S rRNA gene information. A total of 421 moderate halophilic bacteria were isolated from water and mud samples in Qrhan Salt Lake. The 16S rRNA gene information showed that 4 potential novel species belonged to the family Bacillaceae. Eighty-three model strains belonged to 3 phylurms 6 families 16 genus. Among them, Bacillus sp., Oceanobacillus sp. and Halomonas sp. were dominant species. Diversity analysis showed that the diversity of strains isolated from water sample was higher than that from mud sample, but the dominance degree of strains isolated from mud sample was higher than that from water sample. The genetic diversity of moderate halophilic bacteria isolated from Qrhan Salt Lake was abundant. Also, there were dominant and novel species of culturable moderate halophilic bacteria in this lake.

The diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge

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Yuan, Jun; Lai, Qiliang; Sun, Fengqin; Zheng, Tianling; Shao, Zongze

2015-01-01

The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR). After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene, and pyrene), nine bacterial consortia were obtained from depths of 3946–4746 m. While the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene, and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE) analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium, and Rhodovulum occurred most frequently in different PAH-degrading consortia. By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis, and Stappia were found to be PAH degraders. To the best of our knowledge, this is the first time these bacteria have been identified in this context. In summary, this report revealed significant diversity among the PAH-degrading bacteria in the deep-sea water column. These bacteria may play a role in PAH removal in deep-sea environments. PMID:26379634

The diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge.

Science.gov (United States)

Yuan, Jun; Lai, Qiliang; Sun, Fengqin; Zheng, Tianling; Shao, Zongze

2015-01-01

The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR). After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene, and pyrene), nine bacterial consortia were obtained from depths of 3946-4746 m. While the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene, and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE) analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium, and Rhodovulum occurred most frequently in different PAH-degrading consortia. By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis, and Stappia were found to be PAH degraders. To the best of our knowledge, this is the first time these bacteria have been identified in this context. In summary, this report revealed significant diversity among the PAH-degrading bacteria in the deep-sea water column. These bacteria may play a role in PAH removal in deep-sea environments.

Diversity of archaea and bacteria in a biogas reactor fed with ...

African Journals Online (AJOL)

Diversity of archaea and bacteria in a biogas reactor fed with Pennisetum sinese ... AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search · USING ... rumen microbial community in a biogas reactor by 16S rRNA gene analysis, ...

Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

NARCIS (Netherlands)

Lipsewers, Y.A.; Hopmans, E.C.; Meysman, F.J.R.; Sinninghe Damsté, J.S.; Villanueva, L.

2016-01-01

Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox,

Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline lake grevelingen

NARCIS (Netherlands)

Lipsewers, Yvonne A.; Hopmans, Ellen C.; Meysman, Filip J.R.; Sinninghe Damsté, Jaap S.|info:eu-repo/dai/nl/07401370X; Villanueva, Laura

2016-01-01

Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox,

Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria

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2005-06-01

1973. Ecology of Vibrio parahemolyticus in mixed-template amplifications: formation, consequences and elimination by Chesapeake Bay. J. Bacteriol. 113...Science 1930 and Engineering DOCTORAL DISSERTATION Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria by...DYNAMICS IN NATURAL POPULATIONS OF PLANKTONIC VIBRIO BACTERIA by Janelle Ren6e Thompson B.S. Biological Sciences, Stanford University 1998 M.S

Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline.

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Li, Guixiang; Xu, Guorui; Shen, Congcong; Tang, Yong; Zhang, Yuxin; Ma, Keming

2016-11-01

Above- and below-ground organisms are closely linked, but how elevational distribution pattern of soil microbes shifting across the treeline still remains unknown. Sampling of 140 plots with transect, we herein investigated soil bacterial distribution pattern from a temperate forest up to a subalpine meadow along an elevational gradient using Illumina sequencing. Our results revealed distinct elevational patterns of bacterial diversity above and below the treeline in responding to changes in soil conditions: a hollow elevational pattern in the forest (correlated with soil temperature, pH, and C:N ratio) and a significantly decreasing pattern in the meadow (correlated with soil pH, and available phosphorus). The bacterial community structure was also distinct between the forest and meadow, relating to soil pH in the forest and soil temperature in the meadow. Soil bacteria did not follow the distribution pattern of herb diversity, but bacterial community structure could be predicted by herb community composition. These results suggest that plant communities have an important influence on soil characteristics, and thus change the elevational distribution of soil bacteria. Our findings are useful for future assessments of climate change impacts on microbial community.

Implementing sponge physiological and genomic information to enhance the diversity of its culturable associated bacteria.

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Lavy, Adi; Keren, Ray; Haber, Markus; Schwartz, Inbar; Ilan, Micha

2014-02-01

In recent years new approaches have emerged for culturing marine environmental bacteria. They include the use of novel culture media, sometimes with very low-nutrient content, and a variety of growth conditions such as temperature, oxygen levels, and different atmospheric pressures. These approaches have largely been neglected when it came to the cultivation of sponge-associated bacteria. Here, we used physiological and environmental conditions to reflect the environment of sponge-associated bacteria along with genomic data of the prominent sponge symbiont Candidatus Poribacteria sp. WGA-4E, to cultivate bacteria from the Red Sea sponge Theonella swinhoei. Designing culturing conditions to fit the metabolic needs of major bacterial taxa present in the sponge, through a combined use of diverse culture media compositions with aerobic and microaerophilic states, and addition of antibiotics, yielded higher diversity of the cultured bacteria and led to the isolation of novel sponge-associated and sponge-specific bacteria. In this work, 59 OTUs of six phyla were isolated. Of these, 22 have no close type strains at the species level (< 97% similarity of 16S rRNA gene sequence), representing novel bacteria species, and some are probably new genera and even families. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean

OpenAIRE

Allers, Elke; Wright, Jody J; Konwar, Kishori M; Howes, Charles G; Beneze, Erica; Hallam, Steven J; Sullivan, Matthew B

2012-01-01

Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O2 concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and ...

Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.

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Thomas, Pious; Sekhar, Aparna Chandra

2017-05-01

The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.

Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen

NARCIS (Netherlands)

Do, Huyen Thi; Dao, Khoa Trong; Nguyen, Viet Khanh Hoang; Le Ngoc, Giang; Nguyen, Phuong Thi Mai; Le, Lam Tung; Phung, Nguyet Thu; M. van Straalen, Nico; Roelofs, Dick; Truong, Hai Nam

2017-01-01

Objective: In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen

[Diversity and enzyme-producing activity of culturable halophilic bacteria in Daishan Saltern of East China].

Science.gov (United States)

Yang, Dan-Dan; Li, Qian; Huang, Jing-Jing; Chen, Min

2012-11-01

Soil and saline water samples were collected from the Daishan Saltern of East China, and the halophilic bacteria were isolated and cultured by using selective media, aimed to investigate the diversity and enzyme-producing activity of culturable halophilic bacteria in saltern environment. A total of 181 strains were isolated by culture-dependent method. Specific primers were used to amplify the 16S rRNA gene of bacteria and archaea. The operation taxonomy units (OTUs) were determined by ARDRA method, and the representative strain of each OTU was sequenced. The phylogenetic position of all the isolated strains was determined by 16S rRNA sequencing. The results showed that the isolated 181 strains displayed 21 operational taxonomic units (OTUs), of which, 12 OTUs belonged to halophilic bacteria, and the others belonged to halophilic archaea. Phylogenetic analysis indicated that there were 7 genera presented among the halophilic bacteria group, and 4 genera presented among the halophilic archaea group. The dominant halophilic strains were of Halomonas and Haloarcula, with 46.8% in halophilic bacteria and 49.1% in halophilic archaea group, respectively. Enzyme-producing analysis indicated that most strains displayed enzyme-producing activity, including the activities of producing amylase, proteinase and lipase, and the dominant strains capable of enzyme-producing were of Haloarcula. Our results showed that in the environment of Daishan Saltern, there existed a higher diversity of halophilic bacteria, being a source sink for screening enzyme-producing bacterial strains.

Molecular diversity of legume root-nodule bacteria in Kakadu National Park, Northern Territory, Australia.

Directory of Open Access Journals (Sweden)

Bénédicte Lafay

2007-03-01

Full Text Available Symbiotic relationships between leguminous plants (family Fabaceae and nodule-forming bacteria in Australia native ecosystems remain poorly characterized despite their importance. Most studies have focused on temperate parts of the country, where the use of molecular approaches have already revealed the presence of Bradyrhizobium, Ensifer (formerly Sinorhizobium, Mesorhizobium and Rhizobium genera of legume root-nodule bacteria. We here provide the first molecular characterization of nodulating bacteria from tropical Australia.45 nodule-forming bacterial strains, isolated from eight native legume hosts at eight locations in Kakadu National Park, Northern Territory, Australia, were examined for their genetic diversity and phylogenetic position. Using SSU rDNA PCR-RFLPs and phylogenetic analyses, our survey identified nine genospecies, two of which, Bradyrhizobium genospp. B and P, had been previously identified in south-eastern Australia and one, Mesorhizobium genospecies AA, in southern France. Three of the five newly characterized Bradyrhizobium genospecies were more closely related to B. japonicum USDA110, whereas the other two belonged to the B. elkanii group. All five were each more closely related to strains sampled in various tropical areas outside Australia than to strains known to occur in Australia. We also characterized an entirely novel nodule-forming lineage, phylogenetically distant from any previously described rhizobial and non-rhizobial legume-nodulating lineage within the Rhizobiales.Overall, the present results support the hypothesis of tropical areas being centres of biodiversity and diversification for legume root-nodule bacteria and confirm the widespread occurrence of Bradyrhizobium genosp. B in continental Australia.

Structure, diversity and evolution of protein toxins from spore-forming entomopathogenic bacteria

NARCIS (Netherlands)

Maagd, de R.A.; Bravo, A.; Berry, C.; Crickmore, N.; Schnepf, H.E.

2003-01-01

Gram-positive spore-forming entomopathogenic bacteria can utilize a large variety of protein toxins to help them invade, infect, and finally kill their hosts, through their action on the insect midgut. These toxins belong to a number of homology groups containing a diversity of protein structures

Sterol Synthesis in Diverse Bacteria.

Science.gov (United States)

Wei, Jeremy H; Yin, Xinchi; Welander, Paula V

2016-01-01

Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria

High abundance and diversity of nitrite-dependent anaerobic methane-oxidizing bacteria in a paddy field profile.

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Zhou, Leiliu; Wang, Yu; Long, Xi-En; Guo, Jianhua; Zhu, Guibing

2014-11-01

The discovery of nitrite-dependent anaerobic methane oxidation (n-damo) mediated by 'Candidatus Methylomirabilis oxyfera' with nitrite and methane as substrates has connected biogeochemical carbon and nitrogen cycles in a new way. The paddy fields often carry substantial methane and nitrate, thus may be a favorable habitat for n-damo bacteria. In this paper, the vertical-temporal molecular fingerprints of M. oxyfera-like bacteria, including abundance and community composition, were investigated in a paddy soil core in Jiangyin, near the Yangtze River. Through qPCR investigation, high abundance of M. oxyfera-like bacteria up to 1.0 × 10(8) copies (g d.w.s.)(-1) in summer and 8.5 × 10(7) copies (g d.w.s.)(-1) in winter was observed in the ecotone of soil and groundwater in the paddy soil core, which was the highest in natural environments to our knowledge. In the ecotone, the ratio of M. oxyfera-like bacteria to total bacteria reached peak values of 2.80% in summer and 4.41% in winter. Phylogenetic analysis showed n-damo bacteria in the paddy soil were closely related to M. oxyfera and had high diversity in the soil/groundwater ecotone. All of the results indicated the soil/groundwater ecotone of the Jiangyin paddy field was a favorable environment for the growth of n-damo bacteria. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

The abundance and diversity of heterotrophic bacteria as a function of harvesting frequency of duckweed (Lemna minor L.) in recirculating aquaculture systems.

Science.gov (United States)

Ardiansyah, A; Fotedar, R

2016-07-01

Duckweed (Lemna minor L.) is a potential biofilter for nutrient removal and acts as a substrate for heterotrophic bacteria in recirculating aquaculture systems (RAS). Here, we determined the effects of harvesting frequency of duckweed on heterotrophic bacteria in RAS. Twelve independent RAS consisting of fish-rearing tank, biofilter tank and waste-collection tank were used to study the interactions between duckweed harvest frequencies up to 6 days and the composition, abundance and diversity of heterotrophic bacteria. After 36 days, heterotrophic bacteria in the biofilter tank were primarily Gram-negative cocci or ovoid, coccobacilli, Gram-negative bacilli and Gram-positive bacilli. Most bacterial genera were Bacillus and Pseudomonas while the least common was Acinetobacter. Duckweed harvested after every 2 days produced the highest specific growth rates (SGR) and total harvested biomass of duckweed, but harboured less abundant bacteria, whereas 6-day harvests had a higher growth index (GI) of duckweed than 2-day harvests, but caused a poor relationship between SGR and biomass harvest with the abundance and diversity of heterotrophic bacteria. Stronger correlations (R(2)  > 0·65) between duckweed SGR and biomass harvest with the heterotrophic bacteria diversity were observed at 4-day harvest frequency and the control. This study provides significant information on the interaction between the harvest frequency of duckweed and the composition, abundance and diversity of heterotrophic bacteria in recirculating aquaculture systems (RAS). Different harvest frequencies significantly influence the abundance and diversity of heterotrophic bacteria, which in turn may influence the nitrogen uptake efficiency of the system. The research is useful in improving the efficiency of removing nitrogenous metabolites in RAS directly by the duckweed and associated heterotrophic bacteria. © 2016 The Society for Applied Microbiology.

Genetic diversity of culturable bacteria in oil-contaminated rhizosphere of Galega orientalis

International Nuclear Information System (INIS)

Jussila, Minna M.; Jurgens, German; Lindstroem, Kristina; Suominen, Leena

2006-01-01

A collection of 50 indigenous meta-toluate tolerating bacteria isolated from oil-contaminated rhizosphere of Galega orientalis on selective medium was characterized and identified by classical and molecular methods. 16S rDNA partial sequencing showed the presence of five major lineages of the Bacteria domain. Gram-positive Rhodococcus, Bacillus and Arthrobacter and gram-negative Pseudomonas were the most abundant genera. Only one-fifth of the strains that tolerated m-toluate also degraded m-toluate. The inoculum Pseudomonas putida PaW85 was not found in the rhizosphere samples. The ability to degrade m-toluate by the TOL plasmid was detected only in species of the genus Pseudomonas. However, a few Rhodococcus erythropolis strains were found which were able to degrade m-toluate. A new finding was that Pseudomonas migulae strains and a few P. oryzihabitans strains were able to grow on m-toluate and most likely contained the TOL plasmid. Because strain specific differences in degradation abilities were found for P. oryzihabitans, separation at the strain level was important. For strain specific separation (GTG) 5 fingerprinting was the best method. A combination of the single locus ribotyping and the whole genomic fingerprinting techniques with the selective partial sequencing formed a practical molecular toolbox for studying genetic diversity of culturable bacteria in oil-contaminated rhizosphere. - Bacterial diversity during rhizoremediation in oil-contaminated soil is characterized by a combination of molecular methods

Highly task-related diversity vs. less task-related diversity among university staff

DEFF Research Database (Denmark)

Lauring, Jakob; Selmer, Jan

2013-01-01

from 489 university staff members showed that age diversity and cultural diversity, representing highly task-related diversity, were positively associated with most of the variables depicting group cohesiveness. On the other hand, gender diversity, illustrating less task-related diversity, seemed......As only very few large-scale studies have investigated multi-cultural university staff and as none of these studies have dealt with diversity and group processes, this survey was directed toward staffs in 16 science departments from three large universities in Denmark. Results based on the response...

Effect of air pollution on the total bacteria and pathogenic bacteria in different sizes of particulate matter.

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Liu, Huan; Zhang, Xu; Zhang, Hao; Yao, Xiangwu; Zhou, Meng; Wang, Jiaqi; He, Zhanfei; Zhang, Huihui; Lou, Liping; Mao, Weihua; Zheng, Ping; Hu, Baolan

2018-02-01

In recent years, air pollution events have occurred frequently in China during the winter. Most studies have focused on the physical and chemical composition of polluted air. Some studies have examined the bacterial bioaerosols both indoors and outdoors. But few studies have focused on the relationship between air pollution and bacteria, especially pathogenic bacteria. Airborne PM samples with different diameters and different air quality index values were collected in Hangzhou, China from December 2014 to January 2015. High-throughput sequencing of 16S rRNA was used to categorize the airborne bacteria. Based on the NCBI database, the "Human Pathogen Database" was established, which is related to human health. Among all the PM samples, the diversity and concentration of total bacteria were lowest in the moderately or heavily polluted air. However, in the PM2.5 and PM10 samples, the relative abundances of pathogenic bacteria were highest in the heavily and moderately polluted air respectively. Considering the PM samples with different particle sizes, the diversities of total bacteria and the proportion of pathogenic bacteria in the PM10 samples were different from those in the PM2.5 and TSP samples. The composition of PM samples with different sizes range may be responsible for the variances. The relative humidity, carbon monoxide and ozone concentrations were the main factors, which affected the diversity of total bacteria and the proportion of pathogenic bacteria. Among the different environmental samples, the compositions of the total bacteria were very similar in all the airborne PM samples, but different from those in the water, surface soil, and ground dust samples. Which may be attributed to that the long-distance transport of the airflow may influence the composition of the airborne bacteria. This study of the pathogenic bacteria in airborne PM samples can provide a reference for environmental and public health researchers. Copyright © 2017 Elsevier Ltd

Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments

DEFF Research Database (Denmark)

Zeng, Yonghui; Baumbach, Jan; Barbosa, Eudes Guilherme Vieira

2016-01-01

, biofilms, plant surfaces, intertidal sediment, soils, springs, and wastewater treatment plants, but none from marine waters or sediment. Phototrophic Gemmatimonadetes bacteria make up 0.4∼11.9% of whole phototrophic microbial communities in these habitats. Unexpectedly, an almost complete 37.9 kb long...... widely distributed in the environment and exhibit a higher genetic diversity than previously thought....

Diversity analysis of diazotrophic bacteria associated with the roots of tea (Camellia sinensis (L.) O. Kuntze).

Science.gov (United States)

Gulati, Arvind; Sood, Swati; Rahi, Praveen; Thakur, Rishu; Chauhan, Sunita; Chawla, Isha

2011-06-01

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included alpha-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; gamma-Proteobacteria genera Pseudomonas and Stenotrophomonas; and beta-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.

Size variability of the unit building block of peripheral light-harvesting antennas as a strategy for effective functioning of antennas of variable size that is controlled in vivo by light intensity.

Science.gov (United States)

Taisova, A S; Yakovlev, A G; Fetisova, Z G

2014-03-01

This work continuous a series of studies devoted to discovering principles of organization of natural antennas in photosynthetic microorganisms that generate in vivo large and highly effective light-harvesting structures. The largest antenna is observed in green photosynthesizing bacteria, which are able to grow over a wide range of light intensities and adapt to low intensities by increasing of size of peripheral BChl c/d/e antenna. However, increasing antenna size must inevitably cause structural changes needed to maintain high efficiency of its functioning. Our model calculations have demonstrated that aggregation of the light-harvesting antenna pigments represents one of the universal structural factors that optimize functioning of any antenna and manage antenna efficiency. If the degree of aggregation of antenna pigments is a variable parameter, then efficiency of the antenna increases with increasing size of a single aggregate of the antenna. This means that change in degree of pigment aggregation controlled by light-harvesting antenna size is biologically expedient. We showed in our previous work on the oligomeric chlorosomal BChl c superantenna of green bacteria of the Chloroflexaceae family that this principle of optimization of variable antenna structure, whose size is controlled by light intensity during growth of bacteria, is actually realized in vivo. Studies of this phenomenon are continued in the present work, expanding the number of studied biological materials and investigating optical linear and nonlinear spectra of chlorosomes having different structures. We show for oligomeric chlorosomal superantennas of green bacteria (from two different families, Chloroflexaceae and Oscillochloridaceae) that a single BChl c aggregate is of small size, and the degree of BChl c aggregation is a variable parameter, which is controlled by the size of the entire BChl c superantenna, and the latter, in turn, is controlled by light intensity in the course of cell

Diversity of Nitrate-Reducing and Denitrifying Bacteria in a Marine Aquaculture Biofilter and their Response to Sulfide

DEFF Research Database (Denmark)

Krieger, Bärbel; Schwermer, Carsten U.; Rezakhani, Nastaran

2006-01-01

with Alphaproteobacteria but also including Beta- and Gammaproteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. The diversity of the isolates was compared to the cultivation-independent diversity of nitrate-reducing and denitrifying bacteria based on narG and nosZ as functional marker genes. Growth experiments...

Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen

Science.gov (United States)

Lipsewers, Yvonne A.; Hopmans, Ellen C.; Meysman, Filip J. R.; Sinninghe Damsté, Jaap S.; Villanueva, Laura

2016-01-01

Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments. PMID:27812355

Abundance and diversity of denitrifying and anammox bacteria in seasonally hypoxic and sulfidic sediments of the saline Lake Grevelingen

Directory of Open Access Journals (Sweden)

Yvonne A. Lipsewers

2016-10-01

Full Text Available Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution at three different locations before (March and during summer hypoxia (August. The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen- and sulfur cycling in Lake Grevelingen sediments.

Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier.

Science.gov (United States)

Atanasova, Nina S; Pietilä, Maija K; Oksanen, Hanna M

2013-10-01

The significance of antimicrobial substances, halocins, produced by halophilic archaea and bacteria thriving in hypersaline environments is relatively unknown. It is suggested that their production might increase species diversity and give transient competitive advances to the producer strain. Halocin production is considered to be common among halophilic archaea, but there is a lack of information about halocins produced by bacteria in highly saline environments. We studied the antimicrobial activity of 68 halophilic archaea and 22 bacteria isolated from numerous geographically distant hypersaline environments. Altogether 144 antimicrobial interactions were found between the strains and aside haloarchaea, halophilic bacteria from various genera were identified as halocin producers. Close to 80% of the interactions were detected between microorganisms from different genera and in few cases, even across the domain boundary. Several of the strains produced halocins with a wide inhibitory spectrum as has been observed before. Most of the antimicrobial interactions were found between strains from distant sampling sites indicating that hypersaline environments around the world have similar microorganisms with the potential to produce wide activity range antimicrobials. © 2013 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.

Science.gov (United States)

Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha

2017-11-01

Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates

Functionally relevant diversity of closely related Nitrospira in activated sludge.

Science.gov (United States)

Gruber-Dorninger, Christiane; Pester, Michael; Kitzinger, Katharina; Savio, Domenico F; Loy, Alexander; Rattei, Thomas; Wagner, Michael; Daims, Holger

2015-03-01

Nitrospira are chemolithoautotrophic nitrite-oxidizing bacteria that catalyze the second step of nitrification in most oxic habitats and are important for excess nitrogen removal from sewage in wastewater treatment plants (WWTPs). To date, little is known about their diversity and ecological niche partitioning within complex communities. In this study, the fine-scale community structure and function of Nitrospira was analyzed in two full-scale WWTPs as model ecosystems. In Nitrospira-specific 16S rRNA clone libraries retrieved from each plant, closely related phylogenetic clusters (16S rRNA identities between clusters ranged from 95.8% to 99.6%) within Nitrospira lineages I and II were found. Newly designed probes for fluorescence in situ hybridization (FISH) allowed the specific detection of several of these clusters, whose coexistence in the WWTPs was shown for prolonged periods of several years. In situ ecophysiological analyses based on FISH, relative abundance and spatial arrangement quantification, as well as microautoradiography revealed functional differences of these Nitrospira clusters regarding the preferred nitrite concentration, the utilization of formate as substrate and the spatial coaggregation with ammonia-oxidizing bacteria as symbiotic partners. Amplicon pyrosequencing of the nxrB gene, which encodes subunit beta of nitrite oxidoreductase of Nitrospira, revealed in one of the WWTPs as many as 121 species-level nxrB operational taxonomic units with highly uneven relative abundances in the amplicon library. These results show a previously unrecognized high diversity of Nitrospira in engineered systems, which is at least partially linked to niche differentiation and may have important implications for process stability.

Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea

Directory of Open Access Journals (Sweden)

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

Ice nucleation active bacteria in precipitation are genetically diverse and nucleate ice by employing different mechanisms.

Science.gov (United States)

Failor, K C; Schmale, D G; Vinatzer, B A; Monteil, C L

2017-12-01

A growing body of circumstantial evidence suggests that ice nucleation active (Ice + ) bacteria contribute to the initiation of precipitation by heterologous freezing of super-cooled water in clouds. However, little is known about the concentration of Ice + bacteria in precipitation, their genetic and phenotypic diversity, and their relationship to air mass trajectories and precipitation chemistry. In this study, 23 precipitation events were collected over 15 months in Virginia, USA. Air mass trajectories and water chemistry were determined and 33 134 isolates were screened for ice nucleation activity (INA) at -8 °C. Of 1144 isolates that tested positive during initial screening, 593 had confirmed INA at -8 °C in repeated tests. Concentrations of Ice + strains in precipitation were found to range from 0 to 13 219 colony forming units per liter, with a mean of 384±147. Most Ice + bacteria were identified as members of known and unknown Ice + species in the Pseudomonadaceae, Enterobacteriaceae and Xanthomonadaceae families, which nucleate ice employing the well-characterized membrane-bound INA protein. Two Ice + strains, however, were identified as Lysinibacillus, a Gram-positive genus not previously known to include Ice + bacteria. INA of the Lysinibacillus strains is due to a nanometer-sized molecule that is heat resistant, lysozyme and proteinase resistant, and secreted. Ice + bacteria and the INA mechanisms they employ are thus more diverse than expected. We discuss to what extent the concentration of culturable Ice + bacteria in precipitation and the identification of a new heat-resistant biological INA mechanism support a role for Ice + bacteria in the initiation of precipitation.

Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria.

Science.gov (United States)

Raaijmakers, Jos M; Mazzola, Mark

2012-01-01

Soil- and plant-associated environments harbor numerous bacteria that produce antibiotic metabolites with specific or broad-spectrum activities against coexisting microorganisms. The function and ecological importance of antibiotics have long been assumed to yield a survival advantage to the producing bacteria in the highly competitive but resource-limited soil environments through direct suppression. Although specific antibiotics may enhance producer persistence when challenged by competitors or predators in soil habitats, at subinhibitory concentrations antibiotics exhibit a diversity of other roles in the life history of the producing bacteria. Many processes modulated by antibiotics may be inherently critical to the producing bacterium, such as the acquisition of substrates or initiation of developmental changes that will ensure survival under stressful conditions. Antibiotics may also have roles in more complex interactions, including in virulence on host plants or in shaping the outcomes of multitrophic interactions. The innate functions of antibiotics to producing bacteria in their native ecosystem are just beginning to emerge, but current knowledge already reveals a breadth of activities well beyond the historical perspective of antibiotics as weaponry in microbial conflicts.

Improving diversity in cultures of bacteria from an extreme environment.

Science.gov (United States)

Vester, Jan Kjølhede; Glaring, Mikkel Andreas; Stougaard, Peter

2013-08-01

The ikaite columns in the Ikka Fjord in Greenland represent one of the few permanently cold and alkaline environments on Earth, and the interior of the columns is home to a bacterial community adapted to these extreme conditions. The community is characterized by low cell numbers imbedded in a calcium carbonate matrix, making extraction of bacterial cells and DNA a challenge and limiting molecular and genomic studies of this environment. To utilize this genetic resource, cultivation at high pH and low temperature was studied as a method for obtaining biomass and DNA from the fraction of this community that would not otherwise be amenable to genetic analyses. The diversity and community dynamics in mixed cultures of bacteria from ikaite columns was investigated using denaturing gradient gel electrophoresis and pyrosequencing of 16S rDNA. Both medium composition and incubation time influenced the diversity of the culture and many hitherto uncharacterized genera could be brought into culture by extended incubation time. Extended incubation time also gave rise to a more diverse community with a significant number of rare species not detected in the initial community.

Antifungal Bacteria on Woodland Salamander Skin Exhibit High Taxonomic Diversity and Geographic Variability.

Science.gov (United States)

Muletz-Wolz, Carly R; DiRenzo, Graziella V; Yarwood, Stephanie A; Campbell Grant, Evan H; Fleischer, Robert C; Lips, Karen R

2017-05-01

Diverse bacteria inhabit amphibian skin; some of those bacteria inhibit growth of the fungal pathogen Batrachochytrium dendrobatidis Yet there has been no systematic survey of anti- B. dendrobatidis bacteria across localities, species, and elevations. This is important given geographic and taxonomic variations in amphibian susceptibility to B. dendrobatidis Our collection sites were at locations within the Appalachian Mountains where previous sampling had indicated low B. dendrobatidis prevalence. We determined the numbers and identities of anti- B. dendrobatidis bacteria on 61 Plethodon salamanders (37 P. cinereus , 15 P. glutinosus , 9 P. cylindraceus ) via culturing methods and 16S rRNA gene sequencing. We sampled co-occurring species at three localities and sampled P. cinereus along an elevational gradient (700 to 1,000 meters above sea level [masl]) at one locality. We identified 50 anti- B. dendrobatidis bacterial operational taxonomic units (OTUs) and found that the degree of B. dendrobatidis inhibition was not correlated with relatedness. Five anti- B. dendrobatidis bacterial strains occurred on multiple amphibian species at multiple localities, but none were shared among all species and localities. The prevalence of anti- B. dendrobatidis bacteria was higher at Shenandoah National Park (NP), VA, with 96% (25/26) of salamanders hosting at least one anti- B. dendrobatidis bacterial species compared to 50% (7/14) at Catoctin Mountain Park (MP), MD, and 38% (8/21) at Mt. Rogers National Recreation Area (NRA), VA. At the individual level, salamanders at Shenandoah NP had more anti- B. dendrobatidis bacteria per individual (μ = 3.3) than those at Catoctin MP (μ = 0.8) and at Mt. Rogers NRA (μ = 0.4). All salamanders tested negative for B. dendrobatidis Anti- B. dendrobatidis bacterial species are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacterial species that we identified may play a

Co-existence of Anaerobic Ammonium Oxidation Bacteria and Denitrifying Anaerobic Methane Oxidation Bacteria in Sewage Sludge: Community Diversity and Seasonal Dynamics.

Science.gov (United States)

Xu, Sai; Lu, Wenjing; Mustafa, Muhammad Farooq; Caicedo, Luis Miguel; Guo, Hanwen; Fu, Xindi; Wang, Hongtao

2017-11-01

Anaerobic ammonium oxidation (ANAMMOX) and denitrifying anaerobic methane oxidation (DAMO) have been recently discovered as relevant processes in the carbon and nitrogen cycles of wastewater treatment plants. In this study, the seasonal dynamics of ANAMMOX and DAMO bacterial community structures and their abundance in sewage sludge collected from wastewater treatment plants were analysed. Results indicated that ANAMMOX and DAMO bacteria co-existed in sewage sludge in different seasons and their abundance was positively correlated (P bacteria in autumn and winter indicated that these seasons were the preferred time to favour the growth of ANAMMOX and DAMO bacteria. The community structure of ANNAMOX and DAMO bacteria could also shift with seasonal changes. The "Candidatus Brocadia" genus of ANAMMOX bacteria was mainly recovered in spring and summer, and an unknown cluster was primarily detected in autumn and winter. Similar patterns of seasonal variation in the community structure of DAMO bacteria were also observed. Group B was the dominant in spring and summer, whereas in autumn and winter, group A and group B presented almost the same proportion. The redundancy analysis revealed that pH and nitrate were the most significant factors affecting community structures of these two groups (P < 0.01). This study reported the diversity of ANAMMOX and DAMO in wastewater treatment plants that may be the basis for new nitrogen removal technologies.

The Effect of Biofertilizer on The Diversity of N2O Reducing Bacteria in Paddy Fields of Sukabumi, Indonesia

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Alfan Cahyadi

2017-12-01

Full Text Available Some of the methanotrophic bacteria and N2O reducing bacteria have been proven to be able to support the plant growth and increase the productivity of paddy. However effect of the methanotrophic and N2O reducing bacteria application as a biofertilizer to indigenous N2O reducing bacteria is still not well known yet. The aim of this study was to analyze the diversity of N2O reducing bacteria in lowland paddy soil based on a nosZ gene. Soil samples were taken from lowland paddy soils in Pelabuhan Ratu Sukabumi, West Java, Indonesia. There were two treatments for the paddy field soil, ie. biofertilizer-treated field 20% fertilizer (50 kg/ha with the addition of biofertilizer and 100% fertilizer. PCR amplification of nosZ gene was successfully conducted using nosZF and nosZR primer pair. Denaturing Gradient Gel Electrophoresis (DGGE process was conducted at 150 V for 5.5h. There were three differences nosZ bands were sequenced. The phylogenetic analysis showed that they were close to uncultured bacteria. Microbial diversity in the biofertilizer-treated field was higher than that of in the 100% fertilizer-treated field. The biofertilizer treatment has higher in microbial diversity than that of applied non-biofertilizer paddy fields. This research might have impact in the application of biofertilizers due to the emission of N2O as a green house gas from paddy fields farming activity. The biofertilizer has great potential application in sustainable environmental friendly agriculture systems.

Influence of Engineering Bacteria Quantitative Inspection on Diversity of Anpeng Alkali Mine Resources Exploitation

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Yu Tao

2016-03-01

Full Text Available Cadmium (Cd is a heavy metal pollutant seriously threatening creatures, and highly concentrated Cd in soil severely inhibits the activity of microbial populations. Soil in Anpeng Alkali Mine area in Nanyang city (Henan province is seriously polluted by heavy metal. Both copper (Cu and Cd content are found to be over standard, in which, Cu belongs to mild contamination while Cd is a serious contamination. To detect diversity of microbial communities in soil in the process of bioremediation, Cd polluted soil samples are collected from orefield for pot experiment, Biolog micro-plate technology is used to study the influence of applying low, medium and high amount of rice straw (5.3 t/ha, 10.2 t/ha and 23.4 t/ha in polluted soil and combining low, medium and high amount of rice straw with surface displayed engineering bacteria (X4/pCIM on microbial community. In the meantime, X4/pCIM is quantitatively measured by real-time polymerase chain reaction (PCR. Biolog experimental results indicate that the combination of rice straw and engineering bacteria is able to change the composition of soil microbial community, and has a difference in influencing rhizosphere and non-rhizosphere microorganisms. Through real-time PCR, it is found that the number of engineering bacteria falls to 103 after 120 days of bioremediation. Therefore, it can be concluded that combining rice straw with engineering bacteria can change the composition of soil microbial community and have diverse influences as application rate changes, without obvious rules to follow.

Effect of diesel leakage in circulating cooling water system on preponderant bacteria diversity and bactericidal effect of biocides.

Science.gov (United States)

Zhong, Huiyun; Liu, Fang; Lu, Jinjin; Yang, Wei; Zhao, Chaocheng

2015-01-01

Petroleum products leakage results in adverse effect on the normal operation of a circulating cooling water system. However, relatively little research has been done to explore the effect of petroleum products leakage on circulating cooling water quality and biofilm preponderant bacteria diversity. Also, normal biocides application modes cannot fulfil the need for biofilm control. In this study, diesel oil was used as the experimental subject representing leaking petroleum products; the effect of diesel addition on biofilm preponderant bacteria diversity and the bactericidal effect of chlorine dioxide and tetradecyl dimethyl benzyl ammonium chloride (1427) was investigated. Bacterial community structures were examined by PCR-denaturing gradient gel electrophoresis and PCR cloning of 16S rDNA genes. Except for 100 mg/L diesel, increasing diesel concentration enhanced the biofilm detachment ratio compared with the control test. The microstructure of biofilm samples with 0, 300 and 900 mg/L diesel addition was observed. The species of preponderant bacteria in the biofilm sample with 300 mg/L diesel addition were more and the bacterial distribution was more uniform than those in the biofilm sample with 900 mg/L diesel addition. With ClO2 and 1427 addition, chemical oxygen demand increased, lipid phosphorus and bacterial count first decreased and then remained stable, and the bactericidal ratio first increased and then remained stable. Diesel addition variation has more obvious effect on ClO2 than 1427.

Endophytes diversity of bacteria associated with roots of colosuana (bothriochloa pertusa) pasture in three locations of Sucre Department, Colombia

International Nuclear Information System (INIS)

Perez C, Alexander; Rojas S, Johanna; Fuentes C, Justo

2010-01-01

The objective of this study was to isolate endophytes diversity of culturable bacteria associated with grass roots colosuana Bothriochloa pertusa (L) a. camus in three localities of the department of Sucre, Colombia. endophytes bacterial diversity was performed by isolation of colonies on media culture. The population density was estimated by direct counting of colonies on plate and cultural characteristics of each morphotype were obtained by observation of each colony made. We determined the correlation diversity, population density and locations, using ANOVA and principal component analysis or simple correspondence, using the statistical program R, 2009 (4.5). 20 farms livestock were sampled by locality; it was observed the presence of various bacterial morphotypes endophytes. We found significant differences between diversity (morphotypes), population density (UFC.raiz -1 ) and locations. The diversity of bacterial endophytes represents only a small fraction of the total diversity present in nature; being little information we have of the presence of these microorganisms in specific agro-ecosystems, which is why this work becomes the first evidence of association between bacteria and roots of grass endophytes colosuana in Colombia.

Diversity of rare and abundant bacteria in surface waters of the Southern Adriatic Sea.

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Quero, Grazia Marina; Luna, Gian Marco

2014-10-01

Bacteria are fundamental players in the functioning of the ocean, yet relatively little is known about the diversity of bacterioplankton assemblages and the factors shaping their spatial distribution. We investigated the diversity and community composition of bacterioplankton in surface waters of the Southern Adriatic sub-basin (SAd) in the Mediterranean Sea, across an environmental gradient from coastal to offshore stations. Bacterioplankton diversity was investigated using a whole-assemblage genetic fingerprinting technique (Automated Ribosomal Intergenic Spacer Analysis, ARISA) coupled with 16S rDNA amplicon pyrosequencing. The main physico-chemical variables showed clear differences between coastal and offshore stations, with the latter displaying generally higher temperature, salinity and oxygen content. Bacterioplankton richness was higher in coastal than offshore waters. Bacterial community composition (BCC) differed significantly between coastal and offshore waters, and appeared to be influenced by temperature (explaining up to 30% of variance) and by the trophic state. Pyrosequencing evidenced dominance of Alphaproteobacteria (SAR11 cluster), uncultured Gammaproteobacteria (Rhodobacteraceae) and Cyanobacteria (Synechococcus). Members of the Bacteroidetes phylum were also abundant, and accounted for 25% in the station characterized by the higher organic carbon availability. Bacterioplankton assemblages included a few dominant taxa and a very large proportion (85%) of rare (diversity, particularly evident at the level of the rare taxa, suggests to direct future investigations toward larger spatial or temporal scales, to better understand the role of bacterioplankton in the ecosystem functioning and the biogeochemistry of the basin. Copyright © 2014 Elsevier B.V. All rights reserved.

Abundance and diversity of n-alkane-degrading bacteria in a forest soil co-contaminated with hydrocarbons and metals: a molecular study on alkB homologous genes.

Science.gov (United States)

Pérez-de-Mora, Alfredo; Engel, Marion; Schloter, Michael

2011-11-01

Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated, two intermediately contaminated, and a noncontaminated zone. Contaminant concentrations, hydrocarbon profiles, and soil microbial respiration and biomass were studied. Abundance of n-alkane-degrading bacteria was quantified via real-time PCR of alkB, whereas genetic diversity was examined using molecular fingerprints (T-RFLP) and clone libraries. Along the contamination plume, hydrocarbon profiles and increased respiration rates suggested on-going natural attenuation at the site. Gene copy numbers of alkB were similar in contaminated and control areas. However, T-RFLP-based fingerprints suggested lower diversity and evenness of the n-alkane-degrading bacterial community in the highly contaminated zone compared to the other areas; both diversity and evenness were negatively correlated with metal and hydrocarbon concentrations. Phylogenetic analysis of alkB denoted a shift of the hydrocarbon-degrading bacterial community from Gram-positive bacteria in the control zone (most similar to Mycobacterium and Nocardia types) to Gram-negative genotypes in the contaminated zones (Acinetobacter and alkB sequences with little similarity to those of known bacteria). Our results underscore a qualitative rather than a quantitative response of

Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.

Science.gov (United States)

Erwin, Patrick M; Olson, Julie B; Thacker, Robert W

2011-01-01

Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP), might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods. We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6%) of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil). The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the ambient

Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics

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Perron, Gabriel G.; Whyte, Lyle; Turnbaugh, Peter J.; Goordial, Jacqueline; Hanage, William P.; Dantas, Gautam; Desai, Michael M.

2015-01-01

Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes. PMID:25807523

The Structural Diversity of Carbohydrate Antigens of Selected Gram-Negative Marine Bacteria

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Elena P. Ivanova

2011-10-01

Full Text Available Marine microorganisms have evolved for millions of years to survive in the environments characterized by one or more extreme physical or chemical parameters, e.g., high pressure, low temperature or high salinity. Marine bacteria have the ability to produce a range of biologically active molecules, such as antibiotics, toxins and antitoxins, antitumor and antimicrobial agents, and as a result, they have been a topic of research interest for many years. Among these biologically active molecules, the carbohydrate antigens, lipopolysaccharides (LPSs, O-antigens found in cell walls of Gram-negative marine bacteria, show great potential as candidates in the development of drugs to prevent septic shock due to their low virulence. The structural diversity of LPSs is thought to be a reflection of the ability for these bacteria to adapt to an array of habitats, protecting the cell from being compromised by exposure to harsh environmental stress factors. Over the last few years, the variety of structures of core oligosaccharides and O-specific polysaccharides from LPSs of marine microrganisms has been discovered. In this review, we discuss the most recently encountered structures that have been identified from bacteria belonging to the genera Aeromonas, Alteromonas, Idiomarina, Microbulbifer, Pseudoalteromonas, Plesiomonas and Shewanella of the Gammaproteobacteria phylum; Sulfitobacter and Loktanella of the Alphaproteobactera phylum and to the genera Arenibacter, Cellulophaga, Chryseobacterium, Flavobacterium, Flexibacter of the Cytophaga-Flavobacterium-Bacteroides phylum. Particular attention is paid to the particular chemical features of the LPSs, such as the monosaccharide type, non-sugar substituents and phosphate groups, together with some of the typifying traits of LPSs obtained from marine bacteria. A possible correlation is then made between such features and the environmental adaptations undertaken by marine bacteria.

High diversity of nitrogen-fixing bacteria in upper reaches of Heihe River, Northwestern China

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Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.

2013-03-01

Vegetation plays a key role to water conservation in southern Qilian Mountains (Northwestern China), the upper reaches of Heihe River. Nitrogen-fixing bacteria are crucial for vegetation protection because they can supply plants with nitrogen source. Nevertheless, little is known about nitrogen-fixing bacteria in this region. In present study, nifH gene clone libraries were established for detecting the difference of nitrogen-fixing bacterial communities between Potentilla parvifolia shrub and Carex alrofusca meadow in the southern Qilian Mountains. All the identified nitrogen-fixing bacterial clones belonged to Proteobacteria. At the genus level, the Azospirillum sp. was only detected in shrub soil while Thiocapsa sp., Derxiasp., Ectothiorhodospira sp., Mesorhizobium sp., Klebsiella sp., Ensifer sp., Methylocella sp. and Peseudomonas sp. were just detected in meadow soil. Shannon-Wiener index of nifH gene ranged from 1.5 to 2.8 and was higher in meadow soil than shrub soil. Contrarily, the nifH gene copies and CFUs of cultured nitrogen-fixing bacteria ranged from 0.4 × 107 to 6.9 × 107 copies g-1 soil and 0.97 × 106 to 12.78 × 106 g-1 soil, respectively. Furthermore, both of them were lower in meadow soil than shrub soil. Statistical analysis revealed that diversity and copies of nifH gene mostly correlated with aboveground biomass in shrub soil. In meadow soil, nifH gene diversity was principally affected by altitude while copies did by soil available K.

The diversity and abundance of bacteria and oxygenic phototrophs in saline biological desert crusts in Xinjiang, northwest China.

Science.gov (United States)

Li, Ke; Liu, Ruyin; Zhang, Hongxun; Yun, Juanli

2013-07-01

Although microorganisms, particularly oxygenic phototrophs, are known as the major players in the biogeochemical cycles of elements in desert soil ecosystems and have received extensive attention, still little is known about the effects of salinity on the composition and abundances of microbial community in desert soils. In this study, the diversity and abundance of bacteria and oxygenic phototrophs in biological desert crusts from Xinjiang province, which were under different salinity conditions, were investigated by using clone library and quantitative PCR (qPCR). The 16S rRNA gene phylogenetic analysis showed that cyanobacteria, mainly Microcoleus vagnitus of the order Oscillatoriales, were predominant in the low saline crusts, while other phototrophs, such as diatom, were the main microorganism group responsible for the oxygenic photosynthesis in the high saline crusts. Furthermore, the higher salt content in crusts may stimulate the growth of other bacteria, including Deinococcus-Thermus, Bacteroidetes, and some subdivisions of Proteobacteria (β-, γ-, and δ-Proteobacteria). The cpcBA-IGS gene analysis revealed the existence of novel M. vagnitus strains in this area. The qPCR results showed that the abundance of oxygenic phototrophs was significantly higher under lower saline condition than that in the higher saline crusts, suggesting that the higher salinity in desert crusts could suppress the numbers of total bacteria and phototrophic bacteria but did highly improve the diversity of salt-tolerant bacteria.

Heavy metal pollution exerts reduction/adaptation in the diversity and enzyme expression profile of heterotrophic bacteria in Cochin estuary, India

Energy Technology Data Exchange (ETDEWEB)

Jose, Jiya; Giridhar, Rajesh; Anas, Abdulaziz [National Institute of Oceanography (CSIR), Regional Centre, PB 1913, Cochin, Kerala 682018 (India); Loka Bharathi, P.A. [National Institute of Oceanography (CSIR), Dona Paula, Goa 403004 (India); Nair, Shanta, E-mail: shanta@nio.org [National Institute of Oceanography (CSIR), Dona Paula, Goa 403004 (India)

2011-10-15

Over the past three decades heavy metal pollution has increased substantially in Cochin estuary, south west coast of India. Here we studied the distribution, diversity and enzyme expression profile of culturable microbial population along a pollution gradient. The distribution of resistance against 5 mM concentration of Zn, Co, Ni and Cu was observed among 90-100% of bacterial isolates retrieved from highly polluted Eloor, whereas it was less than 40% in Vypin and Munambam. Similarly, there was a difference in the distribution and diversity of bacterial phyla with predominance of Proteobacteria in Eloor and Firmicutes in Munambam and Vypin. We observed that 75-100% of the organisms retrieved from Eloor had low levels of expression for hydrolytic enzyme. In conclusion, the heavy metal pollution in Cochin estuary brought in reduction/adaptation in the distribution, diversity and enzyme expression profile of bacteria, which may impart adverse impacts on ecosystem functioning. - Highlights: > Substantial proliferation of heavy metal pollution in Cochin estuary. > 90-100% of bacteria were resistant against heavy metals. > Proteobacteria dominated in the hot spot sites. > Low Enzyme expression profile among microorganisms in hot spot sites. - Heavy metal pollution exerts pressure on the diversity and enzyme expression profile of estuarine bacteria.

Diversity and importance of filamentous bacteria in biological nutrient removal wastewater treatment plants – a worldwide survey

DEFF Research Database (Denmark)

Nierychlo, Marta; McIlroy, Simon Jon; Ziegler, Anja Sloth

Filamentous bacteria are present in wastewater treatment plants (WWTPs) worldwide where they play an important role by providing structural backbone for activated sludge (AS) flocs and thus ensuring good settling properties. However, their excessive growth may lead to inter-floc bridging, which i...... demonstrated limited diversity of abundant filamentous bacteria in AS community around the globe presenting a hope for solution of sludge settling problems if we can couple the knowledge of filaments identity and their physiology....

Diversity of Endophytic Bacteria in a Fern Species Dryopteris uniformis (Makino) Makino and Evaluation of Their Antibacterial Potential Against Five Foodborne Pathogenic Bacteria.

Science.gov (United States)

Das, Gitishree; Park, Seonjoo; Baek, Kwang-Hyun

2017-05-01

The fern plant Dryopteris uniformis has traditionally been used in herbal medicine and possesses many biological activities. This study was conducted to explore the endophytic bacterial diversity associated with D. uniformis and evaluate their antibacterial potential against foodborne pathogenic bacteria (FPB). Among 51 isolated endophytic bacteria (EB), 26 EB were selected based on their morphological characteristics and identified by 16S rRNA gene analysis. The distribution of EB was diverse in the leaf and the stem/root tissues. When the EB were screened for antibacterial activity against five FPB, Listeria monocytogenes, Salmonella Typhimurium, Bacillus cereus, Staphylococcus aureus, and Escherichia coli O157:H7, four EB Bacillus sp. cryopeg, Paenibacillus sp. rif200865, Staphylococcus warneri, and Bacillus psychrodurans had a broad spectrum of antibacterial activity (9.58 ± 0.66 to 21.47 ± 0.27 mm inhibition zone). The butanol solvent extract of B. sp. cryopeg and P. sp. rif200865 displayed effective antibacterial activity against the five FPB, which was evident from the scanning electron microscopy with irregular or burst cell morphology in the EB-treated bacteria compared to smooth and regular cells in case of the control bacteria. The minimum inhibitory concentration and minimum bactericidal concentration values ranged between 250-500 μg/mL and 500-100 μg/mL, respectively. The above outcomes signify the huge prospective of the selected EB in the food industry. Overall, the above results suggested that D. uniformis contains several culturable EB that possess effective antibacterial compounds, and that EB can be utilized as a source of natural antibacterial agents for their practical application in food industry to control the spread of FPB as a natural antibacterial agent.

Diversity, metabolic properties and arsenic mobilization potential of indigenous bacteria in arsenic contaminated groundwater of West Bengal, India.

Science.gov (United States)

Paul, Dhiraj; Kazy, Sufia K; Gupta, Ashok K; Pal, Taraknath; Sar, Pinaki

2015-01-01

Arsenic (As) mobilization in alluvial aquifers is caused by a complex interplay of hydro-geo-microbiological activities. Nevertheless, diversity and biogeochemical significance of indigenous bacteria in Bengal Delta Plain are not well documented. We have deciphered bacterial community compositions and metabolic properties in As contaminated groundwater of West Bengal to define their role in As mobilization. Groundwater samples showed characteristic high As, low organic carbon and reducing property. Culture-independent and -dependent analyses revealed presence of diverse, yet near consistent community composition mostly represented by genera Pseudomonas, Flavobacterium, Brevundimonas, Polaromonas, Rhodococcus, Methyloversatilis and Methylotenera. Along with As-resistance and -reductase activities, abilities to metabolize a wide range carbon substrates including long chain and polyaromatic hydrocarbons and HCO3, As3+ as electron donor and As5+/Fe3+ as terminal electron acceptor during anaerobic growth were frequently observed within the cultivable bacteria. Genes encoding cytosolic As5+ reductase (arsC) and As3+ efflux/transporter [arsB and acr3(2)] were found to be more abundant than the dissimilatory As5+ reductase gene arrA. The observed metabolic characteristics showed a good agreement with the same derived from phylogenetic lineages of constituent populations. Selected bacterial strains incubated anaerobically over 300 days using natural orange sand of Pleistocene aquifer showed release of soluble As mostly as As3+ along with several other elements (Al, Fe, Mn, K, etc.). Together with the production of oxalic acid within the biotic microcosms, change in sediment composition and mineralogy indicated dissolution of orange sand coupled with As/Fe reduction. Presence of arsC gene, As5+ reductase activity and oxalic acid production by the bacteria were found to be closely related to their ability to mobilize sediment bound As. Overall observations suggest that

Phylogenetic diversity, host-specificity and community profiling of sponge-associated bacteria in the northern Gulf of Mexico.

Directory of Open Access Journals (Sweden)

Patrick M Erwin

Full Text Available Marine sponges can associate with abundant and diverse consortia of microbial symbionts. However, associated bacteria remain unexamined for the majority of host sponges and few studies use phylogenetic metrics to quantify symbiont community diversity. DNA fingerprinting techniques, such as terminal restriction fragment length polymorphisms (T-RFLP, might provide rapid profiling of these communities, but have not been explicitly compared to traditional methods.We investigated the bacterial communities associated with the marine sponges Hymeniacidon heliophila and Haliclona tubifera, a sympatric tunicate, Didemnum sp., and ambient seawater from the northern Gulf of Mexico by combining replicated clone libraries with T-RFLP analyses of 16S rRNA gene sequences. Clone libraries revealed that bacterial communities associated with the two sponges exhibited lower species richness and lower species diversity than seawater and tunicate assemblages, with differences in species composition among all four source groups. T-RFLP profiles clustered microbial communities by source; individual T-RFs were matched to the majority (80.6% of clone library sequences, indicating that T-RFLP analysis can be used to rapidly profile these communities. Phylogenetic metrics of community diversity indicated that the two sponge-associated bacterial communities include dominant and host-specific bacterial lineages that are distinct from bacteria recovered from seawater, tunicates, and unrelated sponge hosts. In addition, a large proportion of the symbionts associated with H. heliophila were shared with distant, conspecific host populations in the southwestern Atlantic (Brazil.The low diversity and species-specific nature of bacterial communities associated with H. heliophila and H. tubifera represent a distinctly different pattern from other, reportedly universal, sponge-associated bacterial communities. Our replicated sampling strategy, which included samples that reflect the

In silico and experimental methods revealed highly diverse bacteria with quorum sensing and aromatics biodegradation systems--a potential broad application on bioremediation.

Science.gov (United States)

Huang, Yili; Zeng, Yanhua; Yu, Zhiliang; Zhang, Jing; Feng, Hao; Lin, Xiuchun

2013-11-01

Phylogenetic overlaps between aromatics-degrading bacteria and acyl-homoserine-lactone (AHL) or autoinducer (AI) based quorum-sensing (QS) bacteria were evident in literatures; however, the diversity of bacteria with both activities had never been finely described. In-silico searching in NCBI genome database revealed that more than 11% of investigated population harbored both aromatic ring-hydroxylating-dioxygenase (RHD) gene and AHL/AI-synthetase gene. These bacteria were distributed in 10 orders, 15 families, 42 genus and 78 species. Horizontal transfers of both genes were common among them. Using enrichment and culture dependent method, 6 Sphingomonadales and 4 Rhizobiales with phenanthrene- or pyrene-degrading ability and AHL-production were isolated from marine, wetland and soil samples. Thin-layer-chromatography and gas-chromatography-mass-spectrum revealed that these Sphingomonads produced various AHL molecules. This is the first report of highly diverse bacteria that harbored both aromatics-degrading and QS systems. QS regulation may have broad impacts on aromatics biodegradation, and would be a new angle for developing bioremediation technology. Copyright © 2013 Elsevier Ltd. All rights reserved.

Co-existence of Rhizobia and Diverse Non-rhizobial Bacteria in the Rhizosphere and Nodules of Dalbergia odorifera Seedlings Inoculated with Bradyrhizobium elkanii, Rhizobium multihospitium–Like and Burkholderia pyrrocinia–Like Strains

Directory of Open Access Journals (Sweden)

Junkun Lu

2017-11-01

relative abundances (0.01–3.41%. Regarding non-rhizobial bacteria, 32 genera were found in the nodules, with non-rhizobial bacteria being predominant in the N omitted potting mix (with a relative abundance of 56–87%. This study suggests that legume nodules are inhabited by a high diversity of non-rhizobial bacteria, which may play a vital role in nodulation and N2 fixation in the host plants.

Plant n-alkane production from litterfall altered the diversity and community structure of alkane degrading bacteria in litter layer in lowland subtropical rainforest in Taiwan

Science.gov (United States)

Huang, Tung-Yi; Hsu, Bing-Mu; Chao, Wei-Chun; Fan, Cheng-Wei

2018-03-01

n-Alkane and alkane-degrading bacteria have long been used as crucial biological indicators of paleoecology, petroleum pollution, and oil and gas prospecting. However, the relationship between n-alkane and alkane-degrading bacteria in natural forests is still poorly understood. In this study, long-chain n-alkane (C14-C35) concentrations in litterfall, litter layer, and topsoil as well as the diversity and abundance of n-alkane-degrading bacterial communities in litter layers were investigated in three habitats across a lowland subtropical rainforest in southern Taiwan: ravine, windward, and leeward habitats in Nanjenshan. Our results demonstrate that the litterfall yield and productivity of long-chain n-alkane were highest in the ravine habitats. However, long-chain n-alkane concentrations in all habitats were decreased drastically to a similar low level from the litterfall to the bulk soil, suggesting a higher rate of long-chain n-alkane degradation in the ravine habitat. Operational taxonomic unit (OTU) analysis using next-generation sequencing data revealed that the relative abundances of microbial communities in the windward and leeward habitats were similar and different from that in the ravine habitat. Data mining of community amplicon sequencing using the NCBI database revealed that alkB-gene-associated bacteria (95 % DNA sequence similarity to alkB-containing bacteria) were most abundant in the ravine habitat. Empirical testing of litter layer samples using semi-quantitative polymerase chain reaction for determining alkB gene levels confirmed that the ravine habitat had higher alkB gene levels than the windward and leeward habitats. Heat map analysis revealed parallels in pattern color between the plant and microbial species compositions of the habitats, suggesting a causal relationship between the plant n-alkane production and microbial community diversity. This finding indicates that the diversity and relative abundance of microbial communities in the

Life with compass: diversity and biogeography of magnetotactic bacteria

Energy Technology Data Exchange (ETDEWEB)

Lin, Wei [Institute of Geology and Geophysics; Bazylinski, Dennis A [Ames Laboratory; Xiao, Tian [Chinese Academy of Sciences; Wu, Long-Fei [v; Pan, Yongxin [Institute of Geology and Geophysics

2013-11-12

Magnetotactic bacteria (MTB) are unique in their ability to synthesize intracellular nano-sized minerals of magnetite and/or greigite magnetosomes for magnetic orientation. Thus, they provide an excellent model system to investigate mechanisms of biomineralization. MTB play important roles in bulk sedimentary magnetism and have numerous versatile applications in paleoenvironmental reconstructions, and biotechnological and biomedical fields. Significant progress has been made in recent years in describing the composition of MTB communities and distribution through innovative cultivation-dependent and -independent techniques. In this review, the most recent contributions to the field of diversity and biogeography of MTB are summarized and reviewed. Emphasis is on the novel insights into various factors/processes potentially affecting MTB community distribution. An understanding of the present-day biogeography of MTB, and the ruling parameters of their spatial distribution, will eventually help us predict MTB community shifts with environmental changes and assess their roles in global iron cycling.

Diversity and phosphate solubilization by bacteria isolated from Laki Island coastal ecosystem

Directory of Open Access Journals (Sweden)

SRI WIDAWATI

2011-01-01

Full Text Available Widawati S (2011 Diversity and phosphate solubilization by bacteria isolated from Laki Island coastal ecosystem. Biodiversitas 12: 17-21. Soil, water, sand, and plant rhizosphere samples collected from coastal ecosystem of Laki Island-Jakarta were screened for phosphate solubilizing bacteria (PSB. While the population was dependent on the cultivation media and the sample type, the highest bacterial population was observed in the rhizosphere of Ipomea aquatica. The PSB strains isolated from the sample registered 18.59 g-1L-1, 18.31 g-1L-1, and 5.68 g-1L-1 of calcium phosphate (Ca-P, Al-P and rock phosphate solubilization after 7-days. Phosphate solubilizing capacity was the highest in the Ca-P medium. Two strains, 13 and 14, registered highest Phosphomonoesterase activities (2.01 µgNP.g-1.h-1 and 1.85NP µg.g-1.h-1 were identified as Serattia marcescens, and Pseudomonas fluorescense, respectively. Both strains were isolated from the crops of Amaranthus hybridus and I. aquatica, respectively, which are commonly observed in coastal ecosystems. The presence of phosphate solubilizing microorganisms and their ability to solubilize various types of phosphate species are indicative of the important role of both species of bacteria in the biogeochemical cycle of phosphorus and the plant growth in coastal ecosystems.

Dietary Corn Bran Fermented by Bacillus subtilis MA139 Decreased Gut Cellulolytic Bacteria and Microbiota Diversity in Finishing Pigs

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Ping Liu

2017-12-01

Full Text Available Solid-state fermentation of feedstuffs by Bacillus subtilis MA139 can reduce insoluble dietary fiber content in vitro and improve growth performance in pigs. This study was conducted to investigate the effects of dietary corn bran (CB fermented by B. subtilis on growth performance and gut microbiota composition in finishing pigs. A total of 60 finishing pigs were allocated to 3 dietary treatments consisting of a control (CON diet, a 10% CB diet, and a 10% fermented CB (FCB diet in a 21 d feeding trial. Growth performance and nutrient digestibility were evaluated. Fecal samples were determined for bacterial community diversity by 16S rRNA gene amplicon sequencing. The dietary CB and FCB did not affect growth performance of finishing pigs. The digestibility of organic matter was decreased in both CB and FCB treatments compared with CON group (P < 0.05. The α-diversity for bacterial community analysis of Chao 1 in FCB treatment was lower than CON treatment (P < 0.05. The Fibrobacteres phylum belongs to cellulolytic bacteria was isolated, and their relative abundance in CB group showed no difference between CON and FCB treatments. The abundance of Lachnospiraceae_NK4A136_group in CB treatment was higher than CON and FCB groups (P < 0.05, whereas the population of norank_f_Prevotellaceae was higher in FCB group compared to CON and CB groups (P < 0.05. In conclusion, dietary FCB decreased the abundance of bacterial communities, particularly the population of bacteria related to cellulolytic degradation.

The Diversity of PAH-degrading bacteria in a deep-sea water column above the Southwest Indian Ridge

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Zongze eShao

2015-08-01

Full Text Available The bacteria involved in organic pollutant degradation in pelagic deep-sea environments are largely unknown. In this report, the diversity of polycyclic aromatic hydrocarbon ( PAH-degrading bacteria was analyzed in deep-sea water on the Southwest Indian Ridge (SWIR. After enrichment with a PAH mixture (phenanthrene, anthracene, fluoranthene and pyrene, 9 nine bacterial consortia were obtained from depths of 3946 m to 4746 m. PAH degradation occurred to all components of the mixture, but when using a single PAH as the sole carbon and energy source, only phenanthrene can be degraded obviously. This indicates the cometabolism of anthracene, fluoranthene and pyrene with phenanthreneWhile the consortia degraded all four PAHs when supplied in a mixture, when PAHs were tested individually, only phenanthrene supported growth. Thus, degradation of the PAH mixture reflected a cometabolism of anthracene, fluoranthene and pyrene with phenanthrene. Further, both culture-dependent and independent methods revealed many new bacteria involved in PAH degradation. Specifically, the alpha and gamma subclasses of Proteobacteria were confirmed as the major groups within the communities. Additionally, Actinobacteria, the CFB group and Firmicutes were detected. Denaturing Gradient Gel Electrophoresis (DGGE analysis showed that bacteria closely affiliated with Alcanivorax, Novosphingobium and Rhodovulum occurred most frequently in different PAH-degrading consortia. More than half of the isolates (34 of 51 isolates were confirmed to have the ability to grow with the PAH mixture By using general heterotrophic media, 51 bacteria were isolated from the consortia and of these 34 grew with the PAH mixture as a sole carbon source. Of these, isolates most closely related to Alterierythrobacter, Citricella, Erythrobacter, Idiomarina, Lutibacterium, Maricaulis, Marinobacter, Martelella, Pseudidiomarina, Rhodobacter, Roseovarius, Salipiger, Sphingopyxis and Stappia were found to

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea

KAUST Repository

Guan, Yue

2015-11-01

Oceanic deep hypersaline anoxic basins (DHABs) are characterized by drastic changes in physico-chemical conditions in the transition from overlaying seawater to brine body. Brine-seawater interfaces (BSIs) of several DHABs across the Mediterranean Sea have been shown to possess methanogenic and sulfate-reducing activities, yet no systematic studies have been conducted to address the potential functional diversity of methanogenic and sulfate-reducing communities in the Red Sea DHABs. Here, we evaluated the relative abundance of Bacteria and Archaea using quantitative PCR and conducted phylogenetic analyses of nearly full-length 16S rRNA genes as well as functional marker genes encoding the alpha subunits of methyl-coenzyme M reductase (mcrA) and dissimilatory sulfite reductase (dsrA). Bacteria predominated over Archaea in most locations, the majority of which were affiliated with Deltaproteobacteria, while Thaumarchaeota were the most prevalent Archaea in all sampled locations. The upper convective layers of Atlantis II Deep, which bear increasingly harsh environmental conditions, were dominated by members of the class Thermoplasmata (Marine Benthic Group E and Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the presence of niche-specific groups, and collectively, a higher diversity of sulfate-reducing communities compared to methanogenic communities in all five studied locations. © 2015 Institut Pasteur.

Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea

KAUST Repository

Guan, Yue; Hikmawan, Tyas; Antunes, Andre; Ngugi, David; Stingl, Ulrich

2015-01-01

Oceanic deep hypersaline anoxic basins (DHABs) are characterized by drastic changes in physico-chemical conditions in the transition from overlaying seawater to brine body. Brine-seawater interfaces (BSIs) of several DHABs across the Mediterranean Sea have been shown to possess methanogenic and sulfate-reducing activities, yet no systematic studies have been conducted to address the potential functional diversity of methanogenic and sulfate-reducing communities in the Red Sea DHABs. Here, we evaluated the relative abundance of Bacteria and Archaea using quantitative PCR and conducted phylogenetic analyses of nearly full-length 16S rRNA genes as well as functional marker genes encoding the alpha subunits of methyl-coenzyme M reductase (mcrA) and dissimilatory sulfite reductase (dsrA). Bacteria predominated over Archaea in most locations, the majority of which were affiliated with Deltaproteobacteria, while Thaumarchaeota were the most prevalent Archaea in all sampled locations. The upper convective layers of Atlantis II Deep, which bear increasingly harsh environmental conditions, were dominated by members of the class Thermoplasmata (Marine Benthic Group E and Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the presence of niche-specific groups, and collectively, a higher diversity of sulfate-reducing communities compared to methanogenic communities in all five studied locations. © 2015 Institut Pasteur.

The seaweed holobiont: understanding seaweed-bacteria interactions.

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Egan, Suhelen; Harder, Tilmann; Burke, Catherine; Steinberg, Peter; Kjelleberg, Staffan; Thomas, Torsten

2013-05-01

Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for aquatic life. Like other eukaryotic organisms, macroalgae harbor a rich diversity of associated microorganisms with functions related to host health and defense. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host, and bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as a unified functional entity or holobiont, analogous to the previously suggested relationship in corals. Moreover, given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal-bacterial interactions with reference to the diversity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Diversity and population structure of Marine Group A bacteria in the Northeast subarctic Pacific Ocean.

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Allers, Elke; Wright, Jody J; Konwar, Kishori M; Howes, Charles G; Beneze, Erica; Hallam, Steven J; Sullivan, Matthew B

2013-02-01

Marine Group A (MGA) is a candidate phylum of Bacteria that is ubiquitous and abundant in the ocean. Despite being prevalent, the structural and functional properties of MGA populations remain poorly constrained. Here, we quantified MGA diversity and population structure in relation to nutrients and O(2) concentrations in the oxygen minimum zone (OMZ) of the Northeast subarctic Pacific Ocean using a combination of catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and 16S small subunit ribosomal RNA (16S rRNA) gene sequencing (clone libraries and 454-pyrotags). Estimates of MGA abundance as a proportion of total bacteria were similar across all three methods although estimates based on CARD-FISH were consistently lower in the OMZ (5.6%±1.9%) than estimates based on 16S rRNA gene clone libraries (11.0%±3.9%) or pyrotags (9.9%±1.8%). Five previously defined MGA subgroups were recovered in 16S rRNA gene clone libraries and five novel subgroups were defined (HF770D10, P262000D03, P41300E03, P262000N21 and A714018). Rarefaction analysis of pyrotag data indicated that the ultimate richness of MGA was very nearly sampled. Spearman's rank analysis of MGA abundances by CARD-FISH and O(2) concentrations resulted in significant correlation. Analyzed in more detail by 16S rRNA pyrotag sequencing, MGA operational taxonomic units affiliated with subgroups Arctic95A-2 and A714018 comprised 0.3-2.4% of total bacterial sequences and displayed strong correlations with decreasing O(2) concentration. This study is the first comprehensive description of MGA diversity using complementary techniques. These results provide a phylogenetic framework for interpreting future studies on ecotype selection among MGA subgroups, and suggest a potentially important role for MGA in the ecology and biogeochemistry of OMZs.

Use of a Packed-Column Bioreactor for Isolation of Diverse Protease-Producing Bacteria from Antarctic Soil

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Wery, Nathalie; Gerike, Ursula; Sharman, Ajay; Chaudhuri, Julian B.; Hough, David W.; Danson, Michael J.

2003-01-01

Seventy-five aerobic heterotrophs have been isolated from a packed-column bioreactor inoculated with soil from Antarctica. The column was maintained at 10°C and continuously fed with a casein-containing medium to enrich protease producers. Twenty-eight isolates were selected for further characterization on the basis of morphology and production of clearing zones on skim milk plates. Phenotypic tests indicated that the strains were mainly psychrotrophs and presented a high morphological and metabolical diversity. The extracellular protease activities tested were optimal at neutral pH and between 30 and 45°C. 16S ribosomal DNA sequence analyses showed that the bioreactor was colonized by a wide variety of taxons, belonging to various bacterial divisions: α-, β-, and γ-Proteobacteria; the Flexibacter-Cytophaga-Bacteroides group; and high G+C gram-positive bacteria and low G+C gram-positive bacteria. Some strains represent candidates for new species of the genera Chryseobacterium and Massilia. This diversity demonstrates that the bioreactor is an efficient enrichment tool compared to traditional isolation strategies. PMID:12620829

Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

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Cui, Yanhua; Hu, Tong; Qu, Xiaojun; Zhang, Lanwei; Ding, Zhongqing; Dong, Aijun

2015-01-01

Plasmids are widely distributed in different sources of lactic acid bacteria (LAB) as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research. PMID:26068451

Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states.

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Šantl-Temkiv, Tina; Gosewinkel, Ulrich; Starnawski, Piotr; Lever, Mark; Finster, Kai

2018-04-01

The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity. The communities consisted of 1.3×103 ± 1.0×103 cells m-3, which were aerosolized from local terrestrial environments or transported from marine, glaciated and terrestrial surfaces over long distances. On average, airborne bacterial cells displayed a high activity potential, reflected in the high 16S rRNA copy number (590 ± 300 rRNA cell-1), that correlated positively with water vapor pressure. We observed that bacterial clades differed in their activity potential. For instance, a high activity potential was seen for Rubrobacteridae and Clostridiales, while a low activity potential was observed for Proteobacteria. Of those bacterial families that harbor ice-nucleation active species, which are known to facilitate freezing and may thus be involved in cloud and rain formation, cells with a high activity potential were rare in air, but were enriched in rain.

Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

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Yanhua Cui

2015-06-01

Full Text Available Plasmids are widely distributed in different sources of lactic acid bacteria (LAB as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.

Influence of land use intensity on the diversity of ammonia oxidizing bacteria and archaea in soils from grassland ecosystems.

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Meyer, Annabel; Focks, Andreas; Radl, Viviane; Welzl, Gerhard; Schöning, Ingo; Schloter, Michael

2014-01-01

In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.

Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea

KAUST Repository

Miyake, Sou

2016-03-14

Epulopiscium is a group of giant bacteria found in high abundance in intestinal tracts of herbivorous surgeonfish. Despite their peculiarly large cell size (can be up to 600 μm), extreme polyploidy (some with over 100,000 genome copies per cell) and viviparity (whereby mother cells produce live offspring), details about their diversity, distribution or their role in the host gut are lacking. Previous studies have highlighted the existence of morphologically distinct Epulopiscium cell types (defined as morphotypes A to J) in some surgeonfish genera, but the corresponding genetic diversity and distribution among other surgeonfishes remain mostly unknown. Therefore, we investigated the phylogenetic diversity of Epulopiscium, distribution and co-occurrence in multiple hosts. Here, we identified eleven new phylogenetic clades, six of which were also morphologically characterized. Three of these novel clades were phylogenetically and morphologically similar to cigar-shaped type A1 cells, found in a wide range of surgeonfishes including Acanthurus nigrofuscus, while three were similar to smaller, rod-shaped type E that has not been phylogenetically classified thus far. Our results also confirmed that biogeography appears to have relatively little influence on Epulopiscium diversity, as clades found in the Great Barrier Reef and Hawaii were also recovered from the Red Sea. Although multiple symbiont clades inhabited a given species of host surgeonfish and multiple host species possessed a given symbiont clade, statistical analysis of host and symbiont phylogenies indicated significant cophylogeny, which in turn suggests co-evolutionary relationships. A cluster analysis of Epulopiscium sequences from previously published amplicon sequencing dataset revealed a similar pattern, where specific clades were consistently found in high abundance amongst closely related surgeonfishes. Differences in abundance may indicate specialization of clades to certain gut environments

Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea

Science.gov (United States)

Miyake, Sou; Ngugi, David K.; Stingl, Ulrich

2016-01-01

Epulopiscium is a group of giant bacteria found in high abundance in intestinal tracts of herbivorous surgeonfish. Despite their peculiarly large cell size (can be up to 600 μm), extreme polyploidy (some with over 100,000 genome copies per cell) and viviparity (whereby mother cells produce live offspring), details about their diversity, distribution or their role in the host gut are lacking. Previous studies have highlighted the existence of morphologically distinct Epulopiscium cell types (defined as morphotypes A to J) in some surgeonfish genera, but the corresponding genetic diversity and distribution among other surgeonfishes remain mostly unknown. Therefore, we investigated the phylogenetic diversity of Epulopiscium, distribution and co-occurrence in multiple hosts. Here, we identified eleven new phylogenetic clades, six of which were also morphologically characterized. Three of these novel clades were phylogenetically and morphologically similar to cigar-shaped type A1 cells, found in a wide range of surgeonfishes including Acanthurus nigrofuscus, while three were similar to smaller, rod-shaped type E that has not been phylogenetically classified thus far. Our results also confirmed that biogeography appears to have relatively little influence on Epulopiscium diversity, as clades found in the Great Barrier Reef and Hawaii were also recovered from the Red Sea. Although multiple symbiont clades inhabited a given species of host surgeonfish and multiple host species possessed a given symbiont clade, statistical analysis of host and symbiont phylogenies indicated significant cophylogeny, which in turn suggests co-evolutionary relationships. A cluster analysis of Epulopiscium sequences from previously published amplicon sequencing dataset revealed a similar pattern, where specific clades were consistently found in high abundance amongst closely related surgeonfishes. Differences in abundance may indicate specialization of clades to certain gut environments

Phylogenetic Diversity, Distribution, and Cophylogeny of Giant Bacteria (Epulopiscium) with their Surgeonfish Hosts in the Red Sea

KAUST Repository

Miyake, Sou; Ngugi, David; Stingl, Ulrich

2016-01-01

Epulopiscium is a group of giant bacteria found in high abundance in intestinal tracts of herbivorous surgeonfish. Despite their peculiarly large cell size (can be up to 600 μm), extreme polyploidy (some with over 100,000 genome copies per cell) and viviparity (whereby mother cells produce live offspring), details about their diversity, distribution or their role in the host gut are lacking. Previous studies have highlighted the existence of morphologically distinct Epulopiscium cell types (defined as morphotypes A to J) in some surgeonfish genera, but the corresponding genetic diversity and distribution among other surgeonfishes remain mostly unknown. Therefore, we investigated the phylogenetic diversity of Epulopiscium, distribution and co-occurrence in multiple hosts. Here, we identified eleven new phylogenetic clades, six of which were also morphologically characterized. Three of these novel clades were phylogenetically and morphologically similar to cigar-shaped type A1 cells, found in a wide range of surgeonfishes including Acanthurus nigrofuscus, while three were similar to smaller, rod-shaped type E that has not been phylogenetically classified thus far. Our results also confirmed that biogeography appears to have relatively little influence on Epulopiscium diversity, as clades found in the Great Barrier Reef and Hawaii were also recovered from the Red Sea. Although multiple symbiont clades inhabited a given species of host surgeonfish and multiple host species possessed a given symbiont clade, statistical analysis of host and symbiont phylogenies indicated significant cophylogeny, which in turn suggests co-evolutionary relationships. A cluster analysis of Epulopiscium sequences from previously published amplicon sequencing dataset revealed a similar pattern, where specific clades were consistently found in high abundance amongst closely related surgeonfishes. Differences in abundance may indicate specialization of clades to certain gut environments

Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting.

Science.gov (United States)

Zeng, Guangming; Zhang, Jiachao; Chen, Yaoning; Yu, Zhen; Yu, Man; Li, Hui; Liu, Zhifeng; Chen, Ming; Lu, Lunhui; Hu, Chunxiao

2011-10-01

The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R²=0.554; Parchaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R²=0.503; P=0.03) especially during the mesophilic and maturation stages. Copyright © 2011 Elsevier Ltd. All rights reserved.

Diversity and antimicrobial potential of culturable heterotrophic bacteria associated with the endemic marine sponge Arenosclera brasiliensis

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Cintia P.J. Rua

2014-06-01

Full Text Available Marine sponges are the oldest Metazoa, very often presenting a complex microbial consortium. Such is the case of the marine sponge Arenosclera brasiliensis, endemic to Rio de Janeiro State, Brazil. In this investigation we characterized the diversity of some of the culturable heterotrophic bacteria living in association with A. brasiliensis and determined their antimicrobial activity. The genera Endozoicomonas (N = 32, Bacillus (N = 26, Shewanella (N = 17, Pseudovibrio (N = 12, and Ruegeria (N = 8 were dominant among the recovered isolates, corresponding to 97% of all isolates. Approximately one third of the isolates living in association with A. brasiliensis produced antibiotics that inhibited the growth of Bacillus subtilis, suggesting that bacteria associated with this sponge play a role in its health.

Diversity of bacteria associated with Bursaphelenchus xylophilus and other nematodes isolated from Pinus pinaster trees with pine wilt disease.

Science.gov (United States)

Proença, Diogo Neves; Francisco, Romeu; Santos, Clara Vieira; Lopes, André; Fonseca, Luís; Abrantes, Isabel M O; Morais, Paula V

2010-12-09

The pinewood nematode (PWN), Bursaphelenchus xylophilus, has been thought to be the only causal agent of pine wilt disease (PWD), however, since bacteria have been suggested to play a role in PWD, it is important to know the diversity of the microbial community associated to it. This study aimed to assess the microbial community associated with B. xylophilus and with other nematodes isolated from pine trees, Pinus pinaster, with PWD from three different affected forest areas in Portugal. One hundred and twenty three bacteria strains were isolated from PWN and other nematodes collected from 14 P. pinaster. The bacteria strains were identified by comparative analysis of the 16S rRNA gene partial sequence. All except one gram-positive strain (Actinobacteria) belonged to the gram-negative Beta and Gammaproteobacteria. Most isolates belonged to the genus Pseudomonas, Burkholderia and to the family Enterobacteriaceae. Species isolated in higher percentage were Pseudomonas lutea, Yersinia intermedia and Burkholderia tuberum. The major bacterial population associated to the nematodes differed according to the forest area and none of the isolated bacterial species was found in all different forest areas. For each of the sampled areas, 60 to 100% of the isolates produced siderophores and at least 40% produced lipases. The ability to produce siderophores and lipases by most isolates enables these bacteria to have a role in plant physiological response. This research showed a high diversity of the microbial community associated with B. xylophilus and other nematodes isolated from P. pinaster with PWD.

Colony contact contributes to the diversity of gut bacteria in bumblebees (Bombus terrestris)

Institute of Scientific and Technical Information of China (English)

Annelies Billiet; Ivan Meeus; Filip Van Nieuwerburgh; Dieter Deforce; Felix W(a)ckers; Guy Smagghe

2017-01-01

Social bees,like honeybees and bumblebees,have a close contact with nest mates of different developmental stages and generations.This could enhance bacterial transfer between nest mates and offers opportunities for direct transfer of symbionts from one generation to the next,resulting in a stable host specific gut microbiota.Gut symbionts of honeybees and bumblebees have been suggested to contribute in digestion and protection against parasites and pathogens.Here we studied the impact of contact with the bumblebee colony on the colonization potential of the bacterial families (i.e.,Neisseriaceae,Orbaceae,Lactobacillaceae and Bifidobacteriaceae) occurring in the gut of adult bumblebees (Bombus terrestris).Bacterial profiles of the gut microbiota of B.terrestris were determined based on the hypervariable V4 region of the 16S rRNA using paired-end Illumina sequencing.In our experiments,we created different groups in which we gradually reduced the contact with nest mates and hive material.We made 3 observations:(i) reducing the contact between the colony and the bumblebee during adult life resulted in a significant drop in the relative abundance of Lactobacillus bombicola and Lactobacillus bombi;(ii) Bifidobacteriaceae required contact with nest mates to colonize the gut of B.terrestris and a significant lower bacterial diversity was observed in bumblebees that were completely excluded from colony contact during the adult life;(iii) Snodgrassella and Gilliamella were able to colonize the gut of the adult bumblebee without any direct contact with nest mates in the adult life stage.These results indicate the impact of the colony life on the diversity of the characteristic bumblebee gut bacteria.

Flea diversity as an element for persistence of plague bacteria in an East African plague focus.

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Rebecca J Eisen

Full Text Available Plague is a flea-borne rodent-associated zoonotic disease that is caused by Yersinia pestis and characterized by long quiescent periods punctuated by rapidly spreading epidemics and epizootics. How plague bacteria persist during inter-epizootic periods is poorly understood, yet is important for predicting when and where epizootics are likely to occur and for designing interventions aimed at local elimination of the pathogen. Existing hypotheses of how Y. pestis is maintained within plague foci typically center on host abundance or diversity, but little attention has been paid to the importance of flea diversity in enzootic maintenance. Our study compares host and flea abundance and diversity along an elevation gradient that spans from low elevation sites outside of a plague focus in the West Nile region of Uganda (~725-1160 m to higher elevation sites within the focus (~1380-1630 m. Based on a year of sampling, we showed that host abundance and diversity, as well as total flea abundance on hosts was similar between sites inside compared with outside the plague focus. By contrast, flea diversity was significantly higher inside the focus than outside. Our study highlights the importance of considering flea diversity in models of Y. pestis persistence.

Diversity of root nodule bacteria from leguminous crops

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Agrawal Pooja

2016-01-01

Full Text Available In the present study, a total of 353 nodule-associated bacteria were isolated from 220 legume plant samples belonging to Cicer arietinum (85, Glycine max (74, Vigna radiata (21 and Cajanus cajan (40. A total of 224 bacteria were identified as fast-growing Rhizobium spp. on the basis of differential staining (Gram staining and carbol fuchsin staining and biochemical tests. All the isolates were tested for indole acetic acid production (IAA, phosphate solubilization and siderophore production on plate assay. To examine the effect of volatile organic metabolites (VOM and water soluble soil components (WSSC on nodule bacteria, culture conditions were optimized by observing the effects of various parameters such as pH, salt content and temperatures on the growth of bacteria. Selected rhizobia were subjected to random amplified polymorphic DNA (RAPD and amplified ribosomal DNA restriction analysis (ARDRA analysis to identify their species. On the basis of RAPD and ARDRA, 10 isolates were identified as Rhizobium meliloti. In this study, Rhizobium GO4, G16, G20, G77, S43, S81, M07, M37, A15 and A55 were observed as the best candidates among the tested bacteria and can be further used as potent bioinoculants.

Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin

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Lina eRuss

2013-08-01

Full Text Available Hydrothermally active sediments are highly productive, chemosynthetic areas which are characterized by the rapid turnover of particulate organic matter under extreme conditions in which ammonia is liberated. These systems might be suitable habitats for anaerobic ammonium oxidizing (anammox bacteria but this has not been investigated in detail. Here we report the diversity and abundance of anammox bacteria in sediments that seep cold hydrocarbon-rich fluids and hydrothermal vent areas of the Guaymas Basin in the Cortés Sea using the unique functional anammox marker gene, hydrazine synthase (hzsA. All clones retrieved were closely associated to the ‘Candidatus Scalindua’ genus. Phylogenetic analysis revealed two distinct clusters of hzsA sequences (Ca. Scalindua hzsA cluster I and II. Comparison of individual sequences from both clusters showed that several of these sequences had a similarity as low as 76% on nucleotide level. Based on the analysis of this phylomarker, a very high interspecies diversity within the marine anammox group is apparent. Absolute numbers of anammox bacteria in the sediments samples were determined by amplification of a 257 bp fragment of the hszA gene in a qPCR assay. The results indicate that numbers of anammox bacteria are generally higher in cold hydrocarbon-rich sediments compared to the vent areas and the reference zone. Ladderanes, lipids unique to anammox bacteria were also detected in several of the sediment samples corroborating the hzsA analysis. Due to the high concentrations of reduced sulfur compounds and its potential impact on the cycling of nitrogen we aimed to get an indication about the key players in the oxidation of sulfide in the Guaymas Basin sediments using the alpha subunit of the adenosine-5’-phosphosulfate (APS reductase (aprA. Amplification of the aprA gene revealed a high number of gammaproteobacterial aprA genes covering the two sulfur-oxidizing bacteria aprA lineages as well as

Presence and diversity of anammox bacteria in cold hydrocarbon-rich seeps and hydrothermal vent sediments of the Guaymas Basin.

Science.gov (United States)

Russ, Lina; Kartal, Boran; Op den Camp, Huub J M; Sollai, Martina; Le Bruchec, Julie; Caprais, Jean-Claude; Godfroy, Anne; Sinninghe Damsté, Jaap S; Jetten, Mike S M

2013-01-01

Hydrothermally active sediments are highly productive, chemosynthetic areas which are characterized by the rapid turnover of particulate organic matter under extreme conditions in which ammonia is liberated. These systems might be suitable habitats for anaerobic ammonium oxidizing (anammox) bacteria but this has not been investigated in detail. Here we report the diversity and abundance of anammox bacteria in sediments that seep cold hydrocarbon-rich fluids and hydrothermal vent areas of the Guaymas Basin in the Cortés Sea using the unique functional anammox marker gene, hydrazine synthase (hzsA). All clones retrieved were closely associated to the "Candidatus Scalindua" genus. Phylogenetic analysis revealed two distinct clusters of hzsA sequences (Ca. Scalindua hzsA cluster I and II). Comparison of individual sequences from both clusters showed that several of these sequences had a similarity as low as 76% on nucleotide level. Based on the analysis of this phylomarker, a very high interspecies diversity within the marine anammox group is apparent. Absolute numbers of anammox bacteria in the sediments samples were determined by amplification of a 257 bp fragment of the hszA gene in a qPCR assay. The results indicate that numbers of anammox bacteria are generally higher in cold hydrocarbon-rich sediments compared to the vent areas and the reference zone. Ladderanes, lipids unique to anammox bacteria were also detected in several of the sediment samples corroborating the hzsA analysis. Due to the high concentrations of reduced sulfur compounds and its potential impact on the cycling of nitrogen we aimed to get an indication about the key players in the oxidation of sulfide in the Guaymas Basin sediments using the alpha subunit of the adenosine-5'-phosphosulfate (APS) reductase (aprA). Amplification of the aprA gene revealed a high number of gammaproteobacterial aprA genes covering the two sulfur-oxidizing bacteria aprA lineages as well as sulfate-reducers.

Diversity of bacteria nesting the plant cover of north Sinai deserts, Egypt

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Amira L. Hanna

2013-01-01

Full Text Available North Sinai deserts were surveyed for the predominant plant cover and for the culturable bacteria nesting their roots and shoots. Among 43 plant species reported, 13 are perennial (e.g. Fagonia spp., Pancratium spp. and 30 annuals (e.g. Bromus spp., Erodium spp.. Eleven species possessed rhizo-sheath, e.g. Cyperus capitatus, Panicum turgidum and Trisetaria koelerioides. Microbiological analyses demonstrated: the great diversity and richness of associated culturable bacteria, in particular nitrogen-fixing bacteria (diazotrophs; the majority of bacterial residents were of true and/or putative diazotrophic nature; the bacterial populations followed an increasing density gradient towards the root surfaces; sizeable populations were able to reside inside the root (endorhizosphere and shoot (endophyllosphere tissues. Three hundred bacterial isolates were secured from studied spheres. The majority of nitrogen-fixing bacilli isolates belonged to Bacillus megaterium, Bacillus pumilus, Bacillus polymexa, Bacillus macerans, Bacillus circulans and Bacillus licheniformis. The family Enterobacteriaceae represented by Enterobacter agglomerans, Enterobacter sackazakii, Enterobacter cloacae, Serratia adorifera, Serratia liquefaciens and Klebsiella oxytoca. The non-Enterobacteriaceae population was rich in Pantoae spp., Agrobacterium rdiobacter, Pseudomonas vesicularis, Pseudomonas putida, Stenotrophomonas maltophilia, Ochrobactrum anthropi, Sphingomonas paucimobilis and Chrysemonas luteola. Gluconacetobacter diazotrophicus were reported inside root and shoot tissues of a number of tested plants. The dense bacterial populations reported speak well to the very possible significant role played by the endophytic bacterial populations in the survival, in respect of nutrition and health, of existing plants. Such groups of diazotrophs are good candidates, as bio-preparates, to support the growth of future field crops grown in deserts of north Sinai and irrigated by the

Anaerobic Ammonium-Oxidizing Bacteria in Cow Manure Composting.

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Wang, Tingting; Cheng, Lijun; Zhang, Wenhao; Xu, Xiuhong; Meng, Qingxin; Sun, Xuewei; Liu, Huajing; Li, Hongtao; Sun, Yu

2017-07-28

Composting is widely used to transform waste into valuable agricultural organic fertilizer. Anaerobic ammonium-oxidizing (anammox) bacteria play an important role in the global nitrogen cycle, but their role in composting remains poorly understood. In the present study, the community structure, diversity, and abundance of anammox bacteria were analyzed using cloning and sequencing methods by targeting the 16S rRNA gene and the hydrazine oxidase gene ( hzo ) in samples isolated from compost produced from cow manure and rice straw. A total of 25 operational taxonomic units were classified based on 16S rRNA gene clone libraries, and 14 operational taxonomic units were classified based on hzo gene clone libraries. The phylogenetic tree analysis of the 16S rRNA gene and deduced HZO protein sequences from the corresponding encoding genes indicated that the majority of the obtained clones were related to the known anammox bacteria Candidatus "Brocadia," Candidatus "Kuenenia," and Candidatus "Scalindua." The abundances of anammox bacteria were determined by quantitative PCR, and between 2.13 × 10 5 and 1.15 × 10 6 16S rRNA gene copies per gram of compost were found. This study provides the first demonstration of the existence of anammox bacteria with limited diversity in cow manure composting.

Diversity of bacteria associated with Bursaphelenchus xylophilus and other nematodes isolated from Pinus pinaster trees with pine wilt disease.

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Diogo Neves Proença

Full Text Available The pinewood nematode (PWN, Bursaphelenchus xylophilus, has been thought to be the only causal agent of pine wilt disease (PWD, however, since bacteria have been suggested to play a role in PWD, it is important to know the diversity of the microbial community associated to it. This study aimed to assess the microbial community associated with B. xylophilus and with other nematodes isolated from pine trees, Pinus pinaster, with PWD from three different affected forest areas in Portugal. One hundred and twenty three bacteria strains were isolated from PWN and other nematodes collected from 14 P. pinaster. The bacteria strains were identified by comparative analysis of the 16S rRNA gene partial sequence. All except one gram-positive strain (Actinobacteria belonged to the gram-negative Beta and Gammaproteobacteria. Most isolates belonged to the genus Pseudomonas, Burkholderia and to the family Enterobacteriaceae. Species isolated in higher percentage were Pseudomonas lutea, Yersinia intermedia and Burkholderia tuberum. The major bacterial population associated to the nematodes differed according to the forest area and none of the isolated bacterial species was found in all different forest areas. For each of the sampled areas, 60 to 100% of the isolates produced siderophores and at least 40% produced lipases. The ability to produce siderophores and lipases by most isolates enables these bacteria to have a role in plant physiological response. This research showed a high diversity of the microbial community associated with B. xylophilus and other nematodes isolated from P. pinaster with PWD.

Metagenomic and PCR-based diversity surveys of [FeFe]-hydrogenases combined with isolation of alkaliphilic hydrogen-producing bacteria from the serpentinite-hosted Prony hydrothermal field, New Caledonia

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Nan Mei

2016-08-01

Full Text Available High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia, where high-pH (~11, low-temperature (<40°C and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e. high-pH, low-salt, mesothermic fluids. In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ.

Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia.

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Mei, Nan; Postec, Anne; Monnin, Christophe; Pelletier, Bernard; Payri, Claude E; Ménez, Bénédicte; Frouin, Eléonore; Ollivier, Bernard; Erauso, Gaël; Quéméneur, Marianne

2016-01-01

High amounts of hydrogen are emitted in the serpentinite-hosted hydrothermal field of the Prony Bay (PHF, New Caledonia), where high-pH (~11), low-temperature (< 40°C), and low-salinity fluids are discharged in both intertidal and shallow submarine environments. In this study, we investigated the diversity and distribution of potentially hydrogen-producing bacteria in Prony hyperalkaline springs by using metagenomic analyses and different PCR-amplified DNA sequencing methods. The retrieved sequences of hydA genes, encoding the catalytic subunit of [FeFe]-hydrogenases and, used as a molecular marker of hydrogen-producing bacteria, were mainly related to those of Firmicutes and clustered into two distinct groups depending on sampling locations. Intertidal samples were dominated by new hydA sequences related to uncultured Firmicutes retrieved from paddy soils, while submarine samples were dominated by diverse hydA sequences affiliated with anaerobic and/or thermophilic submarine Firmicutes pertaining to the orders Thermoanaerobacterales or Clostridiales. The novelty and diversity of these [FeFe]-hydrogenases may reflect the unique environmental conditions prevailing in the PHF (i.e., high-pH, low-salt, mesothermic fluids). In addition, novel alkaliphilic hydrogen-producing Firmicutes (Clostridiales and Bacillales) were successfully isolated from both intertidal and submarine PHF chimney samples. Both molecular and cultivation-based data demonstrated the ability of Firmicutes originating from serpentinite-hosted environments to produce hydrogen by fermentation, potentially contributing to the molecular hydrogen balance in situ.

[Teichoic acids from lactic acid bacteria].

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Livins'ka, O P; Harmasheva, I L; Kovalenko, N K

2012-01-01

The current view of the structural diversity of teichoic acids and their involvement in the biological activity of lactobacilli has been reviewed. The mechanisms of effects of probiotic lactic acid bacteria, in particular adhesive and immunostimulating functions have been described. The prospects of the use of structure data of teichoic acid in the assessment of intraspecific diversity of lactic acid bacteria have been also reflected.

Ubiquity and diversity of heterotrophic bacterial nasA genes in diverse marine environments.

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Xuexia Jiang

Full Text Available Nitrate uptake by heterotrophic bacteria plays an important role in marine N cycling. However, few studies have investigated the diversity of environmental nitrate assimilating bacteria (NAB. In this study, the diversity and biogeographical distribution of NAB in several global oceans and particularly in the western Pacific marginal seas were investigated using both cultivation and culture-independent molecular approaches. Phylogenetic analyses based on 16S rRNA and nasA (encoding the large subunit of the assimilatory nitrate reductase gene sequences indicated that the cultivable NAB in South China Sea belonged to the α-Proteobacteria, γ-Proteobacteria and CFB (Cytophaga-Flavobacteria-Bacteroides bacterial groups. In all the environmental samples of the present study, α-Proteobacteria, γ-Proteobacteria and Bacteroidetes were found to be the dominant nasA-harboring bacteria. Almost all of the α-Proteobacteria OTUs were classified into three Roseobacter-like groups (I to III. Clone library analysis revealed previously underestimated nasA diversity; e.g. the nasA gene sequences affiliated with β-Proteobacteria, ε-Proteobacteria and Lentisphaerae were observed in the field investigation for the first time, to the best of our knowledge. The geographical and vertical distributions of seawater nasA-harboring bacteria indicated that NAB were highly diverse and ubiquitously distributed in the studied marginal seas and world oceans. Niche adaptation and separation and/or limited dispersal might mediate the NAB composition and community structure in different water bodies. In the shallow-water Kueishantao hydrothermal vent environment, chemolithoautotrophic sulfur-oxidizing bacteria were the primary NAB, indicating a unique nitrate-assimilating community in this extreme environment. In the coastal water of the East China Sea, the relative abundance of Alteromonas and Roseobacter-like nasA gene sequences responded closely to algal blooms, indicating

Location-Related Differences in Weathering Behaviors and Populations of Culturable Rock-Weathering Bacteria Along a Hillside of a Rock Mountain.

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Wang, Qi; Wang, Rongrong; He, Linyan; Sheng, Xiafang

2017-05-01

Bacteria play important roles in rock weathering, elemental cycling, and soil formation. However, little is known about the weathering potential and population of bacteria inhabiting surfaces of rocks. In this study, we isolated bacteria from the top, middle, and bottom rock samples along a hillside of a rock (trachyte) mountain as well as adjacent soils and characterized rock-weathering behaviors and populations of the bacteria. Per gram of rock or surface soil, 10 6 -10 7 colony forming units were obtained and total 192 bacteria were isolated. Laboratory rock dissolution experiments indicated that the proportions of the highly effective Fe (ranging from 67 to 92 %), Al (ranging from 40 to 48 %), and Cu (ranging from 54 to 81 %) solubilizers were significantly higher in the top rock and soil samples, while the proportion of the highly effective Si (56 %) solubilizers was significantly higher in the middle rock samples. Furthermore, 78, 96, and 6 % of bacteria from the top rocks, soils, and middle rocks, respectively, significantly acidified the culture medium (pH bacteria (79 %) from the rocks were different to those from the soils and most of them (species level) have not been previously reported. Furthermore, location-specific rock-weathering bacterial populations were found and Bacillus species were the most (66 %) frequently isolated rock-weathering bacteria in the rocks based on cultivation methods. Notably, the top rocks and soils had the highest and lowest diversity of rock-weathering bacterial populations, respectively. The results suggested location-related differences in element (Si, Al, Fe, and Cu) releasing effectiveness and communities of rock-weathering bacteria along the hillside of the rock mountain.

School ethnic diversity and students' interethnic relations.

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Thijs, Jochem; Verkuyten, Maykel

2014-03-01

School ethnic desegregation has been a topic of strong societal and educational concern. Research has examined the effects of ethnic school composition on students' interethnic relations with diverging outcomes and sometimes inconsistent results. In this review paper, we provide an assessment of this literature to explain why and when school desegregation might improve or worsen ethnic relations and to identify important future research directions. We discuss different theoretical perspectives predicting positive versus negative aspects of school ethnic diversity: intergroup contact theory and the perspectives of group threat and power differences. Subsequently, we consider a number of school and educational characteristics that can moderate the impact of ethnic diversity on students' interethnic relations and that could be considered in future research. Furthermore, we discuss the need for studying underlying psychological and social processes as well as the importance of investigating interethnic relations in combination with academic adjustment. School ethnic diversity is not enough to promote interethnic tolerance. It is important to examine diversity in relation to other aspects of the school environment that may influence how students respond to the ethnic diversity within school. Important factors to consider are the presence of multicultural education and inclusive school identities, student-teacher relationships, and peer norms and networks, but also the role of parents and of peer relations outside the school context. © 2013 The British Psychological Society.

Transformation of nitrogen and distribution of nitrogen-related bacteria in a polluted urban stream.

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Jiao, Y; Jin, W B; Zhao, Q L; Zhang, G D; Yan, Y; Wan, J

2009-01-01

Most researchers focused on either nitrogen species or microbial community for polluted urban stream while ignoring the interaction between them and its effect on nitrogen transformation, which restricted the rational selection of an effective and feasible remediation technology. Taking Buji stream in Shenzhen (China) as target stream, the distribution of nitrogen-related bacteria was investigated by most probable number (MPN) besides analysis of nitrogen species etc. The nitrogen-related bacteria in sediment were 10(2) times richer than those in water. Owing to their faster growth, the MPN of ammonifying bacteria and denitrifying bacteria were 10(5) and 10(2) times higher than those of nitrifying bacteria, respectively. The ammonifying bacteria numbers were significantly related to BOD5 in water, while nitrifying bacteria in sediment correlated well with nitrate in water. Thus, nitrification occurred mainly in sediment surface and was limited by low proportion of nitrifying bacteria. The denitrifying bacteria in sediment had good relationship with BOD5 and nitrite and nitrate in water. Low DO and rich organic compounds were beneficial to denitrification but unfavourable to nitrification. Denitrification was restricted by low nitrite and nitrate concentration. These results could be served as a reference for implementing the remediation scheme of nitrogen polluted urban stream.

Phylogenetic diversity of lactic acid bacteria associated with paddy rice silage as determined by 16S ribosomal DNA analysis.

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Ennahar, Saïd; Cai, Yimin; Fujita, Yasuhito

2003-01-01

A total of 161 low-G+C-content gram-positive bacteria isolated from whole-crop paddy rice silage were classified and subjected to phenotypic and genetic analyses. Based on morphological and biochemical characters, these presumptive lactic acid bacterium (LAB) isolates were divided into 10 groups that included members of the genera Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and WEISSELLA: Analysis of the 16S ribosomal DNA (rDNA) was used to confirm the presence of the predominant groups indicated by phenotypic analysis and to determine the phylogenetic affiliation of representative strains. The virtually complete 16S rRNA gene was PCR amplified and sequenced. The sequences from the various LAB isolates showed high degrees of similarity to those of the GenBank reference strains (between 98.7 and 99.8%). Phylogenetic trees based on the 16S rDNA sequence displayed high consistency, with nodes supported by high bootstrap values. With the exception of one species, the genetic data was in agreement with the phenotypic identification. The prevalent LAB, predominantly homofermentative (66%), consisted of Lactobacillus plantarum (24%), Lactococcus lactis (22%), Leuconostoc pseudomesenteroides (20%), Pediococcus acidilactici (11%), Lactobacillus brevis (11%), Enterococcus faecalis (7%), Weissella kimchii (3%), and Pediococcus pentosaceus (2%). The present study, the first to fully document rice-associated LAB, showed a very diverse community of LAB with a relatively high number of species involved in the fermentation process of paddy rice silage. The comprehensive 16S rDNA-based approach to describing LAB community structure was valuable in revealing the large diversity of bacteria inhabiting paddy rice silage and enabling the future design of appropriate inoculants aimed at improving its fermentation quality.

Cluster-distinguishing genotypic and phenotypic diversity of carbapenem-resistant Gram-negative bacteria in solid-organ transplantation patients: a comparative study.

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Karampatakis, Theodoros; Geladari, Anastasia; Politi, Lida; Antachopoulos, Charalampos; Iosifidis, Elias; Tsiatsiou, Olga; Karyoti, Aggeliki; Papanikolaou, Vasileios; Tsakris, Athanassios; Roilides, Emmanuel

2017-07-31

Solid-organ transplant recipients may display high rates of colonization and/or infection by multidrug-resistant bacteria. We analysed and compared the phenotypic and genotypic diversity of carbapenem-resistant (CR) strains of Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii isolated from patients in the Solid Organ Transplantation department of our hospital. Between March 2012 and August 2013, 56 CR strains from various biological fluids underwent antimicrobial susceptibility testing with VITEK 2, molecular analysis by PCR amplification and genotypic analysis with pulsed-field gel electrophoresis (PFGE). They were clustered according to antimicrobial drug susceptibility and genotypic profiles. Diversity analyses were performed by calculating Simpson's diversity index and applying computed rarefaction curves.Results/Key findings. Among K. pneumoniae, KP-producers predominated (57.1 %). VIM and OXA-23 carbapenemases prevailed among P. aeruginosa and A. baumannii (89.4 and 88.9 %, respectively). KPC-producing K. pneumoniae and OXA-23 A. baumannii were assigned in single PFGE pulsotypes. VIM-producing P. aeruginosa generated multiple pulsotypes. CR K. pneumoniae strains displayed phenotypic diversity in tigecycline, colistin (CS), amikacin (AMK), gentamicin (GEN) and co-trimoxazole (SXT) (16 clusters); P. aeruginosa displayed phenotypic diversity in cefepime (FEP), ceftazidime, aztreonam, piperacillin, piperacillin-tazobactam, AMK, GEN and CS (9 clusters); and A. baumannii displayed phenotypic diversity in AMK, GEN, SXT, FEP, tobramycin and rifampicin (8 clusters). The Simpson diversity indices for the interpretative phenotype and PFGE analysis were 0.89 and 0.6, respectively, for K. pneumoniae strains (P<0.001); 0.77 and 0.6 for P. aeruginosa (P=0.22); and 0.86 and 0.19 for A. baumannii (P=0.004). The presence of different antimicrobial susceptibility profiles does not preclude the possibility that two CR K. pneumoniae or A. baumannii

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria.

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Lisa C Crossman

2008-07-01

Full Text Available This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10 are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

Diversity and numbers of root-nodule bacteria (rhizobia in Polish soils

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Stefan Martyniuk

2011-01-01

Full Text Available Using a sand pouch-plant infection method, populations of several species of root-nodule bacteria (rhizobia were enumerated in eighty soils collected throughout Poland. Rhizobium leguminosarum bv. viciae (symbionts of pea, faba bean, vetch and R. leguminosarum bv. trifolii (symbionts of clover were detected in 77 and 76 soils, respectively. Most of these soils contained moderate and high numbers of these species of the rhizobia. Symbionts of beans, R. leguminosarum bv. phaseoli, were assessed in 76 soils; of this number 15 soils had no detectable populations of bean rhizobia and in 40 soils high or moderate numbers of these bacteria were found. Bradyrhizobium sp. (Lupinus, root-nodule bacteria of lupine and serradella, were absent in 19 soils, out of 80 tested, and 34 soils were colonised by high or moderate populations of bradyrhizobia. Sinorhizobium meliloti, rhizobia nodulating alfalfa, were sparse in the examined soils; with 56 soil containing no detectable numbers of S. meliloti and only 6 soils harbouring high or moderate populations of this species. The estimated numbers of the rhizobia in the studied soils were also related to some physical and chemical properties of these soils.

Genomics of Probiotic Bacteria

Science.gov (United States)

O'Flaherty, Sarah; Goh, Yong Jun; Klaenhammer, Todd R.

Probiotic bacteria from the Lactobacillus and Bifidobacterium species belong to the Firmicutes and the Actinobacteria phylum, respectively. Lactobacilli are members of the lactic acid bacteria (LAB) group, a broadly defined family of microorganisms that ferment various hexoses into primarily lactic acid. Lactobacilli are typically low G + C gram-positive species which are phylogenetically diverse, with over 100 species documented to date. Bifidobacteria are heterofermentative, high G + C content bacteria with about 30 species of bifidobacteria described to date.

Analysis of diversity of diazotrophic bacteria associated with the rhizosphere of a tropical Arbor, Melastoma malabathricum L.

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Sato, Atsuya; Watanabe, Toshihiro; Unno, Yusuke; Purnomo, Erry; Osaki, Mitsuru; Shinano, Takuro

2009-01-01

The diversity of diazotrophic bacteria in the rhizosphere of Melastoma malabathricum L. was investigated by cloning-sequencing of the nifH gene directly amplified from DNA extracted from soil. Samples were obtained from the rhizosphere and bulk soil of M. malabathricum growing in three different soil types (acid sulfate, peat and sandy clay soils) located very close to each other in south Kalimantan, Indonesia. Six clone libraries were constructed, generated from bulk and rhizosphere soil samples, and 300 nifH clones were produced, then assembled into 29 operational taxonomic units (OTUs) based on percent identity values. Our results suggested that nifH gene diversity is mainly dependent on soil properties, and did not differ remarkably between the rhizosphere and bulk soil of M. malabathricum except in acid sulfate soil. In acid sulfate soil, as the Shannon diversity index was lower in rhizosphere than in bulk soil, it is suggested that particular bacterial species might accumulate in the rhizosphere.

Characterization of bacterial diversity associated with calcareous deposits and drip-waters, and isolation of calcifying bacteria from two Colombian mines.

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García G, Mariandrea; Márquez G, Marco Antonio; Moreno H, Claudia Ximena

2016-01-01

Bacterial carbonate precipitation has implications in geological processes and important biotechnological applications. Bacteria capable of precipitating carbonates have been isolated from different calcium carbonate deposits (speleothems) in caves, soil, freshwater and seawater around the world. However, the diversity of bacteria from calcareous deposits in Colombia, and their ability to precipitate carbonates, remains unknown. In this study, conventional microbiological methods and molecular tools, such as temporal temperature gradient electrophoresis (TTGE), were used to assess the composition of bacterial communities associated with carbonate deposits and drip-waters from two Colombian mines. A genetic analysis of these bacterial communities revealed a similar level of diversity, based on the number of bands detected using TTGE. The dominant phylogenetic affiliations of the bacteria, determined using 16S rRNA gene sequencing, were grouped into two phyla: Proteobacteria and Firmicutes. Within these phyla, seven genera were capable of precipitating calcium carbonates: Lysinibacillus, Bacillus, Strenotophomonas, Brevibacillus, Methylobacterium, Aeromicrobium and Acinetobacter. FTIR and SEM/EDX were used to analyze calcium carbonate crystals produced by isolated Acinetobacter gyllenbergii. The results showed that rhombohedral and angular calcite crystals with sizes of 90μm were precipitated. This research provides information regarding the presence of complex bacterial communities in secondary carbonate deposits from mines and their ability to precipitate calcium carbonate from calcareous deposits of Colombian mines. Copyright © 2015 Elsevier GmbH. All rights reserved.

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic?Anoxic Interface of the Congo Deep-Sea Fan

OpenAIRE

Bessette, Sandrine; Moalic, Yann; Gautey, S?bastien; Lesongeur, Fran?oise; Godfroy, Anne; Toffin, Laurent

2017-01-01

Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon). This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB) communities at the oxic–anoxic in...

Antagonistic activity of isolated lactic acid bacteria from Pliek U against gram-negative bacteria Escherichia coli ATCC 25922

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Kiti, A. A.; Jamilah, I.; Rusmarilin, H.

2017-09-01

Lactic acid bacteria (LAB) is one group of microbes that has many benefits, notably in food and health industries sector. LAB plays an important role in food fermentation and it has bacteriostatic effect against the growth of pathogenic microorganisms. The research related LAB continued to be done to increase the diversity of potential isolates derived from nature which is indigenous bacteria for biotechnological purposes. This study was aimed to isolate and characterize LAB derived from pliek u sample and to examine the potency to inhibits Escherichia coli ATCC 25922 bacteria growth. A total of 5 isolates were isolated and based on morphological and physiological characteristics of the fifth bacteria, they are allegedly belonging to the genus Bacillus. Result of antagonistic test showed that the five isolates could inhibits the growth of E. coli ATCC 25922. The highest inhibition zone is 8.5 mm was shown by isolates NQ2, while the lowest inhibition is 1.5 mm was shown by isolates NQ3.

Diversity and enumeration of halophilic and alkaliphilic bacteria in Spanish-style green table-olive fermentations.

Science.gov (United States)

Lucena-Padrós, Helena; Ruiz-Barba, José Luis

2016-02-01

The presence and enumeration of halophilic and alkaliphilic bacteria in Spanish-style table-olive fermentations was studied. Twenty 10-tonne fermenters at two large manufacturing companies in Spain, previously studied through both culture dependent and independent (PCR-DGGE) methodologies, were selected. Virtually all this microbiota was isolated during the initial fermentation stage. A total of 203 isolates were obtained and identified based on 16S rRNA gene sequences. They belonged to 13 bacterial species, included in 11 genera. It was noticeable the abundance of halophilic and alkaliphilic lactic acid bacteria (HALAB). These HALAB belonged to the three genera of this group: Alkalibacterium, Marinilactibacillus and Halolactibacillus. Ten bacterial species were isolated for the first time from table olive fermentations, including the genera Amphibacillus, Natronobacillus, Catenococcus and Streptohalobacillus. The isolates were genotyped through RAPD and clustered in a dendrogram where 65 distinct strains were identified. Biodiversity indexes found statistically significant differences between both patios regarding genotype richness, diversity and dominance. However, Jaccard similarity index suggested that the halophilic/alkaliphilic microbiota in both patios was more similar than the overall microbiota at the initial fermentation stage. Thus, up to 7 genotypes of 6 different species were shared, suggesting adaptation of some strains to this fermentation stage. Morisita-Horn similarity index indicated a high level of codominance of the same species in both patios. Halophilic and alkaliphilic bacteria, especially HALAB, appeared to be part of the characteristic microbiota at the initial stage of this table-olive fermentation, and they could contribute to the conditioning of the fermenting brines in readiness for growth of common lactic acid bacteria. Copyright © 2015 Elsevier Ltd. All rights reserved.

Relative feeding rates on free and particle-bound bacteria by freshwater macrozooplankton

International Nuclear Information System (INIS)

Schoenberg, S.A.; Maccubbin, A.E.

1985-01-01

Feeding suspensions of equivalent particle spectra were assembled with either free-living ( 3 H]thymidine. Clearance (ml ind -1 d -1 ) of attached bacteria was 3-29 x that of free bacteria for the cladocerans Acantholeberis, Chydorus, and Eubosmina. Pseudosida and Ceriodaphnia showed weaker discrimination or no selection, indicating a lower size threshold for filtration in these species. Feeding suspensions composed of isolated free bacteria yielded significantly higher or lower estimates of grazing than free bacteria with the full complement of particles, depending on species. Relative clearance (attached:free) tended to increase with body size within a species and varied for different particle environments. Bacteria associated with large particles may increase detrital energy flow to consumers in eutrophic environments

Significance of anaerobic bacteria in postoperative infection after radical cystectomy and urinary diversion or reconstruction.

Science.gov (United States)

Hiyama, Yoshiki; Takahashi, Satoshi; Uehara, Teruhisa; Hashimoto, Jiro; Kurimura, Yuichiro; Tanaka, Toshiaki; Masumori, Naoya; Tsukamoto, Taiji

2013-10-01

Radical cystectomy followed by urinary diversion or reconstruction (RC) is a standard treatment for patients with muscle-invasive bladder cancer. In these operations, a high frequency of complications, especially postoperative infection, has been reported. However, there have only been a few studies about postoperative anaerobic bacterial infection. To clarify the significance and role of anaerobic bacteria in postoperative infection, we retrospectively analyzed cases in which postoperative infection by these organisms developed. A total of 126 patients who underwent RC from 2006 to 2010 were included in this study. Various types of postoperative infection occurred in 66 patients. Anaerobic bacterial infections were detected with cultures for urine and blood in one case, for blood in two cases, and for surgical wound pus in four. The frequency of postoperative anaerobic bacterial infection in RC was less than that of colon surgery. However, this study revealed the possible development of a nonnegligible number of postoperative anaerobic bacterial infections. Therefore, we should consider anaerobic bacteria as possible pathogens in postoperative infection after RC.

Diversity and Distribution of Thermophilic Bacteria in Hot Springs of Pakistan.

Science.gov (United States)

Amin, Arshia; Ahmed, Iftikhar; Salam, Nimaichand; Kim, Byung-Yong; Singh, Dharmesh; Zhi, Xiao-Yang; Xiao, Min; Li, Wen-Jun

2017-07-01

Chilas and Hunza areas, located in the Main Mantle Thrust and Main Karakoram Thrust of the Himalayas, host a range of geochemically diverse hot springs. This Himalayan geothermal region encompassed hot springs ranging in temperature from 60 to 95 °C, in pH from 6.2 to 9.4, and in mineralogy from bicarbonates (Tato Field), sulfates (Tatta Pani) to mixed type (Murtazaabad). Microbial community structures in these geothermal springs remained largely unexplored to date. In this study, we report a comprehensive, culture-independent survey of microbial communities in nine samples from these geothermal fields by employing a bar-coded pyrosequencing technique. The bacterial phyla Proteobacteria and Chloroflexi were dominant in all samples from Tato Field, Tatta Pani, and Murtazaabad. The community structures however depended on temperature, pH, and physicochemical parameters of the geothermal sites. The Murtazaabad hot springs with relatively higher temperature (90-95 °C) favored the growth of phylum Thermotogae, whereas the Tatta Pani thermal spring site TP-H3-b (60 °C) favored the phylum Proteobacteria. At sites with low silica and high temperature, OTUs belonging to phylum Chloroflexi were dominant. Deep water areas of the Murtazaabad hot springs favored the sulfur-reducing bacteria. About 40% of the total OTUs obtained from these samples were unclassified or uncharacterized, suggesting the presence of many undiscovered and unexplored microbiota. This study has provided novel insights into the nature of ecological interactions among important taxa in these communities, which in turn will help in determining future study courses in these sites.

Nitrogen-fixing bacteria in Mediterranean seagrass (Posidonia oceanica) roots

KAUST Repository

Garcias Bonet, Neus

2016-03-09

Biological nitrogen fixation by diazotrophic bacteria in seagrass rhizosphere and leaf epiphytic community is an important source of nitrogen required for plant growth. However, the presence of endophytic diazotrophs remains unclear in seagrass tissues. Here, we assess the presence, diversity and taxonomy of nitrogen-fixing bacteria within surface-sterilized roots of Posidonia oceanica. Moreover, we analyze the nitrogen isotopic signature of seagrass tissues in order to notice atmospheric nitrogen fixation. We detected nitrogen-fixing bacteria by nifH gene amplification in 13 out of the 78 roots sampled, corresponding to 9 locations out of 26 meadows. We detected two different types of bacterial nifH sequences associated with P. oceanica roots, which were closely related to sequences previously isolated from the rhizosphere of a salt marsh cord grass and a putative anaerobe. Nitrogen content of seagrass tissues showed low isotopic signatures in all the sampled meadows, pointing out the atmospheric origin of the assimilated nitrogen by seagrasses. However, this was not related with the presence of endophytic nitrogen fixers, suggesting the nitrogen fixation occurring in rhizosphere and in the epiphytic community could be an important source of nitrogen for P. oceanica. The low diversity of nitrogen-fixing bacteria reported here suggests species-specific relationships between diazotrophs and P. oceanica, revealing possible symbiotic interactions that could play a major role in nitrogen acquisition by seagrasses in oligotrophic environments where they form lush meadows.

Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor.

Science.gov (United States)

Goberna, M; Insam, H; Franke-Whittle, I H

2009-04-01

Prokaryotic diversity was investigated near the inlet and outlet of a plug-flow reactor. After analyzing 800 clones, 50 bacterial and 3 archaeal phylogenetic groups were defined. Clostridia (>92%) dominated among bacteria and Methanoculleus (>90%) among archaea. Significant changes in pH and volatile fatty acids did not invoke a major shift in the phylogenetic groups. We suggest that the environmental filter imposed by the saline conditions (20 g liter(-1)) selected a stable community of halotolerant and halophilic prokaryotes.

Influence of Geographical Origin and Flour Type on Diversity of Lactic Acid Bacteria in Traditional Belgian Sourdoughs▿ †

OpenAIRE

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

2007-01-01

A culture-based approach was used to investigate the diversity of lactic acid bacteria (LAB) in Belgian traditional sourdoughs and to assess the influence of flour type, bakery environment, geographical origin, and technological characteristics on the taxonomic composition of these LAB communities. For this purpose, a total of 714 LAB from 21 sourdoughs sampled at 11 artisan bakeries throughout Belgium were subjected to a polyphasic identification approach. The microbial composition of the tr...

The Relation between Evenness and Diversity

Directory of Open Access Journals (Sweden)

Lou Jost

2010-02-01

Full Text Available Contrary to common belief, decomposition of diversity into independent richness and evenness components is mathematically impossible. However, richness can be decomposed into independent diversity and evenness or inequality components. The evenness or inequality component derived in this way is connected to most of the common measures of evenness and inequality in ecology and economics. This perspective justifies the derivation of measures of relative evenness, which give the amount of evenness relative to the maximum and minimum possible for a given richness. Pielou’s [1] evenness measure J is shown to be such a measure.

Abundance and Diversity of CO2-Assimilating Bacteria and Algae Within Red Agricultural Soils Are Modulated by Changing Management Practice.

Science.gov (United States)

Yuan, Hongzhao; Ge, Tida; Chen, Xiangbi; Liu, Shoulong; Zhu, Zhenke; Wu, Xiaohong; Wei, Wenxue; Whiteley, Andrew Steven; Wu, Jinshui

2015-11-01

Elucidating the biodiversity of CO(2)-assimilating bacterial and algal communities in soils is important for obtaining a mechanistic view of terrestrial carbon sinks operating at global scales. "Red" acidic soils (Orthic Acrisols) cover large geographic areas and are subject to a range of management practices, which may alter the balance between carbon dioxide production and assimilation through changes in microbial CO(2)-assimilating populations. Here, we determined the abundance and diversity of CO(2)-assimilating bacteria and algae in acidic soils using quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP) of the cbbL gene, which encodes the key CO(2) assimilation enzyme (ribulose-1,5-bisphosphate carboxylase/oxygenase) in the Calvin cycle. Within the framework of a long-term experiment (Taoyuan Agro-ecosystem, subtropical China), paddy rice fields were converted in 1995 to four alternative land management regimes: natural forest (NF), paddy rice (PR), maize crops (CL), and tea plantations (TP). In 2012 (17 years after land use transformation), we collected and analyzed the soils from fields under the original and converted land management regimes. Our results indicated that fields under the PR soil management system harbored the greatest abundance of cbbL copies (4.33 × 10(8) copies g(-1) soil). More than a decade after converting PR soils to natural, rotation, and perennial management systems, a decline in both the diversity and abundance of cbbL-harboring bacteria and algae was recorded. The lowest abundance of bacteria (0.98 × 10(8) copies g(-1) soil) and algae (0.23 × 10(6) copies g(-1) soil) was observed for TP soils. When converting PR soil management to alternative management systems (i.e., NF, CL, and TP), soil edaphic factors (soil organic carbon and total nitrogen content) were the major determinants of bacterial autotrophic cbbL gene diversity. In contrast, soil phosphorus concentration was the major regulator

Mimicking microbial interactions under nitrate-reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio.

Science.gov (United States)

Arshad, Arslan; Dalcin Martins, Paula; Frank, Jeroen; Jetten, Mike S M; Op den Camp, Huub J M; Welte, Cornelia U

2017-12-01

Microorganisms are main drivers of the sulfur, nitrogen and carbon biogeochemical cycles. These elemental cycles are interconnected by the activity of different guilds in sediments or wastewater treatment systems. Here, we investigated a nitrate-reducing microbial community in a laboratory-scale bioreactor model that closely mimicked estuary or brackish sediment conditions. The bioreactor simultaneously consumed sulfide, methane and ammonium at the expense of nitrate. Ammonium oxidation occurred solely by the activity of anammox bacteria identified as Candidatus Scalindua brodae and Ca. Kuenenia stuttgartiensis. Fifty-three percent of methane oxidation was catalyzed by archaea affiliated to Ca. Methanoperedens and 47% by Ca. Methylomirabilis bacteria. Sulfide oxidation was mainly shared between two proteobacterial groups. Interestingly, competition for nitrate did not lead to exclusion of one particular group. Metagenomic analysis showed that the most abundant taxonomic group was distantly related to Thermodesulfovibrio sp. (87-89% 16S rRNA gene identity, 52-54% average amino acid identity), representing a new family within the Nitrospirae phylum. A high quality draft genome of the new species was recovered, and analysis showed high metabolic versatility. Related microbial groups are found in diverse environments with sulfur, nitrogen and methane cycling, indicating that these novel Nitrospirae bacteria might contribute to biogeochemical cycling in natural habitats. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Screening and isolation of halophilic bacteria producing industrially important enzymes.

Science.gov (United States)

Kumar, Sumit; Karan, Ram; Kapoor, Sanjay; S P, Singh; S K, Khare

2012-10-01

Halophiles are excellent sources of enzymes that are not only salt stable but also can withstand and carry out reactions efficiently under extreme conditions. The aim of the study was to isolate and study the diversity among halophilic bacteria producing enzymes of industrial value. Screening of halophiles from various saline habitats of India led to isolation of 108 halophilic bacteria producing industrially important hydrolases (amylases, lipases and proteases). Characterization of 21 potential isolates by morphological, biochemical and 16S rRNA gene analysis found them related to Marinobacter, Virgibacillus, Halobacillus, Geomicrobium, Chromohalobacter, Oceanobacillus, Bacillus, Halomonas and Staphylococcus genera. They belonged to moderately halophilic group of bacteria exhibiting salt requirement in the range of 3-20%. There is significant diversity among halophiles from saline habitats of India. Preliminary characterization of crude hydrolases established them to be active and stable under more than one extreme condition of high salt, pH, temperature and presence of organic solvents. It is concluded that these halophilic isolates are not only diverse in phylogeny but also in their enzyme characteristics. Their enzymes may be potentially useful for catalysis under harsh operational conditions encountered in industrial processes. The solvent stability among halophilic enzymes seems a generic novel feature making them potentially useful in non-aqueous enzymology.

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

Directory of Open Access Journals (Sweden)

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.

In vivo IgA coating of anaerobic bacteria in human faeces

NARCIS (Netherlands)

vanderWaaij, LA; Limburg, PC; Mesander, G; vanderWaaij, D

The bacterial flora in the human colon, although extremely diverse, has a relatively stable composition and non-infectious anaerobic bacteria are dominant. The flora forms a pool of numerous different antigens separated from mucosal immunocompetent cells by just a single layer of epithelial cells.

Shotgun metagenomic data reveals signifcant abundance but low diversity of Candidatus Scalindua marine anammox bacteria in the Arabian Sea oxygen minimum zone

Directory of Open Access Journals (Sweden)

laura eVillanueva

2014-02-01

Full Text Available Anaerobic ammonium oxidizing (anammox bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. To date, marine anammox bacteria found in both water columns and sediments worldwide belong almost exclusively to Candidatus Scalindua species. Recently the genome assembly of a marine anammox enrichment culture dominated by Candidatus Scalindua profunda became available and can now be used as a template to study metagenome data obtained from various oxygen minimum zones. Here, we sequenced genomic DNA from suspended particulate matter recovered at the upper (170 m deep and center (600 m area of the oxygen minimum zone in the Arabian Sea by SOLiD and Ion Torrent technology. The genome of Candidatus Scalindua profunda served as a template to collect reads. Based on the mapped reads marine anammox Abundance was estimated to be at least 0.4% in the upper and 1.7% in the center area. Single nucleotide variation (SNV analysis was performed to assess diversity of the Candidatus Scalindua populations. Most highly covered were the two diagnostic anammox genes hydrazine synthase (scal_01318c, hzsA and hydrazine dehydrogenase (scal_03295, hdh, while other genes involved in anammox metabolism (narGH, nirS, amtB, focA and ACS had a lower coverage but could still be assembled and analyzed. The results show that Candidatus Scalindua is abundantly present in the Arabian Sea OMZ, but that the diversity within the ecosystem is relatively low.

High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

Directory of Open Access Journals (Sweden)

X. S. Tai

2013-08-01

Full Text Available Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China, located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon–Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g−1 soil and 0.97 × 106 to 12.78 × 106 g−1 soil, respectively. Redundancy analysis (RDA revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial

High diversity of nitrogen-fixing bacteria in the upper reaches of the Heihe River, northwestern China

Science.gov (United States)

Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.; Zhang, Y.

2013-08-01

Vegetation plays a key role in water conservation in the southern Qilian Mountains (northwestern China), located in the upper reaches of the Heihe River. Nitrogen-fixing bacteria are crucial for the protection of the nitrogen supply for vegetation in the region. In the present study, nifH gene clone libraries were established to determine differences between the nitrogen-fixing bacterial communities of the Potentilla parvifolia shrubland and the Carex alrofusca meadow in the southern Qilian Mountains. All of the identified nitrogen-fixing bacterial clones belonged to the Proteobacteria. At the genus level, Azospirillum was only detected in the shrubland soil, while Thiocapsa, Derxia, Ectothiorhodospira, Mesorhizobium, Klebsiella, Ensifer, Methylocella and Pseudomonas were only detected in the meadow soil. The phylogenetic tree was divided into five lineages: lineages I, II and III mainly contained nifH sequences obtained from the meadow soils, while lineage IV was mainly composed of nifH sequences obtained from the shrubland soils. The Shannon-Wiener index of the nifH genes ranged from 1.5 to 2.8 and was higher in the meadow soils than in the shrubland soils. Based on these analyses of diversity and phylogeny, the plant species were hypothesised to influence N cycling by enhancing the fitness of certain nitrogen-fixing taxa. The number of nifH gene copies and colony-forming units (CFUs) of the cultured nitrogen-fixing bacteria were lower in the meadow soils than in the shrubland soils, ranging from 0.4 × 107 to 6.9 × 107 copies g-1 soil and 0.97 × 106 to 12.78 × 106 g-1 soil, respectively. Redundancy analysis (RDA) revealed that the diversity and number of the nifH gene copies were primarily correlated with aboveground biomass in the shrubland soil. In the meadow soil, nifH gene diversity was most affected by altitude, while copy number was most impacted by soil-available K. These results suggest that the nitrogen-fixing bacterial communities beneath Potentilla

Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis.

Directory of Open Access Journals (Sweden)

Tiago Dos Vultos

Full Text Available BACKGROUND: Mycobacterium tuberculosis complex species display relatively static genomes and 99.9% nucleotide sequence identity. Studying the evolutionary history of such monomorphic bacteria is a difficult and challenging task. PRINCIPAL FINDINGS: We found that single-nucleotide polymorphism (SNP analysis of DNA repair, recombination and replication (3R genes in a comprehensive selection of M. tuberculosis complex strains from across the world, yielded surprisingly high levels of polymorphisms as compared to house-keeping genes, making it possible to distinguish between 80% of clinical isolates analyzed in this study. Bioinformatics analysis suggests that a large number of these polymorphisms are potentially deleterious. Site frequency spectrum comparison of synonymous and non-synonymous variants and Ka/Ks ratio analysis suggest a general negative/purifying selection acting on these sets of genes that may lead to suboptimal 3R system activity. In turn, the relaxed fidelity of 3R genes may allow the occurrence of adaptive variants, some of which will survive. Furthermore, 3R-based phylogenetic trees are a new tool for distinguishing between M. tuberculosis complex strains. CONCLUSIONS/SIGNIFICANCE: This situation, and the consequent lack of fidelity in genome maintenance, may serve as a starting point for the evolution of antibiotic resistance, fitness for survival and pathogenicity, possibly conferring a selective advantage in certain stressful situations. These findings suggest that 3R genes may play an important role in the evolution of highly clonal bacteria, such as M. tuberculosis. They also facilitate further epidemiological studies of these bacteria, through the development of high-resolution tools. With many more microbial genomes being sequenced, our results open the door to 3R gene-based studies of adaptation and evolution of other, highly clonal bacteria.

Frost related dieback in Estonian energy plantations of willows in relation to fertilisation and pathogenic bacteria

Energy Technology Data Exchange (ETDEWEB)

Cambours, M.A.; Nejad, P. [Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala (Sweden); Heinsoo, K. [Institute of Zoology and Botany, Estonian Agricultural University, Riia 181, 51014 Tartu (Estonia); Granhall, U. [Department of Microbiology, Swedish University of Agricultural Sciences, Box 7025, 750 07 Uppsala (Sweden)

2006-03-15

Two 9-year old Estonian Salix plantations suffering from dieback were studied: one situated on poor mineral soil and divided into fertilised and unfertilised plots (Saare plantation) and another growing on a well-decomposed and nitrogen-rich organic soil, without fertiliser application (Kambja plantation). Bacteria from internal tissues of visually damaged shoots from seven clones were isolated in spring and autumn. The strains were subsequently biochemically characterised and tested for ice nucleation activity and pathogenicity on Salix. Some strains were also analysed with 16S rRNA. High numbers of culturable bacteria were found, belonging mainly to Erwinia, Sphingomonas, Pseudomonas and Xanthomonas spp. Fertilised plots were significantly more colonised by bacteria than unfertilised plots and also more extensively damaged, showing a lower density of living plants after 7 years of culture. More ice nucleation active (INA) strains were found in Saare fertilised plots and at Kambja than in Saare unfertilised plots. Likewise, most pathogenic strains were isolated from Saare fertilised plots and from Kambja. For some of the willow clones studied, dieback appeared to be related to both clonal frost sensitivity and abundance of INA and pathogenic bacteria. The plantations probably suffered from the presence of high amounts of pathogens and from frost related injuries aggravated by INA bacteria. Most probably the fertilisation at Saare and the nitrogen-rich soil at Kambja created a favourable environment for bacterial development and led to high dieback levels after the first harvest. (author)

Diversity of sulfate-reducing bacteria in a plant using deep geothermal energy

Science.gov (United States)

Alawi, Mashal; Lerm, Stephanie; Vetter, Alexandra; Wolfgramm, Markus; Seibt, Andrea; Würdemann, Hilke

2011-06-01

Enhanced process understanding of engineered geothermal systems is a prerequisite to optimize plant reliability and economy. We investigated microbial, geochemical and mineralogical aspects of a geothermal groundwater system located in the Molasse Basin by fluid analysis. Fluids are characterized by temperatures ranging from 61°C to 103°C, salinities from 600 to 900 mg/l and a dissolved organic carbon content (DOC) between 6.4 to 19.3 mg C/l. The microbial population of fluid samples was analyzed by genetic fingerprinting techniques based on PCR-amplified 16S rRNA- and dissimilatory sulfite reductase genes. Despite of the high temperatures, microbes were detected in all investigated fluids. Fingerprinting and DNA sequencing enabled a correlation to metabolic classes and biogeochemical processes. The analysis revealed a broad diversity of sulfate-reducing bacteria. Overall, the detection of microbes known to be involved in biocorrosion and mineral precipitation indicates that microorganisms could play an important role for the understanding of processes in engineered geothermal systems.

Functional Diversity of Tandem Substrate-Binding Domains in ABC Transporters from Pathogenic Bacteria

NARCIS (Netherlands)

Fulyani, Faizah; Schuurman-Wolters, Gea K.; Vujicic - Zagar, Andreja; Guskov, Albert; Slotboom, Dirk-Jan; Poolman, Bert

2013-01-01

The ATP-binding cassette (ABC) transporter GInPQ is an essential uptake system for amino acids in gram-positive pathogens and related nonpathogenic bacteria. The transporter has tandem substrate-binding domains (SBDs) fused to each transmembrane domain, giving rise to four SBDs per functional

Genetic diversity of siderophore-producing bacteria of tobacco rhizosphere Diversidade genética de bactérias de rizosfera de tabaco produtoras de sideróforos

OpenAIRE

Fang Tian; Yanqin Ding; Hui Zhu; Liangtong Yao; Binghai Du

2009-01-01

The genetic diversity of siderophore-producing bacteria of tobacco rhizosphere was studied by amplified ribosomal DNA restriction analysis (ARDRA), 16S rRNA sequence homology and phylogenetics analysis methods. Studies demonstrated that 85% of the total 354 isolates produced siderophores in iron limited liquid medium. A total of 28 ARDRA patterns were identified among the 299 siderophore-producing bacterial isolates. The 28 ARDRA patterns represented bacteria of 14 different genera belonging ...

Second generation sequencing for elucidating the diversity of bacteria and plasmids in soil

DEFF Research Database (Denmark)

Holmsgaard, Peter Nikolai

. The relative abundance of IncP-1β1 plasmids also increased. In papers four and five, the mobile genetic elements and bacterial diversity, respectively, was studied over a pesticide spraying season in the same BPS used in paper three. The addition of pesticides decreased overall bacterial diversity...

Plant-associated bacteria and their role in the success or failure of metal phytoextraction projects: first observations of a field-related experiment

Science.gov (United States)

Weyens, Nele; Beckers, Bram; Schellingen, Kerim; Ceulemans, Reinhart; Croes, Sarah; Janssen, Jolien; Haenen, Stefan; Witters, Nele; Vangronsveld, Jaco

2013-01-01

Phytoextraction has been reported as an economically and ecologically sound alternative for the remediation of metal-contaminated soils. Willow is a metal phytoextractor of interest because it allows to combine a gradual contaminant removal with production of biomass that can be valorized in different ways. In this work two willow clones growing on a metal-contaminated site were selected: ‘Belgisch Rood’ (BR) with a moderate metal extraction capacity and ‘Tora’ (TO) with a twice as high metal accumulation. All cultivable bacteria associated with both willow clones were isolated and identified using 16SrDNA ARDRA analysis followed by 16SrDNA sequencing. Further all isolated bacteria were investigated for characteristics that might promote plant growth (production of siderophores, organic acids and indol acetic acid) and for their metal resistance. The genotypic and phenotypic characterization of the isolated bacteria showed that the TO endophytic bacterial population is more diverse and contains a higher percentage of metal-resistant plant growth promoting bacteria than the endophytic population associated with BR. We hypothesize that the difference in the metal accumulation capacity between BR and TO clones might be at least partly related to differences in characteristics of their associated bacterial population. PMID:23425076

Bacterial 16S rRNA gene analysis revealed that bacteria related to Arcobacter spp. constitute an abundant and common component of the oyster microbiota (Tiostrea chilensis).

Science.gov (United States)

Romero, J; García-Varela, M; Laclette, J P; Espejo, R T

2002-11-01

To explore the bacterial microbiota in Chilean oyster (Tiostrea chilensis), a molecular approach that permits detection of different bacteria, independently of their capacity to grow in culture media, was used. Bacterial diversity was assessed by analysis of both the 16S rDNA and the 16S-23S intergenic region, obtained by PCR amplifications of DNA extracted from depurated oysters. RFLP of the PCR amplified 16S rDNA showed a prevailing pattern in most of the individuals analyzed, indicating that a few bacterial species were relatively abundant and common in oysters. Cloning and sequencing of the 16S rDNA with the prevailing RFLP pattern indicated that this rRNA was most closely related to Arcobacter spp. However, analysis by the size of the amplified 16S-23S rRNA intergenic regions revealed not Arcobacter spp. but Staphylococcus spp. related bacteria as a major and common component in oyster. These different results may be caused by the absence of target for one of the primers employed for amplification of the intergenic region. Neither of the two bacteria species found in large abundance was recovered after culturing under aerobic, anaerobic, or microaerophilic conditions. This result, however, is expected because the number of bacteria recovered after cultivation was less than 0.01% of the total. All together, these observations suggest that Arcobacter-related strains are probably abundant and common in the Chilean oyster bacterial microbiota.

Isolation and characterization of biosurfactant producing bacteria from Persian Gulf (Bushehr provenance)

International Nuclear Information System (INIS)

Hassanshahian, Mehdi

2014-01-01

Highlights: • Biosurfactant producing bacteria were isolated from Persian Gulf. • There is high diversity of biosurfactant producing bacteria in the Persian Gulf. • These bacteria are very useful for management of oil pollution in the sea. - Abstract: Biosurfactants are surface active materials that are produced by some microorganisms. These molecules increase biodegradation of insoluble pollutants. In this study sediments and seawater samples were collected from the coastline of Bushehr provenance in the Persian Gulf and their biosurfactant producing bacteria were isolated. Biosurfactant producing bacteria were isolated by using an enrichment method in Bushnell-Hass medium with diesel oil as the sole carbon source. Five screening tests were used for selection of Biosurfactant producing bacteria: hemolysis in blood agar, oil spreading, drop collapse, emulsification activity and Bacterial Adhesion to Hydrocarbon test (BATH). These bacteria were identified using biochemical and molecular methods. Eighty different colonies were isolated from the collected samples. The most biosurfactant producing isolates related to petrochemical plants of Khark Island. Fourteen biosurfactant producing bacteria were selected between these isolates and 7 isolates were screened as these were predominant producers that belong to Shewanella alga, Shewanella upenei, Vibrio furnissii, Gallaecimonas pentaromativorans, Brevibacterium epidermidis, Psychrobacter namhaensis and Pseudomonas fluorescens. The largest clear zone diameters in oil spreading were observed for G. pentaromativorans strain O15. Also, this strain has the best emulsification activity and reduction of surface tension, suggesting it is the best of thee isolated strains. The results of this study confirmed that there is high diversity of biosurfactant producing bacteria in marine ecosystem of Iran and by application of these bacteria in petrochemical waste water environmental problems can be assisted

Functional Encyclopedia of Bacteria and Archaea

Energy Technology Data Exchange (ETDEWEB)

Blow, M. J.; Deutschbauer, A. M.; Hoover, C. A.; Lamson, J.; Lamson, J.; Price, M. N.; Waters, J.; Wetmore, K. M.; Bristow, J.; Arkin, A. P.

2013-03-20

Bacteria and Archaea exhibit a huge diversity of metabolic capabilities with fundamental importance in the environment, and potential applications in biotechnology. However, the genetic bases of these capabilities remain unclear due largely to an absence of technologies that link DNA sequence to molecular function. To address this challenge, we are developing a pipeline for high throughput annotation of gene function using mutagenesis, growth assays and DNA sequencing. By applying this pipeline to annotate gene function in 50 diverse microbes we hope to discover thousands of new gene functions and produce a proof of principle `Functional Encyclopedia of Bacteria and Archaea?.

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin.

Science.gov (United States)

Medina, Daniel; Walke, Jenifer B; Gajewski, Zachary; Becker, Matthew H; Swartwout, Meredith C; Belden, Lisa K

2017-01-01

One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads ( Anaxyrus americanus ) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting

Diverse structural approaches to haem appropriation by pathogenic bacteria.

Science.gov (United States)

Hare, Stephen A

2017-04-01

The critical need for iron presents a challenge for pathogenic bacteria that must survive in an environment bereft of accessible iron due to a natural low bioavailability and their host's nutritional immunity. Appropriating haem, either direct from host haemoproteins or by secreting haem-scavenging haemophores, is one way pathogenic bacteria can overcome this challenge. After capturing their target, haem appropriation systems must remove haem from a high-affinity binding site (on the host haemoprotein or bacterial haemophore) and transfer it to a binding site of lower affinity on a bacterial receptor. Structural information is now available to show how, using a combination of induced structural changes and steric clashes, bacteria are able to extract haem from haemophores, haemopexin and haemoglobin. This review focuses on structural descriptions of these bacterial haem acquisition systems, summarising how they bind haem and their target haemoproteins with particularly emphasis on the mechanism of haem extraction. Copyright © 2017 The Author. Published by Elsevier B.V. All rights reserved.

Microbial Diversity in KURT Groundwater and Biomineralization Characteristics

International Nuclear Information System (INIS)

Roh, Yul; Rhee, Sung Keun; Oh, Jong Min; Park, Byung Jun

2009-03-01

The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxides, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

The Microworld of Marine-Bacteria

DEFF Research Database (Denmark)

JØRGENSEN, BB

1995-01-01

Microsensor studies show that the marine environment in the size scale of bacteria is physically and chemically very different from the macroenvironment. The microbial world of the sediment-water interface is thus dominated by water viscosity and steep diffusion gradients. Because of the diverse...... metabolism types, bacteria in the mostly anoxic sea floor play an important role in the major element cycles of the ocean. The communities of giant, filamentous sulfur bacteria that live in the deep-sea hydrothermal vents or along the Pacific coast of South America are presented here as examples....

[Research on soil bacteria under the impact of sealed CO2 leakage by high-throughput sequencing technology].

Science.gov (United States)

Tian, Di; Ma, Xin; Li, Yu-E; Zha, Liang-Song; Wu, Yang; Zou, Xiao-Xia; Liu, Shuang

2013-10-01

Carbon dioxide Capture and Storage has provided a new option for mitigating global anthropogenic CO2 emission with its unique advantages. However, there is a risk of the sealed CO2 leakage, bringing a serious threat to the ecology system. It is widely known that soil microorganisms are closely related to soil health, while the study on the impact of sequestered CO2 leakage on soil microorganisms is quite deficient. In this study, the leakage scenarios of sealed CO2 were constructed and the 16S rRNA genes of soil bacteria were sequenced by Illumina high-throughput sequencing technology on Miseq platform, and related biological analysis was conducted to explore the changes of soil bacterial abundance, diversity and structure. There were 486,645 reads for 43,017 OTUs of 15 soil samples and the results of biological analysis showed that there were differences in the abundance, diversity and community structure of soil bacterial community under different CO, leakage scenarios while the abundance and diversity of the bacterial community declined with the amplification of CO2 leakage quantity and leakage time, and some bacteria species became the dominant bacteria species in the bacteria community, therefore the increase of Acidobacteria species would be a biological indicator for the impact of sealed CO2 leakage on soil ecology system.

Bacterial Diversity across Individual Lichens▿ †

Science.gov (United States)

Mushegian, Alexandra A.; Peterson, Celeste N.; Baker, Christopher C. M.; Pringle, Anne

2011-01-01

Symbioses are unique habitats for bacteria. We surveyed the spatial diversity of bacterial communities across multiple individuals of closely related lichens using terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing. Centers of lichens house richer, more consistent assemblages than species-poor and compositionally disparate lichen edges, suggesting that ecological succession plays a role in structuring these communities. PMID:21531831

Diversity and activity of methanotrophic related bacteria in subsurface sediments of the Krishna-Godavari Basin, India

Digital Repository Service at National Institute of Oceanography (India)

Sujith, P.P.; Sheba, M.; Gonsalves, M.J.B.D.

system (Bio-Rad, USA). DNA sequencing and phylogenetic analysis: The ampli- fied PCR products were purified prior to sequencing according to the manufacturer’s guidelines, using the GenEluteTM PCR Cleanup Kit (Sigma, USA). The puri- fied PCR... at the interface between the reduced zones of the environment6 in the marine sediments7, where methane production and oxidation may take place. These bacteria can be obligate or facultative methano- trophs8. Based on their physiology and phylogeny...

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

KAUST Repository

Neave, Matthew J.

2016-08-24

Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.

Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas

KAUST Repository

Neave, Matthew J.; Apprill, Amy; Ferrier-Pagè s, Christine; Voolstra, Christian R.

2016-01-01

Endozoicomonas bacteria are emerging as extremely diverse and flexible symbionts of numerous marine hosts inhabiting oceans worldwide. Their hosts range from simple invertebrate species, such as sponges and corals, to complex vertebrates, such as fish. Although widely distributed, the functional role of Endozoicomonas within their host microenvironment is not well understood. In this review, we provide a summary of the currently recognized hosts of Endozoicomonas and their global distribution. Next, the potential functional roles of Endozoicomonas, particularly in light of recent microscopic, genomic, and genetic analyses, are discussed. These analyses suggest that Endozoicomonas typically reside in aggregates within host tissues, have a free-living stage due to their large genome sizes, show signs of host and local adaptation, participate in host-associated protein and carbohydrate transport and cycling, and harbour a high degree of genomic plasticity due to the large proportion of transposable elements residing in their genomes. This review will finish with a discussion on the methodological tools currently employed to study Endozoicomonas and host interactions and review future avenues for studying complex host-microbial symbioses.

[Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

Science.gov (United States)

Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

2015-07-01

To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

[Phylogenetic diversity and cold-adaptive hydrolytic enzymes of culturable psychrophilic bacteria associated with sea ice from high latitude ocean, Artic].

Science.gov (United States)

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

2006-04-01

The phylogenetic diversity of culturable psychrophilic bacteria associated with sea ice from high latitude sea (77 degrees 30'N - 81 degrees 12'N), Canadian Basin and Greenland sea Arctic, was investigated. A total of 37 psychrophilic strains were isolated using three different methods of ( i ) spread plate method: 100 microL of each dilution ice-melt sample was spreaded onto the surface of Marine 2216 agar (DIFCO laboratories, Detroit, MI) and incubated for 2 to 6 weeks at 4 degrees C; ( ii ) bath culture and spread plate method: 1 mL of sample was added to 9mL of NSW (unamended natural seawater, 0.2 microm prefiltered and autoclaved) and incubated for 1 months at - 1 degrees C, then spread plate method was used to isolate bacterial strains from the pre-cultured samples; ( iii ) cold shock, bath culture and spread plate method: samples were exposed to - 20 degrees C for 24h, then bacterial strains isolated by bath culture and spread plate method under aerobic conditions. Nearly half of psychrophilic strains are isolated by using method iii . 16S rDNA nearly full-length sequence analysis reveal that psychrophilic strains fall in two phylogenetic divisions, gamma-proteobacteria (in the genera Colwellia, Marinobacter, Shewanella, Thalassomonas, Glaciecola, Marinomonas and Pseudoalteromonas) and Cytophaga-Flexibacter-Bacteroides (in the genera Flavobacterium and Psychroflexus). Nine of bacterial isolates (BSi20007, BSi20497, BSi20517, BSi20537, BSi20170, BSi20001, BSi20002, BSi20675 and BSi20101) quite likely represent novel species (16S rDNA sequence similarity below 97%). One of strains (BSi20002) from Canadian Basin shows 100% sequence similarity to the Antarctic Weddell sea ice isolate Marinobacter sp. ANT8277, suggesting bacteria may have a bipolar distribution at the species level. AF283859 sequences were submitted to the BLAST search program of the National Center for Biotechnology Information website (NCBI, http://www. ncbi. nlm.nih. gov). Twenty sequences

Visualizing aquatic bacteria by light and transmission electron microscopy.

Science.gov (United States)

Silva, Thiago P; Noyma, Natália P; Duque, Thabata L A; Gamalier, Juliana P; Vidal, Luciana O; Lobão, Lúcia M; Chiarini-Garcia, Hélio; Roland, Fábio; Melo, Rossana C N

2014-01-01

The understanding of the functional role of aquatic bacteria in microbial food webs is largely dependent on methods applied to the direct visualization and enumeration of these organisms. While the ultrastructure of aquatic bacteria is still poorly known, routine observation of aquatic bacteria by light microscopy requires staining with fluorochromes, followed by filtration and direct counting on filter surfaces. Here, we used a new strategy to visualize and enumerate aquatic bacteria by light microscopy. By spinning water samples from varied tropical ecosystems in a cytocentrifuge, we found that bacteria firmly adhere to regular slides, can be stained by fluorochoromes with no background formation and fast enumerated. Significant correlations were found between the cytocentrifugation and filter-based methods. Moreover, preparations through cytocentrifugation were more adequate for bacterial viability evaluation than filter-based preparations. Transmission electron microscopic analyses revealed a morphological diversity of bacteria with different internal and external structures, such as large variation in the cell envelope and capsule thickness, and presence or not of thylakoid membranes. Our results demonstrate that aquatic bacteria represent an ultrastructurally diverse population and open avenues for easy handling/quantification and better visualization of bacteria by light microscopy without the need of filter membranes.

[Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia].

Science.gov (United States)

Kalyzhnaya, O V; Itskovich, V B

2014-07-01

The diversity of bacteria associated with deep-water sponge Baikalospongia intermedia was evaluated by sequence analysis of 16S rRNA genes from two sponge samples collected in Lake Baikal from depths of 550 and 1204 m. A total of 64 operational taxonomic units, belonging to nine bacterial phyla, Proteobacteria (classes Alphaproteobacteria,. Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Planctomycetes, Cloroflexi, Verrucomicrobia, Acidobacteria, Chlorobi, and Nitrospirae, including candidate phylum WS5, were identified. Phylogenetic analysis showed that the examined communities contained phylotypes exhibiting homology to uncultured bacteria from different lake ecosystems, freshwater sediments, soil and geological formations. Moreover, a number of phylotypes were relative to psychrophilic, methane-oxidizing, sulfate-reducing bacteria, and to microorganisms resistant to the influence of heavy metals. It seems likely that the unusual habitation conditions of deep-water sponges contribute to the taxonomic diversity of associated bacteria and have an influence on the presence of functionally important microorganisms in bacterial communities.

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides.

Science.gov (United States)

Brown, Steven D; Utturkar, Sagar M; Klingeman, Dawn M; Johnson, Courtney M; Martin, Stanton L; Land, Miriam L; Lu, Tse-Yuan S; Schadt, Christopher W; Doktycz, Mitchel J; Pelletier, Dale A

2012-11-01

To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.

Morphological diversity in tenrecs (Afrosoricida, Tenrecidae: comparing tenrec skull diversity to their closest relatives

Directory of Open Access Journals (Sweden)

Sive Finlay

2015-04-01

Full Text Available It is important to quantify patterns of morphological diversity to enhance our understanding of variation in ecological and evolutionary traits. Here, we present a quantitative analysis of morphological diversity in a family of small mammals, the tenrecs (Afrosoricida, Tenrecidae. Tenrecs are often cited as an example of an exceptionally morphologically diverse group. However, this assumption has not been tested quantitatively. We use geometric morphometric analyses of skull shape to test whether tenrecs are more morphologically diverse than their closest relatives, the golden moles (Afrosoricida, Chrysochloridae. Tenrecs occupy a wider range of ecological niches than golden moles so we predict that they will be more morphologically diverse. Contrary to our expectations, we find that tenrec skulls are only more morphologically diverse than golden moles when measured in lateral view. Furthermore, similarities among the species-rich Microgale tenrec genus appear to mask higher morphological diversity in the rest of the family. These results reveal new insights into the morphological diversity of tenrecs and highlight the importance of using quantitative methods to test qualitative assumptions about patterns of morphological diversity.

Distribution and Diversity of Bacteria and Fungi Colonization in Stone Monuments Analyzed by High-Throughput Sequencing.

Science.gov (United States)

Li, Qiang; Zhang, Bingjian; He, Zhang; Yang, Xiaoru

The historical and cultural heritage of Qingxing palace and Lingyin and Kaihua temple, located in Hangzhou of China, include a large number of exquisite Buddhist statues and ancient stone sculptures which date back to the Northern Song (960-1219 A.D.) and Qing dynasties (1636-1912 A.D.) and are considered to be some of the best examples of ancient stone sculpting techniques. They were added to the World Heritage List in 2011 because of their unique craftsmanship and importance to the study of ancient Chinese Buddhist culture. However, biodeterioration of the surface of the ancient Buddhist statues and white marble pillars not only severely impairs their aesthetic value but also alters their material structure and thermo-hygric properties. In this study, high-throughput sequencing was utilized to identify the microbial communities colonizing the stone monuments. The diversity and distribution of the microbial communities in six samples collected from three different environmental conditions with signs of deterioration were analyzed by means of bioinformatics software and diversity indices. In addition, the impact of environmental factors, including temperature, light intensity, air humidity, and the concentration of NO2 and SO2, on the microbial communities' diversity and distribution was evaluated. The results indicate that the presence of predominantly phototrophic microorganisms was correlated with light and humidity, while nitrifying bacteria and Thiobacillus were associated with NO2 and SO2 from air pollution.

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

Energy Technology Data Exchange (ETDEWEB)

Brown, Steven D [ORNL; Utturkar, Sagar M [ORNL; Klingeman, Dawn Marie [ORNL; Johnson, Courtney M [ORNL; Martin, Stanton [ORNL; Land, Miriam L [ORNL; Lu, Tse-Yuan [ORNL; Schadt, Christopher Warren [ORNL; Doktycz, Mitchel John [ORNL; Pelletier, Dale A [ORNL

2012-01-01

To aid in the investigation of the Populus deltoides microbiome we generated draft genome sequences for twenty one Pseudomonas and twenty one other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Burkholderia, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium and Variovorax were generated.

Diversity and composition of sediment bacteria in subtropical coastal wetlands of North Stradbroke Island, Queensland, Australia

Science.gov (United States)

Chuvochina, Maria; Sampayo, Eugenia; Welti, Nina; Hayes, Matthew; Lu, Yang; Lovelock, Catherine; Lockington, David

2013-04-01

Coastal wetlands provide a wide variety of important ecosystem services but continue to suffer disturbance, degradation and deforestation. Sediment bacteria are responsible for major nutrient transformation and recycling in these ecosystems. Insight into microbial community composition and the factors that determine them may improve our understanding of biogeochemical processes, food web dynamics, biodegradation processes and, thus, help to develop the management strategies for preserving the ecosystem health and services. Characterizing shifts in community taxa along environmental gradients has been shown to provide a useful tool for determining the major drivers affecting community structure and function. North Stradbroke Island (NSI) in Southern Queensland presents considerable habitat diversity including variety of groundwater dependent ecosystems such as lakes, swamps, sedge-like salt marshes and mangroves. Ecological responses of continuous groundwater extraction for municipal purposes and sand mining operations on NSI are still need to be assessed in order to protect its unique environment. Changes in coastal hydrology due to either climate change or human activity may directly affect microbial populations and, thus, biogeochemical cycles of nutrients. These may result in altering/losing some ecosystem services provided by coastal wetlands. In this study we examine microbial diversity and determine environmental controls on bacterial community structure along a natural transition from freshwater forested wetland (melaleuca woodland), sedge-like salt marsh and into mangroves located at NSI. The study area is characterized by significant groundwater flow, nutrient limitation and sharp transition from one ecosystem type to another. Sediment cores (0-5 cm and 20-25 cm depth) were collected from three representative sites of each zone (mangroves - salt marsh - freshwater wetland) along the salinity gradient in August 2012. Subsamples were set aside for use in

Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

Science.gov (United States)

Dobrijevic, Dragana; Abraham, Anne-Laure; Jamet, Alexandre; Maguin, Emmanuelle; van de Guchte, Maarten

2016-01-01

The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

Directory of Open Access Journals (Sweden)

Dragana Dobrijevic

Full Text Available The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

It's all relative: ranking the diversity of aquatic bacterial communities.

Science.gov (United States)

Shaw, Allison K; Halpern, Aaron L; Beeson, Karen; Tran, Bao; Venter, J Craig; Martiny, Jennifer B H

2008-09-01

The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.

Phylloplane bacteria of Jatropha curcas: diversity, metabolic characteristics, and growth-promoting attributes towards vigor of maize seedling.

Science.gov (United States)

Dubey, Garima; Kollah, Bharati; Ahirwar, Usha; Mandal, Asit; Thakur, Jyoti Kumar; Patra, Ashok Kumar; Mohanty, Santosh Ranjan

2017-10-01

The complex role of phylloplane microorganisms is less understood than that of rhizospheric microorganisms in lieu of their pivotal role in plant's sustainability. This experiment aims to study the diversity of the culturable phylloplane bacteria of Jatropha curcas and evaluate their growth-promoting activities towards maize seedling vigor. Heterotrophic bacteria were isolated from the phylloplane of J. curcas and their 16S rRNA genes were sequenced. Sequences of the 16S rRNA gene were very similar to those of species belonging to the classes Bacillales (50%), Gammaproteobacteria (21.8%), Betaproteobacteria (15.6%), and Alphaproteobacteria (12.5%). The phylloplane bacteria preferred to utilize alcohol rather than monosaccharides and polysaccharides as a carbon source. Isolates exhibited ACC (1-aminocyclopropane-1-carboxylic acid) deaminase, phosphatase, potassium solubilization, and indole acetic acid (IAA) production activities. The phosphate-solubilizing capacity (mg of PO 4 solubilized by 10 8 cells) varied from 0.04 to 0.21. The IAA production potential (μg IAA produced by 10 8 cells in 48 h) of the isolates varied from 0.41 to 9.29. Inoculation of the isolates to maize seed significantly increased shoot and root lengths of maize seedlings. A linear regression model of the plant-growth-promoting activities significantly correlated (p < 0.01) with the growth parameters. Similarly, a correspondence analysis categorized ACC deaminase and IAA production as the major factors contributing 41% and 13.8% variation, respectively, to the growth of maize seedlings.

Influence of compost amendments on the diversity of alkane degrading bacteria in hydrocarbon contaminated soils

Directory of Open Access Journals (Sweden)

Michael eSchloter

2014-03-01

Full Text Available Alkane degrading microorganisms play an important role for bioremediation of petrogenic contaminated environments. In this study, we investigated the effects of compost addition on the diversity of alkane monooxygenase gene (alkB harboring bacteria in oil-contaminated soil originated from an industrial zone in Celje, Slovenia, to improve our understanding about the bacterial community involved in alkane degradation and the effects of amendments. Soil without any amendments (control soil and soil amended with compost of different maturation stages, i 1 year and ii 2 weeks, were incubated under controlled conditions in a microcosm experiment and sampled after 0, 6, 12 and 36 weeks of incubation. By using quantitative real-time PCR higher number of alkB genes could be detected in soil samples with compost compared to the control soil after 6, 12 and 36 weeks mainly if the less maturated compost was added. To get an insight into the composition of the alkB harboring microbial communities, we performed next generation sequencing of alkB gene fragment amplicons. Richness and diversity of alkB gene harboring prokaryotes was higher in soil mixed with compost compared to control soil after 6, 12 and 36 weeks again with stronger effects of the less maturated compost. Comparison of communities detected in different samples and time points based on principle component analysis revealed that the addition of compost in general stimulated the abundance of alkB harboring Actinobacteria during the experiment independent from the maturation stage of the compost compared to the control soils. In addition alkB harboring proteobacteria like Shewanella or Hydrocarboniphaga as well as proteobacteria of the genus Agrobacterium responded positively to the addition of compost to soil The amendment of the less maturated compost resulted in addition in a large increase of alkB harboring bacteria of the Cytophaga group (Microscilla mainly at the early sampling

Enrichment of marine anammox bacteria from seawater-related samples and bacterial community study.

Science.gov (United States)

Kawagoshi, Y; Nakamura, Y; Kawashima, H; Fujisaki, K; Furukawa, K; Fujimoto, A

2010-01-01

Anaerobic ammonium oxidation (anammox) is a novel nitrogen pathway catalyzed by anammox bacteria which are obligate anaerobic chemoautotrophs. In this study, enrichment culture of marine anammox bacteria (MAAOB) from the samples related to seawater was conducted. Simultaneous removal of ammonium and nitrite was confirmed in continuous culture inoculated with sediment of a sea-based waste disposal site within 50 days. However, no simultaneous nitrogen removal was observed in cultures inoculated with seawater-acclimated denitrifying sludge or with muddy sediment of tideland even during 200 days. Nitrogen removal rate of 0.13 kg/m(3)/day was achieved at nitrogen loading rate of 0.16 kg/m(3)/day after 320th days in the culture inoculated with the sediment of waste disposal site. The nitrogen removal ratio between ammonium nitrogen and nitrite nitrogen was 1:1.07. Denaturing gradient gel electrophoresis (DGGE) analysis indicated that an abundance of the bacteria close to MAAOB and coexistence of ammonium oxidizing bacteria and denitrifying bacteria in the culture.

Diversity and antibiotic resistance of uropathogenic bacteria from ...

African Journals Online (AJOL)

Background: Urinary tract infections (UTI) are one of the major causes of prescribing and antibiotic consumption. In order to use the best antibiotic treatment for their patients, reliable and recent data about epidemiology and antibiotic resistance profile of uropathogenic bacteria must be available for clinicians. Therefore ...

Isolation, Characterization, and Genetic Diversity of Ice Nucleation Active Bacteria on Various Plants

Directory of Open Access Journals (Sweden)

DIANA ELIZABETH WATURANGI

2009-06-01

Full Text Available Ice nucleation active (INA bacteria is a group of bacteria with the ability to catalyze the ice formation at temperature above -10 °C and causing frost injury in plants. Since, most of the literature on INA bacteria were from subtropical area, studies of INA bacteria from tropical area are needed. We sampled eight fruits and 36 leaves of 21 plant species, and then identified through biochemical and genetic analysis. INA bacteria were characterized for INA protein classification, pH stability, and optimization of heat endurance. We discovered 15 INA bacteria from seven plants species. Most of bacteria are oxidase and H2S negative, catalase and citrate positive, gram negative, and cocoid formed. These INA bacteria were classified in to three classes based on their freezing temperature. Most of the isolates were active in heat and pH stability assay. Some isolates were analysed for 16S rRNA gene. We observed that isolates from Morinda citrifolia shared 97% similiarity with Pseudomonas sp. Isolate from Piper betle shared 93% similarity with P. pseudoalcaligenes. Isolate from Carica papaya shared 94% similarity with Pseudomonas sp. While isolate from Fragaria vesca shared 90% similarity with Sphingomonas sp.

Isolation, Characterization, and Genetic Diversity of Ice Nucleation Active Bacteria on Various Plants

Directory of Open Access Journals (Sweden)

DIANA ELIZABETH WATURANGI

2009-06-01

Full Text Available Ice nucleation active (INA bacteria is a group of bacteria with the ability to catalyze the ice formation at temperature above -10 oC and causing frost injury in plants. Since, most of the literature on INA bacteria were from subtropical area, studies of INA bacteria from tropical area are needed. We sampled eight fruits and 36 leaves of 21 plant species, and then identified through biochemical and genetic analysis. INA bacteria were characterized for INA protein classification, pH stability, and optimization of heat endurance. We discovered 15 INA bacteria from seven plants species. Most of bacteria are oxidase and H2S negative, catalase and citrate positive, gram negative, and cocoid formed. These INA bacteria were classified in to three classes based on their freezing temperature. Most of the isolates were active in heat and pH stability assay. Some isolates were analysed for 16S rRNA gene. We observed that isolates from Morinda citrifolia shared 97% similiarity with Pseudomonas sp. Isolate from Piper betle shared 93% similarity with P. pseudoalcaligenes. Isolate from Carica papaya shared 94% similarity with Pseudomonas sp. While isolate from Fragaria vesca shared 90% similarity with Sphingomonas sp.

Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon.

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Lemay, Matthew A; Russello, Michael A

2014-11-04

Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with

Diversity and community composition of tributyltin-resistant bacteria under different conditions

International Nuclear Information System (INIS)

Lee, Y. H.; Park, S.; Park, H.; Choi, Y

2009-01-01

Tributyltin (TBT) is an organometallic compound used as anti fouling agent in marine paints. this compound is toxic not only for eukaryotes, but also for bacteria. Based on the literature review, a few researchers have reported evidence for the presence of TBT-resistant bacteria in natural seawater and marine sediment. (Author)

Diversity and community composition of tributyltin-resistant bacteria under different conditions

Energy Technology Data Exchange (ETDEWEB)

Lee, Y. H.; Park, S.; Park, H.; Choi, Y

2009-07-01

Tributyltin (TBT) is an organometallic compound used as anti fouling agent in marine paints. this compound is toxic not only for eukaryotes, but also for bacteria. Based on the literature review, a few researchers have reported evidence for the presence of TBT-resistant bacteria in natural seawater and marine sediment. (Author)

Natural Diversity in Heat Resistance of Bacteria and Bacterial Spores: Impact on Food Safety and Quality.

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den Besten, Heidy M W; Wells-Bennik, Marjon H J; Zwietering, Marcel H

2018-03-25

Heat treatments are widely used in food processing often with the aim of reducing or eliminating spoilage microorganisms and pathogens in food products. The efficacy of applying heat to control microorganisms is challenged by the natural diversity of microorganisms with respect to their heat robustness. This review gives an overview of the variations in heat resistances of various species and strains, describes modeling approaches to quantify heat robustness, and addresses the relevance and impact of the natural diversity of microorganisms when assessing heat inactivation. This comparison of heat resistances of microorganisms facilitates the evaluation of which (groups of) organisms might be troublesome in a production process in which heat treatment is critical to reducing the microbial contaminants, and also allows fine-tuning of the process parameters. Various sources of microbiological variability are discussed and compared for a range of species, including spore-forming and non-spore-forming pathogens and spoilage organisms. This benchmarking of variability factors gives crucial information about the most important factors that should be included in risk assessments to realistically predict heat inactivation of bacteria and spores as part of the measures for controlling shelf life and safety of food products.

The little bacteria that can – diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments

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Taş, Neslihan; Van Eekert, Miriam H. A.; De Vos, Willem M.; Smidt, Hauke

2010-01-01

Summary The fate and persistence of chlorinated organics in the environment have been a concern for the past 50 years. Industrialization and extensive agricultural activities have led to the accumulation of these pollutants in the environment, while their adverse impact on various ecosystems and human health also became evident. This review provides an update on the current knowledge of specialized anaerobic bacteria, namely ‘Dehalococcoides’ spp., which are dedicated to the transformation of various chlorinated organic compounds via reductive dechlorination. Advances in microbiology and molecular techniques shed light into the diversity and functioning of Dehalococcoides spp. in several different locations. Recent genome sequencing projects revealed a large number of genes that are potentially involved in reductive dechlorination. Molecular approaches towards analysis of diversity and expression especially of reductive dehalogenase‐encoding genes are providing a growing body of knowledge on biodegradative pathways active in defined pure and mixed cultures as well as directly in the environment. Moreover, several successful field cases of bioremediation strengthen the notion of dedicated degraders such as Dehalococcoides spp. as key players in the restoration of contaminated environments. PMID:21255338

Diversity of lactic acid bacteria in sian-sianzih (fermented clams), a traditional fermented food in Taiwan.

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Chen, Yi-sheng; Wu, Hui-chung; Li, Ya-han; Leong, Kun-hon; Pua, Xiao-hui; Weng, Ming-kai; Yanagida, Fujitoshi

2012-01-30

Sian-sianzih (fermented clams) is a popular traditional fermented food in Taiwan. The lactic acid bacteria (LAB) microflora in sian-sianzih have not been studied in detail. In this study, LAB from sian-sianzih were isolated, characterized and identified. A total of 186 cultures of LAB were isolated from seven sian-sianzih samples and 29 cultures were isolated from its main raw substrate: clams. The identification results revealed up to 11 distinct bacterial species belonging to five genera in sian-sianzih, and three species belonging to two genera in clams. The most common bacterial genera in sian-sianzih were Lactobacillus and Weissella, followed by Leuconostoc, Pediococcus and Lactococcus. A regional similarity in LAB, with differences in diversity, was observed in the current study. On the other hand, Lactococcus lactis subsp. lactis was the most common species found in raw clam samples. The results also suggested that greater LAB diversity could be observed in wild clams than in cultured ones. Furthermore, antibacterial activities of the isolates were determined, and one Weisella hellenica strain showed inhibitory activity against the indicator strain Lactobacilluas sakei JCM 1157(T) . A sensory assessment of seven sian-sianzih samples was also performed and the results indicated that diversity of LAB has a great effect on its aroma and taste formation. The results demonstrate that various LAB species are distributed in sian-sianzih and have a great effect on the flavor of sian-sianzih. Copyright © 2011 Society of Chemical Industry.

Distribution and Diversity of Bacteria and Fungi Colonization in Stone Monuments Analyzed by High-Throughput Sequencing.

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Qiang Li

Full Text Available The historical and cultural heritage of Qingxing palace and Lingyin and Kaihua temple, located in Hangzhou of China, include a large number of exquisite Buddhist statues and ancient stone sculptures which date back to the Northern Song (960-1219 A.D. and Qing dynasties (1636-1912 A.D. and are considered to be some of the best examples of ancient stone sculpting techniques. They were added to the World Heritage List in 2011 because of their unique craftsmanship and importance to the study of ancient Chinese Buddhist culture. However, biodeterioration of the surface of the ancient Buddhist statues and white marble pillars not only severely impairs their aesthetic value but also alters their material structure and thermo-hygric properties. In this study, high-throughput sequencing was utilized to identify the microbial communities colonizing the stone monuments. The diversity and distribution of the microbial communities in six samples collected from three different environmental conditions with signs of deterioration were analyzed by means of bioinformatics software and diversity indices. In addition, the impact of environmental factors, including temperature, light intensity, air humidity, and the concentration of NO2 and SO2, on the microbial communities' diversity and distribution was evaluated. The results indicate that the presence of predominantly phototrophic microorganisms was correlated with light and humidity, while nitrifying bacteria and Thiobacillus were associated with NO2 and SO2 from air pollution.

Full-scale photobioreactor for biotreatment of olive washing water: Structure and diversity of the microalgae-bacteria consortium.

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Maza-Márquez, P; González-Martínez, A; Rodelas, B; González-López, J

2017-08-01

The performance of a full-scale photobioreactor (PBR) for the treatment of olive washing water (OWW) was evaluated under different HRTs (5-2days). The system was able to treat up to 3926L OWWday -1 , and consisted of an activated-carbon pretreatment column and a tubular PBR unit (80 tubes, 98.17L volume, 2-m height, 0.25m diameter). PBR was an effective and environmentally friendly method for the removal of phenols, COD, BOD 5 , turbidity and color from OWW (average efficiencies 94.84±0.55%, 85.86±1.24%, 99.12±0.17%, 95.86±0.98% and 87.24±0.91%, respectively). The diversity of total bacteria and microalgae in the PBR was analyzed using Illumina-sequencing, evaluating the efficiency of two DNA extraction methods. A stable microalgae-bacteria consortium was developed throughout the whole experimentation period, regardless of changes in HRT, temperature or solar radiation. MDS analyses revealed that the interplay between green algae (Sphaeropleales), cyanobacteria (Hapalosiphon) and Proteobacteria (Rhodopseudomonas, Azotobacter) played important roles in OWW bioremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Study of fecal bacterial diversity in Yunnan snub-nosed monkey ...

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Yomi

The bacterial diversity in fecal samples from Yunnan snub-nosed monkey ... Based on the phylogenetic analysis, the fecal bacteria of R. bieti distributed ... and conservation genetics, but research on fecal bacterial ... The large number of microorganisms in the intestine of .... There was high evolutional relativity between.

Microbial Diversity and Characteristics in Anaerobic Environments in KURT Groundwater

International Nuclear Information System (INIS)

Roh, Yul; Oh, Jong Min; Rhee, Sung Keun; Yong, Jong Joong

2008-03-01

The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxide, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

Culture-dependent and independent studies of microbial diversity in highly copper-contaminated Chilean marine sediments.

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Besaury, Ludovic; Marty, Florence; Buquet, Sylvaine; Mesnage, Valérie; Muyzer, Gerard; Quillet, Laurent

2013-02-01

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions, focusing on sulfate-, thiosulfate-, and iron-reducing bacteria. For both sediments, the cultivable bacteria isolated at oxic conditions were mostly affiliated to the genus Bacillus, while at anoxic conditions the majority of the cultivable bacteria found were closely related to members of the genera Desulfovibrio, Sphingomonas, and Virgibacillus. Copper resistance was between 100 and 400 ppm, with the exception of a strain affiliated to members of the genus Desulfuromonas, which was resistant up to 1,000 ppm of copper. In parallel, cloning and sequencing of 16S rRNA was performed to study the total bacterial diversity in the sediments. A weak correlation was observed between the isolated strains and the 16S rRNA operational taxonomic units detected. The presence of copper resistance genes (copA, cusA, and pcoA) was tested for all the strains isolated; only copA was detected in a few isolates, suggesting that other copper resistance mechanisms could be used by the bacteria in those highly copper-contaminated sediments.

Isolation, diversity, and biotechnological potential of rhizo- and endophytic bacteria associated with mangrove plants from Saudi Arabia.

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Bibi, F; Ullah, I; Alvi, S A; Bakhsh, S A; Yasir, M; Al-Ghamdi, A A K; Azhar, E I

2017-06-20

Marine bacteria have been exceptional sources of halotolerant enzymes since decades. The aim of the present study was to isolate bacteria producing hydrolytic enzymes from seven different mangroves collected from the coastal area of Thuwal, Jeddah, Saudi Arabia, and to further screen them for other enzymatic and antifungal activities. We have isolated 46 different rhizo- and endophytic bacteria from the soil, roots, and leaves of the mangroves using different enzymatic media. These bacterial strains were capable of producing industrially important enzymes (cellulase, protease, lipase, and amylase). The bacteria were screened further for antagonistic activity against fungal pathogens. Finally, these bacterial strains were identified on the basis of the16S rDNA sequence. Taxonomic and phylogenetic analysis revealed 95.9-100% sequence identity to type strains of related species. The dominant phylum was Gammaproteobacteria (γ-Proteobacteria), which comprised 10 different genera - Erwinia, Vibrio, Psychrobacter, Aidingimonas, Marinobacter, Chromohalobacter, Halomonas, Microbulbifer, and Alteromonas. Firmicutes was the second dominant phylum, which contained only the genus Bacillus. Similarly, only Isoptericola belonged to Actinobacteria. Further these enzyme-producing bacteria were tested for the production of other enzymes. Most of the active strains showed cellulytic and lipolytic activities. Several were also active against fungal pathogens. Our results demonstrated that the mangroves represent an important source of potentially active bacteria producing enzymes and antifungal metabolites (bioactive products). These bacteria are a source of novel halophilic enzymes and antibiotics that can find industrial and medicinal use.

[Distribution and Diversity of Ammonium-oxidizing Archaea and Ammonium-oxidizing Bacteria in Surface Sediments of Oujiang River].

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Li, Hu; Huang, Fu-yi; Su, Jian-qiang; Hong, You-wei; Yu, Shen

2015-12-01

Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) play important roles in the biogeochemical nitrogen cycle. Rivers are important ecosystems containing a large number of functional microbes in nitrogen cycle. In this study, denaturing gradient gel electrophoresis (DGGE ) and real-time quantitative PCR (qPCR) technology were used to analyze the distribution and diversity of AOA and AOB in sediments from Oujiang. The results showed that the AOA community structure was similar among various sites, while the AOB community structure was significantly different, in which all detected AOB sequences were classified into Nitrosospira and Nitrosomonas, and 90% affiliated to Nitrosospira. The community composition of AOA was influenced by NH₄⁺ and TS, in addition, the AOB composition was affected by NH₄⁺, EC, pH, NO₃⁻, TC and TN. Total sulfur (TS) and electrical conductivity (EC) were the major factors influencing the diversity of AOA and AOB, respectively. AOA abundance was significantly higher than that of AOB. EC, NH₄⁺-N and NO₃⁻-N were the main environmental factors affecting the abundance of AOA and AOB. This study indicated that the community composition and diversity of AOA and AOB were significantly influenced by environmental factors, and AOA might be dominant drivers in the ammonia oxidation process in Oujiang surface sediment.

Relational Diversity Promotes Cooperation in Prisoner’s Dilemma Games

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Xu, Bo; Wang, Jianwei; Deng, Ruipu; Li, Miao

2014-01-01

Relational diversity can be characterized by heterogeneous distributions of tie strengths in social networks and this diversity is present not only among humans, but throughout the animal world. We account for this observation by analyzing two network datasets from Facebook. We measure the strength of a tie by calculating the extent of overlap of friends between the two individuals. Based on the previous findings in human experiments, we argue that it is very unlikely that players will allocate their investments equally to their neighbors. There is a tendency that players prefer to donate more to their intimate friends. We find that if players preferentially allocate their investments to their good friends, cooperation will be promoted in PDG. We proved that the facilitation of the cooperative strategy relies mostly on the cooperative allies between best friends, resulting in the formation of cooperative clusters which are able to prevail against the defectors even when there is a large cost to cooperate. Moreover, we discover that the effect of relational diversity cannot be analyzed by adopting classical complex networks models, because neither of the artificial networks is able to produce networks with diverse distributions of tie strengths. It is of vital importance to introduce real social networks to study the influence of diverse relations especially when it comes to humans. This research proposes a brand new perspective to understand the influence of social relations on the emergence of cooperation in evolutionary prisoner’s dilemma games. PMID:25474354

Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization.

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Tiago, Igor; Veríssimo, António

2013-06-01

Microbial and functional diversity were assessed, from a serpentinization-driven subterrestrial alkaline aquifer - Cabeço de Vide Aquifer (CVA) in Portugal. DGGE analyses revealed the presence of a stable microbial community. By 16S rRNA gene libraries and pyrosequencing analyses, a diverse bacterial composition was determined, contrasting with low archaeal diversity. Within Bacteria the majority of the populations were related to organisms or sequences affiliated to class Clostridia, but members of classes Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Deinococci, Gammaproteobacteria and of the phyla Bacteroidetes, Chloroflexi and Nitrospira were also detected. Domain Archaea encompassed mainly sequences affiliated to Euryarchaeota. Only form I RuBisCO - cbbL was detected. Autotrophic carbon fixation via the rTCA, 3-HP and 3-HP/4H-B cycles could not be confirmed. The detected APS reductase alpha subunit - aprA sequences were phylogenetically related to sequences of sulfate-reducing bacteria belonging to Clostridia, and also to sequences of chemolithoautothrophic sulfur-oxidizing bacteria belonging to Betaproteobacteria. Sequences of methyl coenzyme M reductase - mcrA were phylogenetically affiliated to sequences belonging to Anaerobic Methanotroph group 1 (ANME-1). The populations found and the functional key markers detected in CVA suggest that metabolisms related to H2 , methane and/or sulfur may be the major driving forces in this environment. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes

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Zhang, Jun; Zhang, Lei; Geng, Alei; Liu, Fanghua; Zhao, Guoping; Wang, Shengyue; Zhou, Zhihua; Yan, Xing

2015-01-01

Diverse cellulolytic bacteria are essential for maintaining high lignocellulose degradation ability in biogas digesters. However, little was known about functional genes and gene clusters of dominant cellulolytic bacteria in biogas digesters. This is the foundation to understand lignocellulose degradation mechanisms of biogas digesters and apply these gene resource for optimizing biofuel production. A combination of metagenomic and 16S rRNA gene clone library methods was used to investigate the dominant cellulolytic bacteria and their glycoside hydrolase (GH) genes in two biogas digesters. The 16S rRNA gene analysis revealed that the dominant cellulolytic bacteria were strains closely related to Clostridium straminisolvens and an uncultured cellulolytic bacterium designated BG-1. To recover GH genes from cellulolytic bacteria in general, and BG-1 in particular, a refined assembly approach developed in this study was used to assemble GH genes from metagenomic reads; 163 GH-containing contigs ≥ 1 kb in length were obtained. Six recovered GH5 genes that were expressed in E. coli demonstrated multiple lignocellulase activities and one had high mannanase activity (1255 U/mg). Eleven fosmid clones harboring the recovered GH-containing contigs were sequenced and assembled into 10 fosmid contigs. The composition of GH genes in the 163 assembled metagenomic contigs and 10 fosmid contigs indicated that diverse GHs and lignocellulose degradation mechanisms were present in the biogas digesters. In particular, a small portion of BG-1 genome information was recovered by PhyloPythiaS analysis. The lignocellulase gene clusters in BG-1 suggested that it might use a possible novel lignocellulose degradation mechanism to efficiently degrade lignocellulose. Dominant cellulolytic bacteria of biogas digester possess diverse GH genes, not only in sequences but also in their functions, which may be applied for production of biofuel in the future. PMID:26070087

Low Prevalence of Carbapenem-Resistant Bacteria in River Water: Resistance Is Mostly Related to Intrinsic Mechanisms.

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Tacão, Marta; Correia, António; Henriques, Isabel S

2015-10-01

Carbapenems are last-resort antibiotics to handle serious infections caused by multiresistant bacteria. The incidence of resistance to these antibiotics has been increasing and new resistance mechanisms have emerged. The dissemination of carbapenem resistance in the environment has been overlooked. The main goal of this research was to assess the prevalence and diversity of carbapenem-resistant bacteria in riverine ecosystems. The presence of frequently reported carbapenemase-encoding genes was inspected. The proportion of imipenem-resistant bacteria was on average 2.24 CFU/ml. Imipenem-resistant strains (n=110) were identified as Pseudomonas spp., Stenotrophomonas maltophilia, Aeromonas spp., Chromobacterium haemolyticum, Shewanella xiamenensis, and members of Enterobacteriaceae. Carbapenem-resistant bacteria were highly resistant to other beta-lactams such as quinolones, aminoglycosides, chloramphenicol, tetracyclines, and sulfamethoxazole/trimethoprim. Carbapenem resistance was mostly associated with intrinsically resistant bacteria. As intrinsic resistance mechanisms, we have identified the blaCphA gene in 77.3% of Aeromonas spp., blaL1 in all S. maltophilia, and blaOXA-48-like in all S. xiamenensis. As acquired resistance mechanisms, we have detected the blaVIM-2 gene in six Pseudomonas spp. (5.45%). Integrons with gene cassettes encoding resistance to aminoglycosides (aacA and aacC genes), trimethoprim (dfrB1b), and carbapenems (blaVIM-2) were found in Pseudomonas spp. Results suggest that carbapenem resistance dissemination in riverine ecosystems is still at an early stage. Nevertheless, monitoring these aquatic compartments for the presence of resistance genes and its host organisms is essential to outline strategies to minimize resistance dissemination.

Diversity structure of culturable bacteria isolated from the Fildes Peninsula (King George Island, Antarctica): A phylogenetic analysis perspective.

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González-Rocha, Gerardo; Muñoz-Cartes, Gabriel; Canales-Aguirre, Cristian B; Lima, Celia A; Domínguez-Yévenes, Mariana; Bello-Toledo, Helia; Hernández, Cristián E

2017-01-01

It has been proposed that Antarctic environments select microorganisms with unique biochemical adaptations, based on the tenet 'Everything is everywhere, but, the environment selects' by Baas-Becking. However, this is a hypothesis that has not been extensively evaluated. This study evaluated the fundamental prediction contained in this hypothesis-in the sense that species are structured in the landscape according to their local habitats-, using as study model the phylogenetic diversity of the culturable bacteria of Fildes Peninsula (King George Island, Antarctica). Eighty bacterial strains isolated from 10 different locations in the area, were recovered. Based on phylogenetic analysis of 16S rRNA gene sequences, the isolates were grouped into twenty-six phylotypes distributed in three main clades, of which only six are exclusive to Antarctica. Results showed that phylotypes do not group significantly by habitat type; however, local habitat types had phylogenetic signal, which support the phylogenetic niche conservatism hypothesis and not a selective role of the environment like the Baas-Becking hypothesis suggests. We propose that, more than habitat selection resulting in new local adaptations and diversity, local historical colonization and species sorting (i.e. differences in speciation and extinction rates that arise by interaction of species level traits with the environment) play a fundamental role on the culturable bacterial diversity in Antarctica.

Diversity of indigenous endophytic bacteria associated with the roots of Chinese cabbage (Brassica campestris L.) cultivars and their antagonism towards pathogens.

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Haque, Md Azizul; Yun, Han Dae; Cho, Kye Man

2016-05-01

The study aimed to reveal the diversity of endophytic bacteria in the roots of Chinese cabbage (CC) cultivated in two areas in Korea, namely, Seosang-gun (SS) and Haenam-gun (HN), and also in a transgenic plant (TP) from the laboratory. A total of 653 colonies were isolated from the interior of CC roots, comprising 118, 302, and 233 isolates from SS, HN, and TP samples, respectively. Based on 16S rRNA gene sequence analysis, the isolates belonged to four major phylogenetic groups: high-G+C Gram-positive bacteria (HGC-GPB), low-G+C Gram-positive bacteria (LGC-GPB), Proteobacteria, and Bacteriodetes. The most dominant groups in the roots of the SS, HN, and TP cultivars were LGC-GPB (48.3%), Proteobacteria (50.2%), and HGC-GPB (38.2%), respectively. Importantly, most of the isolates that produced cell-walldegrading enzymes belonged to the genus Bacillus. Bacillus sp. (HNR03, TPR06), Bacillus pumilus (SSR07, HNR11, TPR07), and Bacillus subtilis (TPR03) showed high antagonism against the tested food-borne pathogenic bacteria. In addition, Bacillus sp. (HNR03, TPR06), Bacillus pumilus (SSR07, HNR11, HNR17, TPR11), Microbacterium oxidans (SSR09, TPR04), Bacillus cereus HNR10, Pseudomonas sp. HNR13, and Bacillus subtilis (TPR02, TPR03) showed strong antagonistic activity against the fungi Phythium ultimum, Phytophthora capsici, Fusarium oxysporum, and Rhizoctonia solani. The endophytes isolated from the TP cultivar showed the strongest antagonistic reactions against pathogens. This study is the first report on endophytic bacteria from Chinese cabbage roots.

Synergistic Antibacterial Effects of Chitosan-Caffeic Acid Conjugate against Antibiotic-Resistant Acne-Related Bacteria.

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Kim, Ji-Hoon; Yu, Daeung; Eom, Sung-Hwan; Kim, Song-Hee; Oh, Junghwan; Jung, Won-Kyo; Kim, Young-Mog

2017-06-08

The object of this study was to discover an alternative therapeutic agent with fewer side effects against acne vulgaris, one of the most common skin diseases. Acne vulgaris is often associated with acne-related bacteria such as Propionibacterium acnes , Staphylococcus epidermidis , Staphylococcus aureus , and Pseudomonas aeruginosa . Some of these bacteria exhibit a resistance against commercial antibiotics that have been used in the treatment of acne vulgaris (tetracycline, erythromycin, and lincomycin). In the current study, we tested in vitro antibacterial effect of chitosan-phytochemical conjugates on acne-related bacteria. Three chitosan-phytochemical conjugates used in this study exhibited stronger antibacterial activity than that of chitosan (unmodified control). Chitosan-caffeic acid conjugate (CCA) showed the highest antibacterial effect on acne-related bacteria along with minimum inhibitory concentration (MIC; 8 to 256 μg/mL). Additionally, the MIC values of antibiotics against antibiotic-resistant P. acnes and P. aeruginosa strains were dramatically reduced in combination with CCA, suggesting that CCA would restore the antibacterial activity of the antibiotics. The analysis of fractional inhibitory concentration (FIC) indices clearly revealed a synergistic antibacterial effect of CCA with antibiotics. Thus, the median sum of FIC (∑FIC) values against the antibiotic-resistant bacterial strains ranged from 0.375 to 0.533 in the combination mode of CCA and antibiotics. The results of the present study suggested a potential possibility of chitosan-phytochemical conjugates in the control of infections related to acne vulgaris.

Diversity of Metabolically Active Bacteria in Water-Flooded High-Temperature Heavy Oil Reservoir

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Tamara N. Nazina

2017-04-01

Full Text Available The goal of this work was to study the overall genomic diversity of microorganisms of the Dagang high-temperature oilfield (PRC and to characterize the metabolically active fraction of these populations. At this water-flooded oilfield, the microbial community of formation water from the near-bottom zone of an injection well where the most active microbial processes of oil degradation occur was investigated using molecular, cultural, radiotracer, and physicochemical techniques. The samples of microbial DNA and RNA from back-flushed water were used to obtain the clone libraries for the 16S rRNA gene and cDNA of 16S rRNA, respectively. The DNA-derived clone libraries were found to contain bacterial and archaeal 16S rRNA genes and the alkB genes encoding alkane monooxygenases similar to those encoded by alkB-geo1 and alkB-geo6 of geobacilli. The 16S rRNA genes of methanogens (Methanomethylovorans, Methanoculleus, Methanolinea, Methanothrix, and Methanocalculus were predominant in the DNA-derived library of Archaea cloned sequences; among the bacterial sequences, the 16S rRNA genes of members of the genus Geobacillus were the most numerous. The RNA-derived library contained only bacterial cDNA of the 16S rRNA sequences belonging to metabolically active aerobic organotrophic bacteria (Tepidimonas, Pseudomonas, Acinetobacter, as well as of denitrifying (Azoarcus, Tepidiphilus, Calditerrivibrio, fermenting (Bellilinea, iron-reducing (Geobacter, and sulfate- and sulfur-reducing bacteria (Desulfomicrobium, Desulfuromonas. The presence of the microorganisms of the main functional groups revealed by molecular techniques was confirmed by the results of cultural, radioisotope, and geochemical research. Functioning of the mesophilic and thermophilic branches was shown for the microbial food chain of the near-bottom zone of the injection well, which included the microorganisms of the carbon, sulfur, iron, and nitrogen cycles.

Comparative Analysis of Glycoside Hydrolases Activities from Phylogenetically Diverse Marine Bacteria of the Genus Arenibacter

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Valery Mikhailov

2013-06-01

Full Text Available A total of 16 marine strains belonging to the genus Arenibacter, recovered from diverse microbial communities associated with various marine habitats and collected from different locations, were evaluated in degradation of natural polysaccharides and chromogenic glycosides. Most strains were affiliated with five recognized species, and some presented three new species within the genus Arenibacter. No strains contained enzymes depolymerizing polysaccharides, but synthesized a wide spectrum of glycosidases. Highly active β-N-acetylglucosaminidases and α-N-acetylgalactosaminidases were the main glycosidases for all Arenibacter. The genes, encoding two new members of glycoside hydrolyses (GH families, 20 and 109, were isolated and characterized from the genomes of Arenibacter latericius. Molecular genetic analysis using glycosidase-specific primers shows the absence of GH27 and GH36 genes. A sequence comparison with functionally-characterized GH20 and GH109 enzymes shows that both sequences are closest to the enzymes of chitinolytic bacteria Vibrio furnissii and Cellulomonas fimi of marine and terrestrial origin, as well as human pathogen Elisabethkingia meningoseptica and simbionts Akkermansia muciniphila, gut and non-gut Bacteroides, respectively. These results revealed that the genus Arenibacter is a highly taxonomic diverse group of microorganisms, which can participate in degradation of natural polymers in marine environments depending on their niche and habitat adaptations. They are new prospective candidates for biotechnological applications due to their production of unique glycosidases.

Diversity of endophytic bacteria of Dendrobium officinale based on culture-dependent and culture-independent methods

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Cong Pei

2017-01-01

Full Text Available Culture-dependent and culture-independent methods were compared and evaluated in the study of the endophytic diversity of Dendrobium officinale. Culture-independent methods consisted of polymerase chain reaction–denaturing gradient gel electrophoresis (PCR-DGGE and metagenome methods. According to the results, differences were found between the three methods. Three phyla, namely Firmicutes, Proteobacteria, and Actinobacteria, were detected using the culture-dependent method, and two phyla, Firmicutes and Proteobacteria, were detected by the DGGE method. Using the metagenome method, four major phyla were determined, including Proteobacteria (76.54%, Actinobacteria (18.56%, Firmicutes (2.27%, and Bacteroidetes (1.56%. A distinct trend was obtained at the genus level in terms of the method and the corresponding number of genera determined. There were 449 genera and 16 genera obtained from the metagenome and DGGE methods, respectively, and only 7 genera were obtained through the culture-dependent method. By comparison, all the genera from the culture-dependent and DGGE methods were contained in the members determined using the metagenome method. Overall, culture-dependent methods are limited to ‘finding’ endophytic bacteria in plants. DGGE is an alternative to investigating primary diversity patterns; however, the metagenome method is still the best choice for determining the endophytic profile in plants. It is essential to use multiphasic approaches to study cultured and uncultured microbes.

Mucosal immunity to pathogenic intestinal bacteria.

Science.gov (United States)

Perez-Lopez, Araceli; Behnsen, Judith; Nuccio, Sean-Paul; Raffatellu, Manuela

2016-03-01

The intestinal mucosa is a particularly dynamic environment in which the host constantly interacts with trillions of commensal microorganisms, known as the microbiota, and periodically interacts with pathogens of diverse nature. In this Review, we discuss how mucosal immunity is controlled in response to enteric bacterial pathogens, with a focus on the species that cause morbidity and mortality in humans. We explain how the microbiota can shape the immune response to pathogenic bacteria, and we detail innate and adaptive immune mechanisms that drive protective immunity against these pathogens. The vast diversity of the microbiota, pathogens and immune responses encountered in the intestines precludes discussion of all of the relevant players in this Review. Instead, we aim to provide a representative overview of how the intestinal immune system responds to pathogenic bacteria.

Abundance and diversity of CO2-fixing bacteria in grassland soils close to natural carbon dioxide springs.

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Videmsek, Urska; Hagn, Alexandra; Suhadolc, Marjetka; Radl, Viviane; Knicker, Heike; Schloter, Michael; Vodnik, Dominik

2009-07-01

Gaseous conditions at natural CO2 springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO2 concentrations ([CO2]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO2-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavesinci mofette, a natural CO2 spring which is known for very pure CO2 emissions, at different distances from the CO2 releasing vents, at locations that clearly differed in soil CO2 efflux (from 12.5 to over 200 micromol CO2 m(-2) s(-1) yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the "red-like" type of cbbL genes could be detected. In contrast, the "green-like" type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of "red-like" cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO2 concentrations. Furthermore, the diversity pattern of "red-like" cbbL genes changed depending on the CO(2) regime. This indicates that only a part of the autotrophic CO2-fixing microbes could adapt to the very high CO2 concentrations and adverse life conditions that are governed by mofette gaseous regime.

Culture-independent analysis of lactic acid bacteria diversity associated with mezcal fermentation.

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Narváez-Zapata, J A; Rojas-Herrera, R A; Rodríguez-Luna, I C; Larralde-Corona, C P

2010-11-01

Mezcal is an alcoholic beverage obtained from the distillation of fermented juices of cooked Agave spp. plant stalks (agave must), and each region in Mexico with denomination of origin uses defined Agave species to prepare mezcal with unique organoleptic characteristics. During fermentation to produce mezcal in the state of Tamaulipas, not only alcohol-producing yeasts are involved, but also a lactic acid bacterial community that has not been characterized yet. In order to address this lack of knowledge on this traditional Mexican beverage, we performed a DGGE-16S rRNA analysis of the lactic acid bacterial diversity and metabolite accumulation during the fermentation of a typical agave must that is rustically produced in San Carlos County (Tamaulipas, Mexico). The analysis of metabolite production indicated a short but important malolactic fermentation stage not previously described for mezcal. The denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA genes showed a distinctive lactic acid bacterial community composed mainly of Pediococcus parvulus, Lactobacillus brevis, Lactobacillus composti, Lactobacillus parabuchneri, and Lactobacillus plantarum. Some atypical genera such as Weissella and Bacillus were also found in the residual must. Our results suggest that the lactic acid bacteria could strongly be implicated in the organoleptic attributes of this traditional Mexican distilled beverage.

Diversity and Distribution of Heavy Metal-Resistant Bacteria in Polluted Sediments of the Araça Bay, São Sebastião (SP), and the Relationship Between Heavy Metals and Organic Matter Concentrations.

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Zampieri, Bruna Del Busso; Pinto, Aline Bartelochi; Schultz, Leonardo; de Oliveira, Marcos Antonio; de Oliveira, Ana Julia Fernandes Cardoso

2016-10-01

Heavy metals influence the population size, diversity, and metabolic activity of bacteria. In turn, bacteria can develop heavy metal resistance mechanisms, and this can be used in bioremediation of contaminated areas. The purpose of the present study was to understand how heavy metals concentration influence on diversity and distribution of heavy metal-resistant bacteria in Araça Bay, São Sebastião, on the São Paulo coast of Brazil. The hypothesis is that activities that contribute for heavy metal disposal and the increase of metals concentrations in environment can influence in density, diversity, and distribution of heavy metal-resistant bacteria. Only 12 % of the isolated bacteria were sensitive to all of the metals tested. We observed that the highest percentage of resistant strains were in areas closest to the São Sebastião channel, where port activity occurs and have bigger heavy metals concentrations. Bacterial isolated were most resistant to Cr, followed by Zn, Cd, and Cu. Few strains resisted to Cd levels greater than 200 mg L(-1). In respect to Cr, 36 % of the strains were able to grow in the presence of as much as 3200 mg L(-1). Few strains were able to grow at concentrations of Zn and Cu as high as 1600 mg L(-1), and none grew at the highest concentration of 3200 mg L(-1). Bacillus sp. was most frequently isolated and may be the dominant genus in heavy metal-polluted areas. Staphylococcus sp., Planococcus maritimus, and Vibrio aginolyticus were also isolated, suggesting their potential in bioremediation of contaminated sites.

Presence, distribution, and diversity of iron-oxidizing bacteria at a landfill leachate-impacted groundwater surface water interface

DEFF Research Database (Denmark)

Yu, R.; Gan, P.; Mackay, A.A.

2010-01-01

) were dominated by members of the Bradyrhizobiaceae and Comamonadaceae; clones from the deeper sediments were phylogenetically more diverse, dominated by members of the Rhodocyclaceae. The iron deposition profiles indicated that active iron oxidation occurred only within the near-to-surface GSI......We examined the presence of iron-oxidizing bacteria (IOB) at a groundwater surface water interface (GSI) impacted by reduced groundwater originating as leachate from an upgradient landfill. IOB enrichments and quantifications were obtained, at high vertical resolution, by an iron/oxygen opposing...... site mirrored the IOB distribution. Clone libraries from two separate IOB enrichments indicated a stratified IOB community with clear differences at short vertical distances. Alpha- and Betaproteobacteria were the dominant phylotypes. Clones from the near-surface sediment (1-2 cm below ground surface...

Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere.

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Delgado-Baquerizo, Manuel; Reith, Frank; Dennis, Paul G; Hamonts, Kelly; Powell, Jeff R; Young, Andrew; Singh, Brajesh K; Bissett, Andrew

2018-03-01

The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere. © 2018 by the Ecological Society of America.

Diverse Expected Gradient Active Learning for Relative Attributes.

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You, Xinge; Wang, Ruxin; Tao, Dacheng

2014-06-02

The use of relative attributes for semantic understanding of images and videos is a promising way to improve communication between humans and machines. However, it is extremely labor- and time-consuming to define multiple attributes for each instance in large amount of data. One option is to incorporate active learning, so that the informative samples can be actively discovered and then labeled. However, most existing active-learning methods select samples one at a time (serial mode), and may therefore lose efficiency when learning multiple attributes. In this paper, we propose a batch-mode active-learning method, called Diverse Expected Gradient Active Learning (DEGAL). This method integrates an informativeness analysis and a diversity analysis to form a diverse batch of queries. Specifically, the informativeness analysis employs the expected pairwise gradient length as a measure of informativeness, while the diversity analysis forces a constraint on the proposed diverse gradient angle. Since simultaneous optimization of these two parts is intractable, we utilize a two-step procedure to obtain the diverse batch of queries. A heuristic method is also introduced to suppress imbalanced multi-class distributions. Empirical evaluations of three different databases demonstrate the effectiveness and efficiency of the proposed approach.

Isolation and characterization of heavy metal tolerant bacteria from ...

African Journals Online (AJOL)

Panteka stream is a flowing stream polluted with wastes from the activities of mechanics. Water samples collected at different points of the stream were analysed in order to determine the level of heavy metal contamination and bacteria diversity with the view to elucidating the bioremediating potentials of the bacteria isolates ...

Relative Abundance and Diversity of Bacterial Methanotrophs at the Oxic–Anoxic Interface of the Congo Deep-Sea Fan

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Laurent Toffin

2017-04-01

Full Text Available Sitting at ∼5,000 m water depth on the Congo-Angola margin and ∼760 km offshore of the West African coast, the recent lobe complex of the Congo deep-sea fan receives large amounts of fluvial sediments (3–5% organic carbon. This organic-rich sedimentation area harbors habitats with chemosynthetic communities similar to those of cold seeps. In this study, we investigated relative abundance, diversity and distribution of aerobic methane-oxidizing bacteria (MOB communities at the oxic–anoxic interface of sedimentary habitats by using fluorescence in situ hybridization and comparative sequence analysis of particulate mono-oxygenase (pmoA genes. Our findings revealed that sedimentary habitats of the recent lobe complex hosted type I and type II MOB cells and comparisons of pmoA community compositions showed variations among the different organic-rich habitats. Furthermore, the pmoA lineages were taxonomically more diverse compared to methane seep environments and were related to those found at cold seeps. Surprisingly, MOB phylogenetic lineages typical of terrestrial environments were observed at such water depth. In contrast, MOB cells or pmoA sequences were not detected at the previous lobe complex that is disconnected from the Congo River inputs.

Diversity and antifungal activity of endophytic diazotrophic bacteria colonizing sugarcane in Egypt

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The price of nitrogen continues to increase and is a major input in sugarcane production. Sugarcane grown in Egypt was screened for the presence of nitrogen-fixing bacteria. Nitrogen-free medium LGI-P was used to isolate bacteria from cane stalks. Among the 52 isolates subjected to acetylene redu...

Molecular genetic studies on obligate anaerobic bacteria

International Nuclear Information System (INIS)

Woods, D.R.

1982-01-01

Molecular genetic studies on obligate anaerobic bacteria have lagged behind similar studies in aerobes. However, the current interest in biotechnology, the involvement of anaerobes in disease and the emergence of antibioticresistant strains have focused attention on the genetics of anaerobes. This article reviews molecular genetic studies in Bacteroides spp., Clostridium spp. and methanogens. Certain genetic systems in some anaerobes differ from those in aerobes and illustrate the genetic diversity among bacteria

Horizontal gene transfer between bacteria.

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Heuer, Holger; Smalla, Kornelia

2007-01-01

Horizontal gene transfer (HGT) refers to the acquisition of foreign genes by organisms. The occurrence of HGT among bacteria in the environment is assumed to have implications in the risk assessment of genetically modified bacteria which are released into the environment. First, introduced genetic sequences from a genetically modified bacterium could be transferred to indigenous micro-organisms and alter their genome and subsequently their ecological niche. Second, the genetically modified bacterium released into the environment might capture mobile genetic elements (MGE) from indigenous micro-organisms which could extend its ecological potential. Thus, for a risk assessment it is important to understand the extent of HGT and genome plasticity of bacteria in the environment. This review summarizes the present state of knowledge on HGT between bacteria as a crucial mechanism contributing to bacterial adaptability and diversity. In view of the use of GM crops and microbes in agricultural settings, in this mini-review we focus particularly on the presence and role of MGE in soil and plant-associated bacteria and the factors affecting gene transfer.

Molecular analysis of microbial diversity in advanced caries.

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Chhour, Kim-Ly; Nadkarni, Mangala A; Byun, Roy; Martin, F Elizabeth; Jacques, Nicholas A; Hunter, Neil

2005-02-01

Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included Selenomonas spp., Dialister spp., Fusobacterium nucleatum, Eubacterium spp., members of the Lachnospiraceae family, Olsenella spp., Bifidobacterium spp., Propionibacterium sp., and Pseudoramibacter alactolyticus. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.

Emerging principles of inorganic nitrogen metabolism in Paracoccus denitrificans and related bacteria

NARCIS (Netherlands)

Stouthamer, A.H.; de Boer, A P; van der Oost, J.; van Spanning, R J

The taxonomy of Paracoccus denitrificans and related bacteria is discussed. Evidence is given which shows that the physiological differences between P. denitrificans and Thiosphaera pantotropha are less fundamental than previously thought. A proposal to consider a species P. pantotropha is

Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change.

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Lladó, Salvador; López-Mondéjar, Rubén; Baldrian, Petr

2017-06-01

The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously. Copyright © 2017 American Society for Microbiology.

More, smaller bacteria in response to ocean's warming?

KAUST Repository

Moran, Xose Anxelu G.

2015-06-10

Heterotrophic bacteria play a major role in organic matter cycling in the ocean. Although the high abundances and relatively fast growth rates of coastal surface bacterioplankton make them suitable sentinels of global change, past analyses have largely overlooked this functional group. Here, time series analysis of a decade of monthly observations in temperate Atlantic coastal waters revealed strong seasonal patterns in the abundance, size and biomass of the ubiquitous flow-cytometric groups of low (LNA) and high nucleic acid (HNA) content bacteria. Over this relatively short period, we also found that bacterioplankton cells were significantly smaller, a trend that is consistent with the hypothesized temperature-driven decrease in body size. Although decadal cell shrinking was observed for both groups, it was only LNA cells that were strongly coherent, with ecological theories linking temperature, abundance and individual size on both the seasonal and interannual scale. We explain this finding because, relative to their HNA counterparts, marine LNA bacteria are less diverse, dominated by members of the SAR11 clade. Temperature manipulation experiments in 2012 confirmed a direct effect of warming on bacterial size. Concurrent with rising temperatures in spring, significant decadal trends of increasing standing stocks (3% per year) accompanied by decreasing mean cell size (-1% per year) suggest a major shift in community structure, with a larger contribution of LNA bacteria to total biomass. The increasing prevalence of these typically oligotrophic taxa may severely impact marine foodwebs and carbon fluxes by an overall decrease in the efficiency of the biological pump. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Relation between chemotaxis and consumption of amino acids in bacteria

Science.gov (United States)

Yang, Yiling; M. Pollard, Abiola; Höfler, Carolin; Poschet, Gernot; Wirtz, Markus; Hell, Rüdiger

2015-01-01

Summary Chemotaxis enables bacteria to navigate chemical gradients in their environment, accumulating toward high concentrations of attractants and avoiding high concentrations of repellents. Although finding nutrients is likely to be an important function of bacterial chemotaxis, not all characterized attractants are nutrients. Moreover, even for potential nutrients, the exact relation between the metabolic value of chemicals and their efficiency as chemoattractants has not been systematically explored. Here we compare the chemotactic response of amino acids with their use by bacteria for two well‐established models of chemotactic behavior, E scherichia coli and B acillus subtilis. We demonstrate that in E . coli chemotaxis toward amino acids indeed strongly correlates with their utilization. However, no such correlation is observed for B . subtilis, suggesting that in this case, the amino acids are not followed because of their nutritional value but rather as environmental cues. PMID:25807888

Symbiotic bacteria contribute to increasing the population size of a freshwater crustacean, Daphnia magna.

Science.gov (United States)

Peerakietkhajorn, Saranya; Tsukada, Koji; Kato, Yasuhiko; Matsuura, Tomoaki; Watanabe, Hajime

2015-04-01

The filter-feeding crustacean Daphnia is a key organism in freshwater ecosystems. Here, we report the effect of symbiotic bacteria on ecologically important life history traits, such as population dynamics and longevity, in Daphnia magna. By disinfection of the daphniid embryos with glutaraldehyde, aposymbiotic daphniids were prepared and cultured under bacteria-free conditions. Removal of bacteria from the daphniids was monitored by quantitative polymerase chain reaction for bacterial 16S rRNA gene. The population of aposymbiotic daphniids was reduced 10-folds compared with that of the control daphniids. Importantly, re-infection with symbiotic bacteria caused daphniids to regain bacteria and increase their fecundity to the level of the control daphniids, suggesting that symbiotic bacteria regulate Daphnia fecundity. To identify the species of symbiotic bacteria, 16S rRNA genes of bacteria in daphniids were sequenced. This revealed that 50% of sequences belonged to the Limnohabitans sp. of the Betaproteobacteria class and that the diversity of bacterial taxa was relatively low. These results suggested that symbiotic bacteria have a beneficial effect on D. magna, and that aposymbiotic Daphnia are useful tools in understanding the role of symbiotic bacteria in the environmental responses and evolution of their hosts. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Bacteria from diverse habitats colonize and compete in the mouse gut.

Science.gov (United States)

Seedorf, Henning; Griffin, Nicholas W; Ridaura, Vanessa K; Reyes, Alejandro; Cheng, Jiye; Rey, Federico E; Smith, Michelle I; Simon, Gabriel M; Scheffrahn, Rudolf H; Woebken, Dagmar; Spormann, Alfred M; Van Treuren, William; Ursell, Luke K; Pirrung, Megan; Robbins-Pianka, Adam; Cantarel, Brandi L; Lombard, Vincent; Henrissat, Bernard; Knight, Rob; Gordon, Jeffrey I

2014-10-09

To study how microbes establish themselves in a mammalian gut environment, we colonized germ-free mice with microbial communities from human, zebrafish, and termite guts, human skin and tongue, soil, and estuarine microbial mats. Bacteria from these foreign environments colonized and persisted in the mouse gut; their capacity to metabolize dietary and host carbohydrates and bile acids correlated with colonization success. Cohousing mice harboring these xenomicrobiota or a mouse cecal microbiota, along with germ-free "bystanders," revealed the success of particular bacterial taxa in invading guts with established communities and empty gut habitats. Unanticipated patterns of ecological succession were observed; for example, a soil-derived bacterium dominated even in the presence of bacteria from other gut communities (zebrafish and termite), and human-derived bacteria colonized germ-free bystander mice before mouse-derived organisms. This approach can be generalized to address a variety of mechanistic questions about succession, including succession in the context of microbiota-directed therapeutics. Copyright © 2014 Elsevier Inc. All rights reserved.

Diversity and activity of nitrogen fixing archaea and bacteria associated with micro-environments of wetland rice

Science.gov (United States)

Schmidt, Hannes; Woebken, Dagmar

2017-04-01

Wetland rice is one of the world's most important crop plants. The cultivation on waterlogged paddy soils is strongly limited by nitrogen (N), which is typically supplied by industrial fertilizers that are not only costly but also exhibit hazardous effects on the environment. It has been reported that "Biological Nitrogen Fixation" through N2-fixing bacteria and archaea (diazotrophs) can alleviate the N-shortage in rice cultivation, thus carrying out an important ecosystem function. However, our understanding of the diversity and in situ N2 fixation activity of diazotrophs in flooded rice fields is still rudimentary. Moreover, knowledge on the impact of biochemical gradients established by root activity (i.e. exudation, radial oxygen loss) on the functioning of N-fixing microorganisms in paddy soil ecosystems is limited. We aimed at studying underlying processes on biologically relevant scales. Greenhouse studies were performed to identify key factors that control rice-diazotroph association and related N2 fixation activities. Paddy soils of different geographical origin were cultivated with two commercially used genotypes of wetland rice. Samples were separated into bulk soil, rhizosphere soil, rhizoplane, and roots at flowering stage of rice plant development. These samples were subjected to functional assays and various molecular biological techniques in order to analyze the associated diazotroph communities. Based on Illumina amplicon sequencing of nifH genes and transcripts, we show that the diversity and potential activity of diazotroph communities varies according to micro-environments. We will comparatively discuss the influence of (a) the soil microbial "seed bank" and (b) plant genotype in shaping the respective microbiomes and selecting for potentially active diazotrophs. Actual N2 fixation activities of soil-genotype combinations and micro-environments will be shown on the basis of incubation assays using 15N2-containing atmospheres. Areas of potential

THE RESURRECTION PLANT TRIPOGON SPICATUS (POACEAE HARBORS A DIVERSITY OF PLANT GROWTH PROMOTING BACTERIA IN NORTHEASTERN BRAZILIAN CAATINGA

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Paulo Ivan Fernandes-Júnior

2015-08-01

Full Text Available Plant species that naturally occur in the Brazilian Caatinga(xeric shrubland adapt in several ways to these harsh conditions, and that can be exploited to increase crop production. Among the strategic adaptations to confront low water availability, desiccation tolerance stands out. Up to now, the association of those species with beneficial soil microorganisms is not well understood. The aim of this study was to characterize Tripogon spicatusdiazotrophic bacterial isolates from the Caatingabiome and evaluate their ability to promote plant growth in rice. Sixteen bacterial isolates were studied in regard to their taxonomic position by partial sequencing of the 16S rRNA gene, putative diazotrophic capacity, in vitro indole-acetic acid (IAA production and calcium phosphate solubilization, metabolism of nine different C sources in semi-solid media, tolerance to different concentrations of NaCl to pHs and intrinsic resistance to nine antibiotics. Finally, the ability of the bacterial isolates to promote plant growth was evaluated using rice (Oryza sativa as a model plant. Among the 16 isolates evaluated, eight of them were classified as Enterobacteriaceae members, related to Enterobacter andPantoeagenera. Six other bacteria were related toBacillus, and the remaining two were related toRhizobiumand Stenotrophomonas.The evaluation of total N incorporation into the semi-solid medium indicated that all the bacteria studied have putative diazotrophic capacity. Two bacteria were able to produce more IAA than that observed for the strain BR 11175Tof Herbaspirillum seropedicae.Bacterial isolates were also able to form a microaerophilic pellicle in a semi-solid medium supplemented with different NaCl concentrations up to 1.27 mol L-1. Intrinsic resistance to antibiotics and the metabolism of different C sources indicated a great variation in physiological profile. Seven isolates were able to promote rice growth, and two bacteria were more efficient than the

Comparative genomics of the lactic acid bacteria

Energy Technology Data Exchange (ETDEWEB)

Makarova, K.; Slesarev, A.; Wolf, Y.; Sorokin, A.; Mirkin, B.; Koonin, E.; Pavlov, A.; Pavlova, N.; Karamychev, V.; Polouchine, N.; Shakhova, V.; Grigoriev, I.; Lou, Y.; Rokhsar, D.; Lucas, S.; Huang, K.; Goodstein, D. M.; Hawkins, T.; Plengvidhya, V.; Welker, D.; Hughes, J.; Goh, Y.; Benson, A.; Baldwin, K.; Lee, J. -H.; Diaz-Muniz, I.; Dosti, B.; Smeianov, V; Wechter, W.; Barabote, R.; Lorca, G.; Altermann, E.; Barrangou, R.; Ganesan, B.; Xie, Y.; Rawsthorne, H.; Tamir, D.; Parker, C.; Breidt, F.; Broadbent, J.; Hutkins, R.; O' Sullivan, D.; Steele, J.; Unlu, G.; Saier, M.; Klaenhammer, T.; Richardson, P.; Kozyavkin, S.; Weimer, B.; Mills, D.

2006-06-01

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive gene loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.

Diversity and ubiquity of bacteria capable of utilizing humic substances as electron donors for anaerobic respiration.

Science.gov (United States)

Coates, John D; Cole, Kimberly A; Chakraborty, Romy; O'Connor, Susan M; Achenbach, Laurie A

2002-05-01

Previous studies have demonstrated that reduced humic substances (HS) can be reoxidized by anaerobic bacteria such as Geobacter, Geothrix, and Wolinella species with a suitable electron acceptor; however, little is known of the importance of this metabolism in the environment. Recently we investigated this metabolism in a diversity of environments including marine and aquatic sediments, forest soils, and drainage ditch soils. Most-probable-number enumeration studies were performed using 2,6-anthrahydroquinone disulfonate (AHDS), an analog for reduced HS, as the electron donor with nitrate as the electron acceptor. Anaerobic organisms capable of utilizing reduced HS as an electron donor were found in all environments tested and ranged from a low of 2.31 x 10(1) in aquifer sediments to a high of 9.33 x 10(6) in lake sediments. As part of this study we isolated six novel organisms capable of anaerobic AHDS oxidation. All of the isolates coupled the oxidation of AHDS to the reduction of nitrate with acetate (0.1 mM) as the carbon source. In the absence of cells, no AHDS oxidation was apparent, and in the absence of AHDS, no cell density increase was observed. Generally, nitrate was reduced to N(2). Analysis of the AHDS and its oxidized form, 2,6-anthraquinone disulfonate (AQDS), in the medium during growth revealed that the anthraquinone was not being biodegraded as a carbon source and was simply being oxidized as an energy source. Determination of the AHDS oxidized and nitrate reduced accounted for 109% of the theoretical electron transfer. In addition to AHDS, all of these isolates could also couple the oxidation of reduced humic substances to the reduction of nitrate. No HS oxidation occurred in the absence of cells and in the absence of a suitable electron acceptor, demonstrating that these organisms were capable of utilizing natural HS as an energy source and that AHDS serves as a suitable analog for studying this metabolism. Alternative electron donors included

Comparison among amoA Primers Suited for Quantification and Diversity Analyses of Ammonia-Oxidizing Bacteria in Soil

Science.gov (United States)

Shimomura, Yumi; Morimoto, Sho; Hoshino, Yuko Takada; Uchida, Yoshitaka; Akiyama, Hiroko; Hayatsu, Masahito

2012-01-01

Ammonia monooxygenase subunit A gene (amoA) is frequently used as a functional gene marker for diversity analysis of ammonia-oxidizing bacteria (AOB). To select a suitable amoA primer for real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE), three reverse primers (degenerate primer amoA-2R; non-degenerate primers amoA-2R-GG and amoA-2IR) were examined. No significant differences were observed among the three primers in terms of quantitative values of amoA from environmental samples using real-time PCR. We found that PCR-DGGE analysis with the amoA-2IR primer gave the best results in this studied soil. These results indicate that amoA-2IR is a suitable primer for community analysis of AOB in the environment. PMID:22075625

Iron encrustations on filamentous algae colonized by Gallionella-related bacteria in a metal-polluted freshwater stream

Science.gov (United States)

Mori, J. F.; Neu, T. R.; Lu, S.; Händel, M.; Totsche, K. U.; Küsel, K.

2015-09-01

Filamentous macroscopic algae were observed in slightly acidic to circumneutral (pH 5.9-6.5), metal-rich stream water that leaked out from a former uranium mining district (Ronneburg, Germany). These algae differed in color and morphology and were encrusted with Fe-deposits. To elucidate their potential interaction with Fe(II)-oxidizing bacteria (FeOB), we collected algal samples at three time points during summer 2013 and studied the algae-bacteria-mineral compositions via confocal laser scanning microscopy (CLSM), scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectra, and a 16S and 18S rRNA gene-based bacterial and algae community analysis. Surprisingly, sequencing analysis of 18S rRNA gene regions of green and brown algae revealed high homologies with the freshwater algae Tribonema (99.9-100 %). CLSM imaging indicated a loss of active chloroplasts in the algae cells, which may be responsible for the change in color in oxidation under the putative oxygen-saturated conditions that occur in association with photosynthetic algae. Quantitative PCR (polymerase chain reaction) revealed even higher Gallionella-related 16S rRNA gene copy numbers on the surface of green algae compared to the brown algae. The latter harbored a higher microbial diversity, including some putative predators of algae. A loss of chloroplasts in the brown algae could have led to lower photosynthetic activities and reduced EPS production, which is known to affect predator colonization. Collectively, our results suggest the coexistence of oxygen-generating algae Tribonema sp. and strictly microaerophilic neutrophilic FeOB in a heavy metal-rich environment.

Long-term nitrogen fertilization decreases bacterial diversity and favors the growth of Actinobacteria and Proteobacteria in agro-ecosystems across the globe

Energy Technology Data Exchange (ETDEWEB)

Dai, Zhongmin [Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Lab. of Agricultural Resources and Environment; Su, Weiqin [Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Lab. of Agricultural Resources and Environment; Chen, Huaihai [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Barberan, Albert [Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Zhao, Haochun [Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Lab. of Agricultural Resources and Environment; Yu, Mengjie [Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Lab. of Agricultural Resources and Environment; Yu, Lu [Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Lab. of Agricultural Resources and Environment; Brookes, Philip C. [Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Lab. of Agricultural Resources and Environment; Schadt, Christopher W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Chang, Scott X. [Univ. of Alberta, Edmonton, AB (Canada). Dept. of Renewable Resources; Xu, Jianming [Zhejiang Univ., Hangzhou (China). Inst. of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Lab. of Agricultural Resources and Environment

2018-04-25

Long-term Elevated nitrogen (N) input from anthropogenic sources may cause soil acidification and decrease crop yield, yet the response of the belowground microbial community to long-term N input and the input of N combined with phosphorus (P) and potassium (K) is still poorly understood. Here, we explored the effect of long-term N and NPK fertilization on soil bacterial diversity and community composition using meta-analysis of a global dataset. Nitrogen fertilization decreased soil pH, and increased soil organic carbon (C) and available N contents. Bacterial taxonomic diversity was decreased by N fertilization alone, but was increased by NPK fertilization. The effect of N fertilization on bacterial diversity depends on soil texture and water management, but independent of crop type or N application rate. Both soil pH and organic C content were positively related to changes in bacterial diversity under N fertilization, while soil organic C was the dominant factor determining changes in bacterial diversity under NPK fertilization. Microbial biomass C decreased with decreasing bacterial diversity under long-term N fertilization. Nitrogen fertilization increased the relative abundance of copiotrophic bacteria (i.e. Proteobacteria and Actinobacteria), but reduced the abundance of oligotrophic taxa (i.e. Acidobacteria), consistent with the general life history strategy theory for bacteria. The relative abundance of Proteobacteria was also increased by NPK fertilization. The positive correlation between N application rate and the relative abundance of Actinobacteria indicates that increased N availability favored the growth of Actinobacteria. This first global analysis of long-term N and NPK fertilization effect on bacterial diversity and community composition suggests that N input decreases bacterial diversity but favors the growth of copiotrophic bacteria, providing a reference for nutrient management strategies for maintaining belowground microbial diversity in agro

Bacterial diversity of biofilm samples from deep mines in South ...

African Journals Online (AJOL)

JTEkanem

Department of Biotechnology, University of The Free State, Box 339, ... Proteobacteria, forty-one percent (41%) of the sequences with yet uncultured bacteria and ..... (1995) Selective solid media for isolating and enumerating acidophilic bacteria. ... Monitoring the Lactic Acid Bacteria diversity during Shochu fermentation by.

Diversity of alkane degrading bacteria associated with plants in a petroleum oil-contaminated environment and expression of alkane monooxygenase (alkB) genes

Science.gov (United States)

Andria, V.; Yousaf, S.; Reichenauer, T. G.; Smalla, K.; Sessitsch, A.

2009-04-01

Among twenty-six different plant species, Italian ryegrass (Lolium multiflorum var. Taurus), Birdsfoot trefoil (Lotus corniculatus var. Leo), and the combination of both plants performed well in a petroleum oil contaminated soil. Hydrocarbon degrading bacteria were isolated from the rhizosphere, root interior and shoot interior and subjected to the analysis of 16S rRNA, the 16S and 23S rRNA intergenic spacer region and alkane hydroxylase genes. Higher numbers of culturable, degrading bacteria were associated with Italian ryegrass, which were also characterized by a higher diversity, particularly in the plant interior. Only half of the isolated bacteria hosted known alkane hydroxylase genes (alkB and cytochrome P153-like). Our results indicated that alkB genes have spread through horizontal gene transfer, particularly in the Italian ryegrass rhizosphere, and suggested mobility of catabolic genes between Gram-negative and Gram-positive bacteria. We furthermore studied the colonization behaviour of selected hydrocarbon-degrading strains (comprising an endopyhte and a rhizosphere strain) as well as the expression of their alkane monooxygenase genes in association with Italian ryegrass. Results showed that the endophyte strain better colonized the plant, particularly the plant interior, and also showed higher expression of alkB genes suggesting a more efficient degradation of the pollutant. Furthermore, plants inoculated with the endophyte were better able to grow in the presence of diesel. The rhizosphere strain colonized primarily the rhizosphere and showed low alkB gene expression in the plant interior.

Effects of inoculation with organic-phosphorus-mineralizing bacteria on soybean (Glycine max) growth and indigenous bacterial community diversity.

Science.gov (United States)

Sun, Wei; Qian, Xun; Gu, Jie; Wang, Xiao-Juan; Li, Yang; Duan, Man-Li

2017-05-01

Three different organic-phosphorus-mineralizing bacteria (OPMB) strains were inoculated to soil planted with soybean (Glycine max), and their effects on soybean growth and indigenous bacterial community diversity were investigated. Inoculation with Pseudomonas fluorescens Z4-1 and Brevibacillus agri L7-1 increased organic phosphorus degradation by 22% and 30%, respectively, compared with the control at the mature stage. Strains P. fluorescens Z4-1 and B. agri L7-1 significantly improved the soil alkaline phosphatase activity, average well color development, and the soybean root activity. Terminal restriction fragment length polymorphism analysis demonstrated that P. fluorescens Z4-1 and B. agri L7-1 could persist in the soil at relative abundances of 2.0%-6.4% throughout soybean growth. Thus, P. fluorescens Z4-1 and B. agri L7-1 could potentially be used in organic-phosphorus-mineralizing biofertilizers. OPMB inoculation altered the genetic structure of the soil bacterial communities but had no apparent influence on the carbon source utilization profiles of the soil bacterial communities. Principal components analysis showed that the changes in the carbon source utilization profiles of bacterial community depended mainly on the plant growth stages rather than inoculation with OPMB. The results help to understand the evolution of the soil bacterial community after OPMB inoculation.

Betaproteobacteria dominance and diversity shifts in the bacterial community of a PAH-contaminated soil exposed to phenanthrene

International Nuclear Information System (INIS)

Martin, Florence; Torelli, Stéphane; Le Paslier, Denis; Barbance, Agnès; Martin-Laurent, Fabrice; Bru, David; Geremia, Roberto; Blake, Gérard; Jouanneau, Yves

2012-01-01

In this study, the PAH-degrading bacteria of a constructed wetland collecting road runoff has been studied through DNA stable isotope probing. Microcosms were spiked with 13 C-phenanthrene at 34 or 337 ppm, and bacterial diversity was monitored over a 14-day period. At 337 ppm, PAH degraders became dominated after 5 days by Betaproteobacteria, including novel Acidovorax, Rhodoferax and Hydrogenophaga members, and unknown bacteria related to Rhodocyclaceae. The prevalence of Betaproteobacteria was further demonstrated by phylum-specific quantitative PCR, and was correlated with a burst of phenanthrene mineralization. Striking shifts in the population of degraders were observed after most of the phenanthrene had been removed. Soil exposed to 34 ppm phenanthrene showed a similar population of degraders, albeit only after 14 days. Results demonstrate that specific Betaproteobacteria are involved in the main response to soil PAH contamination, and illustrate the potential of SIP approaches to investigate PAH biodegradation in soil. - Highlights: ► We explored PAH-degrading bacteria on a chronically polluted site by stable isotope probing. ► Betaproteobacteria appeared as the main phenanthrene degraders in soil. ► Most soil PAH degraders were poorly related to bacteria isolated so far. ► Diversity shifts occurred in the community of degraders when the PAH became less available. - On a site collecting road runoff, implementation of stable isotope probing to identify soil bacteria responsible for phenanthrene degradation, led to the discovery of new Betaproteobacteria distantly related to known PAH degraders.

Influence of geographical origin and flour type on diversity of lactic acid bacteria in traditional Belgian sourdoughs.

Science.gov (United States)

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

2007-10-01

A culture-based approach was used to investigate the diversity of lactic acid bacteria (LAB) in Belgian traditional sourdoughs and to assess the influence of flour type, bakery environment, geographical origin, and technological characteristics on the taxonomic composition of these LAB communities. For this purpose, a total of 714 LAB from 21 sourdoughs sampled at 11 artisan bakeries throughout Belgium were subjected to a polyphasic identification approach. The microbial composition of the traditional sourdoughs was characterized by bacteriological culture in combination with genotypic identification methods, including repetitive element sequence-based PCR fingerprinting and phenylalanyl-tRNA synthase (pheS) gene sequence analysis. LAB from Belgian sourdoughs belonged to the genera Lactobacillus, Pediococcus, Leuconostoc, Weissella, and Enterococcus, with the heterofermentative species Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus plantarum, and Lactobacillus pontis as the most frequently isolated taxa. Statistical analysis of the identification data indicated that the microbial composition of the sourdoughs is mainly affected by the bakery environment rather than the flour type (wheat, rye, spelt, or a mixture of these) used. In conclusion, the polyphasic approach, based on rapid genotypic screening and high-resolution, sequence-dependent identification, proved to be a powerful tool for studying the LAB diversity in traditional fermented foods such as sourdough.

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.

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest.

Science.gov (United States)

Kivlin, Stephanie N; Hawkes, Christine V

2016-01-01

The high diversity of tree species has traditionally been considered an important controller of belowground processes in tropical rainforests. However, soil water availability and resources are also primary regulators of soil bacteria in many ecosystems. Separating the effects of these biotic and abiotic factors in the tropics is challenging because of their high spatial and temporal heterogeneity. To determine the drivers of tropical soil bacteria, we examined tree species effects using experimental tree monocultures and secondary forests at La Selva Biological Station in Costa Rica. A randomized block design captured spatial variation and we sampled at four dates across two years to assess temporal variation. We measured bacteria richness, phylogenetic diversity, community composition, biomass, and functional potential. All bacteria parameters varied significantly across dates. In addition, bacteria richness and phylogenetic diversity were affected by the interaction of vegetation type and date, whereas bacteria community composition was affected by the interaction of vegetation type and block. Shifts in bacteria community richness and composition were unrelated to shifts in enzyme function, suggesting physiological overlap among taxa. Based on the observed temporal and spatial heterogeneity, our understanding of tropical soil bacteria will benefit from additional work to determine the optimal temporal and spatial scales for sampling. Understanding spatial and temporal variation will facilitate prediction of how tropical soil microbes will respond to future environmental change.

Archaea, Bacteria, and Sulfur-Cycling in a Shallow-Sea Hydrothermal Ecosystem

Science.gov (United States)

Amend, J. P.; Huang, C.; Amann, R.; Bach, W.; Meyerdierks, A.; Price, R. E.; Schubotz, F.; Summons, R. E.; Wenzhoefer, F.

2009-12-01

Deep-sea hydrothermal systems are windows to the marine subsurface biosphere. It often is overlooked, however, that their far more accessible shallow-sea counterparts can serve the same purpose. To characterize the extent, diversity, and activity of the subsurface microbial community in the shallow vent ecosystem near Panarea Island (Italy), sediment cores were analyzed with a broad array of analytical techniques. Vent fluid and sediment temperatures reached up to 135 °C, with pHs in porewaters generally measuring 5-6. Microsensor profiles marked a very sharp oxic-anoxic transition, and when coupled to pH and H2S profiles, pointed to aerobic sulfide oxidation. With increasing depth from the sediment-water interface, porewater analyses showed a decrease in sulfate levels from ~30 mM to thermophilic sulfate reducing and acidophilic sulfide oxidizing bacteria. Results from several sites also showed that with increasing depth and temperature, biomass abundance of archaea generally increased relative to that of bacteria. Lastly, DGGE fingerprinting and 16S rRNA clone libraries from several depths at Hot Lake revealed a moderate diversity of bacteria, dominated by Epsilonproteobacteria; this class is known to catalyze both sulfur reduction and oxidation reactions, and to mediate the formation of iron-sulfides, including framboidal pyrite. Archaeal sequences at Hot Lake are dominated by uncultured Thermoplasmatales, plus several sequences in the Korarchaeota.

Presence of Nitrosospiral cluster 2 bacteria corresponds to N transformation rates in nine acid Scots pine forest soils.

NARCIS (Netherlands)

Nugroho, R. Adi; Roling, W.F.M.; Laverman, A.M.; Zoomer, R.; Verhoef, H.A.

2005-01-01

The relation between environmental factors and the presence of ammonia-oxidising bacteria (AOB), and its consequences for the N transformation rates were investigated in nine Scots pine (Pinus sylvestris L.) forest soils. In general, the diversity in AOB appears to be strikingly low compared to

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

Science.gov (United States)

Andam, Cheryl P.; Doroghazi, James R.; Campbell, Ashley N.; Kelly, Peter J.; Choudoir, Mallory J.

2016-01-01

ABSTRACT We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift. PMID:27073097

A Latitudinal Diversity Gradient in Terrestrial Bacteria of the Genus Streptomyces

Directory of Open Access Journals (Sweden)

Cheryl P. Andam

2016-04-01

Full Text Available We show that Streptomyces biogeography in soils across North America is influenced by the regional diversification of microorganisms due to dispersal limitation and genetic drift. Streptomyces spp. form desiccation-resistant spores, which can be dispersed on the wind, allowing for a strong test of whether dispersal limitation governs patterns of terrestrial microbial diversity. We employed an approach that has high sensitivity for determining the effects of genetic drift. Specifically, we examined the genetic diversity and phylogeography of physiologically similar Streptomyces strains isolated from geographically distributed yet ecologically similar habitats. We found that Streptomyces beta diversity scales with geographic distance and both beta diversity and phylogenetic diversity manifest in a latitudinal diversity gradient. This pattern of Streptomyces biogeography resembles patterns seen for diverse species of plants and animals, and we therefore evaluated these data in the context of ecological and evolutionary hypotheses proposed to explain latitudinal diversity gradients. The data are consistent with the hypothesis that niche conservatism limits dispersal, and historical patterns of glaciation have limited the time for speciation in higher-latitude sites. Most notably, higher-latitude sites have lower phylogenetic diversity, higher phylogenetic clustering, and evidence of range expansion from lower latitudes. In addition, patterns of beta diversity partition with respect to the glacial history of sites. Hence, the data support the hypothesis that extant patterns of Streptomyces biogeography have been driven by historical patterns of glaciation and are the result of demographic range expansion, dispersal limitation, and regional diversification due to drift.

Molecular diversity among seven Solanum (eggplant and relatives ...

African Journals Online (AJOL)

Admin

2012-11-08

Nov 8, 2012 ... Seven Solanum species (eggplants) were investigated for molecular diversity. Besides its ... Eggplant comprises three closely related cultivated species .... generated with SSR data was submitted to 2-way Mantel test (Man-.

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Science.gov (United States)

Kovach, Ryan; Muhlfeld, Clint C.; Wade, Alisa A.; Hand, Brian K.; Whited, Diane C.; DeHaan, Patrick W.; Al-Chokhachy, Robert K.; Luikart, Gordon

2015-01-01

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision-making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = −0.77;P bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.

Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

Directory of Open Access Journals (Sweden)

Vidya eDe Gannes

2012-07-01

Full Text Available Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, coffee hulls, which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase and the finished product (mature phase. The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (groub I.1b, in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have signifcant effects on its performanc as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities with nitrification in these systems.

The ecological role of type three secretion systems in the interaction of bacteria with fungi in soil and related habitats is diverse and context-dependent

NARCIS (Netherlands)

Nazir, Rashid; Mazurier, Sylvie; Yang, Pu; Lemanceau, Philippe; van Elsas, Jan Dirk

2017-01-01

Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve

Diversity and natural functions of antibiotices produced by beneficial and pathogenic soil bacteria

Science.gov (United States)

Soil and plant-associated environments harbor numerous bacterial species that produce antibiotic metabolites. Many of these bacteria have been exploited for the discovery of clinical antibiotics and other therapeutics. In the field of plant pathology, antibiotic-producing bacteria are used as a reso...

Molecular diversity of thermophilic bacteria isolated from Pasinler hot spring (Erzurum, Turkey)

OpenAIRE

ADIGÜZEL, Ahmet; İNAN, Kadriye; ŞAHİN, Fikrettin; ARASOĞLU, Tulin; GÜLLÜCE, Medine

2011-01-01

The present study was conducted to determine the phenotypic and genotypic characterization of thermophilic bacteria isolated from Pasinler hot spring, Erzurum, Turkey. Fatty acid profiles, BOX PCR fingerprints, and 16S rDNA sequence data were used for the phenotypic and genotypic characterization of thermophilic bacteria. Totally 9 different bacterial strains were selected based on morphological, physiological, and biochemical tests. These strains were characterized by molecular tests includi...

Bacteria of Phlebotominae Sand Flies Collected in Western Iran

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Somayeh Rafatbakhsh-Iran

2015-08-01

Full Text Available Microorganisms particularly bacteria presenting in insects such as Phlebotominae may play an important role in the epidemiology of human infectious disease. Nowadays, because of vector implications, the routine methods of controlling and spraying have no more beneficial effects on vectors and reservoirs. Little knows about the prevalence and diversity of sand fly bacteria. The main objective of this study was to determine the presence of bacteria of phlebotominae sand flies collected in Hamadan, west of Iran. This information is important in order to development of vector control strategies. The microbial flora of Phlebotomus papatasi and P. sergenti the main vector of Cutaneous Leishmaniasis in the old world, were investigated. We characterized 8 bacteria, including 5 Gram-negative bacteria: Acinetobacter lwoffii, Pseudomonas aeruginosa, Enterobacter cloacae, Edvardsiela sp. and Proteus mirabilis and Gram-positive bacteria: Bacillus subtilis, Staphylococcus saprophyticus and Micrococcus luteus. Our study provides some data on the microbiota diversity of field-collected sand flies for the first time in Hamadan. Our results indicate that there is a range of variation of aerobic bacteria inhabiting sand fly, which possibly reflect the ecological condition of the habitat where the fly breeds. Microbiota is increasingly regarded as an important factor for modulating vector competence in insect vectors. So, mirobiota can be effects on the biology of phlebotominae and their roles in the sandfly-Leishmania interaction. Further experiments are required to clearly delineate the vectorial role of sand flies. Because it is probable that in the future, factors such as environmental changes, migration and urbanization can ease the transmission of leishmaniasis in this area.

Spatial Variability of Cyanobacteria and Heterotrophic Bacteria in Lake Taihu (China).

Science.gov (United States)

Qian, Haifeng; Lu, Tao; Song, Hao; Lavoie, Michel; Xu, Jiahui; Fan, Xiaoji; Pan, Xiangliang

2017-09-01

Cyanobacterial blooms frequently occur in Lake Taihu (China), but the intertwined relationships between biotic and abiotic factors modulating the frequency and duration of the blooms remain enigmatic. To better understand the relationships between the key abiotic and biotic factors and cyanobacterial blooms, we measured the abundance and diversity of prokaryotic organisms by high-throughput sequencing, the abundance of key genes involved in microcystin production and nitrogen fixation or loss as well as several physicochemical parameters at several stations in Lake Taihu during a cyanobacterial bloom of Microcystis sp.. Measurements of the copy number of denitrification-related genes and 16S rRNA analyses show that denitrification potential and denitrifying bacteria abundance increased in concert with non-diazotrophic cyanobacteria (Microcystis sp.), suggesting limited competition between cyanobacteria and heterotrophic denitrifiers for nutrients, although potential bacteria-mediated N loss may hamper Microcystis growth. The present study provides insight into the importance of different abiotic and biotic factors in controlling cyanobacteria and heterotrophic bacteria spatial variability in Lake Taihu.

Chironomus plumosus larvae increase fluxes of denitrification products and diversity of nitrate-reducing bacteria in freshwater sediment

DEFF Research Database (Denmark)

Poulsen, Morten; W. V. Kofoed, Michael; H. Larsen, Lone

2014-01-01

, respectively, which was mostly due to stimulation of sedimentary denitrification; incomplete denitrification in the guts accounted for up to 20% of the N2O efflux. Phylotype richness of the nitrate reductase gene narG was significantly higher in sediment with than without larvae. In the gut, 47 narG phylotypes...... were found expressed, which may contribute to higher phylotype richness in colonized sediment. In contrast, phylotype richness of the nitrous oxide reductase gene nosZ was unaffected by the presence of larvae and very few nosZ phylotypes were expressed in the gut. Gene abundance of neither narG, nor...... nosZ wasdifferent in sediments with and without larvae. Hence, C. plumosus increases activity and diversity, but not overall abundance of nitrate-reducing bacteria, probably by providing additional ecological niches in its burrow and gut....

3D printing of bacteria into functional complex materials.

Science.gov (United States)

Schaffner, Manuel; Rühs, Patrick A; Coulter, Fergal; Kilcher, Samuel; Studart, André R

2017-12-01

Despite recent advances to control the spatial composition and dynamic functionalities of bacteria embedded in materials, bacterial localization into complex three-dimensional (3D) geometries remains a major challenge. We demonstrate a 3D printing approach to create bacteria-derived functional materials by combining the natural diverse metabolism of bacteria with the shape design freedom of additive manufacturing. To achieve this, we embedded bacteria in a biocompatible and functionalized 3D printing ink and printed two types of "living materials" capable of degrading pollutants and of producing medically relevant bacterial cellulose. With this versatile bacteria-printing platform, complex materials displaying spatially specific compositions, geometry, and properties not accessed by standard technologies can be assembled from bottom up for new biotechnological and biomedical applications.

Molecular Diversity, Cultivation, and Improved Detection by Fluorescent In Situ Hybridization of a Dominant Group of Human Gut Bacteria Related to Roseburia spp. or Eubacterium rectale

OpenAIRE

Aminov, Rustam I.; Walker, Alan W.; Duncan, Sylvia H.; Harmsen, Hermie J. M.; Welling, Gjalt W.; Flint, Harry J.

2006-01-01

Phylogenetic analysis was used to compare 16S rRNA sequences from 19 cultured human gut strains of Roseburia and Eubacterium rectale with 356 related sequences derived from clone libraries. The cultured strains were found to represent five of the six phylotypes identified. A new oligonucleotide probe, Rrec584, and the previous group probe Rint623, when used in conjunction with a new helper oligonucleotide, each recognized an average of 7% of bacteria detected by the eubacterial probe Eub338 i...

Oral, intestinal, and skin bacteria in ventral hernia mesh implants

Directory of Open Access Journals (Sweden)

Odd Langbach

2016-07-01

Full Text Available Background: In ventral hernia surgery, mesh implants are used to reduce recurrence. Infection after mesh implantation can be a problem and rates around 6–10% have been reported. Bacterial colonization of mesh implants in patients without clinical signs of infection has not been thoroughly investigated. Molecular techniques have proven effective in demonstrating bacterial diversity in various environments and are able to identify bacteria on a gene-specific level. Objective: The purpose of this study was to detect bacterial biofilm in mesh implants, analyze its bacterial diversity, and look for possible resemblance with bacterial biofilm from the periodontal pocket. Methods: Thirty patients referred to our hospital for recurrence after former ventral hernia mesh repair, were examined for periodontitis in advance of new surgical hernia repair. Oral examination included periapical radiographs, periodontal probing, and subgingival plaque collection. A piece of mesh (1×1 cm from the abdominal wall was harvested during the new surgical hernia repair and analyzed for bacteria by PCR and 16S rRNA gene sequencing. From patients with positive PCR mesh samples, subgingival plaque samples were analyzed with the same techniques. Results: A great variety of taxa were detected in 20 (66.7% mesh samples, including typical oral commensals and periodontopathogens, enterics, and skin bacteria. Mesh and periodontal bacteria were further analyzed for similarity in 16S rRNA gene sequences. In 17 sequences, the level of resemblance between mesh and subgingival bacterial colonization was 98–100% suggesting, but not proving, a transfer of oral bacteria to the mesh. Conclusion: The results show great bacterial diversity on mesh implants from the anterior abdominal wall including oral commensals and periodontopathogens. Mesh can be reached by bacteria in several ways including hematogenous spread from an oral site. However, other sites such as gut and skin may also

Diversity and characterization of mercury-resistant bacteria in snow, freshwater and sea-ice brine from the High Arctic.

Science.gov (United States)

Møller, Annette K; Barkay, Tamar; Abu Al-Soud, Waleed; Sørensen, Søren J; Skov, Henrik; Kroer, Niels

2011-03-01

It is well-established that atmospheric deposition transports mercury from lower latitudes to the Arctic. The role of bacteria in the dynamics of the deposited mercury, however, is unknown. We characterized mercury-resistant bacteria from High Arctic snow, freshwater and sea-ice brine. Bacterial densities were 9.4 × 10(5), 5 × 10(5) and 0.9-3.1 × 10(3) cells mL(-1) in freshwater, brine and snow, respectively. Highest cultivability was observed in snow (11.9%), followed by freshwater (0.3%) and brine (0.03%). In snow, the mercury-resistant bacteria accounted for up to 31% of the culturable bacteria, but levels of most isolates were not temperature dependent. Of the resistant isolates, 25% reduced Hg(II) to Hg(0). No relation between resistance level, ability to reduce Hg(II) and phylogenetic group was observed. An estimation of the potential bacterial reduction of Hg(II) in snow suggested that it was important in the deeper snow layers where light attenuation inhibited photoreduction. Thus, by reducing Hg(II) to Hg(0), mercury-resistant bacteria may limit the supply of substrate for methylation processes and, hence, contribute to lowering the risk that methylmercury is being incorporated into the Arctic food chains. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Isolation and characterization of oxalotrophic bacteria from tropical soils.

Science.gov (United States)

Bravo, Daniel; Braissant, Olivier; Cailleau, Guillaume; Verrecchia, Eric; Junier, Pilar

2015-01-01

The oxalate-carbonate pathway (OCP) is a biogeochemical set of reactions that involves the conversion of atmospheric CO2 fixed by plants into biomass and, after the biological recycling of calcium oxalate by fungi and bacteria, into calcium carbonate in terrestrial environments. Oxalotrophic bacteria are a key element of this process because of their ability to oxidize calcium oxalate. However, the diversity and alternative carbon sources of oxalotrophs participating to this pathway are unknown. Therefore, the aim of this study was to characterize oxalotrophic bacteria in tropical OCP systems from Bolivia, India, and Cameroon. Ninety-five oxalotrophic strains were isolated and identified by sequencing of the 16S rRNA gene. Four genera corresponded to newly reported oxalotrophs (Afipia, Polaromonas, Humihabitans, and Psychrobacillus). Ten strains were selected to perform a more detailed characterization. Kinetic curves and microcalorimetry analyses showed that Variovorax soli C18 has the highest oxalate consumption rate with 0.240 µM h(-1). Moreover, Streptomyces achromogenes A9 displays the highest metabolic plasticity. This study highlights the phylogenetic and physiological diversity of oxalotrophic bacteria in tropical soils under the influence of the oxalate-carbonate pathway.

Novel anammox bacteria and nitrogen loss from Lake Superior

DEFF Research Database (Denmark)

Crowe, Sean A.; Treusch, Alexander H.; Forth, Michael

2017-01-01

and diversity of anammox bacteria in the world's largest freshwater lake - Lake Superior. We found that anammox performed by previously undiscovered bacteria is an important contributor to sediment N2 production. We observed striking differences in the anammox bacterial populations found at different locations...... within Lake Superior and those described from other locations. Our data thus reveal that novel anammox bacteria underpin N-loss from Lake Superior, and if more broadly distributed across inland waters would play an important role in continental N-cycling and mitigation of fixed nitrogen transfer from...

Diversity of H2/CO2-utilizing acetogenic bacteria from feces of non-methane-producing humans.

Science.gov (United States)

Bernalier, A; Rochet, V; Leclerc, M; Doré, J; Pochart, P

1996-08-01

The purpose of this work was to study H2/CO2-utilizing acetogenic population in the colons of non-methane-producing individuals harboring low numbers of methanogenic archaea. Among the 50 H2-consuming acetogenic strains isolated from four fecal samples and an in vitro semi-continuous culture enrichment, with H2/CO2 as sole energy source, 20 were chosen for further studies. All isolates were Gram-positive strict anaerobes. Different morphological types were identified, providing evidence of generic diversity. All acetogenic strains characterized used H2/CO2 to form acetate as the sole metabolite, following the stoichiometric equation of reductive acetogenesis. These bacteria were also able to use a variety of organic compounds for growth. The major end product of glucose fermentation was acetate, except for strains of cocci that mainly produced lactate. Yeast extract was not necessary, but was stimulatory for growth and acetogenesis from H2/CO2.

Decreased waterborne pathogenic bacteria in an urban aquifer related to intense shallow geothermal exploitation.

Science.gov (United States)

García-Gil, Alejandro; Gasco-Cavero, Samanta; Garrido, Eduardo; Mejías, Miguel; Epting, Jannis; Navarro-Elipe, Mercedes; Alejandre, Carmen; Sevilla-Alcaine, Elena

2018-08-15

The implications of intensive use of shallow geothermal energy resources in shallow urban aquifers are still not known for waterborne pathogens relevant to human health. Firstly, we hypothesized that waterborne enteric pathogens would be relatively increased in heated groundwater plumes. To prove this, microbiological sampling of 31 piezometers covering the domain of an urban groundwater body affected by microbiological contamination and energetically exploited by 70 groundwater heat pump systems was performed. Mean differences of pathogenic bacteria contents between impacted and non-impacted monitoring points were assessed with a two-tailed independent Student's t-test or Mann-Whitney U and correlation coefficients were also calculated. Surprisingly, the results obtained revealed a significant and generalized decrease in waterborne pathogen contents in thermally impacted piezometers compared to that of non-impacted piezometers. This decrease is hypothesized to be caused by a heat shock to bacteria within the heat exchangers. The statistically significant negative correlations obtained between waterborne pathogen counts and temperature could be explained by the spatial distribution of the bacteria, finding that bacteria start to recover with increasing distance from the injection point. Also, different behavior groups fitting exponential regression models were found for the bacteria species studied, justified by the different presence and influence of several aquifer parameters and major, minor and trace elements studied, as well as the coexistence with other bacteria species. The results obtained from this work reinforce the concept of shallow geothermal resources as a clean energy source, as they could also provide the basis to control the pathogenic bacteria contents in groundwater bodies. Copyright © 2018 Elsevier B.V. All rights reserved.

Method of Detecting Coliform Bacteria and Escherichia Coli Bacteria from Reflected Light

Science.gov (United States)

Vincent, Robert (Inventor)

2013-01-01

The present invention relates to a method of detecting coliform bacteria in water from reflected light and a method of detecting Eschericha Coli bacteria in water from reflected light, and also includes devices for the measurement, calculation and transmission of data relating to that method.

A direct pre-screen for marine bacteria producing compounds inhibiting quorum sensing reveals diverse planktonic bacteria that are bioactive.

Science.gov (United States)

Linthorne, Jamie S; Chang, Barbara J; Flematti, Gavin R; Ghisalberti, Emilio L; Sutton, David C

2015-02-01

A promising new strategy in antibacterial research is inhibition of the bacterial communication system termed quorum sensing. In this study, a novel and rapid pre-screening method was developed to detect the production of chemical inhibitors of this system (quorum-quenching compounds) by bacteria isolated from marine and estuarine waters. This method involves direct screening of mixed populations on an agar plate, facilitating specific isolation of bioactive colonies. The assay showed that between 4 and 46 % of culturable bacteria from various samples were bioactive, and of the 95 selectively isolated bacteria, 93.7 % inhibited Vibrio harveyi bioluminescence without inhibiting growth, indicating potential production of quorum-quenching compounds. Of the active isolates, 21 % showed further activity against quorum-sensing-regulated pigment production by Serratia marcescens. The majority of bioactive isolates were identified by 16S ribosomal DNA (rDNA) amplification and sequencing as belonging to the genera Vibrio and Pseudoalteromonas. Extracts of two strongly bioactive Pseudoalteromonas isolates (K1 and B2) were quantitatively assessed for inhibition of growth and quorum-sensing-regulated processes in V. harveyi, S. marcescens and Chromobacterium violaceum. Extracts of the isolates reduced V. harveyi bioluminescence by as much as 98 % and C. violaceum pigment production by 36 % at concentrations which had no adverse effect on growth. The activity found in the extracts indicated that the isolates may produce quorum-quenching compounds. This study further supports the suggestion that quorum quenching may be a common attribute among culturable planktonic marine and estuarine bacteria.

Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia.

Science.gov (United States)

Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

2014-10-01

In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

Diversity of acetic acid bacteria present in healthy grapes from the Canary Islands.

Science.gov (United States)

Valera, Maria José; Laich, Federico; González, Sara S; Torija, Maria Jesús; Mateo, Estibaliz; Mas, Albert

2011-11-15

The identification of acetic acid bacteria (AAB) from sound grapes from the Canary Islands is reported in the present study. No direct recovery of bacteria was possible in the most commonly used medium, so microvinifications were performed on grapes from Tenerife, La Palma and Lanzarote islands. Up to 396 AAB were isolated from those microvinifications and identified by 16S rRNA gene sequencing and phylogenetic analysis. With this method, Acetobacter pasteurianus, Acetobacter tropicalis, Gluconobacter japonicus and Gluconacetobacter saccharivorans were identified. However, no discrimination between the closely related species Acetobacter malorum and Acetobacter cerevisiae was possible. As previously described, 16S-23S rRNA gene internal transcribed spacer (ITS) region phylogenetic analysis was required to classify isolates as one of those species. These two species were the most frequently occurring, accounting for more than 60% of the isolates. For typing the AAB isolates, both the Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR and (GTG)5-PCR techniques gave similar resolution. A total of 60 profiles were identified. Thirteen of these profiles were found in more than one vineyard, and only one profile was found on two different islands (Tenerife and La Palma). Copyright © 2011 Elsevier B.V. All rights reserved.

Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin

Science.gov (United States)

Dhillon, Ashita; Teske, Andreas; Dillon, Jesse; Stahl, David A.; Sogin, Mitchell L.

2003-01-01

The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing.

Diversity of lactic acid bacteria associated with traditional fermented dairy products in Mongolia.

Science.gov (United States)

Yu, J; Wang, W H; Menghe, B L G; Jiri, M T; Wang, H M; Liu, W J; Bao, Q H; Lu, Q; Zhang, J C; Wang, F; Xu, H Y; Sun, T S; Zhang, H P

2011-07-01

Spontaneous milk fermentation has a long history in Mongolia, and beneficial microorganisms have been handed down from one generation to the next for use in fermented dairy products. The objective of this study was to investigate the diversity of lactic acid bacteria (LAB) communities in fermented yak, mare, goat, and cow milk products by analyzing 189 samples collected from 13 different regions in Mongolia. The LAB counts in these samples varied from 3.41 to 9.03 log cfu/mL. Fermented yak and mare milks had almost identical mean numbers of LAB, which were significantly higher than those in fermented goat milk but slightly lower than those in fermented cow milk. In total, 668 isolates were obtained from these samples using de Man, Rogosa, and Sharpe agar and M17 agar. Each isolate was considered to be presumptive LAB based on gram-positive and catalase-negative properties, and was identified at the species level by 16S rRNA gene sequencing, multiplex PCR assay, and restriction fragment length polymorphism analysis. All isolates from Mongolian dairy products were accurately identified as Enterococcus faecalis (1 strain), Enterococcus durans (3 strains), Lactobacillus brevis (3 strains), Lactobacillus buchneri (2 strains), Lactobacillus casei (16 strains), Lactobacillus delbrueckii ssp. bulgaricus (142 strains), Lactobacillus diolivorans (17 strains), Lactobacillus fermentum (42 strains), Lactobacillus helveticus (183 strains), Lactobacillus kefiri (6 strains), Lactobacillus plantarum ssp. plantarum (7 strains), Lactococcus lactis ssp. lactis (7 strains), Leuconostoc lactis (22 strains), Leuconostoc mesenteroides (21 strains), Streptococcus thermophilus (195 strains), and Weissella cibaria (1 strain). The predominant LAB were Strep. thermophilus and Lb. helveticus, which were isolated from all sampling sites. The results demonstrate that traditional fermented dairy products from different regions of Mongolia have complex compositions of LAB species. Such diversity of

Influence of Geographical Origin and Flour Type on Diversity of Lactic Acid Bacteria in Traditional Belgian Sourdoughs▿ †

Science.gov (United States)

Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

2007-01-01

A culture-based approach was used to investigate the diversity of lactic acid bacteria (LAB) in Belgian traditional sourdoughs and to assess the influence of flour type, bakery environment, geographical origin, and technological characteristics on the taxonomic composition of these LAB communities. For this purpose, a total of 714 LAB from 21 sourdoughs sampled at 11 artisan bakeries throughout Belgium were subjected to a polyphasic identification approach. The microbial composition of the traditional sourdoughs was characterized by bacteriological culture in combination with genotypic identification methods, including repetitive element sequence-based PCR fingerprinting and phenylalanyl-tRNA synthase (pheS) gene sequence analysis. LAB from Belgian sourdoughs belonged to the genera Lactobacillus, Pediococcus, Leuconostoc, Weissella, and Enterococcus, with the heterofermentative species Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus plantarum, and Lactobacillus pontis as the most frequently isolated taxa. Statistical analysis of the identification data indicated that the microbial composition of the sourdoughs is mainly affected by the bakery environment rather than the flour type (wheat, rye, spelt, or a mixture of these) used. In conclusion, the polyphasic approach, based on rapid genotypic screening and high-resolution, sequence-dependent identification, proved to be a powerful tool for studying the LAB diversity in traditional fermented foods such as sourdough. PMID:17675431

Phylogenetic and functional diversity of Bacteria and Archaea in a unique stratified lagoon, the Clipperton atoll (N Pacific).

Science.gov (United States)

Galand, Pierre E; Bourrain, Muriel; De Maistre, Emmanuel; Catala, Philippe; Desdevises, Yves; Elifantz, Hila; Kirchman, David L; Lebaron, Philippe

2012-01-01

The Clipperton lagoon in the North Pacific Ocean has been isolated from the surrounding sea for c. 160 years. It has a stratified water column that comprises an oxic and brackish upper water layer (mixolimnion) and a deep sulfuric anoxic saline layer (monimolimnion), separated by a steep pycnocline. Here, we test whether the Clipperton lagoon with its distinctive physico-chemical features, geographic isolation, recent water column stratification, and large nutrient input harbors original microbial communities. The combination of capillary electrophoresis single-strand polymorphism (CE-SSCP) fingerprinting and sequencing of cloned bacterial and archaeal 16S rRNA genes, and functional genes for methanogenesis (mcrA), methanotrophy (pmoA), and sulfate reduction (dsrAB), revealed that microbial communities and pathways were highly stratified down the water column. The mixolimnion contained ubiquitous freshwater clades of Alpha- and Betaproteobacteria, while the pycnocline contained mostly green sulfur bacteria (phylum Chlorobi). Sequences of the upper layers were closely related to sequences found in other aquatic ecosystems, suggesting that they have a strong potential for dispersal and colonization. In contrast, the monimolimnion contained new deeply branching bacterial divisions within the OP11 cluster and the Bacteroidetes, and was the most diverse of the layers. The unique environmental conditions characterizing the deep layers of the lagoon may explain the novelty of the microbial communities found at the Clipperton atoll.

New insights into valve-related intramural and intracellular bacterial diversity in infective endocarditis.

Science.gov (United States)

Oberbach, Andreas; Schlichting, Nadine; Feder, Stefan; Lehmann, Stefanie; Kullnick, Yvonne; Buschmann, Tilo; Blumert, Conny; Horn, Friedemann; Neuhaus, Jochen; Neujahr, Ralph; Bagaev, Erik; Hagl, Christian; Pichlmaier, Maximilian; Rodloff, Arne Christian; Gräber, Sandra; Kirsch, Katharina; Sandri, Marcus; Kumbhari, Vivek; Behzadi, Armirhossein; Behzadi, Amirali; Correia, Joao Carlos; Mohr, Friedrich Wilhelm; Friedrich, Maik

2017-01-01

In infective endocarditis (IE), a severe inflammatory disease of the endocardium with an unchanged incidence and mortality rate over the past decades, only 1% of the cases have been described as polymicrobial infections based on microbiological approaches. The aim of this study was to identify potential biodiversity of bacterial species from infected native and prosthetic valves. Furthermore, we compared the ultrastructural micro-environments to detect the localization and distribution patterns of pathogens in IE. Using next-generation sequencing (NGS) of 16S rDNA, which allows analysis of the entire bacterial community within a single sample, we investigated the biodiversity of infectious bacterial species from resected native and prosthetic valves in a clinical cohort of 8 IE patients. Furthermore, we investigated the ultrastructural infected valve micro-environment by focused ion beam scanning electron microscopy (FIB-SEM). Biodiversity was detected in 7 of 8 resected heart valves. This comprised 13 bacterial genera and 16 species. In addition to 11 pathogens already described as being IE related, 5 bacterial species were identified as having a novel association. In contrast, valve and blood culture-based diagnosis revealed only 4 species from 3 bacterial genera and did not show any relevant antibiotic resistance. The antibiotics chosen on this basis for treatment, however, did not cover the bacterial spectra identified by our amplicon sequencing analysis in 4 of 8 cases. In addition to intramural distribution patterns of infective bacteria, intracellular localization with evidence of bacterial immune escape mechanisms was identified. The high frequency of polymicrobial infections, pathogen diversity, and intracellular persistence of common IE-causing bacteria may provide clues to help explain the persistent and devastating mortality rate observed for IE. Improved bacterial diagnosis by 16S rDNA NGS that increases the ability to tailor antibiotic therapy may

Molecular and phenotypic characterization of endophytic bacteria isolated from sulla nodules.

Science.gov (United States)

Beghalem, Hamida; Aliliche, Khadidja; Chriki, Ali; Landoulsi, Ahmed

2017-10-01

In the current study, bacterial diversity was investigated in root nodules of Sulla pallida and Sulla capitata. The isolates were analyzed on the basis of their phenotypic and molecular characteristics. The phylogenetic analysis based on 16S rRNA and housekeeping genes (recA and atpD) showed that the isolated bacteria related to Sinorhizobium, Neorhizobium, Phyllobacterium, Arthrobacter, Variovorax and Pseudomonas genera. This is the first report of Neorhizobium genus associated with Hedysarum genus. Phenotypically, all strains tolerate the elevated temperature of 40 °C, and salt stress at a concentration of 2%. In addition, the isolates failed to induce nodulation on their original host; and the symbiotic genes could not be amplified, suggesting that these strains are endophytic bacteria. Copyright © 2017 Elsevier Ltd. All rights reserved.

Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica.

Science.gov (United States)

Sampaio, Dayanna Souza; Almeida, Juliana Rodrigues Barboza; de Jesus, Hugo E; Rosado, Alexandre S; Seldin, Lucy; Jurelevicius, Diogo

2017-11-01

Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.

Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.

Science.gov (United States)

Niu, Jia; Kasuga, Ikuro; Kurisu, Futoshi; Furumai, Hiroaki; Shigeeda, Takaaki; Takahashi, Kazuhiko

2016-01-01

Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance.

Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site

International Nuclear Information System (INIS)

Chang, Yun-Juan; Peacock, A D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Mcnaughton, Sarah J.; Hussain, A K M A.; Saxton, A M.; White, D C.

2000-01-01

Microbially mediated reduction and immobilization of U(VI) to U(TV) plays a role in both natural attenuation and accelerated bioremediation of uranium contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex,, was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from F-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least,52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0, Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within F-Proteobacteria were mainly recovered from low-uranium (less than or equal to 302 ppb) samples. One Desulfotomaculum like sequence cluster overwhelmingly dominated high-U (> 1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P= 0.0001), This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research

Protein-Injection Machines in Bacteria.

Science.gov (United States)

Galán, Jorge E; Waksman, Gabriel

2018-03-08

Many bacteria have evolved specialized nanomachines with the remarkable ability to inject multiple bacterially encoded effector proteins into eukaryotic or prokaryotic cells. Known as type III, type IV, and type VI secretion systems, these machines play a central role in the pathogenic or symbiotic interactions between multiple bacteria and their eukaryotic hosts, or in the establishment of bacterial communities in a diversity of environments. Here we focus on recent progress elucidating the structure and assembly pathways of these machines. As many of the interactions shaped by these machines are of medical importance, they provide an opportunity to develop novel therapeutic approaches to combat important human diseases. Copyright © 2018 Elsevier Inc. All rights reserved.

Molecular analysis of deep subsurface bacteria

International Nuclear Information System (INIS)

Jimenez Baez, L.E.

1989-09-01

Deep sediments samples from site C10a, in Appleton, and sites, P24, P28, and P29, at the Savannah River Site (SRS), near Aiken, South Carolina were studied to determine their microbial community composition, DNA homology and mol %G+C. Different geological formations with great variability in hydrogeological parameters were found across the depth profile. Phenotypic identification of deep subsurface bacteria underestimated the bacterial diversity at the three SRS sites, since bacteria with the same phenotype have different DNA composition and less than 70% DNA homology. Total DNA hybridization and mol %G+C analysis of deep sediment bacterial isolates suggested that each formation is comprised of different microbial communities. Depositional environment was more important than site and geological formation on the DNA relatedness between deep subsurface bacteria, since more 70% of bacteria with 20% or more of DNA homology came from the same depositional environments. Based on phenotypic and genotypic tests Pseudomonas spp. and Acinetobacter spp.-like bacteria were identified in 85 million years old sediments. This suggests that these microbial communities might have been adapted during a long period of time to the environmental conditions of the deep subsurface

Patterns of microbial diversity along a salinity gradient in the Guerrero Negro solar saltern, Baja CA Sur, Mexico

Directory of Open Access Journals (Sweden)

Jesse G Dillon

2013-12-01

Full Text Available The goal of this study was to use environmental sequencing of 16S rRNA and bop genes to compare the diversity of planktonic bacteria and archaea across ponds with increasing salinity in the Exportadora de Sal (ESSA evaporative saltern in Guerrero Negro, Baja CA S., Mexico. We hypothesized that diverse communities of heterotrophic bacteria and archaea would be found in the ESSA ponds, but that bacterial diversity would decrease relative to archaea at the highest salinities. Archaeal 16S rRNA diversity was higher in Ponds 11 and 12 (370 & 380 g l-1 total salts respectively compared to Pond 9 (180 g l-1 total salts. Both Pond 11 and 12 communities had high representation (47 and 45% of clones respectively by Haloquadratum walsbyi-like (99% similarity lineages. The archaeal community in Pond 9 was dominated (79% by a single uncultured phylotype with 99% similarity to sequences recovered from the Sfax saltern in Tunisia. This pattern was mirrored in bop gene diversity with greater numbers of highly supported phylotypes including many Haloquadratum-like sequences from the two highest salinity ponds. In Pond 9, most bop sequences, were not closely related to sequences in databases. Bacterial 16S rRNA diversity was higher than archaeal in both Pond 9 and Pond 12 samples, but not Pond 11, where a non-Salinibacter lineage within the Bacteroidetes >98% similar to environmental clones recovered from Lake Tuz in Turkey and a saltern in Chula Vista, CA was most abundant (69% of community. This OTU was also the most abundant in Pond 12, but only represented 14% of clones in the more diverse pond. The most abundant OTU in Pond 9 (33% of community was 99% similar to an uncultured gammaproteobacterial clone from the Salton Sea. Results suggest that the communities of saltern bacteria and archaea vary even in ponds with similar salinity and further investigation into the ecology of diverse, uncultured halophile communities is warranted.

Characteristics of airborne bacteria in Mumbai urban environment.

Science.gov (United States)

Gangamma, S

2014-08-01

Components of biological origin constitute small but a significant proportion of the ambient airborne particulate matter (PM). However, their diversity and role in proinflammatory responses of PM are not well understood. The present study characterizes airborne bacterial species diversity in Mumbai City and elucidates the role of bacterial endotoxin in PM induced proinflammatory response in ex vivo. Airborne bacteria and endotoxin samples were collected during April-May 2010 in Mumbai using six stage microbial impactor and biosampler. The culturable bacterial species concentration was measured and factors influencing the composition were identified by principal component analysis (PCA). The biosampler samples were used to stimulate immune cells in whole blood assay. A total of 28 species belonging to 17 genera were identified. Gram positive and spore forming groups of bacteria dominated the airborne culturable bacterial concentration. The study indicated the dominance of spore forming and human or animal flora derived pathogenic/opportunistic bacteria in the ambient air environment. Pathogenic and opportunistic species of bacteria were also present in the samples. TNF-α induction by PM was reduced (35%) by polymyxin B pretreatment and this result was corroborated with the results of blocking endotoxin receptor cluster differentiation (CD14). The study highlights the importance of airborne biological particles and suggests need of further studies on biological characterization of ambient PM. Copyright © 2014 Elsevier B.V. All rights reserved.

Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen.

Science.gov (United States)

Do, Thi Huyen; Dao, Trong Khoa; Nguyen, Khanh Hoang Viet; Le, Ngoc Giang; Nguyen, Thi Mai Phuong; Le, Tung Lam; Phung, Thu Nguyet; van Straalen, Nico M; Roelofs, Dick; Truong, Nam Hai

2018-05-01

In a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats' rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials. The metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information non-redundant sequence database. Here the BLASTX hits were further processed by the Metagenome Analyzer program to statistically analyze the abundance of taxa. Microbial community in the rumen is defined by dominance of Bacteroidetes compared to Firmicutes. The ratio of Firmicutes versus Bacteroidetes was 0.36:1. An abundance of Synergistetes was uniquely identified in the goat microbiome may be formed by host genotype. With regard to bacterial lignocellulose degraders, the ratio of lignocellulolytic genes affiliated with Firmicutes compared to the genes linked to Bacteroidetes was 0.11:1, in which the genes encoding putative hemicellulases, carbohydrate esterases, polysaccharide lyases originated from Bacteroidetes were 14 to 20 times higher than from Firmicutes. Firmicutes seem to possess more cellulose hydrolysis capacity showing a Firmicutes/Bacteroidetes ratio of 0.35:1. Analysis of lignocellulolytic potential degraders shows that four species belonged to Bacteroidetes phylum, while two species belonged to Firmicutes phylum harbouring at least 12 different catalytic domains for all lignocellulose pretreatment, cellulose, as well as hemicellulose saccharification. Based on these findings, we speculate that increasing the members of Bacteroidetes to keep a low ratio of Firmicutes versus Bacteroidetes in goat rumen has resulted most likely in an increased lignocellulose digestion.

Diversity and evolution of Lactobacillus casei group isolated from fermented dairy products in Tibet.

Science.gov (United States)

Feng, Jing; Jiang, Yujun; Li, Mingyu; Zhao, Siyu; Zhang, Yanming; Li, Xuesong; Wang, Hui; Lin, Guangen; Wang, Hao; Li, Tiejing; Man, Chaoxin

2018-05-25

Bacteria in Lactobacillus casei group, including Lactobacillus casei (L. casei), Lactobacillus paracasei (L. paracasei), and Lactobacillus rhamnosus (L. rhamnosus) are important lactic acid bacteria in the production of fermented dairy products and are faced with the controversial nomenclatural status due to their close phylogenetic similarity. To probe the evolution and phylogeny of L. casei group, 100 isolates of lactic acid bacteria originated from naturally fermented dairy products in Tibet of China were subjected to multilocus sequence typing (MLST). The MLST scheme, based on analysis of the housekeeping genes fusA, ileS, lepA, leuS, pyrG, recA and recG, revealed that all the isolates belonged to a group containing the L. paracasei reference strains and were clearly different from the strains of L. casei and L. rhamnosus. Although nucleotide diversity (π) was low for the seven genes (ranging from 0.00341 for fusA to 0.01307 for recG), high genetic diversity represented by 83 sequence types (STs) with a discriminatory index of 0.98 was detected. A network-like structure based on split decomposition analysis, and the high values of the relative effect of recombination and mutation in the diversification of the lineages (r/m = 4.76) and the relative frequency of occurrence of recombination and mutation (ρ/θ = 2.62) indicated that intra-species recombination occurred frequently and homologous recombination played a key role in generating genotypic diversity amongst L. paracasei strains in Tibet. The discovery of 51 new STs and the results of STRUCTURE analysis suggested that the L. casei group in Tibet had an individual and particular population structure in comparison to European isolates. Overall, this research might be the first report about genetic diversity and population structure of Lactobacillus populations isolated from naturally fermented dairy products in Tibet based on MLST scheme.

Isolation and characterization of biosurfactant producing bacteria from Persian Gulf (Bushehr provenance).

Science.gov (United States)

Hassanshahian, Mehdi

2014-09-15

Biosurfactants are surface active materials that are produced by some microorganisms. These molecules increase biodegradation of insoluble pollutants. In this study sediments and seawater samples were collected from the coastline of Bushehr provenance in the Persian Gulf and their biosurfactant producing bacteria were isolated. Biosurfactant producing bacteria were isolated by using an enrichment method in Bushnell-Hass medium with diesel oil as the sole carbon source. Five screening tests were used for selection of Biosurfactant producing bacteria: hemolysis in blood agar, oil spreading, drop collapse, emulsification activity and Bacterial Adhesion to Hydrocarbon test (BATH). These bacteria were identified using biochemical and molecular methods. Eighty different colonies were isolated from the collected samples. The most biosurfactant producing isolates related to petrochemical plants of Khark Island. Fourteen biosurfactant producing bacteria were selected between these isolates and 7 isolates were screened as these were predominant producers that belong to Shewanella alga, Shewanella upenei, Vibrio furnissii, Gallaecimonas pentaromativorans, Brevibacterium epidermidis, Psychrobacter namhaensis and Pseudomonas fluorescens. The largest clear zone diameters in oil spreading were observed for G. pentaromativorans strain O15. Also, this strain has the best emulsification activity and reduction of surface tension, suggesting it is the best of thee isolated strains. The results of this study confirmed that there is high diversity of biosurfactant producing bacteria in marine ecosystem of Iran and by application of these bacteria in petrochemical waste water environmental problems can be assisted. Copyright © 2014 Elsevier Ltd. All rights reserved.

A reservoir of drug-resistant pathogenic bacteria in asymptomatic hosts.

Directory of Open Access Journals (Sweden)

Gabriel G Perron

Full Text Available The population genetics of pathogenic bacteria has been intensively studied in order to understand the spread of disease and the evolution of virulence and drug resistance. However, much less attention has been paid to bacterial carriage populations, which inhabit hosts without producing disease. Since new virulent strains that cause disease can be recruited from the carriage population of bacteria, our understanding of infectious disease is seriously incomplete without knowledge on the population structure of pathogenic bacteria living in an asymptomatic host. We report the first extensive survey of the abundance and diversity of a human pathogen in asymptomatic animal hosts. We have found that asymptomatic swine from livestock productions frequently carry populations of Salmonella enterica with a broad range of drug-resistant strains and genetic diversity greatly exceeding that previously described. This study shows how agricultural practice and human intervention may lead and influence the evolution of a hidden reservoir of pathogens, with important implications for human health.

Energetics and Application of Heterotrophy in Acetogenic Bacteria.

Science.gov (United States)

Schuchmann, Kai; Müller, Volker

2016-07-15

Acetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2 fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogen Acetobacterium woodii Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2 reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Diversity of protists and bacteria determines predation performance and stability.

Science.gov (United States)

Saleem, Muhammad; Fetzer, Ingo; Harms, Hauke; Chatzinotas, Antonis

2013-10-01

Predation influences prey diversity and productivity while it effectuates the flux and reallocation of organic nutrients into biomass at higher trophic levels. However, it is unknown how bacterivorous protists are influenced by the diversity of their bacterial prey. Using 456 microcosms, in which different bacterial mixtures with equal initial cell numbers were exposed to single or multiple predators (Tetrahymena sp., Poterioochromonas sp. and Acanthamoeba sp.), we showed that increasing prey richness enhanced production of single predators. The extent of the response depended, however, on predator identity. Bacterial prey richness had a stabilizing effect on predator performance in that it reduced variability in predator production. Further, prey richness tended to enhance predator evenness in the predation experiment including all three protists predators (multiple predation experiment). However, we also observed a negative relationship between prey richness and predator production in multiple predation experiments. Mathematical analysis of potential ecological mechanisms of positive predator diversity-functioning relationships revealed predator complementarity as a factor responsible for both enhanced predator production and prey reduction. We suggest that the diversity at both trophic levels interactively determines protistan performance and might have implications in microbial ecosystem processes and services.

Bacteria in atmospheric waters: Detection, characteristics and implications

Science.gov (United States)

Hu, Wei; Niu, Hongya; Murata, Kotaro; Wu, Zhijun; Hu, Min; Kojima, Tomoko; Zhang, Daizhou

2018-04-01

In this review paper, we synthesize the current knowledges about bacteria in atmospheric waters, e.g., cloud, fog, rain, and snow, most of which were obtained very recently. First, we briefly describe the importance of bacteria in atmospheric waters, i.e., the essentiality of studying bacteria in atmospheric waters in understanding aerosol-cloud-precipitation-climate interactions in the Earth system. Next, approaches to collect atmospheric water samples for the detection of bacteria and methods to identify the bacteria are summarized and compared. Then the available data on the abundance, viability and community composition of bacteria in atmospheric waters are summarized. The average bacterial concentration in cloud water was usually on the order 104-105 cells mL-1, while that in precipitation on the order 103-104 cells mL-1. Most of the bacteria were viable or metabolically active. Their community composition was highly diverse and differed at various sites. Factors potentially influencing the bacteria, e.g., air pollution levels and sources, meteorological conditions, seasonal effect, and physicochemical properties of atmospheric waters, are described. After that, the implications of bacteria present in atmospheric waters, including their effect on nucleation in clouds, atmospheric chemistry, ecosystems and public health, are briefly discussed. Finally, based on the current knowledges on bacteria in atmospheric waters, which in fact remains largely unknown, we give perspectives that should be paid attention to in future studies.

Diversity of thermophilic bacteria in raw, pasteurized and selectively-cultured milk, as assessed by culturing, PCR-DGGE and pyrosequencing.

Science.gov (United States)

Delgado, Susana; Rachid, Caio T C C; Fernández, Elena; Rychlik, Tomasz; Alegría, Angel; Peixoto, Raquel S; Mayo, Baltasar

2013-10-01

Thermophilic lactic acid bacteria (LAB) species, such as Streptococcus thermophilus, Lactobacillus delbrueckii and Lactobacillus helveticus, enjoy worldwide economic importance as dairy starters. To assess the diversity of thermophilic bacteria in milk, milk samples were enriched in thermophilic organisms through a stepwise procedure which included pasteurization of milk at 63 °C for 30 min (PM samples) and pasteurization followed by incubation at 42 °C for 24 h (IPM samples). The microbial composition of these samples was analyzed by culture-dependent (at 42 °C) and culture-independent (PCR-DGGE and pyrosequencing of 16S rRNA gene amplicons) microbial techniques. The results were then compared to those obtained for their corresponding starting raw milk counterparts (RM samples). Twenty different species were scored by culturing among 352 isolates purified from the counting plates and identified by molecular methods. Mesophilic LAB species (Lactococcus lactis, Lactococcus garvieae) were dominant (87% of the isolates) among the RM samples. However, S. thermophilus and Lb. delbrueckii were found to be the dominant recoverable organisms in both PM and IPM samples. The DGGE profiles of RM and PM samples were found to be very similar; the most prominent bands belonging to Lactococcus, Leuconostoc and Streptococcus species. In contrast, just three DGGE bands were obtained for IPM samples, two of which were assigned to S. thermophilus. The pyrosequencing results scored 95 operational taxonomic units (OTUs) at 3% sequence divergence in an RM sample, while only 13 were encountered in two IPM samples. This technique identified Leuconostoc citreum as the dominant microorganism in the RM sample, while S. thermophilus constituted more than 98% of the reads in the IPM samples. The procedure followed in this study allowed to estimate the bacterial diversity in milk and afford a suitable strategy for the isolation of new thermophilic LAB strains, among which adequate

Quorum Quenching in Culturable Phyllosphere Bacteria from Tobacco

Directory of Open Access Journals (Sweden)

Guoqiang Zhuang

2013-07-01

Full Text Available Many Gram-negative plant pathogenic bacteria employ a N-acylhomoserine lactone (AHL-based quorum sensing (QS system to regulate their virulence traits. A sustainable biocontrol strategy has been developed using quorum quenching (QQ bacteria to interfere with QS and protect plants from pathogens. Here, the prevalence and the diversity of QQ strains inhabiting tobacco leaf surfaces were explored. A total of 1177 leaf-associated isolates were screened for their ability to disrupt AHL-mediated QS, using the biosensor Chromobacterium violaceum CV026. One hundred and sixty-eight strains (14% are capable of interfering with AHL activity. Among these, 106 strains (63% of the culturable quenchers can enzymatically degrade AHL molecules, while the remaining strains might use other QS inhibitors to interrupt the chemical communication. Moreover, almost 79% of the QQ strains capable of inactivating AHLs enzymatically have lactonase activity. Further phylogenetic analysis based on 16S rDNA revealed that the leaf-associated QQ bacteria can be classified as Bacillus sp., Acinetobacter sp., Lysinibacillus sp., Serratia sp., Pseudomonas sp., and Myroides sp. The naturally occurring diversity of bacterial quenchers might provide opportunities to use them as effective biocontrol reagents for suppressing plant pathogen in situ.

Characterization of spoilage bacteria in pork sausage by PCR-DGGE analysis

Directory of Open Access Journals (Sweden)

Francesca Silva Dias

2013-09-01

Full Text Available To investigate microbial diversity and identify spoilage bacteria in fresh pork sausages during storage, twelve industrial pork sausages of different trademarks were stored at 4 ºC for 0, 14, 28 and 42 days, 80% relative humidity and packaged in sterile plastic bags. Microbiological analysis was performed. The pH and water activity (a w were measured. The culture-independent method performed was the Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis (PCR-DGGE. The culture-dependent method showed that the populations of mesophilic bacteria and Lactic Acid Bacteria (LAB increased linearly over storage time. At the end of the storage time, the average population of microorganisms was detected, in general, at the level of 5 log cfu g-1. A significant (P < 0.005 increase was observed in pH and a w values at the end of the storage time. The PCR-DGGE allowed a rapid identification of dominant communities present in sausages. PCR-DGGE discriminated 15 species and seven genera of bacteria that frequently constitute the microbiota in sausage products. The most frequent spoilage bacteria identified in the sausages were Lactobacillus sakei and Brochothrix thermosphacta. The identification of dominant communities present in fresh pork sausages can help in the choice of the most effective preservation method for extending the product shelf-life.

Diversity of nitrogen-fixing bacteria in cyanobacterial mats

NARCIS (Netherlands)

Severin, I.; Acinas, S.G.; Stal, L.J.

2010-01-01

The structure of the microbial community and the diversity of the functional gene for dinitrogenase reductase and its transcripts were investigated by analyzing >1400 16S rRNA gene and nifH sequences from two microbial mats situated in the intertidal zone of the Dutch barrier island Schiermonnikoog.

Diversity and abundance of ammonia oxidizing archaea in tropical compost systems.

Science.gov (United States)

de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H; Hickey, William J

2012-01-01

Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.

Diversidade de bactérias diazotróficas endofíticas associadas a plantas de milho Diversity of diazotrophic endophytic bacteria associated with maize plants

Directory of Open Access Journals (Sweden)

Luiz Fernando Wurdig Roesch

2007-12-01

capazes de colonizar o interior de plantas de milho e que as diferentes condições edafoclimáticas estão correlacionadas com a diversidade dos genes nifH.Endophytic diazotrophic bacteria are capable of promoting maize growth through biological nitrogen fixation (BNF or by the production of plant hormones. The aim of this study was to characterize diversity of endophytic bacteria in maize at sites with different climate and soil conditions in Rio Grande do Sul, Brazil. A PCR-RFLP approach and sequence analysis of nifH Cluster I clone libraries were used to assess diversity in maize plants. The Shannon-Weaver and Equitability indices were calculated to estimate the diazotroph diversity as well as the nucleotide diversity and the average sequence divergence to estimate genetic diversity. To evaluate the variability in populations we performed the F ST test. A greater variation in bacterial communities was detected between rather than within regions, particularly among communities of different soil types and varying water regimes and geographical regions. The Shannon-Weaver index indicated a high difference in terms of diversity of taxonomic units among the communities. The diversity of the communities in the northern region, with higher precipitation and clay content, tended to be higher than that in the south. The Equitability index indicated that there was a dominant taxonomic unit within each community. All clones grouped into nifH gene cluster I. The nifH sequence types from Alpha, Beta and Gammaproteobacteria were recovered. These results demonstrate that there is a large diversity of endophytic nitrogen-fixing bacteria able to colonize maize tissue and that nifH diversity is correlated with the different environmental conditions.

Diverse protist grazers select for virulence-related traits in Legionella

Science.gov (United States)

Amaro, Francisco; Wang, Wen; Gilbert, Jack A; Roger Anderson, O; Shuman, Howard A

2015-01-01

It is generally accepted that selection for resistance to grazing by protists has contributed to the evolution of Legionella pneumophila as a pathogen. Grazing resistance is becoming more generally recognized as having an important role in the ecology and evolution of bacterial pathogenesis. However, selection for grazing resistance presupposes the existence of protist grazers that provide the selective pressure. To determine whether there are protists that graze on pathogenic Legionella species, we investigated the existence of such organisms in a variety of environmental samples. We isolated and characterized diverse protists that graze on L. pneumophila and determined the effects of adding L. pneumophila on the protist community structures in microcosms made from these environmental samples. Several unrelated organisms were able to graze efficiently on L. pneumophila. The community structures of all samples were markedly altered by the addition of L. pneumophila. Surprisingly, some of the Legionella grazers were closely related to species that are known hosts for L. pneumophila, indicating the presence of unknown specificity determinants for this interaction. These results provide the first direct support for the hypothesis that protist grazers exert selective pressure on Legionella to acquire and retain adaptations that contribute to survival, and that these properties are relevant to the ability of the bacteria to cause disease in people. We also report a novel mechanism of killing of amoebae by one Legionella species that requires an intact Type IV secretion system but does not involve intracellular replication. We refer to this phenomenon as ‘food poisoning'. PMID:25575308

Microbial Diversity of Betula Trees: Pollen, Catkins, Leaves Relatively of Flowering

Directory of Open Access Journals (Sweden)

Tetiana V. Shevtsova

2016-01-01

Full Text Available Quantitative microbiological analysis by dilution plating method of pollen and additional male and female catkins, leaves of Betula verrucosa Ehrh. and its two cultivars: ‘Purpurea’ and ‘Youngii’ relatively of flowering period of Betula has been realized with the aim to provide new knowledge of the microbiological quality of anemophilous pollen for processing and its further application. Qualitative microbiological analysis with MALDI-TOF MS Biotyper was used in the identification of aerobic, anaerobic mesophilic bacteria and coliforms. Mixed microbiota was determined, consisting of aerobic (4.68–4.89 log cfu/g and anaerobic (3.30–3.48 log cfu/g mesophilic bacteria, lactobacilli (0–3.48 log cfu/g, coliform bacteria (0–4.57 log cfu/g, fungi and yeast (3.78–3.95 log cfu/g on the pollen grains, that indicates acceptable quality in comparison with the microbiological quality parameters for bee pollen. Pantoea agglomerans was found associated with pollen of Betula verrucosa Ehrh. Recommendations on the collection of anemophilous pollen were established.

Fish Diversity in Relation to Aquatic Macrophytes and ...

African Journals Online (AJOL)

An investigation of fish diversity in relation to aquatic macrophytes and physicochemical parameters of Ona Lake in Asaba was carried out within a period of eighteen months. Fish samples were collected fortnightly from three sampling sites using cast, gill and trigger nets. Aquatic macrophytes found in close association with ...

Diversity and functional properties of acid-tolerant bacteria isolated from tea plantation soil of Assam.

Science.gov (United States)

Goswami, Gunajit; Deka, Priyadarshini; Das, Pompi; Bora, Sudipta Sankar; Samanta, Ramkrishna; Boro, Robin Chandra; Barooah, Madhumita

2017-07-01

In this study, we report on the bacterial diversity and their functional properties prevalent in tea garden soils of Assam that have low pH (3.8-5.5). Culture-dependent studies and phospholipid fatty acid analysis revealed a high abundance of Gram-positive bacteria. Further, 70 acid-tolerant bacterial isolates characterized using a polyphasic taxonomy approach could be grouped to the genus Bacillus, Lysinibacillus, Staphylococcus, Brevundimonas, Alcaligenes, Enterobacter, Klebsiella, Escherichia, and Aeromonas. Among the 70 isolates, 47 most promising isolates were tested for their plant growth promoting activity based on the production of Indole Acetic Acid (IAA), siderophore, and HCN as well as solubilization of phosphate, zinc, and potassium. Out of the 47 isolates, 10 isolates tested positive for the entire aforesaid plant growth promoting tests and further tested for quantitative analyses for production of IAA, siderophore, and phosphate solubilization at the acidic and neutral condition. Results indicated that IAA and siderophore production, as well as phosphate solubilization efficiency of the isolates decreased significantly (P ≤ 0.05) in the acidic environment. This study revealed that low soil pH influences bacterial community structure and their functional properties.

Big bacteria

DEFF Research Database (Denmark)

Schulz, HN; Jørgensen, BB

2001-01-01

A small number of prokaryotic species have a unique physiology or ecology related to their development of unusually large size. The biomass of bacteria varies over more than 10 orders of magnitude, from the 0.2 mum wide nanobacteria to the largest cells of the colorless sulfur bacteria......, Thiomargarita namibiensis, with a diameter of 750 mum. All bacteria, including those that swim around in the environment, obtain their food molecules by molecular diffusion. Only the fastest and largest swimmers known, Thiovulum majus, are able to significantly increase their food supply by motility...... and by actively creating an advective flow through the entire population. Diffusion limitation generally restricts the maximal size of prokaryotic cells and provides a selective advantage for mum-sized cells at the normally low substrate concentrations in the environment. The largest heterotrophic bacteria...

Geobiology of Marine Magnetotactic Bacteria

Science.gov (United States)

2006-06-01

prokaryotic cells of diverse phylogeny when grown in media containing 45 1mM iron, suggesting some kind of detoxification function . The inclusions were...salt marsh productivity. FISH also showed that aggregates consist of genetically identical cells. QPCR data indicated that populations are finely...my advisor Katrina Edwards for taking a chance on someone who initially knew nothing about magnetotactic bacteria, microbial ecology , or microbiology

Assessment of bacterial diversity during composting of agricultural byproducts

Science.gov (United States)

2013-01-01

Background Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts. Results The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 105 to 109 cfu g-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts. Conclusion The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost

The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria.

KAUST Repository

Bayer, Till; Neave, Matthew J.; Alsheikh Hussain, Areej Sameer; Aranda, Manuel; Yum, Lauren K; Mincer, Tracy; Hughen, Konrad; Apprill, Amy; Voolstra, Christian R.

2013-01-01

Endozoicomonas bacteria were found highly associated with the coral Stylophora pistillata, and these bacteria are also ubiquitously associated with diverse corals worldwide. Novel Endozoicomonas-specific probes revealed that Endozoicomonas bacteria were abundant in the endodermal tissues of S. pistillata and appear to have an intimate relationship with the coral.

The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria.

KAUST Repository

Bayer, Till

2013-08-01

Endozoicomonas bacteria were found highly associated with the coral Stylophora pistillata, and these bacteria are also ubiquitously associated with diverse corals worldwide. Novel Endozoicomonas-specific probes revealed that Endozoicomonas bacteria were abundant in the endodermal tissues of S. pistillata and appear to have an intimate relationship with the coral.

[Unique properties of highly radioresistant bacteria].

Science.gov (United States)

Romanovskaia, V A; Rokitko, P V; Malashenko, Iu R

2000-01-01

In connection with the Chernobyl Nuclear Power Plant (ChNPP) accident and the negative ecological after-effects for biota in this zone the interest has arisen to radioresistant bacteria, as to the most dynamic model of the given ecosystem, and to mechanisms which provide resistance of bacteria to ionizing radiation. The analysis of published data has shown that the radioresistant bacteria are not interrelated taxonomically and phylogenetically. The extreme radioresistant bacteria are represented by the Deinococcus species, which form a group phylogenetically close to the line Thermus-Meiothermus. Other radioresistant bacteria are the representatives of the genera Rubrobacter, Methylobacterium, Kocuria, Bacillus and some archebacteria. Data on natural habitats, of radioresistant bacteria are not numerous. In a number of cases it is difficult to distinguish their natural habitats, as they were isolated from the samples which were previously exposed to X-ray or gamma-irradiation, or from the ecosystems with the naturally raised radioactivity. To understand the strategy of survival of radioresistant bacteria, we briefly reviewed the mechanism of action of various species of radiation on cells and macromolecules; physiological signs of the cell damage caused by radiation; mechanisms eliminating (repairing) these damages. More details on mechanisms of the DNA repair in D. radiodurans are described. The extreme resistance of D. radiodurans to the DNA damaging factors is defined by 1) repair mechanisms which fundamentally differ from those in other procaryotes; 2) ability to increase the efficiency of a standard set of the DNA repairing proteins. Literary and own data on the effect of radiation on survival of various groups of bacteria in natural ecosystems are summarized. The ecological consequences of the ChNPP accident for soil bacteria in this region were estimated. The reduction of the number of soil bacteria and recession of microbial diversity under the effect of

Molecular Characterization of Sulfate-Reducing Bacteria in the Guaymas Basin†

Science.gov (United States)

Dhillon, Ashita; Teske, Andreas; Dillon, Jesse; Stahl, David A.; Sogin, Mitchell L.

2003-01-01

The Guaymas Basin (Gulf of California) is a hydrothermal vent site where thermal alteration of deposited planktonic and terrestrial organic matter forms petroliferous material which supports diverse sulfate-reducing bacteria. We explored the phylogenetic and functional diversity of the sulfate-reducing bacteria by characterizing PCR-amplified dissimilatory sulfite reductase (dsrAB) and 16S rRNA genes from the upper 4 cm of the Guaymas sediment. The dsrAB sequences revealed that there was a major clade closely related to the acetate-oxidizing delta-proteobacterial genus Desulfobacter and a clade of novel, deeply branching dsr sequences related to environmental dsr sequences from marine sediments in Aarhus Bay and Kysing Fjord (Denmark). Other dsr clones were affiliated with gram-positive thermophilic sulfate reducers (genus Desulfotomaculum) and the delta-proteobacterial species Desulforhabdus amnigena and Thermodesulforhabdus norvegica. Phylogenetic analysis of 16S rRNAs from the same environmental samples resulted in identification of four clones affiliated with Desulfobacterium niacini, a member of the acetate-oxidizing, nutritionally versatile genus Desulfobacterium, and one clone related to Desulfobacula toluolica and Desulfotignum balticum. Other bacterial 16S rRNA bacterial phylotypes were represented by non-sulfate reducers and uncultured lineages with unknown physiology, like OP9, OP8, as well as a group with no clear affiliation. In summary, analyses of both 16S rRNA and dsrAB clone libraries resulted in identification of members of the Desulfobacteriales in the Guaymas sediments. In addition, the dsrAB sequencing approach revealed a novel group of sulfate-reducing prokaryotes that could not be identified by 16S rRNA sequencing. PMID:12732547

Microbial colonisation in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

Science.gov (United States)

Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

2014-09-01

Colonisation of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focusing on settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associate vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soils types on the surface of the island. Total viable bacterial counts were performed with plate count at 22, 30 and 37 °C for all soils samples and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms aerobic and anaerobic bacteria. The deep subsurface biosphere was investigated by collecting liquid subsurface samples from a 182 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between N deficits and the number of microorganisms in surface soils samples. The lowest number of bacteria (1 × 104-1 × 105 g-1) was detected in almost pure pumice but the count was significant higher (1 × 106-1 × 109 g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 m and 172 m depth at 80 °C and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

Microbial colonization in diverse surface soil types in Surtsey and diversity analysis of its subsurface microbiota

Science.gov (United States)

Marteinsson, V.; Klonowski, A.; Reynisson, E.; Vannier, P.; Sigurdsson, B. D.; Ólafsson, M.

2015-02-01

Colonization of life on Surtsey has been observed systematically since the formation of the island 50 years ago. Although the first colonisers were prokaryotes, such as bacteria and blue-green algae, most studies have been focused on the settlement of plants and animals but less on microbial succession. To explore microbial colonization in diverse soils and the influence of associated vegetation and birds on numbers of environmental bacteria, we collected 45 samples from different soil types on the surface of the island. Total viable bacterial counts were performed with the plate count method at 22, 30 and 37 °C for all soil samples, and the amount of organic matter and nitrogen (N) was measured. Selected samples were also tested for coliforms, faecal coliforms and aerobic and anaerobic bacteria. The subsurface biosphere was investigated by collecting liquid subsurface samples from a 181 m borehole with a special sampler. Diversity analysis of uncultivated biota in samples was performed by 16S rRNA gene sequences analysis and cultivation. Correlation was observed between nutrient deficits and the number of microorganisms in surface soil samples. The lowest number of bacteria (1 × 104-1 × 105 cells g-1) was detected in almost pure pumice but the count was significantly higher (1 × 106-1 × 109 cells g-1) in vegetated soil or pumice with bird droppings. The number of faecal bacteria correlated also to the total number of bacteria and type of soil. Bacteria belonging to Enterobacteriaceae were only detected in vegetated samples and samples containing bird droppings. The human pathogens Salmonella, Campylobacter and Listeria were not in any sample. Both thermophilic bacteria and archaea 16S rDNA sequences were found in the subsurface samples collected at 145 and 172 m depth at 80 and 54 °C, respectively, but no growth was observed in enrichments. The microbiota sequences generally showed low affiliation to any known 16S rRNA gene sequences.

Coevolution of antibiotic production and counter-resistance in soil bacteria.

Science.gov (United States)

Laskaris, Paris; Tolba, Sahar; Calvo-Bado, Leo; Wellington, Elizabeth M; Wellington, Liz

2010-03-01

We present evidence for the coexistence and coevolution of antibiotic resistance and biosynthesis genes in soil bacteria. The distribution of the streptomycin (strA) and viomycin (vph) resistance genes was examined in Streptomyces isolates. strA and vph were found either within a biosynthetic gene cluster or independently. Streptomyces griseus strains possessing the streptomycin cluster formed part of a clonal complex. All S. griseus strains possessing solely strA belonged to two clades; both were closely related to the streptomycin producers. Other more distantly related S. griseus strains did not contain strA. S. griseus strains with only vph also formed two clades, but they were more distantly related to the producers and to one another. The expression of the strA gene was constitutive in a resistance-only strain whereas streptomycin producers showed peak strA expression in late log phase that correlates with the switch on of streptomycin biosynthesis. While there is evidence that antibiotics have diverse roles in nature, our data clearly support the coevolution of resistance in the presence of antibiotic biosynthetic capability within closely related soil dwelling bacteria. This reinforces the view that, for some antibiotics at least, the primary role is one of antibiosis during competition in soil for resources.

Salicornia strobilacea (synonym of Halocnemum strobilaceum) Grown Under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

KAUST Repository

Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira Santillá n, Marí a José ; Fusi, Marco; Bariselli, Paola; Reddy, Muppala P.; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

2016-01-01

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the PGP potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

Salicornia strobilacea (synonym of Halocnemum strobilaceum) Grown Under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

KAUST Repository

Marasco, Ramona

2016-04-01

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the PGP potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

DIVERSITY IN DIAK JÄRVENPÄÄ CAMPUS UNIT : Diversity and Relation among Different Institutions Located Within the Campus Premises

OpenAIRE

Shakya, Samasty; Singh, Sadin Kumar

2012-01-01

Sadin Kumar Singh & Samasty Shakya. Diversity in Diak Järvenpää Campus Unit: Diversity and Relation among Different Institution Located within the campus premises. Järvenpää, Spring 2012. 48p. Diaconia University of Applied Sciences, Diak South, Järvenpää Unit, Degree program in Social Services (UAS) Focus on Community Development Work The primary purpose of this research was to find the biggest issue of diversity in the campus area. All three educational institutions operating from t...

Lactic acid bacteria in a changing legislative environment

NARCIS (Netherlands)

Feord, J.

2002-01-01

The benefits of using lactic acid bacteria in the food chain, both through direct consumption and production of ingredients, are increasingly recognised by the food industry and consumers alike. The regulatory environment surrounding these products is diverse, covering foods and food ingredients,

Nitrogen-fixing bacteria in Mediterranean seagrass (Posidonia oceanica) roots

KAUST Repository

Garcias Bonet, Neus; Arrieta, J M; Duarte, Carlos M.; Marbà , Nú ria

2016-01-01

of nitrogen for P. oceanica. The low diversity of nitrogen-fixing bacteria reported here suggests species-specific relationships between diazotrophs and P. oceanica, revealing possible symbiotic interactions that could play a major role in nitrogen acquisition

Denitrifying bacteria from the terrestrial subsurface exposed to mixed waste contamination

International Nuclear Information System (INIS)

Green, Stefan; Prakash, Om; Gihring, Thomas; Akob, Denise M.; Jasrotia, Puja; Jardine, Philip M.; Watson, David B.; Brown, Steven David; Palumbo, Anthony Vito; Kostka, Joel

2010-01-01

In terrestrial subsurface environments where nitrate is a critical groundwater contaminant, few cultivated representatives are available with which to verify the metabolism of organisms that catalyze denitrification. In this study, five species of denitrifying bacteria from three phyla were isolated from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC). Isolates belonged to the genera Afipia and Hyphomicrobium (Alphaproteobacteria), Rhodanobacter (Gammaproteobacteria), Intrasporangium (Actinobacteria) and Bacillus (Firmicutes). Isolates from the phylum Proteobacteria were confirmed as complete denitrifiers, whereas the Gram-positive isolates reduced nitrate to nitrous oxide. Ribosomal RNA gene analyses reveal that bacteria from the genus Rhodanobacter comprise a diverse population of circumneutral to moderately acidophilic denitrifiers at the ORIFRC site, with a high relative abundance in areas of the acidic source zone. Rhodanobacter species do not contain a periplasmic nitrite reductase and have not been previously detected in functional gene surveys of denitrifying bacteria at the OR-IFRC site. Sequences of nitrite and nitrous oxide reductase genes were recovered from the isolates and from the terrestrial subsurface by designing primer sets mined from genomic and metagenomic data and from draft genomes of two of the isolates. We demonstrate that a combination of cultivation, genomic and metagenomic data are essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifying microorganisms. Our results indicate that the diversity of denitrifiers is significantly underestimated in the terrestrial subsurface.

Metabolic Interactions between Bacteria and Fungi in Commensal Oral Biofilms

OpenAIRE

Lof, Marloes; Janus, Marleen M.; Krom, Bastiaan P.

2017-01-01

Oral health is more than just the absence of disease. The key to oral health is a diverse microbiome in an ecological balance. The oral microbiota is one of the most complex and diverse microbial communities in the human body. To maintain oral health, balance between the human host and the intrinsic microorganisms is essential. The healthy oral cavity is represented by a great microbial diversity, including both bacteria and fungi. The bacterial microbiome is very well studied. In contrast, f...

Diversity and phylogenetic analyses of bacteria from a shallow-waterhydrothermal vent in Milos island (Greece

Directory of Open Access Journals (Sweden)

Donato eGiovannelli

2013-07-01

Full Text Available Studies of shallow-water hydrothermal vents have been lagging behind their deep-sea counterparts. Hence, the importance of these systems and their contribution to the local and regional diversity and biogeochemistry is unclear. This study analyzes the bacterial community along a transect at the shallow-water hydrothermal vent system of Milos island, Greece. The abundance and biomass of the prokaryotic community is comparable to areas not affected by hydrothermal activity and was, on average, 1.34×108 cells g-1. The abundance, biomass and diversity of the prokaryotic community increased with the distance from the center of the vent and appeared to be controlled by the temperature gradient rather than the trophic conditions. The retrieved 16S rRNA gene fragments matched sequences from a variety of geothermal environments, although the average similarity was low (94 %, revealing previously undiscovered taxa. Epsilonproteobacteria constituted the majority of the population along the transect, with an average contribution to the total diversity of 60%. The larger cluster of 16S rRNA gene sequences was related to chemolithoautotrophic Sulfurovum spp., an Epsilonproteobacterium so far detected only at deep-sea hydrothermal vents. The presence of previously unknown lineages of Epsilonproteobacteria could be related to the abundance of organic matter in these systems, which may support alternative metabolic strategies to chemolithoautotrophy. The relative contribution of Gammaproteobacteria to the Milos microbial community increased along the transect as the distance from the center of the vent increased. Further attempts to isolate key species from these ecosystems will be critical to shed light on their evolution and ecology.

Exploring the microbiota dynamics related to vegetable biomasses degradation and study of lignocellulose-degrading bacteria for industrial biotechnological application

Science.gov (United States)

Ventorino, Valeria; Aliberti, Alberto; Faraco, Vincenza; Robertiello, Alessandro; Giacobbe, Simona; Ercolini, Danilo; Amore, Antonella; Fagnano, Massimo; Pepe, Olimpia

2015-02-01

The aims of this study were to evaluate the microbial diversity of different lignocellulosic biomasses during degradation under natural conditions and to isolate, select, characterise new well-adapted bacterial strains to detect potentially improved enzyme-producing bacteria. The microbiota of biomass piles of Arundo donax, Eucalyptus camaldulensis and Populus nigra were evaluated by high-throughput sequencing. A highly complex bacterial community was found, composed of ubiquitous bacteria, with the highest representation by the Actinobacteria, Proteobacteria, Bacteroidetes and Firmicutes phyla. The abundances of the major and minor taxa retrieved during the process were determined by the selective pressure produced by the lignocellulosic plant species and degradation conditions. Moreover, cellulolytic bacteria were isolated using differential substrates and screened for cellulase, cellobiase, xylanase, pectinase and ligninase activities. Forty strains that showed multienzymatic activity were selected and identified. The highest endo-cellulase activity was seen in Promicromonospora sukumoe CE86 and Isoptericola variabilis CA84, which were able to degrade cellulose, cellobiose and xylan. Sixty-two percent of bacterial strains tested exhibited high extracellular endo-1,4-ß-glucanase activity in liquid media. These approaches show that the microbiota of lignocellulosic biomasses can be considered an important source of bacterial strains to upgrade the feasibility of lignocellulose conversion for the `greener' technology of second-generation biofuels.

Broilers fed dietary vitamins harbor higher diversity of cecal bacteria and higher ratio of Clostridium, Faecalibacterium, and Lactobacillus than broilers with no dietary vitamins revealed by 16S rRNA gene clone libraries.

Science.gov (United States)

Luo, Yu-heng; Peng, Huan-wei; Wright, André-Denis G; Bai, Shi-ping; Ding, Xue-mei; Zeng, Qiu-feng; Li, Hua; Zheng, Ping; Su, Zhuo-wei; Cui, Ren-yong; Zhang, Ke-ying

2013-09-01

Research on the interaction between dietary vitamins and intestinal bacteria is poorly understood. To investigate the effect of dietary vitamins on the cecal bacterial communities, 2 bacterial 16S rRNA gene clone libraries were constructed from pooled PCR products obtained from the cecal digesta of 28-d broilers fed diets with vitamins (V) at the NRC level or with no vitamins (NV). The results showed that BW gain and average feed intake of V broilers was significantly higher (P vitamins can increase the ratio of facultative pathogenic bacteria and decrease the diversity of bacteria in the cecum of broilers. Our results provide new leads for further investigations on the interaction between dietary vitamin additives and the gut health of broilers.

Big bacteria

DEFF Research Database (Denmark)

Schulz, HN; Jørgensen, BB

2001-01-01

A small number of prokaryotic species have a unique physiology or ecology related to their development of unusually large size. The biomass of bacteria varies over more than 10 orders of magnitude, from the 0.2 mum wide nanobacteria to the largest cells of the colorless sulfur bacteria...... and by actively creating an advective flow through the entire population. Diffusion limitation generally restricts the maximal size of prokaryotic cells and provides a selective advantage for mum-sized cells at the normally low substrate concentrations in the environment. The largest heterotrophic bacteria......, the 80 x 600 mum large Epulopiscium sp. from the gut of tropical fish, are presumably living in a very nutrient-rich medium. Many large bacteria contain numerous inclusions in the cells that reduce the volume of active cytoplasm. The most striking examples of competitive advantage from large cell size...

Diversity of heavy metal resistant bacteria from Kalimas Surabaya: A phylogenetic taxonomy approach

Science.gov (United States)

Zulaika, Enny; Utomo, Andry Prio; Prima, Adisya; Alami, Nur Hidayatul; Kuswytasari, Nengah Dwianita; Shovitri, Maya; Sembiring, Langkah

2017-06-01

Bacterial resistance to heavy metal is a genetic and physiological adaptation to the environment which contaminated by heavy metal. Kalimas is an important river in Surabaya that is contaminated by some heavy metals and probably as a habitat for heavy metal resistance bacteria. Bacterial resistance to heavy metals are different for each species, and their diversity can be studied by phylogenetic taxonomy approach. Isolates screening was done using nutrient agar which contained 1 mg/L HgCl2, CdCl2 and K2Cr2O7. Bacterial viability were observed by nutrient broth which contained 10 mg/L HgCl2, 30 mg/L CdCl2 and 50 mg/L K2Cr2O7. Isolates that resistant to heavy metal and viable after exposure to heavy metal were identified using 16S rRNA gene marker by Polymerase Chain Reaction (PCR). Phylogenetic tree reconstruction was done by the neighbor-joining algorithm. Genetic assignment showed isolates that resist and viable after exposure of Hg, Cd and Cr are Bacillus S1, SS19 and DA11. Based on BLAST analysis from NCBI gene bank, 16S rRNA sequences, those isolates were similar with the member of Bacillus cereus. Depend on 16S rRNA nucleotide alignment by the neighbor-joining algorithm, Bacillus S1, SS19 and DA11 were belong to Bacillus cereus sensu-lato group.

Diversity of membrane transport proteins for vitamins in bacteria and archaea

NARCIS (Netherlands)

Jähme, Michael; Slotboom, Dirk Jan

BACKGROUND: All organisms use cofactors to extend the catalytic capacities of proteins. Many bacteria and archaea can synthesize cofactors from primary metabolites, but there are also prokaryotes that do not have the complete biosynthetic pathways for all essential cofactors. These organisms are

Genetic and phenotypic diversity of Rhizobium isolates from Southern Ecuador

Directory of Open Access Journals (Sweden)

Roldán Torres-Gutiérrez

Full Text Available ABSTRACT Rhizobium-legume symbioses play relevant roles in agriculture but have not been well studied in Ecuador. The aim of this study was to characterize the genetic and phenotypic diversity of Rhizobium isolates associated with Phaseolus vulgaris from southern Ecuador. Morpho-cultural characterization, biochemical tests and physiological analyses were conducted to authenticate and determine the diversity of bacteria Rhizobium-like isolates. The genetic diversity of the isolates was determined by molecular techniques, which consisted of bacteria DNA extraction and amplification and sequencing of the 16S rRNA gene. The nodulation parameters and nitrogen fixation for P. vulgaris under greenhouse conditions were also assessed to determine the phenotypic diversity among isolates. Furthermore, bacteria indole-acetic-acid production was evaluated by the colorimetric method. Morpho-cultural and biochemical characteristic assessments demonstrated that Rhizobium-like bacteria was associated with the P. vulgaris nodules. The diversity among the isolates, as determined by physiological analyses, revealed the potential of several isolates to grow at different pH values, salinity conditions and temperatures. Partial sequencing of the 16S rRNA gene identified the Rhizobium genus in every sampling site. From a total of 20 aligned sequences, nine species of Rhizobium were identified. Nodule formation and biomass, as well as nitrogen fixation, showed an increase in plant phenotypic parameters, which could be influenced by IAA production, especially for the strains R. mesoamericanum NAM1 and R. leguminosarum bv. viciae COL6. These results demonstrated the efficiency of native symbiotic diazotrophic strains inoculants for legume production. This work can serve as the basis for additional studies of native Rhizobium strains and to help spread the use of biofertilizers in Ecuadorian fields.

Diversity of bacteria and glycosyl hydrolase family 48 genes in cellulolytic consortia enriched from thermophilic biocompost.

Science.gov (United States)

Izquierdo, Javier A; Sizova, Maria V; Lynd, Lee R

2010-06-01

The enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of microbial cellulose degradation. In this work we identify predominant organisms in three cellulolytic enrichment cultures with thermophilic compost as an inoculum. Community structure based on 16S rRNA gene clone libraries featured extensive representation of clostridia from cluster III, with minor representation of clostridial clusters I and XIV and a novel Lutispora species cluster. Our studies reveal different levels of 16S rRNA gene diversity, ranging from 3 to 18 operational taxonomic units (OTUs), as well as variability in community membership across the three enrichment cultures. By comparison, glycosyl hydrolase family 48 (GHF48) diversity analyses revealed a narrower breadth of novel clostridial genes associated with cultured and uncultured cellulose degraders. The novel GHF48 genes identified in this study were related to the novel clostridia Clostridium straminisolvens and Clostridium clariflavum, with one cluster sharing as little as 73% sequence similarity with the closest known relative. In all, 14 new GHF48 gene sequences were added to the known diversity of 35 genes from cultured species.

Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites

Science.gov (United States)

Noda, Satoko; Hongoh, Yuichi; Sato, Tomoyuki; Ohkuma, Moriya

2009-01-01

Background The microbial community in the gut of termites is responsible for the efficient decomposition of recalcitrant lignocellulose. Prominent features of this community are its complexity and the associations of prokaryotes with the cells of cellulolytic flagellated protists. Bacteria in the order Bacteroidales are involved in associations with a wide variety of gut protist species as either intracellular endosymbionts or surface-attached ectosymbionts. In particular, ectosymbionts exhibit distinct morphological patterns of the associations. Therefore, these Bacteroidales symbionts provide an opportunity to investigate not only the coevolutionary relationships with the host protists and their morphological evolution but also how symbiotic associations between prokaryotes and eukaryotes occur and evolve within a complex symbiotic community. Results Molecular phylogeny of 31 taxa of Bacteroidales symbionts from 17 protist genera in 10 families was examined based on 16S rRNA gene sequences. Their localization, morphology, and specificity were also examined by fluorescent in situ hybridizations. Although a monophyletic grouping of the ectosymbionts occurred in three related protist families, the symbionts of different protist genera were usually dispersed among several phylogenetic clusters unique to termite-gut bacteria. Similar morphologies of the associations occurred in multiple lineages of the symbionts. Nevertheless, the symbionts of congeneric protist species were closely related to one another, and in most cases, each host species harbored a unique Bacteroidales species. The endosymbionts were distantly related to the ectosymbionts examined so far. Conclusion The coevolutionary history of gut protists and their associated Bacteroidales symbionts is complex. We suggest multiple independent acquisitions of the Bacteroidales symbionts by different protist genera from a pool of diverse bacteria in the gut community. In this sense, the gut could serve as a

Microbial diversity of the 180 million-year-old Toarcian argillite from Tournemire, France

International Nuclear Information System (INIS)

Urios, Laurent; Marsal, François; Pellegrini, Delphine; Magot, Michel

2012-01-01

Even though the microbiology of various subsurface environments has been investigated for more than 30 a, the microbial diversity of deep argillaceous media is still poorly known. In the context of radioactive waste disposal in clayey formations, the consequence of microbial activity is of concern regarding e.g. the corrosion of metallic components. The purpose of the present work was to characterise the cultivable microbial diversity of different zones of the Toarcian argillite of Tournemire (France) as a preliminary indication regarding the potential of development of microbes in such subterrestrial environments. Cores were drilled in the Excavation Damaged Zone (EDZ) and in the deeper undisturbed zone of the argillite layer, as well as in a zone intersected by a geological fault. Samples from the wall of the drift were also collected. Microorganisms were cultivated from all samples, but the biodiversity differed depending mainly on the O 2 and moisture content. Aerobic bacteria were identified on the wall, in the EDZ and in the wet faulted area, whereas SO 4 -reducing bacteria were isolated from the wet faulted area only. Anaerobic heterotrophs were cultivated from all zones. One hundred and twelve isolates were identified. Small ribosomal subunit gene sequences showed that bacteria of the undisturbed zone were affiliated to three genera only, whereas the three other sampled zones harbour more diverse microflora, including isolates closely related to taxons characterized from subsurface, deep marine and polar environments.

Molecular Phylogenetic Exploration of Bacterial Diversity in a Bakreshwar (India) Hot Spring and Culture of Shewanella-Related Thermophiles

Science.gov (United States)

Ghosh, Dhritiman; Bal, Bijay; Kashyap, V. K.; Pal, Subrata

2003-01-01

The bacterial diversity of a hot spring in Bakreshwar, India, was investigated by a culture-independent approach. 16S ribosomal DNA clones derived from the sediment samples were found to be associated with gamma-Proteobacteria, cyanobacteria, and green nonsulfur and low-GC gram-positive bacteria. The first of the above phylotypes cobranches with Shewanella, a well-known iron reducer. This phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing microorganisms. PMID:12839826

Horizontal gene transfer and bacterial diversity

Indian Academy of Sciences (India)

Unknown

This review discusses how the recent influx of complete chromosomal sequences of various ... enteric bacteria, a great deal of phenotypic diversity among species is ..... E V 1998 Evidence for massive gene exchange between archaeal and ...

Isolation, Identification, Prevalence, and Genetic Diversity of Bacillus cereus Group Bacteria From Different Foodstuffs in Tunisia.

Science.gov (United States)

Gdoura-Ben Amor, Maroua; Siala, Mariam; Zayani, Mariem; Grosset, Noël; Smaoui, Salma; Messadi-Akrout, Feriele; Baron, Florence; Jan, Sophie; Gautier, Michel; Gdoura, Radhouane

2018-01-01

Bacillus cereus group is widespread in nature and foods. Several members of this group are recognized as causing food spoilage and/or health issues. This study was designed to determine the prevalence and genetic diversity of the B. cereus group strains isolated in Tunisia from different foods (cereals, spices, cooked food, fresh-cut vegetables, raw and cooked poultry meats, seafood, canned, pastry, and dairy products). In total, 687 different samples were collected and searched for the presence of the B. cereus group after selective plating on MYP agar and enumeration of each sample. The typical pink-orange uniform colonies surrounded by a zone of precipitate were assumed to belong to the B. cereus group. One typical colony from each sample was subcultured and preserved as cryoculture. Overall, 191 (27.8%) food samples were found positive, giving rise to a collection of 191 B. cereus -like isolates. The concentration of B. cereus -like bacteria were below 10 3 cfu/g or ml in 77.5% of the tested samples. Higher counts (>10 4 cfu/g or ml) were found in 6.8% of samples including fresh-cut vegetables, cooked foods, cereals, and pastry products. To verify whether B. cereus -like isolates belonged to the B. cereus group, a PCR test targeting the sspE gene sequence specific of the group was carried out. Therefore, 174 isolates were found to be positive. Food samples were contaminated as follows: cereals (67.6%), pastry products (46.2%), cooked food (40.8%), cooked poultry meat (32.7%), seafood products (32.3%), spices (28.8%), canned products (16.7%), raw poultry meat (9.4%), fresh-cut vegetables (5.0%), and dairy products (4.8%). The 174 B. cereus isolates were characterized by partial sequencing of the panC gene, using a Sym'Previous software tool to assign them to different phylogenetic groups. Strains were distributed as follows: 61.3, 29.5, 7.5, and 1.7% in the group III, IV, II, and V, respectively. The genetic diversity was further assessed by ERIC-PCR and PFGE

Isolation, Identification, Prevalence, and Genetic Diversity of Bacillus cereus Group Bacteria From Different Foodstuffs in Tunisia

Directory of Open Access Journals (Sweden)

Maroua Gdoura-Ben Amor

2018-03-01

Full Text Available Bacillus cereus group is widespread in nature and foods. Several members of this group are recognized as causing food spoilage and/or health issues. This study was designed to determine the prevalence and genetic diversity of the B. cereus group strains isolated in Tunisia from different foods (cereals, spices, cooked food, fresh-cut vegetables, raw and cooked poultry meats, seafood, canned, pastry, and dairy products. In total, 687 different samples were collected and searched for the presence of the B. cereus group after selective plating on MYP agar and enumeration of each sample. The typical pink-orange uniform colonies surrounded by a zone of precipitate were assumed to belong to the B. cereus group. One typical colony from each sample was subcultured and preserved as cryoculture. Overall, 191 (27.8% food samples were found positive, giving rise to a collection of 191 B. cereus-like isolates. The concentration of B. cereus-like bacteria were below 103 cfu/g or ml in 77.5% of the tested samples. Higher counts (>104 cfu/g or ml were found in 6.8% of samples including fresh-cut vegetables, cooked foods, cereals, and pastry products. To verify whether B. cereus-like isolates belonged to the B. cereus group, a PCR test targeting the sspE gene sequence specific of the group was carried out. Therefore, 174 isolates were found to be positive. Food samples were contaminated as follows: cereals (67.6%, pastry products (46.2%, cooked food (40.8%, cooked poultry meat (32.7%, seafood products (32.3%, spices (28.8%, canned products (16.7%, raw poultry meat (9.4%, fresh-cut vegetables (5.0%, and dairy products (4.8%. The 174 B. cereus isolates were characterized by partial sequencing of the panC gene, using a Sym'Previous software tool to assign them to different phylogenetic groups. Strains were distributed as follows: 61.3, 29.5, 7.5, and 1.7% in the group III, IV, II, and V, respectively. The genetic diversity was further assessed by ERIC-PCR and PFGE

Bacterial diversity in the sediment from polymetallic nodule fields of the Clarion-Clipperton Fracture Zone.

Science.gov (United States)

Wang, Chun-Sheng; Liao, Li; Xu, Hong-Xiang; Xu, Xue-Wei; Wu, Min; Zhu, Li-Zhong

2010-10-01

The Clarion-Clipperton Fracture Zone (CCFZ) is located in the northeastern equatorial Pacific and contains abundant polymetallic nodules. To investigate its bacterial diversity, four libraries of 16S rRNA genes were constructed from sediments of four stations in different areas of the CCFZ. In total, 313 clones sequenced from the 4 libraries were assigned into 14 phylogenetic groups and 1 group of 28 unclassified bacteria. High bacterial diversity was predicted by the rarefaction analysis. The most dominant group overall was Proteobacteria, but there was variation in each library: Gammaproteobacteria was the most dominant group in two libraries, E2005-01 and ES0502, while Alphaproteobacteria and Deltaproteobacteria were the most dominant groups in libraries EP2005-03 and WS0505, respectively. Seven groups, including Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Betaproteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, were common to all four libraries. The remaining minor groups were distributed in libraries with different patterns. Most clones sequenced in this study were clustered with uncultured bacteria obtained from the environment, such as the ocean crust and marine sediment, but only distantly related to isolates. Bacteria involved in the cycling of metals, sulfur and nitrogen were detected, and their relationship with their habitat was discussed. This study sheds light on the bacterial communities associated with polymetallic nodules in the CCFZ and provides primary data on the bacterial diversity of this area.

Characterization of lactic acid bacteria isolated from indigenous dahi ...

African Journals Online (AJOL)

Diversity and density of lactic acid bacteria from indigenous dahi were studied by the determination of morphological, cultural, physiological and biochemical characteristics. A total of 143 isolates were identified phenotypically and divided into three genera: Lactobacillus, Lactococcus and Streptococcus.

Rumen bacteria

International Nuclear Information System (INIS)

McSweeney, C.S.; Denman, S.E.; Mackie, R.I.

2005-01-01

The rumen is the most extensively studied gut community and is characterized by its high population density, wide diversity and complexity of interactions. This complex, mixed microbial culture is comprised of prokaryote organisms including methane-producing archaebacteria, eukaryote organisms, such as ciliate and flagellate protozoa, anaerobic phycomycete fungi and bacteriophage. Bacteria are predominant (up to 10 11 viable cells per g comprising 200 species) but a variety of ciliate protozoa occur widely (10 4 -10 6 /g distributed over 25 genera). The anaerobic fungi are also widely distributed (zoospore population densities of 10 2 -10 4 /g distributed over 5 genera). The occurrence of bacteriophage is well documented (10 7 -10 9 particles/g). This section focuses primarily on the widely used methods for the cultivation and the enumeration of rumen microbes, especially bacteria, which grow under anaerobic conditions. Methods that can be used to measure hydrolytic enzymes (cellulases, xylanases, amylases and proteinases) are also described, along with cell harvesting and fractionation procedures. Brief reference is also made to fungi and protozoa, but detailed explanations for culturing and enumerating these microbes is presented in Chapters 2.4 and 2.5

Improving diversity in cultures of bacteria from an extreme environment

DEFF Research Database (Denmark)

Vester, Jan Kjølhede; Glaring, Mikkel Andreas; Stougaard, Peter

2013-01-01

The ikaite columns in the Ikka Fjord in Greenland represent one of the few permanently cold and alkaline environments on Earth, and the interior of the columns is home to a bacterial community adapted to these extreme conditions. The community is characterized by low cell numbers imbedded in a ca...... the diversity of the culture and many hitherto uncharacterized genera could be brought into culture by extended incubation time. Extended incubation time also gave rise to a more diverse community with a significant number of rare species not detected in the initial community....

Spatio-temporal dynamics of sulfate-reducing bacteria in extreme environment of Rogoznica Lake revealed by 16S rRNA analysis

Science.gov (United States)

Čanković, Milan; Petrić, Ines; Marguš, Marija; Ciglenečki, Irena

2017-08-01

Highly eutrophic and euxinic seawater system of Rogoznica Lake (Croatia) was used as a study site for investigation of distribution, diversity and abundance of sulfate-reducing bacteria (SRB) during stratified conditions in the summer and winter season, by targeting 6 phylogenetic subgroups of SRB. 16S rRNA gene sequences indicated that community cannot be directly related to cultured SRB species but rather that Rogoznica Lake harbors habitat-specific SRB populations associated to bacteria belonging to δ-Proteobacteria with few Firmicutes and Verrucomicrobium-related populations. Clear spatial-temporal shifts in the SRB community structure were observed. Results implied existence of distinct SRB populations between the water column and sediment, as well as higher diversity of the SRB occupying water layer then the ones found in the sediment. Likewise, seasonal variations in populations were observed. While SRB community was more diverse in the winter compared to the summer season in the water layer, situation was opposite in the sediment. Water layer communities seem to be more susceptible to changes of physico-chemical parameters, while those in the sediment have prorogated response to these changes. Results indicate that SRB diversity is still highly underestimated in natural environments, especially in specific habitats such as Rogoznica Lake. Presented data show a complex SRB diversity and distribution supporting the idea that habitat-specific SRB communities are important part of the anaerobic food chain in degradation of organic matter as well as cycling of sulfur and carbon species in the Lake and similar anoxic environment.

Biodiversity of yeasts, lactic acid bacteria and acetic acid bacteria in the fermentation of "Shanxi aged vinegar", a traditional Chinese vinegar.

Science.gov (United States)

Wu, Jia Jia; Ma, Ying Kun; Zhang, Fen Fen; Chen, Fu Sheng

2012-05-01

Shanxi aged vinegar is a famous traditional Chinese vinegar made from several kinds of cereal by spontaneous solid-state fermentation techniques. In order to get a comprehensive understanding of culturable microorganism's diversity present in its fermentation, the indigenous microorganisms including 47 yeast isolates, 28 lactic acid bacteria isolates and 58 acetic acid bacteria isolates were recovered in different fermenting time and characterized based on a combination of phenotypic and genotypic approaches including inter-delta/PCR, PCR-RFLP, ERIC/PCR analysis, as well as 16S rRNA and 26S rRNA partial gene sequencing. In the alcoholic fermentation, the dominant yeast species Saccharomyces (S.) cerevisiae (96%) exhibited low phenotypic and genotypic diversity among the isolates, while Lactobacillus (Lb.) fermentum together with Lb. plantarum, Lb. buchneri, Lb. casei, Pediococcus (P.) acidilactici, P. pentosaceus and Weissella confusa were predominated in the bacterial population at the same stage. Acetobacter (A.) pasteurianus showing great variety both in genotypic and phenotypic tests was the dominant species (76%) in the acetic acid fermentation stage, while the other acetic acid bacteria species including A. senegalensis, A. indonesiensis, A. malorum and A. orientalis, as well as Gluconobacter (G.) oxydans were detected at initial point of alcoholic and acetic acid fermentation stage respectively. Copyright © 2011 Elsevier Ltd. All rights reserved.

Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000

Science.gov (United States)

Hyer, Kenneth; Moyer, Douglas

2003-01-01

(maximum observed concentration of 290,000 colonies/100 milliliters (col/100mL) could occur along the entire length of each stream, and that the samples collected at the downstream monitoring station of each stream were generally representative of the entire upstream reach. Seasonal patterns were observed in the base-flow fecal coliform concentrations of all streams; concentrations were typically highest in the summer and lowest in the winter. Fecal coliform concentrations were lowest during periods of base flow (typically 200?2,000 col/100mL) and increased by 3?4 orders of magnitude during storm events (as high as 700,000 col/100mL). Multiple linear regression models were developed to predict fecal coliform concentrations as a function of streamflow and other water-quality parameters. The source tracking technique provided identification of bacteria contributions from diverse sources that included (but were not limited to) humans, cattle, poultry, horses, dogs, cats, geese, ducks, raccoons, and deer. Seasonal patterns were observed in the contributions of cattle and poultry sources. There were relations between the identified sources of fecal coliform bacteria and the land-use practices within each watershed. There were only minor differences in the distribution of bacteria sources between low-flow periods and high-flow periods. A coupled approach that utilized both a large available source library and a smaller, location-specific source library provided the most success in identifying the unknown E. coli isolates. BST data should provide valuable support and guidance for producing more defendable and scientifically rigorous watershed models. Incorporation of these bacteria-source data into watershed management strategies also should result in the selection of more efficient source-reduction scenarios for improving water quality.

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

Science.gov (United States)

Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

2015-01-01

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

Directory of Open Access Journals (Sweden)

Maryam Yazdani Foshtomi

Full Text Available The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.Our results indicated that bacteria (total and β-AOB showed more spatio-temporal variation than archaea (total and AOA as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal

Detection, phylogeny and population dynamics of syntrophic propionate - oxidizing bacteria in anaerobic granular sludge

NARCIS (Netherlands)

Harmsen, H.J.M.

1996-01-01

The research described this thesis concerns the diversity and phylogeny of syntrophic propionate-oxidizing bacteria and their ecology in granular sludge, from which they were obtained. 16S rRNA was used as a molecular marker to study both the phylogeny and the ecology of these bacteria.

High throughput screening and profiling of high-value carotenoids from a wide diversity of bacteria in surface seawater.

Science.gov (United States)

Asker, Dalal

2018-09-30

Carotenoids are valuable natural colorants that exhibit numerous health promoting properties, and thus are widely used in food, feeds, pharmaceutical and nutraceuticals industries. In this study, we isolated and identified novel microbial sources that produced high-value carotenoids using high throughput screening (HTS). A total of 701 pigmented microbial strains library including marine bacteria and red yeast was constructed. Carotenoids profiling using HPLC-DAD-MS methods showed 88 marine bacterial strains with potential for the production of high-value carotenoids including astaxanthin (28 strains), zeaxanthin (21 strains), lutein (1 strains) and canthaxanthin (2 strains). A comprehensive 16S rRNA gene based phylogenetic analysis revealed that these strains can be classified into 30 species belonging to five bacterial classes (Flavobacteriia, α-Proteobacteria, γ-Proteobacteria, Actinobacteria and Bacilli). Importantly, we discovered novel producers of zeaxanthin and lutein, and a high diversity in both carotenoids and producing microbial strains, which are promising and highly selective biotechnological sources for high-value carotenoids. Copyright © 2018 Elsevier Ltd. All rights reserved.

Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

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Ditte V. Vestergaard

2018-05-01

Full Text Available Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building’s occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers’ homes, and from suburban homes (267 samples in total and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3–V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers’ homes than suburban homes (Wilcoxon rank sum test P < 0.05. Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (ALDEx2 with P < 0.05, including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, and Lactobacillus. Pig stables had significantly lower airborne bacterial diversity than farmers’ homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables

Pig Farmers’ Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes

Science.gov (United States)

Vestergaard, Ditte V.; Holst, Gitte J.; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P. G.

2018-01-01

Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building’s occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers’ homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3–V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers’ homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers’ homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium, and Lactobacillus. Pig stables had significantly lower airborne bacterial diversity than farmers’ homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear

Pig Farmers' Homes Harbor More Diverse Airborne Bacterial Communities Than Pig Stables or Suburban Homes.

Science.gov (United States)

Vestergaard, Ditte V; Holst, Gitte J; Basinas, Ioannis; Elholm, Grethe; Schlünssen, Vivi; Linneberg, Allan; Šantl-Temkiv, Tina; Finster, Kai; Sigsgaard, Torben; Marshall, Ian P G

2018-01-01

Airborne bacterial communities are subject to conditions ill-suited to microbial activity and growth. In spite of this, air is an important transfer medium for bacteria, with the bacteria in indoor air having potentially major consequences for the health of a building's occupants. A major example is the decreased diversity and altered composition of indoor airborne microbial communities as a proposed explanation for the increasing prevalence of asthma and allergies worldwide. Previous research has shown that living on a farm confers protection against development of asthma and allergies, with airborne bacteria suggested as playing a role in this protective effect. However, the composition of this beneficial microbial community has still not been identified. We sampled settled airborne dust using a passive dust sampler from Danish pig stables, associated farmers' homes, and from suburban homes (267 samples in total) and carried out quantitative PCR measurements of bacterial abundance and MiSeq sequencing of the V3-V4 region of bacterial 16S rRNA genes found in these samples. Airborne bacteria had a greater diversity and were significantly more abundant in pig stables and farmers' homes than suburban homes (Wilcoxon rank sum test P < 0.05). Moreover, bacterial taxa previously suggested to contribute to a protective effect had significantly higher relative and absolute abundance in pig stables and farmers' homes than in suburban homes (ALDEx2 with P < 0.05), including Firmicutes, Peptostreptococcaceae, Prevotellaceae, Lachnospiraceae, Ruminococcaceae, Ruminiclostridium , and Lactobacillus . Pig stables had significantly lower airborne bacterial diversity than farmers' homes, and there was no discernable direct transfer of airborne bacteria from stable to home. This study identifies differences in indoor airborne bacterial communities that may be an important component of this putative protective effect, while showing that pig stables themselves do not appear to

Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals

Directory of Open Access Journals (Sweden)

Lukasz eDziewit

2015-03-01

Full Text Available The Lubin underground mine, is one of three mining divisions in the Lubin-Glogow Copper District in Lower Silesia province (Poland. It is the source of polymetallic ore that is rich in copper, silver and several heavy metals. Black shale is also significantly enriched in fossil organic matter in the form of long-chain hydrocarbons, polycyclic aromatic hydrocarbons, organic acids, esters, thiophenes and metalloporphyrins. Biological analyses have revealed that this environment is inhabited by extremophilic bacteria and fungi. Kupfershiefer black shale and samples of water, bottom and mineral sediments from the underground (below 600 m Lubin mine were taken and twenty bacterial strains were isolated and characterized. All exhibited multi-resistant and hypertolerant phenotypes to heavy metals. We analyzed the plasmidome of these strains in order to evaluate the diversity and role of mobile DNA in adaptation to the harsh conditions of the mine environment. Experimental and bioinformatic analyses of 11 extrachromosomal replicons were performed. Three plasmids, including a broad-host-range replicon containing a Tn3 family transposon, carried genes conferring resistance to arsenic, cadmium, cobalt, mercury and zinc. Functional analysis revealed that the resistance modules exhibit host specificity, i.e. they may increase or decrease tolerance to toxic ions depending on the host strain. The other identified replicons showed diverse features. Among them we identified a catabolic plasmid encoding enzymes involved in the utilization of histidine and vanillate, a putative plasmid-like prophage carrying genes responsible for NAD biosynthesis, and two repABC-type plasmids containing virulence-associated genes. These findings provide an unique molecular insight into the pool of extrachromosomal replicons and highlight their role in the biology and adaptation of extremophilic bacteria inhabiting terrestrial deep subsurface.

Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae

Science.gov (United States)

Grose, Julianne H.; Casjens, Sherwood R.

2014-01-01

Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships. PMID:25240328

Quantification and characterization of putative diazotrophic bacteria from forage palm under saline water irrigation

Directory of Open Access Journals (Sweden)

Gabiane dos Reis Antunes

2017-09-01

Full Text Available The aim of this study was to evaluate the density and phenotypical diversity of diazotrophic endophytic bacteria from the forage palm irrigated with different saline water depths. Opuntia stricta (IPA-200016 received five depths of saline water (L1: 80%. ETo; L2: 60%.ETo; L3: 40%; ETo; L4: 20%; ETo and, L5: 0% ETo, where ETo is the reference evapotranspiration. The roots were collected in the field, disinfected, grounded and serial diluted from 10-1 to 10-4. The total concentration of diazotrophic bacteria was determined by the most probable number method (MPN and the isolated bacteria were characterized phenotipically. The concentration of bacteria found in forage palm roots ranged from 0.36 x 104 to 109.89 104 cells per gram of root, with highest occurrence on the 60 and 80% ETo. In the dendrogram of similarity it was possible to observe the formation of 24 phenotypic groups with 100% similarity. All bacteria presented similarity superior to 40%. Among these groups, 14 are rare groups, formed by only a single bacterial isolate. In the Semi-Arid conditions, the forage palm that receives the highest amount of saline water, presents a higher density of putative nitrogen-fixing endophytic bacteria with high phenotypic diversity.

Bacterial diversity in a tropical crude oil-polluted soil undergoing ...

African Journals Online (AJOL)

The bacterial diversity in a tropical soil experimentally polluted with crude oil during a 57 days bioremediation was investigated in five 1 m2 plots using total culturable hydrocarbon utilizing bacteria, heterotrophic bacteria and gas chromatographic analyses. Four out of the five experimental plots received each 4 L of Bonny ...

Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria

KAUST Repository

Ross, Avena C.

2013-01-23

Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multimodule skipping and iteration. Preliminary biochemical analysis of the N-terminal nonribosomal peptide synthetase module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N terminus. © 2012 American Chemical Society.

Biosynthetic multitasking facilitates thalassospiramide structural diversity in marine bacteria

KAUST Repository

Ross, Avena C.; Xü , Ying; Lu, Liang; Kersten, Roland D.; Shao, Zongze; Al-Suwailem, Abdulaziz M.; Dorrestein, Pieter C.; Qian, Peiyuan; Moore, Bradley S.

2013-01-01

Thalassospiramides A and B are immunosuppressant cyclic lipopeptides first reported from the marine α-proteobacterium Thalassospira sp. CNJ-328. We describe here the discovery and characterization of an extended family of 14 new analogues from four Tistrella and Thalassospira isolates. These potent calpain 1 protease inhibitors belong to six structure classes in which the length and composition of the acylpeptide side chain varies extensively. Genomic sequence analysis of the thalassospiramide-producing microbes revealed related, genus-specific biosynthetic loci encoding hybrid nonribosomal peptide synthetase/polyketide synthases consistent with thalassospiramide assembly. The bioinformatics analysis of the gene clusters suggests that structural diversity, which ranges from the 803.4 Da thalassospiramide C to the 1291.7 Da thalassospiramide F, results from a complex sequence of reactions involving amino acid substrate channeling and enzymatic multimodule skipping and iteration. Preliminary biochemical analysis of the N-terminal nonribosomal peptide synthetase module from the Thalassospira TtcA megasynthase supports a biosynthetic model in which in cis amino acid activation competes with in trans activation to increase the range of amino acid substrates incorporated at the N terminus. © 2012 American Chemical Society.

Architectural design influences the diversity and structure of the built environment microbiome.

Science.gov (United States)

Kembel, Steven W; Jones, Evan; Kline, Jeff; Northcutt, Dale; Stenson, Jason; Womack, Ann M; Bohannan, Brendan Jm; Brown, G Z; Green, Jessica L

2012-08-01

Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome--the community of microorganisms that live indoors--is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors.

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats

Directory of Open Access Journals (Sweden)

Guido Bonthond

2018-02-01

Full Text Available Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.

Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

Science.gov (United States)

Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

2013-06-01

Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

Salicornia strobilacea (synonym of Halocnemum strobilaceum Grown Under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

Directory of Open Access Journals (Sweden)

Ramona Marasco

2016-08-01

Full Text Available Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the PGP potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth.

Science.gov (United States)

Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J; Fusi, Marco; Bariselli, Paola; Reddy, Muppala; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

2016-01-01

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

KAUST Repository

Marasco, Ramona; Mapelli, Francesca; Rolli, Eleonora; Mosqueira, Maria J.; Fusi, Marco; Bariselli, Paola; Reddy, Muppala P.; Cherif, Ameur; Tsiamis, George; Borin, Sara; Daffonchio, Daniele

2016-01-01

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

Salicornia strobilacea (Synonym of Halocnemum strobilaceum) Grown under Different Tidal Regimes Selects Rhizosphere Bacteria Capable of Promoting Plant Growth

KAUST Repository

Marasco, Ramona

2016-08-22

Halophytes classified under the common name of salicornia colonize salty and coastal environments across tidal inundation gradients. To unravel the role of tide-related regimes on the structure and functionality of root associated bacteria, the rhizospheric soil of Salicornia strobilacea (synonym of Halocnemum strobilaceum) plants was studied in a tidal zone of the coastline of Southern Tunisia. Although total counts of cultivable bacteria did not change in the rhizosphere of plants grown along a tidal gradient, significant differences were observed in the diversity of both the cultivable and uncultivable bacterial communities. This observation indicates that the tidal regime is contributing to the bacterial species selection in the rhizosphere. Despite the observed diversity in the bacterial community structure, the plant growth promoting (PGP) potential of cultivable rhizospheric bacteria, assessed through in vitro and in vivo tests, was equally distributed along the tidal gradient. Root colonization tests with selected strains proved that halophyte rhizospheric bacteria (i) stably colonize S. strobilacea rhizoplane and the plant shoot suggesting that they move from the root to the shoot and (ii) are capable of improving plant growth. The versatility in the root colonization, the overall PGP traits and the in vivo plant growth promotion under saline condition suggest that such beneficial activities likely take place naturally under a range of tidal regimes.

A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria

Science.gov (United States)

Kauffman, Kathryn M.; Hussain, Fatima A.; Yang, Joy; Arevalo, Philip; Brown, Julia M.; Chang, William K.; Vaninsberghe, David; Elsherbini, Joseph; Sharma, Radhey S.; Cutler, Michael B.; Kelly, Libusha; Polz, Martin F.

2018-02-01

The most abundant viruses on Earth are thought to be double-stranded DNA (dsDNA) viruses that infect bacteria. However, tailed bacterial dsDNA viruses (Caudovirales), which dominate sequence and culture collections, are not representative of the environmental diversity of viruses. In fact, non-tailed viruses often dominate ocean samples numerically, raising the fundamental question of the nature of these viruses. Here we characterize a group of marine dsDNA non-tailed viruses with short 10-kb genomes isolated during a study that quantified the diversity of viruses infecting Vibrionaceae bacteria. These viruses, which we propose to name the Autolykiviridae, represent a novel family within the ancient lineage of double jelly roll (DJR) capsid viruses. Ecologically, members of the Autolykiviridae have a broad host range, killing on average 34 hosts in four Vibrio species, in contrast to tailed viruses which kill on average only two hosts in one species. Biochemical and physical characterization of autolykiviruses reveals multiple virion features that cause systematic loss of DJR viruses in sequencing and culture-based studies, and we describe simple procedural adjustments to recover them. We identify DJR viruses in the genomes of diverse major bacterial and archaeal phyla, and in marine water column and sediment metagenomes, and find that their diversity greatly exceeds the diversity that is currently captured by the three recognized families of such viruses. Overall, these data suggest that viruses of the non-tailed dsDNA DJR lineage are important but often overlooked predators of bacteria and archaea that impose fundamentally different predation and gene transfer regimes on microbial systems than on tailed viruses, which form the basis of all environmental models of bacteria-virus interactions.

Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake.

Science.gov (United States)

Qin, H; Han, C; Jin, Z; Wu, L; Deng, H; Zhu, G; Zhong, W

2018-07-01

The aim of this study was to explore the vertical distribution traits of anaerobic ammonium-oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake. The Illumina Miseq-based sequencing and quantitative polymerase chain reactions were utilized to analyse relative abundance of anammox hydrazine synthase (hzsB) gene in comparison with bacterial 16S rRNA genes, anammox bacterial relative abundance (the number of anammox sequences divided by total number of sequences), community composition and diversity in sediments. The relative abundance of hzsB gene at the low-nitrogen (LN) site in the lake sediments showed that the vertical distribution of anammox bacteria increased to a peak, then decreased with increasing depth. Moreover, the relative abundance of hzsB gene at the high-nitrogen site was significantly lower than that at the LN site. Additionally, the community composition results showed that Candidatus Brocadia sp. was the dominant genus. In addition, the anammox bacterial diversity was also site specific. Redundancy analysis showed that the total N and the NH 4 + -N content might be the most important factors affecting anammox bacterial community composition in the studied sites. The results revealed the specific vertical variance of anammox bacterial distribution and community composition in oxic/anoxic sediments of a eutrophic shallow lake. This is the first study to demonstrate that anammox bacteria displayed the particular distribution in freshwater sediments, which implied a strong response to the anthropogenic eutrophication. © 2018 The Society for Applied Microbiology.

New Insight Into the Diversity of SemiSWEET Sugar Transporters and the Homologs in Prokaryotes

Directory of Open Access Journals (Sweden)

Baolei Jia

2018-05-01

Full Text Available Sugars will eventually be exported transporters (SWEETs and SemiSWEETs represent a family of sugar transporters in eukaryotes and prokaryotes, respectively. SWEETs contain seven transmembrane helices (TMHs, while SemiSWEETs contain three. The functions of SemiSWEETs are less studied. In this perspective article, we analyzed the diversity and conservation of SemiSWEETs and further proposed the possible functions. 1,922 SemiSWEET homologs were retrieved from the UniProt database, which is not proportional to the sequenced prokaryotic genomes. However, these proteins are very diverse in sequences and can be classified into 19 clusters when >50% sequence identity is required. Moreover, a gene context analysis indicated that several SemiSWEETs are located in the operons that are related to diverse carbohydrate metabolism. Several proteins with seven TMHs can be found in bacteria, and sequence alignment suggested that these proteins in bacteria may be formed by the duplication and fusion. Multiple sequence alignments showed that the amino acids for sugar translocation are still conserved and coevolved, although the sequences show diversity. Among them, the functions of a few amino acids are still not clear. These findings highlight the challenges that exist in SemiSWEETs and provide future researchers the foundation to explore these uncharted areas.

Molecular Diversity of Lactic Acid Bacteria on Ileum and Coecum Broiler Chicken Fed by Chrysonilia crassa Fermentation

Science.gov (United States)

Nur Jannah, Siti; Khotimah, Husnul; Siti Ferniah, Rejeki; Sugiharto

2018-05-01

The Lactid Acid Bakteria (LAB) are microflora in the digestive tract which has positive roles in poultry’s health. One of the factors diversity of LAB in the gatrointestinal tract are influenced by feeding factor. The purpose of this study was to analyze the LAB diversity in ileum and coecum after being fed on fermented Chrysonilia crassa molecularly. LAB species diversity was analysed to provide a baseline profile of the microbial community database on the ileum and coecum digestive tract of broiler chicken of control (commercial feed) and treatment (feed with Chrysonilia crassa fermentation) by the method of Terminal Restriction Fragment Lenght Polymorphism The calculated values werethe number of phylotypes, relative abundace, Shannon-Wiener diversity index (H’), evennes index (E’), and similarity. Group of LAB detected in the control group were Lactobacillus delbrueckii (180 bp), Lactobacillus sp. (187 bp), Lactobacillus plantarum (572 bp), uncultured bacterium (87 bp) and unidentified (50 bp, 582bp). The result of this study showed that by feeding on the fermented Chrysonilia crassa feed had resulted in the decreasing of LAB diversity, i.e. ileum (0.66), coecum (0.48) compared with commercial feed (control) that was ileum (0.84), coecum (1.05).

Effect of incubation temperatures for inactivation of Escherichia coli and related bacteria after gamma-irradiation

International Nuclear Information System (INIS)

Nakauma, Makoto; Ito, Hitoshi; Tada, Mikiro

2000-01-01

Irradiated fresh meat or fishery products have been expected to store and distribute under refrigerated temperature below 10degC. From previous reports, growth of coliform bacteria in these products were suppressed by gamma-irradiation below expected doses obtained at 30-37degC. This research was performed to observe the irradiation effect on the inactivation of Escherichia coli and related bacteria at different incubation temperatures of 10-40degC on plate agar after irradiation. From this study, D10 values of all strains decreased 17- 45% at 10degC compared with maximum D10 values at 30- 40degC. Radiation sensitivities were related to the ability to grow at low temperatures in which psychrotrophic type E. coli A4-1 indicated most sensitive to radiation, next of Salmonella enteritidis YK-2, E. coli S2, B4 whereas most resistant at Enterobacter agglomerans K3-1. (author)

Effect of incubation temperatures for inactivation of Escherichia coli and related bacteria after gamma-irradiation

Energy Technology Data Exchange (ETDEWEB)

Nakauma, Makoto; Ito, Hitoshi [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment; Tada, Mikiro [Okayama Univ. (Japan). Faculty of Agriculture

2000-09-01

Irradiated fresh meat or fishery products have been expected to store and distribute under refrigerated temperature below 10degC. From previous reports, growth of coliform bacteria in these products were suppressed by gamma-irradiation below expected doses obtained at 30-37degC. This research was performed to observe the irradiation effect on the inactivation of Escherichia coli and related bacteria at different incubation temperatures of 10-40degC on plate agar after irradiation. From this study, D10 values of all strains decreased 17- 45% at 10degC compared with maximum D10 values at 30- 40degC. Radiation sensitivities were related to the ability to grow at low temperatures in which psychrotrophic type E. coli A4-1 indicated most sensitive to radiation, next of Salmonella enteritidis YK-2, E. coli S2, B4 whereas most resistant at Enterobacter agglomerans K3-1. (author)

Methanol removal efficiency and bacterial diversity of an activated carbon biofilter.

Science.gov (United States)

Babbitt, Callie W; Pacheco, Adriana; Lindner, Angela S

2009-12-01

Motivated by the need to establish an economical and environmentally friendly methanol control technology for the pulp and paper industry, a bench-scale activated carbon biofiltration system was developed. This system was evaluated for its performance in removing methanol from an artificially contaminated air stream and characterized for its bacterial diversity over time, under varied methanol loading rates, and in different spatial regions of the filter. The biofilter system, composed of a novel packing mixture, provided an excellent support for growth and activity of methanol-degrading bacteria, resulting in approximately 100% methanol removal efficiency for loading rates of 1-17 g/m(3) packing/h, when operated both with and without inoculum containing enriched methanol-degrading bacteria. Although bacterial diversity and abundance varied over the length of the biofilter, the populations present rapidly formed a stable community that was maintained over the entire 138-day operation of the system and through variable operating conditions, as observed by PCR-DGGE methods that targeted all bacteria as well as specific methanol-oxidizing microorganisms. Phylogenetic analysis of bands excised and sequenced from DGGE gels indicated that the biofilter system supported a diverse community of methanol-degrading bacteria, with high similarity to species in the genera Methylophilus (beta-proteobacteria), Hyphomicrobium and Methylocella (both alpha-proteobacteria).

Marine Protists Are Not Just Big Bacteria.

Science.gov (United States)

Keeling, Patrick J; Campo, Javier Del

2017-06-05

The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern. In part this is a technical challenge - eukaryotic genomes are more difficult to characterize - but eukaryotic adaptations are also more dependent on morphology and behaviour than they are on the metabolic diversity that typifies bacteria, and these cannot be inferred from genomic data as readily as metabolism can be. We therefore cannot simply follow in the methodological footsteps of bacterial ecology and hope for similar success. Understanding microbial eukaryotes will require different approaches, including greater emphasis on taxonomically and trophically diverse model systems. Molecular sequencing will continue to play a role, and advances in environmental sequence tag studies and single-cell methods for genomic and transcriptomics offer particular promise. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bacteria of the genus Endozoicomonas dominate the microbiome of the Mediterranean gorgonian coral Eunicella cavolini

KAUST Repository

Bayer, T

2013-04-08

Forming dense beds that provide the structural basis of a distinct ecosystem, the gorgonian Eunicella cavolini (Octocorallia) is an important species in the Mediterranean Sea. Despite the importance and prevalence of this temperate gorgonian, little is known about its microbial assemblage, although bacteria are well known to be important to hard and soft coral functioning. Here, we used massively parallel pyrosequencing of 16S rRNA genes to determine the composition and relative abundances of bacteria associated with E. cavolini collected from different depths at a site on the French Mediterranean coast. We found that whereas the bacterial assemblages of E. cavolini were distinct and less diverse than those of the surrounding water column, the water depth did not affect the bacterial assemblages of this gorgonian. Our data show that E. cavolini?s microbiome contains only a few shared species and that it is highly dominated by bacteria from the genus Endozoicomonas, a Gammaproteobacteria that is frequently found to associate with marine invertebrates.

Bacteria of the genus Endozoicomonas dominate the microbiome of the Mediterranean gorgonian coral Eunicella cavolini

KAUST Repository

Bayer, T; Arif, C; Ferrier-Pagè s, C; Zoccola, D; Aranda, Manuel; Voolstra, Christian R.

2013-01-01

Forming dense beds that provide the structural basis of a distinct ecosystem, the gorgonian Eunicella cavolini (Octocorallia) is an important species in the Mediterranean Sea. Despite the importance and prevalence of this temperate gorgonian, little is known about its microbial assemblage, although bacteria are well known to be important to hard and soft coral functioning. Here, we used massively parallel pyrosequencing of 16S rRNA genes to determine the composition and relative abundances of bacteria associated with E. cavolini collected from different depths at a site on the French Mediterranean coast. We found that whereas the bacterial assemblages of E. cavolini were distinct and less diverse than those of the surrounding water column, the water depth did not affect the bacterial assemblages of this gorgonian. Our data show that E. cavolini?s microbiome contains only a few shared species and that it is highly dominated by bacteria from the genus Endozoicomonas, a Gammaproteobacteria that is frequently found to associate with marine invertebrates.

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials

Science.gov (United States)

Zhang, Jian; Zeng, Zhi-gang; Chen, Shuai; Sun, Li

2018-04-01

Shinkaia crosnieri is a galatheid crab endemic to the deep-sea hydrothermal systems in the Okinawa Trough. In this study, we systematically analyzed and compared the diversity and metabolic potentials of the microbial communities in different tissues (setae, gill, and intestine) of S. crosnieri by high-throughput sequencing technology and quantitative real-time polymerase chain reaction. Sequence analysis based on the V3-V4 regions of the 16S rRNA gene obtained 408,079 taxon tags, which covered 15 phyla, 22 classes, 32 orders, 42 families, and 25 genera. Overall, the microbial communities in all tissues were dominated by Epsilonproteobacteria and Gammaproteobacteria, of which Epsilonproteobacteria was the largest class and accounted for 85.24% of the taxon tags. In addition, 20 classes of bacteria were discovered for the first time to be associated with S. crosnieri and no archaea were detected. Comparative analysis showed that (i) bacteria from different tissues fell into different groups by β-diversity analysis, (ii) bacterial communities in intestine were similar to that in gill and much more diverse than that in setae, and the sulfur-oxidizing genus Sulfurovum was markedly enriched in intestine and gill. Furthermore, bacteria potentially involved in methane, nitrogen, and metal metabolisms were detected in all samples. The key genes of aprA/dsrA and pmoA involved in sulfate reducing and methane oxidization, respectively, were detected in the gill and gut communities for the first time, and pmoA was significantly more abundant in gill and setae than in intestine. These results provide the first comparative and relatively complete picture of the diversity and metabolic potentials of the bacteria in different tissues of S. crosnieri. These results also indicate that the composition of the microbial communities in hydrothermal fauna changes with time, suggesting the importance of environmental influence.

Reconcilable differences? Human diversity, cultural relativity, and sense of community.

Science.gov (United States)

Townley, Greg; Kloos, Bret; Green, Eric P; Franco, Margarita M

2011-03-01

Sense of community (SOC) is one of the most widely used and studied constructs in community psychology. As proposed by Sarason in (The Psychological sense of community: prospects for a community psychology, Jossey-Bass, San Francisco, 1974), SOC represents the strength of bonding among community members. It is a valuable component of community life, and it has been linked to positive mental health outcomes, citizen participation, and community connectedness. However, promotion of SOC can become problematic in community psychology praxis when it conflicts with other core values proposed to define the field, namely values of human diversity, cultural relativity, and heterogeneity of experience and perspective. Several commentators have noted that promotion of SOC can conflict with multicultural diversity because it tends to emphasize group member similarity and appears to be higher in homogeneous communities. In this paper, we introduce the idea of a community-diversity dialectic as part of praxis and research in community psychology. We argue that systematic consideration of cultural psychology perspectives can guide efforts to address a community-diversity dialectic and revise SOC formulations that ultimately will invigorate community research and action. We provide a working agenda for addressing this dialectic, proposing that systematic consideration of the creative tension between SOC and diversity can be beneficial to community psychology.

[Bacterial diversity within different sections of summer sea-ice samples from the Prydz Bay, Antarctica].

Science.gov (United States)

Ma, Jifei; Du, Zongjun; Luo, Wei; Yu, Yong; Zeng, Yixin; Chen, Bo; Li, Huirong

2013-02-04

In order to assess bacterial abundance and diversity within three different sections of summer sea-ice samples collected from the Prydz Bay, Antarctica. Fluorescence in situ hybridization was applied to determine the proportions of Bacteria in sea-ice. Bacterial community composition within sea ice was analyzed by 16S rRNA gene clone library construction. Correlation analysis was performed between the physicochemical parameters and the bacterial diversity and abundance within sea ice. The result of fluorescence in situ hybridization shows that bacteria were abundant in the bottom section, and the concentration of total organic carbon, total organic nitrogen and phosphate may be the main factors for bacterial abundance. In bacterial 16S rRNA gene libraries of sea-ice, nearly complete 16S rRNA gene sequences were grouped into three distinct lineages of Bacteria (gamma-Proteobacteria, alpha-Proteobacteria and Bacteroidetes). Most clone sequences were related to cultured bacterial isolates from the marine environment, arctic and Antarctic sea-ice with high similarity. The member of Bacteroidetes was not detected in the bottom section of sea-ice. The bacterial communities within sea-ice were little heterogeneous at the genus-level between different sections, and the concentration of NH4+ may cause this distribution. The number of bacteria was abundant in the bottom section of sea-ice. Gamma-proteobacteria was the dominant bacterial lineage in sea-ice.

Commensal bacteria and MAMPs are necessary for stress-induced increases in IL-1β and IL-18 but not IL-6, IL-10 or MCP-1.

Directory of Open Access Journals (Sweden)

Thomas Maslanik

Full Text Available Regular interactions between commensal bacteria and the enteric mucosal immune environment are necessary for normal immunity. Alterations of the commensal bacterial communities or mucosal barrier can disrupt immune function. Chronic stress interferes with bacterial community structure (specifically, α-diversity and the integrity of the intestinal barrier. These interferences can contribute to chronic stress-induced increases in systemic IL-6 and TNF-α. Chronic stress, however, produces many physiological changes that could indirectly influence immune activity. In addition to IL-6 and TNF-α, exposure to acute stressors upregulates a plethora of inflammatory proteins, each having unique synthesis and release mechanisms. We therefore tested the hypothesis that acute stress-induced inflammatory protein responses are dependent on the commensal bacteria, and more specifically, lipopolysaccharide (LPS shed from Gram-negative intestinal commensal bacteria. We present evidence that both reducing commensal bacteria using antibiotics and neutralizing LPS using endotoxin inhibitor (EI attenuates increases in some (inflammasome dependent, IL-1 and IL-18, but not all (inflammasome independent, IL-6, IL-10, and MCP-1 inflammatory proteins in the blood of male F344 rats exposed to an acute tail shock stressor. Acute stress did not impact α- or β- diversity measured using 16S rRNA diversity analyses, but selectively reduced the relative abundance of Prevotella. These findings indicate that commensal bacteria contribute to acute stress-induced inflammatory protein responses, and support the presence of LPS-mediated signaling in stress-evoked cytokine and chemokine production. The selectivity of the commensal bacteria in stress-evoked IL-1β and IL-18 responses may implicate the inflammasome in this response.

Diversity and phylogenetic analyses of bacteria from a shallow-water hydrothermal vent in Milos island (Greece).

Science.gov (United States)

Giovannelli, Donato; d'Errico, Giuseppe; Manini, Elena; Yakimov, Michail; Vetriani, Costantino

2013-01-01

Studies of shallow-water hydrothermal vents have been lagging behind their deep-sea counterparts. Hence, the importance of these systems and their contribution to the local and regional diversity and biogeochemistry is unclear. This study analyzes the bacterial community along a transect at the shallow-water hydrothermal vent system of Milos island, Greece. The abundance and biomass of the prokaryotic community is comparable to areas not affected by hydrothermal activity and was, on average, 1.34 × 10(8) cells g(-1). The abundance, biomass and diversity of the prokaryotic community increased with the distance from the center of the vent and appeared to be controlled by the temperature gradient rather than the trophic conditions. The retrieved 16S rRNA gene fragments matched sequences from a variety of geothermal environments, although the average similarity was low (94%), revealing previously undiscovered taxa. Epsilonproteobacteria constituted the majority of the population along the transect, with an average contribution to the total diversity of 60%. The larger cluster of 16S rRNA gene sequences was related to chemolithoautotrophic Sulfurovum spp., an Epsilonproteobacterium so far detected only at deep-sea hydrothermal vents. The presence of previously unknown lineages of Epsilonproteobacteria could be related to the abundance of organic matter in these systems, which may support alternative metabolic strategies to chemolithoautotrophy. The relative contribution of Gammaproteobacteria to the Milos microbial community increased along the transect as the distance from the center of the vent increased. Further attempts to isolate key species from these ecosystems will be critical to shed light on their evolution and ecology.

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.

Science.gov (United States)

Bosi, Emanuele; Fondi, Marco; Orlandini, Valerio; Perrin, Elena; Maida, Isabel; de Pascale, Donatella; Tutino, Maria Luisa; Parrilli, Ermenegilda; Lo Giudice, Angelina; Filloux, Alain; Fani, Renato

2017-01-17

Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis. Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds. This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a

Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

Directory of Open Access Journals (Sweden)

Mu Peng

2015-09-01

Full Text Available Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

Science.gov (United States)

Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

2015-09-24

Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

Current strategies for improving food bacteria

NARCIS (Netherlands)

Kuipers, O P; Buist, Girbe; Kok, Jan

2000-01-01

Novel concepts and methodologies are emerging that hold great promise for the directed improvement of food-related bacteria, specifically lactic acid bacteria. Also, the battle against food spoilage and pathogenic bacteria can now be fought more effectively. Here we describe recent advances in

Anaplasma marginale major surface protein 1a: a marker of strain diversity with implications for control of bovine anaplasmosis.

Science.gov (United States)

Cabezas-Cruz, Alejandro; de la Fuente, José

2015-04-01

Classification of bacteria is challenging due to the lack of a theory-based framework. In addition, the adaptation of bacteria to ecological niches often results in selection of strains with diverse virulence, pathogenicity and transmission characteristics. Bacterial strain diversity presents challenges for taxonomic classification, which in turn impacts the ability to develop accurate diagnostics and effective vaccines. Over the past decade, the worldwide diversity of Anaplasma marginale, an economically important tick-borne pathogen of cattle, has become apparent. The extent of A. marginale strain diversity, formerly underappreciated, has contributed to the challenges of classification which, in turn, likely impacts the design and development of improved vaccines. Notably, the A. marginale surface protein 1a (MSP1a) is a model molecule for these studies because it serves as a marker for strain identity, is both an adhesin necessary for infection of cells and an immuno-reactive protein and is also an indicator of the evolution of strain diversity. Herein, we discuss a molecular taxonomic approach for classification of A. marginale strain diversity. Taxonomic analysis of this important molecule provides the opportunity to understand A. marginale strain diversity as it relates geographic and ecological factors and to the development of effective vaccines for control of bovine anaplasmosis worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

Phylogenetic Diversity of aprA Genes in Subseafloor Sediments on the Northwestern Pacific Margin off Japan.

Science.gov (United States)

Aoki, Masataka; Kakiuchi, Ryota; Yamaguchi, Takashi; Takai, Ken; Inagaki, Fumio; Imachi, Hiroyuki

2015-01-01

Markedly diverse sequences of the adenosine-5'-phosphosulfate reductase alpha subunit gene (aprA), which encodes a key enzyme in microbial sulfate reduction and sulfur oxidation, were detected in subseafloor sediments on the northwestern Pacific off Japan. The aprA gene sequences were grouped into 135 operational taxonomic units (90% sequence identity), including genes related to putative sulfur-oxidizing bacteria predominantly detected in sulfate-depleted deep sediments. Our results suggest that microbial ecosystems in the subseafloor biosphere have phylogenetically diverse genetic potentials to mediate cryptic sulfur cycles in sediments, even where sulfate is rarely present.

[Analysis of diversity of vaginal microbiota in healthy Chinese women by using DNA-fingerprinting].

Science.gov (United States)

Xiao, Bing-bing; Liao, Qin-ping

2012-04-18

To analyze the diversity of healthy women's vaginal dominant flora in different physiological states with PCR-denaturing gradient gel electrophoresis (PCR-DGGE), to establish the basis for the future study of lower genital tract infections, and to provide a theoretical basis for the development of vaginal probiotics adapted to Chinese females. Women who underwent routine gynecologic examinations in Peking University First Hospital from October 2009 to January 2010 were enrolled, including 30 at reproductive age and 30 at post menopause age. Vaginal samples were collected and then total bacterial DNA was extracted. Universal bacterial primers were used to amplify the V3 region of 16S rDNA gene. PCR products were analyzed by denatured gradient gel electrophoresis (DGGE). Featured bands on DGGE were recovered, cloned and sequenced. Alignment with known sequence was made by using Blast on GenBank to identify bacterial strains so as to analyze the diversity of healthy women's vaginal dominant flora in different physiological states. (1) Vaginal flora in healthy Chinese women at their reproductive age were relatively simple, Lactobacillus were the dominant bacteria. Common bacteria included: Lactobacillus crispatus, Lactobacillus iners,and Lactobacillus gasseri. While L. iners were the dominant vaginal bacteria that could not be recognized by traditional method. (2) Vaginal bacteria in the women at post menopause age were more complex than in those at reproductive age. Common bacteria included: Lactobacillus iners, Lactobacillus crispatus, Escherichia coli, Streptococcus agalactiae, Streptococcus gallolyticus, Veillonella sp., Streptococcus intermedius, Streptococcus anginosus, Prevotella sp., Anaerococcus lactolyticus and Bacteroides fragilis. Based on the DGGE analysis, the most common vaginal bacteria in Chinese healthy women at reproductive age are Lactobacillus crispatus, Lactobacillus iners,and Lactobacillus gasseri. the most common vaginal bacteria in healthy post

The diversity of reproductive parasites among arthropods: Wolbachia do not walk alone

Directory of Open Access Journals (Sweden)

Zhou Liqin

2008-06-01

Full Text Available Abstract Background Inherited bacteria have come to be recognised as important components of arthropod biology. In addition to mutualistic symbioses, a range of other inherited bacteria are known to act either as reproductive parasites or as secondary symbionts. Whilst the incidence of the α-proteobacterium Wolbachia is relatively well established, the current knowledge of other inherited bacteria is much weaker. Here, we tested 136 arthropod species for a range of inherited bacteria known to demonstrate reproductive parasitism, sampling each species more intensively than in past surveys. Results The inclusion of inherited bacteria other than Wolbachia increased the number of infections recorded in our sample from 33 to 57, and the proportion of species infected from 22.8% to 32.4%. Thus, whilst Wolbachia remained the dominant inherited bacterium, it alone was responsible for around half of all inherited infections of the bacteria sampled, with members of the Cardinium, Arsenophonus and Spiroplasma ixodetis clades each occurring in 4% to 7% of all species. The observation that infection was sometimes rare within host populations, and that there was variation in presence of symbionts between populations indicates that our survey will itself underscore incidence. Conclusion This extensive survey demonstrates that at least a third of arthropod species are infected by a diverse assemblage of maternally inherited bacteria that are likely to strongly influence their hosts' biology, and indicates an urgent need to establish the nature of the interaction between non-Wolbachia bacteria and their hosts.

[Composition diversity of lactic acid bacteria (LAB) community Al2 used for alfalfa silage].

Science.gov (United States)

Wang, Xiao-Fen; Gao, Li-Juan; Yang, Hong-Yan; Wang, Wei-Dong; Cui, Zong-Jun

2006-10-01

Alfalfa is the most important forage grass that is difficult to ensile for good quality. Using silage inoculants are the important way for preservation of alfalfa silage. Through continuous restricted subcultivation, a lactic acid bacteria (LAB) community Al2 was selected from well-fermented alfalfa silage. Plate isolation and Denaturing Gradient Gel Electrophoresis (DGGE), construction of 16S rDNA clone library were used to identify the composition diversity of Al2 community, with 7 strains detected, and they were all belonged to Lactobacillus. The composition ratios of the 7 strains were 55.21%, 19.79%, 14.58%, 3.13%, 3.13%, 3.13%, 1.03% according to 16S rDNA clone library. Al2-1i, Al2-2i, Al2-3i, corresponding to L. plantarum (99.9%), L. kimchii (99.4%), L. farciminis (100%) were detected by plate isolation. Among 3 isolates, Al2-1i had the highest ability of dropping pH and producing lactic acid, and the amount of lactic acid was reach to 18g/L at 24h cultivated in MRS media. The ability of dropping pH and producing lactic acid of Al2-3i was the lowest. From DGGE profiles, the dominant strains in Al2 community were L. plantarum and L. kimchii. L. plantarum was detected during the whole process, and L. kimchii was detected in the later phase.

Aging in bacteria, immortality or not-a critical review.

Science.gov (United States)

Gómez, José M G

2010-12-01

Bacteria were traditionally thought to have a symmetrical binary fission without a clear distinction between soma and germ-line, being thus considered as immortal biological entities. Yet it has been recently described that bacteria also undergo replicative aging (RA). That is, they exhibit finite replicative abilities under good conditions to growth. The apparently initial indistinguishability of sibling cells after cytokinesis is broken. After division, the daughter cell that inherits the "old" pole present in the "mother cell" progressively exhibits a decline in its proliferative capacity with increasing cell pole age. This is a clear hallmark and phenotypic manifestation of a bona fide RA phenomenon in toto. While the exact molecular mechanism(s) underlying to this lost of replicative potential are not yet fully understood, the "old pole cell" is considered as an aging parent that in a repeatedly manner is able to produce rejuvenated offspring which inherit a resetting of the biological clock. On the order hand, bacteria exhibit in addition to this "mandatory" RA the dubbed conditional senescence (CS). CS is defined as a decline in cellular viability observed in arrested-growing bacteria populations, a phenomenon apparently not related to RA under growing active conditions. To understand bacterial aging, it is necessary to put it within the sociality-multicellularity framework. This is a new conceptual paradigm that expresses the natural reality of the bacterial world. From this more ecological perspective these bacterial aging phenomena probably should represent an insurance/bethedging anticipative survival strategy. This is underpinned in a self-generation of an appropriate level of populational phenotypic diversity. That is, bacterial aging could be considered a communitarian adaptive response to cope with different environmental stresses and threats. I have highlighted the necessity to construct an integrative conceptual framework to achieve a unified view

[Effect of Elodea nuttallii-immobilized Nitrogen Cycling Bacteria on Nitrogen Removal Mechanism in an Inflow River, Gonghu Bay].

Science.gov (United States)

Han, Hua-yang; Li, Zheng-kui; Wang, Hao; Zhu, Qian

2016-04-15

Undisturbed sediment cores and surface water from Qinshui River in Gonghu Bay were collected to carry out a simulation experiment in our laboratory. The remediation effect of Elodea nuttallii-Immobilized Nitrogen Cycling Bacteria (INCB) was applied in the polluted inflow river. The denitrification rate, ANAMMOX rate and nitrogen microorganism diversity were measured by ¹⁵N isotope pairing technology and high-throughput sequencing technology based on 16S rRNA. The TN, NH₄⁺-N, NO₃⁻-N concentrations were reduced by 72.03%, 46.67% and 76.65% in the treatment with addition of Elodea nuttallii and INCB in our laboratory experiment. Meanwhile, denitrification bacteria and ANAMMOX bacteria had synergistic effect with each other. The denitrification and ANAMMOX rates were increased by 165 µmol (m² · h)⁻¹ and 269.7 µmol · (m² · h)⁻¹, respectively. The diversities of denitrification and ANAMMOX bacteria also increased in our experiment. From the level of major phylum, Proteobacteria, Planctomycetes, Acidobbacteria and Bacteroidetes all increased significantly. The results showed that the Elodea nuttallii-INCB assemblage technology could increase the bio-diversity of nitrogen cycling bacteria and promote the ability of nitrogen removal in Qinshui River.

Real-time PCR quantification and diversity analysis of the functional genes aprA and dsrA of sulfate-reducing bacteria in marine sediments of the Peru continental margin and the Black Sea

Directory of Open Access Journals (Sweden)

Axel eSchippers

2011-12-01

Full Text Available A quantitative, real-time PCR (Q-PCR assay for the functional gene adenosine 5´-phosphosulfate reductase (aprA of sulfate-reducing bacteria (SRB was designed. This assay was applied together with described Q-PCR assays for dissimilatory sulfite reductase (dsrA and the 16S rRNA gene of total Bacteria to marine sediments from the Peru margin (0 – 121 meters below seafloor (mbsf and the Black Sea (0 – 6 mbsf. Clone libraries of aprA show that all isolated sequences originate from SRB showing a close relationship to aprA of characterised species or form a new cluster with only distant relation to aprA of isolated SRB. Below 40 mbsf no aprA genes could be amplified. This finding corresponds with results of the applied new Q-PCR assay for aprA. In contrast to the aprA the dsrA gene could be amplified up to sediment depths of 121 mbsf. Even in such an extreme environment a high diversity of this gene was detected. The 16S rRNA gene copy numbers of total Bacteria were much higher than those of the functional genes at all sediment depths and used to calculate the proportion of SRB to the total Bacteria. The aprA and dsrA copy numbers comprised in average 0.5 - 1 % of the 16S rRNA gene copy numbers of total Bacteria in the sediments up to a depth of ca. 40 mbsf. Depth profiles of the aprA and dsrA copy numbers were almost equal for all sites. Gene copy numbers decreased concomitantly with depth from around 108 / g sediment close to the sediment surface to less than 105 / g sediment at 5 mbsf. In the zone without detectable sulfate in the pore water from ca. 40 – 121 mbsf (Peru margin ODP site 1227, only dsrA (but not aprA was detected with copy numbers of less than 104 / g sediment, comprising ca. 14 % of the 16S rRNA gene copy numbers of total Bacteria. In this zone sulfate might be provided for SRB by anaerobic sulfide oxidation.

Seeing Streptococcus pneumoniae, a Common Killer Bacteria

DEFF Research Database (Denmark)

Kjærgaard, Rikke Schmidt; Andersen, Ebbe Sloth

2014-01-01

Look around you. The diversity and complexity of life on earth is overwhelming and data continues to grow. In our desire to understand and explain everything scientifically from molecular evolution to supernovas we depend on visual representations. This paper investigates visual representations...... of the bacteria Streptococcus pneumoniae by use of ink, watercolours and computer graphics. We propose a novel artistic visual rendering of Streptococcus pneumoniae and ask what the value of these kind of representations are compared to traditional scientific data. We ask if drawings and computer......-assisted representations can add to our scientific knowledge about this dangerous bacteria. Is there still a role for the scientific illustrator in the scientific process and synthesis of scientific knowledge?...

Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea.

Science.gov (United States)

Empadinhas, Nuno; da Costa, Milton S

2011-08-01

A decade ago the compatible solutes mannosylglycerate (MG) and glucosylglycerate (GG) were considered to be rare in nature. Apart from two species of thermophilic bacteria, Thermus thermophilus and Rhodothermus marinus, and a restricted group of hyperthermophilic archaea, the Thermococcales, MG had only been identified in a few red algae. Glucosylglycerate was considered to be even rarer and had only been detected as an insignificant solute in two halophilic microorganisms, a cyanobacterium, as a component of a polysaccharide and of a glycolipid in two actinobacteria. Unlike the hyper/thermophilic MG-accumulating microorganisms, branching close to the root of the Tree of Life, those harbouring GG shared a mesophilic lifestyle. Exceptionally, the thermophilic bacterium Persephonella marina was reported to accumulate GG. However, and especially owing to the identification of the key-genes for MG and GG synthesis and to the escalating numbers of genomes available, a plethora of new organisms with the resources to synthesize these solutes has been recognized. The accumulation of GG as an 'emergency' compatible solute under combined salt stress and nitrogen-deficient conditions now seems to be a disseminated survival strategy from enterobacteria to marine cyanobacteria. In contrast, the thermophilic and extremely radiation-resistant bacterium Rubrobacter xylanophilus is the only actinobacterium known to accumulate MG, and under all growth conditions tested. This review addresses the environmental factors underlying the accumulation of MG, GG and derivatives in bacteria and archaea and their roles during stress adaptation or as precursors for more elaborated macromolecules. The diversity of pathways for MG and GG synthesis as well as those for some of their derivatives is also discussed. The importance of glycerate-derived organic solutes in the microbial world is only now being recognized. Their stress-dependent accumulation and the molecular aspects of their

FECAL COLIFORM BACTERIA AND FACTORS RELATED TO ITS GROWTH AT THE SEKOTONG SHALLOW WELLS, WEST NUSA TENGGARA, INDONESIA

OpenAIRE

Doni Marisi Sinaga; Mark Gregory Robson; Beatrix Trikurnia Gasong; Adonia Getse Halel; Dian Pertiwi

2016-01-01

Background: The poor sanitation and small numbers of households who own toilet in Sekotong regency may relate to the diarrheal events due to the fecal coliform contamination in drinking water. Aim: This paper aims to provide the concentrations of fecal coliform bacteria in shallow well waters and the factors associated to its growth. Method: Fifteen groundwater samples were collected from 5 shallow wells to provide the concentrations of total fecal coliform bacteria (FC), mercury conce...

Oligotrophic bacteria isolated from clinical materials.

OpenAIRE

Tada, Y; Ihmori, M; Yamaguchi, J

1995-01-01

Oligotrophic bacteria (oligotrophs) are microorganisms that grow in extremely nutritionally deficient conditions in which the concentrations of organic substances are low. Many oligotrophic bacteria were isolated from clinical materials including urine, sputum, swabbings of the throat, vaginal discharges, and others. Seventy-seven strains of oligotrophic bacteria from 871 samples of clinical material were isolated. A relatively higher frequency of isolation of oligotrophic bacteria was shown ...

Diversity and abundance of ammonia-oxidizing

NARCIS (Netherlands)

Cardoso, J.F.M.F.; van Bleijswijk, J.D.L.; Witte, H.; van Duyl, F.C.

2013-01-01

We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in the shallow warm-water sponge Halisarca caerulea and the deep cold-water sponges Higginsia thielei and Nodastrella nodastrella. The abundance of AOA and AOB was analysed using catalyzed reporter

Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo--Brazil).

Science.gov (United States)

Cuadrat, Rafael R C; Ferrera, Isabel; Grossart, Hans-Peter; Dávila, Alberto M R

2016-02-01

Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean.

Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain).

Science.gov (United States)

Portillo, Maria del Carmen; Franquès, Judit; Araque, Isabel; Reguant, Cristina; Bordons, Albert

2016-02-16

Epiphytic bacteria on grape berries play a critical role in grape health and quality, which decisively influence the winemaking process. Despite their importance, the bacteria related with grape berry surface remain understudied and most previous work has been based on culture-dependent methods, which offer a limited view of the actual diversity. Herein, we used high-throughput sequencing to investigate the bacterial diversity on the surface from two grape varieties, Grenache and Carignan, and compared them across five vineyards included within the Priorat region (Spain). We could detect up to 14 bacterial phyla with Firmicutes (37.6% Bacillales and 14% Lactobacillales), Proteobacteria (16.8% Pseudomonadales and 11.6% Enterobacteriales) and Actinobacteria (3.4% Actinomycetales) being the most abundant. Bacterial community was different at each vineyard being grape varietal, geographical situation and orientation related with changes in bacterial populations. The most abundant bacterial taxa and those driving differences between the vineyards and grape varietals were identified. This study indicates that bacterial community heterogeneities can be influenced by geographic factors like orientation. Copyright © 2015 Elsevier B.V. All rights reserved.

The relative role of dispersal and local interactions for alpine plant community diversity under simulated climate warming

Energy Technology Data Exchange (ETDEWEB)

Klanderud, K.; Totland, Oe. [Norwegian Univ. of Life Science, Dept. of Ecology and Natural Resource Management, Aas (Norway)

2007-08-15

Most studies on factors determining diversity are conducted in temperate or warm regions, whereas studies in climatically harsh and low productivity areas, such as alpine regions, are rare. We examined the relative roles of seed availability and different biotic and abiotic factors for the diversity of an alpine plant community in southern Norway. Furthermore, because climate warming is predicted to be an important driver of alpine species diversity, we assessed how the relative impacts of dispersal and local interactions on diversity might change under experimental warming (open top chambers, OTCs). Addition of seeds from 27 regional species increased community diversity. The establishment of the species was negatively related both to the diversity of the existing system and the cover of the abundant dwarf shrub Dryas octopetala. These results show that both species dispersal limitation and local biotic interactions are important factors for alpine plant community diversity. Despite relatively harsh environmental conditions and low productivity, competition from the resident vegetation appeared to have a greater role for species establishment and diversity than facilitation and experimental warming. Higher temperature appeared to increase the negative relationship between resident species diversity and species establishment. This may suggest that climate warming can increase the role of interspecific competition for alpine plant community structure, and thus alter the long-term effects of biotic interactions on diversity. (au)

;Evolution of Photosynthesis' (1970), re-examined thirty years later.

Science.gov (United States)

Olson, J M

2001-01-01

I have re-examined my 1970 article 'Evolution of Photosynthesis' (Olson JM, Science 168: 438-446) to see whether any of my original proposals still survive. My original conviction that the evolution of photosynthesis was intimately connected with the origin of life has been replaced with the realization that photosynthesis may have been invented by the Bacteria after their divergence from the Archea. The common ancestor of all extant photosynthetic bacteria and cyanobacteria probably contained bacteriochlorophyll a, rather than chlorophyll a as originally proposed, and may have carried out CO(2) fixation instead of photoassimilation. The first electron donors were probably reduced sulfur compounds and later ferrous iron. The common ancestor of all extant reaction centers was probably similar to the homodimeric RC1 of present-day green sulfur bacteria (Chlorobiaceae) and heliobacteria. In the common ancestor of proteobacteria and cyanobacteria, the gene for the primordial RC1 was apparently duplicated and one copy split into two genes, one for RC2 and the other for a chlorophyll protein similar to CP43 and CP47 in extant cyanobacteria and chloroplasts. Homodimeric RC1 and homodimeric RC2 functioned in series as in the Z-scheme to deliver electrons from Fe(OH)(+) to NADP(+), while RC1 and/or RC2 separately drove cyclic electron flow for the production of ATP. In the line of evolution leading to proteobacteria, RC1 and the chlorophyll protein were lost, but RC2 was retained and became heterodimeric. In the line leading to cyanobacteria, both RC1 and RC2 replaced bacteriochlorophyll a with chlorophyll a and became heterodimeric. Heterodimeric RC2 further coevolved with a Mn-containing complex to utilize water as the electron donor for CO(2) fixation. The chlorophyll-protein was also retained and evolved into CP43 and CP47. Heliobacteria are the nearest photosynthetic relatives of cyanobacteria. The branching order of photosynthetic genes appears to be (1

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...

Thermophilic bacteria in Moroccan hot springs, salt marshes and desert soils

OpenAIRE

Aanniz,Tarik; Ouadghiri,Mouna; Melloul,Marouane; Swings,Jean; Elfahime,Elmostafa; Ibijbijen,Jamal; Ismaili,Mohamed; Amar,Mohamed

2015-01-01

The diversity of thermophilic bacteria was investigated in four hot springs, three salt marshes and 12 desert sites in Morocco. Two hundred and forty (240) thermophilic bacteria were recovered, identified and characterized. All isolates were Gram positive, rod-shaped, spore forming and halotolerant. Based on BOXA1R-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by the genus Bacillus (97.5%) represented by B. licheniformis (119), B. aerius (44), B. sonorensis (33), B. ...

Bacterial diversity shift determined by different diets in the gut of the spotted wing fly Drosophila suzukii is primarily reflected on acetic acid bacteria

KAUST Repository

Vacchini, Violetta

2016-11-25

The pivotal role of diet in shaping gut microbiota has been evaluated in different animal models, including insects. Drosophila flies harbour an inconstant microbiota among which acetic acid bacteria (AAB) are important components. Here, we investigated the bacterial and AAB components of the invasive pest Drosophila suzukii microbiota, by studying the same insect population separately grown on fruit-based or non-fruit artificial diet. AAB were highly prevalent in the gut under both diets (90 and 92% infection rates with fruits and artificial diet, respectively). Fluorescent in situ hybridization and recolonization experiments with green fluorescent protein (Gfp)-labelled strains showed AAB capability to massively colonize insect gut. High-throughput sequencing on 16S rRNA gene indicated that the bacterial microbiota of guts fed with the two diets clustered separately. By excluding AAB-related OTUs from the analysis, insect bacterial communities did not cluster separately according to the diet, suggesting that diet-based diversification of the community is primarily reflected on the AAB component of the community. Diet influenced also AAB alpha-diversity, with separate OTU distributions based on diets. High prevalence, localization and massive recolonization, together with AAB clustering behaviour in relation to diet, suggest an AAB role in the D. suzukii gut response to diet modification. This article is protected by copyright. All rights reserved.

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats.

Science.gov (United States)

de Lange, Orlando; Wolf, Christina; Thiel, Philipp; Krüger, Jens; Kleusch, Christian; Kohlbacher, Oliver; Lahaye, Thomas

2015-11-16

Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Primers That Target Functional Genes of Organohalide-Respiring Bacteria (online first)

NARCIS (Netherlands)

Lu, Y.; Atashgahi, S.; Hug, L.A.; Smidt, H.

2015-01-01

Halogenated organic hydrocarbons are problematic environmental pollutants that can be reductively dehalogenated by organohalide-respiring bacteria (OHRB) in anoxic environments. This energy-conserving process is mediated by reductive dehalogenases (RDases). To amplify the diversity of reductive

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

Energy Technology Data Exchange (ETDEWEB)

Bernstein, Hans C.; Brislawn, Colin J.; Dana, Karl; Flores-Wentz, Tobias; Cory, Alexandra B.; Fansler, Sarah J.; Fredrickson, James K.; Moran, James J.

2017-10-01

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: 1) How does species diversity relate to the rates of primary and heterotrophic productivity? 2) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline Lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope incorporation that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose and acetate, respectively. Bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, energy constraints imposed by changing irradiance over a diel cycle.

Parent and Family Processes Related to ADHD Management in Ethnically Diverse Youth.

Science.gov (United States)

Paidipati, Cynthia P; Brawner, Bridgette; Eiraldi, Ricardo; Deatrick, Janet A

Previous research has shown major disparities in attention deficit hyperactivity disorder (ADHD) for diverse youth across America. We do not fully understand, however, how parent and family processes are related to the identification, care-seeking approaches, treatment preferences, and engagement with care systems and services for youth with ADHD. The present study aimed to explore parent and family processes related to the management of ADHD in racially and ethnically diverse youth. This integrative review was structured with the methodology proposed by Whittemore and Knafl. Three major electronic databases yielded a final sample of 32 articles (24 quantitative, 6 qualitative, and 2 mixed methods). Nine themes emerged within three overarching meta-themes. Understanding the unique perspectives of families from diverse backgrounds is essential for clinicians, researchers, and policymakers, who are dedicated to understanding racial and ethnic perspectives and developing ecologically appropriate and family-based interventions for youth with ADHD.

High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR.

Science.gov (United States)

Blazejak, Anna; Schippers, Axel

2010-05-01

Sequences of members of the bacterial candidate division JS-1 and the classes Anaerolineae and Caldilineae of the phylum Chloroflexi are frequently found in 16S rRNA gene clone libraries obtained from marine sediments. Using a newly designed quantitative, real-time PCR assay, these bacterial groups were jointly quantified in samples from near-surface and deeply buried marine sediments from the Peru margin, the Black Sea, and a forearc basin off the island of Sumatra. In near-surface sediments, sequences of the JS-1 as well as Anaerolineae- and Caldilineae-related Bacteria were quantified with significantly lower 16S rRNA gene copy numbers than the sequences of total Bacteria. In contrast, in deeply buried sediments below approximately 1 m depth, similar quantities of the 16S rRNA gene copies of these specific groups and Bacteria were found. This finding indicates that JS-1 and Anaerolineae- and Caldilineae-related Bacteria might dominate the bacterial community in deeply buried marine sediments and thus seem to play an important ecological role in the deep biosphere.

Diversity and stratification of archaea in a hypersaline microbial mat.

Science.gov (United States)

Robertson, Charles E; Spear, John R; Harris, J Kirk; Pace, Norman R

2009-04-01

The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.

Characterization of lactic acid bacteria isolated from Algerian arid ...

African Journals Online (AJOL)

Diversity and density of lactic acid bacteria isolated from Algerian raw goats\\' milk in arid zones were studied by determination of morphological, cultural, physiological and biochemical characteristics. 206 lactic acid bacterial strains were isolated, with 115 of them belonging to lactic acid cocci and others to the genus, ...

Diversity of organotrophic bacteria, activity of dehydrogenases and urease as well as seed germination and root growth Lepidium sativum, Sorghum saccharatum and Sinapis alba under the influence of polycyclic aromatic hydrocarbons.

Science.gov (United States)

Lipińska, Aneta; Wyszkowska, Jadwiga; Kucharski, Jan

2015-12-01

Polycyclic aromatic hydrocarbons are organic compounds with highly toxic, carcinogenic, and mutagenic properties, which adversely affect the basic biological parameters of the soil, including the count of microorganisms, and the enzymatic activity. In addition to disturbances to the biological activity of the soil, PAHs may also exhibit toxic effects on plants. In view of the above, the study involved testing aimed at the determination of the effects of polycyclic aromatic hydrocarbons in a form of naphthalene, phenanthrene, anthracene and pyrene on the count, colony development (CD) index, ecophysiological (EP) diversity index of organotrophic bacteria, and the activity of soil dehydrogenases and soil urease. Moreover, an attempt was made to determine the soil's resistance based on the activity of the above-listed enzymes, and the effect of polycyclic aromatic hydrocarbons on seed germination and root growth was assessed by Lepidium sativum, Sorghum saccharatum, and Sinapis alba. In addition, the species of bacteria found in a soil subjected to strong pressure of polycyclic aromatic hydrocarbons were isolated. The experiment was performed in a laboratory on samples of loamy sand. Polycyclic aromatic hydrocarbons were introduced into the soil in an amount of 0, 1000, 2000, and 4000 mg kg(-1) of soil dry matter. Germination and growth of cress (L. sativum), white mustard (S. alba), and sweet sorghum (S. saccharatum) were determined using Phytotoxkit tests. It was found that the tested PAHs increased the average colony counts of organotrophic soil bacteria; pyrene did so to the greatest extent (2.2-fold relative to non-contaminated soil), phenanthrene to the smallest extent (1.4-fold relative to non-contaminated soil). None of the PAHs changed the value of the bacterial colony development (CD) index, while anthracene and pyrene increased the value of the eco-physiological (EP) diversity indicator. PAHs lowered the activity of the tested enzymes. The activity of

Extracellular deoxyribonuclease production by periodontal bacteria.

Science.gov (United States)

Palmer, L J; Chapple, I L C; Wright, H J; Roberts, A; Cooper, P R

2012-08-01

Whilst certain bacteria have long been known to secrete extracellular deoxyribonuclease (DNase), the purpose in microbial physiology was unclear. Recently, however, this enzyme has been demonstrated to confer enhanced virulence, enabling bacteria to evade the host's immune defence of extruded DNA/chromatin filaments, termed neutrophil extracellular traps (NETs). As NETs have recently been identified in infected periodontal tissue, the aim of this study was to screen periodontal bacteria for extracellular DNase activity. To determine whether DNase activity was membrane bound or secreted, 34 periodontal bacteria were cultured in broth and on agar plates. Pelleted bacteria and supernatants from broth cultures were analysed for their ability to degrade DNA, with relative activity levels determined using an agarose gel electrophoresis assay. Following culture on DNA-supplemented agar, expression was determined by the presence of a zone of hydrolysis and DNase activity related to colony size. Twenty-seven bacteria, including red and orange complex members Porphyromonas gingivalis, Tannerella forsythia, Fusobacterium nucleatum, Parvimonas micra, Prevotella intermedia, Streptococcus constellatus, Campylobacter rectus and Prevotella nigrescens, were observed to express extracellular DNase activity. Differences in DNase activity were noted, however, when bacteria were assayed in different culture states. Analysis of the activity of secreted DNase from bacterial broth cultures confirmed their ability to degrade NETs. The present study demonstrates, for the first time, that DNase activity is a relatively common property of bacteria associated with advanced periodontal disease. Further work is required to determine the importance of this bacterial DNase activity in the pathogenesis of periodontitis. © 2011 John Wiley & Sons A/S.

Spatial Heterogeneity of Bacteria: Evidence from Hot Composts by Culture-independent Analysis

Directory of Open Access Journals (Sweden)

Yan Guo

2012-07-01

Full Text Available The phylogenetic diversity of the bacteria in hot composting samples collected from three spatial locations was investigated by molecular tools in order to determine the influence of gradient effect on bacterial communities during the thermophilic phase of composting swine manure with rice straw. Total microbial DNA was extracted and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, restriction fragment length polymorphism-screened and sequenced. The superstratum sample had the highest microbial diversity among the three samples which was possibly related to the surrounding conditions of the sample resulting from the location. The results showed that the sequences related to Bacillus sp. were most common in the composts. In superstratum sample, 45 clones (33% and 36 clones (27% were affiliated with the Bacillus sp. and Clostridium sp., respectively; 74 clones (58% were affiliated with the Clostridium sp. in the middle-level sample; 52 clones (40% and 29 clones (23% were affiliated with the Clostridium sp. and Bacillus sp. in substrate sample, respectively. It indicated that the microbial diversity and community in the samples were different for each sampling site, and different locations of the same pile often contained distinct and different microbial communities.

Community diversity of bacteria in digestive tract of mud snail (Bullacta exarata Philippi) and its rearing shoal

Institute of Scientific and Technical Information of China (English)

王国良; 郑天伦; 陆彤霞; 王一农; 於宏; 金珊

2002-01-01

The bacterial flora in the digestive tract of B. exarata Philippi and its rearing shoal were investigated, respectively. A total of 107 strains of heterotrophic bacteria, isolated from crop, stomach and intestine, mainly belong to genera Photobacterium, Bacillus, Pseudomonas and Vibrio. Varieties of bacteria in crop were significantly more than that in stomach and in intestine. A total of 173 strains of bacteria were isolated from the rearing shoal, belonging to 13 genera. The 5 predominant genera are Photobacterium, Bacillus, Pseudomonas, Vibrio and some genera of Enterobacteriaceae. The number of heterotrophic bacteria and Vibrio in rearing shoal changed in line with the alteration of the temperature, and were significantly affected by the use of pesticide.

GENETIC VARIABILITY OF SUGARCANE-ASSOCIATED DIAZOTROPHIC BACTERIA CAPABLE OF INORGANIC PHOSPHATE SOLUBILIZING

OpenAIRE

Lira-Cadete, Luana; Barbosa de Farias, Andreza Raquel; de Souza Ramos, Andresa Priscila; da Costa, Diogo Paes; Freire, Fernando Jose; Kuklinsky-Sobral, Julia

2013-01-01

The sugarcane is a culture of great importance for the Brazilian agriculture. Every year this culture consumes great amounts of nitrogen and phosphate fertilizers. However, the use of plant growth-promoting bacteria can reduce the use of the chemical fertilizers, contributing to the economy and the environment conservation. So, the goal of this study was to select sugarcane-associated diazotrophic bacteria able to solubilize inorganic phosphate and to evaluate the genetic diversity of these b...

Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity

Directory of Open Access Journals (Sweden)

Binu M Tripathi

2016-04-01

Full Text Available There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

Potential role of bacteria packaging by protozoa in the persistence and transmission of pathogenic bacteria

Directory of Open Access Journals (Sweden)

Alix M Denoncourt

2014-05-01

Full Text Available Many pathogenic bacteria live in close association with protozoa. These unicellular eukaryotic microorganisms are ubiquitous in various environments. A number of protozoa such as amoebae and ciliates ingest pathogenic bacteria, package them usually in membrane structures, and then release them into the environment. Packaged bacteria are more resistant to various stresses and are more apt to survive than free bacteria. New evidence indicates that protozoa and not bacteria control the packaging process. It is possible that packaging is more common than suspected and may play a major role in the persistence and transmission of pathogenic bacteria. To confirm the role of packaging in the propagation of infections, it is vital that the molecular mechanisms governing the packaging of bacteria by protozoa be identified as well as elements related to the ecology of this process in order to determine whether packaging acts as a Trojan Horse.

Distribution and diversity of airborne microflora under mangrove forest at sandspit area karachi, pakistan

International Nuclear Information System (INIS)

Nazim, K.; Khan, M.U.; Ali, Q.M.; Ahmed, M.; Shaukat, S.S.; Sherwani, S.K.

2012-01-01

Fungi and bacteria are heterotrophic decomposers that grow on organic matter and occupy various habitats in mangrove forests. This paper deals with the distribution and diversity of air-borne microbiota (fungi and bacteria) under a mangrove forest at Sandspit, Pakistan. A permanent stand was set up at Sandspit to observe the qualitative and quantitative variations throughout the year, using petri plate techniques. During the study, a total of 16 fungal species, viz., Aspergillus niger, A. fumigatus, A. sulphureus, A. terreus, A. wentii, A. flavus, Alternaria alternata, A. maritima, A. porri, Alternaria sp., Rhizopus varians, Mucormucedo, Penicillium sp., P. notatum, Dreshellera biseptata, Exosporiella fungorum, Cladosporium oxysporum and 14420 +- 267 bacterial colonies were recorded from the selected site. The study revealed that the fungi were the major component of airborne microflora in mangrove environment. It was observed that both fungal species and number of bacterial colonies were higher in summer than in winter. It is anticipated that the temperature and salinity of sea-water directly affect the diversity of fungi and bacteria in mangroves environment. The maximum diversity H' (1.906) was recorded in August whereas the minimum H' (1.053) was recorded in March. It is hoped that this research will add to our knowledge pertaining to the distribution and diversity of the airborne microbiota (bacteria and fungi) in mangrove ecosystem. (author)

Sexually transmitted bacteria affect female cloacal assemblages in a wild bird

Science.gov (United States)

White, Joël; Mirleau, Pascal; Danchin, Etienne; Mulard, Hervé; Hatch, Scott A.; Heeb, Phillipp; Wagner, Richard H.

2010-01-01

Sexual transmission is an important mode of disease propagation, yet its mechanisms remain largely unknown in wild populations. Birds comprise an important model for studying sexually transmitted microbes because their cloaca provides a potential for both gastrointestinal pathogens and endosymbionts to become incorporated into ejaculates. We experimentally demonstrate in a wild population of kittiwakes (Rissa tridactyla) that bacteria are transmitted during copulation and affect the composition and diversity of female bacterial communities. We used an anti-insemination device attached to males in combination with a molecular technique (automated ribosomal intergenic spacer analysis) that describes bacterial communities. After inseminations were experimentally blocked, the cloacal communities of mates became increasingly dissimilar. Moreover, female cloacal diversity decreased and the extinction of mate-shared bacteria increased, indicating that female cloacal assemblages revert to their pre-copulatory state and that the cloaca comprises a resilient microbial ecosystem.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

Science.gov (United States)

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

Molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs.

Science.gov (United States)

Li, Hui; Chen, Shuo; Mu, Bo-Zhong; Gu, Ji-Dong

2010-11-01

Anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. Recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. This study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecular ecology analysis. High concentration (5.31-39.2 mg l(-1)) of ammonium was detected in the production water from these oilfields with temperatures between 55°C and 75°C. Both 16S rRNA and hzo molecular biomarkers indicated the occurrence of anammox bacteria in nine out of 17 samples. Most of 16S rRNA gene phylotypes are closely related to the known anammox bacterial genera Candidatus Brocadia, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia, while hzo gene phylotypes are closely related to the genera Candidatus Anammoxoglobus, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia. The total bacterial and anammox bacterial densities were 6.4 ± 0.5 × 10(3) to 2.0 ± 0.18 × 10(6) cells ml(-1) and 6.6 ± 0.51 × 10(2) to 4.9 ± 0.36 × 10(4) cell ml(-1), respectively. The cluster I of 16S rRNA gene sequences showed distant identity (<92%) to the known Candidatus Scalindua species, inferring this cluster of anammox bacteria to be a new species, and a tentative name Candidatus "Scalindua sinooilfield" was proposed. The results extended the existence of anammox bacteria to the high-temperature oil reservoirs.

R&D manpower and technological performance : The impact of demographic and task-related diversity

NARCIS (Netherlands)

Faems, D.L.M.; Subramaniam, A.

2013-01-01

We assess the impact of R&D manpower diversity on firms' technological performance. Relying on insights from two theoretical perspectives on team diversity (i.e. social categorization perspective and information decision-making perspective), we hypothesize that both demographic and task-related

Diversity and transmission of gut bacteria in Atta and Acromyrmex leaf-cutting ants during development

DEFF Research Database (Denmark)

Zhukova, Mariya; Sapountzis, Panagiotis; Schiøtt, Morten

2017-01-01

. To elucidate the extent to which metamorphosis interrupts associations between bacteria and hosts, we analyzed changes in gut microbiota during development and traced the transmission routes of dominant symbionts from the egg to adult stage in the leaf-cutting ants Acromyrmex echinatior and Atta cephalotes...... was the absolute dominant bacterial species across developmental stages in Acromyrmex and we confirmed that Atta lacks Wolbachia also in the immature stages, and had mostly Mollicutes bacteria in the adult worker guts. Wolbachia in Acromyrmex appeared to be transovarially transmitted similar to transmission...... in solitary insects. In contrast, Mollicutes were socially transmitted from old workers to newly emerged callows. We found that larval and pupal guts of both ant species contained Pseudomonas and Enterobacter bacteria that are also found in fungus gardens, but hardly or not in adult workers, suggesting...

Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline.

Science.gov (United States)

Linares-Otoya, Luis; Linares-Otoya, Virginia; Armas-Mantilla, Lizbeth; Blanco-Olano, Cyntia; Crüsemann, Max; Ganoza-Yupanqui, Mayar L; Campos-Florian, Julio; König, Gabriele M; Schäberle, Till F

2017-10-12

The microbiome of three different sites at the Peruvian Pacific coast was analyzed, revealing a lower bacterial biodiversity at Isla Foca than at Paracas and Manglares, with 89 bacterial genera identified, as compared to 195 and 173 genera, respectively. Only 47 of the bacterial genera identified were common to all three sites. In order to obtain promising strains for the putative production of novel antimicrobials, predatory bacteria were isolated from these sampling sites, using two different bait organisms. Even though the proportion of predatory bacteria was only around 0.5% in the here investigated environmental microbiomes, by this approach in total 138 bacterial strains were isolated as axenic culture. 25% of strains showed antibacterial activity, thereby nine revealed activity against clinically relevant methicillin resistant Staphylococcus aureus (MRSA) and three against enterohemorrhagic Escherichia coli (EHEC) strains. Phylogeny and physiological characteristics of the active strains were investigated. First insights into the chemical basis of the antibacterial activity indicated the biosynthetic production of the known compounds ariakemicin, kocurin, naphthyridinomycin, pumilacidins, resistomycin, and surfactin. However, most compounds remained elusive until now. Hence, the obtained results implicate that the microbiome present at the various habitats at the Peruvian coastline is a promising source for heterotrophic bacterial strains showing high potential for the biotechnological production of antibiotics.

Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline

Directory of Open Access Journals (Sweden)

Luis Linares-Otoya

2017-10-01

Full Text Available The microbiome of three different sites at the Peruvian Pacific coast was analyzed, revealing a lower bacterial biodiversity at Isla Foca than at Paracas and Manglares, with 89 bacterial genera identified, as compared to 195 and 173 genera, respectively. Only 47 of the bacterial genera identified were common to all three sites. In order to obtain promising strains for the putative production of novel antimicrobials, predatory bacteria were isolated from these sampling sites, using two different bait organisms. Even though the proportion of predatory bacteria was only around 0.5% in the here investigated environmental microbiomes, by this approach in total 138 bacterial strains were isolated as axenic culture. 25% of strains showed antibacterial activity, thereby nine revealed activity against clinically relevant methicillin resistant Staphylococcus aureus (MRSA and three against enterohemorrhagic Escherichia coli (EHEC strains. Phylogeny and physiological characteristics of the active strains were investigated. First insights into the chemical basis of the antibacterial activity indicated the biosynthetic production of the known compounds ariakemicin, kocurin, naphthyridinomycin, pumilacidins, resistomycin, and surfactin. However, most compounds remained elusive until now. Hence, the obtained results implicate that the microbiome present at the various habitats at the Peruvian coastline is a promising source for heterotrophic bacterial strains showing high potential for the biotechnological production of antibiotics.

Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments

Science.gov (United States)

Hewson, Ian; Fuhrman, Jed A.

2007-05-01

Viruses are hypothesized to maintain diversity in microbial assemblages by regulating the abundance of dominant competitors and thereby allowing less-dominant competitors to persist in assemblages; however, there have been few empirical data sets to support this idea. In this study, we examined the relationship between the ratio of viral abundance to bacterial abundance, viral production, and the relative richness and diversity of bacterial assemblage fingerprints, in samples taken from geographically widespread locations (North Pacific gyre, the Amazon River plume and adjacent North Atlantic gyre, Gulf of Mexico, Southern California Bight and Arafura—Coral Seas) which are oligo- to mesotrophic. Bacterial assemblage richness and diversity as measured by automated rRNA intergenic spacer (ARISA) fingerprinting were significantly and positively correlated with the ratio of virus abundance to bacteria abundance (VBR) and to the rate of virus production only in the oligotrophic North Pacific gyre. ARISA fingerprint richness/diversity were not significantly correlated to viral parameters when assessed across all samples in surface waters, suggesting there is not a singular global quantitative relationship between viral pressure and host diversity within well evolved host/virus systems in different geographic locations in plankton. In sediments off Southern California, viral parameters significantly and negatively correlated with ARISA diversity, suggesting strong viral interactions in this habitat. To examine covariation of viral parameters and the relative abundance and diversity of rarer bacterial taxa (i.e., less-dominant competitor), the richness and diversity of diazotroph communities was measured using terminal restriction fragment length polymorphism (TRFLP) of a portion ( nifH) of the nitrogenase gene. The richness and diversity of diazotrophic communities were significantly and negatively correlated with viral parameters across all locations. Since diazotrophs

Diverse bacteria isolated from microtherm oil-production water.

Science.gov (United States)

Sun, Ji-Quan; Xu, Lian; Zhang, Zhao; Li, Yan; Tang, Yue-Qin; Wu, Xiao-Lei

2014-02-01

In total, 435 pure bacterial strains were isolated from microtherm oil-production water from the Karamay Oilfield, Xinjiang, China, by using four media: oil-production water medium (Cai medium), oil-production water supplemented with mineral salt medium (CW medium), oil-production water supplemented with yeast extract medium (CY medium), and blood agar medium (X medium). The bacterial isolates were affiliated with 61 phylogenetic groups that belong to 32 genera in the phyla Actinobacteria, Firmicutes, and Proteobacteria. Except for the Rhizobium, Dietzia, and Pseudomonas strains that were isolated using all the four media, using different media led to the isolation of bacteria with different functions. Similarly, nonheme diiron alkane monooxygenase genes (alkB/alkM) also clustered according to the isolation medium. Among the bacterial strains, more than 24 % of the isolates could use n-hexadecane as the sole carbon source for growth. For the first time, the alkane-degrading ability and alkB/alkM were detected in Rhizobium, Rhodobacter, Trichococcus, Micrococcus, Enterococcus, and Bavariicoccus strains, and the alkM gene was detected in Firmicutes strains.

Occurrence, diversity and community structure of culturable atrazine degraders in industrial and agricultural soils exposed to the herbicide in Shandong Province, P.R. China.

Science.gov (United States)

Bazhanov, Dmitry P; Li, Chengyun; Li, Hongmei; Li, Jishun; Zhang, Xinjian; Chen, Xiangfeng; Yang, Hetong

2016-11-08

Soil populations of bacteria rapidly degrading atrazine are critical to the environmental fate of the herbicide. An enrichment bias from the routine isolation procedure prevents studying the diversity of atrazine degraders. In the present work, we analyzed the occurrence, diversity and community structure of soil atrazine-degrading bacteria based on their direct isolation. Atrazine-degrading bacteria were isolated by direct plating on a specially developed SM agar. The atrazine degradation genes trzN and atzABC were detected by multiplex PCR. The diversity of atrazine degraders was characterized by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) genotyping followed by 16S rRNA gene phylogenetic analysis. The occurrence of atrazine-degrading bacteria was also assessed by conventional PCR targeting trzN and atzABC in soil DNA. A total of 116 atrazine-degrading isolates were recovered from bulk and rhizosphere soils sampled near an atrazine factory and from geographically distant maize fields. Fifteen genotypes were distinguished among 56 industrial isolates, with 13 of them representing eight phylogenetic groups of the genus Arthrobacter. The remaining two were closely related to Pseudomonas alcaliphila and Gulosibacter molinativorax and constituted major components of the atrazine-degrading community in the most heavily contaminated industrial plantless soil. All isolates from the adjacent sites inhabited by cogon grass or common reed were various Arthrobacter spp. with a strong prevalence of A. aurescens group. Only three genotypes were distinguished among 60 agricultural strains. Genetically similar Arthrobacter ureafaciens bacteria which occurred as minor inhabitants of cogon grass roots in the industrial soil were ubiquitous and predominant atrazine degraders in the maize rhizosphere. The other two genotypes represented two distant Nocardioides spp. that were specific to their geographic origins. Direct plating on SM agar enabled rapid isolation

Properties and biotechnological applications of ice-binding proteins in bacteria.

Science.gov (United States)

Cid, Fernanda P; Rilling, Joaquín I; Graether, Steffen P; Bravo, Leon A; Mora, María de La Luz; Jorquera, Milko A

2016-06-01

Ice-binding proteins (IBPs), such as antifreeze proteins (AFPs) and ice-nucleating proteins (INPs), have been described in diverse cold-adapted organisms, and their potential applications in biotechnology have been recognized in various fields. Currently, both IBPs are being applied to biotechnological processes, primarily in medicine and the food industry. However, our knowledge regarding the diversity of bacterial IBPs is limited; few studies have purified and characterized AFPs and INPs from bacteria. Phenotypically verified IBPs have been described in members belonging to Gammaproteobacteria, Actinobacteria and Flavobacteriia classes, whereas putative IBPs have been found in Gammaproteobacteria, Alphaproteobacteria and Bacilli classes. Thus, the main goal of this minireview is to summarize the current information on bacterial IBPs and their application in biotechnology, emphasizing the potential application in less explored fields such as agriculture. Investigations have suggested the use of INP-producing bacteria antagonists and AFPs-producing bacteria (or their AFPs) as a very attractive strategy to prevent frost damages in crops. UniProt database analyses of reported IBPs (phenotypically verified) and putative IBPs also show the limited information available on bacterial IBPs and indicate that major studies are required. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

Summary 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. PMID:21936882

Bacterial diversity in water injection systems of Brazilian offshore oil platforms.

Science.gov (United States)

Korenblum, Elisa; Valoni, Erika; Penna, Mônica; Seldin, Lucy

2010-01-01

Biogenic souring and microbial-influenced corrosion is a common scenario in water-flooded petroleum reservoirs. Water injection systems are continuously treated to control bacterial contamination, but some bacteria that cause souring and corrosion can persist even after different treatments have been applied. Our aim was to increase our knowledge of the bacterial communities that persist in the water injection systems of three offshore oil platforms in Brazil. To achieve this goal, we used a culture-independent molecular approach (16S ribosomal RNA gene clone libraries) to analyze seawater samples that had been subjected to different treatments. Phylogenetic analyses revealed that the bacterial communities from the different platforms were taxonomically different. A predominance of bacterial clones affiliated with Gammaproteobacteria, mostly belonging to the genus Marinobacter (60.7%), were observed in the platform A samples. Clones from platform B were mainly related to the genera Colwellia (37.9%) and Achromobacter (24.6%), whereas clones obtained from platform C were all related to unclassified bacteria. Canonical correspondence analyses showed that different treatments such as chlorination, deoxygenation, and biocide addition did not significantly influence the bacterial diversity in the platforms studied. Our results demonstrated that the injection water used in secondary oil recovery procedures contained potentially hazardous bacteria, which may ultimately cause souring and corrosion.

Reduced Oral Microbial Diversity in Individuals Harbor Periodontal Diseases

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Jinghua Sun

2012-02-01

Full Text Available Introduction: Bacteria colonize a variety of surfaces of the hu-man body. The bacterial diversity in the oral cavity is estimated to be more than 700 different species. The oral cavity is home to microbial communities, with important implications for human health and disease. Oral microbial flora is responsible for two major human infectious diseases of the oral cavity, dental caries and periodontal diseases. From the clinical samples, previously, using polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE technique, we found a significantly greater diversity of oral microbes in caries-free individuals compared with caries-active individuals. The hypothesis: We hypothesize that a greater diversity of indigenous bacteria inhabits a healthy oral environment, and that a sig-nificant proportion of oral biota may be absent, suppressed, or replaced in a periodontal diseases environment. Evaluation of the hypothesis: The microbiota undergoes a transition from a commensal to a pathogenic relationship with the host due to factors that trigger a shift in the proportions of resident microorganisms. If our hypothesis is true, many techniques which were used to detect the oral bacterial diversity can be used in diagnosis and prognosis of periodontal diseases.

Shifts in indigenous culture relate to forest tree diversity: a case study from the Tsimane’, Bolivian Amazon

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Guèze, Maximilien; Luz, Ana Catarina; Paneque-Gálvez, Jaime; Macía, Manuel J.; Orta-Martínez, Martí; Pino, Joan; Reyes-García, Victoria

2015-01-01

Understanding how indigenous peoples’ management practices relate to biological diversity requires addressing contemporary changes in indigenous peoples’ way of life. This study explores the association between cultural change among a Bolivian Amazonian indigenous group, the Tsimane’, and tree diversity in forests surrounding their villages. We interviewed 86 informants in six villages about their level of attachment to traditional Tsimane’ values, our proxy for cultural change. We estimated tree diversity (Fisher’s Alpha index) by inventorying trees in 48 0.1-ha plots in old-growth forests distributed in the territory of the same villages. We used multivariate models to assess the relation between cultural change and alpha tree diversity. Cultural change was associated with alpha tree diversity and the relation showed an inverted U-shape, thus suggesting that tree alpha diversity peaked in villages undergoing intermediate cultural change. Although the results do not allow for testing the direction of the relation, we propose that cultural change relates to tree diversity through the changes in practices and behaviors that affect the traditional ecological knowledge of Tsimane’ communities; further research is needed to determine the causality. Our results also find support in the intermediate disturbance hypothesis, and suggest that indigenous management can be seen as an intermediate form of anthropogenic disturbance affecting forest communities in a subtle, non-destructive way. PMID:26097240

Shifts in indigenous culture relate to forest tree diversity: a case study from the Tsimane', Bolivian Amazon.

Science.gov (United States)

Guèze, Maximilien; Luz, Ana Catarina; Paneque-Gálvez, Jaime; Macía, Manuel J; Orta-Martínez, Martí; Pino, Joan; Reyes-García, Victoria

2015-06-01

Understanding how indigenous peoples' management practices relate to biological diversity requires addressing contemporary changes in indigenous peoples' way of life. This study explores the association between cultural change among a Bolivian Amazonian indigenous group, the Tsimane', and tree diversity in forests surrounding their villages. We interviewed 86 informants in six villages about their level of attachment to traditional Tsimane' values, our proxy for cultural change. We estimated tree diversity (Fisher's Alpha index) by inventorying trees in 48 0.1-ha plots in old-growth forests distributed in the territory of the same villages. We used multivariate models to assess the relation between cultural change and alpha tree diversity. Cultural change was associated with alpha tree diversity and the relation showed an inverted U-shape, thus suggesting that tree alpha diversity peaked in villages undergoing intermediate cultural change. Although the results do not allow for testing the direction of the relation, we propose that cultural change relates to tree diversity through the changes in practices and behaviors that affect the traditional ecological knowledge of Tsimane' communities; further research is needed to determine the causality. Our results also find support in the intermediate disturbance hypothesis, and suggest that indigenous management can be seen as an intermediate form of anthropogenic disturbance affecting forest communities in a subtle, non-destructive way.

Diversity of phytases in the rumen.

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Nakashima, Brenda A; McAllister, Tim A; Sharma, Ranjana; Selinger, L Brent

2007-01-01

Examples of a new class of phytase related to protein tyrosine phosphatases (PTP) were recently isolated from several anaerobic bacteria from the rumen of cattle. In this study, the diversity of PTP-like phytase gene sequences in the rumen was surveyed by using the polymerase chain reaction (PCR). Two sets of degenerate primers were used to amplify sequences from rumen fluid total community DNA and genomic DNA from nine bacterial isolates. Four novel PTP-like phytase sequences were retrieved from rumen fluid, whereas all nine of the anaerobic bacterial isolates investigated in this work contained PTP-like phytase sequences. One isolate, Selenomonas lacticifex, contained two distinct PTP-like phytase sequences, suggesting that multiple phytate hydrolyzing enzymes are present in this bacterium. The degenerate primer and PCR conditions described here, as well as novel sequences obtained in this study, will provide a valuable resource for future studies on this new class of phytase. The observed diversity of microbial phytases in the rumen may account for the ability of ruminants to derive a significant proportion of their phosphorus requirements from phytate.

Temporal variability of the bioaerosol background at a subway station: concentration level, size distribution, and diversity of airborne bacteria.

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Dybwad, Marius; Skogan, Gunnar; Blatny, Janet Martha

2014-01-01

Naturally occurring bioaerosol environments may present a challenge to biological detection-identification-monitoring (BIODIM) systems aiming at rapid and reliable warning of bioterrorism incidents. One way to improve the operational performance of BIODIM systems is to increase our understanding of relevant bioaerosol backgrounds. Subway stations are enclosed public environments which may be regarded as potential bioterrorism targets. This study provides novel information concerning the temporal variability of the concentration level, size distribution, and diversity of airborne bacteria in a Norwegian subway station. Three different air samplers were used during a 72-h sampling campaign in February 2011. The results suggested that the airborne bacterial environment was stable between days and seasons, while the intraday variability was found to be substantial, although often following a consistent diurnal pattern. The bacterial levels ranged from not detected to 10(3) CFU m(-3) and generally showed increased levels during the daytime compared to the nighttime levels, as well as during rush hours compared to non-rush hours. The airborne bacterial levels showed rapid temporal variation (up to 270-fold) on some occasions, both consistent and inconsistent with the diurnal profile. Airborne bacterium-containing particles were distributed between different sizes for particles of >1.1 μm, although ∼50% were between 1.1 and 3.3 μm. Anthropogenic activities (mainly passengers) were demonstrated as major sources of airborne bacteria and predominantly contributed 1.1- to 3.3-μm bacterium-containing particles. Our findings contribute to the development of realistic testing and evaluation schemes for BIODIM equipment by providing information that may be used to simulate operational bioaerosol backgrounds during controlled aerosol chamber-based challenge tests with biological threat agents.

Temporal Variability of the Bioaerosol Background at a Subway Station: Concentration Level, Size Distribution, and Diversity of Airborne Bacteria

Science.gov (United States)

Dybwad, Marius; Skogan, Gunnar

2014-01-01

Naturally occurring bioaerosol environments may present a challenge to biological detection-identification-monitoring (BIODIM) systems aiming at rapid and reliable warning of bioterrorism incidents. One way to improve the operational performance of BIODIM systems is to increase our understanding of relevant bioaerosol backgrounds. Subway stations are enclosed public environments which may be regarded as potential bioterrorism targets. This study provides novel information concerning the temporal variability of the concentration level, size distribution, and diversity of airborne bacteria in a Norwegian subway station. Three different air samplers were used during a 72-h sampling campaign in February 2011. The results suggested that the airborne bacterial environment was stable between days and seasons, while the intraday variability was found to be substantial, although often following a consistent diurnal pattern. The bacterial levels ranged from not detected to 103 CFU m−3 and generally showed increased levels during the daytime compared to the nighttime levels, as well as during rush hours compared to non-rush hours. The airborne bacterial levels showed rapid temporal variation (up to 270-fold) on some occasions, both consistent and inconsistent with the diurnal profile. Airborne bacterium-containing particles were distributed between different sizes for particles of >1.1 μm, although ∼50% were between 1.1 and 3.3 μm. Anthropogenic activities (mainly passengers) were demonstrated as major sources of airborne bacteria and predominantly contributed 1.1- to 3.3-μm bacterium-containing particles. Our findings contribute to the development of realistic testing and evaluation schemes for BIODIM equipment by providing information that may be used to simulate operational bioaerosol backgrounds during controlled aerosol chamber-based challenge tests with biological threat agents. PMID:24162566

Evaluating primers for profiling anaerobic ammonia oxidizing bacteria within freshwater environments.

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Puntipar Sonthiphand

Full Text Available Anaerobic ammonia oxidizing (anammox bacteria play an important role in transforming ammonium to nitrogen gas and contribute to fixed nitrogen losses in freshwater environments. Understanding the diversity and abundance of anammox bacteria requires reliable molecular tools, and these are not yet well established for these important Planctomycetes. To help validate PCR primers for the detection of anammox bacteria within freshwater ecosystems, we analyzed representative positive controls and selected samples from Grand River and groundwater sites, both from Ontario, Canada. The objectives of this study were to identify a suitable anammox denaturing gradient gel electrophoresis (DGGE fingerprint method by using GC-clamp modifications to existing primers, and to verify the specificity of anammox-specific primers used for DGGE, cloning and qPCR methods. Six primer combinations were tested from four published primer sets (i.e. A438f/A684r, Amx368f/Amx820r, An7f/An1388r, and Pla46/1392r for both direct and nested PCR amplifications. All PCR products were run subsequently on DGGE gels to compare the resulting patterns. Two anammox-specific primer combinations were also used to generate clone libraries and quantify anammox bacterial 16S rRNA genes with qPCR. The primer set A438f/A684r was highly specific to anammox bacteria, provided reliable DGGE fingerprints and generated a high proportion of anammox-related clones. A second primer set (Amx368f/Amx820r was anammox specific, based on clone library analysis, but PCR products from different candidate species of anammox bacteria resolved poorly using DGGE analysis. Both DGGE and cloning results revealed that Ca. Brocadia and an uncharacterized anammox bacterial cluster represented the majority of anammox bacteria found in Grand River sediment and groundwater samples, respectively. Together, our results demonstrate that although Amx368f/Amx820r was useful for anammox-specific qPCR and clone library

Diversity of sulfate-reducing bacteria in a plant using deep geothermal energy

Energy Technology Data Exchange (ETDEWEB)

Alawi, Mashal; Lerm, Stephanie; Wuerdemann, Hilke [Helmholtz-Zentrum Potsdam, GFZ Deutsches GeoForschungsZentrum, Internationales Geothermiezentrum, Potsdam (Germany); Vetter, Alexandra [Helmholtz-Zentrum Potsdam, GFZ Deutsches GeoForschungsZentrum, Organische Geochemie, Potsdam (Germany); Wolfgramm, Markus [Geothermie Neubrandenburg GmbH (GTN), Neubrandenburg (Germany); Seibt, Andrea [BWG Geochemische Beratung GbR, Neubrandenburg (Germany)

2011-06-15

Abstract Enhanced process understanding of engineered geothermal systems is a prerequisite to optimize plant reliability and economy. We investigated microbial, geochemical and mineralogical aspects of a geothermal groundwater system located in the Molasse Basin by fluid analysis. Fluids are characterized by temperatures ranging from 61 C to 103 C, salinities from 600 to 900 mg/l and a dissolved organic carbon content (DOC) between 6.4 to 19.3 mg C/l. The microbial population of fluid samples was analyzed by genetic fingerprinting techniques based on PCR-amplified 16S rRNA- and dissimilatory sulfite reductase genes. Despite of the high temperatures, microbes were detected in all investigated fluids. Fingerprinting and DNA sequencing enabled a correlation to metabolic classes and biogeochemical processes. The analysis revealed a broad diversity of sulfate-reducing bacteria. Overall, the detection of microbes known to be involved in biocorrosion and mineral precipitation indicates that microorganisms could play an important role for the understanding of processes in engineered geothermal systems. (orig.) [German] Die Verbesserung des Prozessverstaendnisses ist eine grundlegende Voraussetzung fuer eine Optimierung der Betriebssicherheit und der Oekonomie geothermischer Anlagen in Bezug auf die Partikelbildung und Korrosion. Daher wurden Prozessfluide einer Anlage im Molassebecken unter mikrobiologischen, geochemischen und mineralogischen Gesichtspunkten untersucht. Die Fluidtemperatur der vor und nach dem Waermetauscher entnommenen Fluide betrug zwischen 103 C und 61 C. Die Salinitaet variierte zwischen 600 und 900 mg/l und der geloeste organische Kohlenstoff (DOC) lag zwischen 6,4 und 19,3 mg C/l. Die mikrobielle Lebensgemeinschaft in der Anlage wurde mithilfe einer genetischen Fingerprinting-Methode charakterisiert. Hierzu wurde das 16S rRNA Gen sowie die fuer sulfatreduzierende Bakterien (SRB) spezifische dissimilatorische Sulfitreduktase untersucht. In allen

Fuzzy species among recombinogenic bacteria

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Fraser Christophe

2005-03-01

Full Text Available Abstract Background It is a matter of ongoing debate whether a universal species concept is possible for bacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form discrete genotypic clusters that can be assigned as species. The most challenging test of whether species can be clearly delineated is provided by analysis of large populations of closely-related, highly recombinogenic, bacteria that colonise the same body site. We have used concatenated sequences of seven house-keeping loci from 770 strains of 11 named Neisseria species, and phylogenetic trees, to investigate whether genotypic clusters can be resolved among these recombinogenic bacteria and, if so, the extent to which they correspond to named species. Results Alleles at individual loci were widely distributed among the named species but this distorting effect of recombination was largely buffered by using concatenated sequences, which resolved clusters corresponding to the three species most numerous in the sample, N. meningitidis, N. lactamica and N. gonorrhoeae. A few isolates arose from the branch that separated N. meningitidis from N. lactamica leading us to describe these species as 'fuzzy'. Conclusion A multilocus approach using large samples of closely related isolates delineates species even in the highly recombinogenic human Neisseria where individual loci are inadequate for the task. This approach should be applied by taxonomists to large samples of other groups of closely-related bacteria, and especially to those where species delineation has historically been difficult, to determine whether genotypic clusters can be delineated, and to guide the definition of species.

Molecular diversity among wild relatives of Cajanus cajan (L.) Millsp ...

African Journals Online (AJOL)

In the present study, four wild relatives of pigeonpea were evaluated using 24 simple sequence repeat (SSR) markers to assess their genetic diversity at molecular level. Each marker, on average, amplified 3.3 alleles with polymorphic information content (PIC) value of 0.53. The dendrogram pattern revealed two distinct ...

Insights into the diversity of eukaryotes in acid mine drainage biofilm communities.

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Baker, Brett J; Tyson, Gene W; Goosherst, Lindsey; Banfield, Jillian F

2009-04-01

Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.

Granuloma Annulare and Morphea: Correlation with Borrelia burgdorferi Infections and Chlamydia-related Bacteria

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Lauri Tolkki

2017-12-01

Full Text Available A retrospective study of 109 skin biopsies with granuloma annulare (GA or morphea histology from patients with suspected tick bite was performed. Biopsies were tested for cutaneous Borrelia burgdorferi DNA using PCR. The same biopsies were analysed for tick-borne novel agents, Chlamydia-related bacteria (members of the Chlamydiales order, using a PCR-based method. Borrelia DNA was detected in 7/73 (9.6% biopsies with GA and in 1/36 (2.8 % biopsies with morphea, while Chlamydiales DNA was found in 53/73 (72.6% biopsies with GA and 25/34 (73.4% biopsies with morphea. All Borrelia DNA-positive GA samples were also positive for Chlamydiales DNA. The Chlamydiales sequences detected in GA were heterogeneous and contained Waddliaceae and Rhabdochlamydiaceae bacteria, which are also present in Ixodes ricinus ticks, while the Chlamydiales sequences detected in morphea closely resembled those found in healthy skin. In conclusion, tick-mediated infections can trigger GA in some cases, while correlation of either Borrelia or Chlamydiales with morphea is unlikely.

A wide variety of putative extremophiles and large beta-diversity at the Mars Desert Research Station (Utah)

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Direito, Susana O. L.; Ehrenfreund, Pascale; Marees, Andries; Staats, Martijn; Foing, Bernard; Röling, Wilfred F. M.

2011-07-01

Humankind's innate curiosity makes us wonder whether life is or was present on other planetary bodies such as Mars. The EuroGeoMars 2009 campaign was organized at the Mars Desert Research Station (MDRS) to perform multidisciplinary astrobiology research. MDRS in southeast Utah is situated in a cold arid desert with mineralogy and erosion processes comparable to those on Mars. Insight into the microbial community composition of this terrestrial Mars analogue provides essential information for the search for life on Mars: including sampling and life detection methodology optimization and what kind of organisms to expect. Soil samples were collected from different locations. Culture-independent molecular analyses directed at ribosomal RNA genes revealed the presence of all three domains of life (Archaea, Bacteria and Eukarya), but these were not detected in all samples. Spiking experiments revealed that this appears to relate to low DNA recovery, due to adsorption or degradation. Bacteria were most frequently detected and showed high alpha- and beta-diversity. Members of the Actinobacteria, Proteobacteria, Bacteroidetes and Gemmatimonadetes phyla were found in the majority of samples. Archaea alpha- and beta-diversity was very low. For Eukarya, a diverse range of organisms was identified, such as fungi, green algae and several phyla of Protozoa. Phylogenetic analysis revealed an extraordinary variety of putative extremophiles, mainly Bacteria but also Archaea and Eukarya. These comprised radioresistant, endolithic, chasmolithic, xerophilic, hypolithic, thermophilic, thermoacidophilic, psychrophilic, halophilic, haloalkaliphilic and alkaliphilic micro-organisms. Overall, our data revealed large difference in occurrence and diversity over short distances, indicating the need for high-sampling frequency at similar sites. DNA extraction methods need to be optimized to improve extraction efficiencies.

Diversity of cultivable bacteria involved in the formation of macroscopic microbial colonies (Cave silver on the walls of a cave in Slovenia

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Blagajana Herzog Velikonja

2014-01-01

Full Text Available Karstic caves often support white, yellow, grey or pink microbial colonies that are termed ‘cave silver’ by speleologists. Using various sample pre-treatments and culture media, a wide variety of bacteria associated with these colonies were recovered from a cave in Slovenia, Pajsarjeva jama. Decreasing the inoculum size resulted in significant increases in viable counts, while pre-treatments had the opposite effect with the exception of microwave irradiation. While all growth media yielded viable counts, the maximal counts were observed on a low-nutrient TWA medium. Based on the 16S rRNA gene sequence of OTU representatives, the majority of the 80 isolates examined belonged to Streptomyces (25%, Micrococcus (16% and Rhodococcus (10% Other abundant groups were Pseudomonas (9%, Agrobacterium (8%, Lysobacter (6% and Paenibacillus (5%, while members of genera Microbacterium, Agrococcus, Arthrobacter, Bacillus, Kocuria, Oerskovia, Sphingomonas, Aerococcus, and Bosea represented a minor portion of cultivable diversity encountered. Members of Streptomyces and Agrobacterium were common to all samples. Although these microorganisms readily form colonies under laboratory conditions, they were unrelated to abundant environmental phylotypes recovered from same samples in a previous study. However, the comparative 16S rRNA analysis showed that microorganisms highly related to the ones obtained in this study were cultivated from other subterranean environments indicating that they might represent true microbial cave dwellers.