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Sample records for actinobacteria

  1. Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials

    OpenAIRE

    Mahmoud, Huda M.; Kalendar, Aisha A.

    2016-01-01

    Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different cul...

  2. The obligate respiratory supercomplex from Actinobacteria.

    Science.gov (United States)

    Kao, Wei-Chun; Kleinschroth, Thomas; Nitschke, Wolfgang; Baymann, Frauke; Neehaul, Yashvin; Hellwig, Petra; Richers, Sebastian; Vonck, Janet; Bott, Michael; Hunte, Carola

    2016-10-01

    Actinobacteria are closely linked to human life as industrial producers of bioactive molecules and as human pathogens. Respiratory cytochrome bcc complex and cytochrome aa3 oxidase are key components of their aerobic energy metabolism. They form a supercomplex in the actinobacterial species Corynebacterium glutamicum. With comprehensive bioinformatics and phylogenetic analysis we show that genes for cyt bcc-aa3 supercomplex are characteristic for Actinobacteria (Actinobacteria and Acidimicrobiia, except the anaerobic orders Actinomycetales and Bifidobacteriales). An obligatory supercomplex is likely, due to the lack of genes encoding alternative electron transfer partners such as mono-heme cyt c. Instead, subunit QcrC of bcc complex, here classified as short di-heme cyt c, will provide the exclusive electron transfer link between the complexes as in C. glutamicum. Purified to high homogeneity, the C. glutamicum bcc-aa3 supercomplex contained all subunits and cofactors as analyzed by SDS-PAGE, BN-PAGE, absorption and EPR spectroscopy. Highly uniform supercomplex particles in electron microscopy analysis support a distinct structural composition. The supercomplex possesses a dimeric stoichiometry with a ratio of a-type, b-type and c-type hemes close to 1:1:1. Redox titrations revealed a low potential bcc complex (Em(ISP)=+160mV, Em(bL)=-291mV, Em(bH)=-163mV, Em(cc)=+100mV) fined-tuned for oxidation of menaquinol and a mixed potential aa3 oxidase (Em(CuA)=+150mV, Em(a/a3)=+143/+317mV) mediating between low and high redox potential to accomplish dioxygen reduction. The generated molecular model supports a stable assembled supercomplex with defined architecture which permits energetically efficient coupling of menaquinol oxidation and dioxygen reduction in one supramolecular entity. PMID:27472998

  3. Genome Sequences of 11 Human Vaginal Actinobacteria Strains.

    Science.gov (United States)

    Lewis, Amanda L; Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G

    2016-01-01

    The composition of the vaginal microbiota is an important health determinant. Several members of the phylum Actinobacteria have been implicated in bacterial vaginosis, a condition associated with many negative health outcomes. Here, we present 11 strains of vaginal Actinobacteria (now available through BEI Resources) along with draft genome sequences.

  4. Genome Sequences of 11 Human Vaginal Actinobacteria Strains.

    Science.gov (United States)

    Lewis, Amanda L; Deitzler, Grace E; Ruiz, Maria J; Weimer, Cory; Park, SoEun; Robinson, Lloyd S; Hallsworth-Pepin, Kymberlie; Wollam, Aye; Mitreva, Makedonka; Lewis, Warren G

    2016-01-01

    The composition of the vaginal microbiota is an important health determinant. Several members of the phylum Actinobacteria have been implicated in bacterial vaginosis, a condition associated with many negative health outcomes. Here, we present 11 strains of vaginal Actinobacteria (now available through BEI Resources) along with draft genome sequences. PMID:27688328

  5. Surfactants tailored by the class Actinobacteria

    Directory of Open Access Journals (Sweden)

    Johannes H Kügler

    2015-03-01

    Full Text Available Gloablly, the drive towards the establishment of a bio-based economy has resulted in an increased need for bio-based applications. This, in turn, has served as a driving force for the discovery and application of novel biosurfactants. The class Actinobacteria represents a vast group of microorganisms with the ability to produce a diverse range of secondary metabolites, including surfactants. Understanding the extensive nature of the biosurfactants produced by actinobacterial strains can assist in finding novel biosurfactants with new potential applications. This review therefore presents a comprehensive overview of the knowledge available on actinobacterial surfactants, the chemical structures that have been completely or partly elucidated, as well as the identity of the biosurfactant-producing strains. Producer strains of not yet elucidated compounds are discussed, as well as the original habitats of all the producer strains, which seems to indicate that biosurfactant production is environmentally driven. Methodology applied in the isolation, purification and structural elucidation of the different types of surface active compounds, as well as surfactant activity tests, are also discussed. Overall, actinobacterial surfactants can be summarized to include the dominantly occurring trehalose-comprising surfactants, other non-trehalose containing glycolipids, lipopeptides and the more rare actinobacterial surfactants. The lack of structural information on a large proportion of actinobacterial surfactants should be considered as a driving force to further explore the abundance and diversity of these compounds. This would allow for a better understanding of actinobacterial surface active compounds and their potential for biotechnological application.

  6. Antagonistic activity of marine sponges associated Actinobacteria

    Institute of Scientific and Technical Information of China (English)

    Selvakumar Dharmaraj; Dhevendaran Kandasamy

    2016-01-01

    Objective: To focus on the isolation and preliminary characterization of marine sponges associated Actinobacteria particularly Streptomyces species and also their antagonistic activities against bacterial and fungal pathogens. Methods: The sponges were collected from Kovalam and Vizhinjam port of south-west coast of Kerala, India. Isolation of strains was carried out from sponge extracts using international Streptomyces project media. For preliminary identification of the strains, morphological (mycelial colouration, soluble pigments, melanoid pigmentation, spore morphology), nutritional uptake (carbon utilisation, amonoacids influence, sodium chloride tolerance), physiological (pH, temperature) and chemotaxonomical characterization were done. Antimicrobial studies were also carried out for the selected strains. Results: With the help of the spicule structures, the collected marine sponges were identified as Callyspongia diffusa, Mycale mytilorum, Tedania anhelans and Dysidea fragilis. Nearly 94 strains were primarily isolated from these sponges and further they were sub-cultured using international Streptomyces project media. The strains exhibited different mycelial colouration (aerial and substrate), soluble and melanoid pigmentations. The strains possessed three types of sporophore morphology namely rectus flexibilis, spiral and retinaculiaperti. Among the 94 isolates, seven exhibited antibacterial and antifungal activities with maximal zone of inhibition of 30 mm. The nutritional, physiological and chemotaxonomical characteristic study helped in the conventional identification of the seven strains and they all suggest that the strains to be grouped under the genus Streptomyces. Conclusions: The present study clearly helps in the preliminary identification of the isolates associated with marine sponges. Antagonistic activities prove the production of antimicrobial metabolites against the pathogens. Marine sponges associated Streptomyces are universally well

  7. [Identification of environmental Actinobacteria representing an occupational health risk].

    Science.gov (United States)

    Skóra, Justyna; Szponar, Bogumiła; Paściak, Mariola; Gutarowska, Beata

    2013-01-01

    Actinobacteria, the etiologic agents of tuberculosis, actinomycosis, respiratory infections and pathological skin lesions, are also classified as hazardous biological agents at the workplace. An increased number of Actinobacteria primarily occurs at the workplaces in composting plants, agriculture, waste management facilities, libraries and museums. Robust identification of Actinobacteria requires a polyphasic diagnostic strategy including an assessment of morphological, physiological, biochemical and chemotaxonomic features as well as genotyping. Commercially available diagnostic kits often do not include bacteria isolated from the environment and therefore analyses of chemotaxonomic markers--components of peptidoglycan, fatty acids, polar lipids (phospho- and glycolipids) and isoprenoid quinones are recommended. The paper discusses a comprehensive approach to the isolation and identification of Actinobacteria, with emphasis on chemotaxonomic methods. A diagnostic procedure is exemplified by environmental strains obtained from composting plants and libraries. PMID:24379263

  8. [Identification of environmental Actinobacteria representing an occupational health risk].

    Science.gov (United States)

    Skóra, Justyna; Szponar, Bogumiła; Paściak, Mariola; Gutarowska, Beata

    2013-12-06

    Actinobacteria, the etiologic agents of tuberculosis, actinomycosis, respiratory infections and pathological skin lesions, are also classified as hazardous biological agents at the workplace. An increased number of Actinobacteria primarily occurs at the workplaces in composting plants, agriculture, waste management facilities, libraries and museums. Robust identification of Actinobacteria requires a polyphasic diagnostic strategy including an assessment of morphological, physiological, biochemical and chemotaxonomic features as well as genotyping. Commercially available diagnostic kits often do not include bacteria isolated from the environment and therefore analyses of chemotaxonomic markers--components of peptidoglycan, fatty acids, polar lipids (phospho- and glycolipids) and isoprenoid quinones are recommended. The paper discusses a comprehensive approach to the isolation and identification of Actinobacteria, with emphasis on chemotaxonomic methods. A diagnostic procedure is exemplified by environmental strains obtained from composting plants and libraries.

  9. Screening of marine actinobacteria for amylase enzymes inhibitors

    OpenAIRE

    Raja, S.; Ganesan, S.; Sivakumar, K.; Thangaradjou, T.

    2010-01-01

    Amylase inhibitor producing actinobacteria were isolated and characterized from terrestrial environment and there is no much report found from marine environment, hence in the present study, 17 strains isolated from the rhizosphere sediments of mangroves were tested for their amylase inhibition ability. Seawater requirement test for the growth of actinobacteria found that the strains SSR-3, SSR-12 and SSR-16 requires at least 50% and SSR-6 requires at least 25% seawater for their growth. The ...

  10. Actinobacteria from arid and desert habitats: diversity and biological activity

    Directory of Open Access Journals (Sweden)

    Joachim eWink

    2016-01-01

    Full Text Available Abstract The lack of new antibiotics in the pharmaceutical pipeline guides more and more researchers to leave the classical isolation procedures and to look in special niches and ecosystems. Bioprospecting of extremophilic Actinobacteria through mining untapped strains and avoiding resiolation of known biomolecules is among the most promising strategies for this purpose. With this approach, members of acidtolerant, alkalitolerant, psychrotolerant, thermotolerant, halotolerant and xerotolerant Actinobacteria have been obtained from respective habitats. Among these, little survey exists on the diversity of Actinobacteria in arid areas, which are often adapted to relatively high temperatures, salt concentrations, and radiation. Therefore, arid and desert habitats are special ecosystems which can be recruited for the isolation of uncommon Actinobacteria with new metabolic capability.At the time of this writing, members of Streptomyces, Micromonospora, Saccharothrix, Streptosporangium, Cellulomonas, Amycolatopsis, Geodermatophilus, Lechevalieria, Nocardia and Actinomadura are reported from arid habitats. However, metagenomic data present dominant members of the communities in desiccating condition of areas with limited water availability that are not yet isolated. Furthermore, significant diverse types of polyketide synthase (PKS and nonribosomal peptide synthetase (NRPS genes are detected in xerophilic and xerotolerant Actinobacteria and some bioactive compounds are reported from them. Rather than pharmaceutically active metabolites, molecules with protection activity against drying such as Ectoin and Hydroxyectoin with potential application in industry and agriculture have also been identified from xerophilic Actinobacteria. In addition, numerous biologically active small molecules are expected to be discovered from arid adapted Actinobacteria in the future. In the current survey, the diversity and biotechnological potential of Actinobacteria

  11. Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials.

    Science.gov (United States)

    Mahmoud, Huda M; Kalendar, Aisha A

    2016-01-01

    Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications. PMID:26973601

  12. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications.

    Science.gov (United States)

    Lewin, Gina R; Carlos, Camila; Chevrette, Marc G; Horn, Heidi A; McDonald, Bradon R; Stankey, Robert J; Fox, Brian G; Currie, Cameron R

    2016-09-01

    The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.

  13. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications.

    Science.gov (United States)

    Lewin, Gina R; Carlos, Camila; Chevrette, Marc G; Horn, Heidi A; McDonald, Bradon R; Stankey, Robert J; Fox, Brian G; Currie, Cameron R

    2016-09-01

    The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels. PMID:27607553

  14. Coral-associated Actinobacteria from the Arabian Gulf: diversity, abundance and biotechnological potentials

    OpenAIRE

    Huda Mahmoud Mahmoud; Aisha Ahmad Kalendar

    2016-01-01

    Actinobacteria are widely distributed in terrestrial environments, where they are considered a significant source of bioactive compounds, mainly antibiotics. Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with Coscinaraea columna, Platygyra daedalea and Porites harrisoni, north of the Arabian Gulf were investigated. The corals of the Arabian Gulf, one of the world’s...

  15. Diversity and distribution of Actinobacteria associated with reef coral Porites lutea

    OpenAIRE

    Weiqi eKuang; Jie eLi; Si eZhang; Lijuan eLong

    2015-01-01

    Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every three months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene cl...

  16. Diversity and distribution of Actinobacteria associated with reef coral Porites lutea

    OpenAIRE

    Kuang, Weiqi; Li, Jie; Zhang, Si; Long, Lijuan

    2015-01-01

    Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every 3 months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone ...

  17. Antioxidant activity of newly discovered lineage of marine actinobacteria

    Institute of Scientific and Technical Information of China (English)

    Loganathan Karthik; Gaurav Kumar; Kokati Venkata Bhaskara Rao

    2013-01-01

    Objective: To investigate the antioxidant activity of marine actinobacteria. Methods: The content of total phenolics, the level of antioxidant potential by DPPH radical scavenging activity, metal chelating activity, FRAP method, β carotene assay and NO scavenging activity in extract were determined. Results: In all the methods the extract exhibited good scavenging activity except NO scavenging activity. The IC50 values of marine actinobacteria extract on DPPH radical were found to be 41.09 µg/mL. The zone of color retention was 12 mm in β-carotene bleaching assay. DNA protective efficiency of the extracts was also studied using UV- photolysed H2O2-driven oxidative damage to pBR322. HPLC analysis identified some of the major phenolic compounds in extracts, which might be responsible for the antioxidant potential and cyto-protection. It showed a 100% cytotoxic effect in brine shrimp lethality assay within 10 mins. The novel actinobacteria was identified as Streptomyces LK-3 (JF710608) through 16S rDNA Sequencing. Conclusions: The results obtained suggest that the extracts bear anti-cancer metabolites and could be considered as a potential source for anti-cancer drug development.

  18. Genomics of aerobic cellulose utilization systems in actinobacteria.

    Directory of Open Access Journals (Sweden)

    Iain Anderson

    Full Text Available Cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. Anaerobes including Clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. In contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. Numerous actinobacterial genomes have become available through the Genomic Encyclopedia of Bacteria and Archaea (GEBA project. We identified putative cellulose-degrading enzymes belonging to families GH5, GH6, GH8, GH9, GH12, GH48, and GH51 in the genomes of eleven members of the actinobacteria. The eleven organisms were tested in several assays for cellulose degradation, and eight of the organisms showed evidence of cellulase activity. The three with the highest cellulase activity were Actinosynnema mirum, Cellulomonas flavigena, and Xylanimonas cellulosilytica. Cellobiose is known to induce cellulolytic enzymes in the model organism Thermobifida fusca, but only Nocardiopsis dassonvillei showed higher cellulolytic activity in the presence of cellobiose. In T. fusca, cellulases and a putative cellobiose ABC transporter are regulated by the transcriptional regulator CelR. Nine organisms appear to use the CelR site or a closely related binding site to regulate an ABC transporter. In some, CelR also regulates cellulases, while cellulases are controlled by different regulatory sites in three organisms. Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms.

  19. Diversity and distribution of Actinobacteria associated with reef coral Porites lutea

    Directory of Open Access Journals (Sweden)

    Weiqi eKuang

    2015-10-01

    Full Text Available Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every three months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of twenty-five described families and ten unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater.

  20. Diversity and distribution of Actinobacteria associated with reef coral Porites lutea.

    Science.gov (United States)

    Kuang, Weiqi; Li, Jie; Zhang, Si; Long, Lijuan

    2015-01-01

    Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every 3 months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described families and 10 unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater. PMID:26539166

  1. Diversity and novelty of actinobacteria in Arctic marine sediments.

    Science.gov (United States)

    Zhang, Gaiyun; Cao, Tingfeng; Ying, Jianxi; Yang, Yanliu; Ma, Lingqi

    2014-04-01

    The actinobacterial diversity of Arctic marine sediments was investigated using culture-dependent and culture-independent approaches. A total of 152 strains were isolated from seven different media; 18 isolates were selected for phylogenetic analysis on the basis of their 16S rRNA gene sequences. Results showed that the 18 isolates belonged to a potential novel genus and 10 known genera including Actinotalea, Arthrobacter, Brachybacterium, Brevibacterium, Kocuria, Kytococcus, Microbacterium, Micrococcus, Mycobacterium, and Pseudonocardia. Subsequently, 172 rDNA clones were selected by restriction fragment length polymorphism analysis from 692 positive clones within four actinobacteria-specific 16S rDNA libraries of Arctic marine sediments, and then these 172 clones were sequenced. In total, 67 phylotypes were clustered in 11 known genera of actinobacteria including Agrococcus, Cellulomonas, Demequina, Iamia, Ilumatobacter, Janibacter, Kocuria, Microbacterium, Phycicoccus, Propionibacterium, and Pseudonocardia, along with other, unidentified actinobacterial clones. Based on the detection of a substantial number of uncultured phylotypes showing low BLAST identities (<95 %), this study confirms that Arctic marine environments harbour highly diverse actinobacterial communities, many of which appear to be novel, uncultured species. PMID:24519808

  2. Isolation and Characterisation of Antagonistic Actinobacteria from Mangrove Soil

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    Venkata Raghava Rao

    2012-04-01

    Full Text Available 1024x768 The aim of the present study was to isolate and screen actinobacteria having antagonistic activities against pathogenic microorganisms. A total of twenty actinobacteria strains were isolated from the mangrove sediment. Of these four active isolates were identified as Streptomyces species by means of morphological, physiological, biochemical and cultural characteristics. These isolates were subjected to shake flask fermentation and the secondary metabolites were extracted with ethyl acetate and screened for their antimicrobial activities against selected bacterial and fungal pathogens. The results showed that among the active isolates, four isolates (BC 01, BC 02, BC 03 and BC 04 showed promising activities against the selected test pathogens. These four extracted isolates were analyzed for UV Spectrophotometric and HPLC. Spectral data of the extracted compound revealed its antimicrobial nature. The UV spectrum of the methanol extracts for the active isolates showed absorbance peaks ranging between 207-223 nm. Two to three bioactive regions were detected on the HPLC. The results indicate that Streptomyces strains isolated from mangrove sediment produce potential antibacterial, antifungal and broad spectrum antibiotic compounds. Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

  3. The biogeochemical role of Actinobacteria in Altamira Cave, Spain.

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    Cuezva, Soledad; Fernandez-Cortes, Angel; Porca, Estefania; Pašić, Lejla; Jurado, Valme; Hernandez-Marine, Mariona; Serrano-Ortiz, Penelope; Hermosin, Bernardo; Cañaveras, Juan Carlos; Sanchez-Moral, Sergio; Saiz-Jimenez, Cesareo

    2012-07-01

    The walls and ceiling of Altamira Cave, northern Spain, are coated with different coloured spots (yellow, white and grey). Electron microscopy revealed that the grey spots are composed of bacteria and bioinduced CaCO(3) crystals. The morphology of the spots revealed a dense network of microorganisms organized in well-defined radial and dendritic divergent branches from the central area towards the exterior of the spot, which is coated with overlying spheroidal elements of CaCO(3) and CaCO(3) nest-like aggregates. Molecular analysis indicated that the grey spots were mainly formed by an unrecognized species of the genus Actinobacteria. CO(2) efflux measurements in rocks heavily covered by grey spots confirmed that bacteria-forming spots promoted uptake of the gas, which is abundant in the cave. The bacteria can use the captured CO(2) to dissolve the rock and subsequently generate crystals of CaCO(3) in periods of lower humidity and/or CO(2). A tentative model for the formation of these grey spots, supported by scanning electron microscopy and transmission electron microscopy data, is proposed. PMID:22500975

  4. Genomic islands predict functional adaptation in marine actinobacteria

    Energy Technology Data Exchange (ETDEWEB)

    Penn, Kevin; Jenkins, Caroline; Nett, Markus; Udwary, Daniel; Gontang, Erin; McGlinchey, Ryan; Foster, Brian; Lapidus, Alla; Podell, Sheila; Allen, Eric; Moore, Bradley; Jensen, Paul

    2009-04-01

    Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we report the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification

  5. [Actinobacteria and their odor-producing capacities in a surface water in Shanghai].

    Science.gov (United States)

    Chen, Jiao; Bai, Xiao-hui; Lu, Ning; Wang, Xian-yun; Zhang, Yong-hui; Wu, Pan-cheng; Guo, Xin-chi

    2014-10-01

    The odor in raw water is one of the main sources of odor in drinking water. The occurrence of actinobacteria and their odor producing capacities in a reservoir in.Shanghai were investigated. Gauze's medium and membrane filtration were used for actinobacteria isolation. Through combined methods of 16S rRNA sequencing, colony and hyphae morphology, carbon source utilization, physiological and biochemical characteristics, 40 strains of actinobacteria were identified from the reservoir. Results showed that there were 38 Streptomyces, an Aeromicrobium and a Pseudonocardia. Liquid culture medium and the real reservoir water were used to test the odor producing capacity of these 40 strains of actinobacteria, and headspace solid phase microextraction (HS-SPME) and high resolution gas chromatography mass spectroscopy (GC/MS) were used to analyze the odor compounds 2-methylisoborneol (2-MIB) and geosmin (GSM) in the fermentation liquor. The test results showed that, the odor-producing capacities of these actinobacteria in different fermentation media showed different variation trends, even within the genera Streptomyces. The odor-producing capacity of actinobacteria in the liquid culture medium could not represent their states in the reservoir water or their actual odor contribution to the aquatic environment.

  6. Coral-associated Actinobacteria from the Arabian Gulf: diversity, abundance and biotechnological potentials

    Directory of Open Access Journals (Sweden)

    Huda Mahmoud Mahmoud

    2016-02-01

    Full Text Available Actinobacteria are widely distributed in terrestrial environments, where they are considered a significant source of bioactive compounds, mainly antibiotics. Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with Coscinaraea columna, Platygyra daedalea and Porites harrisoni, north of the Arabian Gulf were investigated. The corals of the Arabian Gulf, one of the world’s hottest seas, are thriving under extreme water temperatures that exceed 39°C during the summer. Similar water temperatures cause coral bleaching and death in other water bodies. For this reason, the corals of the Gulf are living models for investigating how corals in other settings may survive at the end of the current century.Different coral hosts have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though

  7. In-vitro antimicrobial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus

    Institute of Scientific and Technical Information of China (English)

    Sathish Kumar S.R; Kokati Venkata Bhaskara Rao

    2012-01-01

    Objective: To investigate the antibacterial activity of marine actinobacteria against Multidrug resistance Staphylococcus aureus (MDRSA). Methods: Fifty one actinobacterial strains were isolated from salt pans soil, costal area in Kothapattanam, Ongole, Andhra Pradesh. Primary screening was done using cross-streak method against MDRSA. The bioactive compounds are extracted from efficient actinobacteria using solvent extraction. The antimicrobial activity of crude and solvent extracts was performed using Kirby-Bauer method. MIC for ethyl acetate extract was determined by modified agar well diffusion method. The potent actinobacteria are identified using Nonomura key, Shirling and Gottlieb 1966 with Bergey’s manual of Determinative Bacteriology. Results: Among the fifty one isolates screened for antibacterial activity, SRB25 were found efficient against MDRSA. The ethyl acetate extracts showed high inhibition against test organism. MIC test was performed with the ethyl acetate extract against MDRSA and found to be 1000μg/ml. The isolated actinobacteria are identified as Streptomyces sp with the help of Nonomura key. Conclusion: The current investigation reveals that the marine actinobacteria from salt pan environment can be able to produce new drug molecules against drug resistant microorganisms.

  8. Distribution of PASTA domains in penicillin-binding proteins and serine/threonine kinases of Actinobacteria.

    Science.gov (United States)

    Ogawara, Hiroshi

    2016-09-01

    PASTA domains (penicillin-binding protein and serine/threonine kinase-associated domains) have been identified in penicillin-binding proteins and serine/threonine kinases of Gram-positive Firmicutes and Actinobacteria. They are believed to bind β-lactam antibiotics, and be involved in peptidoglycan metabolism, although their biological function is not definitively clarified. Actinobacteria, especially Streptomyces species, are distinct in that they undergo complex cellular differentiation and produce various antibiotics including β-lactams. This review focuses on the distribution of PASTA domains in penicillin-binding proteins and serine/threonine kinases in Actinobacteria. In Actinobacteria, PASTA domains are detectable exclusively in class A but not in class B penicillin-binding proteins, in sharp contrast to the cases in other bacteria. In penicillin-binding proteins, PASTA domains distribute independently from taxonomy with some distribution bias. Particularly interesting thing is that no Streptomyces species have penicillin-binding protein with PASTA domains. Protein kinases in Actinobacteria possess 0 to 5 PASTA domains in their molecules. Protein kinases in Streptomyces can be classified into three groups: no PASTA domain, 1 PASTA domain and 4 PASTA domain-containing groups. The 4 PASTA domain-containing groups can be further divided into two subgroups. The serine/threonine kinases in different groups may perform different functions. The pocket region in one of these subgroup is more dense and extended, thus it may be involved in binding of ligands like β-lactams more efficiently.

  9. In-vitro antimicrobial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus

    Institute of Scientific and Technical Information of China (English)

    Sathish; Kumar; SR; Kokati; Venkata; Bhaskara; Rao

    2012-01-01

    Objective:To investigate the antibacterial aclivily of marine actinobacteria against multidrug resistance Staphylococcus aureus(MDRSA).Methods:Fifty one actinobacterial strains were isolated from salt pans soil,costal area in Kothapattanam,Ongole,Andhra Pradesh.Primary screening was done using cross-streak method against MDRSA.The bioaclive compounds are extracted from efficient actinobacteria using solvent extraction.The antimicrobial activity of crude and solvent extracts was perfomied using Kirby-Bauer method.MIC for ethyl acetate extract was determined by modified agar well diffusion method.The potent actinobacteria are identified using Nonomura key,Shirling and Gottlieb 1966 with Bergey’s manual of determinative bacteriology.Results:Among the fifty one isolates screened for antibacterial activity,SRB25were found efficient against MDRSA.The ethyl acetate extracts showed high inhibition against test organism.MIC test was performed with the ethyl acetate extract against MDRSA and found to be 1 000μg/mL.The isolaled actinobacteria are identified as Streptomyces sp with the help of Nonomura key.Conclusions:The current investigation reveals that the marine actinobacteria from salt pan environment can be able to produce new drug molecules against drug resistant microorganisms.

  10. In-vitro antimicrobial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus

    Institute of Scientific and Technical Information of China (English)

    Sathish Kumar SR; Kokati Venkata Bhaskara Rao

    2012-01-01

    To investigate the antibacterial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus (MDRSA). Methods: Fifty one actinobacterial strains were isolated from salt pans soil, costal area in Kothapattanam, Ongole, Andhra Pradesh. Primary screening was done using cross-streak method against MDRSA. The bioactive compounds are extracted from efficient actinobacteria using solvent extraction. The antimicrobial activity of crude and solvent extracts was performed using Kirby-Bauer method. MIC for ethyl acetate extract was determined by modified agar well diffusion method. The potent actinobacteria are identified using Nonomura key, Shirling and Gottlieb 1966 with Bergey's manual of determinative bacteriology. Results: Among the fifty one isolates screened for antibacterial activity, SRB25 were found efficient against MDRSA. The ethyl acetate extracts showed high inhibition against test organism. MIC test was performed with the ethyl acetate extract against MDRSA and found to be 1 000 μg/mL. The isolated actinobacteria are identified as Streptomyces sp with the help of Nonomura key. Conclusions: The current investigation reveals that the marine actinobacteria from salt pan environment can be able to produce new drug molecules against drug resistant microorganisms.

  11. Exploring the potential for actinobacteria as defensive symbionts in fungus-growing termites

    DEFF Research Database (Denmark)

    Visser, Anna A.; Nobre, Tânia; Currie, Cameron R.;

    2012-01-01

    In fungus-growing termites, fungi of the subgenus Pseudoxylaria threaten colony health through substrate competition with the termite fungus (Termitomyces). The potential mechanisms with which termites suppress Pseudoxylaria have remained unknown. Here we explore if Actinobacteria potentially play......-growing termites, indicating lack of specificity. Antibiotic-activity screening of 288 isolates against the fungal cultivar and competitor revealed that most of the Actinobacteria-produced molecules with antifungal activity. A more detailed bioassay on 53 isolates, to test the specificity of antibiotics, showed...

  12. Paratrechina longicornis ants in a tropical dry forest harbor specific Actinobacteria diversity.

    Science.gov (United States)

    Reyes, Ruth D Hernández; Cafaro, Matías J

    2015-01-01

    The diversity of Actinobacteria associated with Paratrechina longicornis, an ant species that prefers a high protein diet, in a subtropical dry forest (Guánica, Puerto Rico) was determined by culture methods and by 16S rDNA clone libraries. The results of both methodologies were integrated to obtain a broader view of the diversity. Streptomyces, Actinomadura, Nocardia, Ornithinimicrobium, Tsukamurella, Brevibacterium, Saccharopolyspora, Nocardioides, Microbacterium, Leifsonia, Pseudonocardia, Corynebacterium, Geodermatophilus, Amycolatopsis, and Nonomuraea were found associated with the ants. The genera Streptomyces and Actinomadura were the most abundant. Also, the diversity of Actinobacteria associated with the soil surrounding the nest was determined using 16S rDNA clone libraries. In total, 27 genera of Actinobacteria were associated with the nest soils. A dominant genus was not observed in any of the soil samples. We compared statistically the Actinobacteria communities among P. longicornis nests and each nest with its surrounding soil using the clone libraries data. We established that the communities associated with the ants were consistent and significantly different from those found in the soil in which the ants live. PMID:24771570

  13. Anti-Candida Properties of Urauchimycins from Actinobacteria Associated with Trachymyrmex Ants

    Directory of Open Access Journals (Sweden)

    Thais D. Mendes

    2013-01-01

    Full Text Available After decades of intensive searching for antimicrobial compounds derived from actinobacteria, the frequency of isolation of new molecules has decreased. To cope with this concern, studies have focused on the exploitation of actinobacteria from unexplored environments and actinobacteria symbionts of plants and animals. In this study, twenty-four actinobacteria strains isolated from workers of Trachymyrmex ants were evaluated for antifungal activity towards a variety of Candida species. Results revealed that seven strains inhibited the tested Candida species. Streptomyces sp. TD025 presented potent and broad spectrum of inhibition of Candida and was selected for the isolation of bioactive molecules. From liquid shake culture of this bacterium, we isolated the rare antimycin urauchimycins A and B. For the first time, these molecules were evaluated for antifungal activity against medically important Candida species. Both antimycins showed antifungal activity, especially urauchimycin B. This compound inhibited the growth of all Candida species tested, with minimum inhibitory concentration values equivalent to the antifungal nystatin. Our results concur with the predictions that the attine ant-microbe symbiosis may be a source of bioactive metabolites for biotechnology and medical applications.

  14. Abundance of actinobacteria and production of geosmin and 2-methylisoborneol in Danish streams and fish ponds.

    Science.gov (United States)

    Klausen, Cecilie; Nicolaisen, Mette H; Strobel, Bjarne W; Warnecke, Falk; Nielsen, Jeppe L; Jørgensen, Niels O G

    2005-04-01

    Occurrence of the odours geosmin and 2-methylisoborneol (MIB) in freshwater environments indicates that odour-producing organisms are commonly occurring. In the present study, we assumed actinomycetes to be a major source of the odours. Seasonal concentrations of odours and abundance of Actinobacteria, which includes actinomycetes and other G+ and high GC bacteria, were determined in one oligotrophic and two eutrophic freshwater streams, as well as in aquacultures connected to these streams, in Denmark. Concentrations of geosmin and MIB ranged from 2 to 9 ng l(-1) and were lowest in the winter. Passage of stream water in the aquacultures increased the amount of geosmin and MIB by up to 55% and 110%, respectively. Densities of actinobacteria were determined by fluorescence in situ hybridization with catalyzed reporter deposition (CARD-FISH) technique and were found to make up from 4 to 38 x 10(7) cells l(-1), corresponding to 3-9% of the total bacterial populations. The lowest densities of actinobacteria occurred in the winter. Filamentous bacteria targeted by the FISH probe made up about 2.7-38% (average was 22%) of the actinobacteria and were expected to be actinomycetes. Combined microautoradiography and CARD-FISH demonstrated that 10-38% (incorporation of 3H-thymidine) and 41-65% (incorporation of 3H-leucine) of the actinobacteria were metabolically active. The proportion of active actinobacteria increased up to 2-fold during passage of stream water in the aquacultures, and up to 98% of the cells became active. Sequencing of 16S rRNA genes in 8 bacterial isolates with typical actinomycete morphology from the streams and ponds demonstrated that most of them belonged to the genus Streptomyces. The isolated actinomycetes produced geosmin at rates from 0.1 to 35 aggeosmin bacterium(-1)h(-1). MIB was produced at similar rates in 5 isolates, whereas no MIB was produced by three of the isolates. Addition of the odours to stream water demonstrated that indigenous stream

  15. Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria.

    Directory of Open Access Journals (Sweden)

    Mariana Gabriela Ghinet

    Full Text Available Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs. While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS, in Actinobacteria a single DNA FtsK/SpoIIIE-like translocation protein is required. To date, the role and diversity of ICEs in Actinobacteria have received little attention. Putative ICEs were searched for in 275 genomes of Actinobacteria using HMM-profiles of proteins involved in ICE maintenance and transfer. These exhaustive analyses revealed 144 putative FtsK/SpoIIIE-type ICEs and 17 putative T4SS-type ICEs. Grouping of the ICEs based on the phylogenetic analyses of maintenance and transfer proteins revealed extensive exchanges between different sub-families of ICEs. 17 ICEs were found in Actinobacteria from the genus Frankia, globally important nitrogen-fixing microorganisms that establish root nodule symbioses with actinorhizal plants. Structural analysis of ICEs from Frankia revealed their unexpected diversity and a vast array of predicted adaptive functions. Frankia ICEs were found to excise by site-specific recombination from their host's chromosome in vitro and in planta suggesting that they are functional mobile elements whether Frankiae live as soil saprophytes or plant endosymbionts. Phylogenetic analyses of proteins involved in ICEs maintenance and transfer suggests that active exchange between ICEs cargo-borne and chromosomal genes took place within the Actinomycetales order. Functionality of Frankia ICEs in vitro as well as in planta lets us anticipate that conjugation and ICEs could allow the development of genetic manipulation tools for this challenging microorganism

  16. Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria

    OpenAIRE

    Mariana Gabriela Ghinet; Eric Bordeleau; Julie Beaudin; Ryszard Brzezinski; Sébastien Roy; Vincent Burrus

    2011-01-01

    Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs). While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS), in Actinobacteria a sing...

  17. Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products

    OpenAIRE

    Juan Pablo Gomez-Escribano; Silke Alt; Bibb, Mervyn J.

    2016-01-01

    Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a subs...

  18. Termite Nests as an Abundant Source of Cultivable Actinobacteria for Biotechnological Purposes

    OpenAIRE

    Sujada, N.; Sungthong, R.; Lumyong, S.

    2014-01-01

    A total of 118 actinobacterial isolates were collected from the three types of termite nests (mound, carton, and subterranean nests) to evaluate their potential as a source of bioactive actinobacteria with antimicrobial activity. The highest number (67 isolates) and generic abundance (7 known genera) of actinobacterial isolates were obtained from carton nests. Streptomyces was the dominant genus in each type of termite nest. In the non-Streptomyces group, Nocardia was the dominant genus detec...

  19. Biogeography of bacterial communities in hot springs: a focus on the actinobacteria.

    Science.gov (United States)

    Valverde, Angel; Tuffin, Marla; Cowan, Don A

    2012-07-01

    Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5 °C and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.

  20. Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation

    Directory of Open Access Journals (Sweden)

    Wiid Ian JF

    2009-02-01

    Full Text Available Abstract Background Although the gene encoding for glutamine synthetase (glnA is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1 is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4 are not. Results In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved. Conclusion Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria.

  1. Isolation, Phylogenetic Analysis and Antibiotic Activity Screening of Red Sea Sponge-Associated Actinobacteria

    KAUST Repository

    Yang, Chen

    2013-06-01

    Infectious disease has always been and will continue to be a heavy burden on human society worldwide. Terrestrial actinobacteria, notable as a source of antibiotics, have been well investigated in the past. In constrast, marine actinobacteria, especially sponge-associated species, have received much less attention and isolates are sparse. With the aim of studying and discovering novel marine actinobacteria, 11 different species of sponges were collected from the Central Red Sea in Saudi Arabia and cultured with three different types of media. 16S rRNA gene-sequencing revealed that among all 75 isolated bacterial strains 13 belonged to the order actinomycetales. These 13 actinomycetes fall into four different families and can be assigned to six different genera. Antibiotic activity tests using disc diffusion assay were performed against Gram-positive bacteria (Bacillus sp.), Gram-negative bacteria (Escherichia coli), fungi (Fusarium sp.) and West Nile virus NS3 protease. Nine strains presented different level of bioactivity against these pathogens. These findings provide evidence that actinomycetes are presented in marine sponges and that they have the potential to be good candidates in the search for new effective antibiotic, antifungal, and antiviral compounds.

  2. Environmental controls over Actinobacteria communities in ecological sensitive Yanshan mountains zone

    Directory of Open Access Journals (Sweden)

    hui etang

    2016-03-01

    Full Text Available The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1–YS10 on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120 oC for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1. However, there were differences (P < 0.05 from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001 in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites.. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line.

  3. Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone.

    Science.gov (United States)

    Tang, Hui; Shi, Xunxun; Wang, Xiaofei; Hao, Huanhuan; Zhang, Xiu-Min; Zhang, Li-Ping

    2016-01-01

    The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1-YS10) on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120°C for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1). However, there were differences (P < 0.05) from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001) in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line. PMID:27047461

  4. On the nature of fur evolution: A phylogenetic approach in Actinobacteria

    Directory of Open Access Journals (Sweden)

    Benson David R

    2008-06-01

    Full Text Available Abstract Background An understanding of the evolution of global transcription regulators is essential for comprehending the complex networks of cellular metabolism that have developed among related organisms. The fur gene encodes one of those regulators – the ferric uptake regulator Fur – widely distributed among bacteria and known to regulate different genes committed to varied metabolic pathways. On the other hand, members of the Actinobacteria comprise an ecologically diverse group of bacteria able to inhabit various natural environments, and for which relatively little is currently understood concerning transcriptional regulation. Results BLAST analyses revealed the presence of more than one fur homologue in most members of the Actinobacteria whose genomes have been fully sequenced. We propose a model to explain the evolutionary history of fur within this well-known bacterial phylum: the postulated scenario includes one duplication event from a primitive regulator, which probably had a broad range of co-factors and DNA-binding sites. This duplication predated the appearance of the last common ancestor of the Actinobacteria, while six other duplications occurred later within specific groups of organisms, particularly in two genera: Frankia and Streptomyces. The resulting paralogues maintained main biochemical properties, but became specialised for regulating specific functions, coordinating different metal ions and binding to unique DNA sequences. The presence of syntenic regions surrounding the different fur orthologues supports the proposed model, as do the evolutionary distances and topology of phylogenetic trees built using both Neighbor-Joining and Maximum-Likelihood methods. Conclusion The proposed fur evolutionary model, which includes one general duplication and two in-genus duplications followed by divergence and specialization, explains the presence and diversity of fur genes within the Actinobacteria. Although a few rare

  5. Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria

    Directory of Open Access Journals (Sweden)

    Gelfand Mikhail S

    2005-10-01

    Full Text Available Abstract Background Formation of alternative structures in mRNA in response to external stimuli, either direct or mediated by proteins or other RNAs, is a major mechanism of regulation of gene expression in bacteria. This mechanism has been studied in detail using experimental and computational approaches in proteobacteria and Firmicutes, but not in other groups of bacteria. Results Comparative analysis of amino acid biosynthesis operons in Actinobacteria resulted in identification of conserved regions upstream of several operons. Classical attenuators were predicted upstream of trp operons in Corynebacterium spp. and Streptomyces spp., and trpS and leuS genes in some Streptomyces spp. Candidate leader peptides with terminators were observed upstream of ilvB genes in Corynebacterium spp., Mycobacterium spp. and Streptomyces spp. Candidate leader peptides without obvious terminators were found upstream of cys operons in Mycobacterium spp. and several other species. A conserved pseudoknot (named LEU element was identified upstream of leuA operons in most Actinobacteria. Finally, T-boxes likely involved in the regulation of translation initiation were observed upstream of ileS genes from several Actinobacteria. Conclusion The metabolism of tryptophan, cysteine and leucine in Actinobacteria seems to be regulated on the RNA level. In some cases the mechanism is classical attenuation, but in many cases some components of attenuators are missing. The most interesting case seems to be the leuA operon preceded by the LEU element that may fold into a conserved pseudoknot or an alternative structure. A LEU element has been observed in a transposase gene from Bifidobacterium longum, but it is not conserved in genes encoding closely related transposases despite a very high level of protein similarity. One possibility is that the regulatory region of the leuA has been co-opted from some element involved in transposition. Analysis of phylogenetic patterns

  6. Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products

    Directory of Open Access Journals (Sweden)

    Juan Pablo Gomez-Escribano

    2016-04-01

    Full Text Available Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS. Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a substantial increase in the quality of the data, having moved from obtaining a draft genome sequence comprised of several hundred short contigs, sometimes of doubtful reliability, to the possibility of obtaining an almost complete and accurate chromosome sequence in a single contig, allowing a detailed study of gene clusters and the design of strategies for refactoring and full gene cluster synthesis. The impact that these technologies are having in the discovery and study of natural products from actinobacteria, including those from the marine environment, is only starting to be realised. In this review we provide a historical perspective of the field, analyse the strengths and limitations of the most relevant technologies, and share the insights acquired during our genome mining projects.

  7. An agar degrading diazotrophic actinobacteria from hyperalkaline meteoric lonar crater lake - a primary study

    Directory of Open Access Journals (Sweden)

    Avinash A. Raut

    2011-09-01

    Full Text Available There are very few reports on agarases being produced by actinobacteria, Streptomyces coelicolor being the only one known since decades for its agar degrading property. Here we report an agar degrading diazotrophic actinobacterium other than Streptomyces coelicolor, isolated from the littoral soil of Lonar Lake situated in Buldhana district of Maharashtra, India, a lake characterised by high alkalinity, carbonates, bicarbonates, and algal blooms. The lake has a mean diameter of 1800 meters. The Gram-positive filamentous rod grew in a simple medium of pH 10.5 containing agar as a sole source of carbon. The agar degrading property was detected by the appearance of depressions around each colony after 48 h of growth. The enzyme responsible for this degradation, agarase was also detected and estimated. The isolate also grew on Ashby’s Nitrogen free Mannitol Medium aerobically and fixed nitrogen. Morphological, physiological and biochemical characteristics of the isolate are presented in this paper.

  8. Diversity, biogeography and biodegradation potential of actinobacteria in the deep-sea sediments along the Southwest Indian Ridge

    Directory of Open Access Journals (Sweden)

    Ping Chen

    2016-08-01

    Full Text Available The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.

  9. Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile.

    Science.gov (United States)

    Undabarrena, Agustina; Beltrametti, Fabrizio; Claverías, Fernanda P; González, Myriam; Moore, Edward R B; Seeger, Michael; Cámara, Beatriz

    2016-01-01

    Bioprospecting natural products in marine bacteria from fjord environments are attractive due to their unique geographical features. Although, Actinobacteria are well known for producing a myriad of bioactive compounds, investigations regarding fjord-derived marine Actinobacteria are scarce. In this study, the diversity and biotechnological potential of Actinobacteria isolated from marine sediments within the Comau fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. The 16S rRNA gene sequences revealed that members phylogenetically related to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, Dietziaceae, Nocardiaceae, and Streptomycetaceae families were present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera) was retrieved by using only five different isolation media. Four isolates belonging to Arthrobacter, Brevibacterium, Corynebacterium and Kocuria genera showed 16S rRNA gene identity <98.7% suggesting that they are novel species. Physiological features such as salt tolerance, artificial sea water requirement, growth temperature, pigmentation and antimicrobial activity were evaluated. Arthrobacter, Brachybacterium, Curtobacterium, Rhodococcus, and Streptomyces isolates showed strong inhibition against both Gram-negative Pseudomonas aeruginosa, Escherichia coli and Salmonella enterica and Gram-positive Staphylococcus aureus, Listeria monocytogenes. Antimicrobial activities in Brachybacterium, Curtobacterium, and Rhodococcus have been scarcely reported, suggesting that non-mycelial strains are a suitable source of bioactive compounds. In addition, all strains bear at least one of the biosynthetic genes coding for NRPS (91%), PKS I (18%), and PKS II (73%). Our results indicate that the Comau fjord is a promising source of novel Actinobacteria with biotechnological potential for producing biologically active compounds. PMID:27486455

  10. Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge

    Science.gov (United States)

    Chen, Ping; Zhang, Limin; Guo, Xiaoxuan; Dai, Xin; Liu, Li; Xi, Lijun; Wang, Jian; Song, Lei; Wang, Yuezhu; Zhu, Yaxin; Huang, Li; Huang, Ying

    2016-01-01

    The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling. PMID:27621725

  11. The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale

    Science.gov (United States)

    Zhang, Binglin; Wu, Xiukun; Zhang, Gaosen; Li, Shuyan; Zhang, Wei; Chen, Ximing; Sun, Likun; Zhang, Baogui; Liu, Guangxiu; Chen, Tuo

    2016-05-01

    Glacier forelands, where the initially exposed area is unvegetated with minimal human influence, are an ideal place for research on the distributions and biogeography of microbial communities. Actinobacteria produce many bioactive substances and have important roles in soil development and biogeochemical cycling. However, little is known about the distribution and biogeography of Actinobacteria in glacier forelands. Therefore, we investigated the patterns of diversity and the biogeography of actinobacterial communities of the inhabited forefields of 5 glaciers in China. Of the bacteria, the mean relative abundance of Actinobacteria was 13.1%, and 6 classes were identified in the phylum Actinobacteria. The dominant class was Actinobacteria (57%), which was followed in abundance by Acidimicrobiia (19%) and Thermoleophilia (19%). When combined, the relative abundance of the other three classes, the MB-A2-108, Nitriliruptoria and Rubrobacteria, was only 2.4%. A biogeographic pattern in the forelands of the 5 glaciers in China was not detected for actinobacterial communities. Compared with 7 other actinobacterial communities found in the forelands of glaciers globally, those in the Southern Hemisphere were significantly different from those in the Northern Hemisphere. Moreover, the communities were significantly different on the separate continents of the Northern Hemisphere. The dissimilarity of the actinobacterial communities increased with geographic distance (r = 0.428, p = 0.0003). Because of environmental factors, the effect of geography was clear when the distance exceeded a certain continent-level threshold. With the analysis of indicator species, we found that each genus had a geographic characteristic, which could explain why the communities with greater diversity were more strongly affected by biogeography.

  12. Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge.

    Science.gov (United States)

    Chen, Ping; Zhang, Limin; Guo, Xiaoxuan; Dai, Xin; Liu, Li; Xi, Lijun; Wang, Jian; Song, Lei; Wang, Yuezhu; Zhu, Yaxin; Huang, Li; Huang, Ying

    2016-01-01

    The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662-4000 m below water surface. Actinobacterial sequences represented 1.2-9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling. PMID:27621725

  13. In silico discovery of the dormancy regulons in a number of Actinobacteria genomes

    Energy Technology Data Exchange (ETDEWEB)

    Gerasimova, Anna; Dubchak, Inna; Arkin, Adam; Gelfand, Mikhail

    2010-11-16

    Mycobacterium tuberculosis is a dangerous Actinobacteria infecting nearly one third of the human population. It becomes dormant and phenotypically drug resistant in response to stresses. An important feature of the M. tuberculosis pathogenesis is the prevalence of latent infection without disease, making understanding of the mechanisms used by the bacteria to exist in this state and to switch to metabolically active infectious form a vital problem to consider. M. tuberculosis dormancy is regulated by the three-component regulatory system of two kinases (DosT and DevS) and transcriprional regulator (DevR). DevR activates transcription of a set of genes, which allow the bacteria to survive long periods of anaerobiosis, and may be important for long-term survival within the host during latent infection. The DevR-regulon is studied experimentally in M. tuberculosis and few other phylogenetically close Mycobacteria spp. As many other two-component systems, the devRS operon is autoregulated. However, the mechanism of the dormancy is not completely clear even for these bacteria and there is no data describing the dormancy regulons in other species.

  14. Isolation and characterization of actinobacteria from Yalujiang coastal wetland, North China

    Institute of Scientific and Technical Information of China (English)

    Jicheng; Yu; Liu; Zhang; Qiu; Liu; Xiaohui; Qi; Ying; Ji; Beom; Seok; Kim

    2015-01-01

    Objective: To evaluate various types of samples from the different marine environments as sources of actinomycetes from the Yalujiang coastal wetland, North China, and to screen their antimicrobial properties. Further, the identified actinomycetes were characterized based on morphological, biochemical, and physiological characteristics.Methods: Eight different production media were used to isolate actinomycets from different stations of marine soil sediments in Yalujiang coastal wetland and the genotypic positions were established by 16 S r DNA.Results: A total of 172 actinomycetal isolates were obtained from 13 samples using five media. The most effective culture media in the isolation of actinobacteria were Gause’s Synthetic agar and Starch-casein agar. Among 172 isolates, 46 isolates(26.74%) showed antibacterial activity, 70.93% belonged to the genus Streptomyces, others were Micromonospora spp. and Rhodococcus spp. Out of the 46 isolates, two cultures were further supported by morphological characterization analysis.Conclusions: This is the first report about actinomycetes isolated from Yalujiang coastal wetland and it seems that the promising isolates from the unusual/unexplored wetland may prove to be an important step in the development of microbial natural product research.

  15. Isolation and characterization of actinobacteria from Yalujiang coastal wetland, North China

    Institute of Scientific and Technical Information of China (English)

    Jicheng Yu; Liu Zhang; Qiu Liu; Xiaohui Qi; Ying Ji; Beom Seok Kim

    2015-01-01

    Objective:To evaluate various types of samples from the different marine environments as sources of actinomycetes from the Yalujiang coastal wetland, North China, and to screen their antimicrobial properties. Further, the identified actinomycetes were characterized based on morphological, biochemical, and physiological characteristics. Methods:Eight different production media were used to isolate actinomycets from different stations of marine soil sediments in Yalujiang coastal wetland and the genotypic positions were established by 16S rDNA. Results:A total of 172 actinomycetal isolates were obtained from 13 samples using five media. The most effective culture media in the isolation of actinobacteria were Gause’s Synthetic agar and Starch-casein agar. Among 172 isolates, 46 isolates (26.74%) showed antibacterial activity, 70.93%belonged to the genus Streptomyces, others were Micromonospora spp. and Rhodococcus spp. Out of the 46 isolates, two cultures were further supported by morphological characterization analysis. Conclusions: This is the first report about actinomycetes isolated from Yalujiang coastal wetland and it seems that the promising isolates from the unusual/unexplored wetland may prove to be an important step in the development of microbial natural product research.

  16. Phylogenetic Diversity and Biological Activity of Actinobacteria Isolated from the Chukchi Shelf Marine Sediments in the Arctic Ocean

    Directory of Open Access Journals (Sweden)

    Meng Yuan

    2014-03-01

    Full Text Available Marine environments are a rich source of Actinobacteria and have the potential to produce a wide variety of biologically active secondary metabolites. In this study, we used four selective isolation media to culture Actinobacteria from the sediments collected from the Chukchi Shelf in the Arctic Ocean. A total of 73 actinobacterial strains were isolated. Based on repetitive DNA fingerprinting analysis, we selected 30 representatives for partial characterization according to their phylogenetic diversity, antimicrobial activities and secondary-metabolite biosynthesis genes. Results from the 16S rRNA gene sequence analysis indicated that the 30 strains could be sorted into 18 phylotypes belonging to 14 different genera: Agrococcus, Arsenicicoccus, Arthrobacter, Brevibacterium, Citricoccus, Janibacter, Kocuria, Microbacterium, Microlunatus, Nocardioides, Nocardiopsis, Saccharopolyspora, Salinibacterium and Streptomyces. To our knowledge, this paper is the first report on the isolation of Microlunatus genus members from marine habitats. Of the 30 isolates, 11 strains exhibited antibacterial and/or antifungal activity, seven of which have activities against Bacillus subtilis and Candida albicans. All 30 strains have at least two biosynthetic genes, one-third of which possess more than four biosynthetic genes. This study demonstrates the significant diversity of Actinobacteria in the Chukchi Shelf sediment and their potential for producing biologically active compounds and novel material for genetic manipulation or combinatorial biosynthesis.

  17. Phylogenetic diversity and biological activity of actinobacteria isolated from the Chukchi Shelf marine sediments in the Arctic Ocean.

    Science.gov (United States)

    Yuan, Meng; Yu, Yong; Li, Hui-Rong; Dong, Ning; Zhang, Xiao-Hua

    2014-03-01

    Marine environments are a rich source of Actinobacteria and have the potential to produce a wide variety of biologically active secondary metabolites. In this study, we used four selective isolation media to culture Actinobacteria from the sediments collected from the Chukchi Shelf in the Arctic Ocean. A total of 73 actinobacterial strains were isolated. Based on repetitive DNA fingerprinting analysis, we selected 30 representatives for partial characterization according to their phylogenetic diversity, antimicrobial activities and secondary-metabolite biosynthesis genes. Results from the 16S rRNA gene sequence analysis indicated that the 30 strains could be sorted into 18 phylotypes belonging to 14 different genera: Agrococcus, Arsenicicoccus, Arthrobacter, Brevibacterium, Citricoccus, Janibacter, Kocuria, Microbacterium, Microlunatus, Nocardioides, Nocardiopsis, Saccharopolyspora, Salinibacterium and Streptomyces. To our knowledge, this paper is the first report on the isolation of Microlunatus genus members from marine habitats. Of the 30 isolates, 11 strains exhibited antibacterial and/or antifungal activity, seven of which have activities against Bacillus subtilis and Candida albicans. All 30 strains have at least two biosynthetic genes, one-third of which possess more than four biosynthetic genes. This study demonstrates the significant diversity of Actinobacteria in the Chukchi Shelf sediment and their potential for producing biologically active compounds and novel material for genetic manipulation or combinatorial biosynthesis. PMID:24663116

  18. Characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria.

    Science.gov (United States)

    Gangoiti, Joana; Santos, Marta; Prieto, María Auxiliadora; de la Mata, Isabel; Serra, Juan L; Llama, María J

    2012-10-01

    Nineteen medium-chain-length (mcl) poly(3-hydroxyalkanoate) (PHA)-degrading microorganisms were isolated from natural sources. From them, seven Gram-positive and three Gram-negative bacteria were identified. The ability of these microorganisms to hydrolyze other biodegradable plastics, such as short-chain-length (scl) PHA, poly(ε-caprolactone) (PCL), poly(ethylene succinate) (PES), and poly(l-lactide) (PLA), has been studied. On the basis of the great ability to degrade different polyesters, Streptomyces roseolus SL3 was selected, and its extracellular depolymerase was biochemically characterized. The enzyme consisted of one polypeptide chain of 28 kDa with a pI value of 5.2. Its maximum activity was observed at pH 9.5 with chromogenic substrates. The purified enzyme hydrolyzed mcl PHA and PCL but not scl PHA, PES, and PLA. Moreover, the mcl PHA depolymerase can hydrolyze various substrates for esterases, such as tributyrin and p-nitrophenyl (pNP)-alkanoates, with its maximum activity being measured with pNP-octanoate. Interestingly, when poly(3-hydroxyoctanoate-co-3-hydroxyhexanoate [11%]) was used as the substrate, the main hydrolysis product was the monomer (R)-3-hydroxyoctanoate. In addition, the genes of several Actinobacteria strains, including S. roseolus SL3, were identified on the basis of the peptide de novo sequencing of the Streptomyces venezuelae SO1 mcl PHA depolymerase by tandem mass spectrometry. These enzymes did not show significant similarity to mcl PHA depolymerases characterized previously. Our results suggest that these distinct enzymes might represent a new subgroup of mcl PHA depolymerases. PMID:22865072

  19. Rape phosphatide concentrate in the technologies of surfactants production by the Actinobacteria

    Directory of Open Access Journals (Sweden)

    N. Koretska

    2015-05-01

    Full Text Available Introduction. Due to the fact that the production of microbial surfactants is limited by the low yield of end products and high cost of processes, the actual task is to optimize and reduce the cost of the technology of biosurfactants synthesis. One of the solutions of this problem is to use the industrial wastes, including rape phosphatide concentrate (PC. Materials and methods. Hexadecane and rape phosphatide concentrate (2% were used as a carbon source in a nutrient medium for the cultivation of bacteria. Lipids were extracted from a cell mass and supernatant by the mixture of chloroform-methanol 2:1. The qualitative analysis of metabolites was performed by a thin layer chromatography. Results and discussion. The peculiarities of synthesis of biosurfactants by strains G. rubripertincta UCM Aс-122 and R. erythropolis Au-1 during the growth on the nutrient media with rape phosphatide concentrate as a carbon source was studied. Quantity of biomass was 9.4 – 10.1 g/l, exopoly mers –8.9-9.5 g/l and the content of cellbound trehalose lipids was 1.37 – 2.26 g/l; whereas the content of exogenous trehalose lipids –metabolites of R. erythropolis Au-1 was 2.95 g/l. It was found that the addition of trehalose lipids (0.01 g/l to the nutrient medium caused the increase of biomass on 14.6 –17.0 % and cell-bound lipids on 13.9 –15.5 %. Conclusions. Rape phosphatide concentrate is economically viable carbon source in the technologies of surfactant production by Actinobacteria. Its use promotes an increasing of exogenous surfactants strain R. erythropolisAu-1 in 3-fold compared with cultivation on nutrient medium with hexadecane. Trehalose lipids show a stimulating effect on growth and synthesis of biosurfactants by strains of G. rubripertincta UCM Ac-122 and R. erythropolisAu-1.

  20. Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles.

    Science.gov (United States)

    Liu, Lan; Salam, Nimaichand; Jiao, Jian-Yu; Jiang, Hong-Chen; Zhou, En-Min; Yin, Yi-Rui; Ming, Hong; Li, Wen-Jun

    2016-07-01

    The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited

  1. Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles.

    Science.gov (United States)

    Liu, Lan; Salam, Nimaichand; Jiao, Jian-Yu; Jiang, Hong-Chen; Zhou, En-Min; Yin, Yi-Rui; Ming, Hong; Li, Wen-Jun

    2016-07-01

    The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited

  2. Studies on a Novel Actinobacteria Species Capable of Oxidizing Ammonium under Iron Reduction Conditions

    Science.gov (United States)

    Huanh, Shan; Ruiz-Urigüen, Melany; Jaffe, Peter R.

    2014-05-01

    Ammonium (NH4+) oxidation coupled to iron reduction in the absence of oxygen and nitrate/nitrite (NO3-/NO2-) was noted in a forested riparian wetland in New Jersey (1,2), and in tropical rainforest soils (3), and was coined Feammox (4). Through a 180-days anaerobic incubation of soil samples collected at the New Jersey site, and using 16S rDNA PCR-DGGE, 454-pyosequecing, and qPCR analysis, we have shown that an Acidimicrobiaceae bacterium A6, belonging to the phylum Actinobacteria, is responsible for this Feammox process, described previously (1,2). We have enriched these Feammox bacteria in a high efficiency Feammox membrane reactor (with 85% NH4+removal per 48h), and isolated the pure Acidimicrobiaceae bacterium A6 strain 5, in an autotrophic medium. To determine if the Feammox bacteria found in this study are common, at least at the regional scale, we analyzed a series of local wetland-, upland-, as well as storm-water detention pond-sediments. Through anaerobic incubations and molecular biology analysis, the Feammox reaction and Acidimicrobiaceae bacterium A6 were found in three of twenty soil samples collected, indicating that the Feammox pathway might be widespread in selected soil environments. Results show that soil pH and Fe(III) content are key environmental factors controlling the distributions of Feammox bacteria, which require acidic conditions and the presence of iron oxides. Results from incubation experiments conducted at different temperatures have shown that, in contrast to another anaerobic ammonium oxidation pathways (e.g., anammox), the optimal temperature of the Feammox process is ~ 20° and that the organisms are still active when the temperature is around 10°. An incubation experiment amended with acetylene gas (C2H2) as a selected inhibitor showed that in the Feammox reaction, Fe(III) is the electron acceptor, which is reduced to Fe(II), and NH4+is the electron donor, which is oxidized to NO2-. After this process, NO2- is converted to

  3. Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds

    Science.gov (United States)

    Tokovenko, Bogdan T.; Protasov, Eugeniy S.; Gamaiunov, Stanislav V.; Rebets, Yuriy V.; Luzhetskyy, Andriy N.; Timofeyev, Maxim A.

    2016-01-01

    Actinobacteria isolated from unstudied ecosystems are one of the most interesting and promising sources of novel biologically active compounds. Cave ecosystems are unusual and rarely studied. Here, we report the isolation and characterization of ten new actinobacteria strains isolated from an ancient underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in Siberia with a focus on the biological activity of the obtained strains and the metabolite dereplication of one active strain. Streptomyces genera isolates from moonmilk speleothem demonstrated antibacterial and antifungal activities. Some of the strains were able to inhibit the growth of pathogenic Candida albicans. PMID:26901168

  4. Degradation of various alkyl ethers by alkyl ether-degrading Actinobacteria isolated from activated sludge of a mixed wastewater treatment.

    Science.gov (United States)

    Kim, Yong-Hak; Cha, Chang-Jun; Engesser, Karl-Heinrich; Kim, Sang-Jong

    2008-11-01

    Various substrate specificity groups of alkyl ether (AE)-degrading Actinobacteria coexisted in activated sewage sludge of a mixed wastewater treatment. There were substrate niche overlaps including diethyl ether between linear AE- and cyclic AE-degrading strains and phenetole between monoalkoxybenzene- and linear AE-degrading strains. Representatives of each group showed different substrate specificities and degradation pathways for the preferred substrates. Determining the rates of initial reactions and the initial metabolite(s) from whole cell biotransformation helped us to get information about the degradation pathways. Rhodococcus sp. strain DEE5311 and Rhodococcus rhodochrous strain 117 both were able to degrade anisole and phenetole through aromatic 2-monooxygenation to form 2-alkoxyphenols. In contrast, diethyl ether-oxidizing strain DEE5311 capable of degrading a broad range of linear AE, dibenzyl ether and monoalkoxybenzenes initially transformed anisole and phenetole to phenol via direct O-dealkylation. Compared to this, cyclic AE-degrading Rhodococcus sp. strain THF100 preferred tetrahydrofuran (265 ± 35 nmol min(-1)mg(-1) protein) to diethyl ether (diethoxybenzene-degrading Rhodococcus sp. strain DEOB100 and Gordonia sp. strain DEOB200 transformed 1,3-/1,4-dialkoxybenzenes to 3-/4-alkoxyphenols by similar manners in the order of rates (nmol min(-1) mg(-1) protein): 1,4-diethoxybenzene (11.1 vs. 3.9)>1,4-dimethoxybenzene (1.6 vs. 2.6)>1,3-dimethoxybenzene (0.6 vs. 0.6). This study suggests that the AE-degrading Actinobacteria can orchestrate various substrate specificity responses to the degradation of various categories of AE pollutants in activated sludge communities.

  5. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea.

    Science.gov (United States)

    Ettoumi, Besma; Chouchane, Habib; Guesmi, Amel; Mahjoubi, Mouna; Brusetti, Lorenzo; Neifar, Mohamed; Borin, Sara; Daffonchio, Daniele; Cherif, Ameur

    2016-01-01

    In the present study, the ecological distribution of marine Actinobacteria isolated from seamount and non-seamount stations in the Tyrrhenian Sea was investigated. A collection of 110 isolates was analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and 16S rRNA gene sequencing of representatives for each ARISA haplotype (n=49). Phylogenetic analysis of 16S rRNA sequences showed a wide diversity of marine isolates and clustered the strains into 11 different genera, Janibacter, Rhodococcus, Arthrobacter, Kocuria, Dietzia, Curtobacterium, Micrococcus, Citricoccus, Brevibacterium, Brachybacterium and Nocardioides. Interestingly, Janibacter limosus was the most encountered species particularly in seamounts stations, suggesting that it represents an endemic species of this particular ecosystem. The application of BOX-PCR fingerprinting on J. limosus sub-collection (n=22), allowed their separation into seven distinct BOX-genotypes suggesting a high intraspecific microdiversity among the collection. Furthermore, by screening the biotechnological potential of selected actinobacterial strains, J. limosus was shown to exhibit the most important biosurfactant activity. Our overall data indicates that Janibacter is a major and active component of seamounts in the Tyrrhenian Sea adapted to low nutrient ecological niche. PMID:27242145

  6. Actinobacteria possessing antimicrobial and antioxidant activities isolated from the pollen of scots pine (Pinus sylvestris) grown on the Baikal shore.

    Science.gov (United States)

    Axenov-Gribanov, Denis V; Voytsekhovskaya, Irina V; Rebets, Yuriy V; Tokovenko, Bogdan T; Penzina, Tatyana A; Gornostay, Tatyana G; Adelshin, Renat V; Protasov, Eugenii S; Luzhetskyy, Andriy N; Timofeyev, Maxim A

    2016-10-01

    Isolated ecosystems existing under specific environmental conditions have been shown to be promising sources of new strains of actinobacteria. The taiga forest of Baikal Siberia has not been well studied, and its actinobacterial population remains uncharacterized. The proximity between the huge water mass of Lake Baikal and high mountain ranges influences the structure and diversity of the plant world in Siberia. Here, we report the isolation of eighteen actinobacterial strains from male cones of Scots pine trees (Pinus sylvestris) growing on the shore of the ancient Lake Baikal in Siberia. In addition to more common representative strains of Streptomyces, several species belonging to the genera Rhodococcus, Amycolatopsis, and Micromonospora were isolated. All isolated strains exhibited antibacterial and antifungal activities. We identified several strains that inhibited the growth of the pathogen Candida albicans but did not hinder the growth of Saccharomyces cerevisiae. Several isolates were active against Gram-positive and Gram-negative bacteria. The high proportion of biologically active strains producing antibacterial and specific antifungal compounds may reflect their role in protecting pollen against phytopathogens. PMID:27392610

  7. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea

    KAUST Repository

    Ettoumi, Besma

    2016-04-01

    In the present study, the ecological distribution of marine Actinobacteria isolated from seamount and non-seamount stations in the Tyrrhenian Sea was investigated. A collection of 110 isolates was analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and 16S rRNA gene sequencing of representatives for each ARISA haplotype (n = 49). Phylogenetic analysis of 16S rRNA sequences showed a wide diversity of marine isolates and clustered the strains into 11 different genera, Janibacter, Rhodococcus, Arthrobacter, Kocuria, Dietzia, Curtobacterium, Micrococcus, Citricoccus, Brevibacterium, Brachybacterium and Nocardioides. Interestingly, Janibacter limosus was the most encountered species particularly in seamounts stations, suggesting that it represents an endemic species of this particular ecosystem. The application of BOX-PCR fingerprinting on J. limosus sub-collection (n = 22), allowed their separation into seven distinct BOX-genotypes suggesting a high intraspecific microdiversity among the collection. Furthermore, by screening the biotechnological potential of selected actinobacterial strains, J. limosus was shown to exhibit the most important biosurfactant activity. Our overall data indicates that Janibacter is a major and active component of seamounts in the Tyrrhenian Sea adapted to low nutrient ecological niche.

  8. MULTIDRUG RESISTANT GRAM NEGATIVE PATHOGENS ANTIBIOTIC PROFILE AND ITS EFFECTIVE CONTROL US ING SECONDARY METABOLITES FROM MARINE ACTINOBACTERIA

    Directory of Open Access Journals (Sweden)

    Shanthi J

    2012-05-01

    Full Text Available Aim:To screen the spread ofresistance in ESBLs producer’s particularly non lactose fermenting gram negative Acinetobacter spp. andPseudomonas spp.and study antimicrobial activity with crude extract from novel marine actinomycetes in India. Methods:Fifty clinical isolates in a period of one year were processed and the antibiotic susceptibility was determined by double disk approximation test, the ESBLs production was screened with phenotypic confirmatory methodsusing disks of amikacin, meropenem, netilimicin, ciprofloxacin, gentamicin, tigecycline and piperacillinalong with cephalosporin disks. Antimicrobial activity of the crude extract was determined by agar plug method. Results:The isolates collected from different samples were found resistant to third and fourth generation cephalosporins. ESBL production was detected in 56 % to 66 % of the isolates, amikacin and netilmicin showed 50% to 60% resistance they were also found resistant to carbapenems,86% resistance wasobserved in Acinetobacter spp. Two strains PM21 and PM27selected from 24 actinobacterial isolates had zone of inhibition >21mm. Conclusion:A high level of antibiotic resistance was found in Acinetobacter spp.in our study and may reflect the scenario in India. Earlier detection and reporting of ESBL producers will help in treating individual cases and also in controlling the spread of these resistant genes to othersensitive nosocomial isolates. The medical need for new agents is most acute and the future of this work aims to identify one such novel compound from marine actinobacteria.

  9. Dextrins from Maize Starch as Substances Activating the Growth of Bacteroidetes and Actinobacteria Simultaneously Inhibiting the Growth of Firmicutes, Responsible for the Occurrence of Obesity.

    Science.gov (United States)

    Barczynska, Renata; Kapusniak, Janusz; Litwin, Mieczyslaw; Slizewska, Katarzyna; Szalecki, Mieczyslaw

    2016-06-01

    Unarguably, diet has a significant impact on human intestinal microbiota. The role of prebiotics as substances supporting the maintenance of appropriate body weight and reducing the demand for energy via stimulation of the growth of beneficial microbiota of the gut and formation products such as short-chain fatty acids, is more and more often highlighted. The objective of this study was to evaluate whether dextrins from maize starch resistant to enzymatic digestion stimulate the growth of Bacteroidetes and Actinobacteria strains representing a majority of the population of colon microbiota in lean individuals and limit the growth of Firmicutes bacterial strains representing a majority of the population of colon microbiota in obese individuals. The study was conducted with the use of in vitro method, using isolates from faeces of children characterized by normal weight, overweight and obesity. It was demonstrated that dextrins from maize starch equally efficient stimulate the growth of the isolates derived from normal-weight, overweight and obese children, and therefore may be added to foods as a beneficial component stimulating growth of strains belonging to Actinobacteria and Bacteroidetes for both overweight, obese and normal-weight children. PMID:27155867

  10. Caracterización de actinobacterias raras, degradadoras de lignocelulosa: demostración de actividad lacasa en dos aislados de Tsukamurella sp y Cellulosimicrobium sp

    Directory of Open Access Journals (Sweden)

    Enrique Luis Revollo Escudero

    2014-01-01

    Full Text Available Título en ingles: Characterization of lignocelluloses-degrading rare actinobacteria: Demostration of laccase activity in two isolates of Tsukamurella sp and Cellulosimicrobium sp Resumen: Las características fisicoquímicas de la lignina y su compactación con la celulosa han dificultado la explotación biotecnológica de enormes cantidades de biomasa vegetal. Las lacasas constituyen una subfamilia de oxidasas multicobre que intervienen en la despolimerización de la lignina. Si bien han sido ampliamente caracterizadas en los hongos, los estudios de la diversidad y las funcionalidades de las lacasas en los procariotas se han centrado especialmente en isoformas enzimáticas de Streptomyces sp. En este trabajo se aislaron 20 cepas de actinobacterias del suelo. La actividad lacasa de 17 de ellas fue evidenciada en ensayos cualitativos con guayacol y dos cepas seleccionadas fueron caracterizadas en detalle. Las pruebas morfológicas y el análisis de las secuencias del gen 16S rRNA apuntan a que estos dos aislados pertenecen a los géneros Tsukamurella y Cellulosimicrobium. En cultivo sumergido con agitación, AC01 (Tsukamurella sp. expresó una máxima actividad de oxidación de ABTS (2,2’-azino-bis-(3-etilbenzotiazolin-6-sulfonato de 108 U/L. Por otra parte, AC18 (Cellulosimicrobium sp. que había exhibido una actividad oxidativa de guayacol superior a las 16 cepas restantes y demostró ser resistente a niveles tóxicos de cobre, logró un valor máximo de oxidación del ABTS de 0,56 U/L. Estos resultados sugieren que en el aislado AC18 operaría un fenómeno de especificidad de sustrato o de inductor, regulador de la expresión y de la actividad lacasa cuantificable. La caracterización genómica y funcional de las lacasas de nuevas actinobacterias lignocelulósicas ampliará la gama de centros redox con aplicaciones biotecnológicas específicas, además de facilitar el establecimiento de sus relaciones evolutivas con las eucariotas

  11. Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis.

    Science.gov (United States)

    Gupta, Radhey S; Khadka, Bijendra

    2016-02-01

    Homologs showing high degree of sequence similarity to the three subunits of the protochlorophyllide oxidoreductase enzyme complex (viz. BchL, BchN, and BchB), which carries out a central role in chlorophyll-bacteriochlorophyll (Bchl) biosynthesis, are uniquely found in photosynthetic organisms. The results of BLAST searches and homology modeling presented here show that proteins exhibiting a high degree of sequence and structural similarity to the BchB and BchN proteins are also present in organisms from the high G+C Gram-positive phylum of Actinobacteria, specifically in members of the genus Rubrobacter (R. x ylanophilus and R. r adiotolerans). The results presented exclude the possibility that the observed BLAST hits are for subunits of the nitrogenase complex or the chlorin reductase complex. The branching in phylogenetic trees and the sequence characteristics of the Rubrobacter BchB/BchN homologs indicate that these homologs are distinct from those found in other photosynthetic bacteria and that they may represent ancestral forms of the BchB/BchN proteins. Although a homolog showing high degree of sequence similarity to the BchL protein was not detected in Rubrobacter, another protein, belonging to the ParA/Soj/MinD family, present in these bacteria, exhibits high degree of structural similarity to the BchL. In addition to the BchB/BchN homologs, Rubrobacter species also contain homologs showing high degree of sequence similarity to different subunits of magnesium chelatase (BchD, BchH, and BchI) as well as proteins showing significant similarity to the BchP and BchG proteins. Interestingly, no homologs corresponding to the BchX, BchY, and BchZ proteins were detected in the Rubrobacter species. These results provide the first suggestive evidence that some form of photosynthesis either exists or was anciently present within the phylum Actinobacteria (high G+C Gram-positive) in members of the genus Rubrobacter. The significance of these results concerning the

  12. Anti-phytopathogen potential of endophytic actinobacteria isolated from tomato plants (Lycopersicon esculentum) in southern Brazil, and characterization of Streptomyces sp. R18(6), a potential biocontrol agent.

    Science.gov (United States)

    de Oliveira, Margaroni Fialho; da Silva, Mariana Germano; Van Der Sand, Sueli T

    2010-09-01

    Tomato plants (Lycopersicon esculentum) are highly susceptible to phytopathogen attack. The resulting intensive application of pesticides on tomato crops can affect the environment and health of humans and animals. The objective of this study was to select potential biocontrol agents among actinobacteria from tomato plants, in a search for alternative phytopathogen control. We evaluated 70 endophytic actinobacteria isolated from tomato plants in southern Brazil, testing their antimicrobial activity, siderophore production, indoleacetic acid production, and phosphate solubility. The actinomycete isolate with the highest antimicrobial potential was selected using the agar-well diffusion method, in order to optimize conditions for the production of compounds with antimicrobial activity. For this study, six growth media (starch casein-SC, ISP2, Bennett's, Sahin, Czapek-Dox, and TSB), three temperatures (25 degrees C, 30 degrees C, and 35 degrees C) and different pH were tested. Of the actinobacteria tested, 88.6% showed antimicrobial activity against at least one phytopathogen, 72.1% showed a positive reaction for indoleacetic acid production, 86.8% produced siderophores and 16.2% showed a positive reaction for phosphate solubility. Isolate R18(6) was selected due to its antagonistic activity against all phytopathogenic microorganisms tested in this study. The best conditions for production were observed in the SC medium, at 30 degrees C and pH 7.0. The isolate R18(6) showed close biochemical and genetic similarity to Streptomyces pluricolorescens. PMID:20542109

  13. 印度洋红树林沉积物可培养海洋放线菌多样性及其活性%Diversity and bioactivities of culturable marine actinobacteria isolated from mangrove sediment in Indian Ocean

    Institute of Scientific and Technical Information of China (English)

    何洁; 张道锋; 徐盈; 张晓梅; 唐蜀昆; 徐丽华; 李文均

    2012-01-01

    [目的]本研究旨在了解印度洋红树林沉积物可培养海洋放线菌多样性、抗菌活性及产酶活性.[方法]选用24种碳源为唯一能源培养基,利用稀释平板涂布方法对8个印度洋红树林沉积物样品进行分离,并基于16S rRNA基因系统发育分析的方法研究样品中海洋放线菌多样性;对分离得到的菌株进行抗菌活性和产酶活性检测.[结果]24种唯一碳源分离培养基中,非糖类碳源特别是甘油、丙氨酸分离效果最好,其次是多糖物质,最后是单糖.共分离得到521株海洋放线菌,经并菌后选取其中的139株代表性菌株测序,结果发现它们主要分布在放线菌纲7个亚目10个科的16个属,其中35个为潜在新种.有43.1%、33.3%、26.9%、25.5%、15.7%的实验菌株分别对枯草芽孢杆菌、白色念珠菌、大肠埃希氏菌、金黄色葡萄球菌、黑曲霉具有抑制作用;有36.5%、26.5%、22.4%、15.9%的实验菌株分别具有蛋白酶活性、纤维素酶活、淀粉酶活性、酯酶活性.[结论]印度洋红树林沉积物蕴藏着丰富的海洋放线菌资源,并具有较高生物活性,为后续工作提供良好的实验材料.%[Objective] In order to explore the diversity, antimicrobial activity and enzyme-producing activity of marine actinobacteria isolated from mangrove sediments in Indian Ocean. [Methods] Eight sediments collected from mangrove sediments in Indian Ocean were treated by the plate dilution method and spread on 24 isolation media only containing sole carbon source for energy. Marine actinobacteria were isolated and identified by 16S rRNA gene sequence analysis. The antimicrobial activity and enzyme-producing activity of isolated strains were further detected by spot planting method [Results] In total 139 representative strains were selected from 521 isolates, and they were further sequenced and performed phylogenetic analysis based on their 16S rRNA gene sequences. There were 35

  14. 药用植物内生放线菌的分离和生物学特性%Isolation and physiological characteristics of endophytic actinobacteria from medicinal plants

    Institute of Scientific and Technical Information of China (English)

    杜慧竟; 苏静; 余利岩; 张玉琴

    2013-01-01

    [Objective] To isolate, incubate and characterize cultivable endophytic antinobacteria from medicinal plants, and analyze the diversity of the endophytic antinobacteria, then explore the novel microbial resources. [Methods] Ten media were used to isolate endophytic antinobacteria from 37 fresh medicinal plant tissue samples. The optimal cultivation conditions for endophytic antinobacteria were determined by comparison. Based on the morphology of the colonies and cells of the new isolates, we chose174 isolates to analyze their 16S rRNA gene sequences and the diversity of the medicinal plant endophytic antinobacteria. The physiological characteristics of 27 representative strains were studied using Biolog GEN Ⅲ MicroPlates, API SOCH and API ZYM kits. [Results] In total 940 endophytics affiliated to 47 genera of 30 families were isolated, among which more than 600 actinobacteria belonged to 34 genera and 7 unknown taxa. Good growth of the endophytic antinobacteria on PYG ( peptone-yeast-glycerol) medium with pH 7.2 at 28 - 32℃ was observed. Physiological characteristics differences of these isolates related to their phylogenetic relationships. Greater differences were shown among the strains from the same host plants than those from different plants grown in the same area. [ Conclusion ] There are great diverse endophytic actinobacteria inside the medicinal plants. No direct relationship of the endophytic actinobacteria from medicinal plants with the host plants in the sole carbon source utilization, fermentation of carbon sources to produce acid and the enzyme activities was found, while it seemed that the physiological characteristics of the isolates related to the geographical distribution of their host.%[目的]探索药用植物内生环境可培养放线菌的分离、培养方法,总结药用植物内生放线菌的生物学特性,探讨其物种多样性,挖掘新的微生物资源.[方法]采用10种分离培养基对37个新鲜的药用植物样品进

  15. Competitive strategies differentiate closely related species of marine actinobacteria.

    Science.gov (United States)

    Patin, Nastassia V; Duncan, Katherine R; Dorrestein, Pieter C; Jensen, Paul R

    2016-02-01

    Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.

  16. Marine actinobacteria showing phosphate-solubilizing efficiency in Chorao Island, Goa, India

    Digital Repository Service at National Institute of Oceanography (India)

    Dastager, S.G.; Damare, S.R.

    H, and salt concentrations. Further, 16S rRNA gene sequence analyses were carried to identify the bacterial groups which are actively solubilized phosphate in vitro. Gene sequencing results reveal that all isolates were clustered into six different...

  17. Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria)

    Science.gov (United States)

    Klein, Brian A.; Faller, Lina L.; Jospin, Guillaume; Eisen, Jonathan A.; Coil, David A.

    2016-01-01

    Here, we present the draft genome sequence of the actinobacterium Curtobacterium sp. strain UCD-KPL2560, which was isolated from the running surface of an indoor track field house in Medford, MA, USA (42.409716°N, -71.115169°W). The genome assembly contains 3,480,487 bp in 156 contigs.

  18. Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes.

    Science.gov (United States)

    Sghaier, Haïtham; Hezbri, Karima; Ghodhbane-Gtari, Faten; Pujic, Petar; Sen, Arnab; Daffonchio, Daniele; Boudabous, Abdellatif; Tisa, Louis S; Klenk, Hans-Peter; Armengaud, Jean; Normand, Philippe; Gtari, Maher

    2016-01-01

    The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including 'molecular tinkering/opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively. PMID:26125681

  19. Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

    KAUST Repository

    Sghaier, Haïtham

    2015-06-30

    The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including ‘molecular tinkering/opportunism’ as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.

  20. Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria)

    Science.gov (United States)

    Koenigsaecker, Tynisha M.; Coil, David A.

    2016-01-01

    Here, we present the draft genome of Gordonia sp. strain UCD-TK1. The assembly contains 5,470,576 bp in 98 contigs. This strain was isolated from a disinfected ambulatory surgery center. PMID:27738036

  1. Protease inhibitors from marine actinobacteria as a potential source for antimalarial compound.

    Directory of Open Access Journals (Sweden)

    L Karthik

    Full Text Available The study was planned to screen the marine actinobacterial extract for the protease inhibitor activity and its anti- Pf activity under in vitro and in vivo conditions. Out of 100 isolates, only 3 isolates exhibited moderate to high protease inhibitor activities on trypsin, chymotrypsin and proteinase K. Based on protease inhibitor activity 3 isolates were chosen for further studies. The potential isolate was characterized by polyphasic approach and identified as Streptomyces sp LK3 (JF710608. The lead compound was identified as peptide from Streptomyces sp LK3. The double-reciprocal plot displayed inhibition mode is non-competitive and it confirms the irreversible nature of protease inhibitor. The peptide from Streptomyces sp LK3 extract showed significant anti plasmodial activity (IC50: 25.78 µg/ml. In in vivo model, the highest level of parasitemia suppression (≈ 45% was observed in 600 mg/kg of the peptide. These analyses revealed no significant changes were observed in the spleen and liver tissue during 8 dpi. The results confirmed up-regulation of TGF-β and down regulation of TNF-α in tissue and serum level in PbA infected peptide treated mice compared to PbA infection. The results obtained infer that the peptide possesses anti- Pf activity activity. It suggests that the extracts have novel metabolites and could be considered as a potential source for drug development.

  2. Evidence of α-, β- and γ-HCH mixture aerobic degradation by the native actinobacteria Streptomyces sp. M7.

    Science.gov (United States)

    Sineli, P E; Tortella, G; Dávila Costa, J S; Benimeli, C S; Cuozzo, S A

    2016-05-01

    The organochlorine insecticide γ-hexachlorocyclohexane (γ-HCH, lindane) and its non-insecticidal α- and β-isomers continue to pose serious environmental and health concerns, although their use has been restricted or completely banned for decades. In this study we report the first evidence of the growth ability of a Streptomyces strain in a mineral salt medium containing high doses of α- and β-HCH (16.6 mg l(-1)) as a carbon source. Degradation of HCH isomers by Streptomyces sp. M7 was investigated after 1, 4, and 7 days of incubation, determining chloride ion release, and residues in the supernatants by GC with µECD detection. The results show that both the α- and β-HCH isomers were effectively metabolized by Streptomyces sp. M7, with 80 and 78 % degradation respectively, after 7 days of incubation. Moreover, pentachlorocyclohexenes and tetrachlorocyclohexenes were detected as metabolites. In addition, the formation of possible persistent compounds such as chlorobenzenes and chlorophenols were studied by GC-MS, while no phenolic compounds were detected. In conclusion, we have demonstrated for the first time that Streptomyces sp. M7 can degrade α- and β-isomers individually or combined with γ-HCH and could be considered as a potential agent for bioremediation of environments contaminated by organochlorine isomers. PMID:27038951

  3. USE OF AGRICULTURAL WASTES FOR BIOMASS PRODUCTION OF THE PLANT GROWTH PROMOTER ACTINOBACTERIA, Streptomyces sp. MCR26

    Directory of Open Access Journals (Sweden)

    Iván Ávila-Cortes

    2014-10-01

    Full Text Available The use of agricultural wastes for plant growth promoting rhizobacteria (PGPR biomass production has not been widely explored. This study focuses on the development a culture medium for PGPR Streptomyces sp. MCR26, evaluating the influence of carnation harvest waste, yeast extract and ammonium sulfate on biomass production, as well as, the effect of biomass produced in the designed culture medium on the maintenance of PGPR MCR26 traits. The experiments were conducted by a full factorial design, varying nutritional sources concentrations, with duplicate experiments at the central point. Yeast extract and carnation harvest waste were the most influential factors, showing a positive effect on biomass production. The statistical model predicted optimal conditions for maximal biomass production at 20.0 g/L carnation harvest waste and 4.0 g/L yeast extract. Shake flask validation experiments resulted in 8.087 g/L of MCR26 biomass, 80.6% higher compared to carboxymetil cellulose (CMC broth. MCR26 biomass produced on designed culture medium enhanced hydroxamate production, and maintained phosphatases and indole-3-acetic acid synthesis. In addition, white clover inoculated plants presented higher shoot biomass accumulation compared to control treatment; nevertheless, there were no effects on seed germination. These results demonstrated that the designed culture medium effectively induced Streptomyces sp. MCR26 biomass production and maintained its plant growth promotion traits.

  4. Actinobacteria from Termite Mounds Show Antiviral Activity against Bovine Viral Diarrhea Virus, a Surrogate Model for Hepatitis C Virus

    Directory of Open Access Journals (Sweden)

    Marina Aiello Padilla

    2015-01-01

    Full Text Available Extracts from termite-associated bacteria were evaluated for in vitro antiviral activity against bovine viral diarrhea virus (BVDV. Two bacterial strains were identified as active, with percentages of inhibition (IP equal to 98%. Both strains were subjected to functional analysis via the addition of virus and extract at different time points in cell culture; the results showed that they were effective as posttreatments. Moreover, we performed MTT colorimetric assays to identify the CC50, IC50, and SI values of these strains, and strain CDPA27 was considered the most promising. In parallel, the isolates were identified as Streptomyces through 16S rRNA gene sequencing analysis. Specifically, CDPA27 was identified as S. chartreusis. The CDPA27 extract was fractionated on a C18-E SPE cartridge, and the fractions were reevaluated. A 100% methanol fraction was identified to contain the compound(s responsible for antiviral activity, which had an SI of 262.41. GC-MS analysis showed that this activity was likely associated with the compound(s that had a peak retention time of 5 min. Taken together, the results of the present study provide new information for antiviral research using natural sources, demonstrate the antiviral potential of Streptomyces chartreusis compounds isolated from termite mounds against BVDV, and lay the foundation for further studies on the treatment of HCV infection.

  5. Modestobacter caceresii sp. nov., novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper-arid Atacama Desert soils.

    Science.gov (United States)

    Busarakam, Kanungnid; Bull, Alan T; Trujillo, Martha E; Riesco, Raul; Sangal, Vartul; van Wezel, Gilles P; Goodfellow, Michael

    2016-06-01

    A polyphasic study was designed to determine the taxonomic provenance of three Modestobacter strains isolated from an extreme hyper-arid Atacama Desert soil. The strains, isolates KNN 45-1a, KNN 45-2b(T) and KNN 45-3b, were shown to have chemotaxonomic and morphological properties in line with their classification in the genus Modestobacter. The isolates had identical 16S rRNA gene sequences and formed a branch in the Modestobacter gene tree that was most closely related to the type strain of Modestobacter marinus (99.6% similarity). All three isolates were distinguished readily from Modestobacter type strains by a broad range of phenotypic properties, by qualitative and quantitative differences in fatty acid profiles and by BOX fingerprint patterns. The whole genome sequence of isolate KNN 45-2b(T) showed 89.3% average nucleotide identity, 90.1% (SD: 10.97%) average amino acid identity and a digital DNA-DNA hybridization value of 42.4±3.1 against the genome sequence of M. marinus DSM 45201(T), values consistent with its assignment to a separate species. On the basis of all of these data, it is proposed that the isolates be assigned to the genus Modestobacter as Modestobacter caceresii sp. nov. with isolate KNN 45-2b(T) (CECT 9023(T)=DSM 101691(T)) as the type strain. Analysis of the whole-genome sequence of M. caceresii KNN 45-2b(T), with 4683 open reading frames and a genome size of ∽4.96Mb, revealed the presence of genes and gene-clusters that encode for properties relevant to its adaptability to harsh environmental conditions prevalent in extreme hyper arid Atacama Desert soils. PMID:27108251

  6. 两种南海海绵放线菌的分离和培养研究%Isolating Actinobacteria from Two Marine Sponges of the South China Sea

    Institute of Scientific and Technical Information of China (English)

    欧阳永长; 梁梓添; 姚雅琪; 冯颖; 王鹏飞

    2014-01-01

    利用3种培养基对两种南海海绵Axinyssa和Halichondria共附生的放线菌(Actinobacterid)进行分离和培养,共得到41个放线菌菌株,分别属于Brachybaste rium、Janibacter、Dermacoccus、Brevibacterium、Saccharomonospora、A rthrobacter、Micromonospora、Tsukamurella和Streptomyces 9个属的14个种,其中Y12和Y13为候选新种属.这些放线菌能抑制金黄色葡萄球菌、大肠杆菌和枯草芽孢杆菌的生长,其分子方法显示这些放线菌具有产生聚酮类化合物和非核糖体多肽的潜力.

  7. Diversity of actinobacteria associated with coral Porites lutea and Galaxea fascicularis%澄黄滨珊瑚和丛生盔型珊瑚非培养放线菌多样性

    Institute of Scientific and Technical Information of China (English)

    陈淇; 龙丽娟; 张偲; 董俊德; 李洁

    2014-01-01

    [目的]研究澄黄滨珊瑚(Porites lutea)和丛生盔型珊瑚(Galaxea fascicularis)联合放线菌物种多样性.[方法]实验提取两种珊瑚的总DNA,利用放线菌特异性引物对样品总DNA进行扩增,通过构建16S rRNA基因克隆文库和系统发育分析,对三亚鹿回头岸礁区优势物种澄黄滨珊瑚和丛生盔型珊瑚联合放线菌的多样性和群落结构进行研究.[结果]118个从澄黄滨珊瑚克隆文库中随机挑选的阳性克隆子归为58个OTUs,主要分布于酸微菌亚目、棒状杆菌亚目、微球菌亚目、丙酸杆菌亚目和未知类群.丛生盔型珊瑚克隆文库共获得96个序列,归为31个OTUs,主要分布于酸微菌亚目和未知的放线菌类群.多样性指数和稀疏度曲线分析结果显示澄黄滨珊瑚联合放线菌物种多样性比丛生盔型珊瑚更高.[结论]澄黄滨珊瑚和丛生盔型珊瑚拥有较高水平的放线菌物种多样性和复杂的群落结构,并隐藏着大量的高等级放线菌新分类单元.

  8. Genome Sequence of the Acidophilic Ferrous Iron-Oxidizing Isolate Acidithrix ferrooxidans Strain Py-F3, the Proposed Type Strain of the Novel Actinobacterial Genus Acidithrix

    Science.gov (United States)

    Eisen, Sebastian; Poehlein, Anja; Johnson, D. Barrie; Daniel, Rolf; Schlömann, Michael

    2015-01-01

    Extremely acidophilic iron-oxidizing Gram-positive bacteria comprise species within the phyla Firmicutes and Actinobacteria. Here, we report the 4.02-Mb draft genome of Acidithrix ferrooxidans Py-F3, which was isolated from a stream draining an abandoned copper mine and proposed as the type species of a new genus of Actinobacteria. PMID:25931603

  9. Ectosymbionts and immunity in the leaf-cutting ant Acromyrmex subterraneus subterraneus.

    Science.gov (United States)

    de Souza, Danival José; Lenoir, Alain; Kasuya, Maria Catarina Megumi; Ribeiro, Myriam Marques Ramos; Devers, Séverine; Couceiro, Joel da Cruz; Della Lucia, Terezinha Maria Castro

    2013-02-01

    Associations with symbiotic organisms can serve as a strategy for social insects to resist pathogens. Antibiotics produced by attine ectosymbionts (Actinobacteria) suppress the growth of Escovopsis spp., the specialized parasite of attine fungus gardens. Our objective was to evaluate whether the presence or absence of symbiotic actinobacteria covering the whole ant cuticle is related to differential immunocompetence, respiratory rate and cuticular hydrocarbons (CHs). We evaluated these parameters in three worker groups of Acromyrmex subterraneus subterraneus: External workers (EXT), internal workers with actinobacteria covering the whole body (INB) and internal workers without actinobacteria covering the whole body (INØ). We also eliminated the actinobacteria by antibiotic treatment and examined worker encapsulation response. INB ants showed lower rates of encapsulation and respiration than did the EXT and INØ ants. The lower encapsulation rate did not seem to be a cost imposed by actinomycetes because the elimination of the actinomycetes did not increase the encapsulation rate. Instead, we propose that actinobacteria confer protection to young workers until the maturation of their immune system. Actinobacteria do not seem to change nestmate recognition in these colonies. Although it is known that actinobacteria have a specific action against Escovopsis spp., our studies, along with other independent studies, indicate that actinomycetes may also be important for the individual health of the workers. PMID:23207105

  10. Speleothem and biofilm formation in a granite/dolerite cave, Northern Sweden

    DEFF Research Database (Denmark)

    Sallstedt, T.; Ivarsson, M.; Lundberg, J.;

    2014-01-01

    incorporated remains of microorganisms. Two types of microbial communities can be distinguished associated with the speleothems: an Actinobacteria-like biofilm and a fungal community. Actinobacteria seem to play an important role in the formation of speleothem while the fungal community acts as both...... a constructive and a destructive agent. A modern biofilm dominated by Actinobacteria is present in the speleothem-free parts of the dolerite and located in cave ceiling cracks. These biofilms may represent sites of early speleothem formation. Because of its unusual position in between two types of host rock...

  11. 16SrRNA and enzymatic diversity of culturable bacteria from the sediments of oxygen minimum zone in the Arabian Sea

    Digital Repository Service at National Institute of Oceanography (India)

    Divya, B.; Soumya, K.V.; Nair, S.

    of organic matter. Multiple enzyme expression (C is greater than or equal to 3) was exhibited by Actinobacteria (100%), followed by unaffiliated group (62.5%) and Firmicutes (61.5%). Besides hydrolytic enzymes, the phylotypes also elaborated functional...

  12. Production and purification of a bioactive substance against multi-drug resistant human pathogens from the marine-sponge-derived Salinispora sp.

    Directory of Open Access Journals (Sweden)

    Satyendra Singh

    2014-10-01

    Conclusions: The present study reported the rifamycin W from sponge-associated Salinispora sp. and it exhibited appreciable antibacterial activity against multi-drug resistant human pathogens which indicated that sponge-associated Actinobacteria are significant sources of bioactive metabolites.

  13. The Actinobacterial mce4 Locus Encodes a Steroid Transporter

    NARCIS (Netherlands)

    Mohn, William W.; van der Geize, Robert; Stewart, Gordon R.; Okamoto, Sachi; Liu, Jie; Dijkhuizen, Lubbert; Eltis, Lindsay D.

    2008-01-01

    Bioinformatic analyses have suggested that Mce proteins in diverse actinobacteria are components of complex ATP-binding cassette transporter systems, comprising more than eight distinct proteins. In Mycobacterium tuberculosis, these proteins are implicated in interactions of this deadly pathogen wit

  14. Ectosymbionts and immunity in the leaf-cutting ant Acromyrmex subterraneus subterraneus

    OpenAIRE

    José De Souza, Danival; Lenoir, Alain; Megumi Kasuya, Maria Catarina; Marques Ramos Ribeiro, Myriam; Devers, Séverine; Couceiro, Joel da Cruz; Castro Della Lucia, Terezinha Maria

    2012-01-01

    International audience Associations with symbiotic organisms can serve as a strategy for social insects to resist pathogens. Antibiotics produced by attine ectosymbionts (Actinobacteria) suppress the growth of Escovopsis spp., the specialized parasite of attine fungus gardens. Our objective was to evaluate whether the presence or absence of symbiotic actinobacteria covering the whole ant cuticle is related to differential immunocompetence, respiratory rate and cuticular hydrocarbons (CHs)....

  15. Aquatic model for engine oil degradation by rhamnolipid producing Nocardiopsis VITSISB

    OpenAIRE

    Roy, Suki; Chandni, Shreta; Das, Ishita; Karthik, Loganathan; Kumar, Gaurav; Bhaskara Rao, Kokati Venkata

    2014-01-01

    The present study was focused on isolation, screening, characterization and application of biosurfactant producing marine actinobacteria. Twenty actinobacteria were isolated from marine water sample and were primarily screened for biosurfactant production using hemolytic activity method. Among the 20 isolates, six showed positive result for hemolytic activity and those were taken for further secondary screening tests such as oil collapse method, oil spreading method and emulsification method....

  16. Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

    Science.gov (United States)

    Riquelme, Cristina; Marshall Hathaway, Jennifer J.; Enes Dapkevicius, Maria de L. N.; Miller, Ana Z.; Kooser, Ara; Northup, Diana E.; Jurado, Valme; Fernandez, Octavio; Saiz-Jimenez, Cesareo; Cheeptham, Naowarat

    2015-01-01

    Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in

  17. Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions.

    Science.gov (United States)

    Riquelme, Cristina; Marshall Hathaway, Jennifer J; Enes Dapkevicius, Maria de L N; Miller, Ana Z; Kooser, Ara; Northup, Diana E; Jurado, Valme; Fernandez, Octavio; Saiz-Jimenez, Cesareo; Cheeptham, Naowarat

    2015-01-01

    Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in

  18. Phylogenetic diversity of culturable bacteria in surface seawater from the Drake Passage, Antarctica

    Science.gov (United States)

    Li, Zhao; Xing, Mengxin; Wang, Wei; Wang, Dan; Zhu, Jiancheng; Sun, Mi

    2016-01-01

    The Drake Passage is located between the Antarctic Peninsula and Tierra del Fuego in the south of South America. Surface seawater samples were collected at seven sites in the Drake Passage during the austral summer of 2012. The 16S rRNA sequences were analyzed from 187 isolated bacterial strains. Three phyla, 29 genera and 56 species were identified. The three phyla were Actinobacteria, Firmicutes and Proteobacteria; the Proteobacteria included α-Proteobacteria, β-Proteobacteria and γ-Proteobacteria. γ-Proteobacteria, Actinobacteria and Firmicutes were the dominant class or phyla in terms of quantity and species. Gram-positive bacteria (Actinobacteria and Firmicutes) accounted for 57.8% of all types identified. There were nine dominant genera, including Curtobacterium, Staphylococcus, and Halomonas, and 14 dominant species including Curtobacterium flaccumfaciens, Curtobacterium pusillum, and Staphylococcus sciuri. Of the strains identified, 87.2% were catalase positive or weakly positive.

  19. Phylogenetic diversity of culturable bacteria in surface seawater from the Drake Passage, Antarctica

    Science.gov (United States)

    Li, Zhao; Xing, Mengxin; Wang, Wei; Wang, Dan; Zhu, Jiancheng; Sun, Mi

    2016-09-01

    The Drake Passage is located between the Antarctic Peninsula and Tierra del Fuego in the south of South America. Surface seawater samples were collected at seven sites in the Drake Passage during the austral summer of 2012. The 16S rRNA sequences were analyzed from 187 isolated bacterial strains. Three phyla, 29 genera and 56 species were identified. The three phyla were Actinobacteria, Firmicutes and Proteobacteria; the Proteobacteria included α-Proteobacteria, β-Proteobacteria and γ-Proteobacteria. γ-Proteobacteria, Actinobacteria and Firmicutes were the dominant class or phyla in terms of quantity and species. Gram-positive bacteria (Actinobacteria and Firmicutes) accounted for 57.8% of all types identified. There were nine dominant genera, including Curtobacterium, Staphylococcus, and Halomonas, and 14 dominant species including Curtobacterium flaccumfaciens, Curtobacterium pusillum, and Staphylococcus sciuri. Of the strains identified, 87.2% were catalase positive or weakly positive.

  20. The gastric caeca of pentatomids as a house for actinomycetes

    Directory of Open Access Journals (Sweden)

    Zucchi Tiago D

    2012-06-01

    Full Text Available Abstract Background Microbes are extensively associated with insects, playing key roles in insect defense, nutrition and reproduction. Most of the associations reported involve Proteobacteria. Despite the fact that Actinobacteria associated with insects were shown to produce antibiotic barriers against pathogens to the hosts or to their food and nutrients, there are few studies focusing on their association with insects. Thus, we surveyed the Actinobacteria diversity on a specific region of the midgut of seven species of stinkbugs (Hemiptera: Pentatomidae known to carry a diversity of symbiotically-associated Proteobacteria. Results A total of 34 phylotypes were placed in 11 different Actinobacteria families. Dichelops melacanthus held the highest diversity with six actinobacteria families represented by nine phylotypes. Thyanta perditor (n = 7, Edessa meditabunda (n = 5, Loxa deducta (n = 4 and Pellaea stictica (n = 3 were all associated with three families. Piezodorus guildini (n = 3 and Nezara viridula (n = 3 had the lowest diversity, being associated with two (Propionibacteriaceae and Mycobacteriaceae and one (Streptomyceataceae families, respectively. Corynebacteriaceae and Mycobacteriaceae were the most common families with phylotypes from three different insect species each one. Conclusions Many phylotypes shared a low 16S rRNA gene similarity with their closest type strains and formed new phyletic lines on the periphery of several genera. This is a strong indicative that stinkbug caeca can harbor new species of actinobacteria, which might be derived from specific associations with the species of stinkbugs studied. Although the well-known role of actinobacteria as a source of biomolecules, the ecological features of these symbionts on the stinkbugs biology remain unknown.

  1. Interaction between workers during a short time window is required for bacterial symbiont transmission in Acromyrmex leaf-cutting ants

    DEFF Research Database (Denmark)

    Marsh, Sarah E.; Thomas-Poulsen, Michael; Pinto-Tomás, Adrián;

    2014-01-01

    a Pseudonocardia Actinobacteria exosymbiont on their bodies that produces antifungal compounds that help inhibit specialized parasites of the ants' fungal garden. Major workers emerge from their pupal cases (eclose) symbiont-free, but exhibit visible Actinobacterial coverage within 14 days post-eclosion. Using...... exosymbiont-carrying major workers did not acquire visible Actinobacteria (0% acquiring, n = 73). We further show that the majority of ants exposed to major workers with exosymbionts within 2 hours of eclosion acquired bacteria (60.7% acquiring, n = 28), while normal acquisition did not occur when exposure...

  2. EFFECTS OF CARBON SOURCE TO RESISTANCE OF HEAVY METALS OF OIL-DESTUCTIVE STRAINS ACTINOBACTERIA USED FOR BIOREMEDIATION Влияние источника углерода на устойчивость к тяжёлым металлам штаммов нефтеокисляющих актинобактерий, используемых в процессах биоремедиации

    Directory of Open Access Journals (Sweden)

    Khudokormov A. A.

    2012-11-01

    Full Text Available We studied the resistance of the eight strains of oil-destructive actinomycetes, isolated from the oil-contaminated ecosystems to heavy metal salts when cultivatiwng with different carbon sources. Furthermore we researched feasibility to use those microorganisms for bioremediation of oil- contaminated sites with high level of heavy metals

  3. A roadmap for natural product discovery based on large-scale genomics and metabolomics

    Science.gov (United States)

    Actinobacteria encode a wealth of natural product biosynthetic gene clusters, whose systematic study is complicated by numerous repetitive motifs. By combining several metrics we developed a method for global classification of these gene clusters into families (GCFs) and analyzed the biosynthetic ca...

  4. Characterization of Thermostable Cellulases Produced by Bacillus and Geobacillus Strains

    Science.gov (United States)

    Bacterial community composition of thermophilic (60 deg C) mixed cellulose-enrichment cultures was examined by constructing a 16S rDNA clone library which demonstrated major lineages affiliated to Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria. A tot...

  5. Association between Pseudonocardia symbionts and Atta leaf-cutting ants suggested by improved isolation methods

    DEFF Research Database (Denmark)

    Marsh, Sarah E.; Poulsen, Michael; Gorosito, Norma B.;

    2013-01-01

    Fungus-growing ants associate with multiple symbiotic microbes, including Actinobacteria for production of antibiotics. The best studied of these bacteria are within the genus Pseudonocardia, which in most fungus-growing ants are conspicuously visible on the external cuticle of workers. However, ...

  6. Genome Sequence of the Acidophilic Iron Oxidizer Ferrimicrobium acidiphilum Strain T23T

    Science.gov (United States)

    Eisen, Sebastian; Poehlein, Anja; Johnson, D. Barrie; Daniel, Rolf; Schlömann, Michael

    2015-01-01

    Extremely acidophilic iron-oxidizing bacteria have largely been characterized for the phyla Proteobacteria and Nitrospira. Here, we report the draft genome of an iron-oxidizing and -reducing heterotrophic mesophile of the Actinobacteria, Ferrimicrobium acidiphilum, which was isolated from an abandoned pyrite mine. The genome sequence comprises 3.08 Mb. PMID:25931604

  7. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery.

    Directory of Open Access Journals (Sweden)

    Michael Poulsen

    Full Text Available Identifying new sources for small molecule discovery is necessary to help mitigate the continuous emergence of antibiotic-resistance in pathogenic microbes. Recent studies indicate that one potentially rich source of novel natural products is Actinobacterial symbionts associated with social and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15 of these isolates identified 11 distinct and structurally diverse secondary metabolites, including a novel polyunsaturated and polyoxygenated macrocyclic lactam, which we name sceliphrolactam. By pairing the 15 Streptomyces strains against a collection of fungi and bacteria, we document their antifungal and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest.

  8. Increase in Bacterial Colony Formation from a Permafrost Ice Wedge Dosed with a Tomitella biformata Recombinant Resuscitation-Promoting Factor Protein.

    Science.gov (United States)

    Puspita, Indun Dewi; Kitagawa, Wataru; Kamagata, Yoichi; Tanaka, Michiko; Nakatsu, Cindy H

    2015-01-01

    Resuscitation-promoting factor (Rpf) is a protein that has been found in a number of different Actinobacteria species and has been shown to promote the growth of active cells and resuscitate dormant (non-dividing) cells. We previously reported the biological activity of an Rpf protein in Tomitella biformata AHU 1821(T), an Actinobacteria isolated from a permafrost ice wedge. This protein is excreted outside the cell; however, few studies have investigated its contribution in environmental samples to the growth or resuscitation of bacteria other than the original host. Therefore, the aim of the present study was to determine whether Rpf from T. biformata impacted the cultivation of other bacteria from the permafrost ice wedge from which it was originally isolated. All experiments used recombinant Rpf proteins produced using a Rhodococcus erythropolis expression system. Dilutions of melted surface sterilized ice wedge samples mixed with different doses of the purified recombinant Rpf (rRpf) protein indicated that the highest concentration tested, 1250 pM, had a significantly (p Brevibacterium antiquum strain VKM Ac-2118 (AY243344), with 98-99% sequence identity. This species is also a member of the phylum Actinobacteria and was originally isolated from Siberian permafrost sediments. The results of the present study demonstrated that rRpf not only promoted the growth of T. biformata from which it was isolated, but also enhanced colony formation by another Actinobacteria in an environmental sample. PMID:25843055

  9. Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina glauca Grown in Tunisia.

    Science.gov (United States)

    Ghodhbane-Gtari, Faten; Hurst, Sheldon G; Oshone, Rediet; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Gtari, Maher; Tisa, Louis S

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casuarina glauca collected in Tunisia. PMID:24874687

  10. Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown in Egypt

    OpenAIRE

    Hurst, Sheldon G.; Oshone, Rediet; Ghodhbane-Gtari, Faten; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Mansour, Samira; Gtari, Maher; Tisa, Louis S.

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.3-Mbp draft genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium isolated from root nodules of Casuarina cunninghamiana collected in Egypt.

  11. Draft Genome Sequence of Frankia sp. Strain Thr, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina cunninghamiana Grown in Egypt.

    Science.gov (United States)

    Hurst, Sheldon G; Oshone, Rediet; Ghodhbane-Gtari, Faten; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Mansour, Samira; Gtari, Maher; Tisa, Louis S

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.3-Mbp draft genome sequence for Frankia sp. stain Thr, a nitrogen-fixing actinobacterium isolated from root nodules of Casuarina cunninghamiana collected in Egypt. PMID:24855310

  12. Draft Genome Sequence of Frankia sp. Strain BMG5.23, a Salt-Tolerant Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina glauca Grown in Tunisia

    OpenAIRE

    Ghodhbane-Gtari, Faten; Hurst, Sheldon G.; Oshone, Rediet; Morris, Krystalynne; Abebe-Akele, Feseha; Thomas, W Kelley; Ktari, Amir; Salem, Karima; Gtari, Maher; Tisa, Louis S.

    2014-01-01

    Nitrogen-fixing actinobacteria of the genus Frankia are symbionts of woody dicotyledonous plants termed actinorhizal plants. We report here a 5.27-Mbp draft genome sequence for Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from root nodules of Casuarina glauca collected in Tunisia.

  13. Genome Sequence of "Candidatus Microthrix parvicella" Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

    OpenAIRE

    Muller, Emilie; Pinel, Nicolás; Gillece, John D.; Schupp, James M.; Lance B Price; Engelthaler, David M.; Levantesi, Caterina; Tandoi, Valter; Luong, Kkai; Baliga, Nitin S.; Korlach, Jonas; Keim, Paul S.; Wilmes, Paul

    2012-01-01

    “Candidatus Microthrix” bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: “Candidatus Microthrix parvicella” strain Bio17-1.

  14. Molecular characterization of Itp3 and Itp4, essential for C24-branched chain sterol-side-chain degradation in Rhodococcus rhodochrous DSM 43269

    NARCIS (Netherlands)

    Wilbrink, Maarten Hotse; van der Geize, Robert; Dijkhuizen, Lubbert; Spanning, R.J.M. van

    2012-01-01

    A previously identified sterol catabolic gene cluster is widely dispersed among actinobacteria, enabling them to degrade and grow on naturally occurring sterols. We investigated the physiological roles of various genes by targeted inactivation in mutant RG32 of Rhodococcus rhodochrous, which selecti

  15. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

    Science.gov (United States)

    Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

    2016-02-25

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.

  16. A potent fish pathogenic bacterial killer Streptomyces sp. isolated from the soils of east coast region, South India

    Institute of Scientific and Technical Information of China (English)

    Durairaj Thirumurugan; Ramasamy Vijayakumar

    2013-01-01

    Objective: To investigate the potentiality of the marine actinobacteria isolated from marine soil against fish pathogenic bacteria.Methods:east coast region (ECR) of Tamilnadu, South India. Then they were used for the isolation of actinobacteria by using conventional serial dilution technique on starch casein agar medium. The antibacterial activities of the actinobacteria were screened primarily by using cross streak plate method against fish pathogenic bacteria namely Vibrio alginolyticus, Vibrio parahaemolyticus,Vibrio cholera, Aeromonas sp. and Pseudomonas sp. The antimicrobial efficacy of the selected isolates was carried out with various organic solvents, and finally the active compound was subjected to chromatographic techniques including TLC and GC-MS.Results:In the present study, a total of 33 soil samples were collected from the Bay of Bengal, against fish pathogenic bacteria. Out of 21 antibacterial isolates, the isolate ECR77 was selected for further study based on its potential activity against fish pathogenic bacteria. Of the various solvents tested, the ethyl acetate extract had good antibacterial activity against the tested bacterial pathogens. The isolate ECR77 grew well on oat meal agar medium with 2% salt level at 35 °C. GC-MS study found that the presence of bioactive compounds namely tetradecanoic acid,n-hexadecanoic acid and octadecanoic acid. The morphological, physiological, biochemical and cultural characteristics of the potential isolate were supported the identity up to generic level asStreptomyces sp. ECR77. Conclusions: The results obtained from this study concludes that the ECR soils of South India is a hot spot of novel bioactive compound producing marine actinobacteria with great pharmaceutical values. Of the 82 actinobacteria isolated, 21 (26%) isolates were possessed antibacterial activity.

  17. Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess Plateau, China.

    Science.gov (United States)

    Zeng, Quanchao; Dong, Yanghong; An, Shaoshan

    2016-01-01

    Soil bacterial communities play an important role in nutrient recycling and storage in terrestrial ecosystems. Loess soils are one of the most important soil resources for maintaining the stability of vegetation ecosystems and are mainly distributed in northwest China. Estimating the distributions and affecting factors of soil bacterial communities associated with various types of vegetation will inform our understanding of the effect of vegetation restoration and climate change on these processes. In this study, we collected soil samples from 15 sites from north to south on the Loess Plateau of China that represent different ecosystem types and analyzed the distributions of soil bacterial communities by high-throughput 454 pyrosequencing. The results showed that the 142444 sequences were grouped into 36816 operational taxonomic units (OTUs) based on 97% similarity. The results of the analysis showed that the dominant taxonomic phyla observed in all samples were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria and Planctomycetes. Actinobacteria and Proteobacteria were the two most abundant groups in all samples. The relative abundance of Actinobacteria increased from 14.73% to 40.22% as the ecosystem changed from forest to sandy, while the relative abundance of Proteobacteria decreased from 35.35% to 21.40%. Actinobacteria and Proteobacteria had significant correlations with mean annual precipitation (MAP), pH, and soil moisture and nutrients. MAP was significantly correlated with soil chemical and physical properties. The relative abundance of Actinobacteria, Proteobacteria and Planctomycetes correlated significantly with MAP, suggesting that MAP was a key factor that affected the soil bacterial community composition. However, along with the MAP gradient, Chloroflexi, Bacteroidetes and Cyanobacteria had narrow ranges that did not significantly vary with the soil and environmental factors. Overall, we conclude that the edaphic properties and/or vegetation

  18. [Main bacterial groups in banana soil under rotated and continuous cropping].

    Science.gov (United States)

    Ouyang, Xian; Ruan, Xiao-Lei; Wu, Chao; Bai, Ting-Ting; Li, Hua-Ping

    2011-06-01

    Banana wilt is the main disease in banana production, while banana-leek rotation can effectively control the occurrence of the disease. In order to understand the variations of soil bacterial groups under banana-leek rotation and banana continuous cropping, soil samples under these two cropping systems were collected to extract crude DNA, and the bacterial 16S rDNA in V3 region was amplified by PCR. The PCR products were then separated by DGGE, and the main different bands were sequenced and compared with the records of NCBI to identify the germs. Under banana-leek rotation, soil bacterial diversity was richer, and the main bacterial groups were Bacteroidetes, Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria; while under banana continuous cropping, the soil bacterial diversity was somewhat decreased, and the main bacterial groups were Firmicutes, Proteobacteria, Actinobacteria, and Chloroflexi.

  19. Actinobacterial Flora in Feces of Healthy Cottontail Rabbits (Sylvilagus auduboni).

    Science.gov (United States)

    Zhang, Yu; Tan, Hongming; Deng, Qingli; Cao, Lixiang

    2015-03-01

    Most known antibiotics from bacteria are produced by Actinobacteria. However, little is known about the community structure and diversity of fecal actinobacteria from rabbit feces. To investigate the actinobacterial community structure in rabbit feces, different actinobacterial-specific primer sets were used to amplify the overlap regions of 16S rRNA genes from the same DNA. At the genus level, 12 actinobacterial genera were detected by the L and S libraries. Arthrobacter, Brachybacterium, Dietzia, Leucobacter, Microbacterium, Promicromonospora and Rhodococcus were detected by L and S libraries. The Nocardioides, Streptomyces and Williamsia were only detected by L library; the Oerskovia and Brevibacterium were only detected by S library. The results indicated that rabbit feces contain diverse nonpathogenic actinobacterial taxa and PCR primer sets could underestimate the actinobacterial diversity besides the DNA extract efficiency. PMID:25424303

  20. Unravelling the microbiome of eggs of the endangered sea turtle Eretmochelys imbricata identifies bacteria with activity against the emerging pathogen Fusarium falciforme.

    Directory of Open Access Journals (Sweden)

    Jullie M Sarmiento-Ramírez

    Full Text Available Habitat bioaugmentation and introduction of protective microbiota have been proposed as potential conservation strategies to rescue endangered mammals and amphibians from emerging diseases. For both strategies, insight into the microbiomes of the endangered species and their habitats is essential. Here, we sampled nests of the endangered sea turtle species Eretmochelys imbricata that were infected with the fungal pathogen Fusarium falciforme. Metagenomic analysis of the bacterial communities associated with the shells of the sea turtle eggs revealed approximately 16,664 operational taxonomic units, with Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes as the most dominant phyla. Subsequent isolation of Actinobacteria from the eggshells led to the identification of several genera (Streptomyces, Amycolaptosis, Micromomospora Plantactinospora and Solwaraspora that inhibit hyphal growth of the pathogen F. falciforme. These bacterial genera constitute a first set of microbial indicators to evaluate the potential role of microbiota in conservation of endangered sea turtle species.

  1. Actinobacterial Flora in Feces of Healthy Cottontail Rabbits (Sylvilagus auduboni).

    Science.gov (United States)

    Zhang, Yu; Tan, Hongming; Deng, Qingli; Cao, Lixiang

    2015-03-01

    Most known antibiotics from bacteria are produced by Actinobacteria. However, little is known about the community structure and diversity of fecal actinobacteria from rabbit feces. To investigate the actinobacterial community structure in rabbit feces, different actinobacterial-specific primer sets were used to amplify the overlap regions of 16S rRNA genes from the same DNA. At the genus level, 12 actinobacterial genera were detected by the L and S libraries. Arthrobacter, Brachybacterium, Dietzia, Leucobacter, Microbacterium, Promicromonospora and Rhodococcus were detected by L and S libraries. The Nocardioides, Streptomyces and Williamsia were only detected by L library; the Oerskovia and Brevibacterium were only detected by S library. The results indicated that rabbit feces contain diverse nonpathogenic actinobacterial taxa and PCR primer sets could underestimate the actinobacterial diversity besides the DNA extract efficiency.

  2. Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

    Energy Technology Data Exchange (ETDEWEB)

    Stackebrandt, Erko [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Zeytun, Ahmet [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Liolios, Konstantinos [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Chang, Yun-Juan [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Pukall, Rudiger [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

    2013-01-01

    Coriobacterium glomerans Haas and Ko nig 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2T is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for which complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  3. Copper Tube Pitting in Santa Fe Municipal Water Caused by Microbial Induced Corrosion

    Directory of Open Access Journals (Sweden)

    Thomas D. Burleigh

    2014-06-01

    Full Text Available Many copper water lines for municipal drinking water in Santa Fe, New Mexico USA, have developed pinhole leaks. The pitting matches the description of Type I pitting of copper, which has historically been attributed to water chemistry and to contaminants on the copper tubing surface. However, more recent studies attribute copper pitting to microbial induced corrosion (MIC. In order to test for microbes, the copper tubing was fixed in hexamethyldisilazane (HMDS, then the tops of the corrosion mounds were broken open, and the interior of the corrosion pits were examined with scanning electron microscopy (SEM. The analysis found that microbes resembling actinobacteria were deep inside the pits and wedged between the crystallographic planes of the corroded copper grains. The presence of actinobacteria confirms the possibility that the cause of this pitting corrosion was MIC. This observation provides better understanding and new methods for preventing the pitting of copper tubing in municipal water.

  4. 信息动态

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Actinobacteria is one of the best studied taxa of prokaryotes due to its great importance in biotechnology, medical science, ecology and etc.. Modern actinobacterial taxonomy is polyphasic taxonomy, which is based on the phylogenetic analysis of sequences of 16S rRNA genes and other conservative molecular sequences, and employs a variety of microbial information for polyphasic systematic study. Currently, with the development of large-scale sequencing, over 100 actinobacterial genomes have been finished. A comprehensive, detailed and robust phylogeny of actinobacteria is thus needed for understanding how this group emerged and maintained such a vast diversity throughout evolution and how every subgroup related to each other from various habitats. “Phylogenomics” and “Genomic Encyclopedia of Bacteria and Archaea, GEBA project” indicated that actinobacterial taxonomy stepped into the era of genomics. This review summarizes the actinobacterial taxonomic methodology of the genomic era, and results from recent studies.

  5. Spider, bacterial and fungal phospholipase D toxins make cyclic phosphate products.

    Science.gov (United States)

    Lajoie, Daniel M; Cordes, Matthew H J

    2015-12-15

    Phospholipase D (PLD) toxins from sicariid spiders, which cause disease in mammals, were recently found to convert their primary substrates, sphingomyelin and lysophosphatidylcholine, to cyclic phospholipids. Here we show that two PLD toxins from pathogenic actinobacteria and ascomycete fungi, which share distant homology with the spider toxins, also generate cyclic phospholipids. This shared function supports divergent evolution of the PLD toxins from a common ancestor and suggests the importance of cyclic phospholipids in pathogenicity.

  6. 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.

  7. Biosynthetic investigations of ansamycin natural products from marine-derived actinomycetes

    OpenAIRE

    Wilson, Micheal Christopher

    2011-01-01

    Ansamycin polyketides from actinobacteria include the potent antibiotic and anticancer agents rifamycin SV, ansamitocin P-3, and geldanamycin. These natural product macrolactams are characterized by an mC₇N structural unit derived from the aromatic acid 3-amino-5-hydroxybenzoate, which is carboxy extended by multimodular polyketide synthases utilizing primarily acetate and propionate building blocks prior to macrolactam cyclization. Herein, I report a multidisciplinary investigation of the bi...

  8. Concluding remarks

    OpenAIRE

    Lerayer, Alda

    2005-01-01

    International audience; The focus of this Symposium was on bifidobacteria and propionibacteria for dairy and probiotic applications.Both genera have many similarities: being phylogenetically closely grouped within the Actinobacteria, they are high G+C branch Gram-positive bacteria, and share several physiological properties, despite having different industrial applications. It was highlighted in this Symposium that, from the point of view of consumers, consumer organizations, and government a...

  9. On the limits of computational functional genomics for bacterial lifestyle prediction

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Röttger, Richard; Hauschild, Anne-Christin;

    2014-01-01

    We review the level of genomic specificity regarding actinobacterial pathogenicity. As they occupy various niches in diverse habitats, one may assume the existence of lifestyle-specific genomic features. We include 240 actinobacteria classified into four pathogenicity classes: human pathogens (HP...... in the post-genome era and despite next-generation sequencing technology, our ability to efficiently deduce real-world conclusions, such as pathogenicity classification, remains quite limited....

  10. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

    Directory of Open Access Journals (Sweden)

    Bruna Rafaella Z. Palermo

    2016-03-01

    Full Text Available Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isolated from mucus of the Brazilian endemic coral Mussismilia hispida. The sequences are available under accession number LDNX01000000 (http://www.ncbi.nlm.nih.gov/nuccore/LDNX00000000. The genomic analysis revealed interesting information about the adaptation of bacteria to the marine environment (such as genes involved in osmotic and oxidative stress and to the nutrient-rich environment provided by the coral mucus.

  11. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus.

    Science.gov (United States)

    Palermo, Bruna Rafaella Z; Castro, Daniel B A; Pereira, Letícia Bianca; Cauz, Ana Carolina G; Magalhães, Beatriz L; Carlos, Camila; da Costa, Fernanda L P; Scagion, Guilherme P; Higa, Juliana S; Almeida, Ludimila D; das Neves, Meiriele da S; Cordeiro, Melina Aparecida; do Prado, Paula F V; da Silva, Thiago M; Balsalobre, Thiago Willian A; Paulino, Luciana C; Vicentini, Renato; Ferraz, Lúcio F C; Ottoboni, Laura M M

    2016-03-01

    Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isolated from mucus of the Brazilian endemic coral Mussismilia hispida. The sequences are available under accession number LDNX01000000 (http://www.ncbi.nlm.nih.gov/nuccore/LDNX00000000). The genomic analysis revealed interesting information about the adaptation of bacteria to the marine environment (such as genes involved in osmotic and oxidative stress) and to the nutrient-rich environment provided by the coral mucus. PMID:26981384

  12. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

    OpenAIRE

    Palermo, Bruna Rafaella Z.; Castro, Daniel B.A.; Pereira, Letícia Bianca; Cauz, Ana Carolina G.; Beatriz L. Magalhães; Carlos, Camila; da Costa, Fernanda L.P.; Guilherme P. Scagion; Higa, Juliana S.; Almeida, Ludimila D.; das Neves, Meiriele da S.; Cordeiro, Melina Aparecida; Paula F.V. do Prado; da Silva, Thiago M.; Balsalobre, Thiago Willian A.

    2015-01-01

    Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isolated from mucus of the Brazilian endemic coral Mussismilia hispida. The sequences are available under accession number LDNX01000000 (http://www.ncbi.nlm.nih.gov/nuccore/LDNX00000000). The genomic analysis revealed interesting information about the adaptation of bacteria to the marine environment (such as genes involved in osmotic and oxidative stress) and to the nutrient-rich environment provided by the cora...

  13. Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

    OpenAIRE

    Palermo, Bruna Rafaella Z.; Castro, Daniel B.A.; Letícia Bianca Pereira; Cauz, Ana Carolina G.; Beatriz L. Magalhães; Camila Carlos; da Costa, Fernanda L.P.; Guilherme P. Scagion; Higa, Juliana S.; Almeida, Ludimila D.; das Neves, Meiriele da S.; Melina Aparecida Cordeiro; Paula F.V. do Prado; da Silva, Thiago M.; Balsalobre, Thiago Willian A.

    2016-01-01

    Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isolated from mucus of the Brazilian endemic coral Mussismilia hispida. The sequences are available under accession number LDNX01000000 (http://www.ncbi.nlm.nih.gov/nuccore/LDNX00000000). The genomic analysis revealed interesting information about the adaptation of bacteria to the marine environment (such as genes involved in osmotic and oxidative stress) and to the nutrient-rich environment provided by the cora...

  14. Concluding remarks

    OpenAIRE

    Lerayer, Alda

    2005-01-01

    International audience The focus of this Symposium was on bifidobacteria and propionibacteria for dairy and probiotic applications.Both genera have many similarities: being phylogenetically closely grouped within the Actinobacteria, they are high G+C branch Gram-positive bacteria, and share several physiological properties, despite having different industrial applications. It was highlighted in this Symposium that, from the point of view of consumers, consumer organizations, and government...

  15. Effects of growth stage and fulvic acid on the diversity and dynamics of endophytic bacterial community in Stevia rebaudiana Bertoni leaves

    OpenAIRE

    Yu, Xuejian; Yang, Jinshui; Wang, Entao; Li, Baozhen; Yuan, Hongli

    2015-01-01

    The aim of this study was to learn the interactions among the endophytic bacteria, the plant growth, the foliar spray of fulvic acid, and the accumulation of steviol glycosides in the leaves of Stevia rebaudiana. Metagenomic DNA was extracted from the Stevia leaves at different growth stages with or without the fulvic acid treatment; and the diversity of endophytic bacteria in Stevia leaves was estimated by pyrosequencing of 16S rRNA genes. As results, Proteobacteria, Actinobacteria, Bacteroi...

  16. Benzoyl Peroxide Formulated Polycarbophil/Carbopol 934P Hydrogel with Selective Antimicrobial Activity, Potentially Beneficial for Treatment and Prevention of Bacterial Vaginosis

    OpenAIRE

    Shiqi Xu; Cavera, Veronica L.; Rogers, Michael A.; Qingrong Huang; Konstantin Zubovskiy; Michael L. Chikindas

    2013-01-01

    The human vagina is colonized by a variety of indigenous microflora; in healthy individuals the predominant bacterial genus is Lactobacillus while those with bacterial vaginosis (BV) carry a variety of anaerobic representatives of the phylum Actinobacteria. In this study, we evaluated the antimicrobial activity of benzoyl peroxide (BPO) encapsulated in a hydrogel against Gardnerella vaginalis, one of the causative agents of BV, as well as indicating its safety for healthy human lactobacilli. ...

  17. Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments

    OpenAIRE

    Crits-Christoph, Alexander; Robinson, Courtney K.; Ma, Bing; Ravel, Jacques; Wierzchos, Jacek; Ascaso, Carmen; Artieda, Octavio; Souza-Egipsy, Virginia; Casero, M. Cristina; DiRuggiero, Jocelyne

    2016-01-01

    Under extreme water deficit, endolithic (inside rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts, yet their diversity and functional adaptations remain vastly unexplored. The metagenomic analyses of the communities from two rock substrates, calcite and ignimbrite, revealed that they were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi. The relative distribution of major phyla was significantly different between the two substrates and...

  18. Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity

    OpenAIRE

    De Wever, Aaike; Muylaert, Koenraad; Van der Gucht, Katleen; Pirlot, Samuel; Cocquyt, Christine; Descy, Jean-Pierre; Plisnier, Pierre-Denis; Vyverman, Wim

    2005-01-01

    Vertical and latitudinal differences in bacterial community composition (BCC) in Lake Tanganyika were studied during the dry season of 2002 by means of denaturing gradient gel electrophoresis analysis of PCR-amplified 16S RNA fragments. Dominant bands were sequenced and identified as members of the Cyanobacteria, Actinobacteria, Nitrospirae, green nonsulfur bacteria, and Firmicutes divisions and the Gamma- and Deltaproteobacteria subdivisions. The BCC in the lake displayed both vertical and l...

  19. Specificity and stability of the Acromyrmex–Pseudonocardia symbiosis

    DEFF Research Database (Denmark)

    Andersen, Sandra Breum; Hansen, Lars H.; Sapountzis, Panagiotis;

    2013-01-01

    The stability of mutualistic interactions is likely to be affected by the genetic diversity of symbionts that compete for the same functional niche. Fungus-growing (attine) ants have multiple complex symbioses and thus provide ample opportunities to address questions of symbiont specificity and d...... diversity. Among the partners are Actinobacteria of the genus Pseudonocardia that are maintained on the ant cuticle to produce antibiotics, primarily against a fungal parasite of the mutualistic gardens. The symbiosis has been assumed to ...

  20. The Population Structure of Antibiotic-Producing Bacterial Symbionts of Apterostigma dentigerum Ants: Impacts of Coevolution and Multipartite Symbiosis

    OpenAIRE

    Caldera, Eric J.; Currie, Cameron R

    2012-01-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to n...

  1. Bacterial succession within an ephemeral hypereutrophic mojave desert playa lake

    Science.gov (United States)

    Navarro, J.B.; Moser, D.P.; Flores, A.; Ross, C.; Rosen, Michael R.; Dong, H.; Zhang, G.; Hedlund, B.P.

    2009-01-01

    Ephemerally wet playas are conspicuous features of arid landscapes worldwide; however, they have not been well studied as habitats for microorganisms. We tracked the geochemistry and microbial community in Silver Lake playa, California, over one flooding/desiccation cycle following the unusually wet winter of 2004-2005. Over the course of the study, total dissolved solids increased by 10-fold and pH increased by nearly one unit. As the lake contracted and temperatures increased over the summer, a moderately dense planktonic population of 1 ?????106 cells ml-1 of culturable heterotrophs was replaced by a dense population of more than 1????????109 cells ml-1, which appears to be the highest concentration of culturable planktonic heterotrophs reported in any natural aquatic ecosystem. This correlated with a dramatic depletion of nitrate as well as changes in the microbial community, as assessed by small subunit ribosomal RNA gene sequencing of bacterial isolates and uncultivated clones. Isolates from the early-phase flooded playa were primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet clone libraries were dominated by Betaproteobacteria and yet uncultivated Actinobacteria. Isolates from the late-flooded phase ecosystem were predominantly Proteobacteria, particularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, Hydrogenophaga, Alishwenella, and relatives of Thauera; however, clone libraries were composed almost entirely of Synechococcus (Cyanobacteria). A sample taken after the playa surface was completely desiccated contained diverse culturable Actinobacteria typically isolated from soils. In total, 205 isolates and 166 clones represented 82 and 44 species-level groups, respectively, including a wide diversity of Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, and Cyanobacteria. ?? 2008 Springer Science+Business Media, LLC.

  2. Genome sequence of the Fleming strain of Micrococcus luteus, a simple free- living actinobacterium

    Energy Technology Data Exchange (ETDEWEB)

    Young, Michael; Artsatbanov, Vladislav; Beller, Harry R.; Chandra, Govind; Chater, Keith F.; Dover, Lynn G.; Goh, Ee-Been; Kahan, Tamar; Kaprelyants, Arseny S.; Kyrpides, Nikos; Lapidus, Alla; Lowry, Stephen R.; Lykidis, Athanasios; Mahillon, Jacques; Markowitz, Viktor; Mavrommatis, Konstantinos; Mukamolova, Galina V.; Oren, Aharon; Rokem, J. Stefan; Smith, Margaret C. M.; Young, Danielle I.; Greenblatt, Charles L.

    2009-11-01

    Micrococcus luteus (NCTC2665, Fleming strain) has one of the smallest genomes of free living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content 73%) predicted to encode 2403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 IS elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the rrs gene of one of only two rrn operons found in M. luteus. The genome encodes only four sigma factors and fourteen response regulators, indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of M. luteus to {Beta}-lactam antibiotics may result from the presence of a reduced set of penicillin binding proteins and the absence of a wblC gene, which plays an important role in antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth, M. luteus has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria, M. luteus appears to be able to metabolize glycogen only via trehalose, and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to other actinobacteria, M. luteus encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy and its complement of other dormancy-related proteins is also much reduced. M. luteus is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three gene cluster essential for this metabolism has been identified in the genome.

  3. Phylogeny and Functions of Bacterial Communities Associated with Field-Grown Rice Shoots

    OpenAIRE

    Okubo, Takashi; Ikeda, Seishi; Sasaki, Kazuhiro; Ohshima, Kenshiro; Hattori, Masahira; Sato, Tadashi; Minamisawa, Kiwamu

    2014-01-01

    Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51–52%), Actinobacteria (11–15%), Gammaproteobacteria (9–10%), and Betaproteobacteria (4–10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminoc...

  4. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil

    OpenAIRE

    Pacchioni, Ralfo G; Fabíola M. Carvalho; Claudia E Thompson; Faustino, André L F; Nicolini, Fernanda; Pereira, Tatiana S; Silva, Rita C B; Cantão, Mauricio E; Gerber, Alexandra; Vasconcelos, Ana T. R.; Agnez-Lima, Lucymara F

    2014-01-01

    Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related...

  5. Diversity of the bacterial community in the rice rhizosphere managed under conventional and no-tillage practices.

    Science.gov (United States)

    Aslam, Zubair; Yasir, Muhammad; Yoon, Hwan Sik; Jeon, Che Ok; Chung, Young Ryun

    2013-12-01

    Bacterial diversity in the rice rhizosphere at different rice growth stages, managed under conventional and no-tillage practices, was explored using a culture-based approach. Actinobacteria are among the bacterial phyla abundant in the rice rhizosphere. Their diversity was further examined by constructing metagenomic libraries based on the 16S rRNA gene, using actinobacterial- and streptomycete-specific polymerase chain reaction (PCR) primers. The study included 132 culturable strains and 125 clones from the 16S rRNA gene libraries. In conventional tillage, there were 38% Proteobacteria, 22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes, and 2% Acidobacteria, whereas with no-tillage management there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes, and 8% Bacteroidetes as estimated using the culture-dependent method during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89-97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera. PMID:24385351

  6. Rhodococcus erythropolis MTHt3 biotransforms ergopeptines to lysergic acid

    OpenAIRE

    Thamhesl, Michaela; Apfelthaler, Elisabeth; Schwartz-Zimmermann, Heidi Elisabeth; Kunz-Vekiru, Elisavet; Krska, Rudolf; Kneifel, Wolfgang; Schatzmayr, Gerd; Moll, Wulf-Dieter

    2015-01-01

    Background Ergopeptines are a predominant class of ergot alkaloids produced by tall fescue grass endophyte Neotyphodium coenophialum or cereal pathogen Claviceps purpurea. The vasoconstrictive activity of ergopeptines makes them toxic for mammals, and they can be a problem in animal husbandry. Results We isolated an ergopeptine degrading bacterial strain, MTHt3, and classified it, based on its 16S rDNA sequence, as a strain of Rhodococcus erythropolis (Nocardiaceae, Actinobacteria). For strai...

  7. Keratinolytic abilities of Micrococcus luteus from poultry waste

    OpenAIRE

    Wojciech Laba; Anna Choinska; Anna Rodziewicz; Michal Piegza

    2015-01-01

    Keratinolytic microorganisms have become the subject of scientific interest due to their ability to biosynthesize specific keratinases and their prospective application in keratinic waste management. Among several bacterial classes, actinobacteria remain one of the most important sources of keratin-degrading strains, however members of the Micrococcaceae family are rarely scrutinized in regard to their applicatory keratinolytic potential. The tested Micrococcus sp. B1pz isolate from poultry f...

  8. Differential distribution of type II CRISPR-Cas systems in agricultural and nonagricultural campylobacter coli and campylobacter jejuni isolates correlates with lack of shared environments

    OpenAIRE

    Pearson, Bruce M.; Louwen, Rogier; Baarlen, van, P.; Vliet, van, L.P.W.

    2015-01-01

    CRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmids which are widespread in prokaryotes. Here we have studied whether phylogenetic relatedness or sharing of environmental niches affects the distribution and dissemination of Type II CRISPR-Cas systems, first in 132 bacterial genomes from 15 phylogenetic classes, ranging from Proteobacteria to Actinobacteria. There was clustering of dist...

  9. Bacterial proteasome activator bpa (rv3780 is a novel ring-shaped interactor of the mycobacterial proteasome.

    Directory of Open Access Journals (Sweden)

    Cyrille L Delley

    Full Text Available The occurrence of the proteasome in bacteria is limited to the phylum of actinobacteria, where it is maintained in parallel to the usual bacterial compartmentalizing proteases. The role it plays in these organisms is still not fully understood, but in the human pathogen Mycobacterium tuberculosis (Mtb the proteasome supports persistence in the host. In complex with the ring-shaped ATPase Mpa (called ARC in other actinobacteria, the proteasome can degrade proteins that have been post-translationally modified with the prokaryotic ubiquitin-like protein Pup. Unlike for the eukaryotic proteasome core particle, no other bacterial proteasome interactors have been identified to date. Here we describe and characterize a novel bacterial proteasome activator of Mycobacterium tuberculosis we termed Bpa (Rv3780, using a combination of biochemical and biophysical methods. Bpa features a canonical C-terminal proteasome interaction motif referred to as the HbYX motif, and its orthologs are only found in those actinobacteria encoding the proteasomal subunits. Bpa can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome. Using negative-stain electron microscopy, we show that Bpa forms a ring-shaped homooligomer that can bind coaxially to the face of the proteasome cylinder. Interestingly, Bpa can stimulate the proteasomal degradation of the model substrate β-casein, which suggests it could play a role in the removal of non-native or damaged proteins.

  10. Bacterial proteasome activator bpa (rv3780) is a novel ring-shaped interactor of the mycobacterial proteasome.

    Science.gov (United States)

    Delley, Cyrille L; Laederach, Juerg; Ziemski, Michal; Bolten, Marcel; Boehringer, Daniel; Weber-Ban, Eilika

    2014-01-01

    The occurrence of the proteasome in bacteria is limited to the phylum of actinobacteria, where it is maintained in parallel to the usual bacterial compartmentalizing proteases. The role it plays in these organisms is still not fully understood, but in the human pathogen Mycobacterium tuberculosis (Mtb) the proteasome supports persistence in the host. In complex with the ring-shaped ATPase Mpa (called ARC in other actinobacteria), the proteasome can degrade proteins that have been post-translationally modified with the prokaryotic ubiquitin-like protein Pup. Unlike for the eukaryotic proteasome core particle, no other bacterial proteasome interactors have been identified to date. Here we describe and characterize a novel bacterial proteasome activator of Mycobacterium tuberculosis we termed Bpa (Rv3780), using a combination of biochemical and biophysical methods. Bpa features a canonical C-terminal proteasome interaction motif referred to as the HbYX motif, and its orthologs are only found in those actinobacteria encoding the proteasomal subunits. Bpa can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome. Using negative-stain electron microscopy, we show that Bpa forms a ring-shaped homooligomer that can bind coaxially to the face of the proteasome cylinder. Interestingly, Bpa can stimulate the proteasomal degradation of the model substrate β-casein, which suggests it could play a role in the removal of non-native or damaged proteins. PMID:25469515

  11. Composition and diversity analysis of the gut bacterial community of the Oriental armyworm, Mythimna separata, determined by culture-independent and culture-dependent techniques.

    Science.gov (United States)

    He, Cai; Nan, Xiaoning; Zhang, Zhengqing; Li, Menglou

    2013-01-01

    The intestinal bacteria community structure and diversity of the Oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae), was studied by analysis of a 16S rDNA clone library, denaturing gradient gel electrophoresis,and culture-dependent techniques. The 16S rDNA clone library revealed a bacterial community diversity comprising Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes and Proteobacteria, among which Escherichia coli (Migula) (Enterobacteriales: Enterobacteriaceae) was the dominant bacteria. The intestinal bacteria isolated by PCR-denaturing gradient gel electrophoresis were classified to Firmicutes, Proteobacteria, and Gracilicutes, and E. coli was again the dominant bacteria. The culture-dependent technique showed that the intestinal bacteria belonged to Firmicutes and Actinobacteria, and Staphylococcus was the dominant bacteria. The intestinal bacteria of M. separata were widely distributed among the groups Cyanobacteria, Firmicutes, Actinobacteria, Gracilicutes, Proteobacteria, and Gracilicutes. 16S rDNA clone library, denaturing gradient gel electrophoresis, and culture-dependent techniques should be integrated to obtain precise results in terms of the microbial community and its diversity. PMID:24773514

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

    Science.gov (United States)

    Otlewska, Anna; Adamiak, Justyna; Gutarowska, Beata

    2015-02-01

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

  13. Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India and their antimicrobial activities

    Directory of Open Access Journals (Sweden)

    Salam eNimaichand

    2015-05-01

    Full Text Available Studies on actinobacterial diversity in limestone habitats are scarce. This paper reports profiling of actinobacteria isolated from Hundung limestone samples in Manipur, India using ARDRA as the molecular tool for preliminary classification. A total of 137 actinobacteria were clustered into 31 phylotypic groups based on the ARDRA pattern generated and representative of each group was subjected to 16S rRNA gene sequencing. Generic diversity of the limestone isolates consisted of Streptomyces (15 phylotypic groups, Micromonospora (4, Amycolatopsis (3, Arthrobacter (3, Kitasatospora (2, Janibacter (1, Nocardia (1, Pseudonocardia (1 and Rhodococcus (1. Considering the antimicrobial potential of these actinobacteria, 19 showed antimicrobial activities against at least one of the bacterial and candidal test pathogens, while 45 exhibit biocontrol activities against at least one of the rice fungal pathogens. Out of the 137 actinobacterial isolates, 118 were found to have at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, NRPS. The results indicate that 86% of the strains isolated from Hundung limestone deposit sites possessed biosynthetic gene clusters of which 40% exhibited antimicrobial activities. It can, therefore, be concluded that limestone habitat is a promising source for search of novel secondary metabolites.

  14. Community of environmental streptomyces related to geosmin development in Chinese liquors.

    Science.gov (United States)

    Du, Hai; Lu, Hu; Xu, Yan; Du, Xiaowei

    2013-02-13

    Diverse Streptomyces species act as geosmin producers in the Chinese liquor-making process. In this paper, the ecology of these Streptomyces species was analyzed using denaturing gradient gel electrophoresis (DGGE) of amplified Actinobacteria -specified rDNA. The result showed that Streptomyces were widely distributed during Daqu incubation, and multiple processing, geographic, and climate factors can affect their distribution and diversity. The genes associated with geosmin production were characterized in four geosmin-producing Streptomyces strains, all of which were isolated from geosmin-contaminated Daqu. On the basis of this information, a real-time PCR method was developed, enabling the detection of traces of Streptomyces in complex solid-state matrices. The primer was targeted at the gene coding for geosmin synthase (geoA). The real-time PCR method was found to be specific for geosmin-producing Streptomyces and did not show any cross-reactivity with geosmin-negative isolates, which are frequently present in the Chinese liquor-brewing process. Quantification of geoA in the Chinese liquor-making process could permit the monitoring of the level of geosmin producers prior to the occurrence of geosmin production. Comparison of the qPCR results based on the gene encoding geosmin synthase and Actinobacteria-specified rDNA showed that about 1-10% of the Actinobacteria carry the geosmin synthesis gene.

  15. Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

    Directory of Open Access Journals (Sweden)

    Lee H. Bergstrand

    2016-03-01

    Full Text Available Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria.

  16. Isolation, identification, and characterization of gut microflora of Perionyx excavatus collected from Midnapore, West Bengal.

    Science.gov (United States)

    Samanta, Tanushree Tulsian; Das, Ankita

    2016-03-01

    Agriculture is an important part of the economy of the undivided Midnapore district. Agricultural land is its asset and most importantly its means of sustenance as well as survival. Earthworms are invertebrates that play a key role in recycling organic matters in soils. Since the intestines of earthworms harbor wide ranges of microorganisms, enzymes, hormones etc., these half digested materials decompose rapidly and are transformed into a stabilized material called vermicompost which is very useful for increasing the soil fertility. One has to look for these characters before recommending any species for vermiculture. In the present study, Perionyx excavatus specimens were collected from the undivided Midnapore district and from the Earthworms gut, bacteria, fungus, actinobacteria, and yeast were isolated and identified using various morphological and biochemical tests. All the bacterial isolates were identified using morphological study, staining techniques, and different biochemical tests such as catalase test, KOH test, H2 SO4 test, Starch hydrolysis test, oxidase test, and sucrose hydrolysis test. All the fungal, actinobacteria, and yeast isolates were subjected to staining and morphological characterization (color and texture of fungal colony). Bacterial isolates of genus Bacillus sp., Staphylococcus sp., Enterococci, Micrococcus sp., Enterobacter sp., and Citrobacter sp. were identified. Among the fungal isolates Aspergilus sp., and P. boydii were identified. Streptomyces sp., Nocardia sp. among the actinobacteria and Candida sp. among yeast were also found to be present in earthworm gut and these might play an important role along with the earthworm to increase the quality and fertility of soil. PMID:26821782

  17. Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic.

    Science.gov (United States)

    Wilhelm, Roland C; Niederberger, Thomas D; Greer, Charles; Whyte, Lyle G

    2011-04-01

    The abundance and structure of archaeal and bacterial communities from the active layer and the associated permafrost of a moderately acidic (pH Canada) were investigated using culture- and molecular-based methods. Aerobic viable cell counts from the active layer were ∼100-fold greater than those from the permafrost (2.5 × 10(5) CFU·(g soil dry mass)(-1)); however, a greater diversity of isolates were cultured from permafrost, as determined by 16S rRNA gene sequencing. Isolates from both layers demonstrated growth characteristics of a psychrotolerant, halotolerant, and acidotolerant community. Archaea constituted 0.1% of the total 16S rRNA gene copy number and, in the 16S rRNA gene clone library, predominantly (71% and 95%) consisted of Crenarchaeota related to Group I. 1b. In contrast, bacterial communities were diverse (Shannon's diversity index, H = ∼4), with Acidobacteria constituting the largest division of active layer clones (30%) and Actinobacteria most abundant in permafrost (28%). Direct comparisons of 16S rRNA gene sequence data highlighted significant differences between the bacterial communities of each layer, with the greatest differences occurring within Actinobacteria. Comparisons of 16S rRNA gene sequences with those from other Arctic permafrost and cold-temperature wetlands revealed commonly occurring taxa within the phyla Chloroflexi, Acidobacteria, and Actinobacteria (families Intrasporangiaceae and Rubrobacteraceae). PMID:21491982

  18. Selective progressive response of soil microbial community to wild oat roots

    Energy Technology Data Exchange (ETDEWEB)

    DeAngelis, K.M.; Brodie, E.L.; DeSantis, T.Z.; Andersen, G.L.; Lindow, S.E.; Firestone, M.K.

    2008-10-01

    Roots moving through soil enact physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. Use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies previously reported compositional changes, including increases in chitinase and protease specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change in 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA T-RFLP analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared to bulk soil, but then increased in older root zones. Quantitative PCR revealed {beta}-Proteobacteria and Actinobacteria present at about 10{sup 8} copies of 16S rRNA genes g{sup -1} soil, with Nitrospira having about 10{sup 5} copies g{sup -1} soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in function in progressively more mature rhizosphere zones.

  19. Comparative analysis of the gastrointestinal microbial communities of bar-headed goose (Anser indicus) in different breeding patterns by high-throughput sequencing.

    Science.gov (United States)

    Wang, Wen; Cao, Jian; Li, Ji-Rong; Yang, Fang; Li, Zhuo; Li, Lai-Xing

    2016-01-01

    The bar-headed goose is currently one of the most popular species for rare birds breeding in China. However, bar-headed geese in captivity display a reduced reproductive rate. The gut microbiome has been shown to influence host factors such as nutrient and energy metabolism, immune homeostasis and reproduction. It is therefore of great scientific and agriculture value to analyze the microbial communities associated with bar-headed geese in order to improve their reproductive rate. Here we describe the first comparative study of the gut microbial communities of bar-headed geese in three different breeding pattern groups by 16SrRNA sequences using the Illumina MiSeq platform. The results showed that Firmicutes predominated (58.33%) among wild bar-headed geese followed by Proteobacteria (30.67%), Actinobacteria (7.33%) and Bacteroidetes (3.33%). In semi-artificial breeding group, Firmicutes was also the most abundant bacteria (62.00%), followed by Bacteroidetes (28.67%), Proteobacteria (4.20%), Actinobacteria (3.27%) and Fusobacteria (1.51%). The microbial communities of artificial breeding group were dominated by Firmicutes (60.67%), Fusobacteria (29.67%) and Proteobacteria (9.33%). Wild bar-headed geese had a significant higher relative abundance of Proteobacteria and Actinobacteria, while semi-artificial breeding bar-headed geese had significantly more Bacteroidetes. The semi-artificial breeding group had the highest microbial community diversity and richness, followed by wild group, and then the artificial breeding group. The marked differences of genus level group-specific microbes create a baseline for future bar-headed goose microbiology research.

  20. Functional divergence of HBHA from Mycobacterium tuberculosis and its evolutionary relationship with TadA from Rhodococcus opacus.

    Science.gov (United States)

    Lanfranconi, Mariana P; Alvarez, Héctor M

    2016-08-01

    Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 are oleaginous bacteria able to synthesize and accumulate triacylglycerols (TAG) in lipid bodies (LB). Highly relevant to the structure of LB is a protein homologous to heparin-binding hemagglutinin (HBHA) (called TadA in rhodococci), which is a virulence factor found in Mycobacterium tuberculosis. HBHA is an adhesin involved in binding to non-phagocytic cells and extrapulmonary dissemination. We observed a conserved synteny of three genes encoding a transcriptional regulator (TR), the HBHA protein and a membrane protein (MP) between TAG-accumulating actinobacteria belonging to Rhodococcus, Mycobacterium, Nocardia and Dietzia genera, among others. A 354 bp-intergenic spacing containing a SigF-binding site was found between hbha and the TR genes in M. tuberculosis, which was absent in genomes of other investigated actinobacteria. Analyses of available "omic" information revealed that TadA and TR were co-induced in rhodococci under TAG-accumulating conditions; whereas in M. tuberculosis and Mycobacterium smegmatis, HBHA and TR were regulated independently under stress conditions occurring during infection. We also found differences in protein lengths, domain content and distribution between HBHA and TadA proteins from mycobacteria and rhodococci, which may explain their different roles in cells. Based on the combination of results obtained in model actinobacteria, we hypothesize that HBHA and TadA proteins originated from a common ancestor, but later suffered a process of functional divergence during evolution. Thus, rhodococcal TadA probably has maintained its original role; whereas HBHA may have evolved as a virulence factor in pathogenic mycobacteria.

  1. Cultural, Transcriptomic, and Proteomic Analyses of Water-Stressed Cells of Actinobacterial Strains Isolated from Compost: Ecological Implications in the Fed-Batch Composting Process.

    Science.gov (United States)

    Narihiro, Takashi; Kanosue, Yuji; Hiraishi, Akira

    2016-06-25

    This study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (FBC) process by comparing culturability and stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (CTC). The FBC reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. During this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of operation. The plate counts of aerobic chemoorganotrophic bacteria were 3.2-fold higher than CTC-positive (CTC+) counts on average at the fully acclimated stage (after 7 weeks of operation), in which Actinobacteria predominated, as shown by lipoquinone profiling and cultivation methods. When the actinobacterial isolates from the FBC process were grown under aw stress, no significant differences were observed in culturability among the cultures, whereas CTC stainability decreased with reductions in aw levels. A cDNA microarray-based transcriptomic analysis of a representative isolate showed that many of the genes involved in cellular metabolism and genetic information processing were down-regulated by aw stress. This result was fully supported by a proteomic analysis. The results of the present study suggest that, in low aw mature compost, the metabolic activity of the community with Actinobacteria predominating is temporarily reduced to a level that hardly reacts with CTC; however, these bacteria are easily recoverable by exposure to a high aw culture medium. This may be a plausible reason why acclimated FBC reactors in which Actinobacteria predominate yields higher plate counts than CTC+ counts. PMID:27246805

  2. Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and and pyrosequencing for the characterisation of the caries-associated microbiome

    Directory of Open Access Journals (Sweden)

    Kathrin eSchulze-Schweifing

    2014-11-01

    Full Text Available Culture-independent analyses have greatly expanded knowledge regarding the composition of complex bacterial communities including those associated with oral diseases. A consistent finding from such studies, however, has been the under-reporting of members of the phylum Actinobacteria. In this study, five pairs of broad range primers targeting 16S rRNA genes were used in clonal analysis of 6 samples collected from tooth lesions involving dentine in subjects with active caries. Samples were also subjected to cultural analysis and pyrosequencing by means of the 454 platform. A diverse bacterial community of 229 species-level taxa was revealed by culture and clonal analysis, dominated by representatives of the genera Prevotella, Lactobacillus, Selenomonas and Streptococcus. The five most abundant species were: Lactobacillus gasseri, Prevotella denticola, Alloprevotella tannerae, S. mutans and Streptococcus sp. HOT 070, which together made up 31.6 % of the sequences. Two samples were dominated by lactobacilli, while the remaining samples had low numbers of lactobacilli but significantly higher numbers of Prevotella species. The different primer pairs produced broadly similar data but proportions of the phylum Bacteroidetes were significantly higher when primer 1387R was used. All of the primer sets underestimated the proportion of Actinobacteria compared to culture. Pyrosequencing analysis of the samples was performed to a depth of sequencing of 4293 sequences per sample which were identified to 264 species-level taxa, and resulted in significantly higher coverage estimates than the clonal analysis. Pyrosequencing, however, also underestimated the relative abundance of Actinobacteria compared to culture.

  3. Determination of physiological, taxonomic, and molecular characteristics of a cultivable arsenic-resistant bacterial community.

    Science.gov (United States)

    Cordi, A; Pagnout, C; Devin, S; Poirel, J; Billard, P; Dollard, M A; Bauda, P

    2015-09-01

    A collection of 219 bacterial arsenic-resistant isolates was constituted from neutral arsenic mine drainage sediments. Isolates were grown aerobically or anaerobically during 21 days on solid DR2A medium using agar or gelan gum as gelling agent, with 7 mM As(III) or 20 mM As(V) as selective pressure. Interestingly, the sum of the different incubation conditions used (arsenic form, gelling agent, oxygen pressure) results in an overall increase of the isolate diversity. Isolated strains mainly belonged to Proteobacteria (63%), Actinobacteria (25%), and Bacteroidetes (10%). The most representative genera were Pseudomonas (20%), Acinetobacter (8%), and Serratia (15%) among the Proteobacteria; Rhodococcus (13%) and Microbacterium (5%) among Actinobacteria; and Flavobacterium (13%) among the Bacteroidetes. Isolates were screened for the presence of arsenic-related genes (arsB, ACR3(1), ACR3(2), aioA, arsM, and arrA). In this way, 106 ACR3(1)-, 74 arsB-, 22 aioA-, 14 ACR3(2)-, and one arsM-positive PCR products were obtained and sequenced. Analysis of isolate sensitivity toward metalloids (arsenite, arsenate, and antimonite) revealed correlations between taxonomy, sensitivity, and genotype. Antimonite sensitivity correlated with the presence of ACR3(1) mainly present in Bacteroidetes and Actinobacteria, and arsenite or antimonite resistance correlated with arsB gene presence. The presence of either aioA gene or several different arsenite carrier genes did not ensure a high level of arsenic resistance in the tested conditions.

  4. Oral imazalil exposure induces gut microbiota dysbiosis and colonic inflammation in mice.

    Science.gov (United States)

    Jin, Cuiyuan; Zeng, Zhaoyang; Fu, Zhengwei; Jin, Yuanxiang

    2016-10-01

    The fungicide imazalil (IMZ) is used extensively in vegetable and fruit plantations and as a post-harvest treatment to avoid rot. Here, we revealed that ingestion of 25, 50 and 100 mg IMZ kg(-1) body weight for 28 d induced gut microbiota dysbiosis and colonic inflammation in mice. The relative abundance of Bacteroidetes, Firmicutes and Actinobacteria in the cecal contents decreased significantly after exposure to 100 mg kg(-1) IMZ for 28 d. In feces, the relative abundance in Bacteroidetes, Firmicutes and Actinobacteria decreased significantly after being exposed to 100 mg kg(-1) IMZ for 1, 14 and 7 d, respectively. High throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed a significant reduction in the richness and diversity of microbiota in cecal contents and feces of IMZ-treated mice. Operational taxonomic units (OTUs) analysis identified 49.3% of OTUs changed in cecal contents, while 55.6% of OTUs changed in the feces after IMZ exposure. Overall, at the phylum level, the relative abundance of Firmicutes, Proteobacteria and Actinobacteria increased and that of Bacteroidetes decreased in IMZ-treated groups. At the genus level, the abundance of Lactobacillus and Bifidobacterium decreased while those of Deltaproteobacteria and Desulfovibrio increased in response to IMZ exposure. In addition, it was observed that IMZ exposure could induce colonic inflammation characterized by infiltration of inflammatory cells, elevated levels of lipocalin-2 (lcn-2) in the feces, and increased mRNA levels of Tnf-α, IL-1β, IL-22 and IFN-γ in the colon. Our findings strongly suggest that ingestion of IMZ has some risks to human health. PMID:27393971

  5. Bioprospecting microbial natural product libraries from the marine environment for drug discovery.

    Science.gov (United States)

    Liu, Xiangyang; Ashforth, Elizabeth; Ren, Biao; Song, Fuhang; Dai, Huanqin; Liu, Mei; Wang, Jian; Xie, Qiong; Zhang, Lixin

    2010-08-01

    Marine microorganisms are fascinating resources due to their production of novel natural products with antimicrobial activities. Increases in both the number of new chemical entities found and the substantiation of indigenous marine actinobacteria present a fundamental difficulty in the future discovery of novel antimicrobials, namely dereplication of those compounds already discovered. This review will share our experience on the taxonomic-based construction of a highly diversified and low redundant marine microbial natural product library for high-throughput antibiotic screening. We anticipate that libraries such as these can drive the drug discovery process now and in the future. PMID:20606699

  6. Phylogenetic analysis of bacteria in sea ice brine sampled from the Canada Basin, Arctic Ocean

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Bacterial diversity in sea ice brine samples which collected from four stations located at the Canada Basin, Arctic Ocean was analyzed by PCR-DGGE. Twenty-three 16S rDNA sequences of bacteria obtained from DGGE bands were cloned and sequenced. Phylogenetic analysis clustered these sequences within γ-proteobacteria, Cytophaga-Flexibacter-Bacteroides (CFB) group, Firmicutes and Actinobacteria. The phylotype of Pseudoalteromonas in the γ-proteobacteria was predominant and members of the CFB group and γ-proteobacteria were highly abundant in studied sea ice brine samples.

  7. Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss)

    DEFF Research Database (Denmark)

    Ingerslev, Hans-Christian; Strube, Mikael Lenz; Jørgensen, Louise von Gersdorff;

    2014-01-01

    This study investigated the influence of the rainbow trout (Oncorhynchus mykiss) commensal intestinal microbiota in connection to an experimental Yersina ruckeri infection, the causative agent of enteric redmouth disease. One marine and one plant diet was administered to two different groups...... of rainbow trout. The plant-based diet gave rise to an intestinal microbiota dominated by the genera Streptococcus, Leuconostoc and Weissella from phylum Firmicutes whereas phylum Proteobacteria/Bacteroidetes/Actinobacteria dominated the community in the marine fed fish. In connection to the Y. ruckeri bath...

  8. Human microbiome: From the bathroom to the bedside

    Institute of Scientific and Technical Information of China (English)

    Stephen; Malnick; Ehud; Melzer

    2015-01-01

    The human gut contains trillions of bacteria, the major phylae of which include Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. Fecal microbial transplantation(FMT) has been known of for manyyears but only recently has been subjected to rigorous examination. We review the evidence regarding FMT for recurrent Clostridium difficile infection which has resulted in it being an approved treatment. In addition there is some evidence for its use in both irritable bowel syndrome and inflammatory bowel disease. Further research is needed in order to define the indications for FMT and the most appropriate method of administration.

  9. [Number, viability, and diversity of the filterable forms of prokaryotes in sphagnous high-moor peat].

    Science.gov (United States)

    Lysak, L V; Lapygina, E V; Kadulin, M S; Konova, I A

    2014-01-01

    The number, potential viability, and taxonomic diversity (at the level of phylum) of the filterable forms of prokaryotes (FFP) are estimated in the main genetic horizons of high-moor peat. It was shown that the number of FFP reached 500 million cells in 1 g, i.e., up to 5% of the general size bacteria. The portion of viable cells among FFP (93-98%) was higher than that for the general size bacteria (60-68%). FISH-analysis (fluorescence in situ hybridization) showed that FFP contained the same phylogenetic groups as the population of general size bacteria (domain Archea and phylum Actinobacteria, Cytophaga, and Proteobacteria of the domain Bacteria).

  10. Comparison of bacterial succession in green waste composts amended with inorganic fertiliser and wastewater treatment plant sludge.

    Science.gov (United States)

    Storey, Sean; Chualain, Dearbháil Ní; Doyle, Owen; Clipson, Nicholas; Doyle, Evelyn

    2015-03-01

    Replacing CAN with DWS resulted in a stable product capable of supporting similar levels of plant growth to conventional compost. Proteobacteria was the dominant phylum detected in both CAN- and DWS-amended composts with Actinobacteria, Bacteroidetes, Firmicutes and Chloroflexi present also. Proteobacteria in both composts negatively correlated with pH, NO3 concentration and temperature, but were positively influenced by NH4 levels. Sphaerobacter was the most abundant genus in the mature phase of both CAN- and DWS-amended composts but bacterial community structure in mature DWS-amended compost appeared more diverse than that present in mature compost made using CAN.

  11. Human microbiome: From the bathroom to the bedside.

    Science.gov (United States)

    Malnick, Stephen; Melzer, Ehud

    2015-08-15

    The human gut contains trillions of bacteria, the major phylae of which include Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. Fecal microbial transplantation (FMT) has been known of for many years but only recently has been subjected to rigorous examination. We review the evidence regarding FMT for recurrent Clostridium difficile infection which has resulted in it being an approved treatment. In addition there is some evidence for its use in both irritable bowel syndrome and inflammatory bowel disease. Further research is needed in order to define the indications for FMT and the most appropriate method of administration. PMID:26301122

  12. Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring

    Directory of Open Access Journals (Sweden)

    Sonu Bhatia

    2015-09-01

    Full Text Available The soil-mousse surrounding a geothermal spring was analyzed for bacterial and archaeal diversity using 16S rRNA gene amplicon metagenomic sequencing which revealed the presence of 18 bacterial phyla distributed across 109 families and 219 genera. Firmicutes, Actinobacteria, and the Deinococcus-Thermus group were the predominant bacterial assemblages with Crenarchaeota and Thaumarchaeota as the main archaeal assemblages in this largely understudied geothermal habitat. Several metagenome sequences remained taxonomically unassigned suggesting the presence of a repertoire of hitherto undescribed microbes in this geothermal soil-mousse econiche.

  13. 四川冬菜中细菌群落组成及多样性%Bacterial biodiversity in Dongcai, a traditional pickled mustard product in Sichuan Province, China

    Institute of Scientific and Technical Information of China (English)

    董玲; 蒲彪; 敖晓琳; 张小平; 郑有坤; 李小林

    2012-01-01

    [ Objective] To investigate the bacteria community and biodiversity of four-years pickled Yanshan Dongcai. [Methods] We studied the bacterial communities of Dongcai by 16S rDNA diversity analysis and the cultured species isolated from Dongcai sample by Restriction Fragment Length Polymorphism ( RFLP) and 16S rRNA gene sequence analysis. [ Results] The 16S rDNA diversity showed that the bacteria belonged to the phyla Proteobacteria (87. 9% ) and Firmicutes (7. 1% ) , including many moderately halophilic bacteria such as Virgibacillus kekensis, Marinococcus albus, Salinicoccus sp. , Lactobacillus halophilus and Halomonas. Only 5% of clone sequences belonged to the phylum Actinobacteria. Thirty-five strains were isolated from Dongcai sample, and 16S rDNA-RFLP analysis indicated that 34 isolates affiliated with the phylum Firmicutes, including Virgibacillus, Bacillus megaterium and Gracilibacillus saliphilus which were moderately halophilic bacteria, but only one isolate belonged to the phylum Actinobacteria. [ Conclusion ] The bacterial diversity is low in Dongcai, dominated by moderately halophilic bacteria.%[目的]了解腌制4年的四川南充冬菜中细菌群落组成及多样性.[方法]通过16S rDNA多样性分析样品细菌落组成;采用16S rDNA-RFLP方法分析从样品中分离出的纯培养细菌.[结果]16S rDNA多样性分析结果表明,样品中细菌主要属于变形杆菌门( Proteobacteria)和厚壁菌门(Firmicutes),分别占克隆文库的87.9%、7.1%,其中包括Virgibacillus kekensis,Marinococcus albus,Salinicoccus sp.,Lactobacillus halophilus和Halomonas等中度嗜盐菌,仅有5%属于放线菌门(Actinobacteria).通过纯培养方法从冬菜中分离到35株菌,16S rDNA-RFLP分析结果表明,34株属于厚壁菌门(Firmicutes),包括Virgibacillus,Bacillus megaterium和Gracilibacillus saliphilus等中度嗜盐菌,1株属于放线菌门(Actinobacteria).[结论]冬菜中细菌群落多样性较低,以中度嗜盐菌为主.

  14. pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment

    DEFF Research Database (Denmark)

    El Azhari, Najoi

    2007-01-01

    cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to Pca......H sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices....

  15. Cultivation of hard-to-culture subsurface mercury-resistant bacteria and discovery of new merA gene sequences

    DEFF Research Database (Denmark)

    Rasmussen, L D; Zawadsky, C; Binnerup, S J;

    2008-01-01

    was increased up to 2,800 times and numbers of mCFU were similar to the total number of mercury-resistant bacteria in the soils. Denaturing gradient gel electrophoresis analysis of DNA extracted from membranes suggested stimulation of growth of hard-to-culture bacteria during the preincubation. A total of 25...... sequencing of merA of selected isolates led to the discovery of new merA sequences. With phylum-specific merA primers, PCR products were obtained for Alpha- and Betaproteobacteria and Actinobacteria but not for Bacteroidetes and Firmicutes. The similarity to known sequences ranged between 89 and 95%. One...

  16. A review of applied aspects of dealing with gut microbiota impact on rodent models

    DEFF Research Database (Denmark)

    Hansen, Axel Kornerup; Krych, Lukasz; Nielsen, Dennis Sandris;

    2015-01-01

    expression. Through subsequent inoculation with selected strains or cocktails of microbes, new "defined flora" models can yield valuable knowledge on the impact of the GM, and of specific GM members and their interactions, on important disease phenotypes and mechanisms. Rodent husbandry and microbial quality......-negative phylum Bacteroidetes. Other important phyla are the gram-negative phyla Proteobacteria and Verrucomicrobia, and the gram-positive phylum Actinobacteria. GM members influence models for diseases, such as inflammatory bowel diseases, allergies, autoimmunity, cancer, and neuropsychiatric diseases. GM...... assurance practices will be important to ensure and confirm appropriate and research relevant GM....

  17. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    Directory of Open Access Journals (Sweden)

    Annette K. Møller

    2013-04-01

    Full Text Available The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition of the microbial assemblages was different within the snow layers and between snow and freshwater. The highest diversity was seen in snow. In the middle and top snow layers, Proteobacteria, Bacteroidetes and Cyanobacteria dominated, although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacteroidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. Thus, differences in the physicochemical conditions may play an important role in the processes leading to distinctive bacterial community structures in High-Arctic snow and freshwater.

  18. Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce

    Science.gov (United States)

    Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

    2016-04-01

    Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3‑-N, and NH4+-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

  19. The Arctic Soil Bacterial Communities in the Vicinity of a Little Auk Colony.

    Science.gov (United States)

    Zielińska, Sylwia; Kidawa, Dorota; Stempniewicz, Lech; Łoś, Marcin; Łoś, Joanna M

    2016-01-01

    Due to deposition of birds' guano, eggshells or feathers, the vicinity of a large seabirds' breeding colony is expected to have a substantial impact on the soil's physicochemical features as well as on diversity of vegetation and the soil invertebrates. Consequently, due to changing physicochemical features the structure of bacterial communities might fluctuate in different soil environments. The aim of this study was to investigate the bacterial assemblages in the Arctic soil within the area of a birds' colony and in a control sample from a topographically similar location but situated away from the colony's impact area. A high number of OTUs found in both areas indicates a highly complex microbial populations structure. The most abundant phyla in both of the tested samples were: Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, with different proportions in the total share. Despite differences in the physicochemical soil characteristics, the soil microbial community structures at the phylum level were similar to some extent in the two samples. The only share that was significantly higher in the control area when compared to the sample obtained within the birds' colony, belonged to the Actinobacteria phylum. Moreover, when analyzing the class level for each phylum, several differences between the samples were observed. Furthermore, lower proportions of Proteobacteria and Acidobacteria were observed in the soil sample under the influence of the bird's colony, which most probably could be linked to higher nitrogen concentrations in that sample. PMID:27667982

  20. Integration of acoustic and light sensors for marine bio-mining

    Science.gov (United States)

    Wiegand, Gordon

    2016-05-01

    Maximum diversity of life exists within the estuaries and coral reefs of the Globe. The absence of vertebrate and other land dwelling adaptations has resulted in an enormous range of complexity among invertebrates and their symbiotic biome resulting in the generation of compounds finding uses in anti-tumor and antibiotic applications. It has been widely reported that the greatest factor limiting progress in characterizing and processing new therapeutics derived from invertebrates is the lack of adequate original material. Symbiotic bacteria within specific tunicates often synthesize antitumor compounds as secondary metabolites. We describe a 3-stage protocol that utilizes acoustic and photonic analysis of large areas of marine ecosystem and life forms. We refer to this as Estuary Assessment System (EAS), which includes a multi-frequency acoustic transducer/sensing instrument mounted on our research vessel. This generates a topological map of surveyed tracks of marine locations known to be habitats of useful actinobacteria laden invertebrates. Photonic devices are used to generate image and pulse data leading to location, identification and isolation of tunicates and actinobacteria.

  1. Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

    Science.gov (United States)

    Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

    2015-07-01

    In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen.

  2. Different continuous cropping spans significantly affect microbial community membership and structure in a vanilla-grown soil as revealed by deep pyrosequencing.

    Science.gov (United States)

    Xiong, Wu; Zhao, Qingyun; Zhao, Jun; Xun, Weibing; Li, Rong; Zhang, Ruifu; Wu, Huasong; Shen, Qirong

    2015-07-01

    In the present study, soil bacterial and fungal communities across vanilla continuous cropping time-series fields were assessed through deep pyrosequencing of 16S ribosomal RNA (rRNA) genes and internal transcribed spacer (ITS) regions. The results demonstrated that the long-term monoculture of vanilla significantly altered soil microbial communities. Soil fungal diversity index increased with consecutive cropping years, whereas soil bacterial diversity was relatively stable. Bray-Curtis dissimilarity cluster and UniFrac-weighted principal coordinate analysis (PCoA) revealed that monoculture time was the major determinant for fungal community structure, but not for bacterial community structure. The relative abundances (RAs) of the Firmicutes, Actinobacteria, Bacteroidetes, and Basidiomycota phyla were depleted along the years of vanilla monoculture. Pearson correlations at the phyla level demonstrated that Actinobacteria, Armatimonadetes, Bacteroidetes, Verrucomicrobia, and Firmicutes had significant negative correlations with vanilla disease index (DI), while no significant correlation for fungal phyla was observed. In addition, the amount of the pathogen Fusarium oxysporum accumulated with increasing years and was significantly positively correlated with vanilla DI. By contrast, the abundance of beneficial bacteria, including Bradyrhizobium and Bacillus, significantly decreased over time. In sum, soil weakness and vanilla stem wilt disease after long-term continuous cropping can be attributed to the alteration of the soil microbial community membership and structure, i.e., the reduction of the beneficial microbes and the accumulation of the fungal pathogen. PMID:25391237

  3. Molecular Biological Analysis of Microorganisms in Petroleum Reservoirs

    Science.gov (United States)

    Ko, J.; Son, H. A.; Im, K. C.; Back, K. H.; Kim, H. T.

    2014-12-01

    Microorganisms in petroleum reservoirs were analyzed to examine the potential to apply for microbial enhanced oil recovery (MEOR). Genomic DNA (16S rDNA) were extracted from two heavy oil samples from Canadian oil sand and six light oil samples from the Salin fore-arc basin in Myanmar, and amplified using a polymerase chain reaction (PCR) method. The microbes were identified by cloning the PCR products and pyrosequencing. Actinobacteria, Firmicutes, and Proteobacteria were common in both Canadian and Myanmar samples. Staphylococcus and Streptococcus belonging to the Firmicutes phylum are abundant in oil sands, while Propionibacteria belonging to the Actinobacteria phylum and Coprothermobacter, Streptococcus, and Clostridia belonging to the Frimicutes phylum are contained in Myanmar samples. Streptococcus is known to use crude oil as nutrient, and produce organic acid, bio-gas and polysaccharide that could reduce oil viscosity, improve permeability by dissolving carbonate cement from pores throat, and reduce interfacial tension between oil and rock/water surface. Clostridia produce acids and gases by methanogenesis that could improve oil recovery.

  4. Evaluation of microbial population dynamics in the co-composting of cow manure and rice straw using high throughput sequencing analysis.

    Science.gov (United States)

    Ren, Guangming; Xu, Xiuhong; Qu, Juanjuan; Zhu, Liping; Wang, Tingting

    2016-06-01

    Microbial population dynamics in co-composting of cow manure and rice straw were evaluated using 16S high throughput sequencing technology. Physicochemical factors, including temperature, pH, nitrogen contents, the ratio of carbon and nitrogen, and germination index, were also determined in this study. 16S high throughput sequencing results showed that bacterial community structure and composition significantly varied in each phase of composting. The major phyla included Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria and Planctomycetes, respectively. Bacteroidetes and Proteobacteria were the most abundant phyla in all phases, and Actinobacteria was just dominant in the mesophilic phase, while Firmicutes and Planctomycetes were ubiquitous. At the genus level, Simiduia, Flavobacterium, unclassified Chitinophagaceae and Flexibacter notably changed in each phase of composting. Bacterial community diversity in the mesophilic phase was higher than that in others based on the Shannon-Wiener index and Simpson diversity index. The ratio of carbon and nitrogen and germination index indicated that the co-composting of cow manure and rice straw reached maturation. The result of nitrogen contents showed that nitrogen loss mainly occurred in the thermophilic phase. In addition, the differences in the distributions of key OTUs between in the late thermophilic phase and the cooling and maturation phase were unobvious compared with other phase's base on the principal component analysis. Redundancy analysis revealed that the changes of nitrogen played a predominant role in the distributions of OTUs during the composting process. PMID:27116967

  5. Antimicrobial Activity of Marine Bacterial Symbionts Retrieved from Shallow Water Hydrothermal Vents.

    Science.gov (United States)

    Eythorsdottir, Arnheidur; Omarsdottir, Sesselja; Einarsson, Hjorleifur

    2016-06-01

    Marine sponges and other sessile macro-organisms were collected at a shallow water hydrothermal site in Eyjafjörður, Iceland. Bacteria were isolated from the organisms using selective media for actinomycetes, and the isolates were screened for antimicrobial activity. A total of 111 isolates revealed antimicrobial activity displaying different antimicrobial patterns which indicates production of various compounds. Known test strains were grown in the presence of ethyl acetate extracts from one selected isolate, and a clear growth inhibition of Staphylococcus aureus was observed down to 0.1 % extract concentration in the medium. Identification of isolates shows different species of Actinobacteria with Streptomyces sp. playing the largest role, but also members of Bacilli, Alphaproteobacteria and Gammaproteobacteria. Sponges have an excellent record regarding production of bioactive compounds, often involving microbial symbionts. At the hydrothermal vents, however, the majority of active isolates originated from other invertebrates such as sea anemones or algae. The results indicate that antimicrobial assays involving isolates in full growth can detect activity not visible by other methods. The macro-organisms inhabiting the Eyjafjörður hydrothermal vent area host diverse microbial species in the phylum Actinobacteria with antimicrobial activity, and the compounds responsible for the activity will be subject to further research. PMID:27147438

  6. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  7. Culture independent characterization of bacteria associated with the mucus of the coral Acropora digitifera from the Gulf of Mannar.

    Science.gov (United States)

    Nithyanand, Paramasivam; Indhumathi, Thiruvalluvan; Ravi, Arumugam Veera; Pandian, Shunmugiah Karutha

    2011-06-01

    Corals are sessile eukaryotic hosts which provide a unique surface for microbial colonization. Culture independent studies show that the coral mucus and tissue harbour diverse and abundant prokaryotic communities. However, little is known about the diversity of bacteria associated with the corals of Gulf of Mannar. The present study characterised the bacterial diversity associated with the mucus of the coral Acropora digitifera from the Gulf of Mannar by 16S rRNA gene clone library construction. The bacterial communities of the mucus of A. digitifera were diverse, with representatives within the Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes and several unclassified bacteria. The culture independent bacterial population was totally different from our previous culture dependent study of the mucus and tissue of the same coral. 36% of the bacteria in the clone library of A. digitifera were found to be novel after full length sequencing of the 16S rRNA gene wherein several clones were found to be novel at the Genus and species level. The current study further supports the findings that Actinobacteria amount to a certain proportion among bacterial communities associated with corals. PMID:25187139

  8. Bioaugmentation of a 4-chloronitrobenzene contaminated soil with Pseudomonas putida ZWL73

    Energy Technology Data Exchange (ETDEWEB)

    Niu Guilan [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China); Graduate School, Chinese Academy of Sciences, Beijing 100049 (China); Zhang Junjie [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China); Zhao Shuo [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China); Graduate School, Chinese Academy of Sciences, Beijing 100049 (China); Liu Hong [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China); Boon, Nico [Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent (Belgium); Zhou Ningyi [State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071 (China)], E-mail: n.zhou@pentium.whiov.ac.cn

    2009-03-15

    The strain Pseudomonas putida ZWL73, which metabolizes 4-chloronitrobenzene (4CNB) by a partial-reductive pathway, was inoculated into lab-scale 4CNB-contaminated soil for bioaugmentation purposes in this study. The degradation of 4CNB was clearly stimulated, as indicated with the gradual accumulation of ammonium and chloride. Simultaneously, the diversity and quantity of cultivable heterotrophic bacteria decreased due to 4CNB contamination, while the quantity of 4CNB-resistant bacteria increased. During the bioaugmentation, denaturing gradient gel electrophoresis analysis showed the changes of diversity in dominant populations of intrinsic soil microbiota. The results showed that Alphaproteobacteria and Betaproteobacteria were not distinctly affected, but Actinobacteria were apparently stimulated. In addition, an interesting dynamic within Acidobacteria was observed, as well as an influence on ammonia-oxidizing bacteria population. These combined findings demonstrate that the removal of 4CNB in soils by inoculating strain ZWL73 is feasible, and that specific populations in soils rapidly changed in response to 4CNB contamination and subsequent bioaugmentation. - Pseudomonas putida ZWL73 can accelerate 4CNB removal in lab-scale soils, causing dynamic changes within intrinsic Actinobacteria and Acidobacteria.

  9. Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil.

    Science.gov (United States)

    Pan, Yao; Cassman, Noriko; de Hollander, Mattias; Mendes, Lucas W; Korevaar, Hein; Geerts, Rob H E M; van Veen, Johannes A; Kuramae, Eiko E

    2014-10-01

    Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem. PMID:25046442

  10. Differential utilization patterns of dissolved organic phosphorus compounds by heterotrophic bacteria in two mountain lakes.

    Science.gov (United States)

    Rofner, Carina; Sommaruga, Ruben; Pérez, María Teresa

    2016-09-01

    Although phosphorus limitation is common in freshwaters and bacteria are known to use dissolved organic phosphorus (DOP), little is known about how efficiently DOP compounds are taken up by individual bacterial taxa. Here, we assessed bacterial uptake of three model DOP substrates in two mountain lakes and examined whether DOP uptake followed concentration-dependent patterns. We determined bulk uptake rates by the bacterioplankton and examined bacterial taxon-specific substrate uptake patterns using microautoradiography combined with catalyzed reporter deposition-fluorescence in situ hybridization. Our results show that in the oligotrophic alpine lake, bacteria took up ATP, glucose-6-phosphate and glycerol-3-phosphate to similar extents (mean 29.7 ± 4.3% Bacteria), whereas in the subalpine mesotrophic lake, ca. 40% of bacteria took up glucose-6-phosphate, but only ∼20% took up ATP or glycerol-3-phosphate. In both lakes, the R-BT cluster of Betaproteobacteria (lineage of genus Limnohabitans) was over-represented in glucose-6-phosphate and glycerol-3-phosphate uptake, whereas AcI Actinobacteria were under-represented in the uptake of those substrates. Alphaproteobacteria and Bacteroidetes contributed to DOP uptake proportionally to their in situ abundance. Our results demonstrate that R-BT Betaproteobacteria are the most active bacteria in DOP acquisition, whereas the abundant AcI Actinobacteria may either lack high affinity DOP uptake systems or have reduced phosphorus requirements. PMID:27312963

  11. Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica

    Directory of Open Access Journals (Sweden)

    Heather N Buelow

    2016-07-01

    Full Text Available The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and organic matter. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8% and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59% dominated water-amended soils and Firmicutes (45% dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34 of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely.

  12. Microbial communities adhering to the obverse and reverse sides of an oil painting on canvas: identification and evaluation of their biodegradative potential.

    Science.gov (United States)

    López-Miras, M; Piñar, G; Romero-Noguera, J; Bolívar-Galiano, F C; Ettenauer, J; Sterflinger, K; Martín-Sánchez, I

    2013-06-01

    In this study, we investigated and compared the microbial communities adhering to the obverse and the reverse sides of an oil painting on canvas exhibiting signs of biodeterioration. Samples showing no visible damage were investigated as controls. Air samples were also analysed, in order to investigate the presence of airborne microorganisms suspended in the indoor atmosphere. The diversity of the cultivable microorganisms adhering to the surface was analysed by molecular techniques, such as RAPD analysis and gene sequencing. DGGE fingerprints derived from DNA directly extracted from canvas material in combination with clone libraries and sequencing were used to evaluate the non-cultivable fraction of the microbial communities associated with the material. By using culture-dependent methods, most of the bacterial strains were found to be common airborne, spore-forming microorganisms and belonged to the phyla Actinobacteria and Firmicutes, whereas culture-independent techniques identified sequenced clones affiliated with members of the phyla Actinobacteria and Proteobacteria. The diversity of fungi was shown to be much lower than that observed for bacteria, and only species of Penicillium spp. could be detected by cultivation techniques. The selected strategy revealed a higher microbial diversity on the obverse than on the reverse side of the painting and the near absence of actively growing microorganisms on areas showing no visible damage. Furthermore, enzymatic activity tests revealed that the most widespread activities involved in biodeterioration were esterase and esterase lipase among the isolated bacterial strains, and esterase and N-acetyl-β-glucosaminidase among fungi strains. PMID:23576841

  13. Bacterial endophytes mediate positive feedback effects of early legume termination times on the yield of subsequent durum wheat crops.

    Science.gov (United States)

    Yang, Chao; Hamel, Chantal; Gan, Yantai; Vujanovic, Vladimir

    2012-12-01

    Field crops influence the biotic properties of the soil, impacting the health and productivity of subsequent crops. Polymerase chain reaction and 454 GS FLX pyrosequencing of amplicons were used to clarify the legacy of chickpea and pea crops on the quality of the bacterial community colonizing the root endosphere of subsequent crops of wheat, in a replicated field study. Similar communities of root endosphere bacteria were formed in durum wheat grown after pea and chickpea crops when chickpea crops were terminated as early as pea (July). Termination of the chickpea crops in September led to the domination of Firmicutes in wheat root endosphere; Actinobacteria dominated the wheat root endosphere following early pulse crop termination. The architecture of wheat plants was correlated with the composition of its root endosphere community. High grain yield was associated with the production of fewer but larger wheat heads, the abundance of endospheric Actinobacteria and Acidobacteria, and the scarcity of endospheric Firmicutes. Pulse termination time affected wheat root endosphere colonization strongly in 2009 but weakly in 2010, an abnormally wet year. This study improved our understanding of the so-called "crop rotation effect" in pulse-wheat systems and showed how this system can be manipulated through agronomic decisions.

  14. Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce.

    Science.gov (United States)

    Li, Jian-Gang; Shen, Min-Chong; Hou, Jin-Feng; Li, Ling; Wu, Jun-Xia; Dong, Yuan-Hua

    2016-04-28

    Pyrosequencing-based analyses revealed significant effects among low (N50), medium (N80), and high (N100) fertilization on community composition involving a long-term monoculture of lettuce in a greenhouse in both summer and winter. The non-fertilized control (CK) treatment was characterized by a higher relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi; however, the average abundance of Firmicutes typically increased in summer, and the relative abundance of Bacteroidetes increased in winter in the N-fertilized treatments. Principle component analysis showed that the distribution of the microbial community was separated by a N gradient with N80 and N100 in the same group in the summer samples, while CK and N50 were in the same group in the winter samples, with the other N-level treatments existing independently. Redundancy analysis revealed that available N, NO3(-)-N, and NH4(+)-N, were the main environmental factors affecting the distribution of the bacterial community. Correlation analysis showed that nitrogen affected the shifts of microbial communities by strongly driving the shifts of Firmicutes, Bacteroidetes, and Proteobacteria in summer samples, and Bacteroidetes, Actinobacteria, and Acidobacteria in winter samples. The study demonstrates a novel example of rhizosphere bacterial diversity and the main factors influencing rizosphere microbial community in continuous vegetable cropping within an intensive greenhouse ecosystem.

  15. Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica.

    Science.gov (United States)

    Buelow, Heather N; Winter, Ara S; Van Horn, David J; Barrett, John E; Gooseff, Michael N; Schwartz, Egbert; Takacs-Vesbach, Cristina D

    2016-01-01

    The soils of the McMurdo Dry Valleys, Antarctica are an extreme polar desert, inhabited exclusively by microscopic taxa. This region is on the threshold of anticipated climate change, with glacial melt, permafrost thaw, and the melting of massive buried ice increasing liquid water availability and mobilizing soil nutrients. Experimental water and organic matter (OM) amendments were applied to investigate how these climate change effects may impact the soil communities. To identify active taxa and their functions, total community RNA transcripts were sequenced and annotated, and amended soils were compared with unamended control soils using differential abundance and expression analyses. Overall, taxonomic diversity declined with amendments of water and OM. The domain Bacteria increased with both amendments while Eukaryota declined from 38% of all taxa in control soils to 8 and 11% in water and OM amended soils, respectively. Among bacterial phyla, Actinobacteria (59%) dominated water-amended soils and Firmicutes (45%) dominated OM amended soils. Three bacterial phyla (Actinobacteria, Proteobacteria, and Firmicutes) were primarily responsible for the observed positive functional responses, while eukaryotic taxa experienced the majority (27 of 34) of significant transcript losses. These results indicated that as climate changes in this region, a replacement of endemic taxa adapted to dry, oligotrophic conditions by generalist, copiotrophic taxa is likely. PMID:27486436

  16. Unraveling the biochemistry and provenance of pupylation: a prokaryotic analog of ubiquitination

    Directory of Open Access Journals (Sweden)

    Aravind L

    2008-11-01

    Full Text Available Abstract Recently Mycobacterium tuberculosis was shown to possess a novel protein modification, in which a small protein Pup is conjugated to the epsilon-amino groups of lysines in target proteins. Analogous to ubiquitin modification in eukaryotes, this remarkable modification recruits proteins for degradation via archaeal-type proteasomes found in mycobacteria and allied actinobacteria. While a mycobacterial protein named PafA was found to be required for this conjugation reaction, its biochemical mechanism has not been elucidated. Using sensitive sequence profile comparison methods we establish that the PafA family proteins are related to the γ-glutamyl-cysteine synthetase and glutamine synthetase. Hence, we predict that PafA is the Pup ligase, which catalyzes the ATP-dependent ligation of the terminal γ-carboxylate of glutamate to lysines, similar to the above enzymes. We further discovered that an ortholog of the eukaryotic PAC2 (e.g. cg2106 is often present in the vicinity of the actinobacterial Pup-proteasome gene neighborhoods and is likely to represent the ancestral proteasomal chaperone. Pup-conjugation is sporadically present outside the actinobacteria in certain lineages, such as verrucomicrobia, nitrospirae, deltaproteobacteria and planctomycetes, and in the latter two lineages it might modify membrane proteins. Reviewers This article was reviewed by M. Madan Babu and Andrei Osterman

  17. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities.

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    Ru Li

    Full Text Available It has been debated how different farming systems influence the composition of soil bacterial communities, which are crucial for maintaining soil health. In this research, we applied high-throughput pyrosequencing of V1 to V3 regions of bacterial 16S rRNA genes to gain further insight into how organic and conventional farming systems and crop rotation influence bulk soil bacterial communities. A 2×2 factorial experiment consisted of two agriculture management systems (organic versus conventional and two crop rotations (flax-oat-fababean-wheat versus flax-alfalfa-alfalfa-wheat was conducted at the Glenlea Long-Term Crop Rotation and Management Station, which is Canada's oldest organic-conventional management study field. Results revealed that there is a significant difference in the composition of bacterial genera between organic and conventional management systems but crop rotation was not a discriminator factor. Organic farming was associated with higher relative abundance of Proteobacteria, while Actinobacteria and Chloroflexi were more abundant in conventional farming. The dominant genera including Blastococcus, Microlunatus, Pseudonocardia, Solirubrobacter, Brevundimonas, Pseudomonas, and Stenotrophomonas exhibited significant variation between the organic and conventional farming systems. The relative abundance of bacterial communities at the phylum and class level was correlated to soil pH rather than other edaphic properties. In addition, it was found that Proteobacteria and Actinobacteria were more sensitive to pH variation.

  18. Identification of active oxalotrophic bacteria by Bromodeoxyuridine DNA labeling in a microcosm soil experiments.

    Science.gov (United States)

    Bravo, Daniel; Martin, Gaëtan; David, Maude M; Cailleau, Guillaume; Verrecchia, Eric; Junier, Pilar

    2013-11-01

    The oxalate-carbonate pathway (OCP) leads to a potential carbon sink in terrestrial environments. This process is linked to the activity of oxalotrophic bacteria. Although isolation and molecular characterizations are used to study oxalotrophic bacteria, these approaches do not give information on the active oxalotrophs present in soil undergoing the OCP. The aim of this study was to assess the diversity of active oxalotrophic bacteria in soil microcosms using the Bromodeoxyuridine (BrdU) DNA labeling technique. Soil was collected near an oxalogenic tree (Milicia excelsa). Different concentrations of calcium oxalate (0.5%, 1%, and 4% w/w) were added to the soil microcosms and compared with an untreated control. After 12 days of incubation, a maximal pH of 7.7 was measured for microcosms with oxalate (initial pH 6.4). At this time point, a DGGE profile of the frc gene was performed from BrdU-labeled soil DNA and unlabeled soil DNA. Actinobacteria (Streptomyces- and Kribbella-like sequences), Gammaproteobacteria and Betaproteobacteria were found as the main active oxalotrophic bacterial groups. This study highlights the relevance of Actinobacteria as members of the active bacterial community and the identification of novel uncultured oxalotrophic groups (i.e. Kribbella) active in soils. PMID:24033776

  19. Diversity rankings among bacterial lineages in soil.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2009-03-01

    We used rarefaction curve analysis and diversity ordering-based approaches to rank the 11 most frequently encountered bacterial lineages in soil according to diversity in 5 previously reported 16S rRNA gene clone libraries derived from agricultural, undisturbed tall grass prairie and forest soils (n=26,140, 28 328, 31 818, 13 001 and 53 533). The Planctomycetes, Firmicutes and the delta-Proteobacteria were consistently ranked among the most diverse lineages in all data sets, whereas the Verrucomicrobia, Gemmatimonadetes and beta-Proteobacteria were consistently ranked among the least diverse. On the other hand, the rankings of alpha-Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes and Chloroflexi varied widely in different soil clone libraries. In general, lineages exhibiting largest differences in diversity rankings also exhibited the largest difference in relative abundance in the data sets examined. Within these lineages, a positive correlation between relative abundance and diversity was observed within the Acidobacteria, Actinobacteria and Chloroflexi, and a negative diversity-abundance correlation was observed within the Bacteroidetes. The ecological and evolutionary implications of these results are discussed. PMID:18987677

  20. The effect of anaerobic-aerobic and feast-famine cultivation pattern on bacterial diversity during poly-β-hydroxybutyrate production from domestic sewage sludge.

    Science.gov (United States)

    Liu, Changli; Liu, Di; Qi, Yingjie; Zhang, Ying; Liu, Xi; Zhao, Min

    2016-07-01

    The main objective of this work was to investigate the influence of different oxygen supply patterns on poly-β-hydroxybutyrate (PHB) yield and bacterial community diversity. The anaerobic-aerobic (A/O) sequencing batch reactors (SBR1) and feast-famine (F/F) SBR2 were used to cultivate activated sludge to produce PHB. The mixed microbial communities were collected and analyzed after 3 months cultivation. The PHB maximum yield was 64 wt% in SBR1 and 53 wt% in SBR2. Pyrosequencing analysis 16S rRNA gene of two microbial communities indicated there were nine and four bacterial phyla in SBR1 and SBR2, respectively. Specifically, Proteobacteria (36.4 % of the total bacterial community), Actinobacteria (19.7 %), Acidobacteria (14.1 %), Firmicutes (4.4 %), Bacteroidetes (1.7 %), Cyanobacteria/Chloroplast (1.5 %), TM7 (0.8 %), Gemmatimonadetes (0.2 %), and Nitrospirae (0.1 %) were present in SBR1. Proteobacteria (94.2 %), Bacteroidetes (2.9 %), Firmicutes (1.9 %), and Actinobacteria (0.7 %) were present in SBR2. Our results indicated the SBR1 fermentation system was more stable than that of SBR2 for PHB accumulation. PMID:26996908

  1. Bioaugmentation of a 4-chloronitrobenzene contaminated soil with Pseudomonas putida ZWL73

    International Nuclear Information System (INIS)

    The strain Pseudomonas putida ZWL73, which metabolizes 4-chloronitrobenzene (4CNB) by a partial-reductive pathway, was inoculated into lab-scale 4CNB-contaminated soil for bioaugmentation purposes in this study. The degradation of 4CNB was clearly stimulated, as indicated with the gradual accumulation of ammonium and chloride. Simultaneously, the diversity and quantity of cultivable heterotrophic bacteria decreased due to 4CNB contamination, while the quantity of 4CNB-resistant bacteria increased. During the bioaugmentation, denaturing gradient gel electrophoresis analysis showed the changes of diversity in dominant populations of intrinsic soil microbiota. The results showed that Alphaproteobacteria and Betaproteobacteria were not distinctly affected, but Actinobacteria were apparently stimulated. In addition, an interesting dynamic within Acidobacteria was observed, as well as an influence on ammonia-oxidizing bacteria population. These combined findings demonstrate that the removal of 4CNB in soils by inoculating strain ZWL73 is feasible, and that specific populations in soils rapidly changed in response to 4CNB contamination and subsequent bioaugmentation. - Pseudomonas putida ZWL73 can accelerate 4CNB removal in lab-scale soils, causing dynamic changes within intrinsic Actinobacteria and Acidobacteria

  2. An endophytic Pseudonocardia species induces the production of artemisinin in Artemisia annua.

    Directory of Open Access Journals (Sweden)

    Jie Li

    Full Text Available Endophytic actinobacteria colonize internal tissues of their host plants and are considered as a rich and reliable source of diverse species and functional microorganisms. In this study, endophytic actinobacterial strain YIM 63111 was isolated from surface-sterilized tissue of the medicinal plant Artemisia annua. We identified strain YIM 63111 as a member of the genus Pseudonocardia. A. annua seedlings grown under both sterile and greenhouse conditions were inoculated with strain YIM 63111. The growth of A. annua seedlings was strongly reduced when YIM 63111 was inoculated at higher concentrations under sterile conditions. However, no growth inhibition was observed when A. annua was grown under greenhouse conditions. Using an enhanced green fluorescent protein (EGFP expressing YIM 63111 strain, we also observed the endophytic colonization of A. annua seedling using confocal laser-scanning microscopy. The transcription levels of the key genes involved in artemisinin biosynthesis were investigated using real time RT-PCR, revealing that cytochrome P450 monooxygenase (CYP71AV1 and cytochrome P450 oxidoreductase (CPR expression were up-regulated in A. annua upon inoculation with strain YIM 63111 under certain conditions. The up-regulation of these genes was associated with the increased accumulation of artemisinin. These results suggest that endophytic actinobacteria effectively stimulate certain plant defense responses. Our data also demonstrate the use of Pseudonocardia sp. strain YIM 63111 as a promising means to enhance artemisinin production in plants.

  3. Dual control system - A novel scaffolding architecture of an inducible regulatory device for the precise regulation of gene expression.

    Science.gov (United States)

    Horbal, L; Luzhetskyy, A

    2016-09-01

    Here, we present a novel scaffolding architecture of an inducible regulatory device. This dual control system is completely silent in the off stage and is coupled to the regulation of gene expression at both the transcriptional and translational levels. This system also functions as an AND gate. We demonstrated the effectiveness of the cumate-riboswitch dual control system for the control of pamamycin production in Streptomyces albus. Placing the cre recombinase gene under the control of this system permitted the construction of synthetic devices with non-volatile memory that sense the signal and respond by altering DNA at the chromosomal level, thereby producing changes that are heritable. In addition, we present a library of synthetic inducible promoters based on the previously described cumate switch. With only one inducer and different promoters, we demonstrate that simultaneous modulation of the expression of several genes to different levels in various operons is possible. Because all modules of the AND gates are functional in bacteria other than Streptomyces, we anticipate that these regulatory devices can be used to control gene expression in other Actinobacteria. The features described in this study make these systems promising tools for metabolic engineering and biotechnology in Actinobacteria. PMID:27040671

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

    Science.gov (United States)

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

    2016-01-01

    The bloom-containing water bodies may have an impact due to cyanotoxins production on other microorganisms and aquatic plants. Where such water is being used for crops irrigation, the presence of cyanotoxins may also have a toxic impact on terrestrial plants and their rhizosphere microbiota. For that purpose, PCR-based 454 pyrosequencing was applied to phylogenetically characterize the bacterial community of Medicago sativa rhizosphere in response to cyanotoxins extract. This analysis revealed a wide diversity at species level, which decreased from unplanted soil to root tissues indicating that only some populations were able to compete for nutrients and niches in this selective habitat. Gemmatimonas, Actinobacteria, Deltaproteobacteria and Opitutae mainly inhabited the bulk soil, whereas, the root-adhering soil and the root tissues were inhabited by Gammaproteobacteria and Alphaproteobacteria. The proportion of these populations fluctuated in response to cyanotoxins extract exposure. Betaproteobacteria proportion increased in the three studied compartments, whereas Gammaproteobacteria proportion decreased except in the bulk soil. This study revealed the potential toxicity of cyanotoxins extract towards Actinobacteria, Gemmatimonas, Deltaproteobacteria, and Gammaproteobacteria, however Clostridia, Opitutae and bacteria related with Betaproteobacteria, were stimulated denoting their tolerance. Altogether, these data indicate that crop irrigation using cyanotoxins containing water might alter the rhizosphere functioning. PMID:26356186

  5. Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis.

    Directory of Open Access Journals (Sweden)

    Robert E Tyx

    Full Text Available The bacterial communities present in smokeless tobacco (ST products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae. The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products.

  6. Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis.

    Science.gov (United States)

    Tyx, Robert E; Stanfill, Stephen B; Keong, Lisa M; Rivera, Angel J; Satten, Glen A; Watson, Clifford H

    2016-01-01

    The bacterial communities present in smokeless tobacco (ST) products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae). The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products.

  7. Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

    Science.gov (United States)

    Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

    2016-06-01

    Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N•ha‑1•yr‑1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations.

  8. Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake.

    Science.gov (United States)

    Woodhouse, Jason Nicholas; Kinsela, Andrew Stephen; Collins, Richard Nicholas; Bowling, Lee Chester; Honeyman, Gordon L; Holliday, Jon K; Neilan, Brett Anthony

    2016-06-01

    The frequency of freshwater cyanobacterial blooms is at risk of increasing as a consequence of climate change and eutrophication of waterways. It is increasingly apparent that abiotic data are insufficient to explain variability within the cyanobacterial community, with biotic factors such as heterotrophic bacterioplankton, viruses and protists emerging as critical drivers. During the Australian summer of 2012-2013, a bloom that occurred in a shallow ephemeral lake over a 6-month period was comprised of 22 distinct cyanobacteria, including Microcystis, Dolichospermum, Oscillatoria and Sphaerospermopsis. Cyanobacterial cell densities, bacterial community composition and abiotic parameters were assessed over this period. Alpha-diversity indices and multivariate analysis were successful at differentiating three distinct bloom phases and the contribution of abiotic parameters to each. Network analysis, assessing correlations between biotic and abiotic variables, reproduced these phases and assessed the relative importance of both abiotic and biotic factors. Variables possessing elevated betweeness centrality included temperature, sodium and operational taxonomic units belonging to the phyla Verrucomicrobia, Planctomyces, Bacteroidetes and Actinobacteria. Species-specific associations between cyanobacteria and bacterioplankton, including the free-living Actinobacteria acI, Bacteroidetes, Betaproteobacteria and Verrucomicrobia, were also identified. We concluded that changes in the abundance and nature of freshwater cyanobacteria are associated with changes in the diversity and composition of lake bacterioplankton. Given this, an increase in the frequency of cyanobacteria blooms has the potential to alter nutrient cycling and contribute to long-term functional perturbation of freshwater systems. PMID:26636552

  9. Bacterial community structure in the rhizosphere of three cactus species from semi-arid highlands in central Mexico.

    Science.gov (United States)

    Aguirre-Garrido, J Félix; Montiel-Lugo, Daniel; Hernández-Rodríguez, César; Torres-Cortes, Gloria; Millán, Vicenta; Toro, Nicolás; Martínez-Abarca, Francisco; Ramírez-Saad, Hugo C

    2012-05-01

    The nature reserve of Tehuacan-Cuicatlan in central Mexico is known for its diversity and endemism mainly in cactus plants. Although the xerophytic flora is reasonably documented, the bacterial communities associated with these species have been largely neglected. We assessed the diversity and composition of bacterial communities in bulk (non-rhizospheric) soil and the rhizosphere of three cactus plant species: Mammillaria carnea, Opuntia pilifera and Stenocereus stellatus, approached using cultivation and molecular techniques, considering the possible effect of dry and rainy seasons. Cultivation-dependent methods were focused on putative N(2)-fixers and heterotrophic aerobic bacteria, in the two media tested the values obtained for dry season samples grouped together regardless of the sample type (rhizospheric or non-rhizospheric), these groups also included the non-rhizospheric sample for rainy season, on each medium. These CFU values were smaller and significantly different from those obtained on rhizospheric samples from rainy season. Genera composition among isolates of the rhizospheric samples was very similar for each season, the most abundant taxa being α-Proteobacteria, Actinobacteria and Firmicutes. Interestingly, the genus Ochrobactrum was highly represented among rhizospheric samples, when cultured in N-free medium. The structure of the bacterial communities was approached with molecular techniques targeting partial 16S rRNA sequences such as denaturing gradient gel electrophoresis and serial analysis of ribosomal sequence tags. Under these approaches, the most represented bacterial phyla were Actinobacteria, Proteobacteria and Acidobacteria. The first two were also highly represented when using isolation techniques.

  10. Changes of soil bacterial diversity as a consequence of agricultural land use in a semi-arid ecosystem.

    Directory of Open Access Journals (Sweden)

    Guo-Chun Ding

    Full Text Available Natural scrublands in semi-arid deserts are increasingly being converted into fields. This results in losses of characteristic flora and fauna, and may also affect microbial diversity. In the present study, the long-term effect (50 years of such a transition on soil bacterial communities was explored at two sites typical of semi-arid deserts. Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods based on 16S rRNA gene fragments amplified from total community DNA. Denaturing gradient gel electrophoresis (DGGE analyses revealed significant effects of the transition on community composition of Bacteria, Actinobacteria, Alpha- and Betaproteobacteria at both sites. PhyloChip hybridization analysis uncovered that the transition negatively affected taxa such as Acidobacteria, Chloroflexi, Acidimicrobiales, Rubrobacterales, Deltaproteobacteria and Clostridia, while Alpha-, Beta- and Gammaproteobacteria, Bacteroidetes and Actinobacteria increased in abundance. Redundancy analysis suggested that the community composition of phyla responding to agricultural use (except for Spirochaetes correlated with soil parameters that were significantly different between the agricultural and scrubland soil. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. The variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses, suggesting reduced beta diversity due to agricultural practices. The long-term use for agriculture resulted in profound changes in the bacterial community and physicochemical characteristics of former scrublands, which may irreversibly affect the natural soil ecosystem.

  11. Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China.

    Science.gov (United States)

    Ren, Chengjie; Sun, Pingsheng; Kang, Di; Zhao, Fazhu; Feng, Yongzhong; Ren, Guangxin; Han, Xinhui; Yang, Gaihe

    2016-01-01

    In the present paper, we investigated the effects of afforestation on nitrogen fractions and microbial communities. A total of 24 soil samples were collected from farmland (FL) and three afforested lands, namely Robinia pseudoacacia L (RP), Caragana korshinskii Kom (CK), and abandoned land (AL), which have been arable for the past 40 years. Quantitative PCR and Illumina sequencing of 16S rRNA genes were used to analyze soil bacterial abundance, diversity, and composition. Additionally, soil nitrogen (N) stocks and fractions were estimated. The results showed that soil N stock, N fractions, and bacterial abundance and diversity increased following afforestation. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of soil bacterial compositions. Overall, soil bacterial compositions generally changed from Actinobacteria (Acidobacteria)-dominant to Proteobacteria-dominant following afforestation. Soil N fractions, especially for dissolved organic nitrogen (DON), were significantly correlated with most bacterial groups and bacterial diversity, while potential competitive interactions between Proteobacteria (order Rhizobiales) and Cyanobacteria were suggested. In contrast, nitrate nitrogen (NO3(-)-N) influenced soil bacterial compositions less than other N fractions. Therefore, the present study demonstrated that bacterial diversity and specific species respond to farmland-to-forest conversion and hence have the potential to affect N dynamic processes in the Loess Plateau. PMID:27334692

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

    Institute of Scientific and Technical Information of China (English)

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

    2016-01-01

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

  13. Comparison of airborne bacterial communities from a hog farm and spray field.

    Science.gov (United States)

    Arfken, Ann M; Song, Bongkeun; Sung, Jung-Suk

    2015-05-01

    Airborne bacteria from hog farms may have detrimental impacts on human health, particularly in terms of antibiotic resistance and pathogen zoonosis. Despite human health risks, very little is known about the composition and diversity of airborne bacteria from hog farms and hog-related spray fields. We used pyrosequencing analysis of 16S rRNA genes to compare airborne bacterial communities in a North Carolina hog farm and lagoon spray field. In addition, we isolated and identified antibiotic-resistant bacteria from both air samples. Based on 16S rRNA gene pyrosequence analysis, Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria were the dominant phyla in airborne bacterial communities from both hog farm and spray field sites. Within the Firmicutes genera, Clostridium spp. were more abundant in the hog farm, whereas Staphylococcus spp. were higher in the spray field. The presence of opportunitic pathogens, including several Staphylococcus species and Propionibacterium acnes, was detected in both bioaerosol communities based on phylogenetic analysis. The isolation and identification of antibiotic-resistant bacteria from air samples also showed similar results with dominance of Actinobacteria and Proteobacteria in both hog farm and spray field air. Thus, the existence of opportunistic pathogens and antibiotic resistant bacteria in airborne communities evidences potential health risks to farmers and other residents from swine bioaerosol exposure.

  14. Seasonal variation of bacterial endophytes in urban trees

    Directory of Open Access Journals (Sweden)

    Shu Yi eShen

    2015-05-01

    Full Text Available Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons. The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp.. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia and Sanguibacter spp.. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests investigations of the studies ofendophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.

  15. Distribution, diversity and abundance of bacterial laccase-like genes in different particle size fractions of sediments in a subtropical mangrove ecosystem.

    Science.gov (United States)

    Luo, Ling; Zhou, Zhi-Chao; Gu, Ji-Dong

    2015-10-01

    This study investigated the diversity and abundance of bacterial lacasse-like genes in different particle size fractions, namely sand, silt, and clay of sediments in a subtropical mangrove ecosystem. Moreover, the effects of nutrient conditions on bacterial laccase-like communities as well as the correlation between nutrients and, both the abundance and diversity indices of laccase-like bacteria in particle size fractions were also studied. Compared to bulk sediments, Bacteroidetes, Caldithrix, Cyanobacteria and Chloroflexi were dominated in all 3 particle-size fractions of intertidal sediment (IZ), but Actinobacteria and Firmicutes were lost after the fractionation procedures used. The diversity index of IZ fractions decreased in the order of bulk > clay > silt > sand. In fractions of mangrove forest sediment (MG), Verrucomicrobia was found in silt, and both Actinobacteria and Bacteroidetes appeared in clay, but no new species were found in sand. The declining order of diversity index in MG fractions was clay > silt > sand > bulk. Furthermore, the abundance of lacasse-like bacteria varied with different particle-size fractions significantly (p clay > silt in both IZ and MG fractions. Additionally, nutrient availability was found to significantly affect the diversity and community structure of laccase-like bacteria (p carbon contents were positively related to the abundance of bacterial laccase-like genes in particle size fractions (p < 0.05). Therefore, this study further provides evidence that bacterial laccase plays a vital role in turnover of sediment organic matter and cycling of nutrients. PMID:25822201

  16. Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils.

    Science.gov (United States)

    Navarro-Noya, Yendi E; Jan-Roblero, Janet; González-Chávez, Maria del Carmen; Hernández-Gama, Regina; Hernández-Rodríguez, César

    2010-05-01

    In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources. PMID:20084459

  17. Recognition of greater diversity of Bacillus species and related bacteria in human faeces.

    Science.gov (United States)

    Hoyles, Lesley; Honda, Harue; Logan, Niall A; Halket, Gillian; La Ragione, Roberto M; McCartney, Anne L

    2012-01-01

    In a study looking at culturable aerobic Actinobacteria associated with the human gastrointestinal tract, the vast majority of isolates obtained from dried human faeces belonged to the genus Bacillus and related bacteria. A total of 124 isolates were recovered from the faeces of 10 healthy adult donors. 16S rRNA gene sequence analyses showed the majority belonged to the families Bacillaceae (n=81) and Paenibacillaceae (n=3), with Bacillus species isolated from all donors. Isolates tentatively identified as Bacillus clausii (n=32) and Bacillus licheniformis (n=28) were recovered most frequently, with the genera Lysinibacillus, Ureibacillus, Oceanobacillus, Ornithinibacillus and Virgibacillus represented in some donors. Phenotypic data confirmed the identities of isolates belonging to well-characterized species. Representatives of the phylum Actinobacteria were recovered in much lower numbers (n=11). Many of the bacilli exhibited antimicrobial activity against one or more strains of Clostridium difficile, Clostridium perfringens, Listeria monocytogenes and Staphylococcus aureus, with some (n=12) found to have no detectable cytopathic effect on HEp-2 cells. This study has revealed greater diversity within gut-associated aerobic spore-formers than previous studies, and suggests that bacilli with potential as probiotics could be isolated from the human gut. PMID:22041546

  18. Role of primary substrate composition on microbial community structure and function and trace organic chemical attenuation in managed aquifer recharge systems

    KAUST Repository

    Li, Dong

    2014-03-26

    This study was performed to reveal the microbial community characteristics in simulated managed aquifer recharge (MAR), a natural water treatment system, under different concentrations and compositions of biodegradable dissolved organic carbon (BDOC) and further link these to the biotransformation of emerging trace organic chemicals (TOrCs). Two pairs of soil-column setups were established in the laboratory receiving synthetic feed solutions composed of different peptone/humic acid ratios and concentrations. Higher BDOC concentration resulted in lower microbial community diversity and higher relative abundance of Betaproteobacteria. Decreasing the peptone/humic acid ratio resulted in higher diversity of the community and higher relative abundances of Firmicutes, Planctomycetes, and Actinobacteria. The metabolic capabilities of microbiome involved in xenobiotics biodegradation were significantly promoted under lower BDOC concentration and higher humic acid content. Cytochrome P450 genes were also more abundant under these primary substrate conditions. Lower peptone/humic acid ratios also promoted the attenuation of most TOrCs. These results suggest that the primary substrate characterized by a more refractory character could increase the relative abundances of Firmicutes, Planctomycetes, and Actinobacteria, as well as associated cytochrome P450 genes, all of which should play important roles in the biotransformation of TOrCs in this natural treatment system. © 2014 Springer-Verlag.

  19. Bacterial Bio-Resources for Remediation of Hexachlorocyclohexane

    Directory of Open Access Journals (Sweden)

    María J. Amoroso

    2012-11-01

    Full Text Available In the last few decades, highly toxic organic compounds like the organochlorine pesticide (OP hexachlorocyclohexane (HCH have been released into the environment. All HCH isomers are acutely toxic to mammals. Although nowadays its use is restricted or completely banned in most countries, it continues posing serious environmental and health concerns. Since HCH toxicity is well known, it is imperative to develop methods to remove it from the environment. Bioremediation technologies, which use microorganisms and/or plants to degrade toxic contaminants, have become the focus of interest. Microorganisms play a significant role in the transformation and degradation of xenobiotic compounds. Many Gram-negative bacteria have been reported to have metabolic abilities to attack HCH. For instance, several Sphingomonas strains have been reported to degrade the pesticide. On the other hand, among Gram-positive microorganisms, actinobacteria have a great potential for biodegradation of organic and inorganic toxic compounds. This review compiles and updates the information available on bacterial removal of HCH, particularly by Streptomyces strains, a prolific genus of actinobacteria. A brief account on the persistence and deleterious effects of these pollutant chemical is also given.

  20. Genetics and Genomics of the Genus Amycolatopsis.

    Science.gov (United States)

    Kumari, Rashmi; Singh, Priya; Lal, Rup

    2016-09-01

    Actinobacteria are gram-positive filamentous bacteria which contains some of the most deadly human pathogens (Mycobacterium tuberculosis, M. leprae, Corynebacterium diphtheriae, Nocardia farcinica), plant pathogens (Streptomyces scabies, Leifsonia xyli) along with organisms that produces antibiotic (Streptomycetes, Amycolatopsis, Salinospora). Interestingly, these bacteria are equipped with an extraordinary capability of producing antibiotics and other metabolites which have medicinal properties. With the advent of inexpensive genome sequencing techniques and their clinical importance, many genomes of Actinobacteria have been successfully sequenced. These days, with the constant increasing number of drug-resistant bacteria, the urgent need for discovering new antibiotics has emerged as a major scientific challenge. And, unfortunately the traditional method of screening bacterial strains for the production of antibiotics has decreased leading to a paradigm shift in the planning and execution of discovery of novel biosynthetic gene clusters via genome mining process. The entire focus has shifted to the evaluation of genetic capacity of organisms for metabolite production and activation of cryptic gene clusters. This has been made possible only due to the availability of genome sequencing and has been augmented by genomic studies and new biotechnological approaches. Through this article, we present the analysis of the genomes of species belonging to the genus Amycolatopsis, sequenced till date with a focus on completely sequenced genomes and their application for further studies. PMID:27407288

  1. The Arctic Soil Bacterial Communities in the Vicinity of a Little Auk Colony

    Science.gov (United States)

    Zielińska, Sylwia; Kidawa, Dorota; Stempniewicz, Lech; Łoś, Marcin; Łoś, Joanna M.

    2016-01-01

    Due to deposition of birds' guano, eggshells or feathers, the vicinity of a large seabirds' breeding colony is expected to have a substantial impact on the soil's physicochemical features as well as on diversity of vegetation and the soil invertebrates. Consequently, due to changing physicochemical features the structure of bacterial communities might fluctuate in different soil environments. The aim of this study was to investigate the bacterial assemblages in the Arctic soil within the area of a birds' colony and in a control sample from a topographically similar location but situated away from the colony's impact area. A high number of OTUs found in both areas indicates a highly complex microbial populations structure. The most abundant phyla in both of the tested samples were: Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, with different proportions in the total share. Despite differences in the physicochemical soil characteristics, the soil microbial community structures at the phylum level were similar to some extent in the two samples. The only share that was significantly higher in the control area when compared to the sample obtained within the birds' colony, belonged to the Actinobacteria phylum. Moreover, when analyzing the class level for each phylum, several differences between the samples were observed. Furthermore, lower proportions of Proteobacteria and Acidobacteria were observed in the soil sample under the influence of the bird's colony, which most probably could be linked to higher nitrogen concentrations in that sample.

  2. Evaluación de la producción de ácidos orgánicos por Streptomyces spp. y solubilización de tres fuentes de fósforo por la cepa T3A

    Directory of Open Access Journals (Sweden)

    Gloria Carolina Prieto Correal

    2015-05-01

    Full Text Available  Título en ingles: Evaluation of organic acid production by Streptomyces spp. and solubilization of three phosphorus sources by strain T3A Título corto: Producción de ácidos orgánicos por Streptomyces spp.  y solubilización de fosfatos por la cepa T3A. Título corto en ingles: Organic acid production by Streptomyces spp. and solubilization by strain T3AResumen: Quince aislamientos de actinobacterias solubilizadoras de fósforo obtenidas a partir de suelos de los andes orientales colombianos fueron identificadas por sus características morfológicas y por la secuenciación del gen 16S ADNr. El análisis BLASTN de las 15 secuencias obtenidas mostró que los aislamientos pertenecían al género Streptomyces. Paralelamente, los aislamientos fueron sometidos a la detección de ácidos orgánicos, durante el proceso de solubilización de fósforo con la presencia mayoritaria de los ácidos oxálico, cítrico y glucónico. Dentro de las cepas evaluadas Streptomyces sp. T3A fue seleccionada para ser evaluada bajo diferentes fuentes de fósforo inorgánico debido a los resultados de evaluaciones cualitativas y cuantitativas realizadas previamente, en las cuales mostró una actividad solubilizadora de fósforo significativamente alta. Los resultados evidenciaron la capacidad de ésta actinobacteria para solubilizar diferentes fuentes de fosfatos insolubles con valores de 122 mgP·L-1 paraCa3(PO42, 14 mgP·L-1 para AlPO4 y 19,6 mgP·L-1 para roca fosfórica. También los ensayos revelaron que la actividad se mantiene en un rango de pH de 5 a 8 con las mismas fuentes de fosfatos evaluadas. Los resultados presentados contribuyen al avance en la caracterización de estas bacterias como promotoras de crecimiento vegetal con el fin de presentarlos como un recurso clave a nivel de biotecnología agrícola. Palabras clave: Streptomyces, Solubilización de fósforo, ácidos orgánicos, actinobacteria, HPLC. Abstrac: Fifteen isolates of Eastern

  3. Bacteria as growth-promoting agents for citrus rootstocks.

    Science.gov (United States)

    Giassi, Valdionei; Kiritani, Camila; Kupper, Katia Cristina

    2016-09-01

    The microbial community plays an essential role in maintaining the ecological balance of soils. Interactions between microorganisms and plants have a major influence on the nutrition and health of the latter, and growth-promoting rhizobacteria can be used to improve plant development through a wide range of mechanisms. Therefore, the objective of the present study was to evaluate bacteria as growth-promoting agents for citrus rootstocks. A total of 30 bacterial isolates (11 of Bacillus spp., 11 actinobacteria, and 8 lactic acid bacteria) were evaluated in vitro for indoleacetic acid production, phosphate solubilization, and nitrogen (N) fixation. In vivo testing consisted of growth promotion trials of the bacterial isolates that yielded the best results on in vitro tests with three rootstocks: Swingle citrumelo [Citrus×paradisi Macfad cv. Duncan×Poncirus trifoliata (L.) Raf.], Sunki mandarin (Citrus sunki Hort. ex Tan), and rangpur (Citrus×limonia Osbeck). The parameters of interest were height, number of leaves, stem diameter, shoot and root dry mass, and total dry mass at 150days after germination. The results showed that most bacterial isolates were capable of IAA production. Only one lactic acid bacterium isolate (BL06) solubilized phosphate, with a high solubilization index (PSI>3). In the actinobacteria group, isolates ACT01 (PSI=2.09) and ACT07 (PSI=2.01) exhibited moderate phosphate-solubilizing properties. Of the Bacillus spp. isolates, only CPMO6 and BM17 solubilized phosphate. The bacterial isolates that most fixated nitrogen were BM17, ACT11, and BL24. In the present study, some bacteria were able to promote growth of citrus rootstocks; however, this response was dependent on plant genotype and isolate. Bacillus spp. BM16 and CPMO4 were able to promote growth of Swingle citrumelo. In Sunki mandarin plants, the best treatment results were obtained with BM17 (Bacillus sp.) and ACT11 (actinobacteria). For Rangpur lime rootstock, only BM05 (Bacillus sp

  4. Microbial monitoring in treated stone at the Royal Chapel of Granada

    Science.gov (United States)

    Jroundi, Fadwa; Pinar, Guadalupe; González-Muñoz, Maria Theresa; Sterflinger, Katja

    2014-05-01

    Biomineralization processes have been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain). In few years, this conservation treatment has gained worth attention as environmentally friendly methodology for protection and consolidation of limestone because of the compatibilities shown between the new calcium carbonate cement and the original stone substrate. Moreover, the success of this approach may be related to the diversity of the microbiota inhabiting the stone and activated upon the biotreatment application and throughout the time. González-Muñoz et al. (2008) proposed a nutritional solution that activate among the bacteria inhabiting the stone those with carbonatogenic activity. In this study, a long-term (one, two and three years) monitoring of the microbiota present on the treated and untreated stones was done using a molecular strategy, including total DNA extraction, PCR amplification of 16S rRNA sequences, construction of clone libraries and fingerprinting by DGGE (Denaturing Gradient Gel Electrophoresis) analysis. Sequencing of the 16S rDNA revealed the dominant occurrence of members of Actinobacteria (44.20%), Gamma-proteobacteria (30.24%) and Chloroflexi (25.56%) after one year of the biotreatment. Whereas after two years, members of Cyanobacteria (22.10%) appeared and three years after, the microbiota consisted of only Actinobacteria and Cyanobacteria with approximately the same percentage in comparison with the untreated stones, dominated exclusively by Actinobacteria (100%). Fungal diversity followed the same dynamic as bacterial diversity being Ascomicota the predominant order before treatment. After one year, members of Basidiomycota and Viridiplantae appeared on the stone while two years after, the Viridiplantae dominated with a percentage of 84.77%. Finally, three years after the treatment, fungi population started to stabilize again and Ascomicota predominated next to 16.67% of

  5. Microorganisms associated particulate matter: a preliminary study.

    Science.gov (United States)

    Alghamdi, Mansour A; Shamy, Magdy; Redal, Maria Ana; Khoder, Mamdouh; Awad, Abdel Hameed; Elserougy, Safaa

    2014-05-01

    This study aims to determine the microbiological quality of particulate matter (PM) in an urban area in Jeddah, Saudi Arabia, during December 2012 to April 2013. This was achieved by the determination of airborne bacteria, fungi, and actinobacteria associated PM10 and PM2.5, as well as their relationships with gaseous pollutants, O3, SO2 and NO2, and meteorological factors (T°C, RH% and Ws). High volume samplers with PM10 and PM2.5 selective sizes, and glass fiber filters were used to collect PM10 and PM2.5, respectively. The filters were suspended in buffer phosphate and aliquots were spread plated onto the surfaces of trypticase soy agar, malt extract agar, and starch casein agar media for counting of bacteria, fungi and actinobacteria-associated PM, respectively. PM10 and PM2.5 concentrations averaged 159.9 μg/m(3) and 60 μg/m(3), respectively, with the ratio of PM2.5/PM10 averaged ~0.4. The concentrations of O3, SO2 and NO2 averaged 35.73 μg/m(3), 38.1μg/m(3) and 52.5 μg/m(3), respectively. Fungi and actinobacteria associated PM were found in lower concentrations than bacteria. The sum of microbial loads was higher in PM10 than PM2.5, however a significant correlation (r=0.57, P ≤ 0.05) was found between the sum of microbial loads associated PM10 and PM2.5. Aspergillus fumigatus and Aspergillus niger were the common fungal types associated PM. Temperature significantly correlated with both PM10 (r=0.44), and PM2.5 (r=0.5). Significant negative correlations were found between O3 and PM2.5 (r=-0.47), and between SO2 with PM10 (r=-0.48). Wind speed positively correlated with airborne microorganisms associated PM. The regression model showed that the inverse PM2.5 concentration (1/PM2.5) was a significant determinant of fungal count associated PM. Chemical processes and environmental factors could affect properties of PM and in turn its biological quality.

  6. Bacteria as growth-promoting agents for citrus rootstocks.

    Science.gov (United States)

    Giassi, Valdionei; Kiritani, Camila; Kupper, Katia Cristina

    2016-09-01

    The microbial community plays an essential role in maintaining the ecological balance of soils. Interactions between microorganisms and plants have a major influence on the nutrition and health of the latter, and growth-promoting rhizobacteria can be used to improve plant development through a wide range of mechanisms. Therefore, the objective of the present study was to evaluate bacteria as growth-promoting agents for citrus rootstocks. A total of 30 bacterial isolates (11 of Bacillus spp., 11 actinobacteria, and 8 lactic acid bacteria) were evaluated in vitro for indoleacetic acid production, phosphate solubilization, and nitrogen (N) fixation. In vivo testing consisted of growth promotion trials of the bacterial isolates that yielded the best results on in vitro tests with three rootstocks: Swingle citrumelo [Citrus×paradisi Macfad cv. Duncan×Poncirus trifoliata (L.) Raf.], Sunki mandarin (Citrus sunki Hort. ex Tan), and rangpur (Citrus×limonia Osbeck). The parameters of interest were height, number of leaves, stem diameter, shoot and root dry mass, and total dry mass at 150days after germination. The results showed that most bacterial isolates were capable of IAA production. Only one lactic acid bacterium isolate (BL06) solubilized phosphate, with a high solubilization index (PSI>3). In the actinobacteria group, isolates ACT01 (PSI=2.09) and ACT07 (PSI=2.01) exhibited moderate phosphate-solubilizing properties. Of the Bacillus spp. isolates, only CPMO6 and BM17 solubilized phosphate. The bacterial isolates that most fixated nitrogen were BM17, ACT11, and BL24. In the present study, some bacteria were able to promote growth of citrus rootstocks; however, this response was dependent on plant genotype and isolate. Bacillus spp. BM16 and CPMO4 were able to promote growth of Swingle citrumelo. In Sunki mandarin plants, the best treatment results were obtained with BM17 (Bacillus sp.) and ACT11 (actinobacteria). For Rangpur lime rootstock, only BM05 (Bacillus sp

  7. A Novel Insecticidal Peptide SLP1 Produced by Streptomyces laindensis H008 against Lipaphis erysimi.

    Science.gov (United States)

    Xu, Lijian; Liang, Kangkang; Duan, Bensha; Yu, Mengdi; Meng, Wei; Wang, Qinggui; Yu, Qiong

    2016-01-01

    Aphids are major insect pests for crops, causing damage by direct feeding and transmission of plant diseases. This paper was completed to discover and characterize a novel insecticidal metabolite against aphids from soil actinobacteria. An insecticidal activity assay was used to screen 180 bacterial strains from soil samples against mustard aphid, Lipaphis erysimi. The bacterial strain H008 showed the strongest activity, and it was identified by the phylogenetic analysis of the 16S rRNA gene and physiological traits as a novel species of genus Streptomyces (named S. laindensis H008). With the bioassay-guided method, the insecticidal extract from S. laindensis H008 was subjected to chromatographic separations. Finally, a novel insecticidal peptide was purified from Streptomyces laindensis H008 against L. erysimi, and it was determined to be S-E-P-A-Q-I-V-I-V-D-G-V-D-Y-W by TOF-MS and amino acid analysis. PMID:27556442

  8. Eukaryotic and prokaryotic microbial communities during microalgal biomass production.

    Science.gov (United States)

    Lakaniemi, Aino-Maija; Hulatt, Chris J; Wakeman, Kathryn D; Thomas, David N; Puhakka, Jaakko A

    2012-11-01

    Eukaryotic and bacterial communities were characterized and quantified in microalgal photobioreactor cultures of freshwater Chlorella vulgaris and marine Dunaliella tertiolecta. The microalgae exhibited good growth, whilst both cultures contained diverse bacterial communities. Both cultures included Proteobacteria and Bacteroidetes, while C. vulgaris cultures also contained Actinobacteria. The bacterial genera present in the cultures were different due to different growth medium salinities and possibly different extracellular products. Bacterial community profiles were relatively stable in D. tertiolecta cultures but not in C. vulgaris cultures likely due to presence of ciliates (Colpoda sp.) in the latter. The presence of ciliates did not, however, cause decrease in total number of C. vulgaris or bacteria during 14 days of cultivation. Quantitative PCR (qPCR) reliably showed relative microalgal and bacterial cell numbers in the batch cultures with stable microbial communities, but was not effective when bacterial communities varied. Raw culture samples were successfully used as qPCR templates. PMID:22995170

  9. Capacity of Aromatic Compound Degradation by Bacteria from Amazon Dark Earth

    Directory of Open Access Journals (Sweden)

    Fernanda Mancini Nakamura

    2014-06-01

    Full Text Available Amazon dark earth (ADE is known for its high organic matter content, biochar concentration and microbial diversity. The biochar amount suggests the existence of microorganisms capable of degrading aromatic hydrocarbons (AHs. In an effort to investigate the influence of bacteria on the resilience and fertility of these soils, we enriched five ADE soils with naphthalene and phenanthrene, and biodegradation assays with phenanthrene and diesel oil were carried out, as well. After DNA extraction, amplification and sequencing of the 16S rRNA bacterial gene, we identified 148 isolates as the Proteobacteria, Firmicutes and Actinobacteria phyla comprising genera closely related to AHs biodegradation. We obtained 128 isolates that degrade diesel oil and 115 isolates that degrade phenanthrene. Some isolates were successful in degrading both substrates within 2 h. In conclusion, the obtained isolates from ADE have degrading aromatic compound activity, and perhaps, the biochar content has a high influence on this.

  10. Three new 2,5-diketopiperazines from the fish intestinal Streptomyces sp. MNU FJ-36.

    Science.gov (United States)

    Ou, Yi-Xin; Huang, Jia-Fu; Li, Xiu-Min; Kang, Qian-Jin; Pan, Yu-Tian

    2016-08-01

    The gut actinobacteria of marine-inhabited fish is one of the most important reservoirs of novel natural products. Currently, the Streptomyces sp. MNU FJ-36 was isolated from the intestinal fabric of Katsuwonus sp. and determined by 16S rRNA analysis. From the cultures of the S. sp. MNU FJ-36, three new 2,5-diketopiperazines (2,5-DKPs) were discovered and identified as 3-(3-hydroxy-4-methoxybenzyl)-6-isobutyl-2,5-diketopiperazine (1), 3-(1,3-benzodioxol-5-ylmethyl)-6-isobutyl-2,5-diketopiperazine (2) and 3-(1,3-benzodioxol-5-ylmethyl)-6-isopropyl-2,5-diketopiperazine (3). Their structures were elucidated on the basis of spectroscopic data analysis. All the compounds were also evaluated for their inhibitory activity against P388, A-549 and HCT-116 cell lines with the MTT assay. PMID:26828674

  11. Lichens as natural sources of biotechnologically relevant bacteria.

    Science.gov (United States)

    Suzuki, Marcelino T; Parrot, Delphine; Berg, Gabriele; Grube, Martin; Tomasi, Sophie

    2016-01-01

    The search for microorganisms from novel sources and in particular microbial symbioses represents a promising approach in biotechnology. In this context, lichens have increasingly become a subject of research in microbial biotechnology, particularly after the recognition that a diverse community of bacteria other than cyanobacteria is an additional partner to the traditionally recognized algae-fungus mutualism. Here, we review recent studies using culture-dependent as well as culture-independent approaches showing that lichens can harbor diverse bacterial families known for the production of compounds of biotechnological interest and that several microorganisms isolated from lichens, in particular Actinobacteria and Cyanobacteria, can produce a number of bioactive compounds, many of them with biotechnological potential.

  12. Physicochemical characteristics and microbial community evolution of biofilms during the start-up period in a moving bed biofilm reactor.

    Science.gov (United States)

    Zhu, Yan; Zhang, Yan; Ren, Hong-Qiang; Geng, Jin-Ju; Xu, Ke; Huang, Hui; Ding, Li-Li

    2015-03-01

    This study aimed to investigate biofilm properties evolution coupled with different ages during the start-up period in a moving bed biofilm reactor system. Physicochemical characteristics including adhesion force, extracellular polymeric substances (EPS), morphology as well as volatile solid and microbial community were studied. Results showed that the formation and development of biofilms exhibited four stages, including (I) initial attachment and young biofilm formation, (II) biofilms accumulation, (III) biofilm sloughing and updating, and (IV) biofilm maturation. During the whole start-up period, adhesion force was positively and significantly correlated with the contents of EPS, especially the content of polysaccharide. In addition, increased adhesion force and EPS were beneficial for biofilm retention. Gram-negative bacteria mainly including Sphaerotilus, Zoogloea and Haliscomenobacter were predominant in the initial stage. Actinobacteria was beneficial to resist sloughing. Furthermore, filamentous bacteria were dominant in maturation biofilm.

  13. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery

    DEFF Research Database (Denmark)

    Poulsen, Michael; Oh, Dong-Chan; Clardy, Jon;

    2011-01-01

    Identifying new sources for small molecule discovery is necessary to help mitigate the continuous emergence of antibiotic-resistance in pathogenic microbes. Recent studies indicate that one potentially rich source of novel natural products is Actinobacterial symbionts associated with social...... of these isolates identified 11 distinct and structurally diverse secondary metabolites, including a novel polyunsaturated and polyoxygenated macrocyclic lactam, which we name sceliphrolactam. By pairing the 15 Streptomyces strains against a collection of fungi and bacteria, we document their antifungal...... and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding...

  14. [Metagenomic Analysis of Microbial Communities of the Sediments of the Kara Sea Shelf and the Yenisei Bay].

    Science.gov (United States)

    Mamaeva, E V; Galach'yants, Yu P; Khabudaev, K V; Petrova, D P; Pogodaeva, T V; Khodzher, T B; Zemskaya, T I

    2016-01-01

    Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and β-Proteo- bacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Gulf sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons. PMID:27476207

  15. Synthesis of silver nanoparticles from two acidophilic strains of Pilimelia columellifera subsp. pallida and their antibacterial activities.

    Science.gov (United States)

    Golińska, Patrycja; Wypij, Magdalena; Rathod, Dnyaneshwar; Tikar, Sagar; Dahm, Hanna; Rai, Mahendra

    2016-05-01

    Biosynthesis of silver nanoparticles (AgNPs) is an eco-friendly approach by using different biological sources; for example, plants and microorganisms such as bacteria, fungi, and actinobacteria. In this report, we present the biological synthesis of silver nanoparticles (AgNPs) by acidophilic actinomycetes SL19 and SL24 strains isolated from pine forest soil (pH Pseudomonas aeruginosa, and uropathogens such as Enterobacter, S. aureus, P. aeruginosa, K. pneumoniae, and E. coli. The lowest MIC (40 μg ml(-1) ) was demonstrated by AgNPs synthesized from SL24 against E. coli. However, the AgNPs of SL19 showed lowest MIC (70 μg ml(-1) ) against S. aureus. The activity of antibiotic was enhanced, when tested in combination with silver nanoparticles synthesized from both actinobacterial strains. PMID:27151174

  16. Sequential sludge digestion after diverse pre-treatment conditions: sludge removal, methane production and microbial community changes.

    Science.gov (United States)

    Park, Sang Kyu; Jang, Hyun Min; Ha, Jeong Hyub; Park, Jong Moon

    2014-06-01

    A lab-scale sequential sludge digestion process which consists of a mesophilic anaerobic digester (MAD) and a thermophilic aerobic digester (TAD) was developed. Thermal, thermal-alkaline and long-term alkaline pre-treatments were applied to the feed sludge to examine their effects on sludge removal and methane production. Especially after thermal-alkaline pre-treatment, high COD removal was maintained; methane production rate was also drastically increased by improving the hydrolysis step of sludge degradation. Polymerase chain reaction-denaturing gel gradient electrophoresis indicated that bacterial communities were represented by three phyla (Firmicutes, Proteobacteria, Actinobacteria) and that Clostridium straminisolvens was the major bacterial species in MAD. Quantitative real-time PCR results indicated that Methanosaeta concilli was the major archaeal species in MAD, and that Ureibacillus sp. was the most abundant bacterial species in TAD.

  17. Effects of Temperature, Acetate and Nitrate on Methane Generation from Petroleum Hydrocarbons

    Institute of Scientific and Technical Information of China (English)

    Liu Chunshuang; Zhao Dongfeng; Zhang Yunbo

    2014-01-01

    In this study, the effects of temperature, acetate and nitrate on methane gas production from biodegradation of petroleum hydrocarbons were investigated. The results indicated that methane gas production at 35℃was higher than that obtained at 55℃. The acetate addition signiifcant enhanced the methane production at 35℃, however, at 55℃the nitrate addition could largely promote the methane production. The microbial community structures were revealed by PCR-DGGE. The Actinobacteria, Clostridia, Clostridiales, Syntrophus, Pseudomonas, and Proteobacteria-like bacteria and Methano-cellales, Methanosaeta, Methanomicrobiales, Methanolinea, Thermoprotei-like archaea had been enriched at 35 ℃in the acetate addition test. The Thermoprotei, Proteobacterium, Thermodesulfovibrio-like bacteria and Methanocellales-like ar-chaea had been enriched at 55℃in the nitrate addition test. The results may shed light on the bio-utilization of marginal oil reservoirs for enhancing energy recovery.

  18. Periodical episodes of foaming involving Gram-negative filaments. Morpho type 0581: an unknown; Episodios periodicos de espumacion con impliaciond e filamentos Gram negativos. El morfotipo 0581: un desconido

    Energy Technology Data Exchange (ETDEWEB)

    Zarnoza, A.; Rodriguez, E.; Isac, L.; Alonso, J. L.; Fernandez, N.; Zorrila, F.; Fajardo, V.

    2006-07-01

    The bacteria GALO and Microthrix parvicella are responsible for foaming in active sludge in WWTP. According to Eikelboom (2000) and Jenkins, et al. (2003), these micro-organisms are classified by morpho types, which sometimes show a diversity of species when specific probes are used. A study of the periodical foaming process in the WWTP in the municipally of Torres-Torres (Valencia, Spain), with a predominance of morpho type 0581, has made it possible to ascertain both the optical and phylogenetic identity of this morpho type. Contrary to what might have been expected in view of its morphological similarity to Microthrix parvicella, morpho type 0581 is photogenically related to the phylum Chloroflexi and not to the phylum Actinobacteria, to which Microthrix parvicella belong. (Author)

  19. Harboring oil-degrading bacteria: a potential mechanism of adaptation and survival in corals inhabiting oil-contaminated reefs.

    Science.gov (United States)

    Al-Dahash, Lulwa M; Mahmoud, Huda M

    2013-07-30

    Certain coral reef systems north of the Arabian Gulf are characterized by corals with a unique ability to thrive and flourish despite the presence of crude oil continuously seeping from natural cracks in the seabed. Harboring oil-degrading bacteria as a part of the holobiont has been investigated as a potential mechanism of adaptation and survival for corals in such systems. The use of conventional and molecular techniques verified a predominance of bacteria affiliated with Gammaproteobacteria, Actinobacteria and Firmicutes in the mucus and tissues of Acropora clathrata and Porites compressa. These bacteria were capable of degrading a wide range of aliphatic (C9-C28) aromatic hydrocarbons (Phenanthrene, Biphenyl, Naphthalene) and crude oil. In addition, microcosms supplied with coral samples and various concentrations of crude oil shifted their bacterial population toward the more advantageous types of oil degraders as oil concentrations increased. PMID:23014479

  20. Molecular characterization of the Corynebacterium pseudotuberculosis hsp60-hsp10 operon, and evaluation of the immune response and protective efficacy induced by hsp60 DNA vaccination in mice

    Directory of Open Access Journals (Sweden)

    Oliveira Sérgio C

    2011-07-01

    Full Text Available Abstract Background Heat shock proteins (HSPs are important candidates for the development of vaccines because they are usually able to promote both humoral and cellular immune responses in mammals. We identified and characterized the hsp60-hsp10 bicistronic operon of the animal pathogen Corynebacterium pseudotuberculosis, a Gram-positive bacterium of the class Actinobacteria, which causes caseous lymphadenitis (CLA in small ruminants. Findings To construct the DNA vaccine, the hsp60 gene of C. pseudotuberculosis was cloned in a mammalian expression vector. BALB/c mice were immunized by intramuscular injection with the recombinant plasmid (pVAX1/hsp60. Conclusion This vaccination induced significant anti-hsp60 IgG, IgG1 and IgG2a isotype production. However, immunization with this DNA vaccine did not confer protective immunity.

  1. Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

    Science.gov (United States)

    Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

    2011-04-01

    Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples. PMID:21563009

  2. Application of a new purification method of West-Kazakhstan chestnut soil microbiota DNA for metagenomic analysis

    Science.gov (United States)

    Sergaliev, N. Kh.; Kakishev, M. G.; Zhiengaliev, A. T.; Volodin, M. A.; Andronov, E. E.; Pinaev, A. G.

    2015-04-01

    A method for the extraction of soil microbial DNA has been tested on chestnut soils (Kastanozems) of the West Kazakhstan region. The taxonomic analysis of soil microbiome libraries has shown that the phyla Actinobacteria and Proteobacteria constitute the largest part of microbial communities in the analyzed soils. The Archaea form an appreciable part of the microbiome in the studied samples. In the underdeveloped dark chestnut soil, their portion is higher than 11%. This is of interest, as the proportion of Archaea in the soil communities of virgin lands usually does not exceed 5%. In addition to the phyla mentioned above, there are representatives of the phyla Acidobacteria, Bacteroidetes, Firmicutes, Gemmatimonadales, Planctomycetes, and Verrucomicrobia, which are all fairly common in soil communities.

  3. A peptidome-based phylogeny pipeline reveals differential peptides at the strain level within Bifidobacterium animalis subsp. lactis.

    Science.gov (United States)

    Blanco-Míguez, Aitor; Gutiérrez-Jácome, Alberto; Fdez-Riverola, Florentino; Lourenço, Anália; Sánchez, Borja

    2016-12-01

    Bifidobacteria are gut commensal microorganisms belonging to the Actinobacteria group. Some specific strains of Bifidobacterium animalis subsp. lactis are used in functional foods as they are able to exert health-promoting effects in the human host. Due to the limited genetic variability within this subspecies, it is sometimes difficult for a manufacturer to properly track its strain once included in dairy products or functional foods. In this paper, we present a peptidome-based analysis in which the proteomes of a set of B. animalis subsp. lactis strains were digested in silico with human gut endopeptidases. The molecular masses were compared along all the strains to detect strain-specific peptides. These peptides may be interesting towards the development of methodologies for strain identification in the final product. PMID:27554155

  4. Biodiversity characterization of cellulolytic bacteria present on native Chaco soil by comparison of ribosomal RNA genes.

    Science.gov (United States)

    Talia, Paola; Sede, Silvana M; Campos, Eleonora; Rorig, Marcela; Principi, Dario; Tosto, Daniela; Hopp, H Esteban; Grasso, Daniel; Cataldi, Angel

    2012-04-01

    Sequence analysis of the 16S ribosomal RNA gene was used to study bacterial diversity of a pristine forest soil and of two cultures of the same soil enriched with cellulolytic bacteria. Our analysis revealed high bacterial diversity in the native soil sample, evidencing at least 10 phyla, in which Actinobacteria, Proteobacteria and Acidobacteria accounted for more than 76% of all sequences. In both enriched samples, members of Proteobacteria were the most frequently represented. The majority of bacterial genera in both enriched samples were identified as Brevundimonas and Caulobacter, but members of Devosia, Sphingomonas, Variovorax, Acidovorax, Pseudomonas, Xanthomonas, Stenotrophomonas, Achromobacter and Delftia were also found. In addition, it was possible to identify cellulolytic taxa such as Acidothermus, Micromonospora, Streptomyces, Paenibacillus and Pseudomonas, which indicates that this ecosystem could be an attractive source for study of novel enzymes for cellulose degradation. PMID:22202170

  5. Development of an Unnatural Amino Acid Incorporation System in the Actinobacterial Natural Product Producer Streptomyces venezuelae ATCC 15439.

    Science.gov (United States)

    He, Jingxuan; Van Treeck, Briana; Nguyen, Han B; Melançon, Charles E

    2016-02-19

    Many Actinobacteria, most notably Streptomyces, produce structurally diverse bioactive natural products, including ribosomally synthesized peptides, by multistep enzymatic pathways. The use of site-specific genetic incorporation of unnatural amino acids to investigate and manipulate the functions of natural product biosynthetic enzymes, enzyme complexes, and ribosomally derived peptides in these organisms would have important implications for drug discovery and development efforts. Here, we have designed, constructed, and optimized unnatural amino acid systems capable of incorporating p-iodo-l-phenylalanine and p-azido-l-phenylalanine site-specifically into proteins in the model natural product producer Streptomyces venezuelae ATCC 15439. We observed notable differences in the fidelity and efficiency of these systems between S. venezuelae and previously used hosts. Our findings serve as a foundation for using an expanded genetic code in Streptomyces to address questions related to natural product biosynthesis and mechanism of action that are relevant to drug discovery and development. PMID:26562751

  6. What stories can the Frankia genomes start to tell us?

    Science.gov (United States)

    Tisa, Louis S; Beauchemin, Nicholas; Gtari, Maher; Sen, Arnab; Wall, Luis G

    2013-11-01

    Among the Actinobacteria, the genus Frankia is well known for its facultative lifestyle as a plant symbiont of dicotyledonous plants and as a free-living soil dweller. Frankia sp. strains are generally classified into one of four major phylogenetic groups that have distinctive plant host ranges. Our understanding of these bacteria has been greatly facilitated by the availability of the first three complete genome sequences, which suggested a correlation between genome size and plant host range. Since that first report, eight more Frankia genomes have been sequenced. Representatives from all four lineages have been sequenced to provide vital baseline information for genomic approaches toward understanding these novel bacteria. An overview of the Frankia genomes will be presented to stimulate discussion on the potential of these organisms and a greater understanding of their physiology and evolution. PMID:24287651

  7. Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment

    DEFF Research Database (Denmark)

    Otani, Saria; Hansen, Lars H.; Sørensen, Søren Johannes;

    2016-01-01

    Fungus-growing termites (subfamily Macrotermitinae) mix plant forage with asexual spores of their plant-degrading fungal symbiont Termitomyces in their guts and deposit this blend in fungus comb structures, within which the plant matter is degraded. As Termitomyces grows, it produces nodules......, Actinobacteria, and Candidate division TM7 jointly accounting for 92 % of the reads. Analyses of gut microbiotas from 25 of the 33 colonies showed that dominant fungus comb taxa originate from the termite gut. While gut communities were consistent between 2011 and 2013, comb community compositions shifted over...... time. These shifts did not appear to be due to changes in the taxa present, but rather due to differences in the relative abundances of primarily gut-derived bacteria within fungus combs. This indicates that fungus comb microbiotas are largely termite species-specific due to major contributions from...

  8. What stories can the Frankia genomes start to tell us?

    Indian Academy of Sciences (India)

    Louis Tisa; Nicholas Beauchemin; Maher Gtari; Arnab Sen; Luis G Wall

    2013-11-01

    Among the Actinobacteria, the genus Frankia is well known for its facultative lifestyle as a plant symbiont of dicotyledonous plants and as a free-living soil dweller. Frankia sp. strains are generally classified into one of four major phylogenetic groups that have distinctive plant host ranges. Our understanding of these bacteria has been greatly facilitated by the availability of the first three complete genome sequences, which suggested a correlation between genome size and plant host range. Since that first report, eight more Frankia genomes have been sequenced. Representatives from all four lineages have been sequenced to provide vital baseline information for genomic approaches toward understanding these novel bacteria. An overview of the Frankia genomes will be presented to stimulate discussion on the potential of these organisms and a greater understanding of their physiology and evolution.

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

    Science.gov (United States)

    Horath, Thomas; Bachofen, Reinhard

    2009-08-01

    Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1-8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the eukaryotic diversity was outside the scope of the study, an amoeba (39 clones), and several green algae (51 clones) have been observed. We conclude that the bacterial diversity in this endolithic habitat, especially of chemotrophic, nonpigmented organisms, is considerable and that Archaea are present as well. PMID:19172216

  10. Epilithic and endolithic bacterial communities in limestone from a Maya archaeological site.

    Science.gov (United States)

    McNamara, Christopher J; Perry, Thomas D; Bearce, Kristen A; Hernandez-Duque, Guillermo; Mitchell, Ralph

    2006-01-01

    Biodeterioration of archaeological sites and historic buildings is a major concern for conservators, archaeologists, and scientists involved in preservation of the world's cultural heritage. The Maya archaeological sites in southern Mexico, some of the most important cultural artifacts in the Western Hemisphere, are constructed of limestone. High temperature and humidity have resulted in substantial microbial growth on stone surfaces at many of the sites. Despite the porous nature of limestone and the common occurrence of endolithic microorganisms in many habitats, little is known about the microbial flora living inside the stone. We found a large endolithic bacterial community in limestone from the interior of the Maya archaeological site Ek' Balam. Analysis of 16S rDNA clones demonstrated disparate communities (endolithic: >80% Actinobacteria, Acidobacteria, and Low GC Firmicutes; epilithic: >50% Proteobacteria). The presence of differing epilithic and endolithic bacterial communities may be a significant factor for conservation of stone cultural heritage materials and quantitative prediction of carbonate weathering. PMID:16391878

  11. Bacterial reduction of mercury in the high arctic

    DEFF Research Database (Denmark)

    Møller, Annette Klæstrup

    from three snow depths and freshwater only showed a scattered representation of the phyla and genera in comparison to strains identified by culture independent methods. The microbial composition of all arctic sample sites was significantly different, with the two uppermost snow layers being most......, Bacteroidetes, Actinobacteria and Planctomycetes in freshwater. The bacteria identified in this study both included phylotypes commonly found in cold environments as well as rare phylotypes. During the time of sampling atmospheric ozone measurements and total Hg measurements in the snow indicated...... suggested that this may be important in the deeper snow layers. This highlights the importance of microbial mercury transformation in the biogeochemical mercury cycling in the High Arctic. While bacterial Hg reduction by the mercuric reductase, MerA, is widespread in temperate environments, its distribution...

  12. Bacterial populations on brewery filling hall surfaces as revealed by next-generation sequencing.

    Science.gov (United States)

    Priha, Outi; Raulio, Mari; Maukonen, Johanna; Vehviläinen, Anna-Kaisa; Storgårds, Erna

    2016-01-01

    Due to the presence of moisture and nutrients, brewery filling line surfaces are susceptible to unwanted microbial attachment. Knowledge of the attaching microbes will aid in designing hygienic control of the process. In this study the bacterial diversity present on brewery filling line surfaces was revealed by next generation sequencing. The two filling lines studied maintained their characteristic bacterial community throughout three sampling times (13-163 days). On the glass bottle line, γ-proteobacteria dominated (35-82% of all OTUs), whereas on the canning line α-, β- and γ-proteobacteria and actinobacteria were most common. The most frequently detected genera were Acinetobacter, Propinobacterium and Pseudomonas. The halophilic genus Halomonas was commonly detected, which might be due to its tolerance to alkaline foam cleaners. This study has revealed a detailed overall picture of the bacterial groups present on filling line surfaces. Further effort should be given to determine the efficacy of washing procedures on different bacterial groups. PMID:27064426

  13. Host-specific microbial communities in three sympatric North Sea sponges

    DEFF Research Database (Denmark)

    Naim, Mohd Azrul; Morillo, Jose A.; Sørensen, Søren Johannes;

    2014-01-01

    The establishment of next generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of bacteria and archaea from a large number of sponge species. In this study we assessed the diversity of the microbial...... communities hosted by three sympatric sponges living in a semi-enclosed North-Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbour species-specific communities each dominated by a different class of Proteobacteria. An α...... phylotypes belonging to Chlamydiae, TM6, Actinobacteria and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4% ± 1.4% of the total reads, which suggests an important ecological role...

  14. Temporal Patterns in Bacterioplankton Community Composition in Three Reservoirs of Similar Trophic Status in Shenzhen, China

    Science.gov (United States)

    Li, Jiancheng; Chen, Cheng; Lu, Jun; Lei, Anping; Hu, Zhangli

    2016-01-01

    The bacterioplankton community composition’s (BCC) spatial and temporal variation patterns in three reservoirs (Shiyan, Xikeng, and LuoTian Reservoir) of similar trophic status in Bao’an District, Shenzhen (China), were investigated using PCR amplification of the 16S rDNA gene and the denaturing gradient gel electrophoresis (DGGE) techniques. Water samples were collected monthly in each reservoir during 12 consecutive months. Distinct differences were detected in band number, pattern, and density of DGGE at different sampling sites and time points. Analysis of the DGGE fingerprints showed that changes in the bacterial community structure mainly varied with seasons, and the patterns of change indicated that seasonal forces might have a more significant impact on the BCC than eutrophic status in the reservoirs, despite the similar Shannon-Weiner index among the three reservoirs. The sequences obtained from excised bands were affiliated with Cyanobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Actinobacteria, Planctomycetes, and Proteobacteria. PMID:27322295

  15. Population dynamics in wastewater treatment plants with enhanced biological phosphorus removal operated with and without nitrogen removal

    DEFF Research Database (Denmark)

    Lee, N.; Jansen, J.l.C.; Aspegren, H.;

    2002-01-01

    to the pilot plant was periodically manipulated by external addition of phosphorus (P), acetate and glucose, respectively. The population dynamics and the in situ physiology were monitored by quantitative fluorescence in situ hybridization (FISH) and microautoradiography. Significant P removal was observed......The population dynamics of activated sludge in a pilot plant with two activated sludge systems, both designed for enhanced biological phosphorus removal (EBPR), but one of them with (BNP) and the other without (BP) nitrogen removal, was monitored during a period of 2.5 years. The influent water...... Proteobacteria (part of them Rhodocyclus-related, the identity of the rest unknown) and the Actinobacteria. However, not all of the Rhodocyclus-related bacteria showed 33Pi uptake. The P removal in the investigated plants is thus believed to be mediated by a mixed population consisting of a part...

  16. The Human Vaginal Bacterial Biota and Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    2008-01-01

    Full Text Available The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. Changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of HIV infection. Cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (BV. PCR methods have shown that women with BV have complex communities of vaginal bacteria that include many fastidious species, particularly from the phyla Bacteroidetes and Actinobacteria. Healthy women are mostly colonized with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners, though a variety of other bacteria may be present. The microbiology of BV is heterogeneous. The presence of Gardnerella vaginalis and Atopobium vaginae coating the vaginal epithelium in some subjects with BV suggests that biofilms may contribute to this condition.

  17. Isolation and characterization of the microbial community of a freshwater distribution system

    International Nuclear Information System (INIS)

    This investigation provides generic information on culturable and non-culturable microbial community of a freshwater distribution system. Culture based and culture independent (16S rRNA gene sequencing) techniques were used to identify the resident microbial community of the system. Selective isolation of the fouling bacteria such as biofilm formers and corrosion causing bacteria was also attempted. Denaturing gradient gel electrophoresis (DGGE) was carried out and the bands were sequenced to obtain the diversity of the total bacterial types. Pseudomonas aeruginosa was predominantly observed in most of the samples. A variety of bacteria, related to groups such as Cyanobacteria, Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes were identified. The study highlights the relevance of the observed microbial diversity with respect to material deterioration in a freshwater distribution system, which can aid in designing effective control methods. (author)

  18. [Diversity and viability of prokaryotes in primitive soils of the larsemann oasis (East Antarctica)].

    Science.gov (United States)

    Kudinova, A G; Lysak, L V; Lapygina, E V; Soina, V S; Mergelov, N S

    2015-01-01

    The diversity and viability of prokaryotic communities in the primitive organomineral soils of East Antarctica have been studied; it has been shown that the total number of bacteria is smaller than and the viability of bacteria is similar to that in soils of the temperate zone. The prokaryotic communities are characterized by the occurrence of a major part of cells in filterable forms, which is higher than the analogous parameter for the temperate soils. The method of fluorescence in situ hybridization (FISH) revealed that the distribution of the main taxons is similar to that in the temperate soils: the portion of the domain Archaea is smaller than that of the domain Bacteria; the total content of Gram-negative bacteria (the phyla Proteobacteria, Acidobacteria, and Planctomycetes) is higher than that of Gram-positive bacteria (Actinobacteria). Within the phylum Proteobacteria, a significant variation of three proteobacterial classes has been noted along the profiles of the soils studied.

  19. On the limits of computational functional genomics for bacterial lifestyle prediction

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Röttger, Richard; Hauschild, Anne-Christin;

    2014-01-01

    of an observation bias, i.e. many HPs might yet be unclassified BPs. (H4) There is no intrinsic genomic characteristic of OPs compared with pathogens, as small mutations are likely to play a more dominant role to survive the immune system. To study these hypotheses, we implemented a bioinformatics pipeline......We review the level of genomic specificity regarding actinobacterial pathogenicity. As they occupy various niches in diverse habitats, one may assume the existence of lifestyle-specific genomic features. We include 240 actinobacteria classified into four pathogenicity classes: human pathogens (HPs...... in the post-genome era and despite next-generation sequencing technology, our ability to efficiently deduce real-world conclusions, such as pathogenicity classification, remains quite limited....

  20. Coevolution of aah: A dps-Like Gene with the Host Bacterium Revealed by Comparative Genomic Analysis

    Directory of Open Access Journals (Sweden)

    Liyan Ping

    2012-01-01

    Full Text Available A protein named AAH was isolated from the bacterium Microbacterium arborescens SE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of the aah gene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes. The phylogeny of dps-like proteins showed strong correlation with the phylogeny of host bacteria. A conserved genomic synteny was identified in some taxonomically related Actinobacteria, suggesting that the ancestor genes had incorporated into the genome before the divergence of Micrococcineae from other families. The aah gene had evolved new function but still retained the typical dodecameric structure.

  1. Discovery of Rickettsia species in Dermacentor niveus Neumann ticks by investigating the diversity of bacterial communities.

    Science.gov (United States)

    Zhuang, Lu; Wang, Cheng-Yan; Tong, Yi-Gang; Tang, Fang; Yang, Hong; Liu, Wei; Cao, Wu-Chun

    2014-09-01

    Ticks (Dermacentor niveus Neumann) were collected from Tacheng, Xinjiang Uygur Autonomous Region, and their bacterial diversity was investigated using the 16S RNA gene library method from one pooled sample. A total of 452 clones was successfully sequenced and assigned to 4 phyla. The dominant phylum was the Proteobacteria, accounting for 62.8% of all the clones of the 16S rRNA gene at the confidence level 80%. The other sequences were assigned to the phyla Bacteroidetes, Firmicutes, Actinobacteria and accounted for 13.5%, 12.4%, and 11.3%, respectively. These results provide an insight into the bacterial diversity associated with D. niveus ticks in the natural environment of Tacheng. They indicate the occurrence of Rickettsia raoultii and Rickettsia slovaca in D. niveus ticks in this area, and as a consequence, cases of TIBOLA/DEBONEL may occur (tick-borne lymphadenopathy/Dermacentor-borne necrosis erythema and lymphadenopathy).

  2. Activity of 2,4-Di-tert-butylphenol produced by a strain of Streptomyces mutabilis isolated from a Saharan soil against Candida albicans and other pathogenic fungi.

    Science.gov (United States)

    Belghit, S; Driche, E H; Bijani, C; Zitouni, A; Sabaou, N; Badji, B; Mathieu, F

    2016-06-01

    In a search for new antifungal antibiotics active against Candida albicans and others pathogenic fungi, a strain of actinobacteria, designated G61, was isolated from a Saharan soil and tested for its activity against these microorganisms. The analysis of its 16S rDNA sequence showed a similarity level of 100% with Streptomyces mutabilis NBRC 12800(T). The highest anticandidal activities produced by the strain G61 were obtained on Bennett medium in the fourth day of incubation. The active product, extracted by n-butanol, contained one bioactive spot detected on thin layer chromatography plates. It was purified by HPLC and its chemical structure was determined by spectroscopic analyses as 2,4-Di-tert-butylphenol. The minimum inhibitory concentrations (MIC) of this product against several strains of pathogenic microorganisms are interesting. PMID:27107984

  3. Widespread abundance of functional bacterial amyloid in Mycolata and other Gram-positive bacteria

    DEFF Research Database (Denmark)

    Jordal, Peter Bruun; Dueholm, Morten Simonsen; Larsen, Poul;

    2009-01-01

    Until recently, extracellular functional bacterial amyloid (FuBA) has been detected and characterized in only a few bacterial species, including Escherichia coli, Salmonella and Gram-positive Streptomyces coelicolor. Here we have probed Gram-positive bacteria with conformationally specific...... antibodies to reveal the existence of FuBA in 12 out of 14 examined Mycolata species as well as six other examined distantly related species belonging to the phyla Actinobacteria and Firmicutes. Most of the bacteria produced extracellular fimbria, sometimes in copious amounts, and in two cases large...... extracellular fibrils were also produced. In three cases, FuBA was only revealed after extensive removal of extracellular material by saponification, indicating an integrated attachment within the cellular envelope. Spores from species within the genera Streptomyces, Bacillus and Nocardia were all coated with...

  4. Deciphering the rhizosphere microbiome for disease-suppressive bacteria.

    Science.gov (United States)

    Mendes, Rodrigo; Kruijt, Marco; de Bruijn, Irene; Dekkers, Ester; van der Voort, Menno; Schneider, Johannes H M; Piceno, Yvette M; DeSantis, Todd Z; Andersen, Gary L; Bakker, Peter A H M; Raaijmakers, Jos M

    2011-05-27

    Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections. PMID:21551032

  5. Phylogeny and functions of bacterial communities associated with field-grown rice shoots.

    Science.gov (United States)

    Okubo, Takashi; Ikeda, Seishi; Sasaki, Kazuhiro; Ohshima, Kenshiro; Hattori, Masahira; Sato, Tadashi; Minamisawa, Kiwamu

    2014-09-17

    Metagenomic analysis was applied to bacterial communities associated with the shoots of two field-grown rice cultivars, Nipponbare and Kasalath. In both cultivars, shoot microbiomes were dominated by Alphaproteobacteria (51-52%), Actinobacteria (11-15%), Gammaproteobacteria (9-10%), and Betaproteobacteria (4-10%). Compared with other rice microbiomes (root, rhizosphere, and phyllosphere) in public databases, the shoot microbiomes harbored abundant genes for C1 compound metabolism and 1-aminocyclopropane-1-carboxylate catabolism, but fewer genes for indole-3-acetic acid production and nitrogen fixation. Salicylate hydroxylase was detected in all microbiomes, except the rhizosphere. These genomic features facilitate understanding of plant-microbe interactions and biogeochemical metabolism in rice shoots. PMID:25130883

  6. Microbial diversity and community structure in an antimony-rich tailings dump.

    Science.gov (United States)

    Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Xiao, Qingxiang; Sun, Weimin

    2016-09-01

    To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities. PMID:27188777

  7. A novel acidophile community populating waste ore deposits at an acid mine drainage site

    Institute of Scientific and Technical Information of China (English)

    HAO Chun-bo; ZHANG Hong-xun; BAI Zhi-hui; HU Qing; ZHANG Bao-guo

    2007-01-01

    Waste ore samples (pH 3.0) were collected at an acid mine drainage site in Anhui, China. The present acidophilic microbial community in the waste ore was studied with 16S rRNA gene clone library and denaturing gradient gel electrophoresis (DGGE). Eighteen different clones were identified and affiliated with Actinobacteria, low G + C Gram-positives, Thermomicrobia, Acidobacteria, Proteobacteria, Candidate division TM7, and Planctomycetes. Phylogenetic analysis of 16S rRNA gene sequences revealed a diversity of acidophiles in the samples that were mostly novel. It is unexpected that the moderately thermophilic acidophiles were abundant in the acidic ecosystem and may play a great role in the generation of AMD. The result of DGGE was consistent with that of clone library analysis. These findings help in the better understanding of the generation mechanism of AMD and in developing a more efficient method to control AMD.

  8. Bacterial Diversity and Composition in Oylat Cave (Turkey) with Combined Sanger/Pyrosequencing Approach.

    Science.gov (United States)

    Gulecal-Pektas, Yasemin

    2016-01-01

    The microbiology of caves is an important topic for better understanding subsurface biosphere diversity. The diversity and taxonomic composition of bacterial communities associated with cave walls of the Oylat Cave was studied first time by molecular cloning based on Sanger/pyrosequencing approach. Results showed an average of 1,822 operational taxonomic units per sample. Clones analyzed from Oylat Cave were found to belong to 10 common phyla within the domain Bacteria. Proteobacteria dominated the phyla, followed by Actinobacteria, Acidobacteria and Nitrospirae. Shannon diversity index was between to 3.76 and 5.35. The robust analysis conducted for this study demonstrated high bacterial diversity on cave rock wall surfaces. PMID:27281996

  9. Introducing GUt Low-Density Array (GULDA) - a validated approach for qPCR-based intestinal microbial community analysis

    DEFF Research Database (Denmark)

    Bergström, Anders; Licht, Tine Rask; Wilcks, Andrea;

    2012-01-01

    . In the present study, we developed and validated a high-throughput real-time quantitative PCR-based analysis platform, termed 'GUt Low-Density Array' (GULDA). The platform was designed for simultaneous analysis of the change in the abundance of 31 different microbial 16S rRNA gene targets in fecal samples......Alterations in the human gut microbiota caused, for example, by diet, functional foods, antibiotics, or occurring as a function of age are now known to be of relevance for host health. Therefore, there is a strong need for methods to detect such alterations in a rapid and comprehensive manner...... obtained from individuals at various points in time. The target genes represent important phyla, genera, species, or other taxonomic groups within the five predominant bacterial phyla of the gut, Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, and Verrucomicrobia and also Euryarchaeota...

  10. A common soil flagellate (Cercomonas sp.) grows slowly when feeding on the bacterium Rhodococcus fascians in isolation, but does not discriminate against it in a mixed culture with Sphingopyxis witflariensis

    DEFF Research Database (Denmark)

    Lekfeldt, Jonas D S; Rønn, Regin

    2008-01-01

    Flagellates are very important predators on bacteria in soil. Because of their high growth rates, flagellate populations respond rapidly to changes in bacterial numbers. Previous results indicate that actinobacteria are generally less suitable than proteobacteria as food for flagellates...... when fed with R. fascians than when fed with S. witflariensis. This supports our initial hypothesis that the actinobacterium is less suitable as food than the alphaproteobacterium. However, after longer periods of growth the peak abundance of flagellates was higher on R. fascians, indicating...... that the food quality of bacterial prey depends on the time perspective of the flagellate-bacterial interaction. There was no evidence that the flagellates selected against the actinobacterium when feeding in mixed cultures of the two bacteria. Experiments where flagellates were fed with washed bacterial cells...

  11. Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil

    International Nuclear Information System (INIS)

    Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success

  12. Microbial community analysis of an Alabama coastal salt marsh impacted by the Deepwater Horizon Oil Spill

    Science.gov (United States)

    Beazley, M. J.; Martinez, R.; Rajan, S.; Powell, J.; Piceno, Y.; Tom, L.; Andersen, G. L.; Hazen, T. C.; Van Nostrand, J. D.; Zhou, J.; Mortazavi, B.; Sobecky, P. A.

    2011-12-01

    Microbial community responses of an Alabama coastal salt marsh environment to the Deepwater Horizon oil spill were studied by 16S rRNA (PhyloChip) and functional gene (GeoChip) microarray-based analysis. Oil and tar balls associated with the oil spill arrived along the Alabama coast in June 2010. Marsh and inlet sediment samples collected in June, July, and September 2010 from a salt marsh ecosystem at Point Aux Pines Alabama were analyzed to determine if bacterial community structure changed as a result of oil perturbation. Sediment total petroleum hydrocarbon (TPH) concentrations ranged from below detection to 189 mg kg-1 and were randomly dispersed throughout the salt marsh sediments. Total DNA extracted from sediment and particulates were used for PhyloChip and GeoChip hybridization. A total of 4000 to 8000 operational taxonomic units (OTUs) were detected in marsh and inlet samples. Distinctive changes in the number of detectable OTUs were observed between June, July, and September 2010. Surficial inlet sediments demonstrated a significant increase in the total number of OTUs between June and September that correlated with TPH concentrations. The most significant increases in bacterial abundance were observed in the phyla Actinobacteria, Firmicutes, Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. Bacterial richness in marsh sediments also correlated with TPH concentrations with significant changes primarily in Acidobacteria, Actinobacteria, Firmicutes, Fusobacteria, Nitrospirae, and Proteobacteria. GeoChip microarray analysis detected 5000 to 8300 functional genes in marsh and inlet samples. Surficial inlet sediments demonstrated distinctive increases in the number of detectable genes and gene signal intensities in July samples compared to June. Signal intensities increased (> 1.5-fold) in genes associated with petroleum degradation. Genes related to metal resistance, stress, and carbon cycling also demonstrated increases in oiled sediments. This study

  13. Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock.

    Science.gov (United States)

    Paul, Dhiraj; Kumbhare, Shreyas V; Mhatre, Snehit S; Chowdhury, Somak P; Shetty, Sudarshan A; Marathe, Nachiket P; Bhute, Shrikant; Shouche, Yogesh S

    2015-01-01

    Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21-47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments.

  14. Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae Using 16S rRNA Gene Pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Michel Diouf

    Full Text Available Previous surveys of the gut microbiota of termites have been limited to the worker caste. Termite gut microbiota has been well documented over the last decades and consists mainly of lineages specific to the gut microbiome which are maintained across generations. Despite this intimate relationship, little is known of how symbionts are transmitted to each generation of the host, especially in higher termites where proctodeal feeding has never been reported. The bacterial succession across life stages of the wood-feeding higher termite Nasutitermes arborum was characterized by 16S rRNA gene deep sequencing. The microbial community in the eggs, mainly affiliated to Proteobacteria and Actinobacteria, was markedly different from the communities in the following developmental stages. In the first instar and last instar larvae and worker caste termites, Proteobacteria and Actinobacteria were less abundant than Firmicutes, Bacteroidetes, Spirochaetes, Fibrobacteres and the candidate phylum TG3 from the last instar larvae. Most of the representatives of these phyla (except Firmicutes were identified as termite-gut specific lineages, although their relative abundances differed. The most salient difference between last instar larvae and worker caste termites was the very high proportion of Spirochaetes, most of which were affiliated to the Treponema Ic, Ia and If subclusters, in workers. The results suggest that termite symbionts are not transmitted from mother to offspring but become established by a gradual process allowing the offspring to have access to the bulk of the microbiota prior to the emergence of workers, and, therefore, presumably through social exchanges with nursing workers.

  15. Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus.

    Directory of Open Access Journals (Sweden)

    Fabienne Ripoll

    Full Text Available Mycobacterium abscessus is an emerging rapidly growing mycobacterium (RGM causing a pseudotuberculous lung disease to which patients with cystic fibrosis (CF are particularly susceptible. We report here its complete genome sequence. The genome of M. abscessus (CIP 104536T consists of a 5,067,172-bp circular chromosome including 4920 predicted coding sequences (CDS, an 81-kb full-length prophage and 5 IS elements, and a 23-kb mercury resistance plasmid almost identical to pMM23 from Mycobacterium marinum. The chromosome encodes many virulence proteins and virulence protein families absent or present in only small numbers in the model RGM species Mycobacterium smegmatis. Many of these proteins are encoded by genes belonging to a "mycobacterial" gene pool (e.g. PE and PPE proteins, MCE and YrbE proteins, lipoprotein LpqH precursors. However, many others (e.g. phospholipase C, MgtC, MsrA, ABC Fe(3+ transporter appear to have been horizontally acquired from distantly related environmental bacteria with a high G+C content, mostly actinobacteria (e.g. Rhodococcus sp., Streptomyces sp. and pseudomonads. We also identified several metabolic regions acquired from actinobacteria and pseudomonads (relating to phenazine biosynthesis, homogentisate catabolism, phenylacetic acid degradation, DNA degradation not present in the M. smegmatis genome. Many of the "non mycobacterial" factors detected in M. abscessus are also present in two of the pathogens most frequently isolated from CF patients, Pseudomonas aeruginosa and Burkholderia cepacia. This study elucidates the genetic basis of the unique pathogenicity of M. abscessus among RGM, and raises the question of similar mechanisms of pathogenicity shared by unrelated organisms in CF patients.

  16. Diverse microbial species survive high ammonia concentrations

    Science.gov (United States)

    Kelly, Laura C.; Cockell, Charles S.; Summers, Stephen

    2012-04-01

    Planetary protection regulations are in place to control the contamination of planets and moons with terrestrial micro-organisms in order to avoid jeopardizing future scientific investigations relating to the search for life. One environmental chemical factor of relevance in extraterrestrial environments, specifically in the moons of the outer solar system, is ammonia (NH3). Ammonia is known to be highly toxic to micro-organisms and may disrupt proton motive force, interfere with cellular redox reactions or cause an increase of cell pH. To test the survival potential of terrestrial micro-organisms exposed to such cold, ammonia-rich environments, and to judge whether current planetary protection regulations are sufficient, soil samples were exposed to concentrations of NH3 from 5 to 35% (v/v) at -80°C and room temperature for periods up to 11 months. Following exposure to 35% NH3, diverse spore-forming taxa survived, including representatives of the Firmicutes (Bacillus, Sporosarcina, Viridibacillus, Paenibacillus, Staphylococcus and Brevibacillus) and Actinobacteria (Streptomyces). Non-spore forming organisms also survived, including Proteobacteria (Pseudomonas) and Actinobacteria (Arthrobacter) that are known to have environmentally resistant resting states. Clostridium spp. were isolated from the exposed soil under anaerobic culture. High NH3 was shown to cause a reduction in viability of spores over time, but spore morphology was not visibly altered. In addition to its implications for planetary protection, these data show that a large number of bacteria, potentially including spore-forming pathogens, but also environmentally resistant non-spore-formers, can survive high ammonia concentrations.

  17. Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock

    Directory of Open Access Journals (Sweden)

    Dhiraj ePaul

    2016-01-01

    Full Text Available Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world created in the basalt rocks. Although culture-dependent studies have been reported, the comprehensive understanding of microbial community composition and structure of Lonar Lake remain obscure. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet near consistent community composition. The predominance of bacterial phyla Proteobacteria (30% followed by Actinobacteria (24%, Firmicutes (11% and Cyanobacteria (5% was observed. Bacterial phylum Bacteroidetes (1.12%, BD1-5 (0.5%, Nitrospirae (0.41% and Verrucomicrobia (0.28% were detected as relatively minor populations in Lonar Lake ecosystem. Within Proteobacteria, Gammaproteobacteria represented the most abundant population (21-47% among all the sediments and as a minor population in water samples. Bacterial members Proteobacteria and Firmicutes were present significantly higher (p≥0.05 in sediment samples, whereas members of Actinobacteria, Candidate_division_TM7 and Cyanobacteria (p≥0.05 were significantly abundant in water samples. It was noted that compared to other hypersaline soda lakes, Lonar Lake samples formed one distinct cluster, suggesting a different microbial community composition and structure. The present study reports for the first time the different composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. Having better insight of community structure of this Lake ecosystem could be useful in understanding the microbial role in the geochemical cycle for future functional exploration of the unique hypersaline Lonar Lake.

  18. Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap.

    Science.gov (United States)

    Gokul, Jarishma K; Hodson, Andrew J; Saetnan, Eli R; Irvine-Fynn, Tristram D L; Westall, Philippa J; Detheridge, Andrew P; Takeuchi, Nozomu; Bussell, Jennifer; Mur, Luis A J; Edwards, Arwyn

    2016-08-01

    Microbial colonization of glacial ice surfaces incurs feedbacks which affect the melting rate of the ice surface. Ecosystems formed as microbe-mineral aggregates termed cryoconite locally reduce ice surface albedo and represent foci of biodiversity and biogeochemical cycling. Consequently, greater understanding the ecological processes in the formation of functional cryoconite ecosystems upon glacier surfaces is sought. Here, we present the first bacterial biogeography of an ice cap, evaluating the respective roles of dispersal, environmental and biotic filtration occurring at local scales in the assembly of cryoconite microbiota. 16S rRNA gene amplicon semiconductor sequencing of cryoconite colonizing a Svalbard ice cap coupled with digital elevation modelling of physical parameters reveals the bacterial community is dominated by a ubiquitous core of generalist taxa, with evidence for a moderate pairwise distance-decay relationship. While geographic position and melt season duration are prominent among environmental predictors of community structure, the core population of taxa appears highly influential in structuring the bacterial community. Taxon co-occurrence network analysis reveals a highly modular community structured by positive interactions with bottleneck taxa, predominantly Actinobacteria affiliated to isolates from soil humus. In contrast, the filamentous cyanobacterial taxon (assigned to Leptolyngbya/Phormidesmis pristleyi) which dominates the community and binds together granular cryoconite are poorly connected to other taxa. While our study targeted one ice cap, the prominent role of generalist core taxa with close environmental relatives across the global cryosphere indicate discrete roles for cosmopolitan Actinobacteria and Cyanobacteria as respective keystone taxa and ecosystem engineers of cryoconite ecosystems colonizing ice caps. PMID:27261672

  19. A novel cold active esterase derived from Colombian high Andean forest soil metagenome.

    Science.gov (United States)

    Jiménez, Diego Javier; Montaña, José Salvador; Alvarez, Diana; Baena, Sandra

    2012-01-01

    In order to search new lipolytic enzymes and conduct bioprospecting of microbial communities from high Andean forest soil, a metagenomic library of approximately 20,000 clones was constructed in Escherichia coli using plasmid p-Bluescript II SK+. The library covered 80 Mb of the metagenomic DNA mainly from Proteobacteria, Actinobacteria and Acidobacteria. Two clones with lipolytic activity in tributyrin as a substrate were recovered. Clone BAA3G2 (pSK-estGX1) was selected and the entire 4.6 Kb insert sequence was determined. The sequence had a GC content of 70.6% and could be derived from an undescribed Actinobacteria genome. One open reading frame encoded a polypeptide of 210 amino acids (gene estGX1) with a molecular mass of 22.4 kDa that contained the pentapeptide G-P-S-G-G near the N-terminus essential for lipase activity and the putative catalytic triad was identified, also a putative ribosomal binding site located 18 bp upstream the estGX1 ATG start codon was identified. The phylogenetic analysis suggested that the protein belonged to a new lipase family. The secreted enzyme showed a preference for short length fatty acids, with specific activity against p-nitrophenyl-butyrate (0.142 U/mg of total protein), it was cold active with relative activity of 30% at 10°C and moderately thermo active with relative activity of 80% at 50°C and had a pH optimum of 8.0 at 40°C. PMID:22806812

  20. Bacterial population structure of the jute-retting environment.

    Science.gov (United States)

    Munshi, Tulika K; Chattoo, Bharat B

    2008-08-01

    Jute is one of the most versatile bast fibers obtained through the process of retting, which is a result of decomposition of stalks by the indigenous microflora. However, bacterial communities associated with the retting of jute are not well characterized. To investigate the presence of microorganisms during the process of jute retting, full-cycle rRNA approach was followed, and two 16S rRNA gene libraries, from jute-retting locations of Krishnanagar and Barrackpore, were constructed. Phylotypes affiliating to seven bacterial divisions were identified in both libraries. The bulk of clones came from Proteobacteria ( approximately 37, 41%) and a comparatively smaller proportion of clones from the divisions-Firmicutes ( approximately 11, 12%), Cytophaga-Flexibacter-Bacteroidetes group (CFB; approximately 9, 7%), Verrucomicrobia ( approximately 6, 5%), Acidobacteria ( approximately 4, 5%), Chlorobiales ( approximately 5, 5%), and Actinobacteria ( approximately 4, 2%) were identified. Percent coverage value and diversity estimations of phylotype richness, Shannon-Weiner index, and evenness confirmed the diverse nature of both the libraries. Evaluation of the retting waters by whole cell rRNA-targeted flourescent in situ hybridization, as detected by domain- and group-specific probes, we observed a considerable dominance of the beta-Proteobacteria (25.9%) along with the CFB group (24.4%). In addition, 32 bacterial species were isolated on culture media from the two retting environments and identified by 16S rDNA analysis, confirming the presence of phyla, Proteobacteria ( approximately 47%), Firmicutes ( approximately 22%), CFB group ( approximately 19%), and Actinobacteria ( approximately 13%) in the retting niche. Thus, our study presents the first quantification of the dominant and diverse bacterial phylotypes in the retting ponds, which will further help in improving the retting efficiency, and hence the fiber quality. PMID:18097714

  1. Metagenomic analysis of microbial community in uranium-contaminated soil.

    Science.gov (United States)

    Yan, Xun; Luo, Xuegang; Zhao, Min

    2016-01-01

    Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.

  2. Rhizospheric Bacterial Community of Endemic Rhododendron arboreum Sm. Ssp. delavayi along Eastern Himalayan Slope in Tawang

    Science.gov (United States)

    Debnath, Rajal; Yadav, Archana; Gupta, Vijai K.; Singh, Bhim P.; Handique, Pratap J.; Saikia, Ratul

    2016-01-01

    Information on rhizosphere microbiome of endemic plants from high mountain ecosystems against those of cultivated plantations is inadequate. Comparative bacterial profiles of endemic medicinal plant Rhododendron arboreum Sm. subsp. delavayi rhizosphere pertaining to four altitudinal zonation Pankang Thang (PTSO), Nagula, Y-junction and Bum La (Indo-China border; in triplicates each) along cold adapted Eastern slope of Himalayan Tawang region, India is described here. Significant differences in DGGE profile between below ground bulk vs. rhizospheric community profile associated with the plant was identified. Tagged 16S amplicon sequencing from PTSO (3912 m) to Bum La (4509 m), revealed that soil pH, total nitrogen (TN), organic matter (OM) significantly influenced the underlying bacterial community structure at different altitudes. The relative abundance of Acidobacteria was inversely related to pH, as opposed to TN which was positively correlated to Acidobacteria and Proteobacteria abundance. TN was also the significant predictor for less abundant taxonomic groups Chloroflexi, Gemmatimonadetes, and Nitrospirae. Bum La soil harbored less bacterial diversity compared to other sites at lower altitudes. The most abundant phyla at 3% genetic difference were Acidobacteria, Actinobacteria, and Proteobacteria amongst others. Analysis of similarity indicated greater similarity within lower altitudinal than higher altitudinal group (ANOSIM, R = 0.287, p = 0.02). Constraining the ordination with the edaphic factor explained 83.13% of variation. Unique phylotypes of Bradyrhizobium and uncultured Rhizobiales were found in significant proportions at the four regions. With over 1% relative abundance Actinobacteria (42.6%), Acidobacteria (24.02%), Proteobacteria (16.00%), AD3 (9.23%), WPS-2 (5.1%), and Chloroflexi (1.48%) dominated the core microbiome. PMID:27642287

  3. Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

    Science.gov (United States)

    Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

    2016-10-01

    Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water

  4. The extended conformation of the 2.9-Å crystal structure of the three-PASTA domain of a Ser/Thr kinase from the human pathogen Staphylococcus aureus.

    Science.gov (United States)

    Paracuellos, Patricia; Ballandras, Allison; Robert, Xavier; Kahn, Richard; Hervé, Mireille; Mengin-Lecreulx, Dominique; Cozzone, Alain J; Duclos, Bertrand; Gouet, Patrice

    2010-12-17

    PASTA (penicillin-binding protein and serine/threonine kinase associated) modules are found in penicillin-binding proteins and bacterial serine/threonine kinases mainly from Gram-positive Firmicutes and Actinobacteria. They may act as extracellular sensors by binding peptidoglycan fragments. We report here the first crystal structure of a multiple-PASTA domain from Ser/Thr kinase, that of the protein serine/threonine kinase 1 (Stk1) from the Firmicute Staphylococcus aureus. The extended conformation of the three PASTA subunits differs strongly from the compact conformation observed in the two-PASTA domain of penicillin-binding protein PBP2x, whereas linear conformations were also reported for two-subunit fragments of the four-PASTA domain of the Actinobacteria Mycobacterium tuberculosis studied by liquid NMR. Thus, a stretched organization appears to be the signature of modular PASTA domains in Ser/Thr kinases. Signal transduction to the kinase domain is supposed to occur via dimerization and ligand binding. A conserved X-shaped crystallographic dimer stabilized by intermolecular interactions between the second PASTA subunits of each monomer is observed in the two crystal forms of Stk1 that we managed to crystallize. Extracellular PASTA domains are composed of at least two subunits, and this molecular assembly is a plausible candidate for the biological dimer. We have also performed docking experiments, which predict that the hinge regions of the PASTA domain can accommodate peptidoglycan. Finally, a three-dimensional homology molecular model of full-length Stk1 was generated, suggesting an interaction between the kinase domain and the cytoplasmic face of the plasma membrane via a eukaryotic-like juxtamembrane domain. A comprehensive activation mechanism for bacterial Ser/Thr kinases is proposed with the support of these structural data.

  5. Prokaryotic Community in Lacustrine Sediments of Byers Peninsula (Livingston Island, Maritime Antarctica).

    Science.gov (United States)

    Gugliandolo, Concetta; Michaud, Luigi; Lo Giudice, Angelina; Lentini, Valeria; Rochera, Carlos; Camacho, Antonio; Maugeri, Teresa Luciana

    2016-02-01

    Byers Peninsula (Livingston Island, Antarctica), the largest seasonally ice-free region of the Maritime Antarctica, holds a large number of lakes, ponds, and streams. The prokaryotic structure and bacterial diversity in sediment samples collected during the 2008-2009 austral summer from five inland lakes, two coastal lakes, and an estuarine site were analyzed by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and 16S rRNA 454 tag pyrosequencing techniques, respectively. Differently from inland lakes, which range around the oligotrophic status, coastal lakes are eutrophic environments, enriched by nutrient inputs from marine animals. Although the prokaryotic abundances (estimated as DAPI stained cells) in sediment samples were quite similar among inland and coastal lakes, Bacteria always far dominated over Archaea. Despite the phylogenetic analysis indicated that most of sequences were affiliated to a few taxonomic groups, mainly referred to Proteobacteria, Bacteroidetes, and Actinobacteria, their relative abundances greatly differed from each site. Differences in bacterial composition showed that lacustrine sediments were more phyla rich than the estuarine sediment. Proteobacterial classes in lacustrine samples were dominated by Betaproteobacteria (followed by Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), while in the estuarine sample, they were mainly related to Gammaproteobacteria (followed by Deltaproteobacteria, Epsilonproteobacteria, Alphaproteobacteria, and Betaproteobacteria). Higher number of sequences of Alphaproteobacteria, Cyanobacteria, Verrucomicrobia, and Planctomycetes were observed in sediments of inland lakes compared to those of coastal lakes, whereas Chloroflexi were relatively more abundant in the sediments of coastal eutrophic lakes. As demonstrated by the great number of dominant bacterial genera, bacterial diversity was higher in the sediments of inland lakes than that in coastal lakes

  6. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification.

    Science.gov (United States)

    Yang, Qi; Franco, Christopher M M; Zhang, Wei

    2015-10-01

    Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.

  7. Perioperative supplementation with bifidobacteria improves postoperative nutritional recovery, inflammatory response, and fecal microbiota in patients undergoing colorectal surgery: a prospective, randomized clinical trial.

    Science.gov (United States)

    Mizuta, Minoru; Endo, Izuru; Yamamoto, Sumiharu; Inokawa, Hidetoshi; Kubo, Masatoshi; Udaka, Tetsunobu; Sogabe, Osanori; Maeda, Hiroya; Shirakawa, Kazutoyo; Okazaki, Eriko; Odamaki, Toshitaka; Abe, Fumiaki; Xiao, Jin-Zhong

    2016-01-01

    The use of probiotics has been widely documented to benefit human health, but their clinical value in surgical patients remains unclear. The present study investigated the effect of perioperative oral administration of probiotic bifidobacteria to patients undergoing colorectal surgery. Sixty patients undergoing colorectal resection were randomized to two groups prior to resection. One group (n=31) received a probiotic supplement, Bifidobacterium longum BB536, preoperatively for 7-14 days and postoperatively for 14 days, while the other group (n=29) received no intervention as a control. The occurrences of postoperative infectious complications were recorded. Blood and fecal samples were collected before and after surgery. No significant difference was found in the incidence of postoperative infectious complications and duration of hospital stay between the two groups. In comparison to the control group, the probiotic group tended to have higher postoperative levels of erythrocytes, hemoglobin, lymphocytes, total protein, and albumin and lower levels of high sensitive C-reactive proteins. Postoperatively, the proportions of fecal bacteria changed significantly; Actinobacteria increased in the probiotic group, Bacteroidetes and Proteobacteria increased in the control group, and Firmicutes decreased in both groups. Significant correlations were found between the proportions of fecal bacteria and blood parameters; Actinobacteria correlated negatively with blood inflammatory parameters, while Bacteroidetes and Proteobacteria correlated positively with blood inflammatory parameters. In the subgroup of patients who received preoperative chemoradiotherapy treatment, the duration of hospital stay was significantly shortened upon probiotic intervention. These results suggest that perioperative oral administration of bifidobacteria may contribute to a balanced intestinal microbiota and attenuated postoperative inflammatory responses, which may subsequently promote a healthy

  8. Pulp and plaque microbiotas of children with severe early childhood caries

    Directory of Open Access Journals (Sweden)

    Natalia I. Chalmers

    2015-02-01

    Full Text Available Background and objective: Bacterial invasion into pulps of primary teeth can lead to infection and premature tooth loss in children. This pilot study aimed to explore whether the microbiota of carious exposures of dental pulps resembles that of carious dentin or that of infected root canals. Design: Children with severe early childhood caries were studied. Children were consented and extent of caries, plaque, and gingivitis measured. Bacteria were sampled from carious lesion biofilms and vital carious exposures of pulps, and processed by anaerobic culture. Isolates were characterized from partial sequences of the 16S rRNA gene and identified by comparison with taxa in the Human Oral Microbiome Database (http://www.HOMD.org. The microbiotas of carious lesions and dental pulps were compared using univariate and multivariate approaches. Results: The microbiota of cariously exposed pulps was similar in composition to that of carious lesion biofilms except that fewer species/taxa were identified from pulps. The major taxa identified belonged to the phyla Firmicutes (mainly streptococci and Actinobacteria (mainly Actinomyces species. Actinomyces and Selenomonas species were associated with carious lesions whereas Veillonella species, particularly Veillonella dispar was associated with pulps. Other bacteria detected in pulps included Streptococcus mutans, Parascardovia denticolens, Bifidobacterium longum, and several Lactobacillus and Actinomyces species. By principal, component analysis pulp microbiotas grouped together, whereas those in caries biofilms were widely dispersed. Conclusions: We conclude that the microbiota of cariously exposed vital primary pulps is composed of a subset of species associated with carious lesions. Vital primary pulps had a dominant Firmicutes and Actinobacteria microbiota which contrasts with reports of endodontic infections which can harbor a gram-negative microbiota. The microbiota of exposed primary pulps may provide

  9. Same, same but different: symbiotic bacterial associations in GBR sponges

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    Nicole S Webster

    2013-01-01

    Full Text Available Symbioses in marine sponges involve diverse consortia of microorganisms that contribute to the health and ecology of their hosts. The microbial communities of 13 taxonomically diverse Great Barrier Reef (GBR sponge species were assessed by DGGE and 16S rRNA gene sequencing to determine intra and inter species variation in bacterial symbiont composition. Microbial profiling revealed communities that were largely conserved within different individuals of each species with intra species similarity ranging from 65-100%. 16S rRNA gene sequencing revealed that the communities were dominated by Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Nitrospira and Cyanobacteria. Sponge-associated microbes were also highly host-specific with no operational taxonomic units (OTUs common to all species and the most ubiquitous OTU found in only 5 of the 13 sponge species. In total, 91% of the OTUs were restricted to a single sponge species. However, GBR sponge microbes were more closely related to other sponge-derived bacteria than they were to environmental communities with sequences falling within 50 of the 173 previously defined sponge-(or sponge-coral specific sequence clusters. These sequence clusters spanned the Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Gemmatimonadetes, Nitrospira and the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. The number of sequences assigned to these sponge-specific clusters across all species ranged from 0% to 92%. No relationship between host phylogeny and symbiont communities were observed across the different sponge orders, although the highest level of similarity was detected in two closely related Xestospongia species. This study identifies the core microbial inhabitants in a range of GBR sponges thereby providing the basis for future studies on sponge symbiotic function and research aiming to predict how sponge holobionts will respond to environmental

  10. Distinct soil bacterial communities revealed under a diversely managed agroecosystem.

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    Raymon S Shange

    Full Text Available Land-use change and management practices are normally enacted to manipulate environments to improve conditions that relate to production, remediation, and accommodation. However, their effect on the soil microbial community and their subsequent influence on soil function is still difficult to quantify. Recent applications of molecular techniques to soil biology, especially the use of 16S rRNA, are helping to bridge this gap. In this study, the influence of three land-use systems within a demonstration farm were evaluated with a view to further understand how these practices may impact observed soil bacterial communities. Replicate soil samples collected from the three land-use systems (grazed pine forest, cultivated crop, and grazed pasture on a single soil type. High throughput 16S rRNA gene pyrosequencing was used to generate sequence datasets. The different land use systems showed distinction in the structure of their bacterial communities with respect to the differences detected in cluster analysis as well as diversity indices. Specific taxa, particularly Actinobacteria, Acidobacteria, and classes of Proteobacteria, showed significant shifts across the land-use strata. Families belonging to these taxa broke with notions of copio- and oligotrphy at the class level, as many of the less abundant groups of families of Actinobacteria showed a propensity for soil environments with reduced carbon/nutrient availability. Orders Actinomycetales and Solirubrobacterales showed their highest abundance in the heavily disturbed cultivated system despite the lowest soil organic carbon (SOC values across the site. Selected soil properties ([SOC], total nitrogen [TN], soil texture, phosphodiesterase [PD], alkaline phosphatase [APA], acid phosphatase [ACP] activity, and pH also differed significantly across land-use regimes, with SOM, PD, and pH showing variation consistent with shifts in community structure and composition. These results suggest that use of

  11. Pyrosequencing-Based Assessment of Bacterial Community Structure Along Different Management Types in German Forest and Grassland Soils

    Science.gov (United States)

    Nacke, Heiko; Thürmer, Andrea; Wollherr, Antje; Will, Christiane; Hodac, Ladislav; Herold, Nadine; Schöning, Ingo; Schrumpf, Marion; Daniel, Rolf

    2011-01-01

    Background Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. Methodology/Principal Findings We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences) were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. Conclusions/Significance Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land use types grassland

  12. Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes ▿ †

    Science.gov (United States)

    Will, Christiane; Thürmer, Andrea; Wollherr, Antje; Nacke, Heiko; Herold, Nadine; Schrumpf, Marion; Gutknecht, Jessica; Wubet, Tesfaye; Buscot, François; Daniel, Rolf

    2010-01-01

    The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (H′) was higher in the A horizons than in the corresponding B horizons. In addition, the H′ was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the Actinobacteria, Bacteroidetes, Cyanobacteria, Fibrobacteres, Firmicutes, Spirochaetes, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were derived from A horizons, whereas the majority of the sequences related to Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospira, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass. PMID:20729324

  13. Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils.

    Directory of Open Access Journals (Sweden)

    Heiko Nacke

    Full Text Available BACKGROUND: Soil bacteria are important drivers for nearly all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil. In contrast to the importance of soil bacteria for ecosystem functioning, we understand little how different management types affect the soil bacterial community composition. METHODOLOGY/PRINCIPAL FINDINGS: We used pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to identify changes in bacterial diversity and community structure in nine forest and nine grassland soils from the Schwäbische Alb that covered six different management types. The dataset comprised 598,962 sequences that were affiliated to the domain Bacteria. The number of classified sequences per sample ranged from 23,515 to 39,259. Bacterial diversity was more phylum rich in grassland soils than in forest soils. The dominant taxonomic groups across all samples (>1% of all sequences were Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, and Firmicutes. Significant variations in relative abundances of bacterial phyla and proteobacterial classes, including Actinobacteria, Firmicutes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes and Alphaproteobacteria, between the land use types forest and grassland were observed. At the genus level, significant differences were also recorded for the dominant genera Phenylobacter, Bacillus, Kribbella, Streptomyces, Agromyces, and Defluviicoccus. In addition, soil bacterial community structure showed significant differences between beech and spruce forest soils. The relative abundances of bacterial groups at different taxonomic levels correlated with soil pH, but little or no relationships to management type and other soil properties were found. CONCLUSIONS/SIGNIFICANCE: Soil bacterial community composition and diversity of the six analyzed management types showed significant differences between the land

  14. The population structure of antibiotic-producing bacterial symbionts of Apterostigma dentigerum ants: impacts of coevolution and multipartite symbiosis.

    Science.gov (United States)

    Caldera, Eric J; Currie, Cameron R

    2012-11-01

    Fungus-growing ants (Attini) are part of a complex symbiosis with Basidiomycetous fungi, which the ants cultivate for food, Ascomycetous fungal pathogens (Escovopsis), which parasitize cultivars, and Actinobacteria, which produce antibiotic compounds that suppress pathogen growth. Earlier studies that have characterized the association between attine ants and their bacterial symbionts have employed broad phylogenetic approaches, with conclusions ranging from a diffuse coevolved mutualism to no specificity being reported. However, the geographic mosaic theory of coevolution proposes that coevolved interactions likely occur at a level above local populations but within species. Moreover, the scale of population subdivision is likely to impact coevolutionary dynamics. Here, we describe the population structure of bacteria associated with the attine Apterostigma dentigerum across Central America using multilocus sequence typing (MLST) of six housekeeping genes. The majority (90%) of bacteria that were isolated grouped into a single clade within the genus Pseudonocardia. In contrast to studies that have suggested that Pseudonocardia dispersal is high and therefore unconstrained by ant associations, we found highly structured ([Formula: see text]) and dispersal-limited (i.e., significant isolation by distance; [Formula: see text], [Formula: see text]) populations over even a relatively small scale (e.g., within the Panama Canal Zone). Estimates of recombination versus mutation were uncharacteristically low compared with estimates for free-living Actinobacteria (e.g., [Formula: see text] in La Selva, Costa Rica), which suggests that recombination is constrained by association with ant hosts. Furthermore, Pseudonocardia population structure was correlated with that of Escovopsis species ([Formula: see text], [Formula: see text]), supporting the bacteria's role in disease suppression. Overall, the population dynamics of symbiotic Pseudonocardia are more consistent with a

  15. Preliminary in vitro insights into the use of natural fungal pathogens of leaf-cutting ants as biocontrol agents.

    Science.gov (United States)

    Folgarait, Patricia; Gorosito, Norma; Poulsen, Michael; Currie, Cameron R

    2011-09-01

    Leaf-cutting ants are one of the main herbivores of the Neotropics, where they represent an important agricultural pest. These ants are particularly difficult to control because of the complex network of microbial symbionts. Leaf-cutting ants have traditionally been controlled through pesticide application, but there is a need for alternative, more environmentally friendly, control methods such as biological control. Potential promising biocontrol candidates include the microfungi Escovopsis spp. (anamorphic Hypocreales), which are specialized pathogens of the fungi the ants cultivate for food. These pathogens are suppressed through ant behaviors and ant-associated antibiotic-producing Actinobacteria. In order to be an effective biocontrol agent, Escovopsis has to overcome these defenses. Here, we evaluate, using microbial in vitro assays, whether defenses in the ant-cultivated fungus strain (Leucoagaricus sp.) and Actinobacteria from the ant pest Acromyrmex lundii have the potential to limit the use of Escovopsis in biocontrol. We also explore, for the first time, possible synergistic biocontrol between Escovopsis and the entomopathogenic fungus Lecanicillium lecanii. All strains of Escovopsis proved to overgrow A. lundii cultivar in less than 7 days, with the Escovopsis strain isolated from a different leaf-cutting ant species being the most efficient. Escovopsis challenged with a Streptomyces strain isolated from A. lundii did not exhibit significant growth inhibition. Both results are encouraging for the use of Escovopsis as a biocontrol agent. Although we found that L. lecanii can suppress the growth of the cultivar, it also had a negative impact on Escovopsis, making the success of simultaneous use of these two fungi for biocontrol of A. lundii questionable. PMID:21739253

  16. Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices.

    Science.gov (United States)

    Battini, Fabio; Cristani, Caterina; Giovannetti, Manuela; Agnolucci, Monica

    2016-02-01

    Arbuscular Mycorrhizal Fungi (AMF) live in symbiosis with most crop plants and represent essential elements of soil fertility and plant nutrition and productivity, facilitating soil mineral nutrient uptake and protecting plants from biotic and abiotic stresses. These beneficial services may be mediated by the dense and active spore-associated bacterial communities, which sustain diverse functions, such as the promotion of mycorrhizal activity, biological control of soilborne diseases, nitrogen fixation, and the supply of nutrients and growth factors. In this work, we utilised culture-dependent methods to isolate and functionally characterize the microbiota strictly associated to Rhizophagus intraradices spores, and molecularly identified the strains with best potential plant growth promoting (PGP) activities by 16S rDNA sequence analysis. We isolated in pure culture 374 bacterial strains belonging to different functional groups-actinobacteria, spore-forming, chitinolytic and N2-fixing bacteria-and screened 122 strains for their potential PGP activities. The most common PGP trait was represented by P solubilization from phytate (69.7%), followed by siderophore production (65.6%), mineral P solubilization (49.2%) and IAA production (42.6%). About 76% of actinobacteria and 65% of chitinolytic bacteria displayed multiple PGP activities. Nineteen strains with best potential PGP activities, assigned to Sinorhizobium meliloti, Streptomyces spp., Arthrobacter phenanthrenivorans, Nocardiodes albus, Bacillus sp. pumilus group, Fictibacillus barbaricus and Lysinibacillus fusiformis, showed the ability to produce IAA and siderophores and to solubilize P from mineral phosphate and phytate, representing suitable candidates as biocontrol agents, biofertilisers and bioenhancers, in the perspective of targeted management of beneficial symbionts and their associated bacteria in sustainable food production systems. PMID:26805620

  17. Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

    Science.gov (United States)

    Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

    2016-01-01

    Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

  18. The Salivary Microbiome in Polycystic Ovary Syndrome (PCOS) and Its Association with Disease-Related Parameters: A Pilot Study

    Science.gov (United States)

    Lindheim, Lisa; Bashir, Mina; Münzker, Julia; Trummer, Christian; Zachhuber, Verena; Pieber, Thomas R.; Gorkiewicz, Gregor; Obermayer-Pietsch, Barbara

    2016-01-01

    Background: Polycystic ovary syndrome (PCOS) is a common female endocrine condition of unclear etiology characterized by hyperandrogenism, oligo/amenorrhoea, and polycystic ovarian morphology. PCOS is often complicated by infertility, overweight/obesity, insulin resistance, and low-grade inflammation. The gut microbiome is known to contribute to several of these conditions. Recently, an association between stool and saliva microbiome community profiles was shown, making saliva a possible convenient, non-invasive sample type for detecting gut microbiome changes in systemic disease. In this study, we describe the saliva microbiome of PCOS patients and the association of microbiome features with PCOS-related parameters. Methods: 16S rRNA gene amplicon sequencing was performed on saliva samples from 24 PCOS patients and 20 healthy controls. Data processing and microbiome analyses were conducted in mothur and QIIME. All study subjects were characterized regarding reproductive, metabolic, and inflammatory parameters. Results: PCOS patients showed a decrease in bacteria from the phylum Actinobacteria and a borderline significant shift in bacterial community composition in unweighted UniFrac analysis. No differences between patients and controls were found in alpha diversity, weighted UniFrac analysis, or on other taxonomic levels. We found no association of saliva alpha diversity, beta diversity, or taxonomic composition with serum testosterone, oligo/amenorrhoea, overweight, insulin resistance, inflammatory markers, age, or diet. Conclusions: In this pilot study, patients with PCOS showed a reduced salivary relative abundance of Actinobacteria. Reproductive and metabolic components of the syndrome were not associated with saliva microbiome parameters, indicating that the majority of between-subject variation in saliva microbiome profiles remains to be explained. PMID:27610099

  19. Pyrosequencing-derived bacterial, archaeal, and fungal diversity of spacecraft hardware destined for Mars.

    Science.gov (United States)

    La Duc, Myron T; Vaishampayan, Parag; Nilsson, Henrik R; Torok, Tamas; Venkateswaran, Kasthuri

    2012-08-01

    Spacecraft hardware and assembly cleanroom surfaces (233 m(2) in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m(2)) than colocated spacecraft hardware (187 OTU; 162 m(2)). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.

  20. Pyrosequencing reveals the effect of mobilizing agents and lignocellulosic substrate amendment on microbial community composition in a real industrial PAH-polluted soil

    Energy Technology Data Exchange (ETDEWEB)

    Lladó, S., E-mail: llado@biomed.cas.cz [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Covino, S., E-mail: covino@biomed.cas.cz [Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 142 20 Prague 4 (Czech Republic); Solanas, A.M., E-mail: asolanas@ub.edu [Department of Microbiology, University of Barcelona, Diagonal 645, E-08028 Barcelona (Spain); Petruccioli, M., E-mail: petrucci@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); D’annibale, A., E-mail: dannib@unitus.it [Department for Innovation in Biological, Agro-Food and Forest Systems [DIBAF], University of Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo (Italy); Viñas, M., E-mail: marc.vinas@irta.cat [GIRO Joint Research Unit IRTA-UPC, Institute of Research and Technology Food and Agriculture [IRTA], Torre Marimon, E-08140 Caldes de Montbui (Spain)

    2015-02-11

    Highlights: • Soil microbial community assessment through classical (MPN) and molecular tools (DGGE and pyrosequencing) is provided. • A failure of exogenous white rot fungi to colonize the polluted soil is shown by DGGE and pyrosequencing. • Surfactant Brij 30 hampers 4-ring PAHs degradation due to toxicity over Actinobacteria and Bacteroidetes populations. • A high prevalence of Fusarium and Scedosporium populations is revealed during soil bioremediation. • Cupriavidus, Mycobacterium and Chithinophagaceae are potential HMW–PAH degraders in the soil. - Abstract: Bacterial and fungal biodiversity throughout different biostimulation and bioaugmentation treatments applied to an industrial creosote-polluted soil were analyzed by means of polyphasic approach in order to gain insight into the microbial community structure and dynamics. Pyrosequencing data obtained from initial creosote polluted soil (after a biopiling step) revealed that Alpha and Gammaproteobacteria were the most abundant bacterial groups, whereas Fusarium and Scedosporium were the main fungal genera in the contaminated soil. At the end of 60-days laboratory scale bioremediation assays, pyrosequencing and DGGE data showed that (i) major bacterial community shifts were caused by the type of mobilizing agent added to the soil and, to a lesser extent, by the addition of lignocellulosic substrate; and (ii) the presence of the non-ionic surfactant (Brij 30) hampered the proliferation of Actinobacteria (Mycobacteriaceae) and Bacteroidetes (Chitinophagaceae) and, in the absence of lignocellulosic substrate, also impeded polycyclic aromatic hydrocarbons (PAHs) degradation. The results show the importance of implementing bioremediation experiments combined with microbiome assessment to gain insight on the effect of crucial parameters (e.g. use of additives) over the potential functions of complex microbial communities harbored in polluted soils, essential for bioremediation success.

  1. 16SrRNA and enzymatic diversity of culturable bacteria from the sediments of oxygen minimum zone in the Arabian Sea.

    Science.gov (United States)

    Divya, Baby; Soumya, K V; Nair, Shanta

    2010-06-01

    Sediment underlying the oxygen minimum zone of the eastern Arabian Sea is rich in organic matter. Bacteria in this sediment-water interface are of great ecological importance as they are responsible for decomposing, mineralizing and subsequent recycling of organic matter. This study has for the first time addressed the phylogenetic and functional description of culturable bacteria of this region. Genotypic characterization of the isolates using amplified rDNA restriction analysis (ARDRA) followed by 16SrRNA sequencing grouped them into various phylogenetic groups such as Firmicutes, Gammaproteobacteria, Low G+C Gram positive bacteria, Actinobacteria and unaffiliated bacteria. Among the enzyme activities, phosphatase was predominant (52%) and was associated with all the phylotypes followed by amylase (37%) and gelatinase (33%). These hydrolytic enzymes were expressed at a wide range of temperature and pH. Firmicutes expressed most of the hydrolytic activities, consistent with a role in degradation of organic matter. Multiple enzyme expression (>/=3) was exhibited by Actinobacteria (100%), followed by unaffiliated group (62.5%) and Firmicutes (61.5%). Besides hydrolytic enzymes, the phylotypes also elaborated functional enzymes such as nitrate reductase and catalase (58 and 81% of the isolates, respectively). In the oxygen minimum zone, the diversity was high with 28 phylotypes. Culturable bacterial assemblages encountered were Bacillus sp., Halobacillus sp., Virgibacillus sp., Paenibacillus sp., Marinilactibacillus sp., Kytococcus sp., Micrococcus sp., Halomonas sp. and Alteromonas sp. The high diversity and high percentage of extracellular hydrolytic enzyme activities of the culturable bacteria reflect their important ecological role in biogeochemical cycling of organic matter in the oxygen minimum zone. PMID:20229220

  2. Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil

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    Viviane eCordovez

    2015-10-01

    Full Text Available In disease-suppressive soils, plants are protected from infections by specific root pathogens due to the antagonistic activities of soil and rhizosphere microorganisms. For most disease-suppressive soils, however, the microorganisms and mechanisms involved in pathogen control are largely unknown. Our recent studies identified Actinobacteria as the most dynamic phylum in a soil suppressive to the fungal root pathogen Rhizoctonia solani. Here we isolated and characterized 300 isolates of rhizospheric Actinobacteria from the Rhizoctonia-suppressive soil. Streptomyces species were the most abundant, representing approximately 70% of the isolates. Streptomyces are renowned for the production of an exceptionally large number of secondary metabolites, including volatile organic compounds (VOCs. VOC profiling of 12 representative Streptomyces isolates by SPME-GC-MS allowed a more refined phylogenetic delineation of the Streptomyces isolates than the sequencing of 16S rRNA and the house-keeping genes atpD and recA only. VOCs of several Streptomyces isolates inhibited hyphal growth of R. solani and significantly enhanced plant shoot and root biomass. Coupling of Streptomyces VOC profiles with their effects on fungal growth, pointed to VOCs potentially involved in antifungal activity. Subsequent assays with five synthetic analogues of the identified VOCs showed that methyl 2-methylpentanoate, 1,3,5-trichloro-2-methoxy benzene and the VOCs mixture have antifungal activity. In conclusion, our results point to a potential role of VOC-producing Streptomyces in disease suppressive soils and show that VOC profiling of rhizospheric Streptomyces can be used as a complementary identification tool to construct strain-specific metabolic signatures.

  3. Dynamics of the surgical microbiota along the cardiothoracic surgery pathway

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    Sara eRomano-Bertrand

    2015-01-01

    Full Text Available Human skin associated microbiota are increasingly described by culture-independent methods that showed an unexpected diversity with variation correlated with several pathologies. A role of microbiota disequilibrium in infection occurrence is hypothesized, particularly in surgical site infections. We study the diversities of operative site microbiota and its dynamics during surgical pathway of patients undergoing coronary-artery by-pass graft (CABG. Pre-, per- and post-operative samples were collected from 25 patients: skin before the surgery, superficially and deeply during the intervention, and healing tissues. Bacterial diversity was assessed by DNA fingerprint using 16S rRNA gene PCR and Temporal Temperature Gel Electrophoresis (TTGE. The diversity of Operational Taxonomic Units (OTUs at the surgical site was analyzed according to the stage of surgery.From all patients and samples, we identified 147 different OTUs belonging to the 6 phyla Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Cyanobacteria and Fusobacteria. High variations were observed among patients but common themes can be observed. The Firmicutes dominated quantitatively but were largely encompassed by the Proteobacteria regarding the OTUs diversity. The genera Propionibacterium and Staphylococcus predominated on the preoperative skin, whereas very diverse Proteobacteria appeared selected in peri-operative samples. The resilience in scar skin was partial with depletion in Actinobacteria and Firmicutes and increase of Gram-negative bacteria. Finally, the thoracic operative site presents an unexpected bacterial diversity, which is partially common to skin microbiota but presents particular dynamics. We described a complex bacterial community that gathers pathobiontes and bacteria deemed to be environmental, opportunistic pathogens and non-pathogenic bacteria. These data stress to consider surgical microbiota as a pathobiome rather than a reservoir of individual

  4. Biological anoxic treatment of O{sub 2}-free VOC emissions from the petrochemical industry: A proof of concept study

    Energy Technology Data Exchange (ETDEWEB)

    Muñoz, Raúl; Souza, Theo S.O. [Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr Mergelina s/n, 47011 Valladolid (Spain); Glittmann, Lina [Ostfalia University of Applied Sciences, Department of Supply Engineering, Wolfenbüttel (Germany); Pérez, Rebeca [Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr Mergelina s/n, 47011 Valladolid (Spain); Quijano, Guillermo, E-mail: gquijano@iq.uva.es [Department of Chemical Engineering and Environmental Technology, University of Valladolid, Dr Mergelina s/n, 47011 Valladolid (Spain)

    2013-09-15

    Highlights: • The treatment of O{sub 2}-free VOC emissions can be done by means of denitrifying processes. •Toluene vapors were successfully removed under anoxic denitrifying conditions. • A high bacterial diversity was observed. • Actinobacteria and Proteobacteria were the predominant phyla. • The nature and number of metabolites accumulated varied with the toluene load -- Abstract: An innovative biofiltration technology based on anoxic biodegradation was proposed in this work for the treatment of inert VOC-laden emissions from the petrochemical industry. Anoxic biofiltration does not require conventional O{sub 2} supply to mineralize VOCs, which increases process safety and allows for the reuse of the residual gas for inertization purposes in plant. The potential of this technology was evaluated in a biotrickling filter using toluene as a model VOC at loads of 3, 5, 12 and 34 g m{sup −3} h{sup −1} (corresponding to empty bed residence times of 16, 8, 4 and 1.3 min) with a maximum elimination capacity of ∼3 g m{sup −3} h{sup −1}. However, significant differences in the nature and number of metabolites accumulated at each toluene load tested were observed, o- and p-cresol being detected only at 34 g m{sup −3} h{sup −1}, while benzyl alcohol, benzaldehyde and phenol were detected at lower loads. A complete toluene removal was maintained after increasing the inlet toluene concentration from 0.5 to 1 g m{sup −3} (which entailed a loading rate increase from 3 to 6 g m{sup −3} h{sup −1}), indicating that the system was limited by mass transfer rather than by biological activity. A high bacterial diversity was observed, the predominant phyla being Actinobacteria and Proteobacteria.

  5. 枸杞岛海藻场沉积物细菌群落组成的初步研究%A preliminary study on the composition of bacterial community in the seaweed bed sediment of Gouqi Island

    Institute of Scientific and Technical Information of China (English)

    尹冰玉; 章守宇

    2011-01-01

    提取枸杞岛海藻场沉积物样品总DNA,以细菌16S rDNA通用引物进行PCR扩增,经分子克隆、测序与序列分析,构建了沉积物细菌16S rDNA文库和系统发育树,进行沉积物中细菌多样性及系统发育分析.结果表明,沉积物中细菌分属5个类群,分别为变形细菌门(Proteobacteria,48.2%)、厚壁菌门(Firmicutes,22.2%)、放线菌门(Actinobacteria,14.8%)、绿屈挠菌门(Chlorofiexi,3.7%)和酸杆菌门(Acidobacteria,3.7%),还有一些尚未确定其分类(7.4%).在枸杞岛海藻场沉积物变形细菌门类群中,γ-变形菌占主导地位,约为46.1%,其次为α-变形菌(23.1%)、β-变形菌(15.4%)、ε-变形菌(7.7%)和δ-变形菌(7.7%).作为海洋沉积物中的优势菌群,不同生态系统中变形细菌门类群的组成略有不同,功能类群的组成与生态系统机制密切相关.厚壁菌门和放线菌门作为革兰氏阳性菌的两个分支,在枸杞岛海藻场中主要参与分解碎屑及异养营养素的循环过程.%The clone library of 16S rDNA and the phylogenetic tree were constructed with extraction of bacterial DNA from seaweed bed sediment sample of Gouqi Island , PCR amplification of bacterial 16S rDNA by universal primers, molecular clone, sequencing of 16S rDNA fragments and sequence analysis.The biodiversity of bacteria and phylogenetic analysis showed that the bacterial community fell into five main lineages: Proteobacteria (48.2%), Firmicutes (22.2%), Actinobacteria ( 14.8% ), Chloroflexi (3.7%),Acidobacteria (3.7%), In addition, a part of unidentified bacteria (7.4%) was detected.Gammaproteobacteria played the dominant role in the Proteobacteria community of the seaweed bed sediment,it was about 46.1%, followed by the Alphaproteobacteria (23.1% ), Betaproteobacteria ( 15.4% ),Epsilonproteobacteria ( 7.7% ), Deltaproteobacteria ( 7.7% ).As the preponderant bacteria of marine sediment, the composition of Proteobacteria community was different in

  6. POTENCIAL DE ALGUNOS MICROORGANISMOS EN EL COMPOSTAJE DE RESIDUOS SÓLIDOS

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    Alejandro D. Camacho

    2014-09-01

    Full Text Available En México se producen diariamente toneladas de residuos sólidos que requieren un tratamiento seguro. El aumento de residuos que contienen hidrocarburos polimerizados muestra la necesidad de implementar un proceso de compostaje. Una alternativa para la mejora de este proceso es la búsqueda de microorganismos presentes en estos residuos que permitan acelerar los procesos de degradación que conduzcan a un compostaje eficiente. El objetivo de este trabajo fue evaluar microorganismos con potencial de ser utilizados en el proceso de compostaje. Se obtuvieron 17 aislados de 5 compostas; los hongos se caracterizaron mediante morfología microscópica y colonial y las actinobacterias por amplificación del 16S rDNA. A los mismos se les hicieron pruebas de crecimiento a diferentes condiciones de pH y temperatura, además de pruebas cualitativas y cuantitativas de hidrólisis de celulosa y pectina. Con base en los resultados de esas pruebas, se seleccionaron 2 cepas de actinobacterias y 1 hongo filamentoso. Se elaboró un inóculo con esos 3 microorganismos para evaluar su potencial de degradación; se inoculó y se incubó durante 70 días a 45 °C un sustrato compuesto por residuos domésticos y de poda de jardín. Se evaluaron nitrógeno total, materia orgánica, pH, azúcares reductores totales, carbono total y la relación C/N de cada tratamiento antes y después del proceso. Los datos obtenidos se sometieron a análisis de varianza (univariado y a un análisis discriminante canónico (multivariado. La eficiencia del proceso de compostaje (baja relación C/N del sustrato, indicador de la estabilidad del producto final mostró la activa participación de los microorganismos inoculados; también se observó la participación de los microorganismos nativos del sustrato natural.

  7. Isolation and structural elucidation of secondary metabolites from marine Streptomyces sp.SCSIO 1934%海洋放线菌Streptomyces sp.SCSIO1934中次生代谢产物的分离和鉴定

    Institute of Scientific and Technical Information of China (English)

    牛四文; 李苏; 田新朋; 胡涛; 鞠建华; 杨晓红; 张偲; 张长生

    2011-01-01

    目的:从1株来源于中国南海沉积环境的海洋链霉菌SCSIO 1934的发酵产物中分离鉴定次生代谢产物.方法:对海洋链霉菌SCSIO 1934的发酵液进行有机溶剂萃取,利用硅胶、凝胶柱色谱等方法分离次生代谢产物,通过核磁数据和理化性质对各单体化合物进行结构鉴定.结果:从菌株Streptomyces sp.SCSIO 1934中分离纯化得到17-脱甲基格尔德霉素(17-O-demethylgeldanamycin,1),lebstatin(2),17-O-demethyllebstatin(3),尼日利亚菌素(nigericin,4),尼日利亚菌素钠盐(nigericin sodium salt,5),abierixin(6).结论:本研究发现了1株能够产生多种抗生素的海洋放线菌Streptomyces sp.SCSIO 1934.%Marine Actinobacteria are emerging as new resources for bioactive natural products with promise in novel drug discovery. In recent years, the richness and diversity of marine Actinobacteria from the South China Sea and their ability in producing bioactive products have been investigated. The objective of this work is to isolate and identify bioactive secondary metabolites from a marine actinobacterium SCSIO 1934 derived from sediments of South China Sea. The strain was identified as a Streptomyces spieces by analyzing its 16S rDNA sequence. Streptomyces sp. SCSIO 1934 was fermented under optimized conditions and seven bioactive secondary metabolites were isolated and purified by chromatographic methods including colum chromatography over silica gel and Sephadex LH-20. Their structures were elucidated as 17-0-demethylgeldanamycin (1) , lebstatin (2) , 17-O-demethyllebstatin (3), nigericin (4) , nigericin sodium salt (5), abierixin (6), respectively, by detailed NMR spectroscopic data ('H.^C, COSY, HSQC and HMBC). This work provided a new marine actinobacterium Streptomyces sp. SCSIO 1934, capable of producing diverse bioactive natural products.

  8. Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

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    M.-C. Ciobanu

    2012-09-01

    Full Text Available An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion. Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG, within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG and Halobacteria within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria within Proteobacteria phylum, and also members of Bacteroidetes phylum. The second most abundant lineages were Actinobacteria and Firmicutes at the Gulf of Lion site and Chloroflexi at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: Alpha-, Gammaproteobacteria, Firmicutes and Actinobacteria. In molecular surveys, the Betaproteobacteria group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea levee. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence

  9. 新疆泥火山细菌遗传多样性%The bacterial diversity from mud volcano in Xinjiang by culture-independent approach

    Institute of Scientific and Technical Information of China (English)

    马小龙; 娄恺; 王芸; 杨红梅; 王纯利; 毛培宏; 金湘; 常玮; 房世杰; 张评浒

    2009-01-01

    In this study, the mixed environmental genomic DNA was isolated directly from the mud volcano soil in Usu county of Xinjiang. The 16S rRNA genes were amplified with bacterial universal primers and cloned into the pGEM-T Easy Vector to construct a16S rRNA clone library.The total 150 clones were selected by amplified rDNA restriction analysis(ARDRA) using restriction enzymes Hae Ⅲ. Of these, 16 restriction fragment length polymorphism(RFLP)types were used for sequencing. A part of these sequences were closely related to the phylum: Proteobacteria,Firmicutes,Fusobacteria and Actinobacteria (>97% sequence similarity), while another portion showed less affiliation with known taxa (<97% sequence similarity) and might represent novel taxa. The results indicated that the mud volcano in Usu county of Xinjiang is rich in microbial species,which is worth further studying.%为了解新疆乌苏泥火山细菌多样性,从泥火山泥浆样品中直接提取总DNA,构建了含150个有效转化子的泥火山细菌16S rDNA基因文库,转化子经菌液PCR及HaeⅢ酶切后获得16个不同带型,克隆测序结果表明,其分属于16个不同的分类单元.一部分序列与已知细菌类群的16S rDNA序列相似性较高,归属变形菌门(Proteobacteria),厚壁菌门(Firmicutes),梭杆菌门(Fusobacteria),放线菌门(Actinobacteria);另外一部分序列与已知细菌类群的16S rDNA序列同源性较低,可能代表新的分类单位.研究结果显示,泥火山环境中微生物种群丰富,值得进一步研究.

  10. Phylogenetic diversity of dominant bacterial communities during bioremediation of crude oil-polluted soil

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    Eugene Thomas Cloete

    2011-08-01

    degradation. Cluster analysis of DGGE bands using simple matching group average setting revealed that poultry droppings-amended soils and calcium ammonium nitrate-amended soils formed distinct clades meaning that the treatment selected similar bacterial populations for each of the treatments whereas NPK soils showed less association. Excision, reamplification and sequencing of dominant DGGE bands in biostimulated soils revealed the presence of distinct hydrocarbon degraders like Corynebacterium spp., Dietzia spp., low G+C Gram positive bacteria and some uncultured bacterial clones. Phylogenetic analysis of the 16S rRNA gene sequences of these dominant bacterial communities was conducted using the neighbour joining method of PHYLIP. Two distinct clades appeared in the tree clustered members of the Actinobacteria and Firmicutes separately. The overall data suggested that Gram positive bacteria especially members of the Actinobacteria may have a key role in bioremediation of crude oil-polluted soil.

  11. Physical and microbiological properties of alluvial calcareous Çumra province soils (Central Anatolia, Turkey

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    Ahmet Sami Erol

    2015-04-01

    Full Text Available Alluvial calcareous soils in Central Anatolia (Konya province, Çumra district has a heavy granulometric composition (average clay, low organic carbon content (less than 1%, but stable pore space structure and favorable agrophysical properties. Studies of the water regime in drip irrigation confirm favorable hydrological properties of these soils. It is assumed that the favorable structure of the pore space due to vigorous activity a large and diverse soil biota. Four phyla dominate in soil biota, among which predominate Actinobacteria. The higher (Streptomyces, and lower (three species Rhodococcus actinobacteria are predominant in large amounts as a part of this phyla. Large biodiversity at a sufficiently high bacteria richness formed the structure of the microbial community that contribute to the balanced production of specific metabolites, including gases (CO2, N2, which allows the soil to function actively, preventing compaction of the pore space and maintaining optimal density, porosity, hydrologic properties of the studied silty clay soils. m the uppermost soil horizons. Analyses of heavy mineral fraction show presence of metamorphic and igneous minerals which indicate participation of weathering products from other rock types in the nearby area. The types of heavy minerals in soils depend more on composition of parent rocks and geomorphic position than on climate type. Soils from Nova Lovcha show similar composition, but the quantity of goethite and hematite significantly increase in soil from plain. Typical high-metamorphic minerals as andalusite, kyanite and sillimanite present only in Nova Lovcha, while garnet dominates in Petrovo and opaque minerals - in Dobrostan. Red soils, formed on slopes, where erosion prevails over accumulation, contain more illite, smectite and vermiculite-smectite, and very few or no kaolinite, whereas the kaolinite is dominant in soils formed on plain. The mineralogical composition of clays in different

  12. Microbial Degradation and Carbon Biosequestration Potential of Biochar in Contrasting Soils

    Science.gov (United States)

    Tas, N.; Castanha, C.; Reichl, K.; Fischer, M. L.; Brodie, E. L.; Torn, M. S.; Jansson, J. K.

    2012-12-01

    Biochar is a carbon-rich product that is produced by high-temperature and low-oxygen pyrolysis of biomass, whose addition to soil has been proposed as a promising method for carbon sequestration. Biochar carbon has been assumed to be stable in soil, but recent research shows that it is at least partly degradable by soil microbes. However, the influence of environmental conditions on microbial transformation of biochar is poorly understood. Our overall goal is to determine the factors that regulate microbial decomposition of biochar in soils. We performed laboratory incubation experiments to compare the potential for biochar decomposition in soils from contrasting ecosystems (tropical forest from Puerto Rico and Mediterranean grassland from California), varied temperatures (ambient and +6°C) and depths (A and B horizons). Soil incubations with pyrolyzed 13C-enriched wood were continuously monitored for heterotrophic respiration using an online Cavity Ringdown Spectrometer. Samples collected after 10 and 150 days of incubation were analyzed for the activity of extracellular enzymes while changes in microbial community composition were assessed via pyrotag sequencing of both 16S rRNA and 16S rRNA genes. 13C-CO2 measurements confirmed that a fraction of added biochar was degraded in both soils during the one-year incubation period. Biochar addition was associated with a decline in cellulose and hemicellulose degrading enzyme activity in grassland soils, although not in tropical soils. In both soils, native soil organic carbon decomposition was not significantly impacted by biochar addition. Principle coordinates analysis of microbial composition showed that both soils harbored different microbial communities and those communities at different depths were distinct. The main bacterial groups enriched by biochar addition were Actinobacteria in the grassland soil, and α-Proteobacteria, Actinobacteria and Acidobacteria in the tropical soil. Analysis of 16S r

  13. [Prokaryotic microbial diversity of the ancient salt deposits in the Kunming Salt Mine, P.R. China].

    Science.gov (United States)

    Xiao, Wei; Peng, Qian; Liu, Hong-wei; Wen, Meng-liang; Cui, Xiao-long; Yang, Ya-ling; Duan, Dong-cheng; Chen, Wei; Deng, Lan; Li, Qin-yuan; Chen, Yi-guang; Wang, Zhi-gang; Ren, Zhen; Liu, Ji-hui

    2007-04-01

    The prokaryotic microbial diversity of the ancient salt deposits in the Kunming Salt Mine, PR China was investigated using PCR-DGGE and rRNA approaches. Total community DNA was extracted and purified by a direct method, which yielded amplified DNA of high molecular weight for samples. A variable region of 16S rRNA gene was then amplified by PCR with bacterial and archaeal primers and analyzed by denaturing gradient gel electrophoresis (DGGE). Twenty-seven major bands were detected in the bacterial DGGE profile of the sample, but only one band of pure culture strains of bacteria isolated from the Kunming Salt Mine matched with one band of sample. No band of pure culture strains of archaea isolated from the Kunming Salt Mine matched with 18 major bands of sample. The results indicated that most of microbes in this environment are likely uncultivable. Clones on the plate were not the predominant species in the community. Two 16S rRNA gene clone libraries (bacteria and archaea) were also constructed, and 36 and 20 clones were selected for amplified ribosomal DNA restriction analysis (ARDRA). ARDRA with enzymes Afa I, Hha I, Hae III revealed 10 bacterial operational taxonomic units (OTUs), with three most abundant OTUs accounting for 38.9%, 25.0%, 16.7% of all the bacterial 16S rDNA clones, respectively. The remaining 7 OTUs presented at low levels, were represented by a single clone. Eight archaeal OTUs were obtained but no predominant OTUs. Some clones were sequenced and each sequence was compared with all nucleotide sequences in GenBank database. Examination of 16S rDNA clones showed that the ancient salt deposits in the Kunming Salt Mine contained a phylogenetically diverse population of organisms from the Bacteria domain with members of three major lineages represented: alpha-proteobacteria, gamma-Proteobacteria and Actinobacteria, especially Pseudomonas. Surprisingly, we recovered a variety of sequence closely related to Actinobacteria which was not found in other

  14. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

    Science.gov (United States)

    Rughöft, Saskia; Herrmann, Martina; Lazar, Cassandre S.; Cesarz, Simone; Levick, Shaun R.; Trumbore, Susan E.; Küsel, Kirsten

    2016-01-01

    Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our

  15. Unicellular cyanobacteria Synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties.

    Science.gov (United States)

    Abdulaziz, Anas; Sageer, Saliha; Chekidhenkuzhiyil, Jasmin; Vijayan, Vijitha; Pavanan, Pratheesh; Athiyanathil, Sujith; Nair, Shanta

    2016-08-01

    The interactions between heterotrophic bacteria and primary producers have a profound impact on the functioning of marine ecosystem. We characterized the enzymatic and metal resistance properties of fourteen heterotrophic bacteria isolated from a unicellular cyanobacterium Synechocystis sp. that came from a heavy metal contaminated region of Cochin estuary, southwest coast of India. Based on 16S rRNA gene sequence similarities, the heterotrophic bacteria were grouped into three phyla: namely Actinobacteria, Firmicute, and Proteobacteria. Overall Proteobacteria showed a higher level of enzyme expression while Actinobacteria and Firmicutes showed higher tolerance to heavy metals. Among Proteobacteria, an isolate of Marinobacter hydrocarbonoclasticus (MMRF-584) showed highest activities of β-glucosidase (1.58 ± 0.2 μMml(-1)  min(-1) ) and laminarinase (1170.17 ± 95.4 μgml(-1)  min(-1) ), while other two isolates of M. hydrocarbonoclasticus, MMRF-578 and 581, showed highest phosphatase (44.71 ± 0.2 μMml(-1)  min(-1) ) and aminopeptidase (33.22 ± 0 μMml(-1)  min(-1) ) activities respectively. Among Firmicutes, the Virgibacillus sp. MMRF-571 showed exceptional resistance against the toxic heavy metals Cd (180 mM), Pb (150 mM), and Hg (0.5 mM). Bacillus cereus, MMRF-575, showed resistance to the highest concentrations of Co (250 mM), Cd (150 mM), Pb (180 mM), Hg (0.5 mM), Ni (280 mM), and Zn (250 mM) tested. Our results show that heterotrophic bacteria with varied enzymatic and metal resistance properties are associated with Synechocystis sp. Further studies to delineate the role of these heterotrophic bacteria in protecting primary producers from toxic effects of heavy metals and their potential application in bioremediation will be appreciated. PMID:27106264

  16. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems.

    Directory of Open Access Journals (Sweden)

    Elizaveta Pershina

    Full Text Available One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years to a conventional and organic farming systems (CFS and OFS accordingly. Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%, Acidobacteria (16.1%, Actinobacteria (7.9%, Verrucomicrobia (2.0%, Bacteroidetes (2.7% and Firmicutes (4.8%. Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas, while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05 increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum and Clostridium. Thus, the fields under OFS and CFS did

  17. Comparative secretome analysis suggests low plant cell wall degrading capacity in Frankia symbionts

    Directory of Open Access Journals (Sweden)

    Normand Philippe

    2008-01-01

    Full Text Available Abstract Background Frankia sp. strains, the nitrogen-fixing facultative endosymbionts of actinorhizal plants, have long been proposed to secrete hydrolytic enzymes such as cellulases, pectinases, and proteases that may contribute to plant root penetration and formation of symbiotic root nodules. These or other secreted proteins might logically be involved in the as yet unknown molecular interactions between Frankia and their host plants. We compared the genome-based secretomes of three Frankia strains representing diverse host specificities. Signal peptide detection algorithms were used to predict the individual secretomes of each strain, and the set of secreted proteins shared among the strains, termed the core Frankia secretome. Proteins in the core secretome may be involved in the actinorhizal symbiosis. Results The Frankia genomes have conserved Sec (general secretory and Tat (twin arginine translocase secretion systems. The potential secretome of each Frankia strain comprised 4–5% of the total proteome, a lower percentage than that found in the genomes of other actinobacteria, legume endosymbionts, and plant pathogens. Hydrolytic enzymes made up only a small fraction of the total number of predicted secreted proteins in each strain. Surprisingly, polysaccharide-degrading enzymes were few in number, especially in strain CcI3, with more esterolytic, lipolytic and proteolytic enzymes having signal peptides. A total of 161 orthologous proteins belong to the core Frankia secretome. Of these, 52 also lack homologs in closely related actinobacteria, and are termed "Frankia-specific." The genes encoding these conserved secreted proteins are often clustered near secretion machinery genes. Conclusion The predicted secretomes of Frankia sp. are relatively small and include few hydrolases, which could reflect adaptation to a symbiotic lifestyle. There are no well-conserved secreted polysaccharide-degrading enzymes present in all three Frankia

  18. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures.

    Science.gov (United States)

    Aira, Manuel; Bybee, Seth; Pérez-Losada, Marcos; Domínguez, Jorge

    2015-11-01

    Earthworms play a key role in nutrient cycling by interacting with microorganisms thus accelerating organic matter turnover in soil systems. As detritivores, some earthworm types ingest and digest a mixture of dead organic matter and microorganisms, like animal manures (i.e. animal gut microbiomes). Here we described the earthworm cast microbiome and the role ingested bacteria play on its composition. We fed Eisenia andrei with cow, horse and pig manures and determined the taxonomic and phylogenetic composition of the these manures before and after passage through the earthworm gut. Earthworm cast microbiomes showed a smaller diversity than the manure they fed on. Manures strongly differed in their taxonomic and phylogenetic composition, but these differences were markedly reduced once transformed into earthworm cast microbiomes after passage through the earthworm gut. The core earthworm cast microbiome comprised 30 OTUs (2.6% of OTUs from cast samples), of which 10 are possibly native to the earthworm gut. Most of the core cast microbiome OTUs belonged to phyla Actinobacteria and Proteobacteria, as opposed to already described animal core gut microbiomes, which are composed mainly of Firmicutes and Bacteroidetes. Our results suggest that earthworms build up their cast microbiome by selecting from the pool of ingested bacteria.

  19. Dynamic changes in the structure of microbial communities in Baltic Sea coastal seawater microcosms modified by crude oil, shale oil or diesel fuel.

    Science.gov (United States)

    Viggor, Signe; Juhanson, Jaanis; Jõesaar, Merike; Mitt, Mario; Truu, Jaak; Vedler, Eve; Heinaru, Ain

    2013-08-25

    The coastal waters of the Baltic Sea are constantly threatened by oil spills, due to the extensive transportation of oil products across the sea. To characterise the hydrocarbon-degrading bacterial community of this marine area, microcosm experiments on diesel fuel, crude oil and shale oil were performed. Analysis of these microcosms, using alkane monooxygenase (alkB) and 16S rRNA marker genes in PCR-DGGE experiments, demonstrated that substrate type and concentration strongly influence species composition and the occurrence of alkB genes in respective oil degrading bacterial communities. Gammaproteobacteria (particularly the genus Pseudomonas) and Alphaproteobacteria were dominant in all microcosms treated with oils. All alkB genes carried by bacterial isolates (40 strains), and 8 of the 11 major DGGE bands from the microcosms, had more than 95% sequence identity with the alkB genes of Pseudomonas fluorescens. However, the closest relatives of the majority of sequences (54 sequences from 79) of the alkB gene library from initially collected seawater DNA were Actinobacteria. alkB gene expression, induced by hexadecane, was recorded in isolated bacterial strains. Thus, complementary culture dependent and independent methods provided a more accurate picture about the complex seawater microbial communities of the Baltic Sea.

  20. Comparison of bacterial community structures in two systems of a sewage treatment plant using PCR-DGGE analysis

    Institute of Scientific and Technical Information of China (English)

    Abd El-Latif Hesham; Rong Qi; MinYang

    2011-01-01

    The combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis (DGGE) analysis was used to reveal the compositions and dynamics of bacterial communities in a sewage treatment plant with two systems,i.e.,an anoxicanaerobic-aerobic system (inverted A2O) and an anaerobic-anoxic-aerobic one (conventional A2O) over a period from February to July 2009,during which both systems experienced serious sludge bulking problems.The DGGE patterns showed that there were many common bands in both systems,suggesting the high similarity of bacterial communities of the two systems.Meanwhile,the moving window correlation analysis showed that the two systems experienced different microbial community structure changes during the period,which might be related with the different situations of the occurrence and disappearance of sludge bulking,as being reflected by sludge volume index (SVI) values.Major bands of DGGE patterns of sludge samples were further sequenced.Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria,Firmicutes,Bacteroidetes/Chlorobi group and α- and β-Proteobacteria.Two sequences showed high similarities to typical filamentous bacteria Microthrix parvicella and Nostocoida limicola I,indicating that these bacterial species have been involved in the sludge bulking problems.

  1. Insect Pathogenic Bacteria in Integrated Pest Management.

    Science.gov (United States)

    Ruiu, Luca

    2015-01-01

    The scientific community working in the field of insect pathology is experiencing an increasing academic and industrial interest in the discovery and development of new bioinsecticides as environmentally friendly pest control tools to be integrated, in combination or rotation, with chemicals in pest management programs. In this scientific context, market data report a significant growth of the biopesticide segment. Acquisition of new technologies by multinational Ag-tech companies is the center of the present industrial environment. This trend is in line with the requirements of new regulations on Integrated Pest Management. After a few decades of research on microbial pest management dominated by Bacillus thuringiensis (Bt), novel bacterial species with innovative modes of action are being discovered and developed into new products. Significant cases include the entomopathogenic nematode symbionts Photorhabdus spp. and Xenorhabdus spp., Serratia species, Yersinia entomophaga, Pseudomonas entomophila, and the recently discovered Betaproteobacteria species Burkholderia spp. and Chromobacterium spp. Lastly, Actinobacteria species like Streptomyces spp. and Saccharopolyspora spp. have gained high commercial interest for the production of a variety of metabolites acting as potent insecticides. With the aim to give a timely picture of the cutting-edge advancements in this renewed research field, different representative cases are reported and discussed. PMID:26463190

  2. Insect Pathogenic Bacteria in Integrated Pest Management

    Directory of Open Access Journals (Sweden)

    Luca Ruiu

    2015-04-01

    Full Text Available The scientific community working in the field of insect pathology is experiencing an increasing academic and industrial interest in the discovery and development of new bioinsecticides as environmentally friendly pest control tools to be integrated, in combination or rotation, with chemicals in pest management programs. In this scientific context, market data report a significant growth of the biopesticide segment. Acquisition of new technologies by multinational Ag-tech companies is the center of the present industrial environment. This trend is in line with the requirements of new regulations on Integrated Pest Management. After a few decades of research on microbial pest management dominated by Bacillus thuringiensis (Bt, novel bacterial species with innovative modes of action are being discovered and developed into new products. Significant cases include the entomopathogenic nematode symbionts Photorhabdus spp. and Xenorhabdus spp., Serratia species, Yersinia entomophaga, Pseudomonas entomophila, and the recently discovered Betaproteobacteria species Burkholderia spp. and Chromobacterium spp. Lastly, Actinobacteria species like Streptomyces spp. and Saccharopolyspora spp. have gained high commercial interest for the production of a variety of metabolites acting as potent insecticides. With the aim to give a timely picture of the cutting-edge advancements in this renewed research field, different representative cases are reported and discussed.

  3. Characterization of Sviceucin from Streptomyces Provides Insight into Enzyme Exchangeability and Disulfide Bond Formation in Lasso Peptides.

    Science.gov (United States)

    Li, Yanyan; Ducasse, Rémi; Zirah, Séverine; Blond, Alain; Goulard, Christophe; Lescop, Ewen; Giraud, Caroline; Hartke, Axel; Guittet, Eric; Pernodet, Jean-Luc; Rebuffat, Sylvie

    2015-11-20

    Lasso peptides are bacterial ribosomally synthesized and post-translationally modified peptides. They have sparked increasing interest in peptide-based drug development because of their compact, interlocked structure, which offers superior stability and protein-binding capacity. Disulfide bond-containing lasso peptides are rare and exhibit highly sought-after activities. In an effort to expand the repertoire of such molecules, we heterologously expressed, in Streptomyces coelicolor, the gene cluster encoding sviceucin, a type I lasso peptide with two disulfide bridges originating from Streptomyces sviceus, which allowed it to be fully characterized. Sviceucin and its reduced forms were characterized by mass spectrometry and peptidase digestion. The three-dimensional structure of sviceucin was determined using NMR. Sviceucin displayed antimicrobial activity selectively against Gram-positive bacteria and inhibition of fsr quorum sensing in Enterococcus faecalis. This study adds sviceucin to the type I lasso peptide family as a new representative. Moreover, new clusters encoding disulfide-bond containing lasso peptides from Actinobacteria were identified by genome mining. Genetic and functional analyses revealed that the formation of disulfide bonds in sviceucin does not require a pathway-encoded thiol-disulfide oxidoreductase. Most importantly, we demonstrated the functional exchangeability of the sviceucin and microcin J25 (a non-disulfide-bridged lasso peptide) macrolactam synthetases in vitro, highlighting the potential of hybrid lasso synthetases in lasso peptide engineering. PMID:26343290

  4. Evaluating the effectiveness of marine actinobacterial extract and its mediated titanium dioxide nanoparticles in the degradation of azo dyes.

    Science.gov (United States)

    Priyaragini, S; Veena, S; Swetha, D; Karthik, L; Kumar, G; Bhaskara Rao, K V

    2014-04-01

    Aim of the present study was to synthesize titanium dioxide nanoparticles (TiO2 NPs) from marine actinobacteria and to develop an eco-friendly azo-dye degradation method. A total of five actinobacterial isolates were isolated from Chennai marine sediments, Tamilnadu, India and analyzed for the synthesis of TiO2 NPs using titanium hydroxide. Among these, the isolate PSV 3 showed positive results for the synthesis of TiO2 NPs, which was confirmed by UV analysis. Further characterization of the synthesized TiO2 NPs was done using XRD, AFM and FT-IR analysis. Actinobacterial crude extract and synthesized TiO2 NPs was found efficient in degrading azo dye such as Acid Red 79 (AR-79) and Acid Red 80 (AR-80). Degradation percentage was found to be 81% for AR-79, 83% for AR-80 using actinobacterial crude extract and 84% for AR-79, 85% for AR-80 using TiO2 NPs. Immobilized actinobacterial cells showed 88% for AR-79 and 81% for AR-80, dye degrading capacity. Degraded components were characterized by FT-IR and GC-MS analysis. The phytotoxicity test with 500 μg/mL of untreated dye showed remarkable phenotypic as well as cellular damage to Tagetes erecta plant. Comparatively no such damage was observed on plants by degraded dye components. In biotoxicity assay, treated dyes showed less toxic effect as compared to the untreated dyes.

  5. Changes in microbial diversity of brined green asparagus upon treatment with high hydrostatic pressure.

    Science.gov (United States)

    Toledo Del Árbol, Julia; Pérez Pulido, Rubén; La Storia, Antonietta; Grande Burgos, Maria José; Lucas, Rosario; Ercolini, Danilo; Gálvez, Antonio

    2016-01-01

    The application of high hydrostatic pressure (HHP, 600MPa, 8 min) on brined green asparagus and the changes in bacterial diversity after treatments and during storage at 4 °C (30 days) or 22 °C (10 days) were studied. HHP treatments reduced viable cell counts by 3.6 log cycles. The residual surviving population did not increase during storage at 4 °C. However, bacterial counts significantly increased at 22 °C by day 3, leading to rapid spoilage. The microbiota of green asparagus was composed mainly by Proteobacteria (mainly Pantoea and Pseudomonas), followed by Firmicutes (mainly Lactococcus and Enterococcus) and to a less extent Bacteroidetes and Actinobacteria. During chill storage of untreated asparagus, the relative abundance of Proteobacteria as well as Enterococcus and Lactococcus decreased while Lactobacillus increased. During storage of untreated asparagus at 22 °C, the abundance of Bacteroidetes decreased while Proteobacteria increased during late storage. The HHP treatment determined a reduction of the Proteobacteria both early after treatment and during chill storage. In the HHP treated samples stored at 22 °C, the relative abundance of Pseudomonas rapidly decreased at day 1, with an increase of Bacteroidetes. This was followed by a marked increase in Enterobacteriaceae (Escherichia) simultaneously with increase in viable counts and spoilage. Results from the study indicate that the effect of HHP treatments on the viability ofmicrobial populations in foods also has an impact on the dynamics of microbial populations during the storage of the treated foods.

  6. Shrinking the FadE proteome of Mycobacterium tuberculosis: insights into cholesterol metabolism through identification of an α2β2 heterotetrameric acyl coenzyme A dehydrogenase family.

    Science.gov (United States)

    Wipperman, Matthew F; Yang, Meng; Thomas, Suzanne T; Sampson, Nicole S

    2013-10-01

    The ability of the pathogen Mycobacterium tuberculosis to metabolize steroids like cholesterol and the roles that these compounds play in the virulence and pathogenesis of this organism are increasingly evident. Here, we demonstrate through experiments and bioinformatic analysis the existence of an architecturally distinct subfamily of acyl coenzyme A (acyl-CoA) dehydrogenase (ACAD) enzymes that are α2β2 heterotetramers with two active sites. These enzymes are encoded by two adjacent ACAD (fadE) genes that are regulated by cholesterol. FadE26-FadE27 catalyzes the dehydrogenation of 3β-hydroxy-chol-5-en-24-oyl-CoA, an analog of the 5-carbon side chain cholesterol degradation intermediate. Genes encoding the α2β2 heterotetrameric ACAD structures are present in multiple regions of the M. tuberculosis genome, and subsets of these genes are regulated by four different transcriptional repressors or activators: KstR1 (also known as KstR), KstR2, Mce3R, and SigE. Homologous ACAD gene pairs are found in other Actinobacteria, as well as Proteobacteria. Their structures and genomic locations suggest that the α2β2 heterotetrameric structural motif has evolved to enable catalysis of dehydrogenation of steroid- or polycyclic-CoA substrates and that they function in four subpathways of cholesterol metabolism.

  7. Phylogenetic diversity and phenotypic characterization of cultivable bacterioplankton isolated from polar oceans

    Institute of Scientific and Technical Information of China (English)

    ZENG Yinxin; LI Huirong; YU Yong; CHEN Bo; ZHENG Tianling

    2007-01-01

    A set of 27 marine planktonic bacteria isolated from the polar regions was characterized by 16S rDNA sequencing and physiological and biochemical testing. More than half of these bacteria were positive for caseinase, gelatinase and β-glucosidase, and could utilize glucose, maltose or malic acid as carbon source for cell growth. Twelve isolates expressed nitrate reduction activities. Except for one antarctic isolate BSw10175 belonging to Actinobacteria phylum, these isolates were classified as γ-Proteobacteria, suggesting that γ-Proteobacteria dominated in cultivable marine bacterioplankton at both poles. Genus Pseudoalteromonas was the predominant group in the Chukchi Sea and the Bering Sea, and genus Shewanella dominated in cultivable bacterioplankton in the Prydz Bay. With sequence similarities above 97%, genus Psychrobacter was found at both poles. These 27 isolates were psychrotolerant, and significant 16S rDNA sequence similarities were found not only between arctic and antarctic marine bacteria ( > 99% ),but also between polar marine bacteria and bacteria from other aquatic environments ( ≥98.8% ) , including temperate ocean,deep sea, pond and lake, suggesting that in the polar oceans less temperature-sensitive bacteria may be cosmopolitan and have a bipolar, even global, distribution at the species level.

  8. Associations between bacterial communities of house dust and infant gut

    Energy Technology Data Exchange (ETDEWEB)

    Konya, T.; Koster, B. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Maughan, H. [Department of Cell and Systems Biology, University of Toronto (Canada); Escobar, M. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Azad, M.B. [Department of Pediatrics, University of Alberta (Canada); Guttman, D.S. [Department of Cell and Systems Biology, University of Toronto (Canada); Sears, M.R. [Department of Medicine, McMaster University (Canada); Becker, A.B. [University of Manitoba (Canada); Brook, J.R. [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada); Environment Canada (Canada); Takaro, T.K. [Faculty of Health Science, Simon Fraser University (Canada); Kozyrskyj, A.L. [Department of Pediatrics, University of Alberta (Canada); Scott, J.A., E-mail: james.scott@utoronto.ca [Division of Occupational and Environmental Health, Dalla Lana School of Public Health, University of Toronto (Canada)

    2014-05-01

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

  9. Molecular Detection and Environment-Specific Diversity of Glycosyl Hydrolase Family 1 β-Glucosidase in Different Habitats

    Science.gov (United States)

    Tiwari, Rameshwar; Kumar, Kanika; Singh, Surender; Nain, Lata; Shukla, Pratyoosh

    2016-01-01

    β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulfur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes, and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community.

  10. Associations between bacterial communities of house dust and infant gut

    International Nuclear Information System (INIS)

    The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust–stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership

  11. Non-Ferrous Metal Industry Waste Disposal Sites As A Source Of Poly-Extremotolerant Bacteria

    Directory of Open Access Journals (Sweden)

    Pristas Peter

    2015-06-01

    Full Text Available Waste disposal sites from non-ferrous metal industry constitute environments very hostile for life due to the presence of very specialized abiotic factors (pH, salt concentration, heavy metals content. In our experiments microflora of two waste disposal sites in Slovakia – brown mud disposal site from aluminium production near Ziar nad Hronom and nickel sludge disposal site near Sered - was analyzed for cultivable bacteria. Isolated bacteria were characterized by a combination of classical microbiological approaches and molecular methods and the most of isolated bacteria shown a poly-extremotolerant phenotype. The most frequently halotolerant (resistant to the high level of salt concentrations and alkalitolerant (resistant to the high pH level bacteria belonging to the Actinobacteria class were detected. The most of bacteria shown very high level of heavy metal resistance e.g. more than 500 μg/ml for Zn2+ or Cu2+. Based on our data, waste disposal sites thus on one side represents an important environmental burden but on other side they are a source of new poly-extremotolerant bacterial strains and species possibly used in many biotechnology and bioremediation applications.

  12. Microbial hitchhikers on intercontinental dust: catching a lift in Chad.

    Science.gov (United States)

    Favet, Jocelyne; Lapanje, Ales; Giongo, Adriana; Kennedy, Suzanne; Aung, Yin-Yin; Cattaneo, Arlette; Davis-Richardson, Austin G; Brown, Christopher T; Kort, Renate; Brumsack, Hans-Jürgen; Schnetger, Bernhard; Chappell, Adrian; Kroijenga, Jaap; Beck, Andreas; Schwibbert, Karin; Mohamed, Ahmed H; Kirchner, Timothy; de Quadros, Patricia Dorr; Triplett, Eric W; Broughton, William J; Gorbushina, Anna A

    2013-04-01

    Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bodélé Depression in the Republic of Chad has been called the dustiest place on earth. We analysed desert sand from various locations in Chad and dust that had blown to the Cape Verde Islands. High throughput sequencing techniques combined with classical microbiological methods showed that the samples contained a large variety of microbes well adapted to the harsh desert conditions. The most abundant bacterial groupings in four different phyla included: (a) Firmicutes-Bacillaceae, (b) Actinobacteria-Geodermatophilaceae, Nocardiodaceae and Solirubrobacteraceae, (c) Proteobacteria-Oxalobacteraceae, Rhizobiales and Sphingomonadaceae, and (d) Bacteroidetes-Cytophagaceae. Ascomycota was the overwhelmingly dominant fungal group followed by Basidiomycota and traces of Chytridiomycota, Microsporidia and Glomeromycota. Two freshwater algae (Trebouxiophyceae) were isolated. Most predominant taxa are widely distributed land inhabitants that are common in soil and on the surfaces of plants. Examples include Bradyrhizobium spp. that nodulate and fix nitrogen in Acacia species, the predominant trees of the Sahara as well as Herbaspirillum (Oxalobacteraceae), a group of chemoorganotrophic free-living soil inhabitants that fix nitrogen in association with Gramineae roots. Few pathogenic strains were found, suggesting that African dust is not a large threat to public health. PMID:23254516

  13. The effects of entombment on water chemistry and bacterial assemblages in closed cryoconite holes on Antarctic glaciers.

    Science.gov (United States)

    Webster-Brown, Jenny G; Hawes, Ian; Jungblut, Anne D; Wood, Susanna A; Christenson, Hannah K

    2015-12-01

    Closed cryoconite holes (CCHs) are small aquatic ecosystems enclosed in glacier surface ice, and they collectively contribute substantial aquatic habitat to inland Antarctica. We examined the morphology, geochemistry and bacterial diversity of 57 CCHs, spread over seven sites, located on five glaciers, covering a range of latitudes, elevations and distance from open seawater. Isotopes confirmed glacial ice as the initial water source, with water chemistry evolving through freeze concentration and photosynthetic processes to have conductivities ranging from 4 mS cm(-1) and pH from 11. Nitrate concentrations were more elevated in inland, higher altitude sites. Bacterial communities were characterized by Automated Ribosomal Intergenic Spacer Analysis and high-throughput sequencing. The dominant phyla were Cyanobacteria, Bacteroides, Proteobacteria and Actinobacteria. CCH bacterial communities predominantly grouped by geographic location, suggesting initial wind-borne inocula from local and regional sources play a role in structuring assemblages. However, multivariate multiple regression analysis indicated that internal CCH conditions also influenced community structure, particularly the ion content and pH of the liquid water. This highlights the importance of founder bacterial populations, isolation and water chemistry in the evolution of CCH bacterial communities. PMID:26572547

  14. Characterising the interspecific variations and convergence of gut microbiota in Anseriformes herbivores at wintering areas

    Science.gov (United States)

    Yang, Yuzhan; Deng, Ye; Cao, Lei

    2016-01-01

    Microorganisms in vertebrate guts have been recognized as important symbionts influencing host life. However, it remains unclear about the gut microbiota in long-distance migratory Anseriformes herbivores, which could be functionally important for these wetland-dependent animals. We collected faeces of the greater white-fronted goose (GWFG), bean goose (BG) and swan goose (SG) from Shengjin Lake (SJL) and Poyang Lake (PYL) in the Yangtze River Floodplain, China. High-throughput sequencing of 16S rRNA V4 region was employed to depict the composition and structure of geese gut microbiota during wintering period. The dominant bacterial phyla across all samples were Firmicutes, Proteobacteria and Actinobacteria, but significant variations were detected among different goose species and sampling sites, in terms of α diversity, community structures and microbial interactions. We found a significant correlation between diet and the microbial community structure in GWFG-SJL samples. These results demonstrated that host species and diet are potential drivers of goose gut microbiota assemblies. Despite these variations, functions of geese gut microbiota were similar, with great abundances of potential genes involved in nutrient metabolism. This preliminary study would be valuable for future, exhaustive investigations of geese gut microbiota and their interactions with host. PMID:27600170

  15. Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota.

    Science.gov (United States)

    Rastogi, Gurdeep; Osman, Shariff; Kukkadapu, Ravi; Engelhard, Mark; Vaishampayan, Parag A; Andersen, Gary L; Sani, Rajesh K

    2010-10-01

    A microbial census on deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Soil mineralogical characterization was carried out using X-ray diffraction, X-ray photoelectron, and Mössbauer spectroscopic techniques which demonstrated silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable similarities in microbial communities (1,360 common OTUs) despite distinct geochemical characteristics. Fifty-seven phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity by capturing several physiological groups such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. High-density microarrays revealed the greatest prokaryotic diversity ever reported from deep subsurface habitat of gold mines. PMID:20386898

  16. Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota

    Energy Technology Data Exchange (ETDEWEB)

    Rastogi, Gurdeep; Osman, Shariff; Kukkadapu, Ravi K.; Engelhard, Mark H.; Vaishampayan, Parag A.; Andersen, Gary L.; Sani, Rajesh K.

    2010-03-13

    A microbial census on the deep biosphere (1.34 km depth) microbial communities was performed in two soil samples collected from the Ross and number 6 Winze sites of the former Homestake gold mine, Lead, South Dakota using high-density 16S microarrays (PhyloChip). Mineralogical characterization of soil samples was carried out using X-ray diffraction, X-ray photoelectron, and Mössbauer spectroscopic techniques which demonstrated the presence of silicates and iron minerals (phyllosilicates and clays) in both samples. Microarray data revealed extensive bacterial diversity in soils and detected the largest number of taxa in Proteobacteria phylum followed by Firmicutes and Actinobacteria. The archael communities in the deep gold mine environments were less diverse and belonged to phyla Euryarchaeota and Crenarchaeota. Both the samples showed remarkable amount of similar microbial communities (1360 common OTUs) despite of distinct geochemical characteristics. A total of 57 phylotypes could not be classified even at phylum level representing a hitherto unidentified diversity in deep biosphere. PhyloChip data also suggested considerable metabolic diversity in deep biosphere by capturing several physiological groups of bacteria such as sulfur-oxidizer, ammonia-oxidizers, iron-oxidizers, methane-oxidizers, and sulfate-reducers in both samples. Application of high-density microarrays revealed the vast prokaryotic diversity ever reported from deep subsurface habitat of gold mines.

  17. Seasonal patterns of bacterial communities in the coastal brackish sediments of the Gulf of Finland, Baltic Sea

    Science.gov (United States)

    Vetterli, Adrien; Hyytiäinen, Kirsi; Ahjos, Minttu; Auvinen, Petri; Paulin, Lars; Hietanen, Susanna; Leskinen, Elina

    2015-11-01

    Coastal areas are critical in mitigating the impact of nutrient runoffs and downstream eutrophication of aquatic ecosystems. In the Gulf of Finland, the easternmost sub-basin of the Baltic Sea, seasonal and long-term oxygen depletion at the surface of the sediment feeds back the eutrophication loop by promoting the release of nutrients locked in the sediment matrix. In order to understand how the bacterial community responds to the seasonal variations, we sequenced ribosomal gene fragments from the top sediment layer at two coastal sites in southern Finland in spring, summer and late autumn during two consecutive years. Analysis of the samples collected at a shallow (11 m) and deep site (33 m) revealed that the overall community composition was rather constant over time with an extensive collection of shared operational taxonomic units (OTU) between sites. The dominant taxa were related to organoheterotrophs and sulfate reducers and the variation in community structure was linked to the availability of organic matter in the surface sediment. Proteobacteria formed the most abundant and diverse group. The taxa characteristic of spring samples belonged primarily to Actinobacteria, possibly of fresh water origin and linked to humic carbon. Summer communities were characterized by an increase in the number of reads associated with heterotrophic bacteria such as Bacteroidetes which feed on labile organic matter from spring bloom. Taxa typical of autumn samples were linked to Cyanobacteria and other bloom-forming bacteria from the overlying water and to bacteria feeding on organic matter drifting from the phytal zone.

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

    Science.gov (United States)

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

    2016-04-01

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

  19. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Natacha Bodenhausen

    Full Text Available Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root and habitat (epiphytes vs endophytes structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024, while the reverse is true for the leaves (P = 0.032. Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001. The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.

  20. Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga.

    Science.gov (United States)

    Brodie, Juliet; Williamson, Christopher; Barker, Gary L; Walker, Rachel H; Briscoe, Andrew; Yallop, Marian

    2016-08-01

    The living prokaryotic microbiome of the calcified geniculate (articulated) red alga, Corallina officinalis from the intertidal seashore is characterised for the first time based on the V6 hypervariable region of 16S rRNA. Results revealed an extraordinary diversity of bacteria associated with the microbiome. Thirty-five prokaryotic phyla were recovered, of which Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Verrucomicrobia, Firmicutes and Chloroflexi made up the core microbiome. Unclassified sequences made up 25% of sequences, suggesting insufficient sampling of the world's oceans/macroalgae. The greatest diversity in the microbiome was on the upper shore, followed by the lower shore then the middle shore, although the microbiome community composition did not vary between shore levels. The C. officinalis core microbiome was broadly similar in composition to those reported in the literature for crustose coralline algae (CCAs) and free-living rhodoliths. Differences in relative abundance of the phyla between the different types of calcified macroalgal species may relate to the intertidal versus subtidal habit of the taxa and functionality of the microbiome components. The results indicate that much work is needed to identify prokaryotic taxa, and to determine the nature of the relationship of the bacteria with the calcified host spatially, temporally and functionally. PMID:27222222

  1. Characterization of endophytic bacteria from cucurbit fruits with potential benefits to agriculture in melons (Cucumis melo L.).

    Science.gov (United States)

    Glassner, Hanoch; Zchori-Fein, Einat; Compant, Stéphane; Sessitsch, Angela; Katzir, Nurit; Portnoy, Vitaly; Yaron, Sima

    2015-07-01

    Endophytes are microorganisms that mainly colonize vegetative parts, but are also found in reproductive and disseminating organs, and may have beneficial characteristics. To identify microorganisms associated with the agriculturally important family, Cucurbitaceae, endophytes were initially determined in fruits of Cucumis melo Reticulatus Group 'Dulce' by a cultivation-independent approach based on fluorescence in situ hybridization using double labeling of oligonucleotide probes. Alpha-, Beta-, Gammaproteobacteria, Firmicutes and Actinobacteria were localized inside the fruits. Culturable bacteria were further isolated and identified from fruit tissues of 'Dulce', from fruits of other cultivated and wild-field-grown Cucurbitaceae, and from wild fruits growing under natural conditions. Low densities of culturable bacteria were detected in the investigated fruits, especially in four out of the five wild species, regardless of their growing environment. Substantial differences were observed between the wild and cultivated cucurbit taxa in regard to the number of colonized fruits as well as the type of endophytes. Bacillus was the most dominant genus of endophytes colonizing fruits of Cucurbitaceae. The antagonistic effects of isolated endophytes were assessed against cucurbit disease agents in dual-culture assays. Several bacterial isolates exhibited antagonistic properties against the tested plant pathogens. The identified bacteria may be useful for protecting plants not only in the field, but also for post-harvest. PMID:26183916

  2. Sensors for isolation of anti-cancer compounds found within marine invertebrates

    Science.gov (United States)

    Wiegand, Gordon; LaRue, Amanda

    2015-05-01

    Highly evolved bacteria living within immobile marine animals are being targeted as a source of antitumor pharmaceuticals. This paper describes 2 electo-optical sensor systems developed for identifying species of tunicates and actinobacteria that live within them. Two stages of identification include 1) a benthic survey apparatus to locate species and 2) a laboratory housed cell analysis platform used to classify their bacterial micro-biome. Marine Optics Sampling- There are over 3000 species of Tunicates that thrive in diverse habitats. We use a system of cameras, GPS and the GPS/photo integration application on a PC laptop to compile a time / location stamp for each image taken during the dive survey. A shape-map of x/y coordinates of photos are stored for later identification and sampling. Flow Cytometers/cell sorters housed at The Medical University of South Carolina and The University of Maryland have been modified to produce low-noise, high signal wave forms used for bacteria analysis. We strive to describe salient contrasts between these two fundamentally different sensor systems. Accents are placed on analog transducers and initial step sensing systems and output.

  3. Culture-independent methods to study subaerial biofilm growing on biodeteriorated surfaces of stone cultural heritage and frescoes.

    Science.gov (United States)

    Cappitelli, Francesca; Villa, Federica; Polo, Andrea

    2014-01-01

    Actinobacteria, cyanobacteria, algae, and fungi form subaerial biofilm (SAB) that can lead to material deterioration on artistic stone and frescoes. In studying SAB on cultural heritage surfaces, a general approach is to combine microscopy observations and molecular analyses. Sampling of biofilm is performed using specific adhesive tape and sampling of SAB and the substrate with sterile scalpels and chisels. Biofilm observations are carried out using optical and scanning electron microscopy. Specific taxa and EPS in biofilm can be readily visualized by fluorochrome staining and subsequent observation using fluorescence or confocal laser scanning microscopy. The observation of cross sections containing both SAB and the substrate shows if biofilm has developed not only on the surface but also underneath. Following nucleic acid extraction, 16S rRNA gene sequencing is used to identify bacterial taxa, while 18S rRNA gene and internal transcribed spacer (ITS) sequence analysis is used to study eukaryotic groups. In this chapter, we illustrate the protocols related to fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), and denaturing gradient gel electrophoresis (DGGE).

  4. Diversity of Bacterial Communities of Fitness Center Surfaces in a U.S. Metropolitan Area

    Directory of Open Access Journals (Sweden)

    Nabanita Mukherjee

    2014-12-01

    Full Text Available Public fitness centers and exercise facilities have been implicated as possible sources for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial community residing on the surfaces in these indoor environments is still unknown. In this study, we investigated the overall bacterial ecology of selected fitness centers in a metropolitan area (Memphis, TN, USA utilizing culture-independent pyrosequencing of the 16S rRNA genes. Samples were collected from the skin-contact surfaces (e.g., exercise instruments, floor mats, handrails, etc. within fitness centers. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Proteobacter and Actinobacteria, with a total of 17 bacterial families and 25 bacterial genera. Most of these bacterial genera are of human and environmental origin (including, air, dust, soil, and water. Additionally, we found the presence of some pathogenic or potential pathogenic bacterial genera including Salmonella, Staphylococcus, Klebsiella, and Micrococcus. Staphylococcus was found to be the most prevalent genus. Presence of viable forms of these pathogens elevates risk of exposure of any susceptible individuals. Several factors (including personal hygiene, surface cleaning and disinfection schedules of the facilities may be the reasons for the rich bacterial diversity found in this study. The current finding underscores the need to increase public awareness on the importance of personal hygiene and sanitation for public gym users.

  5. Interspecific variations in the gastrointestinal microbiota in penguins.

    Science.gov (United States)

    Dewar, Meagan L; Arnould, John P Y; Dann, Peter; Trathan, Phil; Groscolas, Rene; Smith, Stuart

    2013-02-01

    Despite the enormous amount of data available on the importance of the gastrointestinal (GI) microbiota in vertebrate (especially mammals), information on the GI microbiota of seabirds remains incomplete. As with many seabirds, penguins have a unique digestive physiology that enables them to store large reserves of adipose tissue, protein, and lipids. This study used quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA gene pyrosequencing to characterize the interspecific variations of the GI microbiota of four penguin species: the king, gentoo, macaroni, and little penguin. The qPCR results indicated that there were significant differences in the abundance of the major phyla Firmicutes, Bacteroides, Actinobacteria, and Proteobacteria. A total of 132,340, 18,336, 6324, and 4826 near full-length 16S rRNA gene sequences were amplified from fecal samples collected from king, gentoo, macaroni, and little penguins, respectively. A total of 13 phyla were identified with Firmicutes, Bacteroidetes, Proteobacteria, and Fusobacteria dominating the composition; however, there were major differences in the relative abundance of the phyla. In addition, this study documented the presence of known human pathogens, such as Campylobacter, Helicobacter, Prevotella, Veillonella, Erysipelotrichaceae, Neisseria, and Mycoplasma. However, their role in disease in penguins remains unknown. To our knowledge, this is the first study to provide an in-depth investigation of the GI microbiota of penguins.

  6. First microbiota assessments of children's paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis.

    Science.gov (United States)

    Sawabe, Toko; Suda, Wataru; Ohshima, Kenshiro; Hattori, Masahira; Sawabe, Tomoo

    2016-01-01

    Insufficient chloric sterilization of children's paddling pool waters increases the risk of diarrheal illness. Therefore, we investigated the microbiota changes after children use pools. First, we applied 16S rRNA gene-based metagenome analysis to understand the dynamics of microbiota in pool water, especially with respect to the bio-contamination by potential pathogens. Proteobacteria were major taxa detected in every pool water sample after children spent time in the pool. In more detail, Gammaproteobacteria comprised the dominant class, which was followed by Betaproteobacteria. Five phyla, Bacteroidetes, Firmicutes, Actinobacteria and Deinococcus-Thermus phyla were minor groups. The pool water microbiota are likely to be a consortium of intestinal and skin microbiota from humans. Interestingly, the ratio of Gammaproteobacteria and Betaproteobacteria differed according to the age of the children who used the pool, which means the pool water was additionally contaminated by soil microbiota as a result of the children's behavior. Furthermore, potential pathogens, such as Campylobacter spp., Comamonas testosteroni and Burkholderia pseudomallei, were also found. Considering the standard plate counts, the abundances of these human pathogens are unlikely to be a sufficiently infectious dose. We suggest the importance of sanitary measures in paddling pool waters to reduce bio-contamination from both humans and the environment.

  7. Antioxidant activity and free radical scavenging activities of Streptomyces sp. strain MJM 10778

    Institute of Scientific and Technical Information of China (English)

    Dong-Ryung Lee; Sung-Kwon Lee; Bong-Keun Choi; Jinhua Cheng; Young-Sil Lee; Seung Hwan Yang; Joo-Won Suh

    2014-01-01

    Objective:To investigate the antioxidant activity of soil-borne actinobacteria. Methods:The total phenolic contents, the level of antioxidant potential byDPPH radical scavenging activity,NO scavenging activity, andABTS radical scavenging activity in ethyl acetate extract were determined.Results:The16S rDNA sequencing analysis revealed thatStreptomyces sp. strainMJM10778, which was isolated fromHambakMountain,Korea, has99.9% similarity to Streptomyces misionensis(S. misionensis)NBRC13063.The physiological and the morphological test revealed that the strainMJM10778 has different characteristics from the strainNBRC13063. The entire antioxidant assay with the ethyl acetate extract displayed good radical scavenging activity.TheIC50 values of the strainMJM10778 extract onDPPH,NO, andABTS radicals were identified to be92.8 μg/mL,0.02 μg/mL, and134.9 μg/mL, respectively.The ethyl acetate extract of the strainMJM10778 showed an81.50% of cell viability at100 μg/mL inRaw264.7 cell viability assay.Conclusions:The results obtained suggest that the ethyl acetate extract ofStreptomyces sp. strainMJM10778 could be considered as a potential source of drug for the diseases that is caused by free radicals with its anti-oxidant activities and low cytotoxicity.

  8. Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India

    Directory of Open Access Journals (Sweden)

    Gajanan T. Mehetre

    2016-03-01

    Full Text Available Unkeshwar hot springs are located at geographical South East Deccan Continental basalt of India. Here, we report the microbial community analysis of this hot spring using whole metagenome shotgun sequencing approach. The analysis revealed a total of 848,096 reads with 212.87 Mbps with 50.87% G + C content. Metagenomic sequences were deposited in SRA database with accession number (SUB1242219. Community analysis revealed 99.98% sequences belonging to bacteria and 0.01% to archaea and 0.01% to Viruses. The data obtained revealed 41 phyla including bacteria and Archaea and including 719 different species. In taxonomic analysis, the dominant phyla were found as, Actinobacteria (56%, Verrucomicrobia (24%, Bacteriodes (13%, Deinococcus-Thermus (3% and firmicutes (2% and Viruses (2%. Furthermore, functional annotation using pathway information revealed dynamic potential of hot spring community in terms of metabolism, environmental information processing, cellular processes and other important aspects. Kyoto Encyclopedia of Genes and Genomes (KEGG pathway analysis of each contig sequence by assigning KEGG Orthology (KO numbers revealed contig sequences that were assigned to metabolism, organismal system, Environmental Information Processing, cellular processes and human diseases with some unclassified sequences. The Unkeshwar hot springs offer rich phylogenetic diversity and metabolic potential for biotechnological applications.

  9. Allosteric Transitions Direct Protein Tagging by PafA, the Prokaryotic Ubiquitin-like Protein (Pup) Ligase*

    Science.gov (United States)

    Ofer, Naomi; Forer, Nadav; Korman, Maayan; Vishkautzan, Marina; Khalaila, Isam; Gur, Eyal

    2013-01-01

    Protein degradation via prokaryotic ubiquitin-like protein (Pup) tagging is conserved in bacteria belonging to the phyla Actinobacteria and Nitrospira. The physiological role of this novel proteolytic pathway is not yet clear, although in Mycobacterium tuberculosis, the world's most threatening bacterial pathogen, Pup tagging is important for virulence. PafA, the Pup ligase, couples ATP hydrolysis with Pup conjugation to lysine side chains of protein substrates. PafA is the sole Pup ligase in M. tuberculosis and apparently, in other bacteria. Thus, whereas PafA is a key player in the Pup tagging (i.e. pupylation) system, control of its activity and interactions with target protein substrates remain poorly understood. In this study, we examined the mechanism of protein pupylation by PafA in Mycobacterium smegmatis, a model mycobacterial organism. We report that PafA is an allosteric enzyme that binds its target substrates cooperatively and find that PafA allostery is controlled by the binding of target protein substrates, yet is unaffected by Pup binding. Analysis of PafA pupylation using engineered substrates differing in the number of pupylation sites points to PafA acting as a dimer. These findings suggest that protein pupylation can be regulated at the level of PafA allostery. PMID:23471967

  10. Allosteric transitions direct protein tagging by PafA, the prokaryotic ubiquitin-like protein (Pup) ligase.

    Science.gov (United States)

    Ofer, Naomi; Forer, Nadav; Korman, Maayan; Vishkautzan, Marina; Khalaila, Isam; Gur, Eyal

    2013-04-19

    Protein degradation via prokaryotic ubiquitin-like protein (Pup) tagging is conserved in bacteria belonging to the phyla Actinobacteria and Nitrospira. The physiological role of this novel proteolytic pathway is not yet clear, although in Mycobacterium tuberculosis, the world's most threatening bacterial pathogen, Pup tagging is important for virulence. PafA, the Pup ligase, couples ATP hydrolysis with Pup conjugation to lysine side chains of protein substrates. PafA is the sole Pup ligase in M. tuberculosis and apparently, in other bacteria. Thus, whereas PafA is a key player in the Pup tagging (i.e. pupylation) system, control of its activity and interactions with target protein substrates remain poorly understood. In this study, we examined the mechanism of protein pupylation by PafA in Mycobacterium smegmatis, a model mycobacterial organism. We report that PafA is an allosteric enzyme that binds its target substrates cooperatively and find that PafA allostery is controlled by the binding of target protein substrates, yet is unaffected by Pup binding. Analysis of PafA pupylation using engineered substrates differing in the number of pupylation sites points to PafA acting as a dimer. These findings suggest that protein pupylation can be regulated at the level of PafA allostery. PMID:23471967

  11. Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge

    Institute of Scientific and Technical Information of China (English)

    WU Yuehong; CAO Yi; WANG Chunsheng; WU Min; AHARON Oren; XU Xuewei

    2014-01-01

    A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction (PCR) amplification of the 16S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E (MBGE) and marine group I (MGI) belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the South-west Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.

  12. Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River basin, Yangtze River Delta.

    Science.gov (United States)

    Cai, Wei; Li, Yi; Wang, Peifang; Niu, Lihua; Zhang, Wenlong; Wang, Chao

    2016-01-01

    River pollution is one of the most challenging environmental issues, but the effect of river pollution levels on the biofilm communities has not been well-studied. Spatial and temporal distribution characteristics of environmental parameters and the biofilm communities were investigated in the Qinhuai River basin, Nanjing, China. Water samples were grouped into three clusters reflecting their varying pollution levels of relatively slight pollution, moderated pollution, and high pollution by hierarchical cluster analysis. In different clusters, the biofilm communities mainly differed in the proportion of Actinobacteria, Firmicutes, and Proteobacteria. As the dominant classes of Proteobacteria, Alpha-, Beta- and Gammaproteobacteria seemed to show an upward trend followed by a small fluctuation in the abundance with the escalation of water pollution level. Results of redundancy analysis demonstrated that temperature, total nitrogen to total phosphorus ratios (TN/TP) and concentrations of ammonia nitrogen (NH3-N) and TN were mainly responsible for the variation in bacterial community structure. The occurrences of Alpha-, Beta- and Gammaproteobacteria were closely associated with higher temperature, higher concentrations of NH3-N and TN and a lower TN/TP ratio. This study may provide a theoretical basis for the water pollution control and ecological restoration in urban rivers under different pollution levels. PMID:27642836

  13. Microbial diversity and evidence of novel homoacetogens in the gut of both geriatric and adult giant pandas (Ailuropoda melanoleuca.

    Directory of Open Access Journals (Sweden)

    Hein Min Tun

    Full Text Available Recent studies have described the bacterial community residing in the guts of giant pandas, together with the presence of lignocellulolytic enzymes. However, a more comprehensive understanding of the intestinal microbial composition and its functional capacity in giant pandas remains a major goal. Here, we conducted a comparison of bacterial, fungal and homoacetogenic microbial communities from fecal samples taken from two geriatric and two adult captive giant pandas. 16S rDNA amplicon pyrosequencing revealed that Firmicutes and Proteobacteria are the most abundant microbiota in both geriatric and adult giant pandas. However, members of phylum Actinobacteria found in adult giant pandas were absent in their geriatric counterparts. Similarly, ITS1 amplicon pyrosequencing identified developmental changes in the most abundant fungal classes from Sordariomycetes in adult pandas to Saccharomycetes in geriatric pandas. Geriatric pandas exhibited significantly higher abundance of a potential probiotic fungus (Candida tropicalis as compared to adult pandas, indicating their importance in the normal digestive physiology of aged pandas. Our study also reported the presence of a lignocellulolytic white-rot fungus, Perenniporia medulla-panis, and the evidence of novel homoacetogens residing in the guts of giant pandas.

  14. Psychrotrophic lipase producers from Arctic soil and sediment samples.

    Science.gov (United States)

    Rasol, R; Rashidah, A R; Nazuha, R Siti Nur; Smykla, J; Maznah, W O Wan; Alias, S A

    2014-01-01

    Culturable microorganisms were successfully isolated from soil and sediment samples collected in 2011 on the northern coast of Hornsund, West Spitsbergen. A total of 63 single colony isolates from three sampling sites obtained were subjected to temperature dependence study to assess whether they are obligate psychrophilic or psychrotrophic strains. From initial temperature screening, only 53 psychrotrophic isolates were selected that are capable of growing between 4-28 degrees C. The rest that were capable of tolerating higher temperatures up to 37 degrees C were not included in this study. These isolates were chosen for lipase enzyme screening confirmation with the standard plate assay of olive oil and fluorescent dye Rhodamine B. Six lipase positive isolates were also subjected for subsequent lipase enzyme plate screening on tributyrin, triolein, olive oil and palm oil agar. Lipase production by these six isolates was further assayed by using colorimetric method with palm oil and olive oil as the substrate. These isolates with promising lipase activity ranging from 20 U/ml up to 160 U/ml on palm oil and olive oil substrate were successfully identified. Molecular identification by using 16S rRNA revealed that five out of six isolates were Gram-negative Proteobacteria and the other one was a Gram-positive Actinobacteria. PMID:25033666

  15. Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.

    Science.gov (United States)

    Valenzuela-Encinas, César; Neria-González, Isabel; Alcántara-Hernández, Rocio J; Estrada-Alvarado, Isabel; Zavala-Díaz de la Serna, Francisco Javier; Dendooven, Luc; Marsch, Rodolfo

    2009-07-01

    Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m(-1) and pH 7.80 (LOW soil), with EC 56 dS m(-1) and pH 10.11 (MEDIUM soil) and with EC 159 dS m(-1) and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the alpha- and gamma-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.

  16. Respiratory and dissimilatory nitrate-reducing communities from an extreme saline alkaline soil of the former lake Texcoco (Mexico).

    Science.gov (United States)

    Alcántara-Hernández, Rocio J; Valenzuela-Encinas, César; Marsch, Rodolfo; Dendooven, Luc

    2009-01-01

    The diversity of the dissimilatory and respiratory nitrate-reducing communities was studied in two soils of the former lake Texcoco (Mexico). Genes encoding the membrane-bound nitrate reductase (narG) and the periplasmic nitrate reductase (napA) were used as functional markers. To investigate bacterial communities containing napA and narG in saline alkaline soils of the former lake Texcoco, libraries of the two sites were constructed (soil T3 with pH 11 and electrolytic conductivity in saturated extract (EC(SE)) 160 dS m(-1) and soil T1 with pH 8.5 and EC(SE) 0.8 dS m(-1)). Phylogenetic analysis of napA sequences separated the clone families into two main groups: dependent or independent of NapB. Most of napA sequences from site T1 were grouped in the NapB-dependent clade, meanwhile most of the napA sequences from the extreme soil T3 were affiliated to the NapB-independent group. For both sites, partial narG sequences were associated with representatives of the Proteobacteria, Firmicutes and Actinobacteria phyla, but the proportions of the clones were different. Our results support the concept of a specific and complex nitrate-reducing community for each soil of the former lake Texcoco.

  17. Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity.

    Science.gov (United States)

    Gaikwad, Swapnil; Shouche, Yogesh S; Gade, Wasudev N

    2016-12-01

    Sponges are primitive metazoans that are known to harbour diverse and abundant microbes. All over the world attempts are being made to exploit these microbes for their biotechnological potential to produce, bioactive compounds and antimicrobial peptides. However, the majority of the studies are focussed on the marine sponges and studies on the freshwater sponges have been neglected so far. To increase our understanding of the microbial community structure of freshwater sponges, microbiota of two fresh water sponges namely, Eunapius carteri and Corvospongilla lapidosa is explored for the first time using Next Generation Sequencing (NGS) technology. Overall the microbial composition of these sponges comprises of 14 phyla and on an average, more than 2900 OTUs were obtained from C. lapidosa while E. carteri showed 980 OTUs which is higher than OTUs obtained in the marine sponges. Thus, our study showed that, fresh water sponges also posses highly diverse microbial community than previously thought and it is distinct from the marine sponge microbiota. The present study also revealed that microbial community structure of both the sponges is significantly different from each other and their respective water samples. In the present study, we have detected many bacterial lineages belonging to Firmicutes, Actinobacteria, Proteobacteria, Planctomycetes, etc. that are known to produce compounds of biotechnological importance. Overall, this study gives insight into the microbial composition of the freshwater sponges which is highly diverse and needs to be studied further to exploit their biotechnological capabilities. PMID:27299740

  18. Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia.

    Science.gov (United States)

    He, Jizheng; Xu, Zhihong; Hughes, Jane

    2006-01-01

    A major operational change in exotic pine plantations of subtropical Australia has been the decision to retain postharvest residues on site. A long-term field experiment was established in February 1996 to examine the impacts of residue management regimes [i.e. the postharvest residues removed (G0R), natural amount of residues retained (G1R) and residue quantity doubled and retained (G2R)] on tree growth (F1 hybrid pine) and sustainable soil management. Twelve soil samples, which included the above three residue regimes with four replicates, were collected at plantation age 6.4 years. A 16S rRNA gene clone library was established following soil community DNA extraction, polymerase chain reaction amplification and cloning. A total of 324 clones, including 27 from each sample, were randomly selected and sequenced to represent the bacterial composition and diversity of the clone library and thus the soil bacterial community under the residue management regimes. Phylogenetic analyses indicated that Acidobacteria (37.6%) and Proteobacteria (35.6%) were the dominant components of the soil bacterial community, followed by Actinobacteria (14.7%), Chlamydiae/Verrucomicrobia (7.3%), Unclassified Bacteria (3.8%) and Gemmatimonadetes (1.0%). Analysis of molecular variance revealed that there was no significant difference in bacterial composition and diversity among the residue management regimes or their replicated samples. PMID:16420613

  19. Microbial characterization of basalt formation waters targeted for geological carbon sequestration.

    Science.gov (United States)

    Lavalleur, Heather J; Colwell, Frederick S

    2013-07-01

    Geological carbon sequestration in basalts is a promising solution to mitigate carbon emissions into the Earth's atmosphere. The Wallula pilot well in Eastern Washington State, USA provides an opportunity to investigate how native microbial communities in basalts are affected by the injection of supercritical carbon dioxide into deep, alkaline formation waters of the Columbia River Basalt Group. Our objective was to characterize the microbial communities at five depth intervals in the Wallula pilot well prior to CO2 injection to establish a baseline community for comparison after the CO2 is injected. Microbial communities were examined using quantitative polymerase chain reaction to enumerate bacterial cells and 454 pyrosequencing to compare and contrast the diversity of the native microbial communities. The deepest depth sampled contained the greatest amount of bacterial biomass, as well as the highest bacterial diversity. The shallowest depth sampled harbored the greatest archaeal diversity. Pyrosequencing revealed the well to be dominated by the Proteobacteria, Firmicutes, and Actinobacteria, with microorganisms related to hydrogen oxidizers (Hydrogenophaga), methylotrophs (Methylotenera), methanotrophs (Methylomonas), iron reducers (Geoalkalibacter), sulfur oxidizers (Thiovirga), and methanogens (Methermicocccus). Thus, the Wallula pilot well is composed of a unique microbial community in which hydrogen and single-carbon compounds may play a significant role in sustaining the deep biosphere.

  20. A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics

    Science.gov (United States)

    Sasaki, Daisuke; Fukuda, Itsuko; Tanaka, Kosei; Yoshida, Ken-ichi; Kondo, Akihiko; Osawa, Ro

    2016-01-01

    We devised a single-batch fermentation system to simulate human colonic microbiota from fecal samples, enabling the complex mixture of microorganisms to achieve densities of up to 1011 cells/mL in 24 h. 16S rRNA gene sequence analysis of bacteria grown in the system revealed that representatives of the major phyla, including Bacteroidetes, Firmicutes, and Actinobacteria, as well as overall species diversity, were consistent with those of the original feces. On the earlier stages of fermentation (up to 9 h), trace mixtures of acetate, lactate, and succinate were detectable; on the later stages (after 24 h), larger amounts of acetate accumulated along with some of propionate and butyrate. These patterns were similar to those observed in the original feces. Thus, this system could serve as a simple model to simulate the diversity as well as the metabolism of human colonic microbiota. Supplementation of the system with several prebiotic oligosaccharides (including fructo-, galacto-, isomalto-, and xylo-oligosaccharides; lactulose; and lactosucrose) resulted in an increased population in genus Bifidobacterium, concomitant with significant increases in acetate production. The results suggested that this fermentation system may be useful for in vitro, pre-clinical evaluation of the effects of prebiotics prior to testing in humans. PMID:27483470

  1. Enhancing the culturability of bacteria from the gastrointestinal tract of farmed adult turbot Scophthalmus maximus

    Science.gov (United States)

    Xing, Mengxin; Hou, Zhanhui; Qu, Yanmei; Liu, Bin

    2014-03-01

    Eighteen agar media were tested for the culture of gut-associated bacteria from farmed adult turbot ( Scophthalmus maximus), including 16 agar media with or without 1% gastrointestinal (GI) supernatant, or with 2% or 4% GI supernatant. A total of 1 711 colonies were analyzed and 24 operational taxonomic units (OTUs) were identified. The greatest bacterial diversity was isolated on Zobell 2216E/Zobell 2216E+ agar media, whereas MRS/MRS+ agar media produced a low diversity of colonies. Agar media with GI supernatant (1%, 2%, or 4%) showed increased diversity and yielded different profiles of OTUs from the corresponding original media, suggesting that GI supernatant provides substances that enhance the culture efficiency of bacteria from the turbot GI tract. The large majority of the colonies (82%) were γ-Proteobacteria, whereas 15.6% and 2.4% of colonies were Firmicutes and Actinobacteria, respectively. At the genus level, 49.4% of all colonies were assigned to Vibrio. Other potential pathogens, including Pseudomonas, Photobacterium, and Enterobacter, and potential probiotics, including Bacillus, Paenibacillus, and Pseudomonas, were also isolated on agar media. Most cultured bacteria belonged to species that were first described in the turbot GI tract. The impact of these species on turbot physiology and health should be investigated further.

  2. Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans.

    Science.gov (United States)

    Ushida, Kazunari; Segawa, Takahiro; Tsuchida, Sayaka; Murata, Koichi

    2016-02-01

    Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan. PMID:26468217

  3. Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

    Science.gov (United States)

    Steven, Blaire; Gallegos-Graves, La Verne; Yeager, Chris; Belnap, Jayne; Kuske, Cheryl R.

    2013-01-01

    Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO2 Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO2 did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.

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

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  5. Study of azo dye decolorization and determination of cathode microorganism profile in air-cathode microbial fuel cells.

    Science.gov (United States)

    Kumru, Mert; Eren, Hilal; Catal, Tunc; Bermek, Hakan; Akarsubaşi, Alper Tunga

    2012-09-01

    Five textile azo dyes, as part of an artificial mixture, were treated in single-chamber air-cathode microbial fuel cells while simultaneously utilizing acetate for electricity production. Remazol Black, Remazol Brilliant Blue, Remazol Turquoise Blue, Reactive Yellow and Reactive Red at concentrations of 40 or 80 mg L(-1) were decolorized to a similar extent, at averages of 78, 95, 53, 93 and 74%, respectively, in 24 hours. During the process of decolorization, electricity generation from acetate oxidation continued. Power densities obtained in the presence of textile dyes ranged from 347 to 521 mW m(-2) at the current density range of 0.071 - 0.086 mA cm(-2). Microbial community analyses of cathode biofilm exhibited dynamic changes in abundant species following dye decolorization. Upon the addition of the first dye, a major change (63%) in microbial diversity was observed; however, subsequent addition of other dyes did not affect the community profile significantly. Actinobacteria, Aquamicrobium, Mesorhizobium, Ochrobactrum, Thauera, Paracoccus, Achromobacter and Chelatacoccus affiliated phylotypes were the major phylotypes detected. Our results demonstrate that microbial fuel cells could be a promising alternative for treatment of textile wastewaters and an active bacterial community can rapidly be established for simultaneous azo dye decolorization and sustainable electricity generation.

  6. Saturated and Unsaturated Dietary Fats Differentially Modulate Ethanol-Induced Changes in Gut Microbiome and Metabolome in a Mouse Model of Alcoholic Liver Disease.

    Science.gov (United States)

    Kirpich, Irina A; Petrosino, Joseph; Ajami, Nadim; Feng, Wenke; Wang, Yuhua; Liu, Yanlong; Beier, Juliane I; Barve, Shirish S; Yin, Xinmin; Wei, Xiaoli; Zhang, Xiang; McClain, Craig J

    2016-04-01

    Alcoholic liver disease (ALD) ranks among major causes of morbidity and mortality. Diet and crosstalk between the gut and liver are important determinants of ALD. We evaluated the effects of different types of dietary fat and ethanol on the gut microbiota composition and metabolic activity and the effect of these changes on liver injury in ALD. Compared with ethanol and a saturated fat diet (medium chain triglycerides enriched), an unsaturated fat diet (corn oil enriched) exacerbated ethanol-induced endotoxemia, liver steatosis, and injury. Major alterations in gut microbiota, including a reduction in Bacteroidetes and an increase in Proteobacteria and Actinobacteria, were seen in animals fed an unsaturated fat diet and ethanol but not a saturated fat diet and ethanol. Compared with a saturated fat diet and ethanol, an unsaturated fat diet and ethanol caused major fecal metabolomic changes. Moreover, a decrease in certain fecal amino acids was noted in both alcohol-fed groups. These data support an important role of dietary lipids in ALD pathogenesis and provide insight into mechanisms of ALD development. A diet enriched in unsaturated fats enhanced alcohol-induced liver injury and caused major fecal metagenomic and metabolomic changes that may play an etiologic role in observed liver injury. Dietary lipids can potentially serve as inexpensive interventions for the prevention and treatment of ALD.

  7. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana

    Science.gov (United States)

    Berlanga, Mercedes; Llorens, Carlos; Comas, Jaume; Guerrero, Ricardo

    2016-01-01

    Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1–2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P host of providing nutrients in appropriate quantities and balance. PMID:27054320

  8. Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests.

    Science.gov (United States)

    Ding, Junjun; Zhang, Yuguang; Wang, Mengmeng; Sun, Xin; Cong, Jing; Deng, Ye; Lu, Hui; Yuan, Tong; Van Nostrand, Joy D; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

    2015-10-01

    As two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as 'The Oriental Botanic Garden' for its extraordinarily rich biodiversity. We observed higher plant diversity and relatively richer nutrients in the broadleaved evergreen forest than the deciduous forest. In odds to our expectation that plant communities shaped soil microbial communities, we found that soil organic matter quantity and quality, but not plant community parameters, were the best predictors of microbial communities. Actinobacteria, a copiotrophic phylum, was more abundant in the broadleaved evergreen forest, while Verrucomicrobia, an oligotrophic phylum, was more abundant in the broadleaved deciduous forest. The density of the correlation network of microbial OTUs was higher in the broadleaved deciduous forest but its modularity was smaller, reflecting lower resistance to environment changes. In addition, keystone OTUs of the broadleaved deciduous forest were mainly oligotrophic. Microbial functional genes associated with recalcitrant carbon degradation were also more abundant in the broadleaved deciduous forests, resulting in low accumulation of organic matters. Collectively, these findings revealed the important role of soil organic matter in shaping microbial taxonomic and functional traits.

  9. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana.

    Science.gov (United States)

    Berlanga, Mercedes; Llorens, Carlos; Comas, Jaume; Guerrero, Ricardo

    2016-01-01

    Cryptocercus punctulatus and Parasphaeria boleiriana are two distantly related xylophagous and subsocial cockroaches. Cryptocercus is related to termites. Xylophagous cockroaches and termites are excellent model organisms for studying the symbiotic relationship between the insect and their microbiota. In this study, high-throughput 454 pyrosequencing of 16S rRNA was used to investigate the diversity of metagenomic gut communities of C. punctulatus and P. boleiriana, and thereby to identify possible shifts in symbiont allegiances during cockroaches evolution. Our results revealed that the hindgut prokaryotic communities of both xylophagous cockroaches are dominated by members of four Bacteria phyla: Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Other identified phyla were Spirochaetes, Planctomycetes, candidatus Saccharibacteria (formerly TM7), and Acidobacteria, each of which represented 1-2% of the total population detected. Community similarity based on phylogenetic relatedness by unweighted UniFrac analyses indicated that the composition of the bacterial community in the two species was significantly different (P termites and other cockroaches, but not with those from other animals or environments. These results suggest that, during their evolution, those cockroaches conserved several bacterial communities from the microbiota of a common ancestor. The ecological stability of those microbial communities may imply the important functional role for the survival of the host of providing nutrients in appropriate quantities and balance. PMID:27054320

  10. Molecular diversity of bacteria in commercially available "Spirulina" food supplements.

    Science.gov (United States)

    Vardaka, Elisabeth; Kormas, Konstantinos A; Katsiapi, Matina; Genitsaris, Savvas; Moustaka-Gouni, Maria

    2016-01-01

    The cyanobacterium Arthrospira is among the most well-known food supplements worldwide known as "Spirulina." While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of "Spirulina" supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of "Spirulina" dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) of Arthrospira platensis were the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9-157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e., Pseudomonas, Flavobacterium, Vibrio, Aeromonas, Clostridium, Bacillus, Fusobacterium, Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing of Arthrospira biomass for commercial purposes. PMID:26819852

  11. Selective enrichment of commensal gut bacteria protects against Citrobacter rodentium-induced colitis.

    Science.gov (United States)

    Vong, Linda; Pinnell, Lee J; Määttänen, Pekka; Yeung, C William; Lurz, Eberhard; Sherman, Philip M

    2015-08-01

    The intestinal microbiota plays a key role in shaping the host immune system. Perturbation of gut microbial composition, termed dysbiosis, is associated with an increased susceptibility to intestinal pathogens and is a hallmark of a number of inflammatory, metabolic, and infectious diseases. The prospect of mining the commensal gut microbiota for bacterial strains that can impact immune function represents an attractive strategy to counteract dysbiosis and resulting disease. In this study, we show that selective enrichment of commensal gut lactobacilli protects against the murine pathogen Citrobacter rodentium, a well-characterized model of enteropathogenic and enterohemorrhagic Escherichia coli infection. The lactobacilli-enriched bacterial culture prevented the expansion of Gammaproteobacteria and Actinobacteria and was associated with improved indexes of epithelial barrier function (dextran flux), transmissible crypt hyperplasia, and tissue inflammatory cytokine levels. Moreover, cultivation of gut bacteria from Citrobacter rodentium-infected mice reveals the differential capacity of bacterial subsets to mobilize neutrophil oxidative burst and initiate the formation of weblike neutrophil extracellular traps. Our findings highlight the beneficial effects of a lactobacilli-enriched commensal gut microenvironment and, in the context of an intestinal barrier breach, the ability of neutrophils to immobilize both commensal and pathogenic bacteria.

  12. Bacterial communities in the gut and reproductive organs of Bactrocera minax (Diptera: Tephritidae based on 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Ailin Wang

    Full Text Available The citrus fruit fly Bactrocera minax is associated with diverse bacterial communities. We used a 454 pyrosequencing technology to study in depth the microbial communities associated with gut and reproductive organs of Bactrocera minax. Our dataset consisted of 100,749 reads with an average length of 400 bp. The saturated rarefaction curves and species richness indices indicate that the sampling was comprehensive. We found highly diverse bacterial communities, with individual sample containing approximately 361 microbial operational taxonomic units (OTUs. A total of 17 bacterial phyla were obtained from the flies. A phylogenetic analysis of 16S rDNA revealed that Proteobacteria was dominant in all samples (75%-95%. Actinobacteria and Firmicutes were also commonly found in the total clones. Klebsiella, Citrobacter, Enterobacter, and Serratia were the major genera. However, bacterial diversity (Chao1, Shannon and Simpson indices and community structure (PCA analysis varied across samples. Female ovary has the most diverse bacteria, followed by male testis, and the bacteria diversity of reproductive organs is richer than that of the gut. The observed variation can be caused by sex and tissue, possibly to meet the host's physiological demands.

  13. Feline gastrointestinal microbiota.

    Science.gov (United States)

    Minamoto, Yasushi; Hooda, Seema; Swanson, Kelly S; Suchodolski, Jan S

    2012-06-01

    The close relationship between gastrointestinal (GI) microbiota and its host has an impact on the health status of an animal that reaches beyond the GI tract. A balanced microbiome stimulates the immune system, aids in the competitive exclusion of transient pathogens and provides nutritional benefits to the host. With recent rapid advances in high-throughput sequencing technology, molecular approaches have become the routinely used tools for ecological studies of the feline microbiome, and have revealed a highly diverse and complex intestinal ecosystem in the feline GI tract. The major bacterial groups are similar to those found in other mammals, with Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria constituting more than 99% of intestinal microbiota. Several nutritional studies have demonstrated that the feline microbiota can be modulated by the amount of soluble fibers (i.e., prebiotics) and macronutrients (i.e., protein content) in the diet. Initial clinical studies have suggested the presence of a dysbiosis in feline inflammatory bowel disease (IBD). Recently, metagenomic approaches have attempted to characterize the microbial gene pool. However, more studies are needed to describe the phylogenetic and functional changes in the intestinal microbiome in disease states and in response to environmental and dietary modulations. This paper reviews recent studies cataloging the microbial phylotypes in the GI tract of cats.

  14. Bacterial and fungal taxon changes in soil microbial community composition induced by short-term biochar amendment in red oxidized loam soil.

    Science.gov (United States)

    Hu, Liao; Cao, Lixiang; Zhang, Renduo

    2014-03-01

    To take full advantage of biochar as a soil amendment, the objective of this study was to investigate the effects of biochar addition on soil bacterial and fungal diversity and community composition. Incubation experiments with a forest soil (a red oxidized loam soil) with and without biochar amendment were conducted for 96 days. The culture-independent molecular method was utilized to analyze soil bacterial and fungal species after the incubation experiments. Results showed that bacteria and fungi responded differently to the biochar addition during the short-term soil incubation. Twenty four and 18 bacterial genara were observed in the biochar amended and unamended soils, respectively, whereas 11 and 8 fungal genera were observed in the biochar amended and unamended soils, respectively. Microbial taxa analysis indicated that the biochar amendment resulted in significant shifts in both bacterial and fungal taxa during the incubation period. The shift for bacteria occurred at the genus and phylum levels, while for fungi only at the genus level. Specific taxa, such as Actinobacteria of bacteria and Trichoderma and Paecilomyces of fungi, were enriched in the biochar amended soil. The results reveal a pronounced impact of biochar on soil microbial community composition and an enrichment of key bacterial and fungal taxa in the soil during the short time period. PMID:24136343

  15. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Wuttichai Mhuantong

    Full Text Available 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.

  16. Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Antibiotics are often used to prevent sickness and improve production in animal agriculture, and the residues in animal bodies may enter tannery wastewater during leather production. This study aimed to use Illumina high-throughput sequencing to investigate the occurrence, diversity and abundance of antibiotic resistance genes (ARGs and mobile genetic elements (MGEs in aerobic and anaerobic sludge of a full-scale tannery wastewater treatment plant (WWTP. Metagenomic analysis showed that Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria dominated in the WWTP, but the relative abundance of archaea in anaerobic sludge was higher than in aerobic sludge. Sequencing reads from aerobic and anaerobic sludge revealed differences in the abundance of functional genes between both microbial communities. Genes coding for antibiotic resistance were identified in both communities. BLAST analysis against Antibiotic Resistance Genes Database (ARDB further revealed that aerobic and anaerobic sludge contained various ARGs with high abundance, among which sulfonamide resistance gene sul1 had the highest abundance, occupying over 20% of the total ARGs reads. Tetracycline resistance genes (tet were highly rich in the anaerobic sludge, among which tet33 had the highest abundance, but was absent in aerobic sludge. Over 70 types of insertion sequences were detected in each sludge sample, and class 1 integrase genes were prevalent in the WWTP. The results highlighted prevalence of ARGs and MGEs in tannery WWTPs, which may deserve more public health concerns.

  17. Deodorants and antiperspirants affect the axillary bacterial community.

    Science.gov (United States)

    Callewaert, Chris; Hutapea, Prawira; Van de Wiele, Tom; Boon, Nico

    2014-10-01

    The use of underarm cosmetics is common practice in the Western society to obtain better body odor and/or to prevent excessive sweating. A survey indicated that 95 % of the young adult Belgians generally use an underarm deodorant or antiperspirant. The effect of deodorants and antiperspirants on the axillary bacterial community was examined on nine healthy subjects, who were restrained from using deodorant/antiperspirant for 1 month. Denaturing gradient gel electrophoresis was used to investigate the individual microbial dynamics. The microbial profiles were unique for every person. A stable bacterial community was seen when underarm cosmetics were applied on a daily basis and when no underarm cosmetics were applied. A distinct community difference was seen when the habits were changed from daily use to no use of deodorant/antiperspirant and vice versa. The richness was higher when deodorants and antiperspirants were applied. Especially when antiperspirants were applied, the microbiome showed an increase in diversity. Antiperspirant usage led toward an increase of Actinobacteria, which is an unfavorable situation with respect to body odor development. These initial results show that axillary cosmetics modify the microbial community and can stimulate odor-producing bacteria. PMID:25077920

  18. Bacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the Sør Rondane Mountains, Dronning Maud Land, East Antarctica.

    Science.gov (United States)

    Obbels, Dagmar; Verleyen, Elie; Mano, Marie-José; Namsaraev, Zorigto; Sweetlove, Maxime; Tytgat, Bjorn; Fernandez-Carazo, Rafael; De Wever, Aaike; D'hondt, Sofie; Ertz, Damien; Elster, Josef; Sabbe, Koen; Willems, Anne; Wilmotte, Annick; Vyverman, Wim

    2016-06-01

    The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematoda were present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations. PMID:26936447

  19. The influence of long-term copper contaminated agricultural soil at different pH levels on microbial communities and springtail transcriptional regulation.

    Science.gov (United States)

    de Boer, Tjalf E; Taş, Neslihan; Braster, Martin; Temminghoff, Erwin J M; Röling, Wilfred F M; Roelofs, Dick

    2012-01-01

    Copper has long been applied for agricultural practises. Like other metals, copper is highly persistent in the environment and biologically active long after its use has ceased. Here we present a unique study on the long-term effects (27 years) of copper and pH on soil microbial communities and on the springtail Folsomia candida an important representative of the soil macrofauna, in an experiment with a full factorial, random block design. Bacterial communities were mostly affected by pH. These effects were prominent in Acidobacteria, while Actinobacteria and Gammaroteobacteria communities were affected by original and bioavailable copper. Reproduction and survival of the collembolan F. candida was not affected by the studied copper concentrations. However, the transcriptomic responses to copper reflected a mechanism of copper transport and detoxification, while pH exerted effects on nucleotide and protein metabolism and (acute) inflammatory response. We conclude that microbial community structure reflected the history of copper contamination, while gene expression analysis of F. candida is associated with the current level of bioavailable copper. The study is a first step in the development of a molecular strategy aiming at a more comprehensive assessment of various aspects of soil quality and ecotoxicology. PMID:21882881

  20. Optimization, purification, and characterization of L-asparaginase from Actinomycetales bacterium BkSoiiA.

    Science.gov (United States)

    Dash, Chitrangada; Mohapatra, Sukanti Bala; Maiti, Prasanta Kumar

    2016-01-01

    Actinobacteria are promising source of a wide range of important enzymes, some of which are produced in industrial scale, with others yet to be harnessed. L-Asparaginase is used as an antineoplastic agent. The present work deals with the production and optimization of L-asparaginase from Actinomycetales bacterium BkSoiiA using submerged fermentation in M9 medium. Production optimization resulted in a modified M9 medium with yeast extract and fructose as carbon and nitrogen sources, respectively, at pH 8.0, incubated for 120 hr at 30 ± 2 °C. The crude enzyme was purified to near homogeneity by ammonium sulfate precipitation following dialysis, ion-exchange column chromatography, and finally gel filtration. The sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) revealed an apparent molecular weight of 57 kD. The enzyme was purified 95.06-fold and showed a final specific activity of 204.37 U/mg with 3.49% yield. The purified enzyme showed maximum activity at a pH 10.0 and was stable at pH 7.0 to 9.0. The enzyme was activated by Mn(2+) and strongly inhibited by Ba(2+). All these preliminary characterization suggests that the L-asparaginase from the source may be a tool useful to pharmaceutical industries after further research.

  1. Absence of Cospeciation between the Uncultured Frankia Microsymbionts and the Disjunct Actinorhizal Coriaria Species

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    Imen Nouioui

    2014-01-01

    Full Text Available Coriaria is an actinorhizal plant that forms root nodules in symbiosis with nitrogen-fixing actinobacteria of the genus Frankia. This symbiotic association has drawn interest because of the disjunct geographical distribution of Coriaria in four separate areas of the world and in the context of evolutionary relationships between host plants and their uncultured microsymbionts. The evolution of Frankia-Coriaria symbioses was examined from a phylogenetic viewpoint using multiple genetic markers in both bacteria and host-plant partners. Total DNA extracted from root nodules collected from five species: C. myrtifolia, C. arborea, C. nepalensis, C. japonica, and C. microphylla, growing in the Mediterranean area (Morocco and France, New Zealand, Pakistan, Japan, and Mexico, respectively, was used to amplify glnA gene (glutamine synthetase, dnaA gene (chromosome replication initiator, and the nif DK IGS (intergenic spacer between nifD and nifK genes in Frankia and the matK gene (chloroplast-encoded maturase K and the intergenic transcribed spacers (18S rRNA-ITS1-5.8S rRNA-ITS2-28S rRNA in Coriaria species. Phylogenetic reconstruction indicated that the radiations of Frankia strains and Coriaria species are not congruent. The lack of cospeciation between the two symbiotic partners may be explained by host shift at high taxonomic rank together with wind dispersal and/or survival in nonhost rhizosphere.

  2. An initial investigation into the ecology of culturable aerobic postmortem bacteria.

    Science.gov (United States)

    Chun, Lauren P; Miguel, Marcus J; Junkins, Emily N; Forbes, Shari L; Carter, David O

    2015-12-01

    Postmortem microorganisms are increasingly recognized for their potential to serve as physical evidence. Yet, we still understand little about the ecology of postmortem microbes, particularly those associated with the skin and larval masses. We conducted an experiment to characterize microbiological and chemical properties of decomposing swine (Sus scrofa domesticus) carcasses on the island of Oahu, Hawaii, USA, during June 2013. Bacteria were collected from the head, limb, and larval mass during the initial 145h of decomposition. We also measured the pH, temperature, and oxidation-reduction potential of larval masses in situ. Bacteria were cultured aerobically on Standard Nutrient Agar at 22°C and identified using protein or genetic signals. Carcass decomposition followed a typical sigmoidal pattern and associated bacterial communities differed by sampling location and time since death, although all communities were dominated by phyla Actinobacteria, Firmicutes, and Proteobacteria. Larval masses were reducing environments (~-200mV) of neutral pH (6.5-7.5) and high temperature (35°C-40°C). We recommend that culturable postmortem and larval mass microbiology and chemistry be investigated in more detail, as it has potential to complement culture-independent studies and serve as a rapid estimate of PMI. PMID:26654073

  3. Post-translational modification of PII signal transduction proteins

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    Mike eMerrick

    2015-01-01

    Full Text Available The PII proteins constitute one of the most widely distributed families of signal transduction proteins in nature. They are pivotal players in the control of nitrogen metabolism in bacteria and archaea, and are also found in the plastids of plants. Quite remarkably PII proteins control the activities of a diverse range of enzymes, transcription factors and membrane transport proteins, and in all known cases they achieve their regulatory effect by direct interaction with their target. PII proteins in the Proteobacteria and the Actinobacteria are subject to post-translational modification by uridylylation or adenylylation respectively, whilst in some Cyanobacteria they can be modified by phosphorylation. In all these cases the protein’s modification state is influenced by the cellular nitrogen status and is thought to regulate its activity. However in many organisms there is no evidence for modification of PII proteins and indeed the ability of these proteins to respond to the cellular nitrogen status is fundamentally independent of post-translational modification. In this review we explore the role of post-translational modification in PII proteins in the light of recent studies.

  4. Characteristics of the LrhA subfamily of transcriptional regulators from Sinorhizobium meliloti

    Institute of Scientific and Technical Information of China (English)

    Mingsheng Qi; Li Luo; Haiping Cheng; Jiabi Zhu; Guanqiao Yu

    2008-01-01

    In our previous work, we identified 94 putative genes encoding LysR-type transcriptional regulators from Sinorhizobium meliloti. All of these putative lysR genes were mutagenized using plasmid insertions to determine their phenotypes. Six LysR-type regulators, encoded by mutants SMa1979, SMb20715, SMc00820, SMc04163, SMc03975,and SMc04315, showed similar amino acid sequences (30%)and shared the conserved DNA-binding domain with LrhA,HexA, or DgdR. Phenotype analysis of these gene mutants indicated that the regulators control the swimming behaviors of the bacteria, production of quorum-sensing signals, and secretion of extracellular proteins. These characteristics are very similar to those of LrhA, HexA, and DgdR.Thus, we refer to this group as the LrhA subfamily. Sequence analysis showed that a great number of homologous genes of the LrhA subfamily were distributed in the α,β, and γsubdivisions of proteobacteria, and a few in actinobacteria. These findings could provide new clues to the roles of the LysR gene family.

  5. [Molecular analysis of the microbial communities of the Dagang Kongdian flooding bed oilfield].

    Science.gov (United States)

    She, Yue-hui; Zhang, Xue-li; Zhang, Fan; Wang, Ling-hua; Zhao, Li-ping

    2005-06-01

    Both PCR-TGGE (temperature gradient gel electrophoresis, TGGE) and 16S rRNA gene clone library construction were used to comparatively analyze the microbial communities of a water injection well (WW) and an oil well (OW) in Dagang oilfield. TGGE analysis of the PCR amplified 16S rDNA V3 region products showed great difference between these two microbial communities. Six major bands were detected in the TGGE profile of the WW sample, while only one predominant band in the OW sample was found. Two 16S rRNA gene clone libraries were also constructed, and 108 and 50 clones were selected from the WW and OW library respectively for amplified ribosomal DNA restriction analysis (ARDRA). 33 taxanomic operational units (OTUs) were found in the WW library with 6 major OTUs, while only 8 OTUs were found in the OW library with one OTU predominant. The results of TGGE and clone library profiling analysis both indicated that microbial community of the WW had higher diversity than the OW. Sequence analysis of the representative clone of each OTU showed that most bacteria of the WW were affiliated with alpha, beta, and gamma Proteobacteria and Actinobacteria, especially Rhodobacter (47%). Most bacteria of the OW were affiliated with alpha, beta, and gamma Proteobacteria, especially Pseudomonas (62%). Molecular analysis of the microbial diversity in oilfield provides foundation for better application of MEOR (Microbial Enhanced Oil Recovery). PMID:15989220

  6. Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet’s Disease

    Science.gov (United States)

    Shimizu, Jun; Kubota, Takao; Takada, Erika; Takai, Kenji; Fujiwara, Naruyoshi; Arimitsu, Nagisa; Ueda, Yuji; Wakisaka, Sueshige; Suzuki, Tomoko; Suzuki, Noboru

    2016-01-01

    Gut microbiota compositional alteration may have an association with immune dysfunction in patients with Behcet’s disease (BD). We conducted a fecal metagenomic analysis of BD patients. We analyzed fecal microbiota obtained from 12 patients with BD and 12 normal individuals by sequencing of 16S ribosomal RNA gene. We compared the relative abundance of bacterial taxa. Direct comparison of the relative abundance of bacterial taxa demonstrated that the genera Bifidobacterium and Eggerthella increased significantly and the genera Megamonas and Prevotella decreased significantly in BD patients compared with normal individuals. A linear discriminant analysis of bacterial taxa showed that the phylum Actinobacteria, including Bifidobacterium, and the family Lactobacillaceae exhibited larger positive effect sizes than other bacteria in patients with BD. The phylum Firmicutes and the class Clostridia had large effect sizes in normal individuals. There was no significant difference in annotated species numbers (as numbers of operational taxonomic unit; OTU) and bacterial diversity of each sample (alpha diversity) between BD patients and normal individuals. We next assigned each sample to a position using three axes by principal coordinates analysis of the OTU table. The two groups had a significant distance as beta diversity in the 3-axis space. Fecal sIgA concentrations increased significantly in BD patients but did not correlate with any bacterial taxonomic abundance. These data suggest that the compositional changes of gut microbes may be one type of dysbiosis (unfavorable microbiota alteration) in patients with BD. The dysbiosis may have an association with the pathophysiology of BD. PMID:27105322

  7. Genetic diversity of bacterial communities and gene transfer agents in northern South China Sea.

    Directory of Open Access Journals (Sweden)

    Fu-Lin Sun

    Full Text Available Pyrosequencing of the 16S ribosomal RNA gene (rDNA amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA major capsid gene (g5 was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS, temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments.

  8. Highly heterogeneous bacterial communities associated with the South China Sea reef corals Porites lutea, Galaxea fascicularis and Acropora millepora.

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    Jie Li

    Full Text Available Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species.

  9. Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential

    Science.gov (United States)

    Al-Amoudi, Soha; Essack, Magbubah; Simões, Marta F.; Bougouffa, Salim; Soloviev, Irina; Archer, John A. C.; Lafi, Feras F.; Bajic, Vladimir B.

    2016-01-01

    Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds. PMID:27626430

  10. Crude oil treatment leads to shift of bacterial communities in soils from the deep active layer and upper permafrost along the China-Russia Crude Oil Pipeline route.

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    Sizhong Yang

    Full Text Available The buried China-Russia Crude Oil Pipeline (CRCOP across the permafrost-associated cold ecosystem in northeastern China carries a risk of contamination to the deep active layers and upper permafrost in case of accidental rupture of the embedded pipeline or migration of oil spills. As many soil microbes are capable of degrading petroleum, knowledge about the intrinsic degraders and the microbial dynamics in the deep subsurface could extend our understanding of the application of in-situ bioremediation. In this study, an experiment was conducted to investigate the bacterial communities in response to simulated contamination to deep soil samples by using 454 pyrosequencing amplicons. The result showed that bacterial diversity was reduced after 8-weeks contamination. A shift in bacterial community composition was apparent in crude oil-amended soils with Proteobacteria (esp. α-subdivision being the dominant phylum, together with Actinobacteria and Firmicutes. The contamination led to enrichment of indigenous bacterial taxa like Novosphingobium, Sphingobium, Caulobacter, Phenylobacterium, Alicylobacillus and Arthrobacter, which are generally capable of degrading polycyclic aromatic hydrocarbons (PAHs. The community shift highlighted the resilience of PAH degraders and their potential for in-situ degradation of crude oil under favorable conditions in the deep soils.

  11. Relationships between soil water repellency and microbial community composition under different plant species in a Mediterranean semiarid forest

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    Lozano Elena

    2014-06-01

    Full Text Available Soil water repellency (SWR can influence many hydrological soil properties, including water infiltration, uneven moisture distribution or water retention. In the current study we investigated how variable SWR persistence in the field is related to the soil microbial community under different plant species (P. halepensis, Q. rotundifolia, C. albidus and R. officinalis in a Mediterranean forest. The soil microbial community was determined through phospholipid fatty acids (PLFA. The relationships between microbiological community structure and the soil properties pH, Glomalin Related Soil Protein (GRSP and soil organic matter (SOM content were also studied. Different statistical analyses were used: Principal Component Analysis (PCA, ANOVA, Redundancy Analysis and Pearson correlations. The highest concentrations of PLFA were found in the most water repellent samples. PCA showed that microorganism composition was more dependent of the severity of SWR than the type of plant species. In the Redundancy Analysis, SWR was the only significant factor (p<0.05 to explain PLFA distributions. The only PLFA biomarkers directly related to SWR were associated with Actinobacteria (10Me16:0, 10Me17:0 and 10Me18:0. All the results suggest that a strong dependence between SWR and microbial community composition.

  12. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    Science.gov (United States)

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS.

  13. Gastric Bypass Surgery Reverses Diabetic Phenotypes in Bdnf-Deficient Mice.

    Science.gov (United States)

    Jiang, Shujun; Wang, Qinghua; Huang, Zan; Song, Anying; Peng, Yu; Hou, Siyuan; Guo, Shiying; Zhu, Weiyun; Yan, Sheng; Lin, Zhaoyu; Gao, Xiang

    2016-08-01

    Duodenum-jejunum gastric bypass (DJB) has been used to treat morbid diabetic patients. However, neither the suitability among patients nor the mechanisms of this surgical treatment is clear. Previously, we reported a new mouse strain named Timo as type 2 diabetes model caused by brain-derived neurotrophic factor (Bdnf) deficiency. In this study, we found that DJB on Timo mice reversed their metabolic abnormalities without altering the expression of Bdnf. Glucose tolerance and insulin sensitivity were improved greatly, along with reduction of fat accumulation in liver and white adipose tissue. The gut flora population was altered by DJB with increased proportion of Firmicutes and decreased Actinobacteria and Proteobacteria in the ileum after surgery. Systemic inflammation in Timo mice was greatly suppressed with less macrophage infiltration and lower tumor necrosis factor-α levels in liver and white adipose tissue after surgery. Interestingly, the alteration of gut microflora abundance and improved metabolism preceded the inflammation alleviation after DJB surgery. These results suggested that DJB can reverse Bdnf deficiency-associated metabolic abnormality. In addition, the reduced inflammation may not be the initial cause for the DJB-associated metabolic and microbiota alterations. The increased BDNF protein levels in hypothalamus and hippocampus may result from microbiota change after DJB surgery. PMID:27418549

  14. Bacterial community composition of anthropogenic biochar and Amazonian anthrosols assessed by 16S rRNA gene 454 pyrosequencing.

    Science.gov (United States)

    Taketani, Rodrigo Gouvêa; Lima, Amanda Barbosa; da Conceição Jesus, Ederson; Teixeira, Wenceslau Geraldes; Tiedje, James M; Tsai, Siu Mui

    2013-08-01

    Biochar (BC) is a common minor constituent of soils and is usually derived from the burning of wood materials. In the case of Amazonian dark earth (ADE) soils, the increased amount of this material is believed to be due to anthropogenic action by ancient indigenous populations. In this study, we use 16S rRNA gene pyrosequencing to assess the bacterial diversity observed in the BC found in ADEs as well as in the dark earth itself and the adjacent Acrisol. Samples were taken from two sites, one cultivated with manioc and one with secondary forest cover. Analyses revealed that the community structure found in each sample had unique features. At a coarse phylogenetic resolution, the most abundant phyla in all sequence libraries were Actinobacteria, Acidobacteria, Verrucomicrobia and Proteobacteria that were present in similar relative abundance across all samples. However, the class composition varied between them highlighting the difference between the Acrisol and the remaining samples. This result was also corroborated by the comparison of the OTU composition (at 97 % identity). Also, soil coverage has shown an effect over the community structure observed in all samples. This pattern was found to be significant through unweighted UniFrac as well as P tests. These results indicate that, although the ADEs are found in patches within the Acrisols, the contrasting characteristics found between them led to the development of significantly different communities. PMID:23743632

  15. Functional symbiosis and communication in microbial ecosystems. The case of wood-eating termites and cockroaches.

    Science.gov (United States)

    Berlanga, Mercedes

    2015-09-01

    Animal hosts typically have strong specificity for microbial symbionts and their functions. The symbiotic relationships have enhanced the limited metabolic networks of most eukaryotes by contributing several prokaryotic metabolic capabilities, such as methanogenesis, chemolithoautotrophy, nitrogen assimilation, etc. This review will examine the characteristics that determine bacterial "fidelity" to certain groups of animals (e.g., xylophagous insects, such as termites and cockroaches) over generations and throughout evolution. The hindgut bacteria of wood-feeding termites and cockroaches belong to several phyla, including Proteobacteria, especially Deltaproteobacteria, Bacteroidetes, Firmicutes, Actinomycetes, Spirochetes, Verrucomicrobia, and Actinobacteria, as detected by 16S rRNA. Termites effectively feed on many types of lignocelluloses assisted by their gut microbial symbionts. Although the community structures differ between the hosts (termites and cockroaches), with changes in the relative abundances of particular bacterial taxa, the composition of the bacterial community could reflect at least in part the host evolution in that the microbiota may derive from the microbiota of a common ancestor. Therefore, factors other than host phylogeny, such as diet could have had strong influence in shaping the bacterial community structure. PMID:27036743

  16. Bacterial Endophytes Isolated from Plants in Natural Oil Seep Soils with Chronic Hydrocarbon Contamination.

    Science.gov (United States)

    Lumactud, Rhea; Shen, Shu Yi; Lau, Mimas; Fulthorpe, Roberta

    2016-01-01

    The bacterial endophytic communities of four plants growing abundantly in soils highly contaminated by hydrocarbons were analyzed through culturable and culture-independent means. Given their tolerance to the high levels of petroleum contamination at our study site, we sought evidence that Achillea millefolium, Solidago canadensis, Trifolium aureum, and Dactylis glomerata support high levels of hydrocarbon degrading endophytes. A total of 190 isolates were isolated from four plant species. The isolates were identified by partial 16S rDNA sequence analysis, with class Actinobacteria as the dominant group in all species except S. canadensis, which was dominated by Gammaproteobacteria. Microbacterium foliorum and Plantibacter flavus were present in all the plants, with M. foliorum showing predominance in D. glomerata and both endophytic bacterial species dominated T. aureum. More than 50% of the isolates demonstrated degradative capabilities for octanol, toluene, naphthalene, kerosene, or motor oil based on sole carbon source growth screens involving the reduction of tetrazolium dye. P. flavus isolates from all the sampled plants showed growth on all the petroleum hydrocarbons (PHCs) substrates tested. Mineralization of toluene and naphthalene was confirmed using gas-chromatography. 16S based terminal restriction fragment length polymorphism analysis revealed significant differences between the endophytic bacterial communities showing them to be plant host specific at this site. To our knowledge, this is the first account of the degradation potential of bacterial endophytes in these commonly occurring pioneer plants that were not previously known as phytoremediating plants. PMID:27252685

  17. Effects of diurnal temperature variation on microbial community and petroleum hydrocarbon biodegradation in contaminated soils from a sub-Arctic site.

    Science.gov (United States)

    Akbari, Ali; Ghoshal, Subhasis

    2015-12-01

    Contaminated soils are subject to diurnal and seasonal temperature variations during on-site ex-situ bioremediation processes. We assessed how diurnal temperature variations similar to that in summer at the site from which petroleum hydrocarbon-contaminated soil was collected affect the soil microbial community and the extent of biodegradation of petroleum hydrocarbons compared with constant temperature regimes. Microbial community analyses for 16S rRNA and alkB genes by pyrosequencing indicated that the microbial community for soils incubated under diurnal temperature variation from 5°C to 15°C (VART5-15) evolved similarly to that for soils incubated at constant temperature of 15°C (CST15). In contrast, under a constant temperature of 5°C (CST5), the community evolved significantly different. The extent of biodegradation of C10-C16 hydrocarbons in the VART5-15 systems was 48%, comparable with the 41% biodegradation in CST15 systems, but significantly higher than CST5 systems at 11%. The enrichment of Gammaproteobacteria was observed in the alkB gene-harbouring communities in VART5-15 and CST15 but not in CST5 systems. However, the Actinobacteria was abundant at all temperature regimes. The results suggest that changes in microbial community composition as a result of diurnal temperature variations can significantly influence petroleum hydrocarbon bioremediation performance in cold regions. PMID:25808640

  18. Common occurrence of antibacterial agents in human intestinal microbiota

    Directory of Open Access Journals (Sweden)

    Fatima eDrissi

    2015-05-01

    Full Text Available Laboratory experiments have revealed many active mechanisms by which bacteria can inhibit the growth of other organisms. Bacteriocins are a diverse group of natural ribosomally-synthesized antimicrobial peptides produced by a wide range of bacteria and which seem to play an important role in mediating competition within bacterial communities. In this study, we have identified and established the structural classification of putative bacteriocins encoded by 317 microbial genomes in the human intestine. On the basis of homologies to available bacteriocin sequences, mainly from lactic acid bacteria, we report the widespread occurrence of bacteriocins across the gut microbiota: 175 bacteriocins were found to be encoded in Firmicutes, 79 in Proteobacteria, 34 in Bacteroidetes and 25 in Actinobacteria. Bacteriocins from gut bacteria displayed wide differences among phyla with regard to class distribution, net positive charge, hydrophobicity and secondary structure, but the α-helix was the most abundant structure. The peptide structures and physiochemical properties of bacteriocins produced by the most abundant bacteria in the gut, the Firmicutes and the Bacteroidetes, seem to ensure low antibiotic activity and participate in permanent intestinal host defence against the proliferation of harmful bacteria. Meanwhile, the potentially harmful bacteria, including the Proteobacteria, displayed highly effective bacteriocins, probably supporting the virulent character of diseases. These findings highlight the eventual role played by bacteriocins in gut microbial competition and their potential place in antibiotic therapy.

  19. A 24.7-kDa copper-containing oxidase, secreted by Thermobifida fusca, significantly increasing the xylanase/cellulase-catalyzed hydrolysis of sugarcane bagasse.

    Science.gov (United States)

    Chen, Cheng-Yu; Hsieh, Zhi-Shen; Cheepudom, Jatuporn; Yang, Chao-Hsun; Meng, Menghsiao

    2013-10-01

    Thermobifida fusca is a moderately thermophilic soil bacterium belonging to Actinobacteria. It has been known for its capability to degrade plant cell wall polymers except lignin and pectin. To know whether it can produce enzymes to facilitate lignin degradation, the extracellular proteins bound to sugarcane bagasse were harvested and identified by liquid chromatography tandem mass spectrometry. Among the identified proteins, a putative copper-containing polyphenol oxidase of 241 amino acids, encoded by the locus Tfu_1114, was thought to presumably play a role in lignin degradation. This protein (Tfu1114) was thus expressed in E. coli and characterized. Similarly to common laccases, Tfu1114 is able to catalyze the oxidation reaction of phenolic and nonphenolic lignin related compounds such as 2,6-dimethoxyphenol and veratryl alcohol. More interestingly, it can significantly enhance the enzymatic hydrolysis of bagasse by xylanase and cellulase. Tfu1114 is stable against heat, with a half-life of 4.7 h at 90 °C, and organic solvents. It is sensitive to ethylenediaminetetraacetic acid and reducing agents but resistant to sodium azide, a potent inhibitor of laccases. Atomic absorption spectroscopy indicated that the ratio of copper to the protein monomer is 1, instead of 4, a feature of classical laccases. All these data suggest that Tfu1114 is a novel oxidase with laccase-like activity, potentially useful in biotechnology application. PMID:23377789

  20. Caenorhabditis elegans responses to bacteria from its natural habitats

    Science.gov (United States)

    Rowedder, Holli; Braendle, Christian; Félix, Marie-Anne; Ruvkun, Gary

    2016-01-01

    Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology. PMID:27317746

  1. High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors.

    Science.gov (United States)

    Janek, Daniela; Zipperer, Alexander; Kulik, Andreas; Krismer, Bernhard; Peschel, Andreas

    2016-08-01

    The human nasal microbiota is highly variable and dynamic often enclosing major pathogens such as Staphylococcus aureus. The potential roles of bacteriocins or other mechanisms allowing certain bacterial clones to prevail in this nutrient-poor habitat have hardly been studied. Of 89 nasal Staphylococcus isolates, unexpectedly, the vast majority (84%) was found to produce antimicrobial substances in particular under habitat-specific stress conditions, such as iron limitation or exposure to hydrogen peroxide. Activity spectra were generally narrow but highly variable with activities against certain nasal members of the Actinobacteria, Proteobacteria, Firmicutes, or several groups of bacteria. Staphylococcus species and many other Firmicutes were insusceptible to most of the compounds. A representative bacteriocin was identified as a nukacin-related peptide whose inactivation reduced the capacity of the producer Staphylococcus epidermidis IVK45 to limit growth of other nasal bacteria. Of note, the bacteriocin genes were found on mobile genetic elements exhibiting signs of extensive horizontal gene transfer and rearrangements. Thus, continuously evolving bacteriocins appear to govern bacterial competition in the human nose and specific bacteriocins may become important agents for eradication of notorious opportunistic pathogens from human microbiota.

  2. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

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    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.

  3. Unearthing microbial diversity of Taxus rhizosphere via MiSeq high-throughput amplicon sequencing and isolate characterization

    Science.gov (United States)

    Hao, Da Cheng; Song, Si Meng; Mu, Jun; Hu, Wen Li; Xiao, Pei Gen

    2016-04-01

    The species variability and potential environmental functions of Taxus rhizosphere microbial community were studied by comparative analyses of 15 16S rRNA and 15 ITS MiSeq sequencing libraries from Taxus rhizospheres in subtropical and temperate regions of China, as well as by isolating laccase-producing strains and polycyclic aromatic hydrocarbon (PAH)-degrading strains. Total reads could be assigned to 2,141 Operational Taxonomic Units (OTUs) belonging to 31 bacteria phyla and 2,904 OTUs of at least seven fungi phyla. The abundance of Planctomycetes, Actinobacteria, and Chloroflexi was higher in T. cuspidata var. nana and T. × media rhizospheres than in T. mairei rhizosphere (NF), while Acidobacteria, Proteobacteria, Nitrospirae, and unclassified bacteria were more abundant in the latter. Ascomycota and Zygomycota were predominant in NF, while two temperate Taxus rhizospheres had more unclassified fungi, Basidiomycota, and Chytridiomycota. The bacterial/fungal community richness and diversity were lower in NF than in other two. Three dye decolorizing fungal isolates were shown to be highly efficient in removing three classes of reactive dye, while two PAH-degrading fungi were able to degrade recalcitrant benzo[a]pyrene. The present studies extend the knowledge pedigree of the microbial diversity populating rhizospheres, and exemplify the method shift in research and development of resource plant rhizosphere.

  4. Teichoic, teichulosonic and teichuronic acids in the cell wall of Brevibacterium aurantiacum VKM Ac-2111(Т).

    Science.gov (United States)

    Shashkov, Alexander S; Potekhina, Natalia V; Senchenkova, Sofya N; Evtushenko, Lyudmila I

    2016-02-01

    Two different teichoic acids, along with a teichulosonic and a teichuronic acids, were identified in the cell wall of Brevibacterium aurantiacum VKM Ac-2111(Т). One teichoic acid is 1,3-poly(glycerol phosphate) with 2-acetamido-2-deoxy-α-D-galactopyranose and L-glutamic acid as non-stoichiometric substituents at O-2 of the glycerol residue. The second one is a poly(glycosylglycerol phosphate) with -4)-α-D-Galp-(1 → 2)-sn-Gro-(3-P- and/or -6)-α-D-Galp-(1 → 2)-sn-Gro-(3-P- units in the main chain. The structure of the first has not been reported so far, while the latter one is new for actinobacteria. The teichulosonic acid with α-3-deoxy-β-D-glycero-D-galacto-non-2-ulopyranosonic acid (Kdn) and β-D-glucopyranose residues in the backbone represents a novel polymer: → 8)-α-Kdn-(2 → 6)-β-D-Glcp-(1 →. The teichuronic acid has also hitherto unknown structure: → 3)-β-D-Galf(2OAc)0.3-(1 → 3)-β-D-GlcpА-(1 → and is found in members of the genus Brevibacterium for the first time. The polymer structures were elucidated using 1D- and 2D-NMR spectroscopy: (1)H,(1)H COSY, TOCSY, ROESY, (1)H,(13)C HSQC, HSQC-TOCSY, and (1)H,(13)C and (1)H,(31)P HMBC. PMID:26765252

  5. PCR-denaturing gradient gel electrophoresis analysis of microbial community in soy-daddawa, a Nigerian fermented soybean (Glycine max (L.) Merr.) condiment.

    Science.gov (United States)

    Ezeokoli, Obinna T; Gupta, Arvind K; Mienie, Charlotte; Popoola, Temitope O S; Bezuidenhout, Cornelius C

    2016-03-01

    Soy-daddawa, a fermented soybean (Glycine max (L.) Merr.) condiment, plays a significant role in the culinary practice of West Africa. It is essential to understand the microbial community of soy-daddawa for a successful starter culture application. This study investigated the microbial community structure of soy-daddawa samples collected from Nigerian markets, by PCR-denaturing gradient gel electrophoresis (DGGE) targeting the V3-V5 region of the 16S rRNA gene of bacteria and internal transcribed spacer 2 (ITS2) region of fungi. Six bacterial and 16 fungal (nine yeasts and seven molds) operational taxonomic units (OTUs)/species were obtained at 97% sequence similarity. Taxonomic assignments revealed that bacterial OTUs belonged to the phyla Firmicutes and Actinobacteria, and included species from the genera Atopostipes, Bacillus, Brevibacterium and Nosocomiicoccus. Densitometric analysis of DGGE image/bands revealed that Bacillus spp. were the dominant OTU/species in terms of population numbers. Fungal OTUs belonged to the phyla Ascomycota and Zygomycota, and included species from the genera, Alternaria, Aspergillus, Candida, Cladosporium, Dokmaia, Issatchenkia, Kodamaea, Lecythophora, Phoma, Pichia, Rhizopus, Saccharomyces and Starmerella. The majority of fungal species have not been previously reported in soy-daddawa. Potential opportunistic human pathogens such as Atopostipes suicloacalis, Candida rugosa, Candida tropicalis, and Kodamaea ohmeri were detected. Variation in soy-daddawa microbial communities amongst samples and presence of potential opportunistic pathogens emphasises the need for starter culture employment and good handling practices in soy-daddawa processing. PMID:26796580

  6. A methodological approach to screen diverse cheese-related bacteria for their ability to produce aroma compounds.

    Science.gov (United States)

    Pogačić, Tomislav; Maillard, Marie-Bernadette; Leclerc, Aurélie; Hervé, Christophe; Chuat, Victoria; Yee, Alyson L; Valence, Florence; Thierry, Anne

    2015-04-01

    Microorganisms play an important role in the development of cheese flavor. The aim of this study was to develop an approach to facilitate screening of various cheese-related bacteria for their ability to produce aroma compounds. We combined i) curd-based slurry medium incubated under conditions mimicking cheese manufacturing and ripening, ii) powerful method of extraction of volatiles, headspace trap, coupled to gas chromatography-mass spectrometry (HS-trap-GC-MS), and iii) metabolomics-based method of data processing using the XCMS package of R software and multivariate analysis. This approach was applied to eleven species: five lactic acid bacteria (Leuconostoc lactis, Lactobacillus sakei, Lactobacillus paracasei, Lactobacillus fermentum, and Lactobacillus helveticus), four actinobacteria (Brachybacterium articum, Brachybacterium tyrofermentans, Brevibacterium aurantiacum, and Microbacterium gubbeenense), Propionibacterium freudenreichii, and Hafnia alvei. All the strains grew, with maximal populations ranging from 7.4 to 9.2 log (CFU/mL). In total, 52 volatile aroma compounds were identified, of which 49 varied significantly in abundance between bacteria. Principal component analysis of volatile profiles differentiated species by their ability to produce ethyl esters (associated with Brachybacteria), sulfur compounds and branched-chain alcohols (H. alvei), branched-chain acids (H. alvei, P. freudenreichii and L. paracasei), diacetyl and related carbonyl compounds (M. gubbeenense and L. paracasei), among others. PMID:25475278

  7. A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan

    Science.gov (United States)

    Pershina, E. V.; Ivanova, E. A.; Nagieva, A. G.; Zhiengaliev, A. T.; Chirak, E. L.; Andronov, E. E.; Sergaliev, N. Kh.

    2016-06-01

    The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.

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

    Science.gov (United States)

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

    2015-12-01

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

  9. Characterization of Bacterial Communities in Deep-Sea Hydrothermal Vents from Three Oceanic Regions.

    Science.gov (United States)

    He, Tianliang; Zhang, Xiaobo

    2016-04-01

    Deep-sea hydrothermal vents are considered to be one of the most spectacular ecosystems on Earth. Microorganisms form the basis of the food chain in vents controlling the vent communities. However, the diversity of bacterial communities in deep-sea hydrothermal vents from different oceans remains largely unknown. In this study, the pyrosequencing of 16S rRNA gene was used to characterize the bacterial communities of the venting sulfide, seawater, and tubeworm trophosome from East Pacific Rise, South Atlantic Ridge, and Southwest Indian Ridge, respectively. A total of 23,767 operational taxonomic units (OTUs) were assigned into 42 different phyla. Although Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant phyla in all vents, differences of bacterial diversity were observed among different vents from three oceanic regions. The sulfides of East Pacific Rise possessed the most diverse bacterial communities. The bacterial diversities of venting seawater were much lower than those of vent sulfides. The symbiotic bacteria of tubeworm Ridgeia piscesae were included in the bacterial community of vent sulfides, suggesting their significant ecological functions as the primary producers in the deep-sea hydrothermal vent ecosystems. Therefore, our study presented a comprehensive view of bacterial communities in deep-sea hydrothermal vents from different oceans. PMID:26626941

  10. Comparison of the rhizosphere bacterial communities of Zigongdongdou soybean and a high-methionine transgenic line of this cultivar.

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    Jingang Liang

    Full Text Available Previous studies have shown that methionine from root exudates affects the rhizosphere bacterial population involved in soil nitrogen fixation. A transgenic line of Zigongdongdou soybean cultivar (ZD91 that expresses Arabidopsis cystathionine γ-synthase resulting in an increased methionine production was examined for its influence to the rhizosphere bacterial population. Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved. In total, 87,267 sequences (approximately 10,908 per sample were analyzed. We found that Acidobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes, Gemmatimonadetes, Firmicutes, and Verrucomicrobia constitute the dominant taxonomic groups in either the ZD91 transgenic line or parental cultivar ZD, and that there was no statistically significant difference in the rhizosphere bacterial community structure between the two cultivars.

  11. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.

    Science.gov (United States)

    Le, Phuong Thi; Makhalanyane, Thulani P; Guerrero, Leandro D; Vikram, Surendra; Van de Peer, Yves; Cowan, Don A

    2016-01-01

    Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes. PMID:27503299

  12. Metagenomic insights into the effects of fructo-oligosaccharides (FOS) on the composition of fecal microbiota in mice.

    Science.gov (United States)

    Mao, Bingyong; Li, Dongyao; Zhao, Jianxin; Liu, Xiaoming; Gu, Zhennan; Chen, Yong Q; Zhang, Hao; Chen, Wei

    2015-01-28

    Fructo-oligosaccharides (FOS) are usually regarded as a type of prebiotic, favorably stimulating the growth of bifidobacteria and lactobacilli. However, they are not the specific substrates for these target species, and other bacteria, such as Streptococcus, Escherichia, and Clostridium, have been shown to be able to utilize FOS. Previous studies have mainly investigated only a few bacteria groups, and few reports analyzed the global effects of FOS on intestinal microbial communities. In this study the effects of FOS on gut bacteria in mice were investigated through a 16S rRNA metagenomic analysis. In the FOS-low group, the abundance of Actinobacteria significantly increased and that of Bacteroidetes decreased after FOS diet (5%) for 3 weeks. In the FOS-high group, Enterococcus was promoted and levels of Bifidobacterium and Olsenella both notably increased after FOS diet (25%) and the microbiota tended to revert to initial structure 2 weeks after FOS treatment ceased. The most striking observation was that Olsenella became a dominant genus comparable with Bifidobacterium after FOS treatment, and one strain of Olsenella, isolated from mice feces, was confirmed, for the first time, to be capable of using FOS. The results indicated that metagenomic analysis was helpful to reveal the FOS effects on the global composition of gut communities and new target for future studies. PMID:25598242

  13. Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina.

    Science.gov (United States)

    Manfredi, Adriana P; Perotti, Nora I; Martínez, María A

    2015-12-01

    The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction. PMID:26370071

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

    Science.gov (United States)

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

    2016-01-01

    Little is known of the bacterial communities associated with the rhizosphere of wild plant species found in natural settings. The rhizosphere bacterial community associated with wild thyme, Thymus zygis L., plants was analyzed using cultivation, the creation of a near-full length 16S rRNA gene clone library and 454 amplicon pyrosequencing. The bacterial community was dominated by Proteobacteria (mostly Alphaproteobacteria and Betaproteobacteria), Actinobacteria, Acidobacteria, and Gemmatimonadetes. Although each approach gave a different perspective of the bacterial community, all classes/subclasses detected in the clone library and the cultured bacteria could be found in the pyrosequencing datasets. However, an exception caused by inconclusive taxonomic identification as a consequence of the short read length of pyrotags together with the detection of singleton sequences which corresponded to bacterial strains cultivated from the same sample highlight limitations and considerations which should be taken into account when analysing and interpreting amplicon datasets. Amplicon pyrosequencing of replicate rhizosphere soil samples taken a year later permit the definition of the core microbiome associated with Thymus zygis plants. Abundant bacterial families and predicted functional profiles of the core microbiome suggest that the main drivers of the bacterial community in the Thymus zygis rhizosphere are related to the nutrients originating from the plant root and to their participation in biogeochemical cycles thereby creating an intricate relationship with this aromatic plant to allow for a feedback ecological benefit. PMID:26741495

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

    Directory of Open Access Journals (Sweden)

    Javier Pascual

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

  16. A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity.

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    Emmanouil Angelakis

    Full Text Available Few studies have tested the small intestine microbiota in humans, where most nutrient digestion and absorption occur. Here, our objective was to examine the duodenal microbiota between obese and normal volunteers using metagenomic techniques.We tested duodenal samples from five obese and five normal volunteers using 16S rDNA V6 pyrosequencing and Illumina MiSeq deep sequencing. The predominant phyla of the duodenal microbiota were Firmicutes and Actinobacteria, whereas Bacteroidetes were absent. Obese individuals had a significant increase in anaerobic genera (p < 0.001 and a higher abundance of genes encoding Acyl-CoA dehydrogenase (p = 0.0018 compared to the control group. Obese individuals also had a reduced abundance of genes encoding sucrose phosphorylase (p = 0.015 and 1,4-alpha-glucan branching enzyme (p = 0.05. Normal weight people had significantly increased FabK (p = 0.027, and the glycerophospholipid metabolism pathway revealed the presence of phospholipase A1 only in the control group (p = 0.05.The duodenal microbiota of obese individuals exhibit alterations in the fatty acid and sucrose breakdown pathways, probably induced by diet imbalance.

  17. Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes.

    Science.gov (United States)

    Aszalós, Júlia Margit; Krett, Gergely; Anda, Dóra; Márialigeti, Károly; Nagy, Balázs; Borsodi, Andrea K

    2016-09-01

    Ojos del Salado, the highest volcano on Earth is surrounded by a special mountain desert with extreme aridity, great daily temperature range, intense solar radiation, and permafrost from 5000 meters above sea level. Several saline lakes and permafrost derived high-altitude lakes can be found in this area, often surrounded by fumaroles and hot springs. The aim of this study was to gain information about the bacterial communities inhabiting the sediment of high-altitude lakes of the Ojos del Salado region located between 3770 and 6500 m. Altogether 11 sediment samples from 4 different altitudes were examined with 16S rRNA gene based denaturing gradient gel electrophoresis and clone libraries. Members of 17 phyla or candidate divisions were detected with the dominance of Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. The bacterial community composition was determined mainly by the altitude of the sampling sites; nevertheless, the extreme aridity and the active volcanism had a strong influence on it. Most of the sequences showed the highest relation to bacterial species or uncultured clones from similar extreme environments. PMID:27315168

  18. Characterization of microbiota composition and presence of selected antibiotic resistance genes in carriage water of ornamental fish.

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    Lenka Gerzova

    Full Text Available International trade with ornamental fish is gradually recognized as an important source of a wide range of different antibiotic resistant bacteria. In this study we therefore characterized the prevalence of selected antibiotic resistance genes in the microbiota found in the carriage water of ornamental fish originating from 3 different continents. Real-time PCR quantification showed that the sul1 gene was present in 11 out of 100 bacteria. tet(A was present in 6 out of 100 bacteria and strA, tet(G, sul2 and aadA were present in 1-2 copies per 100 bacteria. Class I integrons were quite common in carriage water microbiota, however, pyrosequencing showed that only 12 different antibiotic gene cassettes were present in class I integrons. The microbiota characterized by pyrosequencing of the V3/V4 variable region of 16S rRNA genes consisted of Proteobacteria (48%, Bacteroidetes (29.5%, Firmicutes (17.8%, Actinobacteria (2.1% and Fusobacteria (1.6%. Correlation analysis between antibiotic resistance gene prevalence and microbiota composition verified by bacterial culture showed that major reservoirs of sul1 sul2, tet(A, tet(B tet(G, cat, cml, bla, strA, aacA, aph and aadA could be found among Alpha-, Beta- and Gammaproteobacteria with representatives of Enterobacteriaceae, Pseudomonadaceae, Rhizobiaceae and Comamonadaceae being those most positively associated with the tested antibiotic resistance genes.

  19. Co-occurrence of resistance to different antibiotics among aquatic bacteria

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    Voolaid Veiko

    2012-10-01

    Full Text Available Abstract Background Antibiotic resistance is not confined to pathogens, but is also widespread in various natural environments. In nature the microbes producing antibiotic compounds have been around for millions of years. Heavy use of antibiotics in medicine and veterinary practice may lead to the accumulation of resistance genes in microbial populations, followed by a rise in multiresistant bacteria. Results To test the extent of resistance among aquatic bacteria, we have collected 760 isolates resistant to at least one antibiotic. The phylogeny of the isolates covers a wide range of Proteobacteria, Actinobacteria and Bacteroidetes. In order to determine the extent of multiresistance, the isolates were tested on six antibiotics. As the growth rate of the different bacteria was highly variable, the classical medical resistance tests could not be used, and an alternative method considering the full growth curve was developed. In general, the overall resistances to different antibiotics could be explained by random, independent distribution. An exception to this was the resistances against tetracycline and chloramphenicol, which tended to occur in pairs. Conclusions We conclude that there is no massive spread of multiresistance determinants in the studied environment, although some specific cases can be found, awaiting for molecular characterization of the resistance mechanisms.

  20. Antibiotic resistance genes occurrence and bacterial community composition in the Liuxi River

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    Wenguang eXiong

    2014-12-01

    Full Text Available Antibiotic resistance genes (ARGs in the environment have paid great concern due to their health risk. We investigated antibiotics concentrations (tetracyclines, sulfonamides and fluoroquinolones, ARGs abundances (tetracycline, sulfonamide and plasmid-mediated quinolone resistance (PMQR genes, and bacterial community composition in sediment and water samples in the Liuxi River, China. Antibiotics concentrations were determined by ultra-performance liquid chromatography-electrospray tandem mass spectrometry. ARGs abundances were quantified by a culture-independent method. Bacterial community composition was analyzed by metagenomic approach based on Ion Torrent Personal Genome Machine platform. Antibiotics concentrations were at the levels of 1.19 to 622 ug kg-1 in sediment samples and below the limit of detection to 127 ng L-1 in water samples. Relative abundances (ARGs copies/16S rRNA gene copies of detected ARGs were at the range of 10-5 to 10-2. The dominant phyla were Proteobacteria, Bacteroidetes and Verrucomicrobia in sediment samples, and were Proteobacteria, Actinobacteria and Bacteroidetes in water samples. The results indicated that the river environment was contaminated by antibiotics and may be as a reservoir of ARGs. This study provided quantitative data on antibiotics, ARGs and bacterial community composition in the Liuxi River, a geographical location different from the reported studies.

  1. Marine Drugs from Sponge-Microbe Association—A Review

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    Tresa Remya A. Thomas

    2010-04-01

    Full Text Available The subject of this review is the biodiversity of marine sponges and associated microbes which have been reported to produce therapeutically important compounds, along with the contextual information on their geographic distribution. Class Demospongiae and the orders Halichondrida, Poecilosclerida and Dictyoceratida are the richest sources of these compounds. Among the microbial associates, members of the bacterial phylum Actinobacteria and fungal division Ascomycota have been identified to be the dominant producers of therapeutics. Though the number of bacterial associates outnumber the fungal associates, the documented potential of fungi to produce clinically active compounds is currently more important than that of bacteria. Interestingly, production of a few identical compounds by entirely different host-microbial associations has been detected in both terrestrial and marine environments. In the Demospongiae, microbial association is highly specific and so to the production of compounds. Besides, persistent production of bioactive compounds has also been encountered in highly specific host-symbiont associations. Though spatial and temporal variations are known to have a marked effect on the quality and quantity of bioactive compounds, only a few studies have covered these dimensions. The need to augment production of these compounds through tissue culture and mariculture has also been stressed. The reviewed database of these compounds is available at www.niobioinformatics.in/drug.php.

  2. Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis.

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    Amaro E Trindade-Silva

    Full Text Available The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb. Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

  3. Analysis and characterization of cultivable heavy metal-resistant bacterial endophytes isolated from Cd-hyperaccumulator Solanum nigrum L. and their potential use for phytoremediation.

    Science.gov (United States)

    Luo, Sheng-lian; Chen, Liang; Chen, Jue-liang; Xiao, Xiao; Xu, Tao-ying; Wan, Yong; Rao, Chan; Liu, Cheng-bin; Liu, Yu-tang; Lai, Cui; Zeng, Guang-ming

    2011-11-01

    This study investigates the heavy metal-resistant bacterial endophytes of Cd-hyperaccumulator Solanum nigrum L. grown on a mine tailing by using cultivation-dependent technique. Thirty Cd-tolerant bacterial endophytes were isolated from roots, stems, and leaves of S. nigrum L. and classified by amplified ribosomal DNA-restriction analysis into 18 different types. Phylogenetic analysis based on 16S rDNA sequences showed that these isolates belonged to four groups: Actinobacteria (43%), Proteobacteria (23%), Bacteroidetes (27%) and Firmicutes (7%). All the isolates were then characterized for their plant growth promoting traits as well as their resistances to different heavy metals; and the actual plant growth promotion and colonization ability were also assessed. Four isolates were re-introduced into S. nigrum L. under Cd stress and resulted in Cd phytotoxicity decrease, as dry weights of roots increased from 55% to 143% and dry weights of above-ground from 64% to 100% compared to the uninoculated ones. The total Cd accumulation of inoculated plants increased from 66% to 135% (roots) and from 22% to 64% (above-ground) compared to the uninoculated ones. Our research suggests that bacterial endophytes are a most promising resource and may be the excellent candidates of bio-inoculants for enhancing the phytoremediation efficiency. PMID:21868057

  4. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

    Science.gov (United States)

    Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N.; Berthrong, Sean; Buckley, Daniel H.

    2016-01-01

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes. PMID:27242725

  5. The small 6C RNA of Corynebacterium glutamicum is involved in the SOS response.

    Science.gov (United States)

    Pahlke, Jennifer; Dostálová, Hana; Holátko, Jiří; Degner, Ursula; Bott, Michael; Pátek, Miroslav; Polen, Tino

    2016-09-01

    The 6C RNA family is a class of small RNAs highly conserved in Actinobacteria, including the genera Mycobacterium, Streptomyces and Corynebacterium whose physiological function has not yet been elucidated. We found that strong transcription of the cgb_03605 gene, which encodes 6C RNA in C. glutamicum, was driven by the SigA- and SigB-dependent promoter Pcgb_03605. 6C RNA was detected at high level during exponential growth phase (180 to 240 molcules per cell) which even increased at the entry of the stationary phase. 6C RNA level did not decrease within 240 min after transcription had been stopped with rifampicin, which suggests high 6C RNA stability. The expression of cgb_03605 further increased approximately twofold in the presence of DNA-damaging mitomycin C (MMC) and nearly threefold in the absence of LexA. Deletion of the 6C RNA gene cgb_03605 resulted in a higher sensitivity of C. glutamicum toward MMC and UV radiation. These results indicate that 6C RNA is involved in the DNA damage response. Both 6C RNA level-dependent pausing of cell growth and branched cell morphology in response to MMC suggest that 6C RNA may also be involved in a control of cell division.

  6. Correlation between diet and gut bacteria in a population of young adults.

    Science.gov (United States)

    Mayorga Reyes, Lino; González Vázquez, Raquel; Cruz Arroyo, Schahrasad M; Melendez Avalos, Araceli; Reyes Castillo, Pedro A; Chavaro Pérez, David A; Ramos Terrones, Idalia; Ramos Ibáñez, Norma; Rodríguez Magallanes, Magdalena M; Langella, Philippe; Bermúdez Humarán, Luis; Azaola Espinosa, Alejandro

    2016-06-01

    Dietary habits strongly influence gut microbiota. The aim of this study was to compare and correlated the abundance of Firmicutes and Bacteroidetes phyla, some representative bacteria of these phyla such as Bacteroides thetaiotaomicron, Prevotella, Faecalibacterium prausnitzii, Clostridium leptum and Bifidobacterium longum as a member of Actinobacteria phylum in young adults with their food intake. Faecal samples used came from lean subjects (BMI = 19.83 ± 0.94 kg/m(2)), overweight (BMI = 27.17 ± 0.51 kg/m(2)) and obese (BMI = 41.33 ± 5.25 kg/m(2)). There were significant differences in total studied gut microbiota between the overweight and lean groups. Members of the Firmicutes phylum, and Bifidobacterium longum, were more abundant in the lean group. The results suggest that diet rich in unsaturated fatty acids and fibre promote an abundant population of beneficial bacteria such as B. longum and Bacteroidetes. However, it has been considered that the results may be biased due to the size of the individuals studied; therefore the results could be only valid for the studied population. PMID:27018166

  7. Richness and diversity in dust stormborne biomes at the southeast mediterranean.

    Science.gov (United States)

    Katra, Itzhak; Arotsker, Luba; Krasnov, Helena; Zaritsky, Arieh; Kushmaro, Ariel; Ben-Dov, Eitan

    2014-06-12

    Dust storms include particulate matter that is transported over land and sea with biota that could impact downwind ecosystems. In addition to the physico-chemical compositions, organismal diversities of dust from two storm events in southern Israel, December 2012 (Ev12) and January 2013 (Ev13), were determined by pyro-sequencing using primers universal to 16S and 18S rRNA genes and compared. The bio-assemblages in the collected dust samples were affiliated with scores of different taxa. Distinct patterns of richness and diversity of the two events were influenced by the origins of the air masses: Ev13 was rich with reads affiliated to Betaproteobacteria and Embryophyta, consistent with a European origin. Ev12, originated in north-Africa, contained significantly more of the Actinobacteria and fungi, without conifers. The abundance of bacterial and eukaryotic reads demonstrates dissemination of biological material in dust that may impose health hazards of pathogens and allergens, and influence vegetation migration throughout the world.

  8. Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16S rRNA gene.

    Directory of Open Access Journals (Sweden)

    Marcio C Costa

    Full Text Available The intestinal tract houses one of the richest and most complex microbial populations on the planet, and plays a critical role in health and a wide range of diseases. Limited studies using new sequencing technologies in horses are available. The objective of this study was to characterize the fecal microbiome of healthy horses and to compare the fecal microbiome of healthy horses to that of horses with undifferentiated colitis. A total of 195,748 sequences obtained from 6 healthy horses and 10 horses affected by undifferentiated colitis were analyzed. Firmicutes predominated (68% among healthy horses followed by Bacteroidetes (14% and Proteobacteria (10%. In contrast, Bacteroidetes (40% was the most abundant phylum among horses with colitis, followed by Firmicutes (30% and Proteobacteria (18%. Healthy horses had a significantly higher relative abundance of Actinobacteria and Spirochaetes while horses with colitis had significantly more Fusobacteria. Members of the Clostridia class were more abundant in healthy horses. Members of the Lachnospiraceae family were the most frequently shared among healthy individuals. The species richness reported here indicates the complexity of the equine intestinal microbiome. The predominance of Clostridia demonstrates the importance of this group of bacteria in healthy horses. The marked differences in the microbiome between healthy horses and horses with colitis indicate that colitis may be a disease of gut dysbiosis, rather than one that occurs simply through overgrowth of an individual pathogen.

  9. The lung microbiome in moderate and severe chronic obstructive pulmonary disease.

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    Alexa A Pragman

    Full Text Available Chronic obstructive pulmonary disease (COPD is an inflammatory disorder characterized by incompletely reversible airflow obstruction. Bacterial infection of the lower respiratory tract contributes to approximately 50% of COPD exacerbations. Even during periods of stable lung function, the lung harbors a community of bacteria, termed the microbiome. The role of the lung microbiome in the pathogenesis of COPD remains unknown. The COPD lung microbiome, like the healthy lung microbiome, appears to reflect microaspiration of oral microflora. Here we describe the COPD lung microbiome of 22 patients with Moderate or Severe COPD compared to 10 healthy control patients. The composition of the lung microbiomes was determined using 454 pyrosequencing of 16S rDNA found in bronchoalveolar lavage fluid. Sequences were analyzed using mothur, Ribosomal Database Project, Fast UniFrac, and Metastats. Our results showed a significant increase in microbial diversity with the development of COPD. The main phyla in all samples were Actinobacteria, Firmicutes, and Proteobacteria. Principal coordinate analyses demonstrated separation of control and COPD samples, but samples did not cluster based on disease severity. However, samples did cluster based on the use of inhaled corticosteroids and inhaled bronchodilators. Metastats analyses demonstrated an increased abundance of several oral bacteria in COPD samples.

  10. Diversity analysis of streptomycetes and associated phosphotranspherase genes in soil.

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    Paris Laskaris

    Full Text Available An attempt was made to verify the observation that Streptomyces griseus was prevalent in soil based on isolation work. A genus-specific PCR was developed for Streptomyces based on the housekeeping gene atpD and used to investigate species diversity within selected soils. The presence of S. griseus was investigated to determine coexistence of resistance-only streptomycin phosphotransferase (strA in the same soil as streptomycin producers. Two additional PCR-based assays were developed; one specific for strA in association with production, the other for more diverse strA and other related phosphotranferases. Both the S. griseus atpD and strA genes were below the PCR detection limit in all soils examined. A number of more diverse phosphotransferase genes were amplified, a minority of which may be associated with streptomycin production. We conclude that neither streptomycin producers nor S. griseus are prevalent in the fresh or chitin and starch-amended soils examined (less than 0.1% of soil actinobacteria. One of the soil sites had received plantomycin (active ingredient: streptomycin and diversity studies suggested that this altered the streptomycete populations present in the soil.

  11. Screening of cloud microorganisms isolated at the Puy de Dôme (France) station for the production of biosurfactants

    Science.gov (United States)

    Renard, Pascal; Canet, Isabelle; Sancelme, Martine; Wirgot, Nolwenn; Deguillaume, Laurent; Delort, Anne-Marie

    2016-09-01

    A total of 480 microorganisms collected from 39 clouds sampled at the Puy de Dôme station (alt. 1465 m; 45°46'19'' N, 2°57'52'' E; Massif Central, France) were isolated and identified. This unique collection was screened for biosurfactant (surfactants of microbial origin) production by measuring the surface tension (σ) of the crude extracts, comprising the supernatants of the pure cultures, using the pendant drop technique. The results showed that 41 % of the tested strains were active producers (σ yeast genus (Udeniomyces) from the Basidiomycota phylum (11 %). Some Bacillus strains from the Firmicutes phylum were also active but represented a small fraction of the collected population. Strains from the Actinobacteria phylum in the collection examined in the present study showed moderate biosurfactant production (45<σ < 55 mN m-1). Pseudomonas (Υ-Proteobacteria), the most frequently detected genus in clouds, with some species issued from the phyllosphere, was the dominant group for the production of biosurfactants. We observed some correlations between the chemical composition of cloud water and the presence of biosurfactant-producing microorganisms, suggesting the "biogeography" of this production. Moreover, the potential impact of the production of biosurfactants by cloud microorganisms on atmospheric processes is discussed.

  12. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge.

    Science.gov (United States)

    Forget, Nathalie L; Kim Juniper, S

    2013-04-01

    We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus-Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.

  13. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge.

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-01-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

  14. Phylogenetic characterization of culturable actinomycetes associated with the mucus of the coral Acropora digitifera from Gulf of Mannar.

    Science.gov (United States)

    Nithyanand, Paramasivam; Manju, Sivalingam; Karutha Pandian, Shunmugiah

    2011-01-01

    The marine environment is a virtually untapped source of novel actinomycete diversity and its metabolites. Investigating the diversity of actinomycetes in other marine macroorganisms, like seaweeds and sponges, have resulted in isolation of novel bioactive metabolites. Actinomycetes diversity associated with corals and their produced metabolites have not yet been explored. Hence, in this study we attempted to characterize the culturable actinomycetes population associated with the coral Acropora digitifera. Actinomycetes were isolated from the mucus of the coral wherein the actinomycetes count was much higher when compared with the surrounding seawater and sediment. Actinobacteria-specific 16S rRNA gene primers were used for identifying the isolates at the molecular level in addition to biochemical tests. Amplified ribosomal DNA restriction analysis using three restriction enzymes revealed several polymorphic groups within the isolates. Sequencing and blast analysis of the isolates revealed that some isolates had only 96.7% similarity with its nearest match in GenBank indicating that they may be novel isolates at the species level. The isolated actinomycetes exhibited good antibacterial activity against various human pathogens. This study offers for the first time a prelude about the unexplored culturable actinomycetes diversity associated with a scleractinian coral and their bioactive capabilities. PMID:21105906

  15. Characterization of culturable bacteria isolated from the cold-water coral Lophelia pertusa.

    Science.gov (United States)

    Galkiewicz, Julia P; Pratte, Zoe A; Gray, Michael A; Kellogg, Christina A

    2011-08-01

    Microorganisms associated with corals are hypothesized to contribute to the function of the host animal by cycling nutrients, breaking down carbon sources, fixing nitrogen, and producing antibiotics. This is the first study to culture and characterize bacteria from Lophelia pertusa, a cold-water coral found in the deep sea, in an effort to understand the roles that the microorganisms play in the coral microbial community. Two sites in the northern Gulf of Mexico were sampled over 2 years. Bacteria were cultured from coral tissue, skeleton, and mucus, identified by 16S rRNA genes, and subjected to biochemical testing. Most isolates were members of the Gammaproteobacteria, although there was one isolate each from the Betaproteobacteria and Actinobacteria. Phylogenetic results showed that both sampling sites shared closely related isolates (e.g. Pseudoalteromonas spp.), indicating possible temporally and geographically stable bacterial-coral associations. The Kirby-Bauer antibiotic susceptibility test was used to separate bacteria to the strain level, with the results showing that isolates that were phylogenetically tightly grouped had varying responses to antibiotics. These results support the conclusion that phylogenetic placement cannot predict strain-level differences and further highlight the need for culture-based experiments to supplement culture-independent studies. PMID:21507025

  16. Safety assessment of dairy microorganisms: Propionibacterium and Bifidobacterium.

    Science.gov (United States)

    Meile, Leo; Le Blay, Gwenaelle; Thierry, Anne

    2008-09-01

    The genera Propionibacterium and Bifidobacterium are clustered in the class Actinobacteria and form the anaerobic branch of coryneform bacteria. The dairy propionibacteria comprising four species P. freudenreichii, P. acidipropionici, P. jensenii and P. thoenii are industrially important as starter cultures in hard-cheese ripening and recently also as protective bio-preservatives and probiotics. These four species are considered as safe whereas cutaneous Propionibacterium species (also named "acnes group") are pathogens. In contrast, bifidobacteria in fermented dairy products and milk powder are exclusively used as probiotics; selected strains of several species (out of more than thirty) contribute to this task. It has been only rarely found that commensal bifidobacteria have been connected with certain dental and other infections. Consequently, only one single species, Bifidobacterium dentium, is recognized as pathogenic. Genome sequence analysis of Bifidobacterium longum and molecular biological analysis of other probiotic strains confirmed so far the absence of virulence and pathogenecity factors. However, tetracycline resistance genes tet(W), although probably not easy transferable, were found in Bifidobacterium strains, also in Bifidobacterium animalis subsp. lactis, the worldwide most used industrial strain. Conclusively, strains from the Propionibacterium and Bifidobacterium species in dairy food generally represent so far no health hazards. PMID:17889391

  17. Optimal growth condition of earthworms and their vermicompost features during recycling of five different fresh fruit and vegetable wastes.

    Science.gov (United States)

    Huang, Kui; Xia, Hui; Li, Fusheng; Wei, Yongfen; Cui, Guangyu; Fu, Xiaoyong; Chen, Xuemin

    2016-07-01

    This study aimed to promote vermicomposting performance for recycling fresh fruit and vegetable wastes (FVWs) and to assess microbial population and community of final products. Five fresh FVWs including banana peels, cabbage, lettuce, potato, and watermelon peels were chosen as earthworms' food. The fate test of earthworms showed that 30 g fresh FVWs/day was the optimal loading and the banana peels was harmful for the survival of Eisenia fetida. The followed vermicomposting test revealed lower contents of total carbon and weaker microbial activity in final vermicomposts, relative to those in compared systems without earthworms worked. The leachate from FVWs carried away great amounts of nutrients from reactors. Additionally, different fresh FVWs displayed dissimilar stabilization process. Molecular biological approaches revealed that earthworms could broaden bacterial diversity in their products, with significant greater populations of actinobacteria and ammonia oxidizing bacteria than in control. This study evidences that vermicomposting efficiency differs with the types and loadings of fresh FVWs and vermicomposts are rich in agricultural probiotics. PMID:27184146

  18. Production and purification of a bioactive substance against multi-drug resistant human pathogens from the marine-sponge-derived Salinispora sp.

    Institute of Scientific and Technical Information of China (English)

    Satyendra Singh; Pritesh Prasad; Ramesh Subramani; William Aalbersberg

    2014-01-01

    Objective: To isolate, purify, characterize, elucidate structure and evaluate bioactive compounds from the sponge-derived Salinispora sp. FS-0034. Methods: The symbiotic actinomycete strain FS-0034 with an interesting bioactivity profile was isolated from the Fijian marine sponge Theonella sp. Based on colony morphology and obligatory requirement of seawater for growth, and mycelia morphological characteristics the isolate FS-0034 was identified as a Salinispora sp. The bioactive compound was identified by using various spectral analysis of ultraviolet, high resolution electrospray ionization mass spectroscopy, 1H nuclear magnetic resonance, correlated spectroscopy and heteronuclear multiple bond coherence spectral data. A minimum inhibitory concentration assay were performed to evaluate the biological properties of the pure compound against multi-drug resistant pathogens. Results: Bioassay guided fractionation of the ethyl acetate extract of the culture of Salinispora sp. FS-0034 by different chromatographic methods yielded the isolation of an antibacterial compound, which was identified as rifamycin W (compound 1). Rifamycin W was reported for its potent antibacterial activity against methicillin-resistant Staphylococcus aureus, wild typeStaphylococcus aureus and vancomycin-resistant Enterococcus faecium and displayed minimum inhibitory concentrations of 15.62, 7.80 and 250.00 µg/mL, respectively. Conclusions:The present study reported the rifamycin W from sponge-associated Salinispora sp. and it exhibited appreciable antibacterial activity against multi-drug resistant human pathogens which indicated that sponge-associated Actinobacteria are significant sources of bioactive metabolites.

  19. Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats.

    Science.gov (United States)

    Han, Hongxing; Xiao, Hailong; Zhang, Kai; Lu, Zhenmei

    2016-01-01

    The impact of 4-epi-oxytetracycline (4-EOTC), one of the main oxytetracycline (OTC) metabolites, on the gut microbiota and physiological metabolism of Wistar rats was analyzed to explore the dynamic alterations apparent after repeated oral exposure (0.5, 5.0 or 50.0 mg/kg bw) for 15 days as shown by 16S rRNA pyrosequencing and UPLC-Q-TOF/MS analysis. Both principal component analysis and cluster analysis showed consistently altered patterns with distinct differences in the treated groups versus the control groups. 4-EOTC treatment at 5.0 or 50.0 mg/kg increased the relative abundance of the Actinobacteria, specifically Bifidobacteriaceae, and improved the synthesis of lysophosphatidylcholine (LysoPC), as shown by the lipid biomarkers LysoPC(16:0), LysoPC(18:3), LysoPC(20:3), and LysoPC(20:4). The metabolomic analysis of urine samples also identified four other decreased metabolites: diacylglycerol, sphingomyelin, triacylglycerol, and phosphatidylglycerol. Notably, the significant changes observed in these biomarkers demonstrated the ongoing disorder induced by 4-EOTC. Blood and urine analysis revealed that residual 4-EOTC accumulated in the rats, even two weeks after oral 4-EOTC administration, ceased. Thus, through thorough analysis, it can be concluded that the alteration of the gut microbiota and disorders in blood metabolomics are correlated with 4-EOTC treatment. PMID:26976662

  20. Spatial heterogeneity in a deep artificial lake plankton community revealed by PCR-DGGE fingerprinting

    Science.gov (United States)

    Li, Qiang; Zhao, Yue; Zhang, Xu; Wei, Yuquan; Qiu, Linlin; Wei, Zimin; Li, Fuheng

    2015-05-01

    To explore the spatial heterogeneity of plankton communities in a deep artificial lake (Songhua Lake, China), samples were collected at seven sites. Samples were investigated by denaturing gradient gel electrophoresis (DGGE) analysis of the PCR-amplified 16S and 18S rRNA genes and specific bands were sequenced. Cluster analysis of the DGGE profiles revealed that all of the samples grouped into two distinct clusters, in accordance with sampling site; while in each cluster, the divergence of sub-clusters correlated with sampling depth. Sequence analysis of selected dominant DGGE bands revealed that most sequenced phylotypes (84%) exhibited ≥97% similarity to the closest sequences in GenBank, and were affiliated with ten common freshwater plankton phyla ( Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Bacillariophyta, Pyrrophyta, Cryptophyta, Ciliophora, Stramenopiles, and Rotifera). Several of these groups are also found worldwide, indicating the cosmopolitan distribution of the phylotypes. The relationships between DGGE patterns and environmental factors were analyzed by redundancy analysis (RDA). The results suggested that, total nitrogen, nitrate, nitrite, ammonia, and CODMn concentrations, and water temperature were strongly correlated with the variation in plankton composition.

  1. Richness and Diversity in Dust Stormborne Biomes at the Southeast Mediterranean

    Science.gov (United States)

    Katra, Itzhak; Arotsker, Luba; Krasnov, Helena; Zaritsky, Arieh; Kushmaro, Ariel; Ben-Dov, Eitan

    2014-06-01

    Dust storms include particulate matter that is transported over land and sea with biota that could impact downwind ecosystems. In addition to the physico-chemical compositions, organismal diversities of dust from two storm events in southern Israel, December 2012 (Ev12) and January 2013 (Ev13), were determined by pyro-sequencing using primers universal to 16S and 18S rRNA genes and compared. The bio-assemblages in the collected dust samples were affiliated with scores of different taxa. Distinct patterns of richness and diversity of the two events were influenced by the origins of the air masses: Ev13 was rich with reads affiliated to Betaproteobacteria and Embryophyta, consistent with a European origin. Ev12, originated in north-Africa, contained significantly more of the Actinobacteria and fungi, without conifers. The abundance of bacterial and eukaryotic reads demonstrates dissemination of biological material in dust that may impose health hazards of pathogens and allergens, and influence vegetation migration throughout the world.

  2. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge

    Science.gov (United States)

    Zhang, Likui; Kang, Manyu; Xu, Jiajun; Xu, Jian; Shuai, Yinjie; Zhou, Xiaojian; Yang, Zhihui; Ma, Kesen

    2016-05-01

    Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents in the Southwest India Ridge using the high-throughput sequencing technology of Illumina MiSeq2500 platform. Based on the V4 region of 16S rRNA gene, sequence analysis showed that bacterial communities in the two samples were dominated by Proteobacteria, followed by Bacteroidetes, Actinobacteria and Firmicutes. Furthermore, archaeal communities in the two samples were dominated by Thaumarchaeota and Euryarchaeota. Comparative analysis showed that (i) TVG4 displayed the higher bacterial richness and lower archaeal richness than TVG11; (ii) the two samples had more divergence in archaeal communities than bacterial communities. Bacteria and archaea that are potentially associated with nitrogen, sulfur metal and methane cycling were detected in the two samples. Overall, we first provided a comparative picture of bacterial and archaeal communities and revealed their potentially ecological roles in the deep-sea environments of inactive hydrothermal vents in the Southwest Indian Ridge, augmenting microbial communities in inactive hydrothermal vents.

  3. 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.

  4. Screening of Marine Actinomycetes from Segara Anakan for Natural Pigment and Hydrolytic Activities

    Science.gov (United States)

    Asnani, A.; Ryandini, D.; Suwandri

    2016-02-01

    Marine actinomycetes have become sources of great interest to natural product chemistry due to their new chemical entities and bioactive metabolites. Since April 2010, we have screened actinobacteria from five sites that represent different ecosystems of Segara Anakan lagoon. In this present study we focus on specific isolates, K-2C which covers 1) actinomycetes identification based on morphology observation and 16S rRNA gene; 2) fermentation and isolation of pigment; 3) structure determination of pigment; and 4) hydrolytic enzymes characterization; Methodologies relevant to the studies were implemented accordingly. The results indicated that K-2C was likely Streptomyces fradiae strain RSU15, and the best fermentation medium should contain starch and casein with 21 days of incubation. The isolate has extracellular as well as intracellular pigments. Isolated pigments gave purple color with λmax of 529.00 nm. The pigment was structurally characterized. Interestingly, Streptomyces K-2C was able to produce potential hydrolytic enzymes such as amylase, cellulase, protease, lipase, urease, and nitrate reductase.

  5. Bacteria that Travel: The Quality of Aircraft Water

    Directory of Open Access Journals (Sweden)

    Harald Handschuh

    2015-10-01

    Full Text Available The travelling population is increasing globally year on year. International tourist arrival figures reached 1087 million in 2013 and 1133 million in 2014; of which 53% and 54% respectively accounted for air transport. The water on board aircraft is sourced from surface or ground water; piped to a central filling point and distributed to each aircraft by water service vehicles at the home base or at the destination airport. The purpose of this study was to ascertain the microbial, chemical (pH; Total and Free chlorine and physical (temperature quality of water from two aircraft, long- and short-haul, as well as from the original water source and the water service vehicle. A total of 154 water samples were collected and analysed. Long-haul flights were found to be significantly poorer in terms of microbial quality than short haul flights (p = 0.015. Furthermore, correlation and regression analysis showed that the water service vehicle was a significant source of increased microbial load in aircraft. Microbial diversity was also demonstrated, with 37 bacterial species identified belonging to eight classes: γ-Proteobacteria; β-Proteobacteria; α-Proteobacteria; Bacilli; Actinobacteria; Flavobacteria; Sphingobacteria and Cytophaga; using phenotypic and 16S rDNA sequence-based analysis. We present a novel quantified study of aircraft-related potable water supplies.

  6. Predominant bacteria associated with red snapper from the Northern Gulf of Mexico.

    Science.gov (United States)

    Arias, Covadonga R; Koenders, Kevin; Larsen, Andrea M

    2013-12-01

    Since the Deepwater Horizon oil spill in 2010, anecdotal observations of Red Snapper Lutjanus campechanus from the northern Gulf of Mexico exhibiting unusual external lesions have been reported. Two opportunistic bacterial fish pathogens, Vibrio vulnificus and Photobacterium damselae, were recovered from the fish and were deemed responsible for the abnormalities. However, the culturable microbiota of healthy Red Snapper has not yet been characterized. We analyzed the heterotrophic bacteria associated with healthy Red Snapper caught off the Louisiana coast. In total, 179 isolates from 60 fish were recovered from skin and mucus, and 43 isolates were obtained from anterior kidney. All isolates were identified by 16S ribosomal RNA gene sequencing. The Proteobacteria was the predominant phylum in both external and internal samples, followed by the Firmicutes and the Actinobacteria. Within the Proteobacteria, most isolates were members of the genera Vibrio and Photobacterium, and V. natriegens and P. damselae were the predominant species. The results of this study suggest that both Vibrio spp. and Photobacterium spp. are associated with the normal microbiota of healthy Red Snapper. Thus, the opportunistic fish pathogens recovered in previous studies cannot be deemed lesion-forming until Koch's postulates are fulfilled.

  7. [Characterization of the Structure of the Prokaryotic Complex of Antarctic Permafrost by Molecular Genetic Techniques].

    Science.gov (United States)

    Manucharova, N A; Trosheva, E V; Kol'tsova, E M; Demkina, E V; Karaevskaya, E V; Rivkina, E M; Mardanov, A V; El'-Registan, G I

    2016-01-01

    A prokaryotic mesophilic organotrophic community responsible for 10% of the total microbial number determined by epifluorescence microscopy was reactivated in the samples ofAntarctic permafrost retrieved from the environment favoring long-term preservation of microbial communities (7500 years). No culturable forms were obtained without resuscitation procedures (CFU = 0). Proteobacteria, Actinobacteria, and Firmicutes were the dominant microbial groups in the complex. Initiation of the reactivated microbial complex by addition of chitin (0.1% wt/vol) resulted in an increased share of metabolically active biomass (up to 50%) due to the functional domination of chitinolytics caused by the target resource. Thus, sequential application of resuscitation procedures and initiation of a specific physiological group (in this case, chitinolytics) to a permafrost-preserved microbial community made it possible to reveal a prokaryotic complex capable of reversion of metabolic activity (FISH data), to determine its phylogenetic structure by metagenomic anal-ysis, and to isolate a pure culture of the dominant microorganism with high chitinolytic activity. PMID:27301132

  8. First microbiota assessments of children's paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis.

    Science.gov (United States)

    Sawabe, Toko; Suda, Wataru; Ohshima, Kenshiro; Hattori, Masahira; Sawabe, Tomoo

    2016-01-01

    Insufficient chloric sterilization of children's paddling pool waters increases the risk of diarrheal illness. Therefore, we investigated the microbiota changes after children use pools. First, we applied 16S rRNA gene-based metagenome analysis to understand the dynamics of microbiota in pool water, especially with respect to the bio-contamination by potential pathogens. Proteobacteria were major taxa detected in every pool water sample after children spent time in the pool. In more detail, Gammaproteobacteria comprised the dominant class, which was followed by Betaproteobacteria. Five phyla, Bacteroidetes, Firmicutes, Actinobacteria and Deinococcus-Thermus phyla were minor groups. The pool water microbiota are likely to be a consortium of intestinal and skin microbiota from humans. Interestingly, the ratio of Gammaproteobacteria and Betaproteobacteria differed according to the age of the children who used the pool, which means the pool water was additionally contaminated by soil microbiota as a result of the children's behavior. Furthermore, potential pathogens, such as Campylobacter spp., Comamonas testosteroni and Burkholderia pseudomallei, were also found. Considering the standard plate counts, the abundances of these human pathogens are unlikely to be a sufficiently infectious dose. We suggest the importance of sanitary measures in paddling pool waters to reduce bio-contamination from both humans and the environment. PMID:26671497

  9. Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India.

    Science.gov (United States)

    Rao, Subramanya; Chan, Yuki; Bugler-Lacap, Donnabella C; Bhatnagar, Ashish; Bhatnagar, Monica; Pointing, Stephen B

    2016-03-01

    A culture-independent diversity assessment of archaea, bacteria and fungi in the Thar Desert in India was made. Six locations in Ajmer, Jaisalmer, Jaipur and Jodhupur included semi-arid soils, arid soils, arid sand dunes, plus arid cryptoendolithic substrates. A real-time quantitative PCR approach revealed that bacteria dominated soils and cryptoendoliths, whilst fungi dominated sand dunes. The archaea formed a minor component of all communities. Comparison of rRNA-defined community structure revealed that substrate and climate rather than location were the most parsimonious predictors. Sequence-based identification of 1240 phylotypes revealed that most taxa were common desert microorganisms. Semi-arid soils were dominated by actinobacteria and alpha proteobacteria, arid soils by chloroflexi and alpha proteobacteria, sand dunes by ascomycete fungi and cryptoendoliths by cyanobacteria. Climatic variables that best explained this distribution were mean annual rainfall and maximum annual temperature. Substrate variables that contributed most to observed diversity patterns were conductivity, soluble salts, Ca(2+) and pH. This represents an important addition to the inventory of desert microbiota, novel insight into the abiotic drivers of community assembly, and the first report of biodiversity in a monsoon desert system. PMID:26843695

  10. Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection.

    Science.gov (United States)

    Niu, Qiuhong; Zhang, Lin; Zhang, Keqin; Huang, Xiaowei; Hui, Fengli; Kan, Yunchao; Yao, Lunguang

    2016-01-01

    The effect of pathogenic bacteria on a host and its symbiotic microbiota is vital and widespread in the biotic world. The soil-dwelling opportunistic bacterium Bacillus nematocida B16 uses a "Trojan horse" mechanism to kill Caenorhabditis elegans. The alterations in the intestinal microflora that occur after B16 infection remain unknown. Here, we analyzed the intestinal bacteria presented in normal and infected worms. The gut microbial community experienced a complex change after B16 inoculation, as determined through marked differences in species diversity, structure, distribution and composition between uninfected and infected worms. Regardless of the worm's origin (i.e., from soil or rotten fruits), the diversity of the intestinal microbiome decreased after infection. Firmicutes increased sharply, whereas Proteobacteria, Actinobacteria, Cyanobacteria and Acidobacteria decreased to different degrees. Fusobacteria was only present 12 h post-infection. After 24 h of infection, 1228 and 1109 bacterial species were identified in the uninfected and infected groups, respectively. The shared species reached 21.97%. The infected group had a greater number of Bacillus species but a smaller number of Pediococcus, Halomonas, Escherichia and Shewanella species (P microbiota using C. elegans as the model species. PMID:26830015

  11. Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula angustifolia Mill

    Directory of Open Access Journals (Sweden)

    Giovanni Emiliani

    2014-01-01

    Full Text Available Endophytic bacteria play a crucial role in plant life and are also drawing much attention for their capacity to produce bioactive compounds of relevant biotechnological interest. Here we present the characterisation of the cultivable endophytic bacteria of Lavandula angustifolia Mill.—a species used since antiquity for its therapeutic properties—since the production of bioactive metabolites from medical plants may reside also in the activity of bacterial endophytes through their direct production, PGPR activity on host, and/or elicitation of plant metabolism. Lavender tissues are inhabited by a tissue specific endophytic community dominated by Proteobacteria, highlighting also their difference from the rhizosphere environment where Actinobacteria and Firmicutes are also found. Leaves’ endophytic community resulted as the most diverse from the other ecological niches. Overall, the findings reported here suggest: (i the existence of different entry points for the endophytic community, (ii its differentiation on the basis of the ecological niche variability, and (iii a two-step colonization process for roots endophytes. Lastly, many isolates showed a strong inhibition potential against human pathogens and the molecular characterization demonstrated also the presence of not previously described isolates that may constitute a reservoir of bioactive compounds relevant in the field of pathogen control, phytoremediation, and human health.

  12. Identification of soil bacteria able to degrade phenanthrene bound to a hydrophobic sorbent in situ

    International Nuclear Information System (INIS)

    Efficient bioremediation of PAH-contaminated sites is limited by the hydrophobic character and poor bioavailability of pollutants. In this study, stable isotope probing (SIP) was implemented to track bacteria that can degrade PAHs adsorbed on hydrophobic sorbents. Temperate and tropical soils were incubated with 13C-labeled phenanthrene, supplied by spiking or coated onto membranes. Phenanthrene mineralization was faster in microcosms with PAH-coated membranes than in microcosms containing spiked soil. Upon incubation with temperate soil, phenanthrene degraders found in the biofilms that formed on coated membranes were mainly identified as Sphingomonadaceae and Actinobacteria. In the tropical soil, uncultured Rhodocyclaceae dominated degraders bound to membranes. Accordingly, ring-hydroxylating dioxygenase sequences recovered from this soil matched PAH-specific dioxygenase genes recently found in Rhodocyclaceae. Hence, our SIP approach allowed the detection of novel degraders, mostly uncultured, which differ from those detected after soil spiking, but might play a key role in the bioremediation of PAH-polluted soils. -- Highlights: •Soil bacteria with the ability to degrade sorbent-bound PAHs were investigated. •In soil, membrane-bound phenanthrene was readily mineralized. •PAH degraders found in biofilms were different in temperate and tropical soils. •Uncultured Rhodocyclaceae were dominant phenanthrene degraders in the tropical soil. •PAH-specific ring-hydroxylating dioxygenase sequences were identified in soil DNA. -- Bacteria able to degrade PAHs bound to a hydrophobic sorbent were mainly identified as uncultured Rhodocyclaceae and Sphingomonadaceae in polluted soils from tropical and temperate area, respectively

  13. A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves.

    Science.gov (United States)

    Thompson, Claudia Elizabeth; Beys-da-Silva, Walter Orlando; Santi, Lucélia; Berger, Markus; Vainstein, Marilene Henning; Guima Rães, Jorge Almeida; Vasconcelos, Ana Tereza Ribeiro

    2013-01-01

    The mangroves are among the most productive and biologically important environments. The possible presence of cellulolytic enzymes and microorganisms useful for biomass degradation as well as taxonomic and functional aspects of two Brazilian mangroves were evaluated using cultivation and metagenomic approaches. From a total of 296 microorganisms with visual differences in colony morphology and growth (including bacteria, yeast and filamentous fungus), 179 (60.5%) and 117 (39.5%) were isolated from the Rio de Janeiro (RJ) and Bahia (BA) samples, respectively. RJ metagenome showed the higher number of microbial isolates, which is consistent with its most conserved state and higher diversity. The metagenomic sequencing data showed similar predominant bacterial phyla in the BA and RJ mangroves with an abundance of Proteobacteria (57.8% and 44.6%), Firmicutes (11% and 12.3%) and Actinobacteria (8.4% and 7.5%). A higher number of enzymes involved in the degradation of polycyclic aromatic compounds were found in the BA mangrove. Specific sequences involved in the cellulolytic degradation, belonging to cellulases, hemicellulases, carbohydrate binding domains, dockerins and cohesins were identified, and it was possible to isolate cultivable fungi and bacteria related to biomass decomposition and with potential applications for the production of biofuels. These results showed that the mangroves possess all fundamental molecular tools required for building the cellulosome, which is required for the efficient degradation of cellulose material and sugar release.

  14. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest.

    Science.gov (United States)

    Kembel, Steven W; O'Connor, Timothy K; Arnold, Holly K; Hubbell, Stephen P; Wright, S Joseph; Green, Jessica L

    2014-09-23

    The phyllosphere--the aerial surfaces of plants, including leaves--is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density-growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant-microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function.

  15. Influence of temperature on the characteristics of aerobic granulation in sequencing batch airlift reactors

    Institute of Scientific and Technical Information of China (English)

    SONG Zhiwei; REN Nanqi; ZHANG Kun; TONG Longyan

    2009-01-01

    Aerobic granular sludge were cultivated in sequencing batch airlift reactors (SBAR) at 25, 30 and 35℃,respectively. The effects of temperature on the granules characteristics were analyzed and the microbial community structures of the granules were probed using scanning electron micrograph (SEM) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The results showed that 30℃ is optimum for matured granules cultivated, where the granules had more compact structure, better settling ability and higher bioactivity, the OUR reached to 1.14 mg O2/(g MLVSS·min) with 97% removal rate of COD and 75% removal rate of TP, and the removal efficiency of NH3-N increased along with the temperature rising in the range of 68.5%-87.5%. DGGE profiles revealed that microbial community structure at 25℃ showed the lowest similarity with others, the sequencing results indicated that most of dominant microbes belonged to Actinobacteria and Proteobacterium. Thermomonas sp., Ottowia sp. and Curtobacterium ammoniigenes may act important roles respectively at different temperature.

  16. Microbial communities from different types of natural wastewater treatment systems: vertical and horizontal flow constructed wetlands and biofilters.

    Science.gov (United States)

    Adrados, B; Sánchez, O; Arias, C A; Becares, E; Garrido, L; Mas, J; Brix, H; Morató, J

    2014-05-15

    The prokaryotic microbial communities (Bacteria and Archaea) of three different systems operating in Denmark for the treatment of domestic wastewater (horizontal flow constructed wetlands (HFCW), vertical flow constructed wetlands (VFCW) and biofilters (BF)) was analysed using endpoint PCR followed by Denaturing Gradient Gel Electrophoresis (DGGE). Further sequencing of the most representative bacterial bands revealed that diverse and distinct bacterial communities were found in each system unit, being γ-Proteobacteria and Bacteroidetes present mainly in all of them, while Firmicutes was observed in HFCW and BF. Members of the Actinobacteria group, although found in HFCW and VFCW, seemed to be more abundant in BF units. Finally, some representatives of α, β and δ-Proteobacteria, Acidobacteria and Chloroflexi were also retrieved from some samples. On the other hand, a lower archaeal diversity was found in comparison with the bacterial population. Cluster analysis of the DGGE bacterial band patterns showed that community structure was related to the design of the treatment system and the organic matter load, while no clear relation was established between the microbial assemblage and the wastewater influent.

  17. Isolation and characterization of facultative mixotrophic ammonia-oxidizing bacteria from constructed wetlands

    Institute of Scientific and Technical Information of China (English)

    Soulwène Kouki; Neila Saidi; Fadhel M'hiri; Houda Nasr; Hanène Cherif; Hadda Ouzari; Abdermaceur Hassen

    2011-01-01

    Autotrophic ammonia-oxidizing bacteria (AOB) have been widely studied in constructed wetlands systems,while mixotrophic AOB have been less thoroughly examined.Heterotrophic bacteria were isolated from wastewater and rhizospheres of macrophytes of constructed wetlands,and then cultivated in a mixotrophic medium containing ammonium and acetic acid.A molecular characterization was accomplished using ITS-PCR amplification,and phylogenetic analysis based on 16S rRNA gene sequences.Results showed the presence of 35 bacteria,among 400 initially heterotrophic isolates,that were able to remove ammonia.These 35 isolates were classified into 10 genetically different groups based on ITS pattern.Then,a collection of 10 isolates were selected because of their relatively high ammonia removal efficiencies (ARE ≥ 80%) and their phylogenetic diversity.In conditions of mixotrophy,these strains were shown to be able to grow (increase of optical density OD660 during incubation with assimilation of nitrogen into cellular biomass) and to oxidize ammonia (important ammonia oxidation efficiencies,AOE between 79% and 87%).Among these facultative mixotrophic AOB,four isolates were genetically related to Firmicutes (Bacillus and Exiguobacterium),three isolates were affiliated to Actinobacteria (Arthrobacter) and three other isolates were associated with Proteobacteria (Pseudomonas,Ochrobactrum and Bordetella).

  18. Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area.

    Science.gov (United States)

    Hu, Jinxiang; Yang, Hui; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    Soil nutrients and microbial communities are the two key factors in revegetation of barren environments. Ecological stoichiometry plays an important role in ecosystem function and limitation, but the relationships between above- and belowground stoichiometry and the bacterial communities in a typical karst region are poorly understood. We used pepino (Solanum muricatum) to examine the stoichiometric traits between soil and foliage, and determine diversity and abundance of bacteria in the karst soil. The soil had a relatively high pH, low fertility, and coarse texture. Foliar N:P ratio and the correlations with soil nitrogen and phosphorus suggested nitrogen limitation. The planting of pepino increased soil urease activity and decreased catalase activity. Higher diversity of bacteria was determined in the pepino rhizosphere than bulk soil using a next-generation, Illumina-based sequencing approach. Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in all samples, accounting for more than 80% of the reads. On a genus level, all 625 detected genera were found in all rhizosphere and bulk soils, and 63 genera showed significant differences among samples. Higher Shannon and Chao 1 indices in the rhizosphere than bulk soil indicated that planting of pepino increased diversity and abundance of bacterial communities in karst area. PMID:26902649

  19. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    Science.gov (United States)

    Newman, Molli M; Hoilett, Nigel; Lorenz, Nicola; Dick, Richard P; Liles, Mark R; Ramsier, Cliff; Kloepper, Joseph W

    2016-02-01

    Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.

  20. Feruloylated Oligosaccharides from Maize Bran Modulated the Gut Microbiota in Rats.

    Science.gov (United States)

    Ou, Juan-Ying; Huang, Jun-Qing; Song, Yuan; Yao, Sheng-Wen; Peng, Xi-Chun; Wang, Ming-Fu; Ou, Shi-Yi

    2016-06-01

    Corn bran is a byproduct produced from corn milling; it is rich in ferulic acid and hemicellulose. In this research, the effects of feruloylated oligosaccharides (FOs) from maize bran on the microbial diversity and profiles in rat feces were investigated through 16S rRNA sequencing. FOs significantly increased bacterial richness and diversity compared with the control and xylooligosaccharides (XOS) alone. In comparison with the control group and the group administrated with XOS, FOs orally administered at 300 mg/kg increased OTU in feces by 57.0 and 24.8 %, and Chao value by 93.4 and 37.6 %, respectively. FOs also influenced obesity- and diabetes-associated bacteria. Oral administration of FOs at 300 mg/kg decreased the ratio of Firmicutes to Bacteroidetes from 477.7:1 to 55.1:1; greatly increased the reads of bacteria that were previously found resistant against diabetes in rats, such as Actinobacteria, Bacteroides, and Lactobacillus; whereas decreased diabetes-prone bacteria, such as Clostridium and Firmicutes. PMID:27165128

  1. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis.

    Science.gov (United States)

    Manuse, Sylvie; Fleurie, Aurore; Zucchini, Laure; Lesterlin, Christian; Grangeasse, Christophe

    2016-01-01

    Bacteria possess a repertoire of versatile protein kinases modulating diverse aspects of their physiology by phosphorylating proteins on various amino acids including histidine, cysteine, aspartic acid, arginine, serine, threonine and tyrosine. One class of membrane serine/threonine protein kinases possesses a catalytic domain sharing a common fold with eukaryotic protein kinases and an extracellular mosaic domain found in bacteria only, named PASTA for 'Penicillin binding proteins And Serine/Threonine kinase Associated'. Over the last decade, evidence has been accumulating that these protein kinases are involved in cell division, morphogenesis and developmental processes in Firmicutes and Actinobacteria. However, observations differ from one species to another suggesting that a general mechanism of activation of their kinase activity is unlikely and that species-specific regulation of cell division is at play. In this review, we survey the latest research on the structural aspects and the cellular functions of bacterial serine/threonine kinases with PASTA motifs to illustrate the diversity of the regulatory mechanisms controlling bacterial cell division and morphogenesis.

  2. Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash.

    Science.gov (United States)

    Joa, Jae Ho; Weon, Hang Yeon; Hyun, Hae Nam; Jeun, Young Chull; Koh, Sang Wook

    2014-12-01

    This study was conducted to assess bacterial species richness, diversity and community distribution according to different fertilization regimes for 16 years in citrus orchard soil of volcanic ash. Soil samples were collected and analyzed from Compost (cattle manure, 2,000 kg/10a), 1/2 NPK+compost (14-20-14+2,000 kg/10a), NPK+compost (28-40-28+2,000 kg/10a), NPK (28-40-28 kg/10a), 3 NPK (84-120-84 kg/10a), and Control (no fertilization) plot which have been managed in the same manners with compost and different amount of chemical fertilization. The range of pyrosequencing reads and OTUs were 4,687-7,330 and 1,790-3,695, respectively. Species richness estimates such as Ace, Chao1, and Shannon index were higher in 1/2 NPK+compost than other treatments, which were 15,202, 9,112, 7.7, respectively. Dominant bacterial groups at level of phylum were Proteobacteria, Acidobacteria, and Actinobacteria. Those were occupied at 70.9% in 1/2 NPK+compost. Dominant bacterial groups at level of genus were Pseudolabrys, Bradyrhizobium, and Acidobacteria. Those were distributed at 14.4% of a total of bacteria in Compost. Soil pH displayed significantly closely related to bacterial species richness estimates such as Ace, Chao1 (pfertilization management, soil pH changes and characteristics of volcanic ash. PMID:25467117

  3. Cellulose degrading bacteria isolated from industrial samples and the gut of native insects from Northwest of Argentina.

    Science.gov (United States)

    Manfredi, Adriana P; Perotti, Nora I; Martínez, María A

    2015-12-01

    The raw materials used to produce bioethanol mostly are food crops, which has led to conflicts on food security. It is, therefore, recommended the gradual replacement for second generation substrates such as lignocellulosic materials. Herein, cellulolytic bacteria were isolated from the gut content of native larvae from Lepidoptera, Coleoptera, and adults of Isoptera. Few environmental samples from the pulp and paper feedstock were also assessed. A total of 233 isolates were obtained using enrichment cultures and classic criteria. Interestingly, several halo-forming colonies were found to be bacterial consortia that presented difficulties to take apart the microbial members. Those pure isolates which hydrolyzed cellulose in larger extend (45 strains) were selected and identified by means of 16S rRNA sequence analysis. Firmicutes was the prevalent phylum (62.2%) being Bacillus spp. the most frequent genus, while Paenibacillus, Brevibacillus, Cohnella, and Staphylococcus species were less frequent. The phylum Actinobacteria (6.7%) was represented by isolates related to Agromyces spp. and Microbacterium spp. Regarding Gram-negative bacteria (31.1%), the more depicted genus was Pseudomonas spp., and members of Achromobacter spp., Enterobacter spp., and Bacteroidetes phylum were also selected. These native bacterial strains are expected to enlarge the cellulolytic toolbox for efficient biomass deconstruction.

  4. Characterizing the structural diversity of a bacterial community associated with filter materials in recirculating aquaculture systems of Scortum barcoo.

    Science.gov (United States)

    Zhu, Peng; Ye, Yangfang; Pei, Fangfang; Lu, Kaihong

    2012-03-01

    The bacterial community structure associated with filter materials in the recirculating aquaculture system of Scortum barcoo was investigated using the 16S rRNA gene clone library method. Preliminary results showed that the clone library constructed from the initial operation condition was characterized by 31 taxa of bacteria belonging to eight phyla including Proteobacteria, Acidobacteria, Firmicutes, Fusobacteria, Sphingobacteria, Bacteroidetes, Verrucomicrobiae, and Actinobacteria. There were 14 taxa of bacteria belonging to four phyla including Proteobacteria, Acidobacteria, Planctomycetacia, and Nitrospirae from the stable operation condition where the water quality was well maintained. Nitrospirae was only found under the stable operation condition in this study. Our results further indicated that Nitrospira was dominated by members of the Nitrospira sp. lineages, with a minor fraction related to Nitrospira moscoviensis and an unknown Nitrospira cluster. These great differences of both diversity and composition between two operation conditions suggested that the composition of the microbial community varied with the degree of water quality in the recirculating aquaculture system of S. barcoo. PMID:22339297

  5. Preliminary characterization of human skin microbiome in healthy Egyptian individuals.

    Science.gov (United States)

    Ramadan, M; Solyman, S; Taha, M; Hanora, A

    2016-01-01

    Human skin is a large, complex ecosystem that harbors diverse microbial communities. The rapid advances in molecular techniques facilitate the exploration of skin associated bacterial populations. The objective of this study was to perform a preliminary characterization of skin associated bacterial populations in Egyptian individuals. Samples were collected from five healthy subjects from two skin sites; Antecubital Fossa (AF) and Popliteal Fossa (PF). Genomic DNA was extracted and used to amplify bacterial 16S rRNA genes which were sequenced on Illumina MiSeq platform. The two sites showed distinct diversity where PF was more diverse than AF. Taxonomic analysis of sequences revealed four main phyla Proteobacteria, Firmicutes, Actinobacteria and Deinococcus-Thermus, with Proteobacteria presenting the highest diversity. Klebsiella, Bacillus, Pseudomonas and Escherichia were the most predominant genera. Our data suggest that environmental factors can shape the composition of the skin microbiome in certain geographical regions. This study presents a new insight for subsequent analyses of human microbiome in Egypt. PMID:27545210

  6. Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes.

    Science.gov (United States)

    Li, Meng; Jain, Sunit; Dick, Gregory J

    2016-01-01

    Microbial chemosynthesis within deep-sea hydrothermal vent plumes is a regionally important source of organic carbon to the deep ocean. Although chemolithoautotrophs within hydrothermal plumes have attracted much attention, a gap remains in understanding the fate of organic carbon produced via chemosynthesis. In the present study, we conducted shotgun metagenomic and metatranscriptomic sequencing on samples from deep-sea hydrothermal vent plumes and surrounding background seawaters at Guaymas Basin (GB) in the Gulf of California. De novo assembly of metagenomic reads and binning by tetranucleotide signatures using emergent self-organizing maps (ESOM) revealed 66 partial and nearly complete bacterial genomes. These bacterial genomes belong to 10 different phyla: Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Verrucomicrobia. Although several major transcriptionally active bacterial groups (Methylococcaceae, Methylomicrobium, SUP05, and SAR324) displayed methanotrophic and chemolithoautotrophic metabolisms, most other bacterial groups contain genes encoding extracellular peptidases and carbohydrate metabolizing enzymes with significantly higher transcripts in the plume than in background, indicating they are involved in degrading organic carbon derived from hydrothermal chemosynthesis. Among the most abundant and active heterotrophic bacteria in deep-sea hydrothermal plumes are Planctomycetes, which accounted for seven genomes with distinct functional and transcriptional activities. The Gemmatimonadetes and Verrucomicrobia also had abundant transcripts involved in organic carbon utilization. These results extend our knowledge of heterotrophic metabolism of bacterial communities in deep-sea hydrothermal plumes. PMID:27512389

  7. Bacterial Diversity in Submarine Groundwater along the Coasts of the Yellow Sea

    Directory of Open Access Journals (Sweden)

    Qi eYe

    2016-01-01

    Full Text Available Submarine groundwater (SGD is one of the most significant pathways for the exchange of groundwater and/or source of nutrients, metals and carbon to the ocean, subsequently cause deleterious impacts on the coastal ecosystems. Microorganisms have been recognized as the important participators in the biogeochemical processes in the SGD. In this study, by utilizing 16S rRNA-based Illumina Miseq sequencing technology, we investigated bacterial diversity and distribution in both fresh well water and brackish recirculated porewater along the coasts in the Yellow Sea. The results showed that Actinobacteria and Betaproteobacteria, especially Comamonas spp. and Limnohabitans spp. were dominated in fresh well samples. Distinct patterns of bacterial communities were found among the porewater samples due to different locations, for examples, Cyanbacteria was the most abundant in the porewater samples far from the algal bloomed areas. The analysis of correlation between representative bacterial taxonomic groups and the contexture environmental parameters showed that fresh well water and brackish porewater might provide different nutrients to the coastal waters. Potential key bacterial groups such as Comamonas spp. may be excellent candidates for the bioremediation of the natural pollutants in the SGD. Our comprehensive understanding of bacterial diversity in the SGD along the coasts of the Yellow Sea will create a basis for designing the effective clean-up approach in-situ, and provide valuable information for the coastal management.

  8. High levels of DegU-P activate an Esat-6-like secretion system in Bacillus subtilis.

    Directory of Open Access Journals (Sweden)

    Catarina Baptista

    Full Text Available The recently discovered Type VII/Esat-6 secretion systems seem to be widespread among bacteria of the phyla Actinobacteria and Firmicutes. In some species they play an important role in pathogenic interactions with eukaryotic hosts. Several studies have predicted that the locus yukEDCByueBC of the non-pathogenic, Gram-positive bacterium Bacillus subtilis would encode an Esat-6-like secretion system (Ess. We provide here for the first time evidences for the functioning of this secretion pathway in an undomesticated B. subtilis strain. We show that YukE, a small protein with the typical features of the secretion substrates from the WXG100 superfamily is actively secreted to culture media. YukE secretion depends on intact yukDCByueBC genes, whose products share sequence or structural homology with known components of the S. aureus Ess. Biochemical characterization of YukE indicates that it exists as a dimer both in vitro and in vivo. We also show that the B. subtilis Ess essentially operates in late stationary growth phase in absolute dependence of phosphorylated DegU, the response regulator of the two-component system DegS-DegU. We present possible reasons that eventually have precluded the study of this secretion system in the B. subtilis laboratory strain 168.

  9. Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes

    Science.gov (United States)

    Li, Meng; Jain, Sunit; Dick, Gregory J.

    2016-01-01

    Microbial chemosynthesis within deep-sea hydrothermal vent plumes is a regionally important source of organic carbon to the deep ocean. Although chemolithoautotrophs within hydrothermal plumes have attracted much attention, a gap remains in understanding the fate of organic carbon produced via chemosynthesis. In the present study, we conducted shotgun metagenomic and metatranscriptomic sequencing on samples from deep-sea hydrothermal vent plumes and surrounding background seawaters at Guaymas Basin (GB) in the Gulf of California. De novo assembly of metagenomic reads and binning by tetranucleotide signatures using emergent self-organizing maps (ESOM) revealed 66 partial and nearly complete bacterial genomes. These bacterial genomes belong to 10 different phyla: Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Proteobacteria, Verrucomicrobia. Although several major transcriptionally active bacterial groups (Methylococcaceae, Methylomicrobium, SUP05, and SAR324) displayed methanotrophic and chemolithoautotrophic metabolisms, most other bacterial groups contain genes encoding extracellular peptidases and carbohydrate metabolizing enzymes with significantly higher transcripts in the plume than in background, indicating they are involved in degrading organic carbon derived from hydrothermal chemosynthesis. Among the most abundant and active heterotrophic bacteria in deep-sea hydrothermal plumes are Planctomycetes, which accounted for seven genomes with distinct functional and transcriptional activities. The Gemmatimonadetes and Verrucomicrobia also had abundant transcripts involved in organic carbon utilization. These results extend our knowledge of heterotrophic metabolism of bacterial communities in deep-sea hydrothermal plumes. PMID:27512389

  10. Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis.

    Science.gov (United States)

    Abbasian, Firouz; Palanisami, Thavamani; Megharaj, Mallavarapu; Naidu, Ravi; Lockington, Robin; Ramadass, Kavitha

    2016-05-01

    Soils contaminated with crude oil are rich sources of enzymes suitable for both degradation of hydrocarbons through bioremediation processes and improvement of crude oil during its refining steps. Due to the long term selection, crude oil fields are unique environments for the identification of microorganisms with the ability to produce these enzymes. In this metagenomic study, based on Hiseq Illumina sequencing of samples obtained from a crude oil field and analysis of data on MG-RAST, Actinomycetales (9.8%) were found to be the dominant microorganisms, followed by Rhizobiales (3.3%). Furthermore, several functional genes were found in this study, mostly belong to Actinobacteria (12.35%), which have a role in the metabolism of aliphatic and aromatic hydrocarbons (2.51%), desulfurization (0.03%), element shortage (5.6%), and resistance to heavy metals (1.1%). This information will be useful for assisting in the application of microorganisms in the removal of hydrocarbon contamination and/or for improving the quality of crude oil. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:638-648, 2016. PMID:26914145

  11. Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism.

    Science.gov (United States)

    Zheng, P; Zeng, B; Zhou, C; Liu, M; Fang, Z; Xu, X; Zeng, L; Chen, J; Fan, S; Du, X; Zhang, X; Yang, D; Yang, Y; Meng, H; Li, W; Melgiri, N D; Licinio, J; Wei, H; Xie, P

    2016-06-01

    Major depressive disorder (MDD) is the result of complex gene-environment interactions. According to the World Health Organization, MDD is the leading cause of disability worldwide, and it is a major contributor to the overall global burden of disease. However, the definitive environmental mechanisms underlying the pathophysiology of MDD remain elusive. The gut microbiome is an increasingly recognized environmental factor that can shape the brain through the microbiota-gut-brain axis. We show here that the absence of gut microbiota in germ-free (GF) mice resulted in decreased immobility time in the forced swimming test relative to conventionally raised healthy control mice. Moreover, from clinical sampling, the gut microbiotic compositions of MDD patients and healthy controls were significantly different with MDD patients characterized by significant changes in the relative abundance of Firmicutes, Actinobacteria and Bacteroidetes. Fecal microbiota transplantation of GF mice with 'depression microbiota' derived from MDD patients resulted in depression-like behaviors compared with colonization with 'healthy microbiota' derived from healthy control individuals. Mice harboring 'depression microbiota' primarily exhibited disturbances of microbial genes and host metabolites involved in carbohydrate and amino acid metabolism. This study demonstrates that dysbiosis of the gut microbiome may have a causal role in the development of depressive-like behaviors, in a pathway that is mediated through the host's metabolism. PMID:27067014

  12. The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

    DEFF Research Database (Denmark)

    Sommer, Felix; Ståhlman, Marcus; Ilkayeva, Olga;

    2016-01-01

    Hibernation is an adaptation that helps many animals to conserve energy during food shortage in winter. Brown bears double their fat depots during summer and use these stored lipids during hibernation. Although bears seasonally become obese, they remain metabolically healthy. We analyzed the micr......Hibernation is an adaptation that helps many animals to conserve energy during food shortage in winter. Brown bears double their fat depots during summer and use these stored lipids during hibernation. Although bears seasonally become obese, they remain metabolically healthy. We analyzed...... the microbiota of free-ranging brown bears during their active phase and hibernation. Compared to the active phase, hibernation microbiota had reduced diversity, reduced levels of Firmicutes and Actinobacteria, and increased levels of Bacteroidetes. Several metabolites involved in lipid metabolism, including...... triglycerides, cholesterol, and bile acids, were also affected by hibernation. Transplantation of the bear microbiota from summer and winter to germ-free mice transferred some of the seasonal metabolic features and demonstrated that the summer microbiota promoted adiposity without impairing glucose tolerance...

  13. Characterisation of the first actinobacterial group isolated from a Mexican extremophile environment.

    Science.gov (United States)

    Quintana, Erika T; Badillo, Ricardo Flores; Maldonado, Luis A

    2013-07-01

    The "Cave of Crystals" (aka 'Naica') in Chihuahua Mexico is a natural unique subterranean ecosystem which mainly consists of crystals made of calcium sulfate. The main system of caves are found at a depth of 300 meters (m) below sea level with crystals that range in size from a few centimeters to 15 m. The crystals date from nearly 400,000 years old and are thought to be formed when the cave was fully covered by water. At present time, this place shows a nearly constant temperature of 55 °C over the year and a humidity of 100 % which makes this place incomparable and unbearable to animal and/or human life. In the present study, two actinobacterial groups were isolated from within this system of caves and subjected to a systematic study to establish their phylogenetic relationship to microorganisms belonging to this vast group of Gram positive bacteria. Phenotypic properties, chemotaxonomic and 16S rRNA gene sequencing show that the microorganisms are members of the family Pseudonocardiaceae and are most closely related to the genus Prauserella. The present study is the first to report the isolation and presence of Actinobacteria or any other microbial form of life in this exceptional place. Moreover, this unexpected biodiversity can also provide an insight of the antibiotic resistome present in the isolates reported in this study.

  14. Influence of zinc nanoparticles on survival of worms Eisenia fetida and taxonomic diversity of the gut microflora.

    Science.gov (United States)

    Yausheva, Еlena; Sizova, Еlena; Lebedev, Svyatoslav; Skalny, Anatoliy; Miroshnikov, Sergey; Plotnikov, Andrey; Khlopko, Yuri; Gogoleva, Natalia; Cherkasov, Sergey

    2016-07-01

    The study was conducted to examine the effect of zinc nanoparticles on survival of worms Eisenia fetida and composition of the gut microflora. Analysis of the survival data has shown that the introduction of high doses of the nanoparticles causes death of worms in the second group with 35 % mortality rate and activates protective mechanisms realized as mucous film. DNA from the worm guts was extracted and 16S metagenomic sequencing was fulfilled using MiSeq (Illumina). Regarding the gut microflora of worms in the control group, high diversity of microorganisms (303 OTUs) was noted. Most of those belong to the taxa Firmicutes (51.9 % of the total high-quality united reads), Proteobacteria (24.1 % of the total), and Actinobacteria (13.3 % of the total), which were represented by numerous species of gen. Clostridium (C. saccharobutylicum, C. saccharoperbutylacetonicum, C. beijerinckii), gen. Pseudomonas (P. hydrogenovora, P. aeruginosa, and P. putida), gen. Bacillus (B. megaterium, B. silvestris), gen. Cellulomonas (B. megaterium, B. silvestris), and other numerically smaller genera. Adding of zinc nanoparticles to the substrate decreased the diversity of bacteria (78 OTUs) as well as percentage of bacteria belonging to the taxon Firmicutes (-41.6 %) and increased the proportion of Proteobacteria due to growth in abundance of gen. Verminephrobacter (+46 %) and gen. Ochrobactrum (+19.5 %).

  15. Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.

    Science.gov (United States)

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2015-07-01

    Cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. Agricultural soil with extensive history of CM application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using PCR-DGGE of 16 S rRNA gene. DGGE analysis revealed that dominant members of CM enrichment culture were associated with α-proteobacteria followed by γ-proteobacteria, Firmicutes, and Actinobacteria. Three potential CM-degrading isolates identified as Ochrobactrum anthropi JCm1, Bacillus megaterium JCm2, and Rhodococcus sp. JCm5 degraded 86-100% of CM (100 mg L(-1) ) within 10 days. These isolates were also able to degrade other pyrethroids, carbofuran, and cypermethrin degradation products. Enzyme activity assays revealed that enzymes involved in CM-degradation were inducible and showed activity when strains were grown on cypermethrin. Degradation kinetics of cypermethrin (200 mg kg(-1)) in soils inoculated with isolates JCm1, JCm2, and JCm5 suggested time-dependent disappearance of cypermethrin with rate constants of 0.0516, 0.0425, and 0.0807 d(-1), respectively, following first order rate kinetics. The isolated bacterial strains were among dominant genera selected under CM enriched conditions and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  16. Effects of diurnal temperature variation on microbial community and petroleum hydrocarbon biodegradation in contaminated soils from a sub-Arctic site.

    Science.gov (United States)

    Akbari, Ali; Ghoshal, Subhasis

    2015-12-01

    Contaminated soils are subject to diurnal and seasonal temperature variations during on-site ex-situ bioremediation processes. We assessed how diurnal temperature variations similar to that in summer at the site from which petroleum hydrocarbon-contaminated soil was collected affect the soil microbial community and the extent of biodegradation of petroleum hydrocarbons compared with constant temperature regimes. Microbial community analyses for 16S rRNA and alkB genes by pyrosequencing indicated that the microbial community for soils incubated under diurnal temperature variation from 5°C to 15°C (VART5-15) evolved similarly to that for soils incubated at constant temperature of 15°C (CST15). In contrast, under a constant temperature of 5°C (CST5), the community evolved significantly different. The extent of biodegradation of C10-C16 hydrocarbons in the VART5-15 systems was 48%, comparable with the 41% biodegradation in CST15 systems, but significantly higher than CST5 systems at 11%. The enrichment of Gammaproteobacteria was observed in the alkB gene-harbouring communities in VART5-15 and CST15 but not in CST5 systems. However, the Actinobacteria was abundant at all temperature regimes. The results suggest that changes in microbial community composition as a result of diurnal temperature variations can significantly influence petroleum hydrocarbon bioremediation performance in cold regions.

  17. Unravelling the diversity of grapevine microbiome.

    Directory of Open Access Journals (Sweden)

    Cátia Pinto

    Full Text Available Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines.

  18. Unravelling the diversity of grapevine microbiome.

    Science.gov (United States)

    Pinto, Cátia; Pinho, Diogo; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; Gomes, Ana C

    2014-01-01

    Vitis vinifera is one of the most widely cultivated fruit crops with a great economic impact on the global industry. As a plant, it is naturally colonised by a wide variety of both prokaryotic and eukaryotic microorganisms that interact with grapevine, having either beneficial or phytopathogenic effects, who play a major role in fruit yield, grape quality and, ultimately, in the evolution of grape fermentation and wine production. Therefore, the objective of this study was to extensively characterize the natural microbiome of grapevine. Considering that the majority of microorganisms are uncultivable, we have deeply studied the microflora of grapevine leaves using massive parallel rDNA sequencing, along its vegetative cycle. Among eukaryotic population the most abundant microorganisms belonged to the early diverging fungi lineages and Ascomycota phylum, whereas the Basidiomycota were the least abundant. Regarding prokaryotes, a high diversity of Proteobacteria, Firmicutes and Actinobacteria was unveiled. Indeed, the microbial communities present in the vineyard during its vegetative cycle were shown to be highly structured and dynamic. In all cases, the major abundant microorganisms were the yeast-like fungus Aureobasidium and the prokaryotic Enterobacteriaceae. Herein, we report the first complete microbiome landscape of the vineyard, through a metagenomic approach, and highlight the analysis of the microbial interactions within the vineyard and its importance for the equilibrium of the microecosystem of grapevines. PMID:24454903

  19. Antifungal activity of a Saharan strain of Actinomadura sp. ACD1 against toxigenic fungi and other pathogenic microorganisms.

    Science.gov (United States)

    Lahoum, A; Aouiche, A; Bouras, N; Verheecke, C; Klenk, H-P; Sabaou, N; Mathieu, F

    2016-09-01

    A new strain of actinobacteria, designated ACD1, was isolated from a Saharan soil sample in the Hoggar region (Algeria). Morphological study led to this strain being classified as a member of the Actinomadura genus. Phylogenetic analysis based on the 16S rRNA gene showed that the strain is closely related to Actinomadura sediminis DSM 45500(T) (98.5% sequence similarity). Furthermore, strain ACD1 presented a strong activity against mycotoxigenic and phytopathogenic fungi, including Aspergillus and Fusarium strains, and other pathogenic microorganisms. The kinetics of antimicrobial activity were investigated on ISP-2, Bennett and TSB media. Four solvents (n-hexane, dichloromethane, ethyl acetate and n-butanol) were used for the extraction of the produced antibiotic. The highest antimicrobial activity was obtained using the butanolic extract from the ISP-2 medium after seven days of fermentation culture. The active antibiotic was purified by reverse-phase HPLC using a C18 column. The UV-visible and mass spectra were determined. The minimum inhibitory concentrations (MIC) of this antibiotic were determined against pathogenic microorganisms. PMID:26996355

  20. Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

    Science.gov (United States)

    Perreault, Nancy N.; Greer, Charles W.; Andersen, Dale T.; Tille, Stefanie; Lacrampe-Couloume, Georges; Lollar, Barbara Sherwood; Whyte, Lyle G.

    2008-01-01

    The saline springs of Gypsum Hill in the Canadian high Arctic are a rare example of cold springs originating from deep groundwater and rising to the surface through thick permafrost. The heterotrophic bacteria and autotrophic sulfur-oxidizing bacteria (up to 40% of the total microbial community) isolated from the spring waters and sediments were classified into four phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) based on 16S rRNA gene analysis; heterotrophic isolates were primarily psychrotolerant, salt-tolerant, facultative anaerobes. Some of the isolates contained genes for thiosulfate oxidation (soxB) and anoxygenic photosynthesis (pufM), possibly enabling the strains to better compete in these sulfur-rich environments subject to long periods of illumination in the Arctic summer. Although leucine uptake by the spring water microbial community was low, CO2 uptake was relatively high under dark incubation, reinforcing the idea that primary production by chemoautotrophs is an important process in the springs. The small amounts of hydrocarbons in gases exsolving from the springs (0.38 to 0.51% CH4) were compositionally and isotopically consistent with microbial methanogenesis and possible methanotrophy. Anaerobic heterotrophic sulfur oxidation and aerobic autotrophic sulfur oxidation activities were demonstrated in sediment slurries. Overall, our results describe an active microbial community capable of sustainability in an extreme environment that experiences prolonged periods of continuous light or darkness, low temperatures, and moderate salinity, where life seems to rely on chemolithoautotrophy. PMID:18805995

  1. Particle Size Distribution of Airborne Microorganisms and Pathogens during an Intense African Dust Event in the Eastern Mediterranean

    Science.gov (United States)

    Polymenakou, Paraskevi N.; Mandalakis, Manolis; Stephanou, Euripides G.; Tselepides, Anastasios

    2008-01-01

    Background The distribution of microorganisms, and especially pathogens, over airborne particles of different sizes has been ignored to a large extent, but it could have significant implications regarding the dispersion of these microorganisms across the planet, thus affecting human health. Objectives We examined the microbial quality of the aerosols over the eastern Mediterranean region during an African storm to determine the size distribution of microorganisms in the air. Methods We used a five-stage cascade impactor for bioaerosol collection in a coastal city on the eastern Mediterranean Sea during a north African dust storm. Bacterial communities associated with aerosol particles of six different size ranges were characterized following molecular culture–independent methods, regardless of the cell culturability (analysis of 16S rRNA genes). Results All 16S rDNA clone libraries were diverse, including sequences commonly found in soil and marine ecosystems. Spore-forming bacteria such as Firmicutes dominated large particle sizes (> 3.3 μm), whereas clones affiliated with Actinobacteria (found commonly in soil) and Bacteroidetes (widely distributed in the environment) gradually increased their abundance in aerosol particles of reduced size (< 3.3 μm). A large portion of the clones detected at respiratory particle sizes (< 3.3 μm) were phylogenetic neighbors to human pathogens that have been linked to several diseases. Conclusions The presence of aerosolized bacteria in small size particles may have significant implications to human health via intercontinental transportation of pathogens. PMID:18335093

  2. Effects of different remediation treatments on crude oil contaminated saline soil.

    Science.gov (United States)

    Gao, Yong-Chao; Guo, Shu-Hai; Wang, Jia-Ning; Li, Dan; Wang, Hui; Zeng, De-Hui

    2014-12-01

    Remediation of the petroleum contaminated soil is essential to maintain the sustainable development of soil ecosystem. Bioremediation using microorganisms and plants is a promising method for the degradation of crude oil contaminants. The effects of different remediation treatments, including nitrogen addition, Suaeda salsa planting, and arbuscular mycorrhiza (AM) fungi inoculation individually or combined, on crude oil contaminated saline soil were assessed using a microcosm experiment. The results showed that different remediation treatments significantly affected the physicochemical properties, oil contaminant degradation and bacterial community structure of the oil contaminated saline soil. Nitrogen addition stimulated the degradation of total petroleum hydrocarbon significantly at the initial 30d of remediation. Coupling of different remediation techniques was more effective in degrading crude oil contaminants. Applications of nitrogen, AM fungi and their combination enhanced the phytoremediation efficiency of S. salsa significantly. The main bacterial community composition in the crude oil contaminated saline soil shifted with the remediation processes. γ-Proteobacteria, β-Proteobacteria, and Actinobacteria were the pioneer oil-degraders at the initial stage, and Firmicutes were considered to be able to degrade the recalcitrant components at the later stage.

  3. Molecular characterization of the cloacal microbiota of wild and captive parrots.

    Science.gov (United States)

    Xenoulis, Panagiotis G; Gray, Patricia L; Brightsmith, Donald; Palculict, Blake; Hoppes, Sharman; Steiner, Jörg M; Tizard, Ian; Suchodolski, Jan S

    2010-12-15

    The gastrointestinal microbiota plays a fundamental role in health and disease. Only limited data are available about the composition of the intestinal microbiota of captive animals compared to those of wild animals. The aim of the present study was to characterize the cloacal microbiota of apparently healthy wild and captive parrots. A total of 16 parrots, 8 wild and 8 captive, belonging to 3 different species, were used in this study. Cloacal material was collected via cloacal swabbing. DNA was extracted and 16S rRNA genes were amplified using universal bacterial primers. Constructed 16S rRNA gene clone libraries were compared between groups. A total of 518 clones were analyzed, and 49 operational taxonomic units (OTUs) were identified. The OTUs were classified in 4 bacterial phyla: Firmicutes (72.9%), Proteobacteria (14.9%), Actinobacteria (12%), and Bacteroidetes (0.2%). Bacterial diversity was significantly lower in wild birds than in captive birds. Principal component analysis based on the Unifrac distance metric indicated that the cloacal microbiota differed between wild and captive parrots. Staphylococcus saprophyticus was significantly more abundant in wild birds, while Escherichia coli was significantly more abundant in captive birds. In conclusion, wild and captive parrots appear to have differences in the composition of their cloacal bacterial microbiota. The clinical significance of these differences remains to be determined.

  4. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

    Directory of Open Access Journals (Sweden)

    Charles ePepe-Ranney

    2016-05-01

    Full Text Available We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP. Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs, respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes.

  5. The pupylation machinery is involved in iron homeostasis by targeting the iron storage protein ferritin.

    Science.gov (United States)

    Küberl, Andreas; Polen, Tino; Bott, Michael

    2016-04-26

    The balance of sufficient iron supply and avoidance of iron toxicity by iron homeostasis is a prerequisite for cellular metabolism and growth. Here we provide evidence that, in Actinobacteria, pupylation plays a crucial role in this process. Pupylation is a posttranslational modification in which the prokaryotic ubiquitin-like protein Pup is covalently attached to a lysine residue in target proteins, thus resembling ubiquitination in eukaryotes. Pupylated proteins are recognized and unfolded by a dedicated AAA+ ATPase (Mycobacterium proteasomal AAA+ ATPase; ATPase forming ring-shaped complexes). In Mycobacteria, degradation of pupylated proteins by the proteasome serves as a protection mechanism against several stress conditions. Other bacterial genera capable of pupylation such as Corynebacterium lack a proteasome, and the fate of pupylated proteins is unknown. We discovered that Corynebacterium glutamicum mutants lacking components of the pupylation machinery show a strong growth defect under iron limitation, which was caused by the absence of pupylation and unfolding of the iron storage protein ferritin. Genetic and biochemical data support a model in which the pupylation machinery is responsible for iron release from ferritin independent of degradation. PMID:27078093

  6. Pupylated proteins in Corynebacterium glutamicum revealed by MudPIT analysis.

    Science.gov (United States)

    Küberl, Andreas; Fränzel, Benjamin; Eggeling, Lothar; Polen, Tino; Wolters, Dirk Andreas; Bott, Michael

    2014-06-01

    In a manner similar to ubiquitin, the prokaryotic ubiquitin-like protein (Pup) has been shown to target proteins for degradation via the proteasome in mycobacteria. However, not all actinobacteria possessing the Pup protein also contain a proteasome. In this study, we set out to study pupylation in the proteasome-lacking non-pathogenic model organism Corynebacterium glutamicum. A defined pup deletion mutant of C. glutamicum ATCC 13032 grew aerobically as the parent strain in standard glucose minimal medium, indicating that pupylation is dispensable under these conditions. After expression of a Pup derivative carrying an aminoterminal polyhistidine tag in the Δpup mutant and Ni(2+)-chelate affinity chromatography, pupylated proteins were isolated. Multidimensional protein identification technology (MudPIT) and MALDI-TOF-MS/MS of the elution fraction unraveled 55 proteins being pupylated in C. glutamicum and 66 pupylation sites. Similar to mycobacteria, the majority of pupylated proteins are involved in metabolism or translation. Our results define the first pupylome of an actinobacterial species lacking a proteasome, confirming that other fates besides proteasomal degradation are possible for pupylated proteins. PMID:24737727

  7. The small 6C RNA of Corynebacterium glutamicum is involved in the SOS response.

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    Pahlke, Jennifer; Dostálová, Hana; Holátko, Jiří; Degner, Ursula; Bott, Michael; Pátek, Miroslav; Polen, Tino

    2016-09-01

    The 6C RNA family is a class of small RNAs highly conserved in Actinobacteria, including the genera Mycobacterium, Streptomyces and Corynebacterium whose physiological function has not yet been elucidated. We found that strong transcription of the cgb_03605 gene, which encodes 6C RNA in C. glutamicum, was driven by the SigA- and SigB-dependent promoter Pcgb_03605. 6C RNA was detected at high level during exponential growth phase (180 to 240 molcules per cell) which even increased at the entry of the stationary phase. 6C RNA level did not decrease within 240 min after transcription had been stopped with rifampicin, which suggests high 6C RNA stability. The expression of cgb_03605 further increased approximately twofold in the presence of DNA-damaging mitomycin C (MMC) and nearly threefold in the absence of LexA. Deletion of the 6C RNA gene cgb_03605 resulted in a higher sensitivity of C. glutamicum toward MMC and UV radiation. These results indicate that 6C RNA is involved in the DNA damage response. Both 6C RNA level-dependent pausing of cell growth and branched cell morphology in response to MMC suggest that 6C RNA may also be involved in a control of cell division. PMID:27362471

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

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

    2016-01-01

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

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

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    Lee F Stanish

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

  10. Illumina-based analysis of core actinobacteriome in roots, stems, and grains of rice.

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    Wang, Wenfeng; Zhai, Yanyan; Cao, Lixiang; Tan, Hongming; Zhang, Renduo

    2016-09-01

    Seed-borne microbiota can transmit vertically from generation to generation and be a favour mutualism between the endosymbionts and hosts. The aim of this study was to investigate the rice-associated actinobacterial taxa in roots, stems, and grains and explore vertically transmitted core actinobacteriome of rice plants. Illumina sequencing analyses of samples of rice grains, stems, and roots showed that the roots contained the most diverse actinobacteria among the tissues. The grains contained 78 actinobacterial operational taxonomic units (OTUs), among which 44 were shared with those in the stems, 30 shared with those in the roots. The coexisted OTUs in the three types of samples mainly belong to genera of Pseudonocardia, Dietzia, Nocardioides, Streptomyces, Mycobacterium, Corynebacterium, Citricoccus, Salinibacterium, and Agrococcus, and other unclassified taxa. The dominant actinobacterial genera Pseudonocardia and Dietzia in the stems and roots were still detected in relatively high abundance in the grains. The Streptomyces isolated from surface sterilized grains could improve nitrogen use efficiency of rice seedlings and the resistance to rice blast fungus. The results suggested that the rice grains contained diverse actinobacterial taxa deriving from stems and roots and showed intimate correlation with the host plants. PMID:27393994

  11. Microbial communities in a coastal cave: Cova des Pas de Vallgornera (Mallorca, Western Mediterranean

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    Antoni Busquets

    2014-05-01

    Full Text Available As a part of an ongoing project on the role of microbes in the biogeochemistry of Majorcan caves, the species diversity of microbial communities present in cave pools of anchialine waters in the Cova des Pas de Vallgornera (Mallorca, western Mediterranean is investigated by a culture-dependent method. Two-hundred and forty-eight strains isolated from this characteristic cave environment of the littoral karst are identified by whole-cell-MALDI-TOF mass spectrometry and phylogeneticaly by 16S rRNA gene sequences. Total cell counts and species diversity of the bacterial communities decreas with the distance to the entrance of the cave and to the sea. Strains are mainly identified as members of the Gammaproteobacteria and Actinobacteria. Around 20% of the isolates are able to precipitate carbonates. Calcite is the predominant phase, growing in all the precipitates, although struvite is also found in one Pseudomonas and in one Aspergillus cultures. Differences in crystal characteristics of external shape (habit and growth are observed according to the bacterial species promoting the precipitates. Bacteria associated with multicolored ferromanganese deposits, present in several parts of the cave, are also studied and are identified as Pseudomonas benzenivorans and Nocardioides luteus. The preponderance of Pseudomonas species and the possible contribution of bacteria in calcite deposition are discussed.

  12. Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga.

    Science.gov (United States)

    Brodie, Juliet; Williamson, Christopher; Barker, Gary L; Walker, Rachel H; Briscoe, Andrew; Yallop, Marian

    2016-08-01

    The living prokaryotic microbiome of the calcified geniculate (articulated) red alga, Corallina officinalis from the intertidal seashore is characterised for the first time based on the V6 hypervariable region of 16S rRNA. Results revealed an extraordinary diversity of bacteria associated with the microbiome. Thirty-five prokaryotic phyla were recovered, of which Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Verrucomicrobia, Firmicutes and Chloroflexi made up the core microbiome. Unclassified sequences made up 25% of sequences, suggesting insufficient sampling of the world's oceans/macroalgae. The greatest diversity in the microbiome was on the upper shore, followed by the lower shore then the middle shore, although the microbiome community composition did not vary between shore levels. The C. officinalis core microbiome was broadly similar in composition to those reported in the literature for crustose coralline algae (CCAs) and free-living rhodoliths. Differences in relative abundance of the phyla between the different types of calcified macroalgal species may relate to the intertidal versus subtidal habit of the taxa and functionality of the microbiome components. The results indicate that much work is needed to identify prokaryotic taxa, and to determine the nature of the relationship of the bacteria with the calcified host spatially, temporally and functionally.

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

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

    2015-12-01

    Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance. PMID:25932616

  14. The Diversity and Co-occurrence Patterns of N₂-Fixing Communities in a CO₂-Enriched Grassland Ecosystem.

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    Tu, Qichao; Zhou, Xishu; He, Zhili; Xue, Kai; Wu, Liyou; Reich, Peter; Hobbie, Sarah; Zhou, Jizhong

    2016-04-01

    Diazotrophs are the major organismal group responsible for atmospheric nitrogen (N2) fixation in natural ecosystems. The extensive diversity and structure of N2-fixing communities in grassland ecosystems and their responses to increasing atmospheric CO2 remain to be further explored. Through pyrosequencing of nifH gene amplicons and extraction of nifH genes from shotgun metagenomes, coupled with co-occurrence ecological network analysis approaches, we comprehensively analyzed the diazotrophic community in a grassland ecosystem exposed to elevated CO2 (eCO2) for 12 years. Long-term eCO2 increased the abundance of nifH genes but did not change the overall nifH diversity and diazotrophic community structure. Taxonomic and phylogenetic analysis of amplified nifH sequences suggested a high diversity of nifH genes in the soil ecosystem, the majority belonging to nifH clusters I and II. Co-occurrence ecological network analysis identified different co-occurrence patterns for different groups of diazotrophs, such as Azospirillum/Actinobacteria, Mesorhizobium/Conexibacter, and Bradyrhizobium/Acidobacteria. This indicated a potential attraction of non-N2-fixers by diazotrophs in the soil ecosystem. Interestingly, more complex co-occurrence patterns were found for free-living diazotrophs than commonly known symbiotic diazotrophs, which is consistent with the physical isolation nature of symbiotic diazotrophs from the environment by root nodules. The study provides novel insights into our understanding of the microbial ecology of soil diazotrophs in natural ecosystems. PMID:26280746

  15. The amphibian skin-associated microbiome across species, space and life history stages.

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    Kueneman, Jordan G; Parfrey, Laura Wegener; Woodhams, Douglas C; Archer, Holly M; Knight, Rob; McKenzie, Valerie J

    2014-03-01

    Skin-associated bacteria of amphibians are increasingly recognized for their role in defence against pathogens, yet we have little understanding of their basic ecology. Here, we use high-throughput 16S rRNA gene sequencing to examine the host and environmental influences on the skin microbiota of the cohabiting amphibian species Anaxyrus boreas, Pseudacris regilla, Taricha torosa and Lithobates catesbeianus from the Central Valley in California. We also studied populations of Rana cascadae over a large geographic range in the Klamath Mountain range of Northern California, and across developmental stages within a single site. Dominant bacterial phylotypes on amphibian skin included taxa from Bacteroidetes, Gammaproteobacteria, Alphaproteobacteria, Firmicutes, Sphingobacteria and Actinobacteria. Amphibian species identity was the strongest predictor of microbial community composition. Secondarily, within a given amphibian species, wetland site explained significant variation. Amphibian-associated microbiota differed systematically from microbial assemblages in their environments. Rana cascadae tadpoles have skin bacterial communities distinct from postmetamorphic conspecifics, indicating a strong developmental shift in the skin microbes following metamorphosis. Establishing patterns observed in the skin microbiota of wild amphibians and environmental factors that underlie them is necessary to understand skin symbiont community assembly, and ultimately, the role skin microbiota play in the extended host phenotype including disease resistance. PMID:24171949

  16. Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology.

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    Akinsanya, Mushafau Adewale; Goh, Joo Kheng; Lim, Siew Ping; Ting, Adeline Su Yien

    2015-12-01

    Next generation sequencing (NGS) enables rapid analysis of the composition and diversity of microbial communities in several habitats. We applied the high throughput techniques of NGS to the metagenomics study of endophytic bacteria in Aloe vera plant, by assessing its PCR amplicon of 16S rDNA sequences (V3-V4 regions) with the Illumina metagenomics technique used to generate a total of 5,199,102 reads from the samples. The analyses revealed Proteobacteria, Firmicutes, Actinobacteria and Bacteriodetes as the predominant genera. The roots have the largest composition with 23% not present in other tissues. The stems have more of the genus-Pseudomonas and the unclassified Pseudomonadaceae. The α-diversity analysis indicated the richness and inverse Simpson diversity index of the bacterial endophyte communities for the leaf, root and stem tissues to be 2.221, 6.603 and 1.491 respectively. In a similar study on culturable endophytic bacteria in the same A. vera plants (unpublished work), the dominance of Pseudomonas and Bacillus genera was similar, with equal proportion of four species each in root, stem and leaf tissues. It is evident that NGS technology captured effectively the metagenomics of microbiota in plant tissues and this can improve our understanding of the microbial-plant host interactions. PMID:26697361

  17. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures.

    Science.gov (United States)

    Aira, Manuel; Bybee, Seth; Pérez-Losada, Marcos; Domínguez, Jorge

    2015-11-01

    Earthworms play a key role in nutrient cycling by interacting with microorganisms thus accelerating organic matter turnover in soil systems. As detritivores, some earthworm types ingest and digest a mixture of dead organic matter and microorganisms, like animal manures (i.e. animal gut microbiomes). Here we described the earthworm cast microbiome and the role ingested bacteria play on its composition. We fed Eisenia andrei with cow, horse and pig manures and determined the taxonomic and phylogenetic composition of the these manures before and after passage through the earthworm gut. Earthworm cast microbiomes showed a smaller diversity than the manure they fed on. Manures strongly differed in their taxonomic and phylogenetic composition, but these differences were markedly reduced once transformed into earthworm cast microbiomes after passage through the earthworm gut. The core earthworm cast microbiome comprised 30 OTUs (2.6% of OTUs from cast samples), of which 10 are possibly native to the earthworm gut. Most of the core cast microbiome OTUs belonged to phyla Actinobacteria and Proteobacteria, as opposed to already described animal core gut microbiomes, which are composed mainly of Firmicutes and Bacteroidetes. Our results suggest that earthworms build up their cast microbiome by selecting from the pool of ingested bacteria. PMID:26432803

  18. Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae.

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    Ana Patrícia Graça

    Full Text Available Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA, Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus, fish pathogen (Aliivibrio fischeri and environmentally relevant bacteria (Vibrio harveyi. The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%, Vibrio (22.7% and Bacillus (7.6%. Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I and nonribosomal peptide synthetases (NRPSs genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sp