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Sample records for actinobacteria

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

    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.

    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. Surfactants tailored by the class Actinobacteria

    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.

  4. Antagonistic activity of marine sponges associated Actinobacteria

    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

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

    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

  6. Screening of marine actinobacteria for amylase enzymes inhibitors

    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 ...

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

    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

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

    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

  9. DESTRUCTION OF HYDROCARBONS WITH VARIOUS MORPHOTYPES OF OIL OXIDIZING ACTINOBACTERIA

    Khudokormov A. A.

    2013-10-01

    Full Text Available In this article we have carried out a comparative study of hydro-carbon-oxidizing activity of S-and R-morphological types of oil oxidizing Actinobacteria from the collection of Kuban State University. Signifi-cant differences observed in parameters of growth between S- and R-forms of oil oxidizing Actinobacte-ria. In S-forms it is higher than the maximum specific growth rate, which is typical for a wide range of hy-drocarbon degradation and a high degree of degrada-tion of pollutants. In experiments with the use of oil as a substrate and heavy oil S-forms, Actinobacteria quickly adapted to the environmental conditions

  10. DESTRUCTION OF HYDROCARBONS WITH VARIOUS MORPHOTYPES OF OIL OXIDIZING ACTINOBACTERIA

    Khudokormov A. A.; Karaseva E. V.; Samkov A. A.; Volchenko N. N.; Kozitsin A. E.

    2013-01-01

    In this article we have carried out a comparative study of hydro-carbon-oxidizing activity of S-and R-morphological types of oil oxidizing Actinobacteria from the collection of Kuban State University. Signifi-cant differences observed in parameters of growth between S- and R-forms of oil oxidizing Actinobacte-ria. In S-forms it is higher than the maximum specific growth rate, which is typical for a wide range of hy-drocarbon degradation and a high degree of degrada-tion of pollutants. In expe...

  11. Characterization of actinobacteria associated with three ant-plant mutualisms.

    Hanshew, Alissa S; McDonald, Bradon R; Díaz Díaz, Carol; Djiéto-Lordon, Champlain; Blatrix, Rumsaïs; Currie, Cameron R

    2015-01-01

    Ant-plant mutualisms are conspicuous and ecologically important components of tropical ecosystems that remain largely unexplored in terms of insect-associated microbial communities. Recent work has revealed that ants in some ant-plant systems cultivate fungi (Chaetothyriales) within their domatia, which are fed to larvae. Using Pseudomyrmex penetrator/Tachigali sp. from French Guiana and Petalomyrmex phylax/Leonardoxa africana and Crematogaster margaritae/Keetia hispida, both from Cameroon, as models, we tested the hypothesis that ant-plant-fungus mutualisms co-occur with culturable Actinobacteria. Using selective media, we isolated 861 putative Actinobacteria from the three systems. All C. margaritae/K. hispida samples had culturable Actinobacteria with a mean of 10.0 colony forming units (CFUs) per sample, while 26 % of P. penetrator/Tachigali samples (mean CFUs 1.3) and 67 % of P. phylax/L. africana samples (mean CFUs 3.6) yielded Actinobacteria. The largest number of CFUs was obtained from P. penetrator workers, P. phylax alates, and C. margaritae pupae. 16S rRNA gene sequencing and phylogenetic analysis revealed the presence of four main clades of Streptomyces and one clade of Nocardioides within these three ant-plant mutualisms. Streptomyces with antifungal properties were isolated from all three systems, suggesting that they could serve as protective symbionts, as found in other insects. In addition, a number of isolates from a clade of Streptomyces associated with P. phylax/L. africana and C. margaritae/K. hispida were capable of degrading cellulose, suggesting that Streptomyces in these systems may serve a nutritional role. Repeated isolation of particular clades of Actinobacteria from two geographically distant locations supports these isolates as residents in ant-plant-fungi niches. PMID:25096989

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

    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...

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

    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...

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

    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 ...

  15. Genomics of aerobic cellulose utilization systems in actinobacteria.

    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.

  16. Antioxidant activity of newly discovered lineage of marine actinobacteria

    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.

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

    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.

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

    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

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

    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

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

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

    2012-01-01

    for morphological (288 isolates, grouped in 44 morphotypes) and for 16S rRNA (35 isolates, spanning the majority of morphotypes) characterisation. Actinobacteria were found throughout all sampled nests and colony parts and, phylogenetically, they are interspersed with Actinobacteria from origins other than fungus...... a role as defensive symbionts against Pseudoxylaria in fungus-growing termites. We sampled for Actinobacteria from 30 fungus-growing termite colonies, spanning the three main termite genera and two geographically distant sites. Our isolations yielded 360 Actinobacteria, from which we selected subsets......-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...

  1. Isolation and Characterisation of Antagonistic Actinobacteria from Mangrove Soil

    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;}

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

    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

  3. Analysis of Actinobacteria from mould-colonized water damaged building material

    Schäfer, Jenny; Jäckel, Udo; Kämpfer, Peter

    2010-01-01

    Mould-colonized water damaged building materials are frequently co-colonized by actinomycetes. Here, we report the results of the analyses of Actinobacteria on different wall materials from water damaged buildings obtained by both cultivation-dependent and cultivation-independent methods. Actinobacteria were detected in all but one of the investigated materials by both methods. The detected concentrations of Actinobacteria ranged between 1.8 x 10(4) and 7.6 x 10(7) CFUg(-1) of investigated ma...

  4. Genomic islands predict functional adaptation in marine actinobacteria

    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. Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria

    Ságová-Marečková, M.; Ulanová, Dana; Šanderová, P.; Omelka, M.; Kameník, Zdeněk; Olšovská, J.; Kopecký, J.

    2015-01-01

    Roč. 15, APR 2015 (2015). ISSN 1471-2180 Institutional support: RVO:61388971 Keywords : Actinobacteria * 16S rRNA diversity * Resistance genes Subject RIV: EE - Microbiology , Virology Impact factor: 2.729, year: 2014

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

    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

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

    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.

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

    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.

  10. Quorum Sensing: An Under-Explored Phenomenon in the Phylum Actinobacteria

    Polkade, Ashish V.; Mantri, Shailesh S.; Patwekar, Umera J.; Jangid, Kamlesh

    2016-01-01

    Quorum sensing is known to play a major role in the regulation of secondary metabolite production, especially, antibiotics, and morphogenesis in the phylum Actinobacteria. Although it is one of the largest bacterial phylum, only 25 of the 342 genera have been reported to use quorum sensing. Of these, only nine have accompanying experimental evidence; the rest are only known through bioinformatic analysis of gene/genome sequences. It is evident that this important communication mechanism is not extensively explored in Actinobacteria. In this review, we summarize the different quorum sensing systems while identifying the limitations of the existing screening strategies and addressing the improvements that have taken place in this field in recent years. The γ-butyrolactone system turned out to be almost exclusively limited to this phylum. In addition, methylenomycin furans, AI-2 and other putative AHL-like signaling molecules are also reported in Actinobacteria. The lack of existing screening systems in detecting minute quantities and of a wider range of signaling molecules was a major reason behind the limited information available on quorum sensing in this phylum. However, recent improvements in screening strategies hold a promising future and are likely to increase the discovery of new signaling molecules. Further, the quorum quenching ability in many Actinobacteria has a great potential in controlling the spread of plant and animal pathogens. A systematic and coordinated effort is required to screen and exploit the enormous potential that quorum sensing in the phylum Actinobacteria has to offer for human benefit. PMID:26904007

  11. The isolation and characterization of actinobacteria from dominant benthic macroinvertebrates endemic to Lake Baikal.

    Axenov-Gribanov, Denis; Rebets, Yuriy; Tokovenko, Bogdan; Voytsekhovskaya, Irina; Timofeyev, Maxim; Luzhetskyy, Andriy

    2016-03-01

    The high demand for new antibacterials fosters the isolation of new biologically active compounds producing actinobacteria. Here, we report the isolation and initial characterization of cultured actinobacteria from dominant benthic organisms' communities of Lake Baikal. Twenty-five distinct strains were obtained from 5 species of Baikal endemic macroinvertebrates of amphipods, freshwater sponges, turbellaria worms, and insects (caddisfly larvae). The 16S ribosomal RNA (rRNA)-based phylogenic analysis of obtained strains showed their affiliation to Streptomyces, Nocardia, Pseudonocardia, Micromonospora, Aeromicrobium, and Agromyces genera, revealing the diversity of actinobacteria associated with the benthic organisms of Lake Baikal. The biological activity assays showed that 24 out of 25 strains are producing compounds active against at least one of the test cultures used, including Gram-negative bacteria and Candida albicans. Complete dereplication of secondary metabolite profiles of two isolated strains led to identification of only few known compounds, while the majority of detected metabolites are not listed in existing antibiotic databases. PMID:26347255

  12. Isolation and characterization of culturable endophytic actinobacteria associated with Artemisia annua L.

    Li, Jie; Zhao, Guo-Zhen; Huang, Hai-Yu; Qin, Sheng; Zhu, Wen-Yong; Zhao, Li-Xing; Xu, Li-Hua; Zhang, Si; Li, Wen-Jun; Strobel, Gary

    2012-03-01

    Endophytic actinobacteria isolated from Artemisia annua were characterized and evaluated for their bioactivities. A total of 228 isolates representing at least 19 different genera of actinobacteria were obtained and several of them seemed to be novel taxa. An evaluation of antimicrobial activity showed that more isolates possessed activity towards plant pathogens than activity against other pathogenic bacteria or yeasts. High frequencies of PCR amplification were obtained for type I polyketide synthases (PKS-I, 21.1%), type II polyketide synthases (PKS-II, 45.2%) and nonribosomal peptide synthetases (NRPS, 32.5%). The results of herbicidal activity screening indicated that 19 out of 117 samples of fermentation broths completely inhibited the germination of Echinochloa crusgalli. This study indicated that endophytic actinobacteria associated with A. annua are abundant and have potentially beneficial and diverse bioactivities which should be pursued for their biotechnical promise. PMID:22038129

  13. Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater .i.Actinobacteria./i

    Sharma, A. K.; Sommerfeld, K.; Bullerjahn, G. S.; Matteson, A. R.; Wilhelm, S. W.; Jezbera, Jan; Brandt, U.; Doolittle, W.F.; Hahn, M.W.

    2009-01-01

    Roč. 3, č. 6 (2009), s. 726-737. ISSN 1751-7362 Institutional research plan: CEZ:AV0Z60170517 Keywords : rhodopsins * actinorhodopsin * freshwater * Actinobacteria * Superior * Erie Subject RIV: EE - Microbiology, Virology Impact factor: 6.397, year: 2009

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

    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

  15. Metagenomic Classification and Characterization Marine Actinobacteria from the Gulf of Maine without Representative Genomes

    Sachdeva, R.; Heidelberg, J.

    2012-12-01

    Actinobacteria represent one of the largest and most diverse bacterial phyla and unlike most marine prokaryotes are gram-positive. This phylum encompasses a broad range of physiologies, morphologies, and metabolic properties with a broad array of lifestyles. The marine actinobacterial assemblage is dominated by the orders Actinomycetales and Acidimicrobiales (also known as the marine Actinobacteria clade). The Acidimicrobiales bacteria typically outnumber the Actinomycetales bacteria and are mostly represented by the OCS155 group. Although bacteria of the order Acidimicrobiales make up ~7.6% of the 16S matches from the Global Ocean Survey shotgun metagenomic libraries; very little is known about their potential function and role in biogeochemical cycling. Samples were collected from surface seawater samples in the Gulf of Maine (GOM) from the summer and winter of 2006. Sanger sequences were generated from the 0.1-0.8 μm fractions using paired-end medium insert shotgun libraries. The resulting 2.2 Gb were assembled using the Celera Assembler package into 280 Mb of non-redundant scaffolds. Putative actinobacterial assemblies were identified using (1) ribosomal RNA genes (16S and 23S), (2) phylogenetically informative non-ribosomal core genes thought to be resistant to horizontal gene transfer (e.g. RecA and RpoB) and (3) compositional binning using oligonucleotide frequency pattern based hierarchical clustering. Binning resulted in 3.6 Mb (4.2X coverage) of actinobacterial scaffolds that were comprised of 15.1 Mb of unassembled reads. Putative actinobacterial assemblies included both summer and winter reads demonstrating that the Actinobacteria are abundant year round. Classification reveals that all of the sampled Actinobacteria are from the orders Acidimicrobiales and Actinomycetales and are similar to those found in the global ocean. The GOM Actinobacteria show a broad range of G+C % content (32-66%) indicating a high level of genomic diversity. Those assemblies

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

    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

  17. An airborne actinobacteria Nocardiopsis alba isolated from bioaerosol of a mushroom compost facility

    Paściak, Mariola; Pawlik, Krzysztof; Gamian, Andrzej; Szponar, Bogumiła; Skóra, Justyna; Gutarowska, Beata

    2014-01-01

    Actinobacteria are widely distributed in many environments and represent the most important trigger to the occupant respiratory health. Health complaints, including hypersensitivity pneumonitis of the workers, were recorded in a mushroom compost facility (MCF). The studies on the airborne bacteria were carried out to find a possible microbiological source of these symptoms. Culture analysis of compost bioaerosols collected in different location of the MCF was performed. An assessment of the i...

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

    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...

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

    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...

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

    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...

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

    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. Use of Metagenomics and Isolation of Actinobacteria in Brazil's Atlantic Rainforest Soil for Antimicrobial Prospecting.

    Assis, Danyelle Alves Martins; Rezende, Rachel Passos; Dias, João Carlos Teixeira

    2014-01-01

    Modern techniques involving molecular biology, such as metagenomics, have the advantage of exploiting a higher number of microorganisms; however, classic isolation and culture methods used to obtain antimicrobials continue to be promising, especially in the isolation of Actinobacteria, which are responsible for the production of many of these compounds. In this work, two methodologies were used to search for antimicrobial substances-isolation of Actinobacteria and metagenomics of the Atlantic Rainforest soil and of the cultivation of cocoa intercropped with acai berry in the Atlantic Rainforest. The metagenomic libraries were constructed with the CopyControl Fosmid Library kit EPICENTRE, resulting in a total of 2688 clones, 1344 of each soil sample. None of the clones presented antimicrobial activity against the microorganisms tested: S. aureus, Bacillus subtilis, and Salmonella choleraesuis. A total of 46 isolates were obtained from the isolation of soil Actinobacteria: 24 isolates from Atlantic Rainforest soil and 22 isolates from the intercrop cultivation soil. Of these, two Atlantic Rainforest soil isolates inhibited the growth of S. aureus including a clinical isolate of S. aureus MRSA-a promising result, since it is an important multidrug-resistant human pathogen. PMID:25937991

  3. [Storage of Actinobacteria of the Genera Streptomyces and Nonomuraea by Low Temperature Preservation].

    Sineva, O N; Kulikova, N G; Filippova, S N; Terekhova, L P

    2014-01-01

    The influence of storage of actinobacteria Streptomyces hygroscopicus RIA 1433T, Nonomuraea roseoviolacea subsp. carminata INA 4281 and Nonomuraea sp. INA 34-06 at extremely low temperatures (-70 degrees C) for 1.5 years was studied with respect to their viability and antibiotic activity. The spores of the actinobacteria preserved their high viability when freezed at a concentration of 10(5)-10(7) CFU/ml. As for the antibiotic activity against the test culture Micrococcus luteus ATCC 9341, the strains differed: the S. hygroscopicus RIA 1433T colonies preserved their antibiotic activity against the test culture, the antibiotic activity of Nonomuraea roseoviolacea subsp. carminata lowered by 5% and that of N. sp. INA 34-06 lowered by 44%. Differences in the resistance of the strains to the storage at the extremely low temperatures were observed when the suspensions contained low concentrations of the spores (10(2) CFU/ml): S. hygroscopicus RIA 1433T preserved its viability and antibiotic activity during 1.5 years, while N. roseoviolacea subsp. carminata INA 4281 and N. sp. INA 34-06 lost the viability by the 8th month of the storage. The study showed that 10% glycerol solution used as a cryoprotector during the storage had no effect on viability and antibiotic activity of the actinobacteria. PMID:26448987

  4. Structural and Phylogenetic Analysis of a Conserved Actinobacteria-Specific Protein (ASP1; SCO1997) from Streptomyces Coelicolor

    Gao, B.; Sugiman-Marangos, S; Junop, M; Gupta, R

    2009-01-01

    The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum [1]. The cellular functions of these actinobacteria-specific proteins (ASP) are not known.

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

    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.

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

    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

  7. Draft genome sequence of Paenibacillus dauci sp. nov., a carrot-associated endophytic actinobacteria.

    Wu, Qian; Zhu, Liying; Jiang, Ling; Xu, Xian; Xu, Qing; Zhang, Zhidong; Huang, He

    2015-09-01

    Paenibacillus dauci sp. nov., a new kind of endophytic actinobacteria, is separated from the inner tissues of carrot sample, which forms intimated associations with carrot acting as biological control agents. Here we report a 5.37-Mb assembly of its genome sequence and other useful information, including the coding sequences (CDSs) responsible for biological processes such as antibiotic metabolic process, antimicrobial metabolism, anaerobic regulation and the biosynthesis of vitamin B and polysaccharide. This novel strain can be a potential source of novel lead products for exploitation in the field of pharmaceutical, agriculture and industry. PMID:26484263

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

    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

  9. Carbonate Mineral Formation under the Influence of Limestone-Colonizing Actinobacteria: Morphology and Polymorphism

    Cao, Chengliang; Jiang, Jihong; Sun, Henry; Huang, Ying; Tao, Faxiang; Lian, Bin

    2016-01-01

    Microorganisms and their biomineralization processes are widespread in almost every environment on earth. In this work, Streptomyces luteogriseus DHS C014, a dominant lithophilous actinobacteria isolated from microbial mats on limestone rocks, was used to investigate its potential biomineralization to allow a better understanding of bacterial contributions to carbonate mineralization in nature. The ammonium carbonate free-drift method was used with mycelium pellets, culture supernatant, and spent culture of the strain. Mineralogical analyses showed that hexagonal prism calcite was only observed in the sub-surfaces of the mycelium pellets, which is a novel morphology mediated by microbes. Hemispheroidal vaterite appeared in the presence of spent culture, mainly because of the effects of soluble microbial products (SMP) during mineralization. When using the culture supernatant, doughnut-like vaterite was favored by actinobacterial mycelia, which has not yet been captured in previous studies. Our analyses suggested that the effects of mycelium pellets as a molecular template almost gained an advantage over SMP both in crystal nucleation and growth, having nothing to do with biological activity. It is thereby convinced that lithophilous actinobacteria, S. luteogriseus DHS C014, owing to its advantageous genetic metabolism and filamentous structure, showed good biomineralization abilities, maybe it would have geoactive potential for biogenic carbonate in local microenvironments.

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

    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.

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

    Gomez-Escribano, Juan Pablo; Alt, Silke; 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 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. PMID:27089350

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

    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.

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

    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

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

    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.

  15. Structure of Mycobacterium tuberculosis Rv2714, a representative of a duplicated gene family in Actinobacteria

    The crystal structure of Rv2714, a protein of unknown function from M. tuberculosis, has been determined at 2.6 Å resolution using single-wavelength anomalous diffraction methods. The gene Rv2714 from Mycobacterium tuberculosis, which codes for a hypothetical protein of unknown function, is a representative member of a gene family that is largely confined to the order Actinomycetales of Actinobacteria. Sequence analysis indicates the presence of two paralogous genes in most mycobacterial genomes and suggests that gene duplication was an ancient event in bacterial evolution. The crystal structure of Rv2714 has been determined at 2.6 Å resolution, revealing a trimer in which the topology of the protomer core is similar to that observed in a functionally diverse set of enzymes, including purine nucleoside phosphorylases, some carboxypeptidases, bacterial peptidyl-tRNA hydrolases and even the plastidic form of an intron splicing factor. However, some structural elements, such as a β-hairpin insertion involved in protein oligomerization and a C-terminal α-helical domain that serves as a lid to the putative substrate-binding (or ligand-binding) site, are only found in Rv2714 bacterial homologues and represent specific signatures of this protein family

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

    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.

  17. Phylogenetic Diversity and Antimicrobial Activities of Culturable Endophytic Actinobacteria Isolated from Different Egyptian Marine Sponges and Soft Corals

    El-Bondkly, Ahmed-Mohammed; El-Gendy, Mervat M. A. A.; Wiese, Jutta; Imhoff, Johannes F.

    2012-01-01

    A cultivation-based approach was employed to isolate and compare the endophytic culturable actinobacterial diversity associated with different Egyptian marine sponges and soft corals. A total of 13 culturable actinobacteria isolates were obtained, five of which isolated from different sponges, two (AE27 and AE32) and three (AE29, AE41 and AE46) were isolated from Haliclona sp. and Callyspongia sp. collected from Sharm El-Sheikh and Hurghada, Egypt, respectively. Eight were isolated from diffe...

  18. Endophytic Actinobacteria from the Brazilian Medicinal Plant Lychnophora ericoides Mart. and the Biological Potential of Their Secondary Metabolites.

    Conti, Raphael; Chagas, Fernanda Oliveira; Caraballo-Rodriguez, Andrés Mauricio; Melo, Weilan Gomes da Paixão; do Nascimento, Andréa Mendes; Cavalcanti, Bruno Coêlho; de Moraes, Manoel Odorico; Pessoa, Cláudia; Costa-Lotufo, Letícia Veras; Krogh, Renata; Andricopulo, Adriano Defini; Lopes, Norberto Peporine; Pupo, Mônica Tallarico

    2016-06-01

    Endophytic actinobacteria from the Brazilian medicinal plant Lychnophora ericoides were isolated for the first time, and the biological potential of their secondary metabolites was evaluated. A phylogenic analysis of isolated actinobacteria was accomplished with 16S rRNA gene sequencing, and the predominance of the genus Streptomyces was observed. All strains were cultured on solid rice medium, and ethanol extracts were evaluated with antimicrobial and cytotoxic assays against cancer cell lines. As a result, 92% of the extracts showed a high or moderate activity against at least one pathogenic microbial strain or cancer cell line. Based on the biological and chemical analyses of crude extracts, three endophytic strains were selected for further investigation of their chemical profiles. Sixteen compounds were isolated, and 3-hydroxy-4-methoxybenzamide (9) and 2,3-dihydro-2,2-dimethyl-4(1H)-quinazolinone (15) are reported as natural products for the first time in this study. The biological activity of the pure compounds was also assessed. Compound 15 displayed potent cytotoxic activity against all four tested cancer cell lines. Nocardamine (2) was only moderately active against two cancer cell lines but showed strong activity against Trypanosoma cruzi. Our results show that endophytic actinobacteria from L. ericoides are a promising source of bioactive compounds. PMID:27128202

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

    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.

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

    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

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

    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.

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

    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

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

    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

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

    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

  5. Kenaf biomass biodecomposition by basidiomycetes and actinobacteria in submerged fermentation for production of carbohydrates and phenolic compounds.

    Brzonova, Ivana; Kozliak, Evguenii; Kubátová, Alena; Chebeir, Michelle; Qin, Wensheng; Christopher, Lew; Ji, Yun

    2014-12-01

    The efficiency and dynamics of simultaneous kenaf biomass decomposition by basidiomycetous fungi and actinobacteria were investigated. After 8weeks of incubation, up to 34wt.% of the kenaf biomass was degraded, with the combination of fungi and bacteria being the most efficient. Lignin decomposition accounted for ∼20% of the observed biomass reduction, regardless of the culture used. The remaining 80% of biomass degradation was due to carbohydrate based polymers. Major monosaccharides were produced in tangible yields (26-38%) at different times. Glucose, fructose and xylose were then fully consumed by day 25 while some galactose persisted until day 45. Once monosaccharides were depleted, the production of laccase, manganese-dependent peroxidase and lignin peroxidase enzymes, essential for lignin decomposition, was induced. The products of lignin biodecomposition were shown to be water-soluble and characterized by thermal desorption-pyrolysis-gas chromatography. PMID:25314665

  6. Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea.

    Karuppiah, Valliappan; Li, Yingxin; Sun, Wei; Feng, Guofang; Li, Zhiyong

    2015-07-01

    Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different marine sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA gene. Based on the screening of phzE genes, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE gene expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of gene screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria. PMID:25820602

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

    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

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

    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

  10. Classification of thermophilic actinobacteria isolated from arid desert soils, including the description of Amycolatopsis deserti sp. nov.

    Busarakam, Kanungnid; Brown, Ros; Bull, Alan T; Tan, Geok Yuan Annie; Zucchi, Tiago D; da Silva, Leonardo José; de Souza, Wallace Rafael; Goodfellow, Michael

    2016-02-01

    The taxonomic position of 26 filamentous actinobacteria isolated from a hyper-arid Atacama Desert soil and 2 from an arid Australian composite soil was established using a polyphasic approach. All of the isolates gave the diagnostic amplification product using 16S rRNA oligonucleotide primers specific for the genus Amycolatopsis. Representative isolates had chemotaxonomic and morphological properties typical of members of the genus Amycolatopsis. 16S rRNA gene analyses showed that all of the isolates belong to the Amycolatopsis methanolica 16S rRNA gene clade. The Atacama Desert isolates were assigned to one or other of two recognised species, namely Amycolatopsis ruanii and Amycolatopsis thermalba, based on 16S rRNA gene sequence, DNA:DNA relatedness and phenotypic data; emended descriptions are given for these species. In contrast, the two strains from the arid Australian composite soil, isolates GY024(T) and GY142, formed a distinct branch at the periphery of the A. methanolica 16S rRNA phyletic line, a taxon that was supported by all of the tree-making algorithms and by a 100 % bootstrap value. These strains shared a high degree of DNA:DNA relatedness and have many phenotypic properties in common, some of which distinguished them from all of the constituent species classified in the A. methanolica 16S rRNA clade. Isolates GY024(T) and GY142 merit recognition as a new species within the A. methanolica group of thermophilic strains. The name proposed for the new species is Amycolatopsis deserti sp. nov.; the type strain is GY024(T) (=NCIMB 14972(T) = NRRL B-65266(T)). PMID:26809280

  11. Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov., two novel actinobacteria isolated from a cave.

    Groth, Ingrid; Schumann, Peter; Schütze, Barbara; Augsten, Kurt; Stackebrandt, Erko

    2002-01-01

    Two novel strains of the class Actinobacteria were isolated from a cave in China. Cells of both strains were gram-positive, non-motile, non-spore-forming and not acid-fast and exhibited a rod/coccus growth cycle. Both isolates grew well on complex organic media under aerobic conditions. Their cell wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The acyl type of the glycan chain of peptidoglycan was acetyl. The major respiratory quinone was MK-8(H4). The cellular fatty acid profile was characterized by the predominance of 13-methyltetradecanoic (i-C15:0), 15-methylhexadecanoic (i-C17:0), 14-methylpentadecanoic (i-C16:0) and 14-methylhexadecanoic (ai-C17:0) acids. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were absent. The DNA G+C composition was 68-69 mol%. 16S rDNA-based phylogenetic analysis revealed an intermediate phylogenetic position of the cave isolates between the genera Janibacter and Tetrasphaera, which did not permit their unambiguous affiliation to either genus. Differences in morphological, physiological and chemotaxonomic properties between the two isolates and their closest phylogenetic neighbours support the proposal of a new genus and two novel species, Knoellia sinensis gen. nov., sp. nov. and Knoellia subterranea sp. nov. The type and only strains of the species are respectively HKI 0119T (= DSM 12331T = CIP 106775T) and HKI 0120T (= DSM 12332T = CIP 106776T). PMID:11837319

  12. Caracterización de actinobacterias raras, degradadoras de lignocelulosa: demostración de actividad lacasa en dos aislados de tsukamurella sp y cellulosimicrobium sp

    Enrique Luis Revollo Escudero; Oriana Danuta Serna Daza; Jorge Hernández Torres

    2014-01-01

    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 ampl...

  13. 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.

    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

  14. Distinct Spatial Patterns of SAR11, SAR86, and Actinobacteria Diversity along a Transect in the Ultra-oligotrophic South Pacific Ocean.

    West, Nyree J; Lepère, Cécile; Manes, Carmem-Lara de O; Catala, Philippe; Scanlan, David J; Lebaron, Philippe

    2016-01-01

    Distinct distribution patterns of members of the major bacterial clades SAR11, SAR86, and Actinobacteria were observed across a transect from the Marquesas islands through the ultra-oligotrophic South Pacific Gyre into the Chilean upwelling using 16S rRNA gene sequencing and RNA-DNA fingerprinting. Three different Actinobacteria sequence clusters belonging to "Candidatus Actinomarinidae" were localized in the western half of the transect, one was limited to the gyre deep chlorophyll maximum (DCM) and sequences affiliated to the OCS155 clade were unique to the upwelling. The structure of the surface bacterial community was highly correlated with water mass and remained similar across the whole central gyre (1300 nautical miles). The surface hyperoligotrophic gyre was dominated (>70% of all sequences) by highly diverse SAR11 and SAR86 operational taxonomic units and these communities were significantly different from those in the DCM. Analysis of 16S rRNA fingerprints generated from RNA allowed insights into the potential activity of assigned bacterial groups. SAR11 and Prochlorococcus showed the highest potential activity in all water masses except for the upwelling, accounting together for 65% of the total bacterial 16S rRNA in the gyre surface waters in equal proportions whereas the contribution of SAR11 decreased significantly at the DCM. PMID:27014192

  15. A Survey of Nucleotide Cyclases in Actinobacteria: Unique Domain Organization and Expansion of the Class III Cyclase Family in Mycobacterium tuberculosis

    Sandhya S. Visweswariah

    2004-01-01

    Full Text Available Cyclic nucleotides are well-known second messengers involved in the regulation of important metabolic pathways or virulence factors. There are six different classes of nucleotide cyclases that can accomplish the task of generating cAMP, and four of these are restricted to the prokaryotes. The role of cAMP has been implicated in the virulence and regulation of secondary metabolites in the phylum Actinobacteria, which contains important pathogens, such as Mycobacterium tuberculosis, M. leprae, M. bovis and Corynebacterium, and industrial organisms from the genus Streptomyces. We have analysed the actinobacterial genome sequences found in current databases for the presence of different classes of nucleotide cyclases, and find that only class III cyclases are present in these organisms. Importantly, prominent members such as M. tuberculosis and M. leprae have 17 and 4 class III cyclases, respectively, encoded in their genomes, some of which display interesting domain fusions seen for the first time. In addition, a pseudogene corresponding to a cyclase from M. avium has been identified as the only cyclase pseudogene in M. tuberculosis and M. bovis. The Corynebacterium and Streptomyces genomes encode only a single adenylyl cyclase each, both of which have corresponding orthologues in M. tuberculosis. A clustering of the cyclase domains in Actinobacteria reveals the presence of typical eukaryote-like, fungi-like and other bacteria-like class III cyclase sequences within this phylum, suggesting that these proteins may have significant roles to play in this important group of organisms.

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

    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

  17. 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.

    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

  18. 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

    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

  19. Diversity of integrating conjugative elements in actinobacteria

    Bordeleau, Eric; Ghinet, Mariana Gabriela; Burrus, Vincent

    2012-01-01

    Conjugation is certainly the most widespread and promiscuous mechanism of horizontal gene transfer in bacteria. During conjugation, DNA translocation across membranes of two cells forming a mating pair is mediated by two types of mobile genetic elements: conjugative plasmids and integrating conjugative elements (ICEs). The vast majority of conjugative plasmids and ICEs employ a sophisticated protein secretion apparatus called type IV secretion system to transfer to a recipient cell. Yet anoth...

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

    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. PMID:26241505

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

    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.

  2. Micromonospora endophytica sp. nov., an endophytic actinobacteria of Thai upland rice (Oryza sativa).

    Thanaboripat, Dusanee; Thawai, Chitti; Kittiwongwattana, Chokchai; Laosinwattana, Chamroon; Koohakan, Prommart; Parinthawong, Nonglak

    2015-11-01

    An actinobacterial strain, DCWR9-8-2(T), was isolated from a leaf of Thai upland rice (Oryza sativa) collected in Chumporn province, Thailand. Strain DCWR9-8-2(T) is Gram-stain-positive aerobic bacteria that produce single spores directly on the vegetative hypha. Cell wall peptidoglycan of this strain exhibits meso-diaminopimelic acid and glycine, the reducing sugars of whole-cell hydrolysate are arabinose, glucose, ribose, xylose and small amount of mannose. The phospholipid profiles in the membrane are comprised of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides. The major menaquinones are MK-9(H4) and MK-10(H6). The diagnostic cellular fatty acids are iso-C16:0 and iso-C15:0. The G+C content of the genomic DNA is 72.5 mol%. The result of 16S rRNA sequence analysis of the strain revealed that this strain was closely related to Micromonospora auratinigra TT1-11(T) (99.25%). On the other hand, the result of gyrB gene sequence analysis revealed that this strain was closed to M. eburnea JCM 12345(T) (96.30%). In addition, a combination of DNA-DNA hybridization results and some phenotypic properties supported that this strain should be judged as a novel species of the genus Micromonospora, for which the name M. endophytica sp. nov. is proposed. The type strain is DCWR9-8-2(T) (=BCC 67267(T)=NBRC 110008(T)). PMID:25966850

  3. Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture

    Pernthaler, J.; Posch, T.; Šimek, Karel; Vrba, Jaroslav; Pernthaler, A.; Glöckner, F. O.; Nübel, U.; Psenner, R.; Amann, R.

    2001-01-01

    Roč. 67, č. 5 (2001), s. 2145-2155. ISSN 0099-2240 R&D Projects: GA ČR GA206/99/0028 Grant ostatní: ANB(AT) OENB6513; AKTION(AT) 23P5 Keywords : protistan bacterivory * Cyclidium glaucoma * Ochromonas sp. Subject RIV: EE - Microbiology, Virology Impact factor: 3.688, year: 2001

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

    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

  5. Mycelial actinobacteria in salt-affected soils of arid territories of Ukraine and Russia

    Grishko, V. N.; Syshchikova, O. V.; Zenova, G. M.; Kozhevin, P. A.; Dubrova, M. S.; Lubsanova, D. A.; Chernov, I. Yu.

    2015-01-01

    A high population density (up to hundreds of thousands or millions CFU/g soil) of mycelial bacteria (actinomycetes) is determined in salt-affected soils of arid territories of Ukraine, Russia, and Turkmenistan. Of all the studied soils, the lowest amounts of actinomycetes (thousands and tens of thousands CFU/g soil) are isolated from sor (playa) and soda solonchaks developed on the bottoms of drying salt lakes in Buryatia and in the Amu Darya Delta. Actinomycetes of the Streptomyces, Micromonospora, and Nocardiopsis genera were recorded in the studied soils. It is found that conditions of preincubation greatly affect the activity of substrate consumption by the cultures of actinomycetes. This could be attributed to changes in the metabolism of actinomycetes as a mechanism of their adaptation to the increased osmotic pressure of the medium. The alkali tolerance of halotolerant actinomycetes isolated from the salt-affected soils is experimentally proved.

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

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

    Sci.12, 213–217. 29. Whitelaw M.A., Harden T.J., Heylar K.R., 1999, Phosphate solubilization in solution culture by the soil fungus Penicillium radicum. Soil Biol.Biochem. 31, 655-665. 30. Widawati S., Suliasih., Latupuapua H.J.D., Sugiharto A...

  7. Predator-Specific Enrichment of Actinobacteria from a Cosmopolitan Freshwater Clade in Mixed Continuous Culture

    Pernthaler, Jakob; Posch, Thomas; S̆imek, Karel; Vrba, Jaroslav; Pernthaler, Annelie; Glöckner, Frank Oliver; Nübel, Ulrich; Psenner, Roland; Amann, Rudolf

    2001-01-01

    We investigated whether individual populations of freshwater bacteria in mixed experimental communities may exhibit specific responses to the presence of different bacterivorous protists. In two successive experiments, a two-stage continuous cultivation system was inoculated with nonaxenic batch cultures of the cryptophyte Cryptomonas sp. Algal exudates provided the sole source of organic carbon for growth of the accompanying microflora. The dynamics of several 16S rRNA-defined bacterial popu...

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

    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

  9. Antiviral Activity of Marine Actinobacteria against Bovine Viral Diarrhea Virus, a Surrogate Model of the Hepatitis C Virus

    Juliana Cristina Santiago Bastos

    2015-12-01

    Full Text Available The Hepatitis C virus (Flaviviridae family, Hepacivirus genus represents a major public health problem worldwide and it is responsible for chronic infections in humans, which can develop to liver cirrhosis and hepatocellular carcinoma. As this virus does not replicate efficiently in cell culture and in animals, bovine viral diarrhea virus (BVDV is used as a surrogate model for screening assays of antiviral activity, and mechanism of action assays. From marine invertebrates and their microorganisms isolated, we prepared extracts and fractions, and we isolated substances for assessment of their possible antiviral activity. Of the 71 tested, seven were considered promising presenting protection percentage of more than 80%. The best inhibition results were obtained from the extracts produced by the Gordonia bacteria samples with 99.9% inhibition and by Micrococcus with 99% inhibition. Furthermore, most of the extracts selected by the protection percentage showed selectivity index values considered promising, especially the extracts of the bacteria Williansia (SI=27 and Brachybacterium (SI=39. On the action mechanism, most of the promising extracts showed activity in the inhibition of intracellular replication steps, although it has been observed action of different extracts in several stages of viral replicative cycle. Thus, various extracts stood out and may lead to the development of drugs that ensure an alternative therapy for the treatment of hepatitis C.

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

    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.

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

    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.

  12. Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition

    Wang, Cheng; Dong, Da; Wang, Haoshu; Müller, Karin; Qin, Yong; Wang, Hailong; Wu, Weixiang

    2016-01-01

    Background Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenom...

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

    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

  14. 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

    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.

  15. 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

    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.

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

    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

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

    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)....

  18. Reassessment of the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria

    Swithers, Kristen S.; Fournier, Gregory P.; Anna G Green; Gogarten, J. Peter; Lapierre, Pascal

    2011-01-01

    In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of Gram-negative bacteria (Nature 460: 967–971). The presented data supported the Gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia. His conclusion was based on a presence-absence analysis of protein families that divided all prokaryotes into five groups: Actinobacteria, Double Membrane bacteria (DM), Clostridia, ...

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

    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....

  20. Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

    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

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

    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.

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

    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.

  3. Structural-functional specificity of the complexes of psychrotolerant soil actinomycetes

    Zenova, G. M.; Dubrova, M. S.; Zvyagintsev, D. G.

    2010-04-01

    The active growth and development of psychrotolerant actinomycetes take place in peat and podzolic soils of the tundra and taiga at temperatures below 10°C. The population density of psychrotolerant mycelial prokaryotes in these soils reaches thousands and tens of thousands of CFU/g of soil, and the length of their mycelium is up to 380 m/g of soil. The application of fluorescent in situ hybridization (the FISH method) demonstrated that the metabolically active psychrotolerant representatives of the phylogenetic group of Actinobacteria comprise up to 30% of the total number of bacteria in prokaryotic microbial communities of oligotrophic peat bog and podzolic soils. The portion of metabolically active mycelial actinobacteria exceeds the portion of unicellular actinobacteria. Psychrotolerant streptomycetes isolated from peat bog soils possess pectinolytic, amylolytic, and antagonistic activities at low temperatures (5°C).

  4. 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

    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

  5. Bacterial diversity and abundance of a creek valley sites reflected soil pH and season

    Ságová-Marečková, M.; Čermák, L.; Omelka, M.; Kyselková, Martina; Kopecký, J.

    2015-01-01

    Roč. 10, č. 1 (2015), s. 61-70. ISSN 2391-5412 Grant ostatní: GA AV ČR(CZ) IAA603020901 Institutional support: RVO:60077344 Keywords : bacterial communities * actinobacteria * OM quantity and quality * T-RFLP Subject RIV: EE - Microbiology, Virology

  6. 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.

    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

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

    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.

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

    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

  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

    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.

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

    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.

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

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

    2008-01-01

    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 of...

  12. Cell division in Corynebacterineae

    CatrionaDonovan

    2014-04-01

    Full Text Available Bacterial cells must coordinate a number of events during the cell cycle. Spatio-temporal regulation of bacterial cytokinesis is indispensable for the production of viable, genetically identical offspring. In many rod-shaped bacteria, precise midcell assembly of the division machinery relies on inhibitory systems such as Min and Noc. In rod-shaped Actinobacteria, for example Corynebacterium glutamicum and Mycobacterium tuberculosis, the divisome assembles in the proximity of the midcell region, however more spatial flexibility is observed compared to Escherichia coli and Bacillus subtilis. Actinobacteria represent a group of bacteria that spatially regulate cytokinesis in the absence of recognizable Min and Noc homologs. The key cell division steps in E. coli and B. subtilis have been subject to intensive study and are well understood. In comparison, only a minimal set of positive and negative regulators of cytokinesis are known in Actinobacteria. Nonetheless, the timing of cytokinesis and the placement of the division septum is coordinated with growth as well as initiation of chromosome replication and segregation. We summarize here the current knowledge on cytokinesis and division site selection in the Actinobacteria suborder Corynebacterineae.

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

    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.

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

    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...

  15. .i.Candidatus./i. Planktophila limnetica, an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton

    Jezbera, Jan; Sharma, A. K.; Brandt, U.; Doolittle, W.F.; Hahn, M.W.

    2009-01-01

    Roč. 59, č. 11 (2009), s. 2864-2869. ISSN 1466-5026 Institutional research plan: CEZ:AV0Z60170517 Keywords : Actinobacteria * Planktophila * freshwater * bacterioplankton Subject RIV: EE - Microbiology, Virology Impact factor: 2.113, year: 2009

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

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

    2016-01-01

    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.

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

    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

  18. Isolation of Bacterial Strains Capable of Sulfamethoxazole Mineralization from an Acclimated Membrane Bioreactor

    Bouju, H.; Ricken, B.; Beffa, T; Corvini, P. F.- X.; Kolvenbach, B.A.

    2011-01-01

    In this study, we isolated five strains capable of degrading 14C-labeled sulfamethoxazole to 14CO2 from a membrane bioreactor acclimatized to sulfamethoxazole, carbamazepine, and diclofenac. Of these strains, two belonged to the phylum Actinobacteria, while three were members of the Proteobacteria.

  19. Insights into variability of actinorhodopsin genes of the LG1 cluster in two different freshwater habitats

    Jezberová, Jitka; Jezbera, Jan; Hahn, M.W.

    2013-01-01

    Roč. 8, č. 7 (2013), e68542. E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GEEEF/10/E011 Institutional support: RVO:60077344 Keywords : actinobacteria * bacteria * bacterioplankton * diversity * sequences * lakes Subject RIV: EE - Microbiology, Virology Impact factor: 3.534, year: 2013

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

    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

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

    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.

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

    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.

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

    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.

  4. New insight into influence of mechanical stirring on membrane fouling of membrane bioreactor: Mixed liquor properties and hydrodynamic conditions.

    Qi, Chao; Wang, Jinnan; Lin, Yaohua

    2016-07-01

    Although membrane bioreactor is widely used in wastewater treatment, the problem of membrane fouling remains to be resolved. This paper focused on the influence of mechanical stirring on membrane fouling. Ammonium removal decreased with viscous bulking when stirring rates slowed down. Trans-membrane pressure increased more rapidly when the stirring rate decreased. The resistance of the gel layer increased significantly under low stirring rates, which indicated that the fouling rates of MBR in different stages were attributed to gel layer variation. The proportion of small particles increased when stirring rates slowed down. Furthermore, 16S rRNA gene amplicon sequencing showed that Proteobacteria and Actinobacteria were dominant in the mixed liquor. The relative abundance of Actinobacteria increased from 41% to 50% in the entire experiment. The computational fluid dynamics model was used to simulate the fluid flow characteristics. The model indicated velocities and directions of the fluid flow changes with different stirring rates. PMID:27058400

  5. 信息动态

    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.

  6. Insect symbioses: a case study of past, present, and future fungus-growing ant research

    Caldera, Eric J; Poulsen, Michael; Suen, Garret;

    2009-01-01

    Fungus-growing ants (Attini: Formicidae) engage in an obligate mutualism with fungi they cultivate for food. Although biologists have been fascinated with fungus-growing ants since the resurgence of natural history in the modern era, the early stages of research focused mainly on the foraging......'s fungus garden, antibiotic-producing actinobacteria that help protect the fungus garden from the parasite, and a black yeast that parasitizes the ant-actinobacteria mutualism. The fungus-growing ant symbiosis serves as a particularly useful model system for studying insect-microbe symbioses, because, to...... date, it contains four well-characterized microbial symbionts, including mutualists and parasites that encompass micro-fungi, macro-fungi, yeasts, and bacteria. Here, we discuss approaches for studying insect-microbe symbioses, using the attine ant-microbial symbiosis as our framework. We draw...

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

    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.

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

    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

  9. [Taxonomical status of the psychrotolerant Antarctic microorganisms].

    Romanovskaia, V A; Gladka, G V; Tashireva, A A; Tashirev, A B

    2013-01-01

    The aerobic chemoorganotrophic bacteria, dominating in soils and phytocenosis of the Antarctic Region, on combination of morphological and biochemical properties belong to several taxons of Bacteria domain. Gram-negative strains 3189, 3415 (fam. Halomonadaceae, Halomonas sp.) and 3088, 3468, 3469 (fam. Moraxellaceae, Psychrobacter sp.) belong to phylum Proteobacteria, to class Gammaproteobacteria. Gram-negative strains 3294 3392 (Rhizobiales, fam. Methylobacteriaceae, Methylobacterium sp.) relate to class Alphaproteobacteria of this phylum. Gram-positive strains 3179, 3275, 3470, 3471 (fam. Microbacteriaceae, Cryobacterium sp.), 3054, 3058, 3411 (fam. Corynebacteriaceae, Corynebacterium sp.) and 3194, 3398 (fam. Micrococcaceae, Micrococcus sp.) relate to phylum Actinobacteria, class Actinobacteria. Thus, the psychrophilic and psychrotolerant Antarctic bacteria (aerobic chemoorganotrophic) isolated from phytocenosis and soils of polar region are characterized by wide taxonomic variety. PMID:24450178

  10. Insights into the molecular bases of the interaction of Bifidobacterium bifidum PRL2010 with the human host and with other human gut commensals.

    Serafini, Fausta

    2014-01-01

    I bifidobatteri sono tra i microrganismi maggiormente presenti nel tratto gastro-intestinale (GIT) dei mammiferi. Sono batteri anaerobi obbligati appartenenti al phylum degli Actinobacteria, Gram-positivi ad alto contenuto di G+C nel genoma. Sono state identificate 47 taxa di bifidobatteri, 11 delle quali isolate dal GIT umano. Sono i primi colonizzatori del tratto gastro-intestinale dei neonati e predominano in quelli allattati al seno, invece dopo lo svezzamento sono in quantità minore risp...

  11. Genetic adaptation of bifidobacteria to the human gut: insights from genomics and transcriptomics analyses

    Duranti, Sabrina

    2015-01-01

    I bifidobatteri sono batteri Gram positivi che appartengono al phylum degli Actinobacteria, caratterizzati dall’avere alto contenuto in GC nel loro DNA, dall’essere non mobili, asporigeni e anaerobi. I bifidobatteri sono parte del microbiota intestinale umano dove sono ritenuti in grado di esplicare degli effetti benefici sull’ospite. Nell’intestino i bifidobatteri sono in grado di influenzare la fisiologia, lo stato di salute e la risposta immunitaria dell’ospite. Tuttavia, poco si cono...

  12. Genomic and ecological studies to understand bifidobacterial adaptation to the human gastro-intestinal tract

    Turroni, Francesca

    2010-01-01

    The Bifidobacterium genus comprises a high GC Gram positive bacteria belonging to the Actinobacteria phylum, which has been found to represent a common inhabitant of the gastro-intestinal tract (GIT) of mammals. In particular focusing on the GIT of human, the overall microorganisms that colonize such environment represent the “gut microbiota”. The human gut microbiota is an extremely complex microbial community whose functions are believed to have a significant impact on human physiology. Dif...

  13. Spatial distribution of marine airborne bacterial communities

    Seifried, Jasmin S; Wichels, Antje; Gerdts, Gunnar

    2015-01-01

    The spatial distribution of bacterial populations in marine bioaerosol samples was investigated during a cruise from the North Sea to the Baltic Sea via Skagerrak and Kattegat. The analysis of the sampled bacterial communities with a pyrosequencing approach revealed that the most abundant phyla were represented by the Proteobacteria (49.3%), Bacteroidetes (22.9%), Actinobacteria (16.3%), and Firmicutes (8.3%). Cyanobacteria were assigned to 1.5% of all bacterial reads. A core of 37 bacterial ...

  14. Genomics of Probiotic Bacteria

    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.

  15. Quantitative comparison of bacterial communities in two Mediterranean sponges

    Noyer, Charlotte; Hamilton, A.; Sacristan-Soriano, Oriol; Becerro, Mikel

    2010-01-01

    Marine sponges can host in their tissues abundant and diverse bacterial communities. Lack of truly quantitative data on bacterial abundance and dynamics limits our understanding of the organization and functioning of these endobiotic communities. In this technical note, we describe a quantitative polymerase chain reaction approach to quantify the relative abundance of multiple clades of three major sponge-associated bacterial phyla: Chloroflexi, Acidobacteria, and Actinobacteria. To test our ...

  16. Comparative genomics reveals evidence of marine adaptation in Salinispora species

    Penn Kevin

    2012-03-01

    Full Text Available Abstract Background Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed.

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

    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...

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

    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...

  19. Genome-wide bioinformatics analysis of steroid metabolism-associated genes in Nocardioides simplex VKM Ac-2033D.

    Shtratnikova, Victoria Y; Schelkunov, Mikhail I; Fokina, Victoria V; Pekov, Yury A; Ivashina, Tanya; Donova, Marina V

    2016-08-01

    Actinobacteria comprise diverse groups of bacteria capable of full degradation, or modification of different steroid compounds. Steroid catabolism has been characterized best for the representatives of suborder Corynebacterineae, such as Mycobacteria, Rhodococcus and Gordonia, with high content of mycolic acids in the cell envelope, while it is poorly understood for other steroid-transforming actinobacteria, such as representatives of Nocardioides genus belonging to suborder Propionibacterineae. Nocardioides simplex VKM Ac-2033D is an important biotechnological strain which is known for its ability to introduce ∆(1)-double bond in various 1(2)-saturated 3-ketosteroids, and perform convertion of 3β-hydroxy-5-ene steroids to 3-oxo-4-ene steroids, hydrolysis of acetylated steroids, reduction of carbonyl groups at C-17 and C-20 of androstanes and pregnanes, respectively. The strain is also capable of utilizing cholesterol and phytosterol as carbon and energy sources. In this study, a comprehensive bioinformatics genome-wide screening was carried out to predict genes related to steroid metabolism in this organism, their clustering and possible regulation. The predicted operon structure and number of candidate gene copies paralogs have been estimated. Binding sites of steroid catabolism regulators KstR and KstR2 specified for N. simplex VKM Ac-2033D have been calculated de novo. Most of the candidate genes grouped within three main clusters, one of the predicted clusters having no analogs in other actinobacteria studied so far. The results offer a base for further functional studies, expand the understanding of steroid catabolism by actinobacteria, and will contribute to modifying of metabolic pathways in order to generate effective biocatalysts capable of producing valuable bioactive steroids. PMID:26832142

  20. Specificity and stability of the Acromyrmex–Pseudonocardia symbiosis

    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 ...

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

    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...

  2. Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis

    Oh, Dong-Chan; Poulsen, Michael; Currie, Cameron R; Clardy, Jon

    2009-01-01

    Fungus-growing ants engage in mutualistic associations with both the fungus they cultivate for food and actinobacteria (Pseudonocardia spp.) that produce selective antibiotics to defend that fungus from specialized fungal parasites. We have analyzed one such system at the molecular level and found...... that the bacterium associated with the ant Apterostigma dentigerum produces dentigerumycin, a cyclic depsipeptide with highly modified amino acids, to selectively inhibit the associated parasitic fungus (Escovopsis sp.)....

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

    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.

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

    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

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

    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...

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

    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...

  7. Concluding remarks

    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...

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

    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...

  9. Co-operation between different targeting pathways during integration of a membrane protein

    Keller, Rebecca; de Keyzer, Jeanine; Driessen, Arnold J. M.; Palmer, Tracy

    2012-01-01

    Membrane protein assembly is a fundamental process in all cells. The membrane-bound Rieske iron-sulfur protein is an essential component of the cytochrome bc(1) and cytochrome b(6)f complexes, and it is exported across the energy-coupling membranes of bacteria and plants in a folded conformation by the twin arginine protein transport pathway (Tat) transport pathway. Although the Rieske protein in most organisms is a monotopic membrane protein, in actinobacteria, it is a polytopic protein with...

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

    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.

  11. Actinomycetes from the South China Sea sponges: isolation, diversity, and potential for aromatic polyketides discovery

    Sun, Wei; Zhang, Fengli; He, Liming; Karthik, Loganathan; Li, Zhiyong

    2015-01-01

    Marine sponges often harbor dense and diverse microbial communities including actinobacteria. To date no comprehensive investigation has been performed on the culturable diversity of the actinomycetes associated with South China Sea sponges. Structurally novel aromatic polyketides were recently discovered from marine sponge-derived Streptomyces and Saccharopolyspora strains, suggesting that sponge-associated actinomycetes can serve as a new source of aromatic polyketides. In this study, a tot...

  12. Actinomycetes as host cells for production of recombinant proteins

    Tamura Tomohiro; Mitani Yasuo; Nakashima Nobutaka

    2005-01-01

    Abstract Actinomycetes (Actinobacteria) are highly attractive as cell factories or bioreactors for applications in industrial, agricultural, environmental, and pharmaceutical fields. Genome sequencing of several species of actinomycetes has paved the way for biochemical and structural analysis of important proteins and the production of such proteins as recombinants on a commercial scale. In this regard, there is a need for improved expression vectors that will be applicable to actinomycetes....

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

    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...

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

    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...

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

    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

  16. The pupylation machinery is involved in iron homeostasis by targeting the iron storage protein ferritin

    Küberl, Andreas; Polen, Tino; Bott, Michael

    2016-01-01

    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 ...

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

    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...

  18. Concluding remarks

    Lerayer, Alda

    2005-01-01

    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 agencies, clarity regardi...

  19. Rhodococcus erythropolis MTHt3 biotransforms ergopeptines to lysergic acid

    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...

  20. Keratinolytic abilities of Micrococcus luteus from poultry waste

    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...

  1. Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes

    Gupta, Radhey S.

    2011-01-01

    The prokaryotic organisms can be divided into two main groups depending upon whether their cell envelopes contain one membrane (monoderms) or two membranes (diderms). It is important to understand how these and other variations that are observed in the cell envelopes of prokaryotic organisms have originated. In 2009, James Lake proposed that cells with two membranes (primarily Gram-negative bacteria) originated from an ancient endosymbiotic event involving an Actinobacteria and a Clostridia (...

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

    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.

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

    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...

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

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

    2016-01-01

    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. PMID:26950332

  5. Diversity and biocatalytic potential of epoxide hydrolases identified by genome analysis

    van der Loo, B; Kingma, J.; Arand, M; Wubbolts, Marcel; Janssen, D B

    2006-01-01

    Epoxide hydrolases play an important role in the biodegradation of organic compounds and are potentially useful in enantioselective biocatalysis. An analysis of various genomic databases revealed that about 20% of sequenced organisms contain one or more putative epoxide hydrolase genes. They were found in all domains of life, and many fungi and actinobacteria contain several putative epoxide hydrolase-encoding genes. Multiple sequence alignments of epoxide hydrolases with other known and puta...

  6. Morphological, Physiological, and Taxonomic Characterization of Actinobacterial Isolates Living as Endophytes of Cacao Pods and Cacao Seeds.

    Tchinda, Romaric Armel Mouafo; Boudjeko, Thaddée; Simao-Beaunoir, Anne-Marie; Lerat, Sylvain; Tsala, Éric; Monga, Ernest; Beaulieu, Carole

    2016-03-26

    Vascular plants are commonly colonized by endophytic actinobacteria. However, very little is known about the relationship between these microorganisms and cacao fruits. In order to determine the physiological and taxonomic relationships between the members of this community, actinobacteria were isolated from cacao fruits and seeds. Among the 49 isolates recovered, 11 morphologically distinct isolates were selected for further characterization. Sequencing of the 16S rRNA gene allowed the partition of the selected isolates into three phylogenetic clades. Most of the selected endophytic isolates belonged to the Streptomyces violaceusniger clade. Physiological characterization was carried out and a similarity index was used to cluster the isolates. However, clustering based on physiological properties did not match phylogenetic lineages. Isolates were also characterized for traits commonly associated with plant growth-promoting bacteria, including antibiosis and auxin biosynthesis. All isolates exhibited resistance to geldanamycin, whereas only two isolates were shown to produce this antibiotic. Endophytes were inoculated on radish seedlings and most isolates were found to possess plant growth-promoting abilities. These endophytic actinobacteria inhibited the growth of various plant pathogenic fungi and/or bacteria. The present study showed that S. violaceusniger clade members represent a significant part of the actinobacterial community living as endophytes in cacao fruits and seeds. While several members of this clade are known to be geldanamycin producers and efficient biocontrol agents of plant diseases, we herein established the endophytic lifestyle of some of these microorganisms, demonstrating their potential as plant health agents. PMID:26947442

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

    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

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

    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.

  9. Spatial and temporal changes in Actinobacterial dominance in experimental artificial groundwater recharge.

    Kolehmainen, Reija E; Tiirola, Marja; Puhakka, Jaakko A

    2008-11-01

    Artificial groundwater recharge (AGR) is used in the drinking water industry to supplement groundwater resources and to minimise the use of chemicals in water treatment. This study analysed the spatial and temporal changes of microbial communities in AGR using two test systems: a nutrient-amended fluidized-bed reactor (FBR) and a sand column. Structural changes in the feed lake water (Lake Roine), FBR, and sand column bacterial communities were determined by denaturing gradient gel electrophoresis (DGGE) and the length heterogeneity analysis of amplified 16S rRNA genes (LH-PCR). Two clone libraries were created to link the LH-PCR results to the dominant bacterial groups. The lake water bacterial community was relatively stable, with three bands dominating in all LH-PCR products. The most dominant fragment accounted for up to 72% and was derived from Actinobacteria. Based on the clone libraries and LH-PCR data, Actinobacteria also dominated in the unattached bacterial community of the FBR, whereas several Proteobacterial groups were more abundant on the FBR carrier particles. In the stabilised AGR system a major change in the community structure of the lake water bacteria took place during passage within the first 0.6m in the sand column as the community composition shifted from Actinobacteria-dominated populations to a diverse, mainly Proteobacterial communities. Concurrently, most of the dissolved organic carbon (DOC) was removed at this stage. In summary, the study showed that the make-up of microbial communities in experimental AGR systems responded to changes in their environment. LH-PCR showed potential as a method to determine microbial community dynamics in long-term studies at real-scale AGR sites. This is the first step to provide data on microbial community dynamics in AGR for drinking water production. PMID:18757075

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

    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.

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

    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

  12. Differences between Bacterial Communities in the Gut of a Soil-Feeding Termite (Cubitermes niokoloensis) and Its Mounds▿ †

    Fall, Saliou; Hamelin, Jérôme; Ndiaye, Farma; Assigbetse, Komi; Aragno, Michel; Chotte, Jean Luc; Brauman, Alain

    2007-01-01

    In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics. PMID:17574999

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

    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

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

    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.

  15. Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing.

    Lee, Soo Eon; Nam, Ok Hyung; Lee, Hyo-Seol; Choi, Sung Chul

    2016-07-01

    Objectives The purpose of this study was designed to identify the oral microbiota in healthy Korean pre-school children using pyrosequencing. Materials and methods Dental plaque samples were obtained form 10 caries-free pre-school children. The samples were analysed using pyrosequencing. Results The pyrosequencing analysis revealed that, at the phylum level, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria showed high abundance. Also, predominant genera were identified as core microbiome, such as Streptococcus, Neisseria, Capnocytophaga, Haemophilus and Veilonella. Conclusions The diversity and homogeneity was shown in the dental plaque microbiota in healthy Korean pre-school children. PMID:26758186

  16. The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos

    Sommer, Felix; Ståhlman, Marcus; Ilkayeva, Olga;

    2016-01-01

    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......, suggesting that seasonal variation in the microbiota may contribute to host energy metabolism in the hibernating brown bear....

  17. Functional and phenotypic profiling of innate immunity during Salmonella infection

    Sørensen, Rikke Brandt; Pedersen, Susanne Brix

    bacterial infections, whereas the other major dendritic cell subset, plasmacytoid DC (pDC), plays an important part in antiviral responses, and is less well characterised in regard to antibacterial immunity. Using multi-parametric flow cytometry, we were able to show for the first time that pDC accumulated...... observed that DC responded to six different bacteria in a phyla-specific manner giving rise to similar inflammatory signatures within the groups of proteobacteria, firmicutes and actinobacteria, hence being independent on pathogenic versus non-pathogenic properties, and also on the bacteria-to-cell ratio...

  18. Isolation of putative probionts from cod rearing environment

    Lauzon, H.L.; Gudmundsdottir, S.; Pedersen, M.H.;

    2008-01-01

    Survival problems are encountered at early stages of intensive fish rearing and antibiotics are widely used to remedy the situation. Probiotics may provide a potential alternative method to protect larvae from opportunistic and pathogenic bacteria and promote a balanced environment. This study was......, metabolite production and adhesion to fish cell lines. Our study demonstrated that 14% of screened bacteria (n = 188) had antagonistic properties towards fish pathogens. The majority of these isolates were Gram-positive (81%), belonging to Firmicutes (69.2%) and Actinobacteria (11.5%) phyla based on 16S r...

  19. 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

    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.

  20. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems.

    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui

    2015-01-01

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and

  1. Sbírka kultur půdních aktinomycetů v Ústavu půdní biologie BC AV ČR, v.v.i. České Budějovice

    Krištůfek, Václav; Chroňáková, Alica; Elhottová, Dana; Petrásek, Jiří; Němec, Jan

    České Budějovice: Ústav půdní biologie BC AV ČR, 2009, s. 88-91. ISBN 978-80-86525-16-7. [Život v půdě /10./. České Budějovice (CZ), 27.01.2009-28.01.2009] R&D Projects: GA MŠk LC06066; GA MŠk 2B06154; GA AV ČR IAA600660607 Institutional research plan: CEZ:AV0Z60660521 Keywords : Actinobacteria * culture collection * microorganisms Subject RIV: EH - Ecology, Behaviour

  2. Isolation, screening and characterization of uranium microremediable actinomycetes from fallen leaves of Azadirachta indica in Western Ghats

    Microremediation of harmful radioactive waste such as uranium has been carried out by the endophytic actinomycetes strains isolated from the unnoticed fallen leaves of commonly available medicinal plant Azadirachta indica, which are considered as unique source. Among six actinobacteria isolates, one microbe (A5) effectively removed uranium in 12 h at temperature 30 deg C and pH 8-9. Molecular characterization and phylogenetic analysis support the classification of the isolate A5 as a new strain which was named as Streptomyces sp. MINIYAA7 (Genbank accession number KF909129). (author)

  3. The structural-functional organization of thermotolerant complexes of actinomycetes in desert and volcanic soils

    Zenova, G. M.; Kurapova, A. I.; Lysenko, A. M.; Zvyagintsev, D. G.

    2009-05-01

    It has been found that the number of thermotolerant actinomycetes in strongly heated soils of deserts and volcanic regions is comparable to or exceeds the number of mesophilic actinomycetes. Among the latter group, streptomyces usually predominate; among thermotolerant actinomycetes, representatives of the Micromonospora, Streptosporangium, Actinomadura, Saccharopolyspora, Microtetraspora, and Microbispora genera are identified. Thermotolerant actinomycetes display the full cycle of their development in these soils. The method of fluorescent in situ hybridization has made it possible to determine that mycelial forms predominate among the metabolically active representatives of Actinobacteria; their portion increases with the rise in the temperature of soil incubation.

  4. Human microbiome: From the bathroom to the bedside

    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.

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

    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....

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

    Bhatia, Sonu; Batra, Navneet; Pathak, Ashish; Joshi, Amit; Souza, Leila; Almeida, Paulo; Chauhan, Ashvini

    2015-09-01

    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. PMID:26484255

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

    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.

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

    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.

  9. Bacterial community analysis of contaminant soils from Chernobyl

    Complete text of publication follows: Shortly after the Chernobyl accident in 1986, vegetation, contaminated soil and other radioactive debris were buried in situ in trenches. The aims of this work are to analyse the structure of bacterial communities evolving in this environment since 20 years, and to evaluate the potential role of microorganisms in radionuclide migration in soils. Therefore, soil samples exhibiting contrasted radionuclides content were collected in and around the trench number 22. Bacterial communities were examined using a genetic fingerprinting method that allowed a comparative profiling of the samples (DGGE), with universal and group-specific PCR primers. Our results indicate that Chernobyl soil samples host a wide diversity of Bacteria, with stable patterns for Firmicutes and Actinobacteria and more variable for Proteobacteria. A collection of 650 aerobic and anaerobic culturable isolates was also constructed. A phylogenetic analysis of 250 heterotrophic aerobic isolates revealed that 5 phyla are represented: Beta-, Gamma-proteobacteria, Actinobacteria, Bacteroidetes and spore-forming Firmicutes, which is largely dominant. These collection will be screened for the presence of radionuclide-accumulating species in order to estimate the potential influence of microorganisms in radionuclides migration in soils

  10. Molecular Biological Analysis of Microorganisms in Petroleum Reservoirs

    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.

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

    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

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

    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.

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

    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.

  14. Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria.

    Kristen S Swithers

    Full Text Available In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of gram-negative bacteria (Nature 460: 967-971. The presented data supported the gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia. His conclusion was based on a presence-absence analysis of protein families that divided all prokaryotes into five groups: Actinobacteria, Double Membrane bacteria (DM, Clostridia, Archaea and Bacilli. Of these five groups, the DM are by far the largest and most diverse group compared to the other groupings. While the fusion hypothesis for the origin of double membrane bacteria is enticing, we show that the signal supporting an ancient symbiosis is lost when the DM group is broken down into smaller subgroups. We conclude that the signal detected in James Lake's analysis in part results from a systematic artifact due to group size and diversity combined with low levels of horizontal gene transfer.

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

    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

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

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

    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

  18. Soil bacterial diversity changes in response to agricultural land use in semi-arid soils

    Ding, Guo-Chun; Piceno, Yvette M.; Heuer, Holger; Weinert, Nicole; Dohrmann, Anja B.; Carrillo, Angel; Andersen, Gary L.; Castellanos, Thelma; Tebbe, Christoph C.; Smalla, Kornelia

    2013-04-01

    Natural scrublands in semi-arid deserts are increasingly being converted into agricultural lands. The long-term effect of such a transition in land use on soil bacterial communities was explored at two sites typical of semi-arid deserts in Mexico (Baja California). Comparisons were made between soil samples from alfalfa fields and the adjacent scrublands by two complementary methods - denaturing gradient gel electrophoresis (DGGE) and PhyloChip hybridization -employed to analyze 16S rRNA gene fragments amplified from total community DNA. 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. The arable soils were lower in organic matter and phosphate concentration, and higher in salinity. Soil parameters that differed between land uses were highly correlated with the community composition of taxa responding to land use. Variation in the bacterial community composition was higher in soils from scrubland than from agriculture, as revealed by DGGE and PhyloChip analyses. The long term use for agriculture resulted in profound changes in the bacterial community composition and physicochemical characteristics of former scrublands, which may affect various soil ecosystem functions.

  19. Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China.

    Liu, Zhenghui; Huang, Shaobin; Sun, Guoping; Xu, Zhencheng; Xu, Meiying

    2012-04-01

    Bacterioplankton community compositions in the Dongjiang River were characterized using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library construction. Water samples in nine different sites were taken along the mainstem and three tributaries. In total, 24 bands from DGGE gels and 406 clones from the libraries were selected and sequenced, subsequently analyzed for the bacterial diversity and composition of those microbial communities. Bacterial 16S rRNA gene sequences from freshwater bacteria exhibited board phylogenetic diversity, including sequences representing the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteriodetes, Verrucomicrobia, and candidate division TM7. Members of Betaproteobacteria group were the most dominant in all sampling sites, followed by Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria. DGGE profiles and the ∫-LIBSHUFF analysis revealed similar patterns of bacterial diversity among most sampling sites, while spatial distribution variances existed in all sites along the river basin. Statistical analysis showed that bacterial species distribution strongly correlated with environmental variables, such as nitrate and ammonia, suggesting that nitrogen nutrients may shape the microbial community structure and composition in the Dongjiang River. This study had important implications for the comparison with other rivers elsewhere and contributed to the growing data set on the factors that structure bacterial communities in freshwater ecosystems. PMID:22133045

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

    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

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

    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.

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

    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.

  3. Diversity rankings among bacterial lineages in soil.

    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

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

    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

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

    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

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

    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

  7. A diversified approach to evaluate biostimulation and bioaugmentation strategies for heavy-oil-contaminated soil.

    Lladó, S; Solanas, A M; de Lapuente, J; Borràs, M; Viñas, M

    2012-10-01

    A diversified approach involving chemical, microbiological and ecotoxicity assessment of soil polluted by heavy mineral oil was adopted, in order to improve our understanding of the biodegradability of pollutants, microbial community dynamics and ecotoxicological effects of various bioremediation strategies. With the aim of improving hydrocarbon degradation, the following bioremediation treatments were assayed: i) addition of inorganic nutrients; ii) addition of the rhamnolipid-based biosurfactant M(AT10); iii) inoculation of an aliphatic hydrocarbon-degrading microbial consortium (TD); and iv) inoculation of a known hydrocarbon-degrading white-rot fungus strain of Trametes versicolor. After 200 days, all the bioremediation assays achieved between 30% and 50% total petroleum hydrocarbon (TPH) biodegradation, with the T. versicolor inoculation degrading it the most. Biostimulation and T. versicolor inoculation promoted the Brevundimonas genus concurrently with other α-proteobacteria, β-proteobacteria and Cytophaga-Flexibacter-Bacteroides (CFB) as well as Actinobacteria groups. However, T. versicolor inoculation, which produced the highest hydrocarbon degradation in soil, also promoted autochthonous Gram-positive bacterial groups, such as Firmicutes and Actinobacteria. An acute toxicity test using Eisenia fetida confirmed the improvement in the quality of the soil after all biostimulation and bioaugmentation strategies. PMID:22858534

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

    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.

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

    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

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

    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

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

    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.

  12. Genetics and Genomics of the Genus Amycolatopsis.

    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

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

    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

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

    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

  15. Bacterial Bio-Resources for Remediation of Hexachlorocyclohexane

    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.

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

    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

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

    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.

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

    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

  19. Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway

    Gaigalat Lars

    2006-08-01

    Full Text Available Abstract Background Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. An efficient transposon mutagenesis system for the completely sequenced type strain ATCC 13032 would significantly advance functional genome analysis in this bacterium. Results A comprehensive transposon mutant library comprising 10,080 independent clones was constructed by electrotransformation of the restriction-deficient derivative of strain ATCC 13032, C. glutamicum RES167, with an IS6100-containing non-replicative plasmid. Transposon mutants had stable cointegrates between the transposon vector and the chromosome. Altogether 172 transposon integration sites have been determined by sequencing of the chromosomal inserts, revealing that each integration occurred at a different locus. Statistical target site analyses revealed an apparent absence of a target site preference. From the library, auxotrophic mutants were obtained with a frequency of 2.9%. By auxanography analyses nearly two thirds of the auxotrophs were further characterized, including mutants with single, double and alternative nutritional requirements. In most cases the nutritional requirement observed could be correlated to the annotation of the mutated gene involved in the biosynthesis of an amino acid, a nucleotide or a vitamin. One notable exception was a clone mutagenized by transposition into the gene cg0910, which exhibited an auxotrophy for histidine. The protein sequence deduced from cg0910 showed high sequence similarities to inositol-1(or 4-monophosphatases (EC 3.1.3.25. Subsequent genetic deletion of cg0910 delivered the same histidine-auxotrophic phenotype. Genetic complementation of the mutants as well as supplementation by histidinol suggests that cg0910 encodes the hitherto unknown

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

    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

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

    Møller, Annette; Søborg, Ditte Andreasen; Al-Soud, Waleed Abu;

    2013-01-01

    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......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...

  2. Doença de Whipple : um diagnóstico difícil

    Fevereiro, Marta Andrade

    2013-01-01

    A doença de Whipple é uma doença bacteriana, multissistémica e rara. O agente etiológico é a bactéria Tropheryma whipplei, um bacilo gram-positivo da família das Actinobacterias e do grupo Actinomycetes. Por ser uma doença sistémica, a doença de Whipple tem manifestações clínicas muito variadas com particular envolvimento do intestino delgado, do sistema nervoso central, das articulações e do coração. A forma mais comum de apresentação inicial é na forma de uma doença gastrointestinal manifes...

  3. Long-term population dynamics and in situ physiology in activated sludge systems with enhanced biological phosphorus removal operated with and without nitrogen removal

    Lee, N.; Nielsen, P.H.; Aspegren, H.; Henze, Mogens; Schleifer, K.-H.; Jansen, J.l.C.

    2003-01-01

    Quantitative fluorescence in situ hybridization (FISH) and the combination of FISH with microautoradiography (MAR) were used in order to study the long-term population dynamics (2.5 years) and the in situ physiology in two parallel activated sludge pilot systems with enhanced biological phosphorus...... removal (EBPR). The two systems received the same influent wastewater, but were differently operated (with and without nitrogen removal, respectively). Both systems showed a significant P removal that increased when different substrates (phosphorus (P), acetate and glucose, respectively) were added to the....... However, we observed a lower correlation (0.9). The Actinobacteria were the only additional group of bacteria which showed a similar degree of correlation to the P content in activated sludge as the Rhodocyclus-related bacteria - but only for the system without nitrogen removal. Significant amounts (less...

  4. Heterotrophic bacteria from an extremely phosphate-poor lake have conditionally reduced phosphorus demand and utilize diverse sources of phosphorus.

    Yao, Mengyin; Elling, Felix J; Jones, CarriAyne; Nomosatryo, Sulung; Long, Christopher P; Crowe, Sean A; Antoniewicz, Maciek R; Hinrichs, Kai-Uwe; Maresca, Julia A

    2016-02-01

    Heterotrophic Proteobacteria and Actinobacteria were isolated from Lake Matano, Indonesia, a stratified, ferruginous (iron-rich), ultra-oligotrophic lake with phosphate concentrations below 50 nM. Here, we describe the growth of eight strains of heterotrophic bacteria on a variety of soluble and insoluble sources of phosphorus. When transferred to medium without added phosphorus (P), the isolates grow slowly, their RNA content falls to as low as 1% of cellular dry weight, and 86-100% of the membrane lipids are replaced with amino- or glycolipids. Similar changes in lipid composition have been observed in marine photoautotrophs and soil heterotrophs, and similar flexibility in phosphorus sources has been demonstrated in marine and soil-dwelling heterotrophs. Our results demonstrate that heterotrophs isolated from this unusual environment alter their macromolecular composition, which allows the organisms to grow efficiently even in their extremely phosphorus-limited environment. PMID:26415900

  5. Bacteria and archaea paleomicrobiology of the dental calculus: a review.

    Huynh, H T T; Verneau, J; Levasseur, A; Drancourt, M; Aboudharam, G

    2016-06-01

    Dental calculus, a material observed in the majority of adults worldwide, emerged as a source for correlating paleomicrobiology with human health and diet. This mini review of 48 articles on the paleomicrobiology of dental calculus over 7550 years discloses a secular core microbiota comprising nine bacterial phyla - Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, TM7, Synergistetes, Chloroflexi, Fusobacteria, Spirochetes - and one archaeal phylum Euryarchaeota; and some accessory microbiota that appear and disappear according to time frame. The diet residues and oral microbes, including bacteria, archaea, viruses and fungi, consisting of harmless organisms and pathogens associated with local and systemic infections have been found trapped in ancient dental calculus by morphological approaches, immunolabeling techniques, isotope analyses, fluorescent in situ hybridization, DNA-based approaches, and protein-based approaches. These observations led to correlation of paleomicrobiology, particularly Streptococcus mutans and archaea, with past human health and diet. PMID:26194817

  6. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

    Klümper, Uli; Riber, Leise; Dechesne, Arnaud;

    2014-01-01

    to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the...... transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes...... and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different...

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

    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.

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

    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.

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

    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

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

    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.

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

    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)

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

    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

  13. ESTIMATING BACTERIAL DIVERSITY IN SCIRTOTHRIPS DORSALIS (THYSANOPTERA: THRIPIDAE) VIA NEXT GENERATION SEQUENCING

    Dickey, Aaron M.; Trease, Andrew J.; Jara-Cavieres, Antonella; Kumar, Vivek; Christenson, Matthew K.; Potluri, Lakshmi-Prasad; Morgan, J. Kent; Shatters, Robert G.; Mckenzie, Cindy L.; Davis, Paul H.; Osborne, Lance S.

    2014-01-01

    The last 2 decades have produced a better understanding of insect-microbial associations and yielded some important opportunities for insect control. However, most of our knowledge comes from model systems. Thrips (Thysanoptera: Thripidae) have been understudied despite their global importance as invasive species, plant pests and disease vectors. Using a culture and primer independent next-generation sequencing and metagenomics pipeline, we surveyed the bacteria of the globally important pest, Scirtothrips dorsalis Hood. The most abundant bacterial phyla identified were Actinobacteria and Proteobacteria and the most abundant genera were Propionibacterium, Stenotrophomonas, and Pseudomonas. A total of 189 genera of bacteria were identified. The absence of any vertically transferred symbiont taxa commonly found in insects is consistent with other studies suggesting that thrips primarilly acquire resident microbes from their environment. This does not preclude a possible beneficial/intimate association between S. dorsalis and the dominant taxa identified and future work should determine the nature of these associations. PMID:25382863

  14. First report of bacterial community from a Bat Guano using Illumina next-generation sequencing

    Surajit De Mandal

    2015-06-01

    Full Text Available V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave — Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach.

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

    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

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

    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

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

    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.

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

    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

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

    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

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

    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

  1. Psychrotolerant actinomycetes of plants and organic horizons in tundra and taiga soils

    Dubrova, M. S.; Zenova, G. M.; Yakushev, A. V.; Manucharova, N. A.; Makarova, E. P.; Zvyagintsev, D. G.; Chernov, I. Yu.

    2013-08-01

    It has been revealed that in organic horizons and plants of the tundra and taiga ecosystems under low temperatures, actinomycetal complexes form. The population density of psychrotolerant actinomycetes in organic horizons and plants reaches tens and hundreds of thousands CFU/g of substrate or soil, and decreases in the sequence litters > plants > soils > undecomposed plant remains > moss growths. The mycelium length of psychrotolerant actinomycetes reaches 220 m/g of substrate. Application of the FISH method has demonstrated that metabolically active psychrotolerant bacteria of the phylum Actinobacteria constitute 30% of all metabolically active psychrotolerant representatives of the Bacterià domain of the prokaryotic microbial community of soils and plants. Psychrotolerant actinomycetes in tundra and taiga ecosystems possess antimicrobial properties.

  2. Ecological and Taxonomic Features of Actinomycetal Complexes in Soils of the Lake Elton Basin

    Zenova, G. M.; Dubrova, M. S.; Kuznetsova, A. I.; Gracheva, T. A.; Manucharova, N. A.; Zvyagintsev, D. G.

    2016-02-01

    In the sor (playa) solonchaks of chloride and sulfate-chloride salinity (the content of readily soluble salts is 0.9-1.0%) in the delta of the Khara River discharging into Lake Elton, the number of mycelial actinobacteria (actinomycetes) is low ((2-3) × 103 CFU/g of soil). At a distance from the water's edge, these soils are substituted for the light chestnut ones, for which an elevated number of actinomycetes (an order of magnitude higher than in the sor solonchaks) and a wider generic spectrum are characteristic. The actinomycetal complex is included the Streptomyces and Micromonospora genera, whereas in the sor solonchaks around the lake, representatives of Micromonospora were not found.

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

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

    2014-01-01

    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...... challenge there was no effect of the diet type on the cumulative survival, but the number of Y. ruckeri positive fish as measured by plate count and the number of fish with a 'high' number of reads belonging to genus Yersinia as measured by 16S rRNA next-generation sequencing was higher for marine diet fed...... fish. Furthermore, the two experimental groups of fish showed a differential immune response, where Y. ruckeri challenged marine fed fish had a higher transcription of IL-1β and MBL-2 relative to challenged plant diet fed fish. The data suggest that the plant diet gave rise to a prebiotic effect...

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

    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...

  5. Bacterial reduction of mercury in the high arctic

    Møller, Annette Klæstrup

    It is well-established that mercury (Hg) from lower latitudes is transferred to and pollutes the Arctic environment. One mechanism of Hg transfer is through the atmosphere where Hg is deposited in the Arctic in the spring time during Atmospheric Mercury Depletion Events (AMDE): large amounts of Hg...... is believed to be depleted from the atmosphere and deposited onto snow and sea-ice through photochemical reactions. The faith of mercury after deposition is poorly understood and while bacteria are known to play an important role in the bio-geochemical Hg cycle in various temperate environments, their role......, 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...

  6. Microbial Colonization of the Salt Deposits in the Driest Place of the Atacama Desert (Chile)

    Stivaletta, Nunzia; Barbieri, Roberto; Billi, Daniela

    2012-06-01

    The Atacama Desert (Chile), one of the most arid places on Earth, shows hostile conditions for the development of epilithic microbial communities. In this study, we report the association of cyanobacteria ( Chroococcidiopsis sp.) and bacteria belonging to Actinobacteria and Beta-Gammaproteobacteria and Firmicutes phyla inhabiting the near surface of salt (halite) deposits of the Salar Grande Basin, Atacama Desert (Chile). The halite deposits were investigated by using optical, confocal and field emission scanning electron microscopes, whereas culture-independent molecular techniques, 16S rDNA clone library, alongside RFLP analysis and 16S rRNA gene sequencing were applied to investigate the bacterial diversity. These microbial communities are an example of life that has adapted to extreme environmental conditions caused by dryness, high irradiation, and metal concentrations. Their adaptation is, therefore, important in the investigation of the environmental conditions that might be expected for life outside of Earth.

  7. Toxicity of Bioactive and Probiotic Marine Bacteria and Their Secondary Metabolites in Artemia sp. and Caenorhabditis elegans as Eukaryotic Model Organisms

    Neu, Anna; Månsson, Maria; Gram, Lone;

    2014-01-01

    applied point of view as fish probiotics or as a source of pharmaceutical compounds. The application of either organisms or compounds requires that they do not cause any side effects, such as toxicity in eukaryotic organisms. The purpose of this study was to determine whether these bacteria or their...... holomycin nor andrimid, the respective antibiotic compounds in these organisms. In contrast, the tropodithietic acid (TDA)-producing bacteria Phaeobacter inhibens DSM17395 and Ruegeria mobilis F1926 and TDA itself had no adverse effect on the target organisms. These results reaffirm TDA......-producing Roseobacter bacteria as a promising group to be used as probiotics in aquaculture, whereas Actinobacteria, Pseudoalteromonas, Photobacteriaceae, and Vibrionaceae should be used with caution....

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

    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

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

    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

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

    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

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

    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

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

    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

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

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

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

    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.

  16. Metagenomic characterization of biodiversity in the extremely arid desert soils of Kazakhstan

    Kutovaya, O. V.; Lebedeva, M. P.; Tkhakakhova, A. K.; Ivanova, E. A.; Andronov, E. E.

    2015-05-01

    For the first time, the composition of microbiomes in the biological crust (AKL) horizons of extremely arid desert soils (Aridic Calcisols) developed from saline and nonsaline alluvial deposits in the Ili Depression (eastern Kazakhstan) was analyzed. To describe the diversity of microorganisms in the soil samples, a novel method of pyrosequencing (Roche/454 Life Sciences) was applied. It was shown that bacteria from the Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, Acidobacteria, and Bacteroidetes phyla predominate in all the samples; these are typical representatives of the microbiome of soil crusts. A distinctive feature of the extremely arid soils is the high contribution of cyanobacteria (25-30%) to the total DNA. In the soils developed from saline sediments, representatives from the Rubrobacteraceae, Streptococcaceae, and Caulobacteraceae families and from the Firmicutes phylum predominated. In the soils developed from nonsaline gypsiferous deposits, bacteria from the class of Acidobacteria, subgroup Gp3, of the Methylobacteriaceae family and the class of Subdivision 3 from the Verrucomicrobia phylum predominated.

  17. 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.

    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

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

    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

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

    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

  20. Long-term population dynamics and in situ physiology in activated sludge systems with enhanced biological phosphorus removal operated with and without nitrogen removal

    Lee, N.; Nielsen, P.H.; Aspegren, H.;

    2003-01-01

    removal (EBPR). The two systems received the same influent wastewater, but were differently operated (with and without nitrogen removal, respectively). Both systems showed a significant P removal that increased when different substrates (phosphorus (P), acetate and glucose, respectively) were added......Quantitative fluorescence in situ hybridization (FISH) and the combination of FISH with microautoradiography (MAR) were used in order to study the long-term population dynamics (2.5 years) and the in situ physiology in two parallel activated sludge pilot systems with enhanced biological phosphorus....... However, we observed a lower correlation (0.9). The Actinobacteria were the only additional group of bacteria which showed a similar degree of correlation to the P content in activated sludge as the Rhodocyclus-related bacteria - but only for the system without nitrogen removal. Significant amounts (less...

  1. The human vaginal bacterial biota and bacterial vaginosis.

    Srinivasan, Sujatha; Fredricks, David N

    2008-01-01

    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. PMID:19282975

  2. A novel approach to enhance biological nutrient removal using a culture supernatant from Micrococcus luteus containing resuscitation-promoting factor (Rpf) in SBR process.

    Liu, Yindong; Su, Xiaomei; Lu, Lian; Ding, Linxian; Shen, Chaofeng

    2016-03-01

    A culture supernatant from Micrococcus luteus containing resuscitation-promoting factor (SRpf) was used to enhance the biological nutrient removal of potentially functional bacteria. The obtained results suggest that SRpf accelerated the start-up process and significantly enhanced the biological nutrient removal in sequencing batch reactor (SBR). PO4 (3-)-P removal efficiency increased by over 12 % and total nitrogen removal efficiency increased by over 8 % in treatment reactor acclimated by SRpf compared with those without SRpf addition. The Illumina high-throughput sequencing analysis showed that SRpf played an essential role in shifts in the composition and diversity of bacterial community. The phyla of Proteobacteria and Actinobacteria, which were closely related to biological nutrient removal, were greatly abundant after SRpf addition. This study demonstrates that SRpf acclimation or addition might hold great potential as an efficient and cost-effective alternative for wastewater treatment plants (WWTPs) to meet more stringent operation conditions and legislations. PMID:26514565

  3. Permanent draft genome sequence of the probiotic strain Propionibacterium freudenreichii CIRM-BIA 129 (ITG P20).

    Falentin, Hélène; Deutsch, Stéphanie-Marie; Loux, Valentin; Hammani, Amal; Buratti, Julien; Parayre, Sandrine; Chuat, Victoria; Barbe, Valérie; Aury, Jean-Marc; Jan, Gwenaël; Le Loir, Yves

    2016-01-01

    Propionibacterium freudenreichii belongs to the class Actinobacteria (Gram positive with a high GC content). This "Generally Recognized As Safe" (GRAS) species is traditionally used as (i) a starter for Swiss-type cheeses where it is responsible for holes and aroma production, (ii) a vitamin B12 and propionic acid producer in white biotechnologies, and (iii) a probiotic for use in humans and animals because of its bifidogenic and anti-inflammatory properties. Until now, only strain CIRM-BIA1T had been sequenced, annotated and become publicly available. Strain CIRM-BIA129 (commercially available as ITG P20) has considerable anti-inflammatory potential. Its gene content was compared to that of CIRM-BIA1 T. This strain contains 2384 genes including 1 ribosomal operon, 45 tRNA and 30 pseudogenes. PMID:26779303

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

    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

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

    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. PMID:26245685

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

    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

  7. Diversity of bacteria in the marine sponge Aplysina fulva in Brazilian coastal waters.

    Hardoim, C C P; Costa, R; Araújo, F V; Hajdu, E; Peixoto, R; Lins, U; Rosado, A S; van Elsas, J D

    2009-05-01

    Microorganisms can account for up to 60% of the fresh weight of marine sponges. Marine sponges have been hypothesized to serve as accumulation spots of particular microbial communities, but it is unknown to what extent these communities are directed by the organism or the site or occur randomly. To address this question, we assessed the composition of specific bacterial communities associated with Aplysina fulva, one of the prevalent sponge species inhabiting Brazilian waters. Specimens of A. fulva and surrounding seawater were collected in triplicate in shallow water at two sites, Caboclo Island and Tartaruga beach, Búzios, Brazil. Total community DNA was extracted from the samples using "direct" and "indirect" approaches. 16S rRNA-based PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the total bacterial community and of specific bacterial groups--Pseudomonas and Actinobacteria--revealed that the structure of these assemblages in A. fulva differed drastically from that observed in seawater. The DNA extraction methodology and sampling site were determinative for the composition of actinobacterial communities in A. fulva. However, no such effects could be gleaned from total bacterial and Pseudomonas PCR-DGGE profiles. Bacterial 16S rRNA gene clone libraries constructed from directly and indirectly extracted DNA did not differ significantly with respect to diversity and composition. Altogether, the libraries encompassed 15 bacterial phyla and the candidate division TM7. Clone sequences affiliated with the Cyanobacteria, Chloroflexi, Gamma- and Alphaproteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were, in this order, most abundant. The bacterial communities associated with the A. fulva specimens were distinct and differed from those described in studies of sponge-associated microbiota performed with other sponge species. PMID:19304829

  8. [Effect of free surface flow wetland and subsurface flow wetland on bacterial diversity in Beijing Cuihu Wetland Park].

    Wang, Xiao-dan; Zhai, Zhen-hua; Zhao, Shuang; Li, Rong-qi; Ma, Wen-lin; Li, Yan-hong

    2009-01-01

    To achieve the effects of artificial wetland on the bacterial diversity, the culturable bacteria and total cell counts of three wetland cells, including sewage pond (SP), free surface wetland (SF) and subsurface flow wetland (SSF), were investigated using the traditional culture-dependent approach and flow cytometry method, based on the detecting the water quality. The bacterial diversity and dominant groups were also compared by PCR-DGGE profiles and 16S rDNA library technique based on its V3 region. Results show that SF and SSF cells can remove the nutrients effectively, the highest removal ratio of COD, total nitrogen, and total phosphorus reach to 42.33%, 52.92% and 41.4%, respectively; The total microbes are increased continuously with the treatment by SF and SSF, and the culturable bacteria clones are decreased after treatment by SF, and increased after further train by SSF. The Shannon-Weaver index is increased to 3.2850 from 3.0819 while the water flowing through SF, but decreased to 3.0181 after flowing through SSF; The dominant groups in SP include Actinobacteria, Cyanobacteria and alpha-Proteobacteria, reach to 38%, 18% and 18%, respectively; but the most dominant bacteria is changed to beta-Proteobacteria with the ratio of 32% and 44%, after treatment by SF and SSF, respectively. Cytophagal Flexibacter/Bacteroides (CFB) phylum is also increased to 24% finally. Therefore, while the Cuihu Wetland removing the nutrients,the bacterial counts, diversity and dominant groups are also changed,some beneficial bacteria in beta-Proteobacteria and CFB phylum increased, and part of those deleterious bacteria in Actinobacteria and Cyanobacteria decreased. PMID:19353894

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

    NicoleSWebster

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

    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

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

    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.

  12. Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina.

    Vega-Avila, A D; Gumiere, T; Andrade, P A M; Lima-Perim, J E; Durrer, A; Baigori, M; Vazquez, F; Andreote, F D

    2015-02-01

    Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices. PMID:25527391

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

    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

  14. Endolithic microbial communities in carbonate precipitates from serpentinite-hosted hyperalkaline springs of the Voltri Massif (Ligurian Alps, Northern Italy).

    Quéméneur, Marianne; Palvadeau, Alexandra; Postec, Anne; Monnin, Christophe; Chavagnac, Valérie; Ollivier, Bernard; Erauso, Gaël

    2015-09-01

    The Voltri Massif is an ophiolitic complex located in the Ligurian Alps close to the city of Genova (Northern Italy) where several springs discharge high pH (up to 11.7), low salinity waters produced by the active serpentinization of the ultramafic basement. Mixing of these hyperalkaline waters with the river waters along with the uptake of atmospheric carbon dioxide forms brownish carbonate precipitates covering the bedrock at the springs. Diverse archaeal and bacterial communities were detected in these carbonate precipitates using 454 pyrosequencing analyses of 16S ribosomal RNA (rRNA) genes. Archaeal communities were dominated by members of potential methane-producing and/or methane-oxidizing Methanobacteriales and Methanosarcinales (Euryarchaeota) together with ammonia-oxidizing Nitrososphaerales (Thaumarchaeota) similar to those found in other serpentinization-driven submarine and terrestrial ecosystems. Bacterial communities consisted of members of the Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, and Verrucomicrobia phyla, altogether accounting for 92.2% of total retrieved bacterial 16S rRNA gene sequences. Amongst Bacteria, potential chemolithotrophy was mainly associated with Alpha- and Betaproteobacteria classes, including nitrogen-fixing, methane-oxidizing or hydrogen-oxidizing representatives of the genera Azospirillum, Methylosinus, and Hydrogenophaga/'Serpentinomonas', respectively. Besides, potential chemoorganotrophy was attributed mainly to representatives of Actinobacteria and Planctomycetales phyla. The reported 16S rRNA gene data strongly suggested that hydrogen, methane, and nitrogen-based chemolithotrophy can sustain growth of the microbial communities inhabiting the carbonate precipitates in the hyperalkaline springs of the Voltri Massif, similarly to what was previously observed in other serpentinite-hosted ecosystems. PMID:25874424

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

    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

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

    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

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

    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

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

    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

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

    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

  20. Diverse microbial species survive high ammonia concentrations

    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.

  1. Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen.

    Schellenberger, Stefanie; Kolb, Steffen; Drake, Harold L

    2010-04-01

    Cellulose is the most abundant biopolymer in terrestrial ecosystems and is degraded by microbial communities in soils. However, relatively little is known about the diversity and function of soil prokaryotes that might participate in the overall degradation of this biopolymer. The active cellulolytic and saccharolytic Bacteria in an agricultural soil were evaluated by 16S rRNA (13)C-based stable isotope probing. Cellulose, cellobiose and glucose were mineralized under oxic conditions in soil slurries to carbon dioxide. Under anoxic conditions, these substrates were converted primarily to acetate, butyrate, carbon dioxide, hydrogen and traces of propionate and iso-butyrate; the production of these fermentation end-products was concomitant with the apparent reduction of iron(III). [(13)C]-cellulose was mainly degraded under oxic conditions by novel family-level taxa of the Bacteroidetes and Chloroflexi, and a known family-level taxon of Planctomycetes, whereas degradation under anoxic conditions was facilitated by the Kineosporiaceae (Actinobacteria) and cluster III Clostridiaceae and novel clusters within Bacteroidetes. Active aerobic sub-communities in oxic [(13)C]-cellobiose and [(13)C]-glucose treatments were dominated by Intrasporangiaceae and Micrococcaceae (Actinobacteria) whereas active cluster I Clostridiaceae (Firmicutes) were prevalent in anoxic treatments. A very large number (i.e. 28) of the detected taxa did not closely affiliate with known families, and active Archaea were not detected in any of the treatments. These collective findings suggest that: (i) a large uncultured diversity of soil Bacteria was involved in the utilization of cellulose and products of its hydrolysis, (ii) the active saccharolytic community differed phylogenetically from the active cellulolytic community, (iii) oxygen availability impacted differentially on the activity of taxa and (iv) different redox guilds (e.g. fermenters and iron reducers) compete or interact during

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

    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.

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

    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

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

    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

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

    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

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

    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

  7. Comparison of the Oral Microbiomes of Canines and Their Owners Using Next-Generation Sequencing.

    Changin Oh

    Full Text Available The oral microbiome, which is closely associated with many diseases, and the resident pathogenic oral bacteria, which can be transferred by close physical contact, are important public health considerations. Although the dog is the most common companion animal, the composition of the canine oral microbiome, which may include human pathogenic bacteria, and its relationship with that of their owners are unclear. In this study, 16S rDNA pyrosequencing was used to compare the oral microbiomes of 10 dogs and their owners and to identify zoonotic pathogens. Pyrosequencing revealed 246 operational taxonomic units in the 10 samples, representing 57 genera from eight bacterial phyla. Firmicutes (57.6%, Proteobacteria (21.6%, Bacteroidetes (9.8%, Actinobacteria (7.1%, and Fusobacteria (3.9% were the predominant phyla in the human oral samples, whereas Proteobacteria (25.7%, Actinobacteria (21%, Bacteroidetes (19.7%, Firmicutes (19.3%, and Fusobacteria (12.3% were predominant in the canine oral samples. The predominant genera in the human samples were Streptococcus (43.9%, Neisseria (10.3%, Haemophilus (9.6%, Prevotella (8.4%, and Veillonella (8.1%, whereas the predominant genera in the canine samples were Actinomyces (17.2%, Unknown (16.8, Porphyromonas (14.8, Fusobacterium (11.8, and Neisseria (7.2%. The oral microbiomes of dogs and their owners were appreciably different, and similarity in the microbiomes of canines and their owners was not correlated with residing in the same household. Oral-to-oral transfer of Neisseria shayeganii, Porphyromonas canigingivalis, Tannerella forsythia, and Streptococcus minor from dogs to humans was suspected. The finding of potentially zoonotic and periodontopathic bacteria in the canine oral microbiome may be a public health concern.

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

    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. PMID:26433967

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

    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.

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

    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

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

    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.

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

    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

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

    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

  14. Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin.

    Mancuso, Francesco P; D'Hondt, Sofie; Willems, Anne; Airoldi, Laura; De Clerck, Olivier

    2016-01-01

    Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti-Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria, and Cyanobacteria especially of the Rhodobacteriaceae, Flavobacteriaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobacteriaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegeria, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of

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

    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. Study of human microecology by mass spectrometry of microbial markers.

    Osipov, G A; Verkhovtseva, N V

    2011-03-01

    This review shows that mass spectrometry of microbial markers (MSMM) permits simultaneous in situ determination of more than one hundred microbial fatty acids in clinical, biotechnological or environmental samples, without precultivation and use of biochemical test materials and primers. Unprecedented information about the quantity of anaerobes and uncultivated aerobes, as well as actinobacteria, yeasts, viruses and microscopic fungi in one sample has provided a full understanding of microbial etiology in clinical conditions of patients. The study of intestine dysbiosis has confirmed the hypothesis about the nosological specificity of changes in the intestinal microbiota. It has been proven that infectious processes are polymicrobial. Measurements have shown that anaerobes dominate in number and functional activities in inflammation. The division of microbes into pathogenic and non- pathogenic is artificial. All microbes living in a human body simultaneously stay in both forms. Lactobacilli and bifidobacteria appear as agents of septic conditions and endocarditis. МSММ data confirm that anaerobes of Clostridium, Eubacterium, Propionibacterium, as well as actinobacteria of Streptomyces, Nocardia, Rhodococcus are mixed infection dominants. The data testify translocation of these microbes in inflammation loci from the intestine. Quantitative comparison of concentration of markers in the inflamed organ and blood proves reproduction of microorganisms in this locus. The current hypothesis is confirmed that the goal of translocation is not only infection, but also a biofilm formation similar to intestines, which stimulate local immunity, protection from local pathogens and restoration of the damaged tissues. Quantification using GC-MS revealed that the influence of antibiotics on the normal intestine's microbiota are not as dramatic as believed. Growth-promoting effects are the most important benefits of probiotic applications. The probiotic essence is not the

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

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

    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.

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

    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

  20. High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet.

    Wang, Wen; Cao, Jian; Yang, Fang; Wang, Xuelian; Zheng, Sisi; Sharshov, Kirill; Li, Laixing

    2016-04-01

    Elucidating the spatial dynamic and core gut microbiome related to wild bar-headed goose is of crucial importance for probiotics development that may meet the demands of bar-headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar-headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar-headed geese gut microbial communities by Illumina high-throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar-headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in-depth assessment, to date, of the gut microbes that associated with bar-headed geese. These data create a baseline for future bar-headed goose microbiology research, and make an original contribution to probiotics development for bar-headed goose artificial breeding industries. PMID:26842811

  1. 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

    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

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

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

    2009-01-01

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

  3. Influence of vegetation on the in situ bacterial community and polycyclic aromatic hydrocarbon (PAH) degraders in aged PAH-contaminated or thermal-desorption-treated soil.

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

    2009-10-01

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

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

    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.

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

    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

  6. 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

    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.

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

    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

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

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

    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

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

    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

  11. A TatABC-type Tat translocase is required for unimpaired aerobic growth of Corynebacterium glutamicum ATCC13032.

    Dan Oertel

    Full Text Available The twin-arginine translocation (Tat system transports folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of plant chloroplasts. Escherichia coli and other Gram-negative bacteria possess a TatABC-type Tat translocase in which each of the three inner membrane proteins TatA, TatB, and TatC performs a mechanistically distinct function. In contrast, low-GC Gram-positive bacteria, such as Bacillus subtilis, use a TatAC-type minimal Tat translocase in which the TatB function is carried out by a bifunctional TatA. In high-GC Gram-positive Actinobacteria, such as Mycobacterium tuberculosis and Corynebacterium glutamicum, tatA, tatB, and tatC genes can be identified, suggesting that these organisms, just like E. coli, might use TatABC-type Tat translocases as well. However, since contrary to this view a previous study has suggested that C. glutamicum might in fact use a TatAC translocase with TatB only playing a minor role, we reexamined the requirement of TatB for Tat-dependent protein translocation in this microorganism. Under aerobic conditions, the misassembly of the Rieske iron-sulfur protein QcrA was identified as a major reason for the severe growth defect of Tat-defective C. glutamicum mutant strains. Furthermore, our results clearly show that TatB, besides TatA and TatC, is strictly required for unimpaired aerobic growth. In addition, TatB was also found to be essential for the secretion of a heterologous Tat-dependent model protein into the C. glutamicum culture supernatant. Together with our finding that expression of the C. glutamicum TatB in an E. coli ΔtatB mutant strain resulted in the formation of an active Tat translocase, our results clearly indicate that a TatABC translocase is used as the physiologically relevant functional unit for Tat-dependent protein translocation in C. glutamicum and, most likely, also in other TatB-containing Actinobacteria.

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

    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.

  13. Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada.

    Fadwa Jroundi

    Full Text Available Biomineralization processes have recently been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain. While this promising method has demonstrated its efficacy regarding strengthening of the stone, little is known about its ecological sustainability.Here, we report molecular monitoring of the stone-autochthonous microbiota before and at 5, 12 and 30 months after the bio-consolidation treatment (medium/long-term monitoring, employing the well-known molecular strategy of DGGE analyses. Before the bio-consolidation treatment, the bacterial diversity showed the exclusive dominance of Actinobacteria (100%, which decreased in the community (44.2% after 5 months, and Gamma-proteobacteria (30.24% and Chloroflexi (25.56% appeared. After 12 months, Gamma-proteobacteria vanished from the community and Cyanobacteria (22.1% appeared and remained dominant after thirty months, when the microbiota consisted of Actinobacteria (42.2% and Cyanobacteria (57.8% only. Fungal diversity showed that the Ascomycota phylum was dominant before treatment (100%, while, after five months, Basidiomycota (6.38% appeared on the stone, and vanished again after twelve months. Thirty months after the treatment, the fungal population started to stabilize and Ascomycota dominated on the stone (83.33% once again. Members of green algae (Chlorophyta, Viridiplantae appeared on the stone at 5, 12 and 30 months after the treatment and accounted for 4.25%, 84.77% and 16.77%, respectively.The results clearly show that, although a temporary shift in the bacterial and fungal diversity was observed during the first five months, most probably promoted by the application of the bio-consolidation treatment, the microbiota tends to regain its initial stability in a few months. Thus, the treatment does not seem to have any negative side effects on the stone-autochthonous microbiota over that time. The molecular strategy employed here is suggested

  14. Characterization of Sviceucin from Streptomyces Provides Insight into Enzyme Exchangeability and Disulfide Bond Formation in Lasso Peptides.

    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

  15. Bacterial Endophytes Isolated from Plants in Natural Oil Seep Soils with Chronic Hydrocarbon Contamination

    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

  16. Characterising the microbiome of Corallina officinalis, a dominant calcified intertidal red alga.

    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

  17. Characterization of endophytic bacteria from cucurbit fruits with potential benefits to agriculture in melons (Cucumis melo L.).

    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

  18. Changes in the Synechococcus Assemblage Composition at the Surface of the East China Sea Due to Flooding of the Changjiang River.

    Chung, Chih-Ching; Gong, Gwo-Ching; Huang, Chin-Yi; Lin, Jer-Young; Lin, Yun-Chi

    2015-10-01

    The aim of this study was to elucidate how flooding of the Changjiang River affects the assemblage composition of phycoerythrin-rich (PE-rich) Synechococcus at the surface of the East China Sea (ECS). During non-flooding summers (e.g., 2009), PE-rich Synechococcus usually thrive at the outer edge of the Changjiang River diluted water coverage (CDW; salinity ≤31 PSU). In the summer of 2010, a severe flood occurred in the Changjiang River basin. The plentiful freshwater injection resulted in the expansion of the CDW over half of the ECS and caused PE-rich cells to show a uniform distribution pattern, with decreased abundance compared with the non-flooding summer. The phylogenetic diversity of 16S rRNA gene sequences indicated that the flooding event also shifted the picoplankton community composition from being dominated by Synechococcus, mainly attributed to the clade II lineage, to various orders of heterotrophic bacteria, including Actinobacteria, Flavobacteria, α-Proteobacteria, and γ-Proteobacteria. As an increasing number of studies have proposed that global warming might result in more frequent floods, combining this perspective with the information obtained from our previous [1] and this studies yield a more comprehensive understanding of the relationship between the composition of the marine Synechococcus assemblage and global environmental changes. PMID:25851446

  19. Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota.

    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

  20. Microbial and Mineralogical Characterizations of Soils Collected from the Deep Biosphere of the Former Homestake Gold Mine, South Dakota

    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.

  1. Bovine vaginal strain Kocuria kristinae and its characterization.

    Styková, Eva; Nemcová, Radomíra; Gancarčíková, Soňa; Valocký, Igor; Lauková, Andrea

    2016-05-01

    Kocuria spp. are widely distributed in nature. They are Gram-positive, coagulase-negative, coccoid bacteria belonging to the family Micrococcaceae, suborder Micrococcineae, order Actinomycetales, class Actinobacteria. In general, limited knowledge exists concerning the properties associated with the representants of the genus Kocuria, Kocuria kristinae as well. Following our previous results, K. kristinae Kk2014 Biocenol(™) (CCM 8628) was isolated from vagina of a healthy cow. Its taxonomical allottation was confirmed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) identification system and phenotypic characteristics. Kk2014 strain showed strong adherence capability to the vaginal mucus, produced organic acids which can play a role in prevention of unsuitable contamination, and showed in vitro antagonistic/antimicrobial activity against strains Arcanobacterium pyogenes CCM 5753, Fusobacterium necrophorum CCM 5982, Streptococcus equi subsp. zooepidemicus CCM 7316, and Gardnerella vaginalis CCM 6221. Antimicrobial activity ranged from 100 to 200 AU/mL, up to 32 mm in size, respectively. PMID:26494240

  2. Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia).

    Kovács, G; Burghardt, J; Pradella, S; Schumann, P; Stackebrandt, E; Màrialigeti, K

    1999-01-01

    Two Gram-positive, aerobic spherical actinobacteria were isolated from the rhizoplane of narrow-leaved cattail (Typha angustifolia) collected from a floating mat in the Soroksár tributary of the Danube river, Hungary. Sequence comparisons of the 16S rDNA indicated these isolates to be phylogenetic neighbours of members of the genus Kocuria, family Micrococcaceae, in which they represent two novel lineages. The phylogenetic distinctness of the two organisms TA68T and TAGA27T was supported by DNA-DNA similarity values of less than 55% between each other and with the type strains of Kocuria rosea, Kocuria kristinae and Kocuria varians. Chemotaxonomic properties supported the placement of the two isolates in the genus Kocuria. The diagnostic diamino acid of the cell-wall peptidoglycan is lysine, the interpeptide bridge is composed of three alanine residues. Predominant menaquinone was MK-7(H2). The fatty acid pattern represents the straight-chain saturated iso-anteiso type. Main fatty acid was anteiso-C15:0. The phospholipids are diphosphatidylglycerol, phosphatidylglycerol and an unknown component. The DNA base composition of strains TA68T and TAGA27T is 69.4 and 69.6 mol% G+C, respectively. Genotypic, morphological and physiological characteristics are used to describe two new species of Kocuria, for which we propose the names Kocuria palustris, type strain DSM 11925T and Kocuria rhizophila, type strain DSM 11926T. PMID:10028258

  3. Sensors for isolation of anti-cancer compounds found within marine invertebrates

    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.

  4. Metagenomics of the Water Column in the Pristine Upper Course of the Amazon River

    McMahon, Katherine D.; Toyama, Danyelle; Rinke, Raquel; Cristina Souza de Oliveira, Tereza; Wagner Garcia, José; Pellon de Miranda, Fernando; Henrique-Silva, Flavio

    2011-01-01

    River water is a small percentage of the total freshwater on Earth but represents an essential resource for mankind. Microbes in rivers perform essential ecosystem roles including the mineralization of significant quantities of organic matter originating from terrestrial habitats. The Amazon river in particular is famous for its size and importance in the mobilization of both water and carbon out of its enormous basin. Here we present the first metagenomic study on the microbiota of this river. It presents many features in common with the other freshwater metagenome available (Lake Gatun in Panama) and much less similarity with marine samples. Among the microbial taxa found, the cosmopolitan freshwater acI lineage of the actinobacteria was clearly dominant. Group I Crenarchaea and the freshwater sister group of the marine SAR11 clade, LD12, were found alongside more exclusive and well known freshwater taxa such as Polynucleobacter. A metabolism-centric analysis revealed a disproportionate representation of pathways involved in heterotrophic carbon processing, as compared to those found in marine samples. In particular, these river microbes appear to be specialized in taking up and mineralizing allochthonous carbon derived from plant material. PMID:21915244

  5. Comparison of the diversity of root-associated bacteria in Phragmites australis and Typha angustifolia L. in artificial wetlands.

    Li, Yan Hong; Zhu, Jing Nan; Liu, Qun Fang; Liu, Yin; Liu, Min; Liu, Lei; Zhang, Qiang

    2013-08-01

    Common reed (Phragmites australis) and narrow-leaved cattail (Typha angustifolia L.) are two plant species used widely in artificial wetlands constructed to treat wastewater. In this study, the community structure and diversity of root-associated bacteria of common reed and narrow-leaved cattail growing in the Beijing Cuihu Wetland, China, were investigated using 16S rDNA library and PCR-denaturing gradient gel electrophoresis methods. Root-associated bacterial diversity was higher in common reed than in narrow-leaved cattail. In both plant species, the dominant root-associated bacterial species were Alpha, Beta and Gamma Proteobacteria, including the genera Aeromonas, Hydrogenophaga, Ideonella, Uliginosibacterium and Vogesella. Acidobacteria, Actinobacteria, Nitrospirae and Spirochaetes were only found in the roots of common reed. Comparing the root-associated bacterial communities of reed and cattail in our system, many more species of bacteria related involved in the total nitrogen cycle were observed in reed versus cattail, while species involved in total phosphorus and organic matter removal were mainly found in cattail. Although we cannot determine their nutrient removal capacity separately, differences in the root-associated bacterial communities may be an important factor contributing to the differing water purification effects mediated by T. angustifolia and P. australis wetlands. Thus, further work describing the ecosystem functions of these bacterial species is needed, in order to fully understand how effective common reed- and narrow-leaved cattail-dominated wetlands are for phytoremediation. PMID:23504190

  6. Phylogenetic diversity of bacteria associated with Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma).

    Schabereiter-Gurtner, Claudia; Saiz-Jimenez, Cesareo; Piñar, Guadalupe; Lubitz, Werner; Rölleke, Sabine

    2004-02-01

    Bacterial diversity in caves is still rarely investigated using culture-independent techniques. In the present study, bacterial communities on Paleolithic paintings and surrounding rock walls in two Spanish caves (Llonín and La Garma) were analyzed, using 16S rDNA-based denaturing gradient gel electrophoresis community fingerprinting and phylogenetic analyses without prior cultivation. Results revealed complex bacterial communities consisting of a high number of novel 16S rDNA sequence types and indicated a high biodiversity of lithotrophic and heterotrophic bacteria. Identified bacteria were related to already cultured bacteria (39 clones) and to environmental 16S rDNA clones (46 clones). The nearest phylogenetic relatives were members of the Proteobacteria (41.1%), of the Acidobacterium division (16.5%), Actinobacteria (20%), Firmicutes (10.6%), of the Cytophaga/Flexibacter/Bacteroides division (5.9%), Nitrospira group (3.5%), green non-sulfur bacteria (1.2%), and candidate WS3 division (1.2%). Thirteen of these clones were most closely related to those obtained from the previous studies on Tito Bustillo Cave. The comparison of the present data with the data obtained previously from Altamira and Tito Bustillo Caves revealed similarities in the bacterial community components, especially in the high abundance of the Acidobacteria and Rhizobiaceae, and in the presence of bacteria related to ammonia and sulfur oxidizers. PMID:19712338

  7. Differences in crop bacterial community structure between hoatzins from different geographical locations.

    Godoy-Vitorino, Filipa; Leal, Sara J; Díaz, Wilmer A; Rosales, Judith; Goldfarb, Katherine C; García-Amado, María A; Michelangeli, Fabían; Brodie, Eoin L; Domínguez-Bello, María G

    2012-04-01

    The hoatzin is the only known folivorous bird with foregut fermentation, and is distributed in Venezuela in rivers of the central savannas to the eastern Orinoco River. Differences in diet are expected to affect the digestive microbiota and we hypothesized that hoatzins from different habitats might have a different crop microbiota. We thus characterized the microbiota of six birds from the Cojedes and Orinoco Rivers using the G2 PhyloChip and, in parallel, we compared plant availability and foraging behavior of the hoatzins from the two locations. Plant composition differed between the 2 locations, which shared 5 out of 18 plant families and 1 plant genus--Coccoloba--that was highly consumed in both locations. The PhyloChip detected ∼1600 phylotypes from 42 phyla. There was a core microbiota with ~50% of the OTUs shared by at least 4 of the 6 individuals, but there were also differences in the crop microbiota of animals from the two regions. There existed a higher relative abundance of Alphaproteobacteria and Actinobacteria in the crops of birds from the Cojedes River and of Clostridia and Deltaproteobacteria in the crops of birds from the Orinoco River. The results showed both a core crop microbiota and also the bacterial taxa responsible for geographical differences among individuals from the two locations with different vegetation, suggesting an effect of both diet and geography in shaping the crop bacterial community of the hoatzin. PMID:22313738

  8. The Anabaena sensory rhodopsin transducer defines a novel superfamily of prokaryotic small-molecule binding domains

    De Souza Robson F

    2009-08-01

    Full Text Available Abstract The Anabaena sensory rhodopsin transducer (ASRT is a small protein that has been claimed to function as a signaling molecule downstream of the cyanobacterial sensory rhodopsin. However, orthologs of ASRT have been detected in several bacteria that lack rhodopsin, raising questions about the generality of this function. Using sequence profile searches we show that ASRT defines a novel superfamily of β-sandwich fold domains. Through contextual inference based on domain architectures and predicted operons and structural analysis we present strong evidence that these domains bind small molecules, most probably sugars. We propose that the intracellular versions like ASRT probably participate as sensors that regulate a diverse range of sugar metabolism operons or even the light sensory behavior in Anabaena by binding sugars or related metabolites. We also show that one of the extracellular versions define a predicted sugar-binding structure in a novel cell-surface lipoprotein found across actinobacteria, including several pathogens such as Tropheryma, Actinomyces and Thermobifida. The analysis of this superfamily also provides new data to investigate the evolution of carbohydrate binding modes in β-sandwich domains with very different topologies. Reviewers: This article was reviewed by M. Madan Babu and Mark A. Ragan.

  9. Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity.

    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

  10. Psychrotrophic lipase producers from Arctic soil and sediment samples.

    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

  11. Population Dynamic of Dendronephthya sp.-Associated Bacteria in Natural and Artificial Habitats

    SUSAN SOKA

    2011-06-01

    Full Text Available Dendronephthya sp. is a soft coral that has huge distribution starting from Indopacific, Tonga, Solomon Islands to Great Barrier Reef in Australia. However, this soft corals survive only in short period after cultivation in artificial habitat (aquarium. Recent study showed that the soft coral Dendronephtya sp. has an association or symbiotic relationship with several bacteria, commonly known as coral associated bacteria (CAB. In this study, we compared the population dynamic of Dendronephthya sp.-associated bacteria in natural and artificial habitat, resulting different bacterial community profiles using terminal restriction fragment length polymorphism (T-RFLP analysis of bacterial community DNA. There were 15 main classes of bacterial population identified along with uncultured microorganism, uncultured organism, uncultured bacteria and unidentified organism. Members of Actinobacteria, Arthrobacteria, Chlorobia, Caldilineae, -proteobacteria and Proteobacteria were predicted to give contributions in the survival ability of both Dendronephthya sp. The cultivation of soft corals after 2 weeks in artificial habitat increases bacterial population similarity on 2 different samples by 10%. Bacterial population similarity in artificial habitat would increase along with the longer cultivation time of soft corals.

  12. Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities.

    Barbosa Lima, Amanda; Cannavan, Fabiana Souza; Navarrete, Acacio Aparecido; Teixeira, Wenceslau Geraldes; Kuramae, Eiko Eurya; Tsai, Siu Mui

    2015-05-01

    Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes. PMID:25103911

  13. SACCHAROTHRIX SP. ABH26, A NEW ACTINOBACTERIAL STRAIN FROM ALGERIAN SAHARAN SOIL: ISOLATION, IDENTIFICATION AND ANTIMICROBIAL ACTIVITY

    Abdelhadi Lahoum

    2015-04-01

    Full Text Available A new strain of actinobacteria, designated ABH26, was isolated from a Saharan soil in the Adrar region (Algeria, by the dilution agar plating method using a chitin-vitamins B medium supplemented with polymyxin and penicillin. The morphological studies showed that this strain represents a member of the Saccharothrix genus. Phylogenetic analysis showed that this strain had 16S rRNA gene sequence similarities ranging from 97.63% (with Saccharothrix violaceirubra NBRC 102064T to 99.86% (with Saccharothrix xinjiangensis NBRC 101911T. Furthermore, strain ABH26 presented a strong activity against mycotoxigenic and phytopathogenic fungi including Aspergillus carbonarius (M333, A. flavus (NRRL 3251, A. westerdijkiae (ATCC 3174, Fusarium oxysporum f. sp. lini (Fol and F. solani (Fsol. Additionally, the strain exhibited an important antimicrobial activity against many strains of the pathogenic yeast Candida albicans (M2, M3 and IPA200 and against methicillin resistant Staphylococcus aureus (MRSA 639c. Thus, four solvents (n-hexane, dichloromethane, ethyl acetate and n-butanol were used for the extraction of produced antibiotic compounds. The highest antimicrobial activities were obtained using the butanolic extract. The thin layer chromatography (TLC method showed two bioactive spots, named HAD1 and HAD2, which were reveled negatively by using chemical revelators (ninhydrin, naphtoresorcinol-sulfuric acid, ferrous iron chloride and formaldehyde-sulfuric. These results indicated the absence of amine group, sugar, hydroxamic acid, phenol and aromatic compound.

  14. Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia.

    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

  15. A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics

    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

  16. Diversity and ecology of oxalotrophic bacteria.

    Hervé, Vincent; Junier, Thomas; Bindschedler, Saskia; Verrecchia, Eric; Junier, Pilar

    2016-02-01

    Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed. PMID:26748805

  17. Microbiota associated with pollen, bee bread, larvae and adults of solitary bee Osmia cornuta (Hymenoptera: Megachilidae).

    Lozo, J; Berić, T; Terzić-Vidojević, A; Stanković, S; Fira, D; Stanisavljević, L

    2015-08-01

    Using cultivation-dependant method, we isolated 184 strains from fresh and old bee bread, pollen, larvae and adults of solitary bee Osmia cornuta. The 16S rDNA sequencing of 79 selected isolates gave the final species-specific identification of strains. Phylogenetic analysis indicated that microbiota isolated from five different sources were represented with 29 species within three different phyla, Firmicutes with 25 species, Actinobacteria with only one species and Proteobacteria with three species of Enterobacteriaceae. Bacterial biodiversity presented with Shannon-Wiener index (H') was highest in the alimentary tract of adults and old bee bread (H' = 2.43 and H' = 2.53, respectively) and in the same time no dominance of any species was scored. On the contrary, results obtained for Simpson index (D) showed that in pollen samples the dominant species was Pantoea agglomerans (D = 0.42) while in fresh bee bread that was Staphylococcus sp. (D = 0.27). We assume that microbial diversity detected in the tested samples of solitary bee O. cornuta probably come from environment. PMID:25895542

  18. Electricity generation from cattle dung using microbial fuel cell technology during anaerobic acidogenesis and the development of microbial populations.

    Zhao, Guang; Ma, Fang; Wei, Li; Chua, Hong; Chang, Chein-Chi; Zhang, Xiao-Jun

    2012-09-01

    A microbial fuel cell (MFC) was constructed to investigate the possible generation of electricity using cattle dung as a substrate. After 30 days of operation, stable electricity was generated, and the maximum volumetric power density was 0.220 W/m(3). The total chemical oxygen demand (TCOD) removal and coulombic efficiency (CE) of the MFC reached 73.9±1.8% and 2.79±0.6%, respectively, after 120 days of operation. Acetate was the main metabolite in the anolyte, and other volatile fatty acids (VFAs) (propionate and butyrate) were present in minor amounts. The PCR-DGGE analysis indicated that the following five groups of microbes were present: Proteobacteria, Bacteroides, Chloroflexi, Actinobacteria and Firmicutes. Proteobacteria and Firmicutes were the dominant phyla in the sample; specifically, 36.3% and 24.2% of the sequences obtained were Proteobacteria and Firmicutes, respectively. Clostridium sp., Pseudomonas luteola and Ochrobactrum pseudogrignonense were the most dominant groups during the electricity generation process. The diversity of archaea dramatically decreased after 20 days of operation. The detected archaea were hydrogenotrophic methanogens, and the Methanobacterium genus disappeared during the periods of stable electricity generation via acidogenesis. PMID:22595839

  19. Efficient electricity generation from sewage sludge using biocathode microbial fuel cell.

    Zhang, Guodong; Zhao, Qingliang; Jiao, Yan; Wang, Kun; Lee, Duu-Jong; Ren, Nanqi

    2012-01-01

    Microbial fuel cells (MFCs) with abiotic cathodes require expensive catalyst (such as Pt) or catholyte (such as hexacynoferrate) to facilitate oxidation reactions. This study incorporated biocathodes into a three-chamber MFC to yield electricity from sewage sludge at maximum power output of 13.2 ± 1.7 W/m(3) during polarization, much higher than those previously reported. After 15 d operation, the total chemical oxygen demand (TCOD) removal and coulombic efficiency (CE) of cell reached 40.8 ± 9.0% and 19.4 ± 4.3%, respectively. The anolyte comprised principally acetate and propionate (minor) as metabolites. The use of biocathodes produced an internal resistance of 36-46 Ω, lower than those reported in literature works, hence yielding higher maximum power density from MFC. The massively parallel sequencing technology, 454 pyrosequencing technique, was adopted to probe microbial community on anode biofilm, with dominant phyla belonging to Proteobacteria (45% of total bacteria), Bacteroidetes (19%), Uncultured bacteria (9%), Actinobacteria (7%), Firmicutes (7%), Chloroflex (7%). At genera level, Rhodoferax, Ferruginibacter, Propionibacterium, Rhodopseudomonas, Ferribacterium, Clostridium, Chlorobaculum, Rhodobacter, Bradyrhizobium were the abundant taxa (relative abundances>2.0%). PMID:22078254

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

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

    2013-01-01

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

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

    Fábio Lino Soares Júnior

    2013-09-01

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

  2. Engineering propionibacteria as versatile cell factories for the production of industrially important chemicals: advances, challenges, and prospects.

    Guan, Ningzi; Zhuge, Xin; Li, Jianghua; Shin, Hyun-Dong; Wu, Jing; Shi, Zhongping; Liu, Long

    2015-01-01

    Propionibacteria are actinobacteria consisting of two principal groups: cutaneous and dairy. Cutaneous propionibacteria are considered primary pathogens to humans, whereas dairy propionibacteria are widely used in the food and pharmaceutical industries. Increasing attention has been focused on improving the performance of dairy propionibacteria for the production of industrially important chemicals, and significant advances have been made through strain engineering and process optimization in the production of flavor compounds, nutraceuticals, and antimicrobial compounds. In addition, genome sequencing of several propionibacteria species has been completed, deepening understanding of the metabolic and physiological features of these organisms. However, the metabolic engineering of propionibacteria still faces several challenges owing to the lack of efficient genome manipulation tools and the existence of various types of strong restriction-modification systems. The emergence of systems and synthetic biology provides new opportunities to overcome these bottlenecks. In this review, we first introduce the major species of propionibacteria and their properties and provide an overview of their functions and applications. We then discuss advances in the genome sequencing and metabolic engineering of these bacteria. Finally, we discuss systems and synthetic biology approaches for engineering propionibacteria as efficient and robust cell factories for the production of industrially important chemicals. PMID:25431012

  3. The potential role of 'Candidatus Microthrix parvicella' in phosphorus removal during sludge bulking in two full-scale enhanced biological phosphorus removal plants.

    Wang, Juan; Qi, Rong; Liu, Miaomiao; Li, Qian; Bao, Haipeng; Li, Yaming; Wang, Shen; Tandoi, Valter; Yang, Min

    2014-01-01

    We investigated the bacterial community compositions and phosphorus removal performance under sludge bulking and non-bulking conditions in two biological wastewater treatment systems (conventional A²/O (anaerobic/anoxic/aerobic) and inverted A²/O (anoxic/anaerobic/aerobic) processes) receiving the same raw wastewater. Sludge bulking resulted in significant shift in bacterial compositions from Proteobacteria dominance to Actinobacteria dominance, characterized by the significant presence of filamentous 'Candidatus Microthrix parvicella'. Quantitative real-time polymerase chain reaction (PCR) analysis revealed that the relative abundance of 'Candidatus Accumulibacter phosphatis', a key polyphosphate-accumulating organism responsible for phosphorus removal, with respect to 16s rRNA genes of total bacteria was 0.8 and 0.7%, respectively, for the conventional and inverted A²/O systems when sludge bulking occurred, which increased to 8.2 and 12.3% during the non-bulking period. However, the total phosphorus removal performance during the bulking period (2-week average: 97 ± 1 and 96 ± 1%, respectively) was not adversely affected comparable to that during the non-bulking period (2-week average: 96 ± 1 and 96 ± 1%, respectively). Neisser staining revealed the presence of large polyphosphate granules in 'Candidatus Microthrix parvicella', suggesting that this microbial group might have been responsible for phosphorus removal during the sludge bulking period when 'Candidatus Accumulibacter phosphatis' was excluded from the systems. PMID:25051486

  4. Isolation and Identification of Cellulolytic Bacteria from the Gut of Holotrichia parallela Larvae (Coleoptera: Scarabaeidae

    Hongyu Zhang

    2012-02-01

    Full Text Available In this study, 207 strains of aerobic and facultatively anaerobic cellulolytic bacteria were isolated from the gut of Holotrichia parallela larvae. These bacterial isolates were assigned to 21 genotypes by amplified ribosomal DNA restriction analysis (ARDRA. A partial 16S rDNA sequence analysis and standard biochemical and physiological tests were used for the assignment of the 21 representative isolates. Our results show that the cellulolytic bacterial community is dominated by the Proteobacteria (70.05%, followed by the Actinobacteria (24.15%, the Firmicutes (4.35%, and the Bacteroidetes (1.45%. At the genus level, Gram-negative bacteria including Pseudomonas, Ochrobactrum, Rhizobium, Cellulosimicrobium, and Microbacterium were the predominant groups, but members of Bacillus, Dyadobacter, Siphonobacter, Paracoccus, Kaistia, Devosia, Labrys, Ensifer, Variovorax, Shinella, Citrobacter, and Stenotrophomonas were also found. Furthermore, our results suggest that a significant amount of bacterial diversity exists among the cellulolytic bacteria, and that Siphonobacter aquaeclarae, Cellulosimicrobium funkei, Paracoccus sulfuroxidans, Ochrobactrum cytisi, Ochrobactrum haematophilum, Kaistia adipata, Devosia riboflavina, Labrys neptuniae, Ensifer adhaerens, Shinella zoogloeoides, Citrobacter freundii, and Pseudomonas nitroreducens are reported to be cellulolytic for the first time in this study. Our results indicate that the scarab gut is an attractive source for the study of novel cellulolytic microorganisms and enzymes useful for cellulose degradation.

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

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

    2013-01-01

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

  6. Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke.

    Yang, Hui; Hu, Jinxiang; Long, Xiaohua; Liu, Zhaopu; Rengel, Zed

    2016-01-01

    The interaction between roots and bacterial communities in halophytic species is poorly understood. Here, we used Jerusalem artichoke cultivar Nanyu 1 (NY-1) to characterise root distribution patterns and determine diversity and abundance of bacteria in the rhizosphere soil under variable salinity. Root growth was not inhibited within the salinity range 1.2 to 1.9 g salt/kg, but roots were mainly confined to 0-20 cm soil layer vertically and 0-30 cm horizontally from the plant centre. Root concentrations of K(+), Na(+), Mg(2+) and particularly Ca(2+) were relatively high under salinity stress. High salinity stress decreased soil invertase and catalase activity. Using a next-generation, Illumina-based sequencing approach, we determined higher diversity of bacteria in the rhizosphere soil at high than low salinity. More than 15,500 valid reads were obtained, and Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria predominated in all samples, accounting for >80% of the reads. On a genus level, 636 genera were common to the low and high salinity treatments at 0-5 cm and 5-10 cm depth. The abundance of Steroidobacter and Sphingomonas was significantly decreased by increasing salinity. Higher Shannon and Chao 1 indices with increasing severity of salt stress indicated that high salt stress increased diversity in the bacterial communities. PMID:26852800

  7. Suitability of the microbial community composition and function in a semiarid mine soil for assessing phytomanagement practices based on mycorrhizal inoculation and amendment addition.

    Kohler, J; Caravaca, F; Azcón, R; Díaz, G; Roldán, A

    2016-03-15

    The recovery of species composition and functions of soil microbial community of degraded lands is crucial in order to guarantee the long-term self-sustainability of the ecosystems. A field experiment was carried out to test the influence of combining fermented sugar beet residue (SBR) addition and inoculation with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae on the plant growth parameters and microbial community composition and function in the rhizosphere of two autochthonous plant species (Dorycnium pentaphyllum L. and Asteriscus maritimus L.) growing in a semiarid soil contaminated by heavy metals. We analysed the phospholipid fatty acids (PLFAs), neutral lipids fatty acids (NLFAs) and enzyme activities to study the soil microbial community composition and function, respectively. The combined treatment was not effective for increasing plant growth. The SBR promoted the growth of both plant species, whilst the AM fungus was effective only for D. pentaphyllum. The effect of the treatments on plant growth was linked to shifts in the rhizosphere microbial community composition and function. The highest increase in dehydrogenase and β-glucosidase activities was recorded in SBR-amended soil. The SBR increased the abundance of marker PLFAs for saprophytic fungi, Gram+ and Gram- bacteria and actinobacteria, whereas the AM fungus enhanced the abundance of AM fungi-related NLFA and marker PLFAs for Gram- bacteria. Measurement of the soil microbial community composition and function was useful to assess the success of phytomanagement technologies in a semiarid, contaminated soil. PMID:26773427

  8. Soil biological attributes in arsenic-contaminated gold mining sites after revegetation.

    Dos Santos, Jessé Valentim; de Melo Rangel, Wesley; Azarias Guimarães, Amanda; Duque Jaramillo, Paula Marcela; Rufini, Márcia; Marra, Leandro Marciano; Varón López, Maryeimy; Pereira da Silva, Michele Aparecida; Fonsêca Sousa Soares, Cláudio Roberto; de Souza Moreira, Fatima Maria

    2013-12-01

    Recovery of arsenic contaminated areas is a challenge society faces throughout the world. Revegetation associated with microbial activity can play an essential role in this process. This work investigated biological attributes in a gold mining area with different arsenic contents at different sites under two types of extant revegetation associated with cover layers of the soil: BS, Brachiaria sp. and Stizolobium sp., and LEGS, Acacia crassicarpa, A. holosericea, A. mangium, Sesbania virgata, Albizia lebbeck and Pseudosamanea guachapele. References were also evaluated, comprising the following three sites: B1, weathered sulfide substrate without revegetation; BM, barren material after gold extraction and PRNH (private reserve of natural heritage), an uncontaminated forest site near the mining area. The organic and microbial biomass carbon contents and substrate-induced respiration rates for these sites from highest to lowest were: PRNH > LEGS > BS > B1 and BM. These attributes were negatively correlated with soluble and total arsenic concentration in the soil. The sites that have undergone revegetation (LEGS and BS) had higher densities of bacteria, fungi, phosphate solubilizers and ammonium oxidizers than the sites without vegetation. Principal component analysis showed that the LEGS site grouped with PRNH, indicating that the use of leguminous species associated with an uncontaminated soil cover layer contributed to the improvement of the biological attributes. With the exception of acid phosphatase, all the biological attributes were indicators of soil recovery, particularly the following: microbial carbon, substrate-induced respiration, density of culturable bacteria, fungi and actinobacteria, phosphate solubilizers and metabolic quotient. PMID:24114185

  9. Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters.

    Gannoun, Hana; Omri, Ilhem; Chouari, Rakia; Khelifi, Eltaief; Keskes, Sajiaa; Godon, Jean-Jacques; Hamdi, Moktar; Sghir, Abdelghani; Bouallagui, Hassib

    2016-02-01

    The effect of increasing the organic loading rates (OLRs) on the performance of the anaerobic codigestion of olive mill (OMW) and abattoir wastewaters (AW) was investigated under mesophilic and thermophilic conditions. The structure of the microbial community was also monitored. Increasing OLR to 9g of chemical oxygen demand (COD) L(-1)d(-1) affected significantly the biogas yield and microbial diversity at 35°C. However, at 55°C digester remained stable until OLR of 12g of CODL(-1)d(-1) with higher COD removal (80%) and biogas yield (0.52Lg(-1) COD removed). Significant differences in the bacterial communities were detected between mesophilic and thermophilic conditions. The dominant phyla detected in the digester at both phases were the Firmicutes, Actinobacteria, Bacteroidetes, Synergistetes and Spirochaete. However, Verrucomicrobia, Proteobacteria and the candidate division BRC1 were only detected at thermophilic conditions. The Methanobacteriales and the Thermoplasmales were found as a high predominant archaeal member in the anaerobic sludge. PMID:26687494

  10. Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

    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.

  11. Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans.

    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

  12. Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

    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.

  13. [Molecular analysis of the microbial communities of the Dagang Kongdian flooding bed oilfield].

    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

  14. Bifidobacteria Abundance-Featured Gut Microbiota Compositional Change in Patients with Behcet’s Disease

    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

  15. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana.

    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

  16. Molecular diversity of bacteria in commercially available "Spirulina" food supplements.

    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

  17. Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control.

    Andreolli, Marco; Lampis, Silvia; Zapparoli, Giacomo; Angelini, Elisa; Vallini, Giovanni

    2016-02-01

    This study represents the first investigation on ecology of endophytic bacteria isolated from 3 and 15 year-old vine stems of Vitis vinifera cv. Corvina. The analysis was performed by means of culture-dependent techniques. The obtained results showed that new grapevine endophytic genera are being discovered. Moreover, Bacilli and Actinobacteria are frequently isolated from 3 year-old plants, whereas Alpha- and Gamma- Proteobacteria classes are more prevalent in the 15 year-old plants. Shannon-Wiener (H) index and analysis of rarefaction curves revealed greater genus richness in young grapevine plants. Furthermore, results evidenced an increase of genotypic group number within specific genera (e.g., Rhizobium and Pantoea). Among isolated strains from 3 and 15 year-old stems, respectively, 34 and 39% produce siderophores; 22 and 15% secrete ammonia; 22 and 21% produce indole-3-acetic acid; 8.7 and 41% solubilize phosphate. Besides, two strains isolated from 15 year-old grapevines showed 1-aminocyclopropane-1-carboxylate deaminase activity. Antifungal activity analysis evidenced that two Bacillus strains possess growth antagonistic effect toward all the tested fungal strains. Therefore, the present study extends our knowledge of the diversity of the endophytic bacteria by providing new insights into the complexity of the grapevine microbiome. PMID:26805617

  18. Survey of bacterial contamination of environment of swimming pools in Yazd city, in 2013

    Hossein Jafari Mansoorian

    2015-09-01

    Full Text Available Background: Infections are readily transmitted as a result of bacterial contamination of swimming pools. Therefore, hygiene and preventing the contamination of swimming pools is of particular importance. The objective of this study was to determine the amount of bacterial contamination in indoor pools of Yazd in 2013. Methods: In this descriptive and analytical study, all indoor swimming pools of Yazd (12 pools were evaluated during the spring and summer of 2013, in terms of bacterial contamination. In order to determine contamination, a sterile cotton swab was used for sampling. On average, 45 samples were taken from different surfaces in each pool (shower, dressing room, sitting places in sauna, platforms and around the pool. In total, about 540 samples from all pools were tested for bacterial contamination. Results: The results show that from 540 samples, bacterial contamination was observed in about 93 samples (17.22%; and was seen more in showers, edges of the pool and jacuzzis, and the slippers used in swimming pools. The most important isolated bacteria types were E. coli, Actinobacteria, Pseudomonas alcaligenes, Pseudomonas aeruginosa and Klebsiella pneumonia. Conclusion: The results indicate the presence of bacterial contamination on the surface of these places. It is recommended that health authorities should pay more attention to cleaning and disinfecting surfaces around the pool, showers, dressing rooms etc, to prevent infectious disease transfer as a result of contact with contaminated swimming pool surfaces.

  19. Characterization of microbiota composition and presence of selected antibiotic resistance genes in carriage water of ornamental fish.

    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.

  20. Characterizing the Intestinal Microbiome in Infantile Colic: Findings Based on an Integrative Review of the Literature.

    Dubois, Nancy E; Gregory, Katherine E

    2016-05-01

    Approximately 20% of newborns will develop symptoms of infantile colic starting around 2 weeks of age. While health care providers have a greater understanding of the impact that inconsolable crying has on family dynamics, maternal-infant bonding, and health care resources, opportunities for study still exist in the area of intestinal microbiome research. Advances in molecular technologies utilizing 16S ribosomal RNA and ribosomal DNA created the opportunity for researchers to index the intestinal microbial composition to better understand its association with infantile colic. This integrative review provides a synopsis of the findings from five recent studies that utilized nonculture-based approaches to characterize the intestinal microbiome of infants with colic. Articles were identified through PubMed, CINAHL, and Google Scholar using the search termscolic,crying,fussiness,microbiome, andmicrobiota The general aim of the research studies was to better understand the potential association of intestinal dysbiosis with the development of colic symptoms. The research found that infants who expressed symptoms of colic were colonized with significantly higher levels of Proteobacteria and exhibited lower bacterial diversity when compared to their unaffected counterparts. Additionally, colonization levels of ActinobacteriaBifidobacteriumand FirmicuteLactobacilliwere inversely related to the amount of crying and fussiness in newborns. The observed association of an imbalanced colonization of the intestines by noncommensal bacteria with the expression of infantile colic symptoms warrants further exploration. PMID:26721871

  1. Microbial communities in acid water environments of two mines, China

    Xiao Shengmu; Xie Xuehui [College of Environmental Science and Engineering, Donghua University, Shanghai (China); Liu Jianshe [College of Environmental Science and Engineering, Donghua University, Shanghai (China); School of Resources Processing and Bioengineering, Central South University, Changsha (China)], E-mail: xiaoshengmu@gmail.com

    2009-03-15

    To understand the compositions and structures of microbial communities in different acid-aqueous environments, a PCR-based cloning approach was used. A total of five samples were collected from two mines in China. Two samples, named as G1 and G2, were acid mine drainage (AMD) samples and from Yunfu sulfide mine in Guangdong province, China. The rest of the three samples named as D1, DY and D3, were from three sites undertaking bioleaching in Yinshan lead-zinc mine in Jiangxi province, China. Phylogenetic analysis revealed that bacteria in the five samples fell into six putative divisions, which were {alpha}-Proteobacteria, {beta}-Proteobacteria, {gamma}-Proteobacteria, Firmicutes, Actinobacteria and Nitrospira. Archaea was only detected in the three samples from Yinshan lead-zinc mine, which fell into two phylogenentic divisions, Thermoplsma and Ferroplasma. In addition, the results of principal component analysis (PCA) suggested that more similar the geochemical properties in samples were, more similar microbial community structures in samples were. - Microbial community compositions in acid-aqueous environments from Chinese mines were studied, and the relationship with geochemical properties was obtained.

  2. A new group in the Leptospirillum clade: cultivation-independent community genomics, proteomics and transcriptomics of the new species Leptospirillum group IV UBA BS.

    Goltsman, Daniela [University of California, Berkeley; Dasari, Mauna [University of California, Berkeley; Thomas, BC [University of California, Berkeley; Shah, Manesh B [ORNL; Verberkmoes, Nathan C [ORNL; Hettich, Robert {Bob} L [ORNL; Banfield, Jillian F. [University of California, Berkeley

    2013-01-01

    Leptospirillum spp. are widespread members of acidophilic microbial communities that catalyze ferrous iron oxidation, thereby increasing sulfide mineral dissolution rates. These bacteria play important roles in environmental acidification and are harnessed for bioleaching-based metal recovery. Known members of the Leptospirillum clade of the Nitrospira phylum are Leptospirillum ferrooxidans (group I), Leptospirillum ferriphilum and Leptospirillum rubarum (group II), and Leptospirillum ferrodiazotrophum (group III). In the Richmond Mine acid mine drainage (AMD) system, biofilm formation is initiated by L. rubarum; L. ferrodiazotrophum appears in later developmental stages. Here we used community metagenomic data from unusual, thick floating biofilms to identify distinguishing metabolic traits in a rare and uncultivated community member, the new species Leptospirillum group IV UBA BS. These biofilms typically also contain a variety of Archaea, Actinobacteria, and a few other Leptospirillum spp. The Leptospirillum group IV UBA BS species shares 98% 16S rRNA sequence identity and 70% average amino acid identity between orthologs with its closest relative, L. ferrodiazotrophum. The presence of nitrogen fixation and reverse tricarboxylic acid (TCA) cycle proteins suggest an autotrophic metabolism similar to that of L. ferrodiazotrophum, while hydrogenase proteins suggest anaerobic metabolism. Community transcriptomic and proteomic analyses demonstrate expression of a multicopper oxidase unique to this species, as well as hydrogenases and core metabolic genes. Results suggest that the Leptospirillum group IV UBA BS species might play important roles in carbon fixation, nitrogen fixation, hydrogen metabolism, and iron oxidation in some acidic environments.

  3. Microbial communities in acid water environments of two mines, China

    To understand the compositions and structures of microbial communities in different acid-aqueous environments, a PCR-based cloning approach was used. A total of five samples were collected from two mines in China. Two samples, named as G1 and G2, were acid mine drainage (AMD) samples and from Yunfu sulfide mine in Guangdong province, China. The rest of the three samples named as D1, DY and D3, were from three sites undertaking bioleaching in Yinshan lead-zinc mine in Jiangxi province, China. Phylogenetic analysis revealed that bacteria in the five samples fell into six putative divisions, which were α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Firmicutes, Actinobacteria and Nitrospira. Archaea was only detected in the three samples from Yinshan lead-zinc mine, which fell into two phylogenentic divisions, Thermoplsma and Ferroplasma. In addition, the results of principal component analysis (PCA) suggested that more similar the geochemical properties in samples were, more similar microbial community structures in samples were. - Microbial community compositions in acid-aqueous environments from Chinese mines were studied, and the relationship with geochemical properties was obtained

  4. Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern South Atlantic Ocean.

    da Silva, Marcus Adonai Castro; Cavalett, Angélica; Spinner, Ananda; Rosa, Daniele Cristina; Jasper, Regina Beltrame; Quecine, Maria Carolina; Bonatelli, Maria Letícia; Pizzirani-Kleiner, Aline; Corção, Gertrudes; Lima, André Oliveira de Souza

    2013-12-01

    The deep-sea environments of the South Atlantic Ocean are less studied in comparison to the North Atlantic and Pacific Oceans. With the aim of identifying the deep-sea bacteria in this less known ocean, 70 strains were isolated from eight sediment samples (depth range between 1905 to 5560 m) collected in the eastern part of the South Atlantic, from the equatorial region to the Cape Abyssal Plain, using three different culture media. The strains were classified into three phylogenetic groups, Gammaproteobacteria, Firmicutes and Actinobacteria, by the analysis of 16s rRNA gene sequences. Gammaproteobacteria and Firmicutes were the most frequently identified groups, with Halomonas the most frequent genus among the strains. Microorganisms belonging to Firmicutes were the only ones observed in all samples. Sixteen of the 41 identified operational taxonomic units probably represent new species. The presence of potentially new species reinforces the need for new studies in the deep-sea environments of the South Atlantic. PMID:23565357

  5. Diversity of Bacterial Biofilm Communities on Sprinklers from Dairy Farm Cooling Systems in Israel.

    Shpigel, Nahum Y; Pasternak, Zohar; Factor, Gilad; Gottlieb, Yuval

    2015-01-01

    On dairy farms in hot climates worldwide, cows suffer from heat stress, which is alleviated by the use of water cooling systems. Sprinklers and showerheads are known to support the development of microbial biofilms, which can be a source of infection by pathogenic microorganisms. The aim of this study was to investigate the presence of microbial biofilms in dairy cooling systems, and to analyze their population compositions using culture-independent technique, 16S rRNA gene sequencing. Biofilm samples were collected on eight dairy farms from 40 sprinklers and the microbial constituents were identified by deep sequencing of the 16S rRNA gene. A total of 9,374 operational taxonomic units (OTUs) was obtained from all samples. The mean richness of the samples was 465 ± 268 OTUs which were classified into 26 different phyla; 76% of the reads belonged to only three phyla: Proteobacteria, Actinobacteria and Firmicutes. Although the most prevalent OTUs (Paracoccus, Methyloversatilis, Brevundimonas, Porphyrobacter, Gp4, Mycobacterium, Hyphomicrobium, Corynebacterium and Clostridium) were shared by all farms, each farm formed a unique microbial pattern. Some known potential human and livestock pathogens were found to be closely related to the OTUs found in this study. This work demonstrates the presence of biofilm in dairy cooling systems which may potentially serve as a live source for microbial pathogens. PMID:26407190

  6. Microbial communities in a coastal cave: Cova des Pas de Vallgornera (Mallorca, Western Mediterranean

    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.

  7. The Truffle Microbiome: Species and Geography Effects on Bacteria Associated with Fruiting Bodies of Hypogeous Pezizales.

    Benucci, Gian Maria Niccolò; Bonito, Gregory M

    2016-07-01

    Fungi that produce their fruiting bodies underground within the soil profile are known commonly as truffles. Truffle fruiting bodies harbor a diverse but poorly understood microbial community of bacteria, yeasts, and filamentous fungi. In this study, we used next-generation 454 amplicon pyrosequencing of the V1 and V4 region of the bacterial 16S ribosomal DNA (rDNA) in order to characterize and compare effects of truffle species and geographic origin on the truffle microbiome. We compared truffle microbiomes of the glebal tissue for eight truffle species belonging to four distinct genera within the Pezizales: Tuber, Terfezia, Leucangium, and Kalapuya. The bacterial community within truffles was dominated by Proteobacteria, Bacterioides, Actinobacteria, and Firmicutes. Bacterial richness within truffles was quite low overall, with between 2-23 operational taxonomic units (OTUs). Notably, we found a single Bradyrhizobium OTU to be dominant within truffle species belonging to the genus Tuber, irrespective of geographic origin, but not in other truffle genera sampled. This study offers relevant insights into the truffle microbiome and raises questions concerning the recruitment and function of these fungal-associated bacteria consortia. PMID:27026101

  8. Impact of Chloramination on the Development of Laboratory-Grown Biofilms Fed with Filter-Pretreated Groundwater

    Ling, Fangqiong

    2013-01-01

    This study evaluated the continuous impact of monochloramine disinfection on laboratory-grown biofilms through the characterization of biofilm architecture and microbial community structure. Biofilm development and disinfection were achieved using CDC (Centers for Disease Control and Prevention) biofilm reactor systems with polyvinyl chloride (PVC) coupons as the substratum and sand filter-pretreated groundwater as the source of microbial seeding and growth nutrient. After 2 weeks of growth, the biofilms were subjected to chloramination for 8 more weeks at concentrations of 7.5±1.4 to 9.1±0.4 mg Cl2 L-1. Control reactors received no disinfection during the development of biofilms. Confocal laser scanning microscopy and image analysis indicated that chloramination could lead to 81.4-83.5% and 86.3-95.6% reduction in biofilm biomass and thickness, respectively, but could not eliminate biofilm growth. 16S rRNA gene terminal restriction fragment length polymorphism analysis indicated that microbial community structures between chloraminated and non-chloraminated biofilms exhibited different successional trends. 16S rRNA gene pyrosequencing analysis further revealed that chloramination could select members of Actinobacteria and Acidobacteria as the dominant populations, whereas natural development leads to the selection of members of Nitrospira and Bacteroidetes as dominant biofilm populations. Overall, chloramination treatment could alter the growth of multi-species biofilms on the PVC surface, shape the biofilm architecture, and select a certain microbial community that can survive or proliferate under chloramination.

  9. Glyphosate effects on soil rhizosphere-associated bacterial communities.

    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. PMID:26580738

  10. Phylogenetic diversity and antimicrobial activities of bryozoan-associated bacteria isolated from Mediterranean and Baltic Sea habitats.

    Heindl, Herwig; Wiese, Jutta; Thiel, Vera; Imhoff, Johannes F

    2010-03-01

    To date, only a small number of investigations covering microbe-bryozoa associations have been carried out. Most of them have focused on a few bryozoan species and none have covered the antibacterial activities of associated bacteria. In the current study, the proportion and phylogenetic classification of Bryozoan-associated bacteria with antimicrobial properties were investigated. Twenty-one specimens of 14 different bryozoan species were collected from several sites in the Baltic and the Mediterranean Sea. A total of 340 associated bacteria were isolated, and 101 displayed antibiotic activities. While antibiosis was predominantly directed against Gram-positive test strains, 16S rRNA gene sequencing revealed affiliation of the isolates to Gram-negative classes (Flavobacteria, Alpha- and Gammaproteobacteria). One isolate was related to the Gram-positive Actinobacteria. The sequences were grouped into 27 phylotypes on the basis of similarity values >or=99.5%. A host-specific affiliation was not revealed as members of the same phylotype were derived from different bryozoan species. Site-specific patterns, however, were demonstrated. Strains of the genera Sphingomonas and Alteromonas were exclusively isolated from Mediterranean sites, whereas Shewanella, Marinomonas and Vibrio-related isolates were only from Baltic sites. Although Pseudoalteromonas affiliated strains were found in both habitats, they were separated into respective phylotypes. Isolates with 16S rDNA similarity values Tenacibaculum. PMID:20153592

  11. Gut Bacterial Community of the Xylophagous Cockroaches Cryptocercus punctulatus and Parasphaeria boleiriana

    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

  12. Bacterial and fungal taxon changes in soil microbial community composition induced by short-term biochar amendment in red oxidized loam soil.

    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

  13. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts

    Mason, Olivia U.; Di Meo-Savoie, Carol A.; Van Nostrand, Joy D.; Zhou, Jizhong; Fisk, Martin R.; Giovannoni, Stephen J.

    2008-09-30

    We used molecular techniques to analyze basalts of varying ages that were collected from the East Pacific Rise, 9 oN, from the rift axis of the Juan de Fuca Ridge, and from neighboring seamounts. Cluster analysis of 16S rDNA Terminal Restriction Fragment Polymorphism data revealed that basalt endoliths are distinct from seawater and that communities clustered, to some degree, based on the age of the host rock. This age-based clustering suggests that alteration processes may affect community structure. Cloning and sequencing of bacterial and archaeal 16S rRNA genes revealed twelve different phyla and sub-phyla associated with basalts. These include the Gemmatimonadetes, Nitrospirae, the candidate phylum SBR1093 in the c, andin the Archaea Marine Benthic Group B, none of which have been previously reported in basalts. We delineated novel ocean crust clades in the gamma-Proteobacteria, Planctomycetes, and Actinobacteria that are composed entirely of basalt associated microflora, and may represent basalt ecotypes. Finally, microarray analysis of functional genes in basalt revealed that genes coding for previously unreported processes such as carbon fixation, methane-oxidation, methanogenesis, and nitrogen fixation are present, suggesting that basalts harbor previously unrecognized metabolic diversity. These novel processes could exert a profound influence on ocean chemistry.

  14. Deodorants and antiperspirants affect the axillary bacterial community.

    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

  15. An initial investigation into the ecology of culturable aerobic postmortem bacteria.

    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

  16. Metagenomic profiling of antibiotic resistance genes and mobile genetic elements in a tannery wastewater treatment plant.

    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. Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond.

    Simachew, Addis; Lanzén, Anders; Gessesse, Amare; Øvreås, Lise

    2016-02-01

    The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 prokaryotic phyla were detected, and the dominant prokaryotic phyla accounted for more than 95 % of the reads consisting of Planctomycetes, Bacteroidetes, candidate division TM7, Deinococcus-Thermus, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota. Diversity indices indicated that operational taxonomic unit (OTU) richness decreases drastically with increasing salinity in the pond system. A total of 471 OTUs were found at 3.4 % salinity whereas 49 OTUs were detected in pond SP211 (25 % salinity), and only 19 OTUs in the crystallization pond at 32 % salinity (SP230F). Along the salinity gradient, archaeal community gradually replaced bacterial community. Thus, archaeal community accounted for 0.4 % in Lake Abijata while 99.0 % in pond SP230F. This study demonstrates that salinity appears to be the key environmental parameter in structuring the prokaryotic communities of haloalkaline environments. Further, it confirmed that the prokaryotic diversity in Lake Abijata is high and it harbors taxa with low or no phylogenetic similarities to existing prokaryotic taxa and thus represents novel microorganisms. PMID:26408190

  18. Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital.

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Felix, Alvina Clara; Sanabani, Sabri Saeed

    2016-01-01

    Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB), bank machine keyboard buttons (BMKB), restroom surfaces, and the employee biometric time clock system (EBTCS), in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients. PMID:26805866

  19. Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge.

    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. PMID:27169490

  20. Broad Escovopsis-inhibition activity of Pseudonocardia associated with Trachymyrmex ants.

    Meirelles, Lucas A; Mendes, Thaís D; Solomon, Scott E; Bueno, Odair C; Pagnocca, Fernando C; Rodrigues, Andre

    2014-08-01

    Attine ants maintain an association with antibiotic-producing Actinobacteria found on their integuments. Evidence supports these bacteria as auxiliary symbionts that help ants to defend the fungus gardens against pathogens. Using Pseudonocardia strains isolated from Trachymyrmex ants, we tested whether the inhibitory capabilities of such strains are restricted to Escovopsis parasites that infect gardens of this ant genus. Twelve Pseudonocardia strains were tested in in vitro bioassays against Escovopsis strains derived from fungus gardens of Trachymyrmex (n = 1) and leaf-cutting ants (n = 3). Overall, significant differences were observed in the mycelial growth among each Escovopsis strain in the presence of Pseudonocardia. Particularly, Escovopsis from Acromyrmex and Trachymyrmex were the most inhibited strains in comparison to Escovopsis isolated from Atta. This result suggests that Pseudonocardia isolated from Trachymyrmex possibly secrete antimicrobial compounds effective against diverse Escovopsis strains. The fact that Trachymyrmex ants harbour Pseudonocardia strains with broad spectrum of activity and its defensive role on attine gardens are discussed. PMID:24992532

  1. Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers.

    Kõiv, Viia; Roosaare, Märt; Vedler, Eve; Kivistik, Paula Ann; Toppi, Kristel; Schryer, David W; Remm, Maido; Tenson, Tanel; Mäe, Andres

    2015-01-01

    Endophytes are microbes and fungi that live inside plant tissues without damaging the host. Herein we examine the dynamic changes in the endophytic bacterial community in potato (Solanum tuberosum) tuber in response to pathogenic infection by Pectobacterium atrosepticum, which causes soft rot in numerous economically important crops. We quantified community changes using both cultivation and next-generation sequencing of the 16S rRNA gene and found that, despite observing significant variability in both the mass of macerated tissue and structure of the endophytic community between individual potato tubers, P. atrosepticum is always taken over by the endophytes during maceration. 16S rDNA sequencing revealed bacteria from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Verrucomicrobia, Acidobacteria, TM7, and Deinococcus-Thermus. Prior to infection, Propionibacterium acnes is frequently among the dominant taxa, yet is out competed by relatively few dominant taxa as the infection proceeds. Two days post-infection, the most abundant sequences in macerated potato tissue are Gammaproteobacteria. The most dominant genera are Enterobacter and Pseudomonas. Eight days post-infection, the number of anaerobic pectolytic Clostridia increases, probably due to oxygen depletion. These results demonstrate that the pathogenesis is strictly initiated by the pathogen (sensu stricto) and proceeds with a major contribution from the endophytic community. PMID:26118792

  2. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. PMID:25314594

  3. Identification of household bacterial community and analysis of species shared with human microbiome.

    Jeon, Yoon-Seong; Chun, Jongsik; Kim, Bong-Soo

    2013-11-01

    Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, which is recognized as highly colonized by microorganisms, in ten houses using high-throughput sequencing. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were predominant in refrigerator and toilet samples. However, Proteobacteria was more abundant in the refrigerator, and Firmicutes was more abundant in the toilet. These household bacterial communities were compared with those of human skin and gut to identify potential sources of household bacteria. Bacterial communities from refrigerators and toilets shared more species in common with human skin than gut. Opportunistic pathogens, including Propionibacterium acnes, Bacteroides vulgatus, and Staphylococcus epidermidis, were identified as species shared with human skin and gut microbiota. This approach can provide a general background of the household microbiota and a potential method of source-tracking for public health purposes. PMID:23743600

  4. Purification, crystallization and preliminary X-ray analysis of SGR6054, a Streptomyces homologue of the mycobacterial integration host factor mIHF

    A Streptomyces homologue of the mycobacterial integration host factor mIHF was heterologously produced, purified and crystallized in the presence of a 16-mer duplex DNA by the sitting-drop vapour-diffusion method. The best crystal diffracted X-rays to 2.22 Å resolution and belonged to space group C2. The mycobacterial integration host factor (mIHF) is a small nonspecific DNA-binding protein that is essential for the growth of Mycobacterium smegmatis. mIHF homologues are widely distributed among Actinobacteria, and a Streptomyces homologue of mIHF is involved in control of sporulation and antibiotic production in S. coelicolor A3(2). Despite their important biological functions, a structure of mIHF or its homologues has not been elucidated to date. Here, the S. griseus mIHF homologue (SGR6054) was expressed and purified from Escherichia coli and crystallized in the presence of a 16-mer duplex DNA by the sitting-drop vapour-diffusion method. The plate-shaped crystal belonged to space group C2, with unit-cell parameters a = 88.53, b = 69.35, c = 77.71 Å, β = 96.63°, and diffracted X-rays to 2.22 Å resolution

  5. Metagenomic Analysis of Antibiotic-Induced Changes in Gut Microbiota in a Pregnant Rat Model

    Khan, Imran; Azhar, Esam I.; Abbas, Aymn T.; Kumosani, Taha; Barbour, Elie K.; Raoult, Didier; Yasir, Muhammad

    2016-01-01

    Food and Drug Administration (FDA, USA)-approved category B antibiotics are commonly prescribed to treat infections during pregnancy. The aim of this study was to investigate antibiotic-induced changes in gut microbiota (GM) that occur during pregnancy. The 16S rRNA amplicon deep-sequencing method was used to analyze the effect of category B antibiotics (azithromycin, amoxicillin and cefaclor) on GM during pregnancy using a rat model. The GM composition was substantially modulated by pregnancy and antibiotics administration. Firmicutes, Bacteroidetes, Proteobacteria, Chlamydiae, Actinobacteria, and Cyanobacteria were the dominant phyla. Antibiotic treatment during pregnancy increased the relative abundance of Proteobacteria and reduced Firmicutes. The genera Shigella, Streptococcus, Candidatus Arthromitus, and Helicobacter were significantly (p < 0.05) more abundant during pregnancy. Antibiotics significantly (p < 0.05) reduced the relative abundance of Lactobacillus but increased that of Enterobacter. There was a significant (p < 0.05) decrease in Lactobacillus sp., Lactobacillus gallinarum and Lactobacillus crispatus during pregnancy. Antibiotic treatment reduced bacterial diversity; the lowest number of operational taxonomic units (OTUs) were detected in the cefaclor-treated groups. Antibiotics significantly (p < 0.05) promoted weight gain during pregnancy, and increased relative abundance of Shigella sonnei, Enterococcus hormaechei, and Acinetobacter sp. GM perturbations were accompanied by increases in Proteobacteria abundance and weight gain in pregnancy following antibiotic treatment. PMID:27199748

  6. Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode-water eddy.

    Nelson, Craig E; Carlson, Craig A; Ewart, Courtney S; Halewood, Elisa R

    2014-03-01

    Eddies are mesoscale oceanographic features (∼ 200 km diameter) that can cause transient blooms of phytoplankton by shifting density isoclines in relation to light and nutrient resources. To better understand how bacterioplankton respond to eddies, we examined depth-resolved distributions of bacterial populations across an anticyclonic mode-water eddy in the Sargasso Sea. Previous work on this eddy has documented elevated phytoplankton productivity and diatom abundance within the eddy centre with coincident bacterial productivity and biomass maxima. We illustrate bacterial community shifts within the eddy centre, differentiating populations uplifted along isopycnals from those enriched or depleted at horizons of enhanced bacterial and primary productivity. Phylotypes belonging to the Roseobacter, OCS116 and marine Actinobacteria clades were enriched in the eddy core and were highly correlated with pigment-based indicators of diatom abundance, supporting developing hypotheses that members of these clades associate with phytoplankton blooms. Typical mesopelagic clades (SAR202, SAR324, SAR406 and SAR11 IIb) were uplifted within the eddy centre, increasing bacterial diversity in the lower euphotic zone. Typical surface oligotrophic clades (SAR116, OM75, Prochlorococcus and SAR11 Ia) were relatively depleted in the eddy centre. The biogeochemical context of a bloom-inducing eddy provides insight into the ecology of the diverse uncultured bacterioplankton dominating the oligotrophic oceans. PMID:24589288

  7. Tracking differential incorporation of dissolved organic carbon types among diverse lineages of Sargasso Sea bacterioplankton.

    Nelson, Craig E; Carlson, Craig A

    2012-06-01

    Bacterioplankton are the primary trophic conduit for dissolved organic carbon (DOC) and linking community structure with DOC utilization is central to understanding global carbon cycling. We coupled stable isotope probing (SIP) with 16S rRNA pyrosequencing in dark seawater culture experiments on euphotic and mesopelagic communities from the Sargasso Sea. Parallel cultures were amended with equimolar quantities of four DO(13) C substrates to simultaneously evaluate community utilization and population-specific incorporation. Of the substrates tested - two cyanobacterial products (exudates or lysates from a culture of Synechococcus) and two defined monosaccharides (glucose or gluconic acid) - the cyanobacterial exudates were incorporated by the greatest diversity of oligotrophic bacterioplankton populations in surface waters, including taxa from > 10 major subclades within the Flavobacteria, Actinobacteria, Verrucomicrobia and Proteobacteria (including SAR11). In contrast, the monosaccharide glucose was not incorporated by any taxa belonging to extant oligotrophic oceanic clades. Conversely, proteobacterial copiotrophs, which were rare in the ambient water (< 0.1% of sequences), grew rapidly on all DOC amendments at both depths, but with different substrate preferences among lineages. We present a new analytical framework for using SIP to detect DOC incorporation across diverse oligotrophic bacterioplankton and discuss implications for the ecology of bacterial-DOC interactions among populations of diverging trophic strategies. PMID:22507662

  8. Ecology of Subglacial Lake Vostok (Antarctica, Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice

    Tom D'Elia

    2013-03-01

    Full Text Available Lake Vostok is the largest of the nearly 400 subglacial Antarctic lakes and has been continuously buried by glacial ice for 15 million years. Extreme cold, heat (from possible hydrothermal activity, pressure (from the overriding glacier and dissolved oxygen (delivered by melting meteoric ice, in addition to limited nutrients and complete darkness, combine to produce one of the most extreme environments on Earth. Metagenomic/metatranscriptomic analyses of ice that accreted over a shallow embayment and over the southern main lake basin indicate the presence of thousands of species of organisms (94% Bacteria, 6% Eukarya, and two Archaea. The predominant bacterial sequences were closest to those from species of Firmicutes, Proteobacteria and Actinobacteria, while the predominant eukaryotic sequences were most similar to those from species of ascomycetous and basidiomycetous Fungi. Based on the sequence data, the lake appears to contain a mixture of autotrophs and heterotrophs capable of performing nitrogen fixation, nitrogen cycling, carbon fixation and nutrient recycling. Sequences closest to those of psychrophiles and thermophiles indicate a cold lake with possible hydrothermal activity. Sequences most similar to those from marine and aquatic species suggest the presence of marine and freshwater regions.

  9. Culture-independent methods to study subaerial biofilm growing on biodeteriorated surfaces of stone cultural heritage and frescoes.

    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). PMID:24664845

  10. A Meta-Analysis of the Bacterial and Archaeal Diversity Observed in Wetland Soils

    Xiaofei Lv

    2014-01-01

    Full Text Available This study examined the bacterial and archaeal diversity from a worldwide range of wetlands soils and sediments using a meta-analysis approach. All available 16S rRNA gene sequences recovered from wetlands in public databases were retrieved. In November 2012, a total of 12677 bacterial and 1747 archaeal sequences were collected in GenBank. All the bacterial sequences were assigned into 6383 operational taxonomic units (OTUs 0.03, representing 31 known bacterial phyla, predominant with Proteobacteria (2791 OTUs, Bacteroidetes (868 OTUs, Acidobacteria (731 OTUs, Firmicutes (540 OTUs, and Actinobacteria (418 OTUs. The genus Flavobacterium (11.6% of bacterial sequences was the dominate bacteria in wetlands, followed by Gp1, Nitrosospira, and Nitrosomonas. Archaeal sequences were assigned to 521 OTUs from phyla Euryarchaeota and Crenarchaeota. The dominating archaeal genera were Fervidicoccus and Methanosaeta. Rarefaction analysis indicated that approximately 40% of bacterial and 83% of archaeal diversity in wetland soils and sediments have been presented. Our results should be significant for well-understanding the microbial diversity involved in worldwide wetlands.

  11. A novel alkaloid from marine-derived actinomycete Streptomyces xinghaiensis with broad-spectrum antibacterial and cytotoxic activities.

    Wence Jiao

    Full Text Available Due to the increasing emergence of drug-resistant bacteria and tumor cell lines, novel antibiotics with antibacterial and cytotoxic activities are urgently needed. Marine actinobacteria are rich sources of novel antibiotics, and here we report the discovery of a novel alkaloid, xinghaiamine A, from a marine-derived actinomycete Streptomyces xinghaiensis NRRL B24674(T. Xinghaiamine A was purified from the fermentation broth, and its structure was elucidated based on extensive spectroscopic analysis, including 1D and 2D NMR spectrum as well as mass spectrometry. Xinghaiamine A was identified to be a novel alkaloid with highly symmetric structure on the basis of sulfoxide functional group, and sulfoxide containing compound has so far never been reported in microorganisms. Biological assays revealed that xinghaiamine A exhibited broad-spectrum antibacterial activities to both Gram-negative persistent hospital pathogens (e.g. Acinetobacter baumannii, Pseudomonas aeruginosa and Escherichia coli and Gram-positive ones, which include Staphylococcus aureus and Bacillus subtilis. In addition, xinghaiamine A also exhibited potent cytotoxic activity to human cancer cell lines of MCF-7 and U-937 with the IC50 of 0.6 and 0.5 µM, respectively.

  12. Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

    Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

    2015-11-01

    The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria. PMID:26024740

  13. Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas).

    Kueneman, Jordan G; Woodhams, Douglas C; Van Treuren, Will; Archer, Holly M; Knight, Rob; McKenzie, Valerie J

    2016-04-01

    Increasingly, host-associated microbiota are recognized to mediate pathogen establishment, providing new ecological perspectives on health and disease. Amphibian skin-associated microbiota interact with the fungal pathogen, Batrachochytrium dendrobatidis (Bd), but little is known about microbial turnover during host development and associations with host immune function. We surveyed skin microbiota of Colorado's endangered boreal toads (Anaxyrus boreas), sampling 181 toads across four life stages (tadpoles, metamorphs, subadults and adults). Our goals were to (1) understand variation in microbial community structure among individuals and sites, (2) characterize shifts in communities during development and (3) examine the prevalence and abundance of known Bd-inhibitory bacteria. We used high-throughput 16S and 18S rRNA gene sequencing (Illumina MiSeq) to characterize bacteria and microeukaryotes, respectively. Life stage had the largest effect on the toad skin microbial community, and site and Bd presence also contributed. Proteobacteria dominated tadpole microbial communities, but were later replaced by Actinobacteria. Microeukaryotes on tadpoles were dominated by the classes Alveolata and Stramenopiles, while fungal groups replaced these groups after metamorphosis. Using a novel database of Bd-inhibitory bacteria, we found fewer Bd-inhibitory bacteria in post-metamorphic stages correlated with increased skin fungi, suggesting that bacteria have a strong role in early developmental stages and reduce skin-associated fungi. PMID:26565725

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

    The rates of crude oil degradation by the extant microorganisms in intertidal sediments from a northern Gulf of Mexico beach were determined. The enhancement in crude oil degradation by amending the microbial communities with marine organic matter was also examined. Replicate mesocosm treatments consisted of: (i) controls (intertidal sand), (ii) sand contaminated with crude oil, (iii) sand plus organic matter, and (iv) sand plus crude oil and organic matter. Carbon dioxide (CO2) production was measured daily for 42 days and the carbon isotopic ratio of CO2 (δ13CO2) was used to determine the fraction of CO2 derived from microbial respiration of crude oil. Bacterial 16S rRNA clone library analyses indicated members of Actinobacteria, Bacteroidetes, and Chloroflexi occurred exclusively in control sediments whereas Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Firmicutes occurred in both control and oil contaminated sediments. Members of the hydrocarbon-degrading genera Hydrocarboniphaga, Pseudomonas, and Pseudoxanthomonas were found primarily in oil contaminated treatments. Hydrocarbon mineralization was 76% higher in the crude oil amended with organic matter treatment compared to the rate in the crude oil only treatment indicating that biodegradation of crude oil in the intertidal zone by an extant microbial community is enhanced by input of organic matter

  15. Efficiency of fluorescence in situ hybridization for bacterial cell identification in temporary river sediments with contrasting water content.

    Fazi, Stefano; Amalfitano, Stefano; Pizzetti, Ilaria; Pernthaler, Jakob

    2007-09-01

    We studied the efficiency of two hybridization techniques for the analysis of benthic bacterial community composition under varying sediment water content. Microcosms were set up with sediments from four European temporary rivers. Wet sediments were dried, and dry sediments were artificially rewetted. The percentage of bacterial cells detected by fluorescence in situ hybridization with fluorescently monolabeled probes (FISH) significantly increased from dry to wet sediments, showing a positive correlation with the community activity measured via incorporation of (3)H leucine. FISH and signal amplification by catalyzed reporter deposition (CARD-FISH) could significantly better detect cells with low activity in dried sediments. Through the application of an optimized cell permeabilization protocol, the percentage of hybridized cells by CARD-FISH showed comparable values in dry and wet conditions. This approach was unrelated to (3)H leucine incorporation rates. Moreover, the optimized protocol allowed a significantly better visualization of Gram-positive Actinobacteria in the studied samples. CARD-FISH is, therefore, proposed as an effective technique to compare bacterial communities residing in sediments with contrasting water content, irrespective of differences in the activity state of target cells. Considering the increasing frequencies of flood and drought cycles in European temporary rivers, our approach may help to better understand the dynamics of microbial communities in such systems. PMID:17452089

  16. Bacterial Diversity of Gut Content in Sea Cucumber (Apostichopus japonicus) and Its Habitat Surface Sediment

    GAO Fei; TAN Jie; SUN Huiling; YAN Jingping

    2014-01-01

    This study investigated the bacterial diversity of gut content of sea cucumber (Apostichopus japonicus) and its habitat surface sediment in a bottom enhancement area using PCR-based denaturing gradient gel electrophoresis (DGGE) technique. Bacte-rial diversity evaluation showed that the value of the Shannon-Wiener index of gut content in different intestinal segments of A. ja-ponicus varied between 2.88 and 3.00, lower than that of the surrounding sediment (3.23). Phylogenetic analysis showed that bacte-rial phylotypes in gut content and the surrounding sediment of A. japonicus were closely related to Proteobacteria includingγ-,α-,δ-andε-proteobacteria, Bacteroidetes, Firmicute, and Actinobacteria, of whichγ-proteobacteria were predominant. These results sug-gested that the sea cucumber A. japonicus was capable of feeding selectively, and PCR-DGGE was applicable for characterizing the bacterial community composition in gut content and the surrounding sediment of sea cucumber. Further investigation targeting longer 16S rDNA gene fragments and/or functional genes was recommended for obtaining more information of the diversity and function of bacterial community in the gut content of sea cucumber.

  17. Functionally redundant cellobiose-degrading soil bacteria respond differentially to oxygen.

    Schellenberger, Stefanie; Drake, Harold L; Kolb, Steffen

    2011-09-01

    The availability of oxygen (O(2)) in aerated (i.e., water-unsaturated) soils affects the metabolic activities of aerobic and anaerobic soil prokaryotes that degrade plant-derived saccharides. Fluctuating availabilities of O(2) were imposed on agricultural soil slurries supplemented with cellobiose. Slurries were subjected to oxic conditions (48 h), followed by an anoxic period (120 h) and a final oxic period (24 h). Redox potential was stable at 500 mV during oxic periods but decreased rapidly (within 10 h) under anoxic conditions to -330 mV. The consumption of cellobiose occurred without apparent delay at all redox potentials. The metabolic activities of seven previously identified saccharolytic family-level taxa of the investigated soil were measured with newly designed quantitative PCR assays targeting the 16S rRNA. Four taxa responded to the experimental conditions. The amounts of rRNAs of Micrococcaceae and Cellulomonadaceae (Actinobacteria) increased under oxic conditions. In contrast, the RNA contents of Clostridiaceae (cluster I, Firmicutes) and two uncultured family-level-taxa, i.e., "Cellu" and "Sphingo" (both Bacteroidetes) increased under anoxic conditions. That the degradation of cellobiose was independent of the availability of O(2) and that redox potentials decreased in response to anaerobic activities indicated that the degradation of cellobiose was linked to functionally redundant cellobiose-degrading taxa capable of altering redox conditions. PMID:21742909

  18. Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils

    Jing eLi

    2015-02-01

    Full Text Available Copper contamination on China’s arable land could pose severe economic, ecological and healthy consequences in the coming decades. As the drivers in maintaining ecosystem functioning, the responses of soil microorganisms to long-term copper contamination in different soil ecosystems are still debated. This study investigated the impacts of copper gradients on soil bacterial communities in two agricultural fields with contrasting soil properties. Our results revealed consistent reduction in soil microbial biomass carbon (SMBC with increasing copper levels in both soils, coupled by significant declines in bacterial abundance in most cases. Despite of contrasting bacterial community structures between the two soils, the bacterial diversity in the copper-contaminated soils showed considerably decreasing patterns when copper levels elevated. High-throughput sequencing revealed copper selection for major bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Chloroflexi were highly sensitive to copper. The thresholds that bacterial communities changed sharply were 800 and 200 added copper mg kg-1 in the fluvo-aquic soil and red soil, respectively, which were similar to the toxicity thresholds (EC50 values characterized by SMBC. Structural equation model (SEM analysis ascertained that the shifts of bacterial community composition and diversity were closely related with the changes of SMBC in both soils. Our results provide field-based evidence that copper contamination exhibits consistently negative impacts on soil bacterial communities, and the shifts of bacterial communities could have largely determined the variations of the microbial biomass.

  19. Pyrosequencing-based assessment of bacterial community structure in mine soils affected by mining subsidence

    Li Yuanyuan a; Chen Longqian a; ⇑; Wen Hongyu b; Zhou Tianjian a; Zhang Ting a

    2014-01-01

    Based on the 454 pyrosequencing approach, this research evaluated the influence of coal mining subsi-dence on soil bacterial diversity and community structure in Chinese mining area. In order to characterize the bacterial community comparatively, this study selected a field experiment site with coal-excavated subsidence soils and an adjacent site with non-disturbed agricultural soils, respectively. The dataset com-prises 24512 sequences that are affiliated to the 7 phylogenetic groups: proteobacteria, actinobacteria, bacteroidetes, gemmatimonadetes, chloroflexi, nitrospirae and unclassified phylum. Proteobacteria is the largest bacterial phylum in all samples, with a marked shift of the proportions of alpha-, beta-, and gammaproteobacteria. The results show that undisturbed soils are relatively more diverse and rich than subsided soils, and differences in abundances of dominant taxonomic groups between the two soil groups are visible. Compared with the control, soil nutrient contents decline achieves significant level in subsided soils. Correlational analysis showed bacterial diversity indices have significantly positive corre-lation with soil organic matter, total N, total P, and available K, but in negative relation with soil salinity. Ground subsidence noticeably affects the diversity and composition of soil microbial community. Degen-eration of soil fertility and soil salinization inhibits the sole-carbon-source metabolic ability of microbial community, leading to the simplification of advantage species and uneven distribution of microbial spe-cies. This work demonstrates the great potential of pyrosequencing technique in revealing microbial diversity and presents background information of microbial communities of mine subsidence land.

  20. Life at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile

    Neilson, Julia W.; Quade, Jay; Ortiz, Marianyoly; Nelson, William M.; Legatzki, Antje; Tian, Fei; LaComb, Michelle; Betancourt, Julio L.; Wing, Rod A.; Soderlund, Carol A.; Maier, Raina M.

    2012-01-01

    Nearly half the earth's surface is occupied by dryland ecosystems, regions susceptible to reduced states of biological productivity caused by climate fluctuations. Of these regions, arid zones located at the interface between vegetated semiarid regions and biologically unproductive hyperarid zones are considered most vulnerable. The objective of this study was to conduct a deep diversity analysis of bacterial communities in unvegetated arid soils of the Atacama Desert, to characterize community structure and infer the functional potential of these communities based on observed phylogenetic associations. A 454-pyrotag analysis was conducted of three unvegetated arid sites located at the hyperarid-arid margin. The analysis revealed communities with unique bacterial diversity marked by high abundances of novel Actinobacteria and Chloroflexi and low levels of Acidobacteria and Proteobacteria, phyla that are dominant in many biomes. A 16S rRNA gene library of one site revealed the presence of clones with phylogenetic associations to chemoautotrophic taxa able to obtain energy through oxidation of nitrite, carbon monoxide, iron, or sulfur. Thus, soils at the hyperarid margin were found to harbor a wealth of novel bacteria and to support potentially viable communities with phylogenetic associations to non-phototrophic primary producers and bacteria capable of biogeochemical cycling.

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

    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

  2. Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing

    Kreisinger, Jakub; Čížková, Dagmar; Kropáčková, Lucie; Albrecht, Tomáš

    2015-01-01

    Effects of vertebrate-associated microbiota on physiology and health are of significant interest in current biological research. Most previous studies have focused on host-microbiota interactions in captive-bred mammalian models. These interactions and their outcomes are still relatively understudied, however, in wild populations and non-mammalian taxa. Using deep pyrosequencing, we described the cloacal microbiome (CM) composition in free living barn swallows Hirundo rustica, a long-distance migratory passerine bird. Barn swallow CM was dominated by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla. Bacteroidetes, which represent an important proportion of the digestive tract microbiome in many vertebrate species, was relatively rare in barn swallow CM (< 5%). CM composition did not differ between males and females. A significant correlation of CM within breeding pair members is consistent with the hypothesis that cloacal contact during within-pair copulation may promote transfer of bacterial assemblages. This effect on CM composition had a relatively low effect size, however, possibly due to the species’ high level of sexual promiscuity. PMID:26360776

  3. [Analysis of Prokaryotic Community Structure in River Waters of the Ningbo Sanjiang Mouth].

    Hu, An-yi; Li, Jiang-wei; Yang, Xiao-yong; Wang, Hong-jie; Yu, Chang-ping

    2015-07-01

    The prokaryotic community structure in river waters of the Ningbo Sanjiang Mouth was analyzed for the first time using 16S rRNA gene based-Illumina Miseq high-throughput sequencing. A total of 215 504 high-quality sequences were obtained, and the results of alpha-diversity analysis revealed that Yongjiang River Watershed (YRW) harbored high diversity and richness of prokaryotic communities. Taxonomic assignment analysis indicated that β-Proteobacterium, Actinobacteria and Bacteroidetes dominated in the river water of YRW, and accounted for 78. 88% of the total prokaryotic communities. Hydrological condition may play an important role in influencing the composition and structure of YRW prokaryotic community. In addition, several kinds of sewer- and fecal-pollution indicator bacterial groups were observed in this area with the highest abundance of pollution indicator bacteria occurring in the water sample of Yuyao River, implying that the Yuyao River might have a high potential risk of sewer- and fecal-pollution. Moreover, a total of 76 species and 18 subspecies of potential pathogenic bacteria, which accounted for 2. 19% and 0. 40% of total sequences respectively, were identified using BLASTN analysis with a local pathogenic bacteria database. Overall, this study provided an important basic data for shedding light on the structure and ecological function of YRW prokaryotic community. PMID:26489316

  4. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    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.

  5. Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes.

    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

  6. A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins

    Teresa Milano

    2016-01-01

    Full Text Available The MocR bacterial transcriptional regulators are characterized by an N-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (wHTH architecture responsible for DNA recognition and binding, linked to a large C-terminal domain (350 residues on average that is homologous to fold type-I pyridoxal 5′-phosphate (PLP dependent enzymes like aspartate aminotransferase (AAT. These regulators are involved in the expression of genes taking part in several metabolic pathways directly or indirectly connected to PLP chemistry, many of which are still uncharacterized. A bioinformatics analysis is here reported that studied the features of a distinct group of MocR regulators predicted to be functionally linked to a family of homologous genes coding for integral membrane proteins of unknown function. This group occurs mainly in the Actinobacteria and Gammaproteobacteria phyla. An analysis of the multiple sequence alignments of their wHTH and AAT domains suggested the presence of specificity-determining positions (SDPs. Mapping of SDPs onto a homology model of the AAT domain hinted at possible structural/functional roles in effector recognition. Likewise, SDPs in wHTH domain suggested the basis of specificity of Transcription Factor Binding Site recognition. The results reported represent a framework for rational design of experiments and for bioinformatics analysis of other MocR subgroups.

  7. Analysis and characterization of cultivable heavy metal-resistant bacterial endophytes isolated from Cd-hyperaccumulator Solanum nigrum L. and their potential use for phytoremediation.

    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

  8. Microbiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid.

    Chan, Xin-Yue; Hong, Kar-Wai; Yin, Wai-Fong; Chan, Kok-Gan

    2016-01-01

    Tropical carnivorous plant, Nepenthes, locally known as "monkey cup", utilises its pitcher as a passive trap to capture insects. It then secretes enzymes into the pitcher fluid to digest the insects for nutrients acquisition. However, little is known about the microbiota and their activity in its pitcher fluid. Eighteen bacteria phyla were detected from the metagenome study in the Nepenthes pitcher fluid. Proteobacteria, Bacteroidetes and Actinobacteria are the dominant phyla in the Nepenthes pitcher fluid. We also performed culturomics approach by isolating 18 bacteria from the Nepenthes pitcher fluid. Most of the bacterial isolates possess chitinolytic, proteolytic, amylolytic, and cellulolytic and xylanolytic activities. Fifteen putative chitinase genes were identified from the whole genome analysis on the genomes of the 18 bacteria isolated from Nepenthes pitcher fluid and expressed for chitinase assay. Of these, six clones possessed chitinase activity. In conclusion, our metagenome result shows that the Nepenthes pitcher fluid contains vast bacterial diversity and the culturomic studies confirmed the presence of biocatalytic bacteria within the Nepenthes pitcher juice which may act in symbiosis for the turn over of insects trapped in the Nepenthes pitcher fluid. PMID:26817720

  9. Correlation between diet and gut bacteria in a population of young adults.

    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

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

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

    2013-01-15

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

  11. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

    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

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

    Itani, Ghida Nouhad; Smith, Colin Andrew

    2016-03-01

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

  13. Photosynthesis within Mars' volcanic craters?: Insights from Cerro Negro Volcano, Nicaragua

    Rogers, K. L.; Hynek, B. M.; McCollom, T. M.

    2011-12-01

    Discrete locales of sulfate-rich bedrocks exist on Mars and in many cases represent the products of acid-sulfate alteration of martian basalt. In some places, the products have been attributed to hydrothermal processes from local volcanism. In order to evaluate the habitability of such an environment, we are investigating the geochemical and biological composition of active fumaroles at Cerro Negro Volcano, Nicaragua, where fresh basaltic cinders similar in composition to martian basalts are altered by acidic, sulfur-bearing gases. Temperatures at active fumaroles can reach as high as 400°C and the pH of the steam ranges from red algae that inhabit acidic, geothermal environments. Many of sequences related to Ktedonobacteria and Actinobacteria have also been found in acid mine drainage environments. The Archaeal community was far less diverse, with sequences matching those of unclassified Desulfurococcales and unclassified Thermoprotei. These sequences were more distant from isolated species than the bacterial sequences. Similar bacterial and archaeal communities have been found in hot spring environments in Yellowstone National Park, Greenland, Iceland, New Zealand and Costa Rica. Some of Mars' volcanoes were active for billions of years and by analogy to Cerro Negro, may have hosted photosynthetic organisms that could have been preserved in alteration mineral assemblages. Even on a generally cold and dry Mars, volcanic craters likely provided long-lived warm and wet conditions and should be a key target for future exploration assessing habitability.

  14. A Genomic, Transcriptomic and Proteomic Look at the GE2270 Producer Planobispora rosea, an Uncommon Actinomycete.

    Arianna Tocchetti

    Full Text Available We report the genome sequence of Planobispora rosea ATCC 53733, a mycelium-forming soil-dweller belonging to one of the lesser studied genera of Actinobacteria and producing the thiopeptide GE2270. The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44% of shared orthologs. Patterns of gene expression in P. rosea cultures during exponential and stationary phase have been analyzed using whole transcriptome shotgun sequencing and by proteome analysis. Among the differentially abundant proteins, those involved in protein metabolism are particularly represented, including the GE2270-insensitive EF-Tu. Two proteins from the pbt cluster, directing GE2270 biosynthesis, slightly increase their abundance values over time. While GE2270 production starts during the exponential phase, most pbt genes, as analyzed by qRT-PCR, are down-regulated. The exception is represented by pbtA, encoding the precursor peptide of the ribosomally synthesized GE2270, whose expression reached the highest level at the entry into stationary phase.

  15. Bacterial diversity and tetrodotoxin analysis in the viscera of the gastropods from Portuguese coast.

    Pratheepa, Vijayakumari; Alex, Anoop; Silva, Marisa; Vasconcelos, Vitor

    2016-09-01

    To trace the pathway of tetrodotoxin (TTX) producing microorganism in the Atlantic coast of Portugal, culture-dependent evaluation of the bacterial isolates from the viscera of the gastropods Monodonta lineata, Gibbula umbilicalis, Nucella lapillus and Patella intermedia, and from the environmental samples (biofilm and surrounding sea water) was carried out. Samples were collected from eight different coastal locations of Northern Portugal. A total of 311 isolates were identified. The observed bacterial diversity was distributed over five different classes (Gammaproteobacteria, Alphaproteobacteria, Flavobacteria, Bacilli and Actinobacteria) with the greatest number of 16S rRNA gene sequence derived from the Gammaproteobacteria (75%). Phylogenetic analysis based on the 16S rRNA gene showed that bacterial isolates were highly diverse and most of which were found in other marine environment. Among the different species isolated, Vibrio was found abundant. Eventhough TTX was not detected (UPLC-MS/MS) in the isolates from this study, PCR screening identified some natural product biosynthesis genes (PKS and NRPS) involved in its assembly. Further PCR screening of the TTX producing two ATCC Vibrio sp. reveals that NRPS might be involved in the biosynthesis of TTX through the incorporation of arginine. PMID:27312988

  16. Microbial diversity in contaminated soils along the T22 trench of the Chernobyl experimental platform

    The diversity of bacterial communities exposed to radioactive contamination in Chernobyl soils was examined by a combination of molecular and culture-based approaches. A set of six radioactive soil samples, exhibiting high levels of 137Cs contamination, were collected from the T22 trench. Three samples were also collected in nearby soils with low contamination. Complex bacterial community structures were observed in both highly and weakly contaminated samples, using a molecular approach targeting the 16S rRNA gene. However, the presence of specific populations within samples from highly contaminated soils could not be revealed by statistical analysis of the DGGE profiles. More than 200 culturable isolates, representative of dominant morphotypes, were grouped into 83 Operational Taxonomic Units (OTUs) and affiliated to Firmicutes, Actinobacteria, Alpha-, Beta-, Gamma-Proteobacteria and Bacteroïdetes. No specific pattern linked to contamination was observed for these culturable bacteria. The results show that both highly and weakly contaminated soils host a wide diversity of bacteria, suggesting that long term exposure to radionuclides does not lead to the extinction of bacterial diversity.

  17. Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water.

    Narciso-da-Rocha, Carlos; Manaia, Célia M

    2016-09-01

    The environment is the original and most ancient source of the antibiotic resistance determinants that threat the human health nowadays. In the environment, water is a privileged habitat and mode of dissemination of bacteria of different origins. Freshwater bodies that cross urban areas are supposed to hold a complex mixture of both human/animal origin and strictly environmental bacteria. In this study, we were interested in unveiling the bacterial diversity in urban river transects and, simultaneously, investigate the occurrence of antibiotic resistant bacteria, in particular the multidrug resistant (MDR). With this aim, water and sediments of two rivers were sampled from an urban transect and the bacterial diversity was assessed based on 16S rRNA gene-based community analysis and, simultaneously, total heterotrophic bacteria were isolated in the presence and in the absence of antibiotics. The three predominant phyla were Proteobacteria, Bacteroidetes and Actinobacteria, in water, or Acidobacteria, in sediments. MDR bacteria were observed to belong to the predominant phyla observed in water, mostly of the classes Gamma- and Betaproteobacteria (Proteobacteria) and Sphingobacteriia and Flavobacteriia (Bacteroidetes) and belonged to genera of ubiquitous (Pseudomonas, Acinetobacter, Stenotrophomonas) or mainly environmental (Chitinophaga, Chryseobacterium) bacteria. The observation that MDR bacteria are widespread in the environment and over distinct phylogenetic lineages has two relevant implications: i) the potential of environmental bacteria as source or facilitators for antibiotic resistance acquisition; ii) the need to complement culture-independent methods with culture-based approaches in order to identify major sources of MDR profiles. PMID:27131885

  18. The microbiome of North Sea copepods

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

    2013-12-01

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

  19. Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression.

    van der Voort, Menno; Kempenaar, Marcel; van Driel, Marc; Raaijmakers, Jos M; Mendes, Rodrigo

    2016-04-01

    The rhizosphere microbiome offers a range of ecosystem services to the plant, including nutrient acquisition and tolerance to (a)biotic stress. Here, analysing the data by Mendes et al. (2011), we show that short heat disturbances (50 or 80 °C, 1 h) of a soil suppressive to the root pathogenic fungus Rhizoctonia solani caused significant increase in alpha diversity of the rhizobacterial community and led to partial or complete loss of disease protection. A reassembly model is proposed where bacterial families that are heat tolerant and have high growth rates significantly increase in relative abundance after heat disturbance, while temperature-sensitive and slow-growing bacteria have a disadvantage. The results also pointed to a potential role of slow-growing, heat-tolerant bacterial families from Actinobacteria and Acidobacteria phyla in plant disease protection. In conclusion, short heat disturbance of soil results in rearrangement of rhizobacterial communities and this is correlated with changes in the ecosystem service disease suppression. PMID:26833547

  20. Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy.

    Shintani, Masaki; Sanchez, Zoe K; Kimbara, Kazuhide

    2015-01-01

    Plasmids are important "vehicles" for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed. PMID:25873913

  1. Influence of bacterial communities based on 454-pyrosequencing on the survival of Escherichia coli O157:H7 in soils.

    Ma, Jincai; Ibekwe, Abasiofiok M; Yang, Ching-Hong; Crowley, David E

    2013-06-01

    Shiga toxin-producing Escherichia coli O157:H7 has been implicated in many foodborne illnesses. In this study, survival of E. coli O157:H7 in 32 soils from California (CA) and Arizona (AZ) was investigated. Our goal was to correlate the survival time of E. coli O157:H7 in soils with 16S rRNA pyrosequencing based bacterial community composition. Kohonen self-organizing map of survival and associated soil chemical, physical and biological variables using artificial neural network analysis showed that survival of E. coli O157:H7 in soils was negatively correlated with salinity (EC), but positively correlated with total nitrogen (TN) and water soluble organic carbon (WSOC). Bacterial diversity as determined by the Shannon diversity index had no significant (P = 0.635) effect on ttd, but individual bacterial phyla had different effects. The survival of E. coli O157:H7 was positively correlated with the abundances of Actinobacteria (P < 0.001) and Acidobacteria (P < 0.05), and negatively correlated with those of Proteobacteria and Bacteroidetes (P < 0.05). Our data showed that specific groups of bacteria correlate with the persistence of E. coli O157:H7 in soils thus opening new ways to study the influence of certain bacterial phyla on persistence of this pathogen and other related pathogens in complex environments. PMID:23360569

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

    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.

  3. Genomics and ecological overview of the genus Bifidobacterium.

    Turroni, Francesca; van Sinderen, Douwe; Ventura, Marco

    2011-09-01

    Members of the genus Bifidobacterium are high G+C Gram positive bacteria belonging to the phylum Actinobacteria, and represent common inhabitants of the gastro-intestinal tract (GIT) of mammals, birds and certain cold-blooded animals. The overall microbial population that resides in the GIT, referred to as the "gut microbiota", is an extremely complex community of microorganisms whose functions are believed to have a significant impact on human physiology. Different ecological relationships between bifidobacteria and their host can be developed, ranging from opportunistic pathogenic interactions (e.g. in the case of Bifidobacterium dentium) to a commensal or even health-promoting relationship (e.g. in the case of Bifidobacterium bifidum and Bifidobacterium breve species). Among the known health-promoting or probiotic microorganisms, bifidobacteria represent one of the most dominant group and some bifidobacterial species are frequently used as the probiotic ingredient in many functional foods. However, despite the generally accepted importance of bifidobacteria as constituents of the human microbiota, there is only limited information available on their phylogeny, physiology and genetics. Moreover, host-microbiota interactions and cross-talk between different members of the gut microbiota are far from completely understood although they represent a crucial factor in the development and maintenance of human physiology and immune system. The aim of this review is to highlight the genetic and functional features of bifidobacteria residing in the human GIT using genomic and ecology-based information. PMID:21276626

  4. Bacterial Diversity within the Extreme Arid Atacama Desert Soils of the Yungay Region, Chile

    Connon, S. A.; Lester, E. D.; Shafaat, H. S.; Obenhuber, D. C.; Ponce, A.

    2006-12-01

    Surface and subsurface soil samples analyzed for this study were collected from the hyper-arid Yungay region of the Atacama Desert, Chile. This is the first report of microbial diversity from DNA extracted directly from these extremely desiccated soils. Our data shows that 94% of the 16S rRNA genes cloned from these soils belong to the Actinobacteria phylum. A 24-hour time course series showed a diurnal water activity (aw) cycle that peaked at 0.52 in the early predawn hours, and ranged from 0.08 0.01 during the day. All measured water activity values were below the level required for microbial growth or enzyme activity. Total organic carbon (TOC) levels in this region were just above the limits of detection and ranged from 220 660 μg/g of soil. Phospholipid fatty acid (PLFA) levels indicated cellular biomass ranging from 2 ×105 to 7 ×106 cell equivalents per gram of soil. The culturable counts were low with most samples showing no growth on standard plates of R2A medium; the highest single count was 47 colony forming units (CFU) per gram.

  5. Microbial hitchhikers on intercontinental dust: catching a lift in Chad.

    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

  6. Associations between bacterial communities of house dust and infant gut

    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

  7. Common occurrence of antibacterial agents in human intestinal microbiota

    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.

  8. Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica.

    Shi, Ying-wu; Lou, Kai; Li, Chun; Wang, Lei; Zhao, Zhen-yong; Zhao, Shuai; Tian, Chang-yan

    2015-10-01

    We used Illumina-based 16S rRNA V3 amplicon pyrosequencing to investigate the community structure of soil bacteria from the rhizosphere surrounding Salicornia europaea, and endophytic bacteria living in Salicornia europaea plants and Sueada aralocaspica seeds growing at the Fukang Desert Ecosystem Observation and Experimental Station (FDEOES) in Xinjiang Province, China, using an Illumina genome analyzer. A total of 89.23 M effective sequences of the 16S rRNA gene V3 region were obtained from the two halophyte species. These sequences revealed a number of operational taxonomic units (OTUs) in the halophytes. There were between 22-2,206 OTUs in the halophyte plant sample, at the 3% cutoff level, and a sequencing depth of 30,000 sequences. We identified 25 different phyla, 39 classes and 141 genera from the resulting 134,435 sequences. The most dominant phylum in all the samples was Proteobacteria (41.61%-99.26%; average, 43.30%). The other large phyla were Firmicutes (0%- 7.19%; average, 1.15%), Bacteroidetes (0%-1.64%; average, 0.44%) and Actinobacteria (0%-0.46%; average, 0.24%). This result suggested that the diversity of bacteria is abundant in the rhizosphere soil, while the diversity of bacteria was poor within Salicornia europaea plant samples. To the extent of our knowledge, this study is the first to characterize and compare the endophytic bacteria found within different halophytic plant species roots using PCR-based Illumina pyrosequencing method. PMID:26428918

  9. In silico dissection of Type VII Secretion System components across bacteria: New directions towards functional characterization

    Chandrani Das; Tarini Shankar Ghosh; Sharmila S Mande

    2016-03-01

    Type VII Secretion System (T7SS) is one of the factors involved in virulence of Mycobacteriun tuberculosis H37Rv. Numerous research efforts have been made in the last decade towards characterizing the components of this secretion system. An extensive genome-wide analysis through compilation of isolated information is required to obtain a global view of diverse characteristics and pathogenicity-related aspects of this machinery. The present study suggests that differences in structural components (of T7SS) between Actinobacteria and Firmicutes, observed earlier in a few organisms, is indeed a global trend. A few hitherto uncharacterized T7SS-like clusters have been identified in the pathogenic bacteria Enterococcus faecalis, Saccharomonospora viridis, Streptococcus equi, Streptococcuss gordonii and Streptococcus sanguinis. Experimental verification of these clusters can shed lights on their role in bacterial pathogenesis. Similarly, verification of the identified variants of T7SS clusters consisting additional membrane components may help in unraveling new mechanism of protein translocation through T7SS. A database of various components of T7SS has been developed to facilitate easy access and interpretation of T7SS related data.

  10. Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae).

    Snyman, Maxi; Gupta, Arvind Kumar; Bezuidenhout, Cornelius Carlos; Claassens, Sarina; van den Berg, Johnnie

    2016-07-01

    Busseola fusca (Fuller) (Lepidoptera: Noctuidae) is a stemborer pest that attacks maize (Zea mays) throughout sub-Saharan Africa. Genetically modified maize has been shown to be effective against B. fusca. However, resistance of B. fusca against Bt-maize has developed and spread throughout South Africa. Previous studies suggested that gut microbiota contribute to mortality across a range of Lepidoptera. To fully assess the role of microbiota within the gut, it is essential to understand the microbiota harboured by natural B. fusca populations. This study aimed to identify the gut-associated bacteria by 16S rRNA gene sequencing. A total of 78 bacterial strains were characterised from the midgut of B. fusca larvae that were collected from 30 sites across the maize producing region of South Africa. Molecular phylogenetic analyses revealed bacteria affiliated to Proteobacteria, Actinobacteria, and Firmicutes. Taxonomic distribution placed these isolates into 15 different genera representing 20 species. The majority of bacteria identified belong to the genera Bacillus, Enterococcus, and Klebsiella. The B. fusca gut represents an intriguing and unexplored niche for analysing microbial ecology. The study could provide opportunities for developing new targets for pest management and contribute to understanding the phenomenon of resistance evolution of this species. PMID:27263010

  11. Picoplankton seasonal variation and community structure in the northeast Adriatic coastal zone.

    Silović, Tina; Balagué, Vanessa; Orlić, Sandi; Pedrós-Alió, Carlos

    2012-12-01

    The bacterial community in coastal waters of northeastern Adriatic Sea was dominated by SAR11 and Sulfitobacter taxa throughout the year. The seasonal distribution of bacterioplankton taxa showed continual differences between surface (0 m) and bottom (27 m) layers. The surface assemblage was represented by Actinobacteria, Cyanobacteria, Alphaproteobacteria, and Gammaproteobacteria, while the bottom assemblage was made up of Bacteroidetes, Cyanobacteria and Alphaproteobacteria. As SAR11 was more dominant in the bottom layer, its appearance may be linked to northward transport of oligotrophic waters of higher salinity from the south. Gammaproteobacteria appeared only in the surface layer during summer, influenced by higher amounts of nutrients, brought in by the Po River. Synechococcus was the most abundant taxon at the genus level. Dominance of Synechococcus during the whole season agrees with its dominance in terms of abundance determined by flow cytometry, and confirms its utmost importance in the picoplankton community of this area. We found two different types of Synechococcus: one type with high similarity to Synechococcus CC9902, present in the surface and bottom layers, and another one similar to Synechococcus WH7803, present only in the surface layer. Oligotrophic conditions together with complex hydrological features of this area were reflected in diversification and dynamic shifts of surface and bottom assemblages. PMID:22748097

  12. Effects of large river dam regulation on bacterioplankton community structure.

    Ruiz-González, Clara; Proia, Lorenzo; Ferrera, Isabel; Gasol, Josep M; Sabater, Sergi

    2013-05-01

    Large rivers are commonly regulated by damming, yet the effects of such disruption on prokaryotic communities have seldom been studied. We describe the effects of the three large reservoirs of the Ebro River (NE Iberian Peninsula) on bacterioplankton assemblages by comparing several sites located before and after the impoundments on three occasions. We monitored the abundances of several bacterial phylotypes identified by rRNA gene probing, and those of two functional groups (picocyanobacteria and aerobic anoxygenic phototrophic bacteria-AAPs). Much greater numbers of particles colonized by bacteria were found in upstream waters than downstream sites. Picocyanobacteria were found in negligible numbers at most sites, whereas AAPs constituted up to 14% of total prokaryotes, but there was no clear effect of reservoirs on the spatial dynamics of these two groups. Instead, damming caused a pronounced decline in Betaproteobacteria, Gammaproteobacteria and Bacteroidetes from upstream to downstream sites, whereas Alphaproteobacteria and Actinobacteria significantly increased after the reservoirs. Redundancy analysis revealed that conductivity, temperature and dissolved inorganic nitrogen were the environmental predictors that best explained the observed variability in bacterial community composition. Our data show that impoundments exerted significant impacts on bacterial riverine assemblages and call attention to the unforeseen ecological consequences of river regulation. PMID:23278359

  13. Catchment-scale biogeography of riverine bacterioplankton.

    Read, Daniel S; Gweon, Hyun S; Bowes, Michael J; Newbold, Lindsay K; Field, Dawn; Bailey, Mark J; Griffiths, Robert I

    2015-02-01

    Lotic ecosystems such as rivers and streams are unique in that they represent a continuum of both space and time during the transition from headwaters to the river mouth. As microbes have very different controls over their ecology, distribution and dispersion compared with macrobiota, we wished to explore biogeographical patterns within a river catchment and uncover the major drivers structuring bacterioplankton communities. Water samples collected across the River Thames Basin, UK, covering the transition from headwater tributaries to the lower reaches of the main river channel were characterised using 16S rRNA gene pyrosequencing. This approach revealed an ecological succession in the bacterial community composition along the river continuum, moving from a community dominated by Bacteroidetes in the headwaters to Actinobacteria-dominated downstream. Location of the sampling point in the river network (measured as the cumulative water channel distance upstream) was found to be the most predictive spatial feature; inferring that ecological processes pertaining to temporal community succession are of prime importance in driving the assemblages of riverine bacterioplankton communities. A decrease in bacterial activity rates and an increase in the abundance of low nucleic acid bacteria relative to high nucleic acid bacteria were found to correspond with these downstream changes in community structure, suggesting corresponding functional changes. Our findings show that bacterial communities across the Thames basin exhibit an ecological succession along the river continuum, and that this is primarily driven by water residence time rather than the physico-chemical status of the river. PMID:25238398

  14. Influence of freshwater discharge on the microbial degradation processes of dissolved organic nitrogen in a subtropical estuary.

    Garcia, Juan C; Ketover, Rheannon D J; Loh, Ai Ning; Parsons, Michael L; Urakawa, Hidetoshi

    2015-02-01

    River bacterioplankton communities, influenced by watershed usage, are responsible for water purification. Bacterioplankton may be critical in the degradation of dissolved organic nitrogen (DON), the major nitrogen pool in the Caloosahatchee River, Florida. We investigated how freshwater discharge influences estuarine bacterioplankton and how the freshwater-originated DON is utilized by estuarine bacterioplankton. Microcosm experiments were conducted during low and high discharge using two upstream freshwater samples: one site primarily influenced by Lake Okeechobee and the other site moderately influenced by an agricultural watershed. These freshwater samples were filtered to eliminate indigenous microbial populations, then mixed with estuarine bacterioplankton. High-throughput sequencing revealed that bacterioplankton differed between low and high discharge and were influenced by salinity. Alphaproteobacteria and Bacteroidetes dominated in low discharge while Bacteroidetes and Cyanobacteria dominated during high discharge. In the microcosm experiment, DON concentration decreased with increasing cell densities, suggesting that the DON was utilized as a carbon and nitrogen source. Band signals in denaturing gradient gel electrophoresis corresponding to Alphaproteobacteria and Actinobacteria decreased while Gammaproteobacteria increased during the 1 month incubation. This data suggests that estuarine bacterioplankton communities are influenced by variations in discharge patterns and use freshwater-originated DON as demonstrated by a shift in community structure. PMID:25542211

  15. Bacterial activity and bacterioplankton diversity in the eutrophic River Warnow--direct measurement of bacterial growth efficiency and its effect on carbon utilization.

    Warkentin, Mareike; Freese, Heike M; Schumann, Rhena

    2011-01-01

    The influence of bacterial activity and diversity on bacterial growth efficiency was investigated in a flatland river. Eutrophic River Warnow drains predominantly agricultural land and is heavily loaded with nutrients, dissolved and particulate organic matter (DOM and POM), especially humic substances. Although the water column bacterial community consists of many inactive or damaged cells, bacterioplankton sustained a high bacterial secondary production of 0.2-14.5 μg C L(-1) h(-1) and a high DNA synthesis (thymidine uptake) of 6.1-15.5 μg C L(-1) h(-1). The direct and short-term measurement of bacterial respiration (by optodes) revealed high respiration rates especially in summer leading to directly estimated bacterial growth efficiencies (BGE) of 2-28%. These values are compared to calculations based only on bacterial production, which considerably overestimated BGEs. From all these data, River Warnow can be characterized as a strongly remineralizing system. River Warnow was dominated among others by Cytophaga/Flavobacteria and Actinobacteria which are typical for organic rich waters because of their ability to degrade high molecular weight compounds. However, community composition did not significantly affect BGE. PMID:20676625

  16. Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time.

    Crump, Byron C; Hopkinson, Charles S; Sogin, Mitchell L; Hobbie, John E

    2004-03-01

    Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([(14)C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and ACTINOBACTERIA: Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil. PMID:15006771

  17. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana.

    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.

  18. Phylogenetic characterization of culturable actinomycetes associated with the mucus of the coral Acropora digitifera from Gulf of Mannar.

    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

  19. Characterization of culturable bacteria isolated from the cold-water coral Lophelia pertusa.

    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

  20. Safety assessment of dairy microorganisms: Propionibacterium and Bifidobacterium.

    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

  1. Streptomyces malaysiense sp. nov.: A novel Malaysian mangrove soil actinobacterium with antioxidative activity and cytotoxic potential against human cancer cell lines

    Ser, Hooi-Leng; Palanisamy, Uma Devi; Yin, Wai-Fong; Chan, Kok-Gan; Goh, Bey-Hing; Lee, Learn-Han

    2016-01-01

    Actinobacteria from the unique intertidal ecosystem of the mangroves are known to produce novel, bioactive secondary metabolites. A novel strain known as MUSC 136T (=DSM 100712T = MCCC 1K01246T) which was isolated from Malaysian mangrove forest soil has proven to be no exception. Assessed by a polyphasic approach, its taxonomy showed a range of phylogenetic and chemotaxonomic properties consistent with the genus of Streptomyces. Phylogenetically, highest similarity was to Streptomyces misionensis NBRC 13063T (99.6%) along with two other strains (>98.9% sequence similarities). The DNA–DNA relatedness between MUSC 136T and these type strains ranged from 22.7 ± 0.5% to 46.5 ± 0.2%. Overall, polyphasic approach studies indicated this strain represents a novel species, for which the name Streptomyces malaysiense sp. nov. is proposed. The potential bioactivities of this strain were explored by means of antioxidant and cytotoxic assays. Intriguingly, MUSC 136T exhibited strong antioxidative activities as evaluated by a panel of antioxidant assays. It was also found to possess high cytotoxic effect against HCT-116 cells, which probably mediated through altering p53 protein and intracellular glutathione levels. Chemical analysis of the extract using GC-MS further affirms that the strain produces chemopreventive related metabolites. PMID:27072394

  2. Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production

    Hollister, Emily B.; Gentry, Terry J. [Texas A and M Univ., College Station, TX (United States). Dept. of Soil and Crop Sciences; Forrest, Andrea K.; Holtzapple, Mark T. [Texas A and M Univ., College Station, TX (United States). Dept. of Chemical Engineering; Wilkinson, Heather H.; Ebbole, Daniel J. [Texas A and M Univ., College Station, TX (United States). Dept. of Plant Pathology and Microbiology; Malfatti, Stephanie A.; Tringe, Susannah G. [DOE Joint Genome Institute, Walnut Creek, CA (United States)

    2010-09-15

    The carboxylate platform utilizes a mixed microbial community to convert lignocellulosic biomass into chemicals and fuels. While much of the platform is well understood, little is known about its microbiology. Mesophilic (40 C) and thermophilic (55 C) fermentations employing a sorghum feedstock and marine sediment inoculum were profiled using 16S rRNA tag-pyrosequencing over the course of a 30-day incubation. The contrasting fermentation temperatures converted similar amounts of biomass, but the mesophilic community was significantly more productive, and the two temperatures differed significantly with respect to propionic and butyric acid production. Pyrotag sequencing revealed the presence of dynamic communities that responded rapidly to temperature and changed substantially over time. Both temperatures were dominated by bacteria resembling Clostridia, but they shared few taxa in common. The species-rich mesophilic community harbored a variety of Bacteroidetes, Actinobacteria, and {gamma}-Proteobacteria, whereas the thermophilic community was composed mainly of Clostridia and Bacilli. Despite differences in composition and productivity, similar patterns of functional class dynamics were observed. Over time, organisms resembling known cellulose degraders decreased in abundance, while organisms resembling known xylose degraders increased. Improved understanding of the carboxylate platform's microbiology will help refine platform performance and contribute to our growing knowledge regarding biomass conversion and biofuel production processes. (orig.)

  3. Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats.

    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

  4. Characterization and in-vivo evaluation of potential probiotics of the bacterial flora within the water column of a healthy shrimp larviculture system

    Xue, Ming; Liang, Huafang; He, Yaoyao; Wen, Chongqing

    2016-05-01

    A thorough understanding of the normal bacterial flora associated with shrimp larviculture systems contributes to probiotic screening and disease control. The bacterial community of the water column over a commercial Litopenaeus vannamei larval rearing run was characterized with both culture-dependent and culture-independent methods. A total of 27 phylotypes at the species level were isolated and identified based on 16S rDNA sequence analysis. Denaturing gradient gel electrophoresis (DGGE) analysis of the V3-V5 region of 16S rRNA genes showed a dynamic bacterial community with major changes occurred from stages zoea to mysis during the rearing run. The sequences retrieved were affiliated to four phyla, Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with the family Rhodobacteraceae being the most frequently recovered one. Subsequently, 13 representative strains conferred higher larval survival than the control when evaluated in the in-vivo experiments; in particular, three candidates, assigned to Phaeobacter sp., Arthrobacter sp., and Microbacterium sp., significantly improved larval survival ( P < 0.05). Therefore, the healthy shrimp larviculture system harbored a diverse and favorable bacterial flora, which contribute to larval development and are of great importance in exploiting novel probiotics.

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

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

    2015-02-01

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

  6. Effect of long-term different fertilization on bacterial community structures and diversity in citrus orchard soil of volcanic ash.

    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

  7. [Characterization of the Structure of the Prokaryotic Complex of Antarctic Permafrost by Molecular Genetic Techniques].

    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. Diversity of Bacterial Communities on Four Frequently Used Surfaces in a Large Brazilian Teaching Hospital

    Tairacan Augusto Pereira da Fonseca

    2016-01-01

    Full Text Available Frequently used hand-touch surfaces in hospital settings have been implicated as a vehicle of microbial transmission. In this study, we aimed to investigate the overall bacterial population on four frequently used surfaces using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Surface samples were collected from four sites, namely elevator buttons (EB, bank machine keyboard buttons (BMKB, restroom surfaces, and the employee biometric time clock system (EBTCS, in a large public and teaching hospital in São Paulo. Taxonomical composition revealed the abundance of Firmicutes phyla, followed by Actinobacteria and Proteobacteria, with a total of 926 bacterial families and 2832 bacterial genera. Moreover, our analysis revealed the presence of some potential pathogenic bacterial genera, including Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus. The presence of these pathogens in frequently used surfaces enhances the risk of exposure to any susceptible individuals. Some of the factors that may contribute to the richness of bacterial diversity on these surfaces are poor personal hygiene and ineffective routine schedules of cleaning, sanitizing, and disinfecting. Strict standards of infection control in hospitals and increased public education about hand hygiene are recommended to decrease the risk of transmission in hospitals among patients.

  9. First microbiota assessments of children's paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis.

    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

  10. Molecular characterization of the stomach microbiota in patients with gastric cancer and controls

    Dicksved, J.; Lindberg, M.; Rosenquist, M.; Enroth, H.; Jansson, J.K.; Engstrand, L.

    2009-01-15

    Persistent infection of the gastric mucosa by Helicobacter pylori, can initiate an inflammatory cascade that progresses into atrophic gastritis, a condition associated with reduced capacity for secretion of gastric acid and an increased risk in developing gastric cancer. The role of H. pylori as an initiator of inflammation is evident but the mechanism for development into gastric cancer has not yet been proven. A reduced capacity for gastric acid secretion allows survival and proliferation of other microbes that normally are killed by the acidic environment. It has been postulated that some of these species may be involved in the development of gastric cancer, however their identities are poorly defined. In this study, the gastric microbiota from ten patients with gastric cancer was characterized and compared with five dyspeptic controls using the molecular profiling approach, terminal-restriction fragment length polymorphism (T-RFLP), in combination with 16S rRNA gene cloning and sequencing. T-RFLP analysis revealed a complex bacterial community in the cancer patients that was not significantly different from the controls. Sequencing of 140 clones revealed 102 phylotypes, with representatives from five bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria). The data revealed a relatively low abundance of H. pylori and showed that the gastric cancer microbiota was instead dominated by different species of the genera Streptococcus, Lactobacillus, Veillonella and Prevotella. The respective role of these species in development of gastric cancer remains to be determined.

  11. Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India.

    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

  12. Changes in intestinal microflora of Caenorhabditis elegans following Bacillus nematocida B16 infection.

    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

  13. Application of Molecular Techniques to Elucidate the Influence of Cellulosic Waste on the Bacterial Community Structure at a Simulated Low-Level-Radioactive-Waste Site

    Low-level radioactive waste sites, including those at various U.S. Department of Energy (DOE) sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a non-radioactive model low-level waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rDNA clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both the clone library and PhyloChip results revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more unique Operational Taxonomic Units (OTUs), and therefore more relative diversity, than the clone libraries. Calculated diversity indices suggest that diversity is lowest in the Fill (F) and Fill Waste (FW) layers and greater in the Wood Waste (WW) and Waste Clay (WC) layers. Principal coordinates analysis and lineage specific analysis determined that Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose degrading microorganisms suggests the FW layer is an enrichment environment for cellulose degradation. Overall, these results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system.

  14. Identification of soil bacteria able to degrade phenanthrene bound to a hydrophobic sorbent in situ

    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

  15. Molecular Techniques Revealed Highly Diverse Microbial Communities in Natural Marine Biofilms on Polystyrene Dishes for Invertebrate Larval Settlement

    Lee, On On

    2014-01-09

    Biofilm microbial communities play an important role in the larval settlement response of marine invertebrates. However, the underlying mechanism has yet to be resolved, mainly because of the uncertainties in characterizing members in the communities using traditional 16S rRNA gene-based molecular methods and in identifying the chemical signals involved. In this study, pyrosequencing was used to characterize the bacterial communities in intertidal and subtidal marine biofilms developed during two seasons. We revealed highly diverse biofilm bacterial communities that varied with season and tidal level. Over 3,000 operational taxonomic units with estimates of up to 8,000 species were recovered in a biofilm sample, which is by far the highest number recorded in subtropical marine biofilms. Nineteen phyla were found, of which Cyanobacteria and Proteobacteria were the most dominant one in the intertidal and subtidal biofilms, respectively. Apart from these, Actinobacteria, Bacteroidetes, and Planctomycetes were the major groups recovered in both intertidal and subtidal biofilms, although their relative abundance varied among samples. Full-length 16S rRNA gene clone libraries were constructed for the four biofilm samples and showed similar bacterial compositions at the phylum level to those revealed by pyrosequencing. Laboratory assays confirmed that cyrids of the barnacle Balanus amphitrite preferred to settle on the intertidal rather than subtidal biofilms. This preference was independent of the biofilm bacterial density or biomass but was probably related to the biofilm community structure, particularly, the Proteobacterial and Cyanobacterial groups. © 2014 Springer Science+Business Media New York.

  16. Microbial community structure in major habitats above 6000 m on Mount Everest

    2007-01-01

    Bacterial abundance in surface snow between 6600 and 8000 m a.s.l. On the northern slope of Mt. Everest was investigated by flow cytometry. Bacterial diversity in serac ice at 6000 m a.s.l., glacier meltwater at 6350 m, and surface snow at 6600 m a.s.l. Was examined by constructing a 16S rRNA gene clone library. Bacterial abundance in snow was higher than that in the Antarctic but similar to other mountain regions in the world. Bacterial abundance in surface snow increased with altitude but showed no correlation with chemical parameters. Bacteria in the cryosphere on Mt. Everest were closely related to those isolated from soil, aquatic environments, plants, animals, humans and other frozen environments. Bacterial community structures in major habitats above 6000 m were variable. The Cytophaga-Flavobacterium-Bacteroides (CFB) group absolutely dominated in glacial meltwater, while β-Proteobacteria and the CFB group dominated in serac ice, and β-Proteobacteria and Actinobacteria dominated in surface snow. The remarkable differences among the habitats were most likely due to the bacterial post-deposition changes during acclimation processes.

  17. Understanding diversity patterns in bacterioplankton communities from a sub-Antarctic peatland.

    Quiroga, María Victoria; Valverde, Angel; Mataloni, Gabriela; Cowan, Don

    2015-06-01

    Bacterioplankton communities inhabiting peatlands have the potential to influence local ecosystem functions. However, most microbial ecology research in such wetlands has been done in ecosystems (mostly peat soils) of the Northern Hemisphere, and very little is known of the factors that drive bacterial community assembly in other regions of the world. In this study, we used high-throughput sequencing to analyse the structure of the bacterial communities in five pools located in a sub-Antarctic peat bog (Tierra del Fuego, Argentina), and tested for relationships between bacterial communities and environmental conditions. Bacterioplankton communities in peat bog pools were diverse and dominated by members of the Proteobacteria, Actinobacteria, Bacteroidetes and Verrucomicrobia. Community structure was largely explained by differences in hydrological connectivity, pH and nutrient status (ombrotrophic versus minerotrophic pools). Bacterioplankton communities in ombrotrophic pools showed phylogenetic clustering, suggesting a dominant role of deterministic processes in shaping these assemblages. These correlations between habitat characteristics and bacterial diversity patterns provide new insights into the factors regulating microbial populations in peatland ecosystems. PMID:25727763

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

    Xuejian eYu

    2015-08-01

    Full Text Available 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, Bacteroidetes and Firmicutes were found to be the dominant phyla despite the growth stages and fulvic acid application. Stevia growth stages strongly regulated composition of endophytic community. The genera Agrobacterium (12.3 % and Erwinia (7.2 % dominated in seedling stage were apparently declined in the vegetable and initial flowering stages, while Sphingomonas and Methylobacterium increased in mature leaves at harvest time, which showed that the mature leaves of Stevia preferred to accumulate some certain endophytic bacteria. Sphingomonas and Methylobacterium constituted an important part of the core endophytic community and were positively correlated with the stevioside content and UGT74G1 gene expression, respectively; while Erwinia, Agrobacterium and Bacillus were negatively correlated with the stevioside accumulation. Fulvic acid treatment accelerated the variation of endophytes along the growth stages.

  19. Characteristics of the LrhA subfamily of transcriptional regulators from Sinorhizobium meliloti

    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.

  20. Genomics of Methylotrophy in Gram-Positive Methylamine-Utilizing Bacteria

    Tami L. McTaggart

    2015-03-01

    Full Text Available Gram-positive methylotrophic bacteria have been known for a long period of time, some serving as model organisms for characterizing the specific details of methylotrophy pathways/enzymes within this group. However, genome-based knowledge of methylotrophy within this group has been so far limited to a single species, Bacillus methanolicus (Firmicutes. The paucity of whole-genome data for Gram-positive methylotrophs limits our global understanding of methylotrophy within this group, including their roles in specific biogeochemical cycles, as well as their biotechnological potential. Here, we describe the isolation of seven novel strains of Gram-positive methylotrophs that include two strains of Bacillus and five representatives of Actinobacteria classified within two genera, Arthrobacter and Mycobacterium. We report whole-genome sequences for these isolates and present comparative analysis of the methylotrophy functional modules within these genomes. The genomic sequences of these seven novel organisms, all capable of growth on methylated amines, present an important reference dataset for understanding the genomic basis of methylotrophy in Gram-positive methylotrophic bacteria. This study is a major contribution to the field of methylotrophy, aimed at closing the gap in the genomic knowledge of methylotrophy within this diverse group of bacteria.

  1. A comprehensive repertoire of prokaryotic species identified in human beings.

    Hugon, Perrine; Dufour, Jean-Charles; Colson, Philippe; Fournier, Pierre-Edouard; Sallah, Kankoe; Raoult, Didier

    2015-10-01

    The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents. PMID:26311042

  2. Preliminary characterization of human skin microbiome in healthy Egyptian individuals.

    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

  3. Composition, variability, and temporal stability of the intestinal microbiota of the elderly.

    Claesson, Marcus J

    2011-03-15

    Alterations in the human intestinal microbiota are linked to conditions including inflammatory bowel disease, irritable bowel syndrome, and obesity. The microbiota also undergoes substantial changes at the extremes of life, in infants and older people, the ramifications of which are still being explored. We applied pyrosequencing of over 40,000 16S rRNA gene V4 region amplicons per subject to characterize the fecal microbiota in 161 subjects aged 65 y and older and 9 younger control subjects. The microbiota of each individual subject constituted a unique profile that was separable from all others. In 68% of the individuals, the microbiota was dominated by phylum Bacteroides, with an average proportion of 57% across all 161 baseline samples. Phylum Firmicutes had an average proportion of 40%. The proportions of some phyla and genera associated with disease or health also varied dramatically, including Proteobacteria, Actinobacteria, and Faecalibacteria. The core microbiota of elderly subjects was distinct from that previously established for younger adults, with a greater proportion of Bacteroides spp. and distinct abundance patterns of Clostridium groups. Analyses of 26 fecal microbiota datasets from 3-month follow-up samples indicated that in 85% of the subjects, the microbiota composition was more like the corresponding time-0 sample than any other dataset. We conclude that the fecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability.

  4. Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues

    Jenny Chun-Yee Ng

    2015-10-01

    Full Text Available Corals are rapidly declining globally due to coral diseases. Skeletal growth anomalies (SGA or coral tumors are a group of coral diseases that affect coral reefs worldwide, including Hong Kong waters in the Indo-Pacific region. To better understand how bacterial communities may vary in corals with SGA, for the first time, we examined the bacterial composition associated with the apparently healthy and the diseased tissues of SGA-affected Platgyra carnosus using 16S ribosomal rRNA gene pyrosequencing. Taxonomic analysis revealed Proteobacteria, Bacteroidetes, Cyanobacteria, and Actinobacteria as the main phyla in both the apparently healthy and the diseased tissues. A significant difference in the bacterial community composition was observed between the two conditions at the OTU level. Diseased tissues were associated with higher abundances of Acidobacteria and Gemmatimonadetes, and a lower abundance of Spirochaetes. Several OTUs belonging to Rhodobacteraceae, Rhizobiales, Gammaproteobacteria, and Cytophaga-Flavobacterium-Bacteroidetes (CFB were strongly associated with the diseased tissues. These groups of bacteria may contain potential pathogens involved with the development of SGA or opportunistic secondary or tertiary colonizers that proliferated upon the health-compromised coral host. We suggest that these bacterial groups to be further studied based on inoculation experiments and testing of Koch’s postulates in efforts to understand the etiology and progression of SGA.

  5. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

    Li, Dong

    2015-09-24

    To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants. © 2015, Springer Science+Business Media New York.

  6. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts.

    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

  7. INTRACELLULAR COPPER ACCUMULATION ENHANCES THE GROWTH OF KINEOCOCCUS RADIOTOLERANS DURING CHRONIC IRRADIATION

    Bagwell, C; Charles Milliken, C

    2007-07-24

    The actinobacteria Kineococcus radiotolerans is highly resistant to ionizing radiation, desiccation, and oxidative stress; though the underlying biochemical mechanisms are unknown. The purpose of this study was to explore a possible linkage between the uptake of transition metals and extreme resistance to ionizing radiation and oxidative stress. The effects of 6 different divalent cationic metals on growth were examined in the absence of ionizing radiation. None of the metals tested were stimulatory, though cobalt was inhibitory to growth. In contrast, copper supplementation dramatically increased cell growth during chronic irradiation. K. radiotolerans exhibited specific uptake and intracellular accumulation of copper compared to only a weak response to both iron and manganese supplementation. Copper accumulation sensitized cells to hydrogen peroxide. Acute irradiation induced DNA damage was similar between the copper-loaded culture as the age-synchronized no copper control culture, though low molecular weight DNA was more persistent during post-irradiation recovery in the Cu-loaded culture. Still, the estimated times for genome restoration differed by only 1 hr between treatments. While we cannot discount the possibility that copper fulfills an unexpectedly important biochemical role in a radioactive environment; K. radiotolerans has a high capacity for intracellular copper sequestration, and presumably efficiently coordinated oxidative stress defenses and detoxification systems, which confers cross-protection from the damaging affects ionizing radiation.

  8. Genome Sequence and Analysis of the Soil Cellulolytic ActinomyceteThermobifida fusca

    Lykidis, Athanasios; Mavromatis, Konstantinos; Ivanova, Natalia; Anderson, Iain; Land, Miriam; DiBartolo, Genevieve; Martinez, Michele; Lapidus, Alla; Lucas, Susan; Copeland, Alex; Richardson, Paul; Wilson,David B.; Kyrpides, Nikos

    2007-02-01

    Thermobifida fusca is a moderately thermophilic soilbacterium that belongs to Actinobacteria. 3 It is a major degrader ofplant cell walls and has been used as a model organism for the study of 4secreted, thermostable cellulases. The complete genome sequence showedthat T. fusca has a 5 single circular chromosome of 3642249 bp predictedto encode 3117 proteins and 65 RNA6 species with a coding densityof 85percent. Genome analysis revealed the existence of 29 putative 7glycoside hydrolases in addition to the previously identified cellulasesand xylanases. The 8 glycosyl hydrolases include enzymes predicted toexhibit mainly dextran/starch and xylan 9 degrading functions. T. fuscapossesses two protein secretion systems: the sec general secretion 10system and the twin-arginine translocation system. Several of thesecreted cellulases have 11 sequence signatures indicating theirsecretion may be mediated by the twin-arginine12 translocation system. T.fusca has extensive transport systems for import of carbohydrates 13coupled to transcriptional regulators controlling the expression of thetransporters and14 glycosylhydrolases. In addition to providing anoverview of the physiology of a soil 15 actinomycete, this study presentsinsights on the transcriptional regulation and secretion of16 cellulaseswhich may facilitate the industrial exploitation of thesesystems.

  9. Culturable diversity of halophilic bacteria in foreshore soils

    Aarzoo Irshad

    2014-06-01

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

  10. High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea.

    Zhao, Shuai; Zhou, Na; Zhao, Zheng-Yong; Zhang, Ke; Tian, Chang-Yan

    2016-05-01

    Endophytic bacterial communities of halophyte Salicornia europaea roots were analyzed by 16S rRNA gene pyrosequencing. A total of 20,151 partial 16S rRNA gene sequences were obtained. These sequences revealed huge amounts of operational taxonomic units (OTUs), that is, 747-1405 OTUs in a root sample, at 3 % cut-off level. Root endophytes mainly comprised four phyla, among which Proteobacteria was the most represented, followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria was the most abundant class of Proteobacteria, followed by Betaproteobacteria and Alphaproteobacteria. Genera Pantoea, Halomonas, Azomonas, Serpens, and Pseudomonas were shared by all growth periods. A marked difference in endophytic bacterial communities was evident in roots from different host life-history stages. Gammaproteobacteria increased during the five periods, while Betaproteobacteria decreased. The richest endophytic bacteria diversity was detected in the seedling stage. Endophytic bacteria diversity was reduced during the flowering stage and fruiting stage. The five libraries contained 2321 different OTUs with 41 OTUs in common. As a whole, this study first surveys communities of endophytic bacteria by tracing crucial stages in the process of halophyte growth using high-throughput sequencing methods. PMID:26787546

  11. Diversity and ecological tolerance of bacteria isolated from the rhizosphere of halophyton plants living nearby Kiskunság soda ponds, Hungary.

    Borsodi, Andrea K; Bárány, Ágnes; Krett, Gergely; Márialigeti, Károly; Szili-Kovács, Tibor

    2015-06-01

    Many halophytes and halophilic microorganisms are capable to adapt to the extremities of saline habitats. This study reveals the taxonomic diversity and ecological tolerance of bacteria isolated from the rhizosphere of three different halophytes (Bolboschoenus maritimus, Puccinellia limosa and Aster tripolium) living in the vicinity of Kiskunság soda ponds. Following a sampling in September 2013, altogether 76 bacterial strains were isolated using two different media. The strains were identified on the basis of 16S rRNA gene sequencing following ARDRA grouping. Salt and pH tolerance of the strains were examined by measuring their growth in broths containing 0-15% NaCl (w/V) and characterized with pH 7-12 values. Among the strains genera of Anaerobacillus, Bacillus and Exiguobacterium (Firmicutes), Agromyces, Isoptericola, Microbacterium, Micrococcus, Nocardiopsis, Nesterenkonia and Streptomyces (Actinobacteria), Halomonas and Idiomarina (Proteobacteria) and Anditalea (Bacteroidetes) were identified. The Bolboschoenus and Puccinellia samples characterized with the highest pH and electric conductivity values were dominated by Bacillus, Halomonas and Nesterenkonia, respectively. The salt tolerance of the bacterial strains was strongly dependent on the sampling location and plant species. In contrast, growth of bacterial strains in broths with alkaline pH values was more balanced. The strains from the Puccinellia sample showed the widest salt and pH tolerance. PMID:26132838

  12. DIVERSITY OF CULTIVABLE MICROORGANISMS IN THE EASTERN PART OF URMIA SALT LAKE, IRAN

    Fereshteh Jookar Kashi

    2014-08-01

    Full Text Available In this study we employed culture techniques to study microbial diversity in Urmia Lake, a hypersaline lake in northwest of Iran. Water, soil and salt samples were taken from the Eastern part of Urmia Salt Lake in September 2011. A total of 11 water samples and 30 soil and salt samples were taken from 41 sites in the Lake. Bacterial isolates were cultured on different growth media and taxonomically affiliated based on their 16S rDNA gene sequence. Three hundred bacterial isolates were obtained from samples collected. Of these, 53 bacterial isolates were selected for sequencing and phylogenetic analysis, based on their growth characteristics and colony morphology. Results showed that these 53 isolates represented 39 species, belonging to 18 genera (Bacillus, Oceanobacillus, Thalassobacillus, Planomicrobium, Halobacillus, Planococcus, Terribacillus, Staphylococcus, Piscibacillus, Virgibacillus, Gracilibacillus, Ornithinibacillus, Halomonas, Pseudomonas, Providencia, Salicola, Psychrobacter, Kocuria and they were from 9 families (Bacillaceae, Planococcaceae, Staphylococcaceae, Halomonadaceae, Pseudomonadaceae, Enterobacteriaceae, Moraxellaceae, Alteromonadaceae, Micrococcaceae pertaining to three phyla (Actinobacteria 1.8%, Firmicutes 78.6%, Proteobacteria 21.4%. The present study showed that Urmia Lake is a rich source for moderately halophilic and halotolerant bacteria. The phylogenetic analysis of sequences from Urmia Lake had some common 16S rDNA sequences from other hypersaline lakes previously reported.

  13. A Freshwater Streptomyces, Isolated from Tyume River, Produces a Predominantly Extracellular Glycoprotein Bioflocculant

    Anthony I. Okoh

    2012-07-01

    Full Text Available We evaluated bioflocculant production by a freshwater actinobacteria whose 16S rDNA nucleotide sequence was deposited in GenBank as Streptomyces sp. Gansen (accession number HQ537129. Optimum culture conditions for bioflocculant production were an initial medium pH of 6.8, incubation temperature of 30 °C, agitation speed of 160 rpm and an inoculum size of 2% (v/v of cell density 1.5 × 108 cfu/mL. The carbon, nitrogen and cation sources for optimum bioflocculant production were glucose (89% flocculating activity, ammonium sulfate (76% flocculating activity and MgCl2. Bioflocculant pyrolysis showed three step decomposition indicative of three components while chemical analyses showed 78% carbohydrate and 22% protein (wt/wt. The mass ratio of neutral sugar, amino sugar and uronic acids was 4.6:2.4:3. FTIR spectrometry indicated the presence of carboxyl, hydroxyl and amino groups, typical for heteropolysaccharide. The bioflocculant showed a lattice structure as seen by SEM imaging. Its high flocculation activity suggests its suitability for industrial applicability.

  14. Characterization of culturable bacteria isolated from the cold-water coral Lophelia pertusa

    Galkiewicz, Julia P.; Pratte, Zoe A.; Gray, Michael A.; Kellogg, Christina A.

    2011-01-01

    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.

  15. Bacterial community survey of sediments at Naracoorte Caves, Australia

    Ball Andrew S.

    2012-07-01

    Full Text Available Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits and Strawhaven Cave was used as control (no tourist access. Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces. The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.

  16. Microbial diversity at the moderate acidic stage in three different sulfidic mine tailings dumps generating acid mine drainage.

    Korehi, Hananeh; Blöthe, Marco; Schippers, Axel

    2014-11-01

    In freshly deposited sulfidic mine tailings the pH is alkaline or circumneutral. Due to pyrite or pyrrhotite oxidation the pH is dropping over time to pH values <3 at which acidophilic iron- and sulfur-oxidizing prokaryotes prevail and accelerate the oxidation processes, well described for several mine waste sites. The microbial communities at the moderate acidic stage in mine tailings are only scarcely studied. Here we investigated the microbial diversity via 16S rRNA gene sequence analysis in eight samples (pH range 3.2-6.5) from three different sulfidic mine tailings dumps in Botswana, Germany and Sweden. In total 701 partial 16S rRNA gene sequences revealed a divergent microbial community between the three sites and at different tailings depths. Proteobacteria and Firmicutes were overall the most abundant phyla in the clone libraries. Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospira occurred less frequently. The found microbial communities were completely different to microbial communities in tailings at

  17. Characterization of the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (Arctocephalus tropicalis).

    Medeiros, Aline Weber; Giongo, Adriana; Valdez, Fernanda P; Blaese de Amorin, Derek; Tavares, Maurício; d'Azevedo, Pedro A; Franco, Ana Claudia; Frazzon, Jeverson; Frazzon, Ana P G

    2016-03-01

    The microbiota of wild marine mammals is poorly understood, perhaps due to the migratory habits of some species and the difficulty in obtaining samples. Using high-throughput sequencing, the present study examines the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (A. tropicalis). Faecal samples from South American (n = 6) and Subantarctic fur seals (n = 4) found dead along the south coast of Brazil were collected. Sequences were assigned to taxa using the Ribosomal Database Project-Bayesian classifier. Diversity of the microbiota was assessed by categorization of sequence reads into operational taxonomic units. Results indicate that Firmicutes (88.556%-84.016%) was the predominant phylum in South American and Subantarctic fur seals. The distribution of Actinobacteria and Proteobacteria varied according to the fur seal species. Fusobacteria and Bacteroidetes represented less than 1% of the sequences. The most abundant order in both fur seals was Clostridiales (88.64% and 87.49%). Individual variable incidences were observed in the composition of family among the fur seals, though the families Lachnospiraceae, Peptostreptococcaceae, Ruminococcaceae and Coriobacteriaceae were more prevalent. This study provides insight into the faecal bacterial community of wild young South American and Subantarctic fur seals. PMID:26880785

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

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

    2016-07-15

    Compost-amended landfill reactors were developed to reduce polychlorinated-p-dioxins and dibenzofurans (PCDD/Fs) in contaminated soils. By periodically recirculating leachate and suppling oxygen, the online monitoring of the oxidation reduction potential confirmed that the reactors were maintained under hypoxic conditions, with redox levels constantly fluctuating between -400 and +80mV. The subsequent reactor operation demonstrated that PCDD/F degradation in soil could be facilitated by amending compost originating from the cow manure and waste sludge and that the degradation might be affected by the availability of easily degradable substrates in the soil and compost. The pyrosequencing analysis of V4/V5 regions of bacterial 16S rRNA genes suggested that species richness of the soil microbial community was increased by a factor of 1.37-1.61. Although the bacterial community varied with the compost origin and changed markedly during reactor operation, it was dominated by Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Firmicutes. The aerotolerant anaerobic Sedimentibacter and Propionibacterium spp., and the uncultured Chloroflexi group could be temporarily induced to a high abundance by amending the cow manure compost; the bacterial growths were associated with the rapid degradation of PCDD/Fs. Overall, the novel bioremediation method for PCDD/F-contaminated soils using hypoxic conditions was effective, simple, energy saving, and thus easily practicable. PMID:27037469

  19. Abundance and Diversity of Bacterial, Archaeal, and Fungal Communities Along an Altitudinal Gradient in Alpine Forest Soils: What Are the Driving Factors?

    Siles, José A; Margesin, Rosa

    2016-07-01

    Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site. PMID:26961712

  20. Genomes of three facultatively symbiotic Frankia sp. strainsreflect host plant biogeography

    Normand, Philippe; Lapierre, Pascal; Tisa, Louis S.; Gogarten, J.Peter; Alloisio, Nicole; Bagnarol, Emilie; Bassi, Carla A.; Berry,Alison; Bickhart, Derek M.; Choisne, Nathalie; Couloux, Arnaud; Cournoyer, Benoit; Cruveiller, Stephane; Daubin, Vincent; Demange, Nadia; Francino, M. Pilar; Ggoltsman, Eugene; Huang, Ying; Kopp, Olga; Labarre,Laurent; Lapidus, Alla; Lavire, Celine; Marechal, Joelle; Martinez,Michele; Mastronunzio, Juliana E.; Mullin, Beth; Niemann, James; Pujic,Pierre; Rawnsley, Tania; Rouy, Zoe; Schenowitz, Chantal; Sellstedt,Anita; Tavares, Fernando; Tomkins, Jeffrey P.; Vallenet, David; Valverde,Claudio; Wall, Luis; Wang, Ying; Medigue, Claudine; Benson, David R.

    2006-02-01

    Filamentous actinobacteria from the genus Frankia anddiverse woody trees and shrubs together form N2-fixing actinorhizal rootnodule symbioses that are a major source of new soil nitrogen in widelydiverse biomes 1. Three major clades of Frankia sp. strains are defined;each clade is associated with a defined subset of plants from among theeight actinorhizal plant families 2,3. The evolution arytrajectoriesfollowed by the ancestors of both symbionts leading to current patternsof symbiont compatibility are unknown. Here we show that the competingprocesses of genome expansion and contraction have operated in differentgroups of Frankia strains in a manner that can be related to thespeciation of the plant hosts and their geographic distribution. Wesequenced and compared the genomes from three Frankia sp. strains havingdifferent host plant specificities. The sizes of their genomes variedfrom 5.38 Mbp for a narrow host range strain (HFPCcI3) to 7.50Mbp for amedium host range strain (ACN14a) to 9.08 Mbp for a broad host rangestrain (EAN1pec.) This size divergence is the largest yet reported forsuch closely related bacteria. Since the order of divergence of thestrains is known, the extent of gene deletion, duplication andacquisition could be estimated and was found to be inconcert with thebiogeographic history of the symbioses. Host plant isolation favoredgenome contraction, whereas host plant diversification favored genomeexpansion. The results support the idea that major genome reductions aswell as expansions can occur in facultatively symbiotic soil bacteria asthey respond to new environments in the context of theirsymbioses.

  1. Continous application of bioorganic fertilizer induced resilient culturable bacteria community associated with banana Fusarium wilt suppression

    Fu, Lin; Ruan, Yunze; Tao, Chengyuan; Li, Rong; Shen, Qirong

    2016-01-01

    Fusarium wilt of banana always drives farmers to find new land for banana cultivation due to the comeback of the disease after a few cropping years. A novel idea for solving this problem is the continuous application of bioorganic fertilizer (BIO), which should be practiced from the beginning of banana planting. In this study, BIO was applied in newly reclaimed fields to pre-control banana Fusarium wilt and the culturable rhizobacteria community were evaluated using Biolog Ecoplates and culture-dependent denaturing gradient gel electrophoresis (CD-DGGE). The results showed that BIO application significantly reduced disease incidences and increased crop yields, respectivly. And the stabilized general bacterial metabolic potential, especially for the utilization of carbohydrates, carboxylic acids and phenolic compounds, was induced by BIO application. DGGE profiles demonstrated that resilient community structure of culturable rhizobacteria with higher richness and diversity were observed in BIO treated soils. Morever, enriched culturable bacteria affiliated with Firmicutes, Gammaproteobacteria and Actinobacteria were also detected. In total, continuous application of BIO effectively suppressed Fusarium wilt disease by stabilizing culturable bacterial metabolic potential and community structure. This study revealed a new method to control Fusarium wilt of banana for long term banana cultivation. PMID:27306096

  2. Associations between bacterial communities of house dust and infant gut

    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.

  3. Screening of Marine Actinomycetes from Segara Anakan for Natural Pigment and Hydrolytic Activities

    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.

  4. Discovery of pentangular polyphenols hexaricins A-C from marine Streptosporangium sp. CGMCC 4.7309 by genome mining.

    Tian, Jun; Chen, Haiyan; Guo, Zhengyan; Liu, Ning; Li, Jine; Huang, Ying; Xiang, Wensheng; Chen, Yihua

    2016-05-01

    Many novel microbial nature products were discovered from Actinobacteria by genome mining methods. However, only a few number of genome mining works were carried out in rare actinomycetes. An important reason precluding the genome mining efforts in rare actinomycetes is that most of them are recalcitrant to genetic manipulation. Herein, we chose the rare marine actinomycete Streptosporangium sp. CGMCC 4.7309 to explore its secondary metabolite diversity by genome mining. The genetic manipulation method has never been established for Streptosporangium strains. At first, we set up the genetic system of Streptosporangium sp. CGMCC 4.7309 unprecedentedly. The draft genome sequencing of Streptosporangium sp. CGMCC 4.7309 revealed that it contains more than 20 cryptic secondary metabolite biosynthetic clusters. A type II polyketide synthases-containing cluster (the hex cluster) was predicted to encode compounds with a pentangular polyphenol scaffold by in silico analysis. The products of the hex cluster were uncovered by comparing the metabolic profile of Streptosporangium sp. CGMCC 4.7309 with that of the hex30 inactivated mutant, in which a key ketoreductase gene was disrupted. Finally, three pentangular polyphenols were isolated and named as hexaricins A (1), B (2), and C (3). The inconsistency of the stereochemistry of C-15 in hexaricins A, B, and C indicates a branch point in their biosynthesis. Finally, the biosynthetic pathway of the hexaricins was proposed based on bioinformatics analysis. PMID:26754814

  5. Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents.

    Blaser, Martin J; Dominguez-Bello, Maria G; Contreras, Monica; Magris, Magda; Hidalgo, Glida; Estrada, Isidoro; Gao, Zhan; Clemente, Jose C; Costello, Elizabeth K; Knight, Rob

    2013-01-01

    The human skin harbors complex bacterial communities. Prior studies showing high inter-individual variation focused on subjects from developed countries. We therefore compared cutaneous bacterial communities of Amerindians in the Venezuelan Amazon with subjects in the United States. Forearm skin specimens were studied from healthy Amerindians in Platanillal village in Amazonas State, and from healthy persons in New York and Colorado. All skin sampling used similar swab/buffer techniques. Multiplexed V2-targeted 16S rRNA gene pyrosequencing yielded high quality sequences from 112 samples. The results show 20 phyla, with three (Proteobacteria, Firmicutes, Actinobacteria) predominating. US residents and Venezuelan Amerindians had significantly different forearm skin bacterial community compositions, with United States dominated by Propionibacterium. Among the Amerindians, there was a deep split based on bacterial community membership, with 30 and 42 samples, respectively, falling into each of the two groups, not associated with age, gender, or body mass index. One Amerindian group had diversity similar to the United States, but was dominated by Staphylococcus rather than Propionibacterium. The other Amerindian group was significantly more diverse and even than the US or the other Amerindian group, and featured a broad range of Proteobacteria. The results provide evidence that ethnicity, lifestyle and/or geography are associated with the structure of human cutaneous bacterial communities. PMID:22895161

  6. No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls.

    Dlugosz, Aldona; Winckler, Björn; Lundin, Elin; Zakikhany, Katherina; Sandström, Gunnar; Ye, Weimin; Engstrand, Lars; Lindberg, Greger

    2015-01-01

    Several studies have indicated that colonic microbiota may exhibit important differences between patients with irritable bowel syndrome (IBS) and healthy controls. Less is known about the microbiota of the small bowel. We used massive parallel sequencing to explore the composition of small bowel mucosa-associated microbiota in patients with IBS and healthy controls. We analysed capsule biopsies from the jejunum of 35 patients (26 females) with IBS aged 18-(36)-57 years and 16 healthy volunteers (11 females) aged 20-(32)-48 years. Sequences were analysed based on taxonomic classification. The phyla with the highest total abundance across all samples were: Firmicutes (43%), Proteobacteria (23%), Bacteroidetes (15%), Actinobacteria (9.3%) and Fusobacteria (7.0%). The most abundant genera were: Streptococcus (19%), Veillonella (13%), Prevotella (12%), Rothia (6.4%), Haemophilus (5.7%), Actinobacillus (5.5%), Escherichia (4.6%) and Fusobacterium (4.3%). We found no difference among major phyla or genera between patients with IBS and controls. We identified a cluster of samples in the small bowel microbiota dominated by Prevotella, which may represent a common enterotype of the upper small intestine. The remaining samples formed a gradient, dominated by Streptococcus at one end and Escherichia at the other. PMID:25687743

  7. Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core.

    Kaci, Assia; Petit, Fabienne; Fournier, Matthieu; Cécillon, Sébastien; Boust, Dominique; Lesueur, Patrick; Berthe, Thierry

    2016-03-01

    In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha-Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community. PMID:25934230

  8. Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive Japanese barberry (Berberis thunbergii DC.).

    Coats, V C; Pelletreau, K N; Rumpho, M E

    2014-03-01

    The soil microbial community acts as a reservoir of microbes that directly influences the structure and composition of the aboveground plant community, promotes plant growth, increases stress tolerance and mediates local patterns of nutrient cycling. Direct interactions between plants and rhizosphere-dwelling microorganisms occur at, or near, the surface of the root. Upon introduction and establishment, invasive plants modify the soil microbial communities and soil biochemistry affecting bioremediation efforts and future plant communities. Here, we used tag-encoded FLX amplicon 454 pyrosequencing (TEFAP) to characterize the bacterial and fungal community diversity in the rhizosphere of Berberis thunbergii DC. (Japanese barberry) from invasive stands in coastal Maine to investigate effects of soil type, soil chemistry and surrounding plant cover on the soil microbial community structure. Acidobacteria, Actinobacteria, Proteobacteria and Verrucomicrobia were the dominant bacterial phyla, whereas fungal communities were comprised mostly of Ascomycota and Basidiomycota phyla members, including Agaricomycetes and Sordariomycetes. Bulk soil chemistry had more effect on the bacterial community structure than the fungal community. An effect of geographic location was apparent in the rhizosphere microbial communities, yet it was less significant than the effect of surrounding plant cover. These data demonstrate a high degree of spatial variation in the rhizosphere microbial communities of Japanese barberry with apparent effects of soil chemistry, location and canopy cover on the microbial community structure. PMID:24118303

  9. 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.

    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.

  10. Characterization of bromate-reducing bacterial isolates and their potential for drinking water treatment.

    Davidson, Andrew N; Chee-Sanford, Joanne; Lai, Hoi Yi Mandy; Ho, Chi-hua; Klenzendorf, J Brandon; Kirisits, Mary Jo

    2011-11-15

    The objective of the current study was to isolate and characterize several bromate-reducing bacteria and to examine their potential for bioaugmentation to a drinking water treatment process. Fifteen bromate-reducing bacteria were isolated from three sources. According to 16S rRNA gene sequencing, the bromate-reducing bacteria are phylogenetically diverse, representing the Actinobacteria, Bacteroidetes, Firmicutes, and α-, β-, and γ-Proteobacteria. The broad diversity of bromate-reducing bacteria suggests the widespread capability for microbial bromate reduction. While the cometabolism of bromate via nitrate reductase and (per)chlorate reductase has been postulated, five of our bromate-reducing isolates were unable to reduce nitrate or perchlorate. This suggests that a bromate-specific reduction pathway might exist in some microorganisms. Bioaugmentation of activated carbon filters with eight of the bromate-reducing isolates did not significantly decrease start-up time or increase bromate removal as compared to control filters. To optimize bromate reduction in a biological drinking water treatment process, the predominant mechanism of bromate reduction (i.e., cometabolic or respiratory) needs to be assessed so that appropriate measures can be taken to improve bromate removal. PMID:21943884

  11. Optimal growth condition of earthworms and their vermicompost features during recycling of five different fresh fruit and vegetable wastes.

    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

  12. High levels of DegU-P activate an Esat-6-like secretion system in Bacillus subtilis.

    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.

  13. Survival of mycobacteria depends on proteasome-mediated amino acid recycling under nutrient limitation

    Elharar, Yifat; Roth, Ziv; Hermelin, Inna; Moon, Alexandra; Peretz, Gabriella; Shenkerman, Yael; Vishkautzan, Marina; Khalaila, Isam; Gur, Eyal

    2014-01-01

    Intracellular protein degradation is an essential process in all life domains. While in all eukaryotes regulated protein degradation involves ubiquitin tagging and the 26S-proteasome, bacterial prokaryotic ubiquitin-like protein (Pup) tagging and proteasomes are conserved only in species belonging to the phyla Actinobacteria and Nitrospira. In Mycobacterium tuberculosis, the Pup-proteasome system (PPS) is important for virulence, yet its physiological role in non-pathogenic species has remained an enigma. We now report, using Mycobacterium smegmatis as a model organism, that the PPS is essential for survival under starvation. Upon nitrogen limitation, PPS activity is induced, leading to accelerated tagging and degradation of many cytoplasmic proteins. We suggest a model in which the PPS functions to recycle amino acids under nitrogen starvation, thereby enabling the cell to maintain basal metabolic activities. We also find that the PPS auto-regulates its own activity via pupylation and degradation of its components in a manner that promotes the oscillatory expression of PPS components. As such, the destructive activity of the PPS is carefully balanced to maintain cellular functions during starvation. PMID:24986881

  14. Genomic and Transcriptomic Resolution of Organic Matter Utilization Among Deep-Sea Bacteria in Guaymas Basin Hydrothermal Plumes

    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

  15. Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis.

    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

  16. Heterotrophic and Autotrophic Microbial Populations in Cold Perennial Springs of the High Arctic ▿ †

    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

  17. Compost-induced suppression of Pythium damping-off is mediated by fatty-acid-metabolizing seed-colonizing microbial communities.

    McKellar, Mary E; Nelson, Eric B

    2003-01-01

    Leaf composts were studied for their suppressive effects on Pythium ultimum sporangium germination, cottonseed colonization, and the severity of Pythium damping-off of cotton. A focus of the work was to assess the role of fatty-acid-metabolizing microbial communities in disease suppression. Suppressiveness was expressed within the first few hours of seed germination as revealed by reduced P. ultimum sporangium germination, reduced seed colonization, and reduced damping-off in transplant experiments. These reductions were not observed when cottonseeds were sown in a conducive leaf compost. Microbial consortia recovered from the surface of cottonseeds during the first few hours of germination in suppressive compost (suppressive consortia) induced significant levels of damping-off suppression, whereas no suppression was induced by microbial consortia recovered from cottonseeds germinated in conducive compost (conducive consortia). Suppressive consortia rapidly metabolized linoleic acid, whereas conducive consortia did not. Furthermore, populations of fatty-acid-metabolizing bacteria and actinobacteria were higher in suppressive consortia than in conducive consortia. Individual bacterial isolates varied in their ability to metabolize linoleic acid and protect seedlings from damping-off. Results indicate that communities of compost-inhabiting microorganisms colonizing cottonseeds within the first few hours after sowing in a Pythium-suppressive compost play a major role in the suppression of P. ultimum sporangium germination, seed colonization, and damping-off. Results further indicate that fatty acid metabolism by these seed-colonizing bacterial consortia can explain the Pythium suppression observed. PMID:12514027

  18. Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism.

    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

  19. Unravelling the diversity of grapevine microbiome.

    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.

  20. Unravelling the diversity of grapevine microbiome.

    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