Microbial Communities (microbial + community)

Distribution by Scientific Domains
Distribution within Life Sciences

Kinds of Microbial Communities

  • anaerobic microbial community
  • complex microbial community
  • diverse microbial community
  • natural microbial community
  • soil microbial community

  • Terms modified by Microbial Communities

  • microbial community analysis
  • microbial community composition
  • microbial community dynamics
  • microbial community structure

  • Selected Abstracts


    Molecular Characterization of Anaerobic Microbial Communities from Benzene-Degrading Sediments under Methanogenic Conditions

    BIOTECHNOLOGY PROGRESS, Issue 6 2005
    Wook Chang
    Anaerobic benzene degradation was confirmed in microbial communities enriched from Baltimore Harbor (Baltimore, MD) sediments under methanogenic conditions. Molecular characterization based on 16S rDNA gene sequences revealed that the strains in the communities were diversely affiliated with such phylogenetic branches as the Bacteroidetes, Euryarchaeota, Firmicutes, and Thermotogaephyla. Of interest was that the majority of the microbial populations detected in these cultures were closely related to the members of dechlorinating microbial communities. Further, some of those species were previously found in naphthalene- or phenanthrene-degrading methanogenic communities. Finally, this result could be used to design targeted isolation strategies for anaerobic benzene-degrading strains under methanogenic conditions. [source]


    Variations of Microbial Communities and the Contents and Isotopic Compositions of Total Organic Carbon and Total Nitrogen in Soil Samples during Their Preservation

    ACTA GEOLOGICA SINICA (ENGLISH EDITION), Issue 1 2009
    Qianye TAO
    Abstract: Semi-sealed preservation of soil samples at different moisture of 4% and 23%, respectively, was simulated to observe the variations of soil microbial communities and determine the contents and isotopic compositions of the total organic carbon and total nitrogen on the 7th and 30th day, respectively. The results show that during preservation, the quantity of microbial communities tended to increase first and then decrease, with a wider variation range at higher moisture (23%). At the moisture content of 23%, the microbial communities became more active on the 7th day, but less after 30 days, and their activity was stable with little fluctuation at the moisture content of 4%. However, there were no significant changes in the contents and isotopic compositions of the total organic carbon and total nitrogen. During preservation, the responses of soil microbes to the environment are more sensitive to changes in the total nitrogen and organic carbon contents. It is thus suggested that the variations of microbial communities have not exerted remarkable impacts on the isotope compositions of the total nitrogen and total organic carbon. [source]


    Extremely Alkaline (pH > 12) Ground Water Hosts Diverse Microbial Community

    GROUND WATER, Issue 4 2006
    George S. Roadcap
    Chemically unusual ground water can provide an environment for novel communities of bacteria to develop. Here, we describe a diverse microbial community that inhabits extremely alkaline (pH > 12) ground water from the Lake Calumet area of Chicago, Illinois, where historic dumping of steel slag has filled in a wetland. Using microbial 16S ribosomal ribonucleic acid gene sequencing and microcosm experiments, we confirmed the presence and growth of a variety of alkaliphilic ,-Proteobacteria, Bacillus, and Clostridium species at pH up to 13.2. Many of the bacterial sequences most closely matched those of other alkaliphiles found in more moderately alkaline water around the world. Oxidation of dihydrogen produced by reaction of water with steel slag is likely a primary energy source to the community. The widespread occurrence of iron-oxidizing bacteria suggests that reduced iron serves as an additional energy source. These results extend upward the known range of pH tolerance for a microbial community by as much as 2 pH units. The community may provide a source of novel microbes and enzymes that can be exploited under alkaline conditions. [source]


    The Role of Amoeboid Protists and the Microbial Community in Moss-Rich Terrestrial Ecosystems: Biogeochemical Implications for the Carbon Budget and Carbon Cycle, Especially at Higher Latitudes,

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2008
    O. ROGER ANDERSON
    ABSTRACT. Moss-rich terrestrial communities are widely distributed in low- and high-latitude environments, covering vast surface areas in the boreal forests and tundra. The microbial biota in these organic-rich communities may contribute substantially to the carbon budget of terrestrial communities and the carbon cycle on a global scale. Recent research is reported on the carbon content of microbial communities in some temperate and high-latitude moss communities. The total carbon content and potential respiratory carbon dioxide (CO2) efflux is reported for bacteria, microflagellates, naked amoebae, and testate amoebae within sampling sites at a northeastern forest and the tundra at Toolik, Alaska. Quantitative models of the predicted total CO2 efflux from the microbes, based on microscopic observations and enumeration of the microbiota in samples from the research sites, are described and predictions are compared with published field-based data of CO2 efflux. The significance of the predictions for climate change and global warming are discussed. [source]


    Microbial communities in a porphyry copper tailings impoundment and their impact on the geochemical dynamics of the mine waste

    ENVIRONMENTAL MICROBIOLOGY, Issue 2 2007
    Nouhou Diaby
    Summary The distribution and diversity of acidophilic bacteria of a tailings impoundment at the La Andina copper mine, Chile, was examined. The tailings have low sulfide (1.7% pyrite equivalent) and carbonate (1.4% calcite equivalent) contents and are stratified into three distinct zones: a surface (0-70-80 cm) ,oxidation zone' characterized by low-pH (2.5,4), a ,neutralization zone' (70,80 to 300,400 cm) and an unaltered ,primary zone' below 400 cm. A combined cultivation-dependent and biomolecular approach (terminal restriction enzyme fragment length polymorphism and 16S rRNA clone library analysis) was used to characterize the indigenous prokaryotic communities in the mine tailings. Total cell counts showed that the microbial biomass was greatest in the top 125 cm of the tailings. The largest numbers of bacteria (109 g,1 dry weight of tailings) were found at the oxidation front (the junction between the oxidation and neutralization zones), where sulfide minerals and oxygen were both present. The dominant iron-/sulfur-oxidizing bacteria identified at the oxidation front included bacteria of the genus Leptospirillum (detected by molecular methods), and Gram-positive iron-oxidizing acidophiles related to Sulfobacillus (identified both by molecular and cultivation methods). Acidithiobacillus ferrooxidans was also detected, albeit in relatively small numbers. Heterotrophic acidophiles related to Acidobacterium capsulatum were found by molecular methods, while another Acidobacterium -like bacterium and an Acidiphilium sp. were isolated from oxidation zone samples. A conceptual model was developed, based on microbiological and geochemical data derived from the tailings, to account for the biogeochemical evolution of the Piuquenes tailings impoundment. [source]


    Molecular analysis of ammonia-oxidizing bacteria community in intermittent aeration sequencing batch reactors used for animal wastewater treatment

    ENVIRONMENTAL MICROBIOLOGY, Issue 11 2006
    Kenichi Otawa
    Summary Bacterial communities and betaproteobacterial ammonia-oxidizing bacteria (AOB) communities were evaluated seasonally in an intermittent-aeration sequencing batch process (SBR, plant A) and in 12 other livestock wastewater treatment plants (WWTP): eight SBRs and four conventional activated-sludge systems. Microbial communities were analysed by reverse transcription polymerase chain reaction followed by denaturing-gradient gel electrophoresis (DGGE) and the construction of clone libraries for 16S rRNA and ammonia monooxygenase (amoA) genes. In plant A, the dominant bacteria were as-yet-uncultured bacteria of Bacteroidetes and Proteobacteria, and the DGGE profiles showed that the bacterial communities were stable during a given treatment cycle, but changed seasonally. In betaproteobacterial AOB communities, two AOB phylotypes (members of the Nitrosomonas ureae,oligotropha,marina cluster) were dominant during the seasons in plant A. Although the dominant AOB phylotypes differed among the 13 WWTPs, dominance by one or two AOB phylotypes was commonly observed in all plants. Sequencing of the DGGE bands indicated that amoA sequences belonging to the Nitrosomonas europaea,eutropha cluster were dominant in 11 plants, where the ammonia-nitrogen concentration was high in the raw wastewater, whereas those belonging to the Nitrosomonas ureae,oligotropha,marina cluster were dominant in two plants where the concentration was relatively low. Even though we detected many minor amoA sequences by means of five clone libraries for the A to D plants, no libraries comprised both amoA sequences belonging to the two clusters, indicating that the dominant AOBs were defined by cluster level in each plant. [source]


    The effects of copper on the microbial community of a coral reef sponge

    ENVIRONMENTAL MICROBIOLOGY, Issue 1 2001
    Nicole S. Webster
    Marine sponges often harbour communities of symbiotic microorganisms that fulfil necessary functions for the well-being of their hosts. Microbial communities associated with the sponge Rhopaloeides odorabile were used as bioindicators for sublethal cupric ion (Cu2+) stress. A combined strategy incorporating molecular, cultivation and electron microscopy techniques was adopted to monitor changes in microbial diversity. The total density of sponge-associated bacteria and counts of the predominant cultivated symbiont (,-proteobacterium strain NW001) were significantly reduced in response to Cu2+ concentrations of 1.7 g l,1 and above after 14 days of exposure. The number of operational taxonomic units (OTUs) detected by restriction fragment length polymorphism (RFLP) decreased by 64% in sponges exposed to 223 g l,1 Cu2+ for 48 h and by 46% in sponges exposed to 19.4 g l,1 Cu2+ for 14 days. Electron microscopy was used to identify 17 predominant bacterial morphotypes, composing 47% of the total observed cells in control sponges. A reduction in the proportion of these morphotypes to 25% of observed cells was evident in sponges exposed to a Cu2+ concentration of 19.4 g l,1. Although the abundance of most morphotypes decreased under Cu2+ stress, three morphotypes were not reduced in numbers and a single morphotype actually increased in abundance. Bacterial numbers, as detected using fluorescence in situ hybridization (FISH), decreased significantly after 48 h exposure to 19.4 g l,1 Cu2+. Archaea, which are normally prolific in R. odorabile, were not detected after exposure to a Cu2+ concentration of 19.4 g l,1 for 14 days, indicating that many of the microorganisms associated with R. odorabile are sensitive to free copper. Sponges exposed to a Cu2+ concentration of 223 g l,1 became highly necrosed after 48 h and accumulated 142 18 mg kg,1 copper, whereas sponges exposed to 19.4 g l,1 Cu2+ accumulated 306 15 mg kg,1 copper after 14 days without apoptosis or mortality. Not only do sponges have potential for monitoring elevated concentrations of heavy metals but also examining changes in their microbial symbionts is a novel and sensitive bioindicator for the assessment of pollution on important microbial communities. [source]


    Reproducibility of a microbial river water community to self-organize upon perturbation with the natural chemical enantiomers, R - and S -carvone

    FEMS MICROBIOLOGY ECOLOGY, Issue 2 2008
    Katja Lehmann
    Abstract A river water microbial community was studied in response to perturbation with the monoterpene enantiomers R - and S -carvone. The microbial community structure and function was also evaluated after enantiomers exposure was switched. Microbial communities were evaluated by length heterogeneity PCR. The addition of R - and S -carvone enriched for a range of functionally different communities: enantiomer-selective, racemic and ones that contain both. After 5 days incubation, the R - and S -carvone treatments developed a range of dominant microbial communities, which were increasingly dissimilar from the ones in which no carvone degradation had taken place (R -values: R -carvone 0.743, S -carvone 0.5007). There was an increase in the evenness of the microbial community structure upon carvone depletion. After the cross-over, the rate of carvone utilization was significantly faster than after the first carvone addition (P=0.008) as demonstrated by concomitant carvone and oxygen depletion. The main R -degrading community (450,456 bp) appeared enantioselective and largely unable to degrade S -carvone, whereas the S -carvone-degrading community (502,508 bp) appeared to have racemic catabolic capacity. In conclusion, chemical perturbations, such as enantiomers, might generate a significant shift in the river microbial ecology that can have implications for the function of a river in both a spatial and temporal context. [source]


    Microbial communities in roots of Pinus sylvestris seedlings with damping-off symptoms in two forest nurseries as determined by ITS1/2 rDNA sequencing

    FOREST PATHOLOGY, Issue 4 2009
    H. Kwa
    Summary A methodological molecular procedure, which included extraction and cloning of the ITS1/2 rDNA of root-associated organisms with subsequent transformation and sequencing of representative clones, was effective for detection, discrimination and determination of the frequency of the main damping-off pathogens in roots of Pinus sylvestris seedlings growing in different forest-tree nursery soils and exhibiting different rates of disease progress. Roots exhibiting slower damping-off progression were colonized by Fusarium oxysporum, Neonectria radicicola (Ascomycota) and Pythium spp. (Oomycota), which comprised 50% of the microbial community. Roots exhibiting faster damping-off progression were dominated by Thanatephorus cucumeris (Basidiomycota), which comprised 80% of the microbial community. The microbial community was more diverse in roots with slower damping-off progression (14 species) than in roots with faster disease progression (seven species). [source]


    DOE genomics: Applications to in situ subsurface bioremediation

    REMEDIATION, Issue 1 2006
    Robert T. AndersonArticle first published online: 22 DEC 200
    Microbial communities can greatly affect the mobility and fate of subsurface contaminants, yet relatively little is known about the functioning of microorganisms in subsurface environments. Major advances in DNA sequencing capability and the advent of genome-enabled studies have produced key insights into how microorganisms adapt to environmental conditions and/or biotransform subsurface contaminants starting from analyses of genome content. These techniques enable the researcher to detect how an organism responds to its environment and, potentially, to devise better methods to promote specific microbial activity in subsurface environments. The U.S. Department of Energy sponsors genome research through the Genomics:GTL program. One of the applications of this research is to better understand and control biological processes influencing the mobility of contaminants of concern to DOE such as metals and radionuclides. Genome and gene expression techniques have led to new insights into the functioning of subsurface microbial communities, but the true potential of these techniques is still to be revealed. As genome-enabled science progresses, techniques for evaluating gene expression patterns of whole communities will advance the understanding and development of optimized in situ bioremediation and more realistic simulations of microbial contaminant biotransformation. 2006 Wiley Periodicals, Inc.* [source]


    Microbial communities of ultramafic soils in maquis and rainforest at Mont Do, New Caledonia

    AUSTRAL ECOLOGY, Issue 5 2009
    MELISSA LENCZEWSKI
    Abstract We analysed variation in microbial community richness and function in soils associated with a fire-induced vegetation successional gradient from low maquis (shrubland) through tall maquis to rainforest on metal-rich ultramafic soils at Mt Do, New Caledonia. Random amplified polymorphic DNA fingerprinting was used to determine the extent of genetic relatedness among the microbial communities and indicated that the open and tall maquis microbial communities were more similar to each other than they were to the rainforest community. Sole-source carbon utilization indicated variation in the microbial communities, again with greater diversity in rainforest soils. Plate counts showed that both rainforest and maquis soils contained bacteria that can grow in the presence of up to 20 mmol L,1 nickel and 10 mmol L,1 chromium. Understanding microbial community composition and dynamics in these ultramafic soils may lead to a better understanding of the processes facilitating vegetation succession from shrubland to forest on these high-metal substrates, and of approaches to successful revegetation following mining for metals including nickel, chromium and cobalt. [source]


    Containment of Biogenic Sulfide Production in Continuous Up-Flow Packed-Bed Bioreactors with Nitrate or Nitrite

    BIOTECHNOLOGY PROGRESS, Issue 2 2003
    Casey Hubert
    Produced water from the Coleville oil field in Saskatchewan, Canada was used to inoculate continuous up-flow packed-bed bioreactors. When 7.8 mM sulfate and 25 mM lactate were present in the in-flowing medium, H2S production (souring) by sulfate-reducing bacteria (SRB) was prevented by addition of 17.5 mM nitrate or 20 mM nitrite. Changing the sulfate or lactate concentration of the in-flowing medium indicated that the concentrations of nitrate or nitrite required for containment of souring decreased proportionally with a lowered concentration of the electron donor lactate, while the sulfate concentration of the medium had no effect. Microbial communities were dominated by SRB. Nitrate addition did not give rise to changes in community composition, indicating that lactate oxidation and H2S removal were caused by the combined action of SRB and nitrate-reducing, sulfide-oxidizing bacteria (NR-SOB). Apparently the nitrite concentrations formed by these NR-SOB did not inhibit the SRB sufficiently to cause community shifts. In contrast, significant community shifts were observed upon direct addition of high concentrations (20 mM) of nitrite. Strains NO3A and NO2B, two newly isolated, nitrate-reducing bacteria (NRB) emerged as major community members. These were found to belong to the ,-division of the Proteobacteria, to be most closely related to Campylobacter lari, and to oxidize lactate with nitrate or nitrite as the electron acceptor. Thus the mechanism of microbial H2S removal in up-flow packed-bed bioreactors depended on whether nitrate (SRB/NR-SOB) or nitrite (SRB/NR-SOB as well as NRB) was used. However, the amount of nitrate or nitrite needed to completely remove H2S was dictated by the electron donor (lactate) concentration, irrespective of mechanism. [source]


    An integrative approach to understanding microbial diversity: from intracellular mechanisms to community structure

    ECOLOGY LETTERS, Issue 9 2010
    Ivana Gudelj
    Ecology Letters (2010) 13: 1073,1084 Abstract Trade-offs have been put forward as essential to the generation and maintenance of diversity. However, variation in trade-offs is often determined at the molecular level, outside the scope of conventional ecological inquiry. In this study, we propose that understanding the intracellular basis for trade-offs in microbial systems can aid in predicting and interpreting patterns of diversity. First, we show how laboratory experiments and mathematical models have unveiled the hidden intracellular mechanisms underlying trade-offs key to microbial diversity: (i) metabolic and regulatory trade-offs in bacteria and yeast; (ii) life-history trade-offs in bacterial viruses. Next, we examine recent studies of marine microbes that have taken steps toward reconciling the molecular and the ecological views of trade-offs, despite the challenges in doing so in natural settings. Finally, we suggest avenues for research where mathematical modelling, experiments and studies of natural microbial communities provide a unique opportunity to integrate studies of diversity across multiple scales. [source]


    Integrating physiological, ecological and evolutionary change: a Price equation approach

    ECOLOGY LETTERS, Issue 8 2009
    Sinad Collins
    Abstract We use a general quantitative framework , the Price equation , to partition phenotypic responses to environmental change into separate physiological, evolutionary and ecological components. We demonstrate how these responses, which potentially occur over different timescales and are usually studied in isolation, can be combined in an additive way; and we discuss the main advantages of doing this. We illustrate our approach using two worked examples, concerning the emergence of toxin resistance within microbial communities, and the estimation of carbon uptake by marine phytoplankton in high-CO2 environments. We find that this approach allows us to exclude particular mechanistic hypotheses with regard to community-level transformations, and to identify specific instances where appropriate data are lacking. Thus Price's equation provides not only a powerful conceptual aid, but also a means for testing hypotheses and for directing empirical research programmes. [source]


    Plant,soil feedbacks and invasive spread

    ECOLOGY LETTERS, Issue 9 2006
    Jonathan M. Levine
    Abstract Plant invaders have been suggested to change soil microbial communities and biogeochemical cycling in ways that can feedback to benefit themselves. In this paper, we ask when do these feedbacks influence the spread of exotic plants. Because answering this question is empirically challenging, we show how ecological theory on ,pushed' and ,pulled' invasions can be used to examine the problem. We incorporate soil feedbacks into annual plant invasion models, derive the conditions under which such feedbacks affect spread, and support our approach with simulations. We show that in homogeneous landscapes, strong positive feedbacks can influence spreading velocity for annual invaders, but that empirically documented feedbacks are not strong enough to do so. Moreover, to influence spread, invaders must modify the soil environment over a spatial scale larger than is biologically realistic. Though unimportant for annual invader spread in our models, feedbacks do affect invader density and potential impact. We discuss how future research might consider the way landscape structure, dispersal patterns, and the time scales over which plant,soil feedbacks develop regulate the effects of such feedbacks on invader spread. [source]


    Molecular evidence for widespread occurrence of Foraminifera in soils

    ENVIRONMENTAL MICROBIOLOGY, Issue 9 2010
    Franck Lejzerowicz
    Summary Environmental SSU rDNA-based surveys are contributing to the dramatic revision of eukaryotic high-level diversity and phylogeny as the number of sequence data increases. This ongoing revolution gives the opportunity to test for the presence of some eukaryotic taxa in environments where they have not been found using classical microscopic observations. Here, we test whether the foraminifera, a group of single-celled eukaryotes, considered generally as typical for the marine ecosystems are present in soil. We performed foraminiferal-specific nested PCR on 20 soil DNA samples collected in contrasted environments. Unexpectedly, we found that the majority of the samples contain foraminiferal SSU rDNA sequences. In total, we obtained 49 sequences from 17 localities. Phylogenetic analysis clusters them in four groups branching among the radiation of early foraminiferal lineages. Three of these groups also include sequences originated from previous freshwater surveys, suggesting that there were up to four independent colonization events of terrestrial and/or freshwater ecosystems by ancestral foraminifera. As shown by our data, foraminifera are a widespread and diverse component of soil microbial communities. Yet, identification of terrestrial foraminiferal species and understanding of their ecological role represent an exciting challenge for future research. [source]


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

    ENVIRONMENTAL MICROBIOLOGY, Issue 4 2010
    Stefanie Schellenberger
    Summary 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 13C-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). [13C]-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 [13C]-cellobiose and [13C]-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 cellulose degradation in aerated soils. [source]


    Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology

    ENVIRONMENTAL MICROBIOLOGY, Issue 4 2010
    Xavier Mayali
    Summary Heterotrophic bacteria and phytoplankton dominate the biomass and play major roles in the biogeochemical cycles of the surface ocean. Here, we designed and tested a fast, high-throughput and multiplexed hybridization-based assay to detect populations of marine heterotrophic bacteria and phytoplankton based on their small subunit ribosomal DNA sequences. The assay is based on established liquid bead array technology, an approach that is gaining acceptance in biomedical research but remains underutilized in ecology. End-labelled PCR products are hybridized to taxon-specific oligonucleotide probes attached to fluorescently coded beads followed by flow cytometric detection. We used ribosomal DNA environmental clone libraries (a total of 450 clones) and cultured isolates to design and test 26 bacterial and 10 eukaryotic probes specific to various ribotypes and genera of heterotrophic bacteria and eukaryotic phytoplankton. Pure environmental clones or cultures were used as controls and demonstrated specificity of the probes to their target taxa. The quantitative nature of the assay was demonstrated by a significant relationship between the number of target molecules and fluorescence signal. Clone library sequencing and bead array fluorescence from the same sample provided consistent results. We then applied the assay to a 37-day time series of coastal surface seawater samples from the Southern California Bight to examine the temporal dynamics of microbial communities on the scale of days to weeks. As expected, several bacterial phylotypes were positively correlated with total bacterial abundances and chlorophyll a concentrations, but others were negatively correlated. Bacterial taxa belonging to the same broad taxonomic groups did not necessarily correlate with one another, confirming recent results suggesting that inferring ecological role from broad taxonomic identity may not always be accurate. [source]


    Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased colonies

    ENVIRONMENTAL MICROBIOLOGY, Issue 2 2010
    Nikole E. Kimes
    Summary A functional gene array (FGA), GeoChip 2.0, was used to assess the biogeochemical cycling potential of microbial communities associated with healthy and Caribbean yellow band diseased (YBD) Montastraea faveolata. Over 6700 genes were detected, providing evidence that the coral microbiome contains a diverse community of archaea, bacteria and fungi capable of fulfilling numerous functional niches. These included carbon, nitrogen and sulfur cycling, metal homeostasis and resistance, and xenobiotic contaminant degradation. A significant difference in functional structure was found between healthy and YBD M. faveolata colonies and those differences were specific to the physical niche examined. In the surface mucopolysaccharide layer (SML), only two of 31 functional categories investigated, cellulose degradation and nitrification, revealed significant differences, implying a very specific change in microbial functional potential. Coral tissue slurry, on the other hand, revealed significant changes in 10 of the 31 categories, suggesting a more generalized shift in functional potential involving various aspects of nutrient cycling, metal transformations and contaminant degradation. This study is the first broad screening of functional genes in coral-associated microbial communities and provides insights regarding their biogeochemical cycling capacity in healthy and diseased states. [source]


    Antagonistic interactions among coral-associated bacteria

    ENVIRONMENTAL MICROBIOLOGY, Issue 1 2010
    Krystal L. Rypien
    Summary Reef-building corals are comprised of close associations between the coral animal, symbiotic zooxanthellae, and a diversity of associated microbes (including Bacteria, Archaea and Fungi). Together, these comprise the coral holobiont , a paradigm that emphasizes the potential contributions of each component to the overall function and health of the coral. Little is known about the ecology of the coral-associated microbial community and its hypothesized role in coral health. We explored bacteria,bacteria antagonism among 67 bacterial isolates from the scleractinian coral Montastrea annularis at two temperatures using Burkholder agar diffusion assays. A majority of isolates exhibited inhibitory activity (69.6% of isolates at 25C, 52.2% at 31C), with members of the ,-proteobacteria (Vibrionales and Alteromonadales) being especially antagonistic. Elevated temperatures generally reduced levels of antagonism, although the effects were complex. Several potential pathogens were observed in the microbial community of apparently healthy corals, and 11.6% of isolates were able to inhibit the growth of the coral pathogen Vibrio shiloi at 25C. Overall, this study demonstrates that antagonism could be a structuring force in coral-associated microbial communities and may contribute to pathogenesis as well as disease resistance. [source]


    GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer

    ENVIRONMENTAL MICROBIOLOGY, Issue 10 2009
    Joy D. Van Nostrand
    Summary A pilot-scale system was established for in situ biostimulation of U(VI) reduction by ethanol addition at the US Department of Energy's (DOE's) Field Research Center (Oak Ridge, TN). After achieving U(VI) reduction, stability of the bioreduced U(IV) was evaluated under conditions of (i) resting (no ethanol injection), (ii) reoxidation by introducing dissolved oxygen (DO), and (iii) reinjection of ethanol. GeoChip, a functional gene array with probes for N, S and C cycling, metal resistance and contaminant degradation genes, was used for monitoring groundwater microbial communities. High diversity of all major functional groups was observed during all experimental phases. The microbial community was extremely responsive to ethanol, showing a substantial change in community structure with increased gene number and diversity after ethanol injections resumed. While gene numbers showed considerable variations, the relative abundance (i.e. percentage of each gene category) of most gene groups changed little. During the reoxidation period, U(VI) increased, suggesting reoxidation of reduced U(IV). However, when introduction of DO was stopped, U(VI) reduction resumed and returned to pre-reoxidation levels. These findings suggest that the community in this system can be stimulated and that the ability to reduce U(VI) can be maintained by the addition of electron donors. This biostimulation approach may potentially offer an effective means for the bioremediation of U(VI)-contaminated sites. [source]


    Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield

    ENVIRONMENTAL MICROBIOLOGY, Issue 8 2009
    Laurence Duc
    Summary Functional microarrays are powerful tools that allow the parallel detection of multiple strains at the species level and therefore to rapidly obtain information on microbial communities in the environment. However, the design of suitable probes is prone to uncertainties, as it is based so far on in silico predictions including weighted mismatch number and Gibbs free-energy values. This study describes the experimental selection of probes targeting subsequences of the nifH gene to study the community structure of diazotrophic populations present in Damma glacier (Swiss Central Alps) forefield soils. Using the Geniom One in situ synthesis technology (Febit, Germany), 2727 in silico designed candidate probes were tested. A total of 946 specific probes were selected and validated. This probe set covered a large diversity of the NifH phylotypes (35 out of the 45) found in the forefield. Hybridization predictors were tested statistically. Gibbs free-energy value for probe-target binding gave the best prediction for hybridization efficiency, while the weighted mismatch number was not significantly associated to probe specificity. In this study, we demonstrate that extensive experimental tests of probe-hybridization behaviour against sequences present in the studied environment remain a prerequisite for meaningful probe selection. [source]


    Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

    ENVIRONMENTAL MICROBIOLOGY, Issue 5 2009
    Julie A. Huber
    Summary PCR-based surveys of microbial communities commonly use regions of the small-subunit ribosomal RNA (SSU rRNA) gene to determine taxonomic membership and estimate total diversity. Here we show that the length of the target amplicon has a significant effect on assessments of microbial richness and community membership. Using operational taxonomic unit (OTU)- and taxonomy-based tools, we compared the V6 hypervariable region of the bacterial SSU rRNA gene of three amplicon libraries of c. 100, 400 and 1000 base pairs (bp) from each of two hydrothermal vent fluid samples. We found that the smallest amplicon libraries contained more unique sequences, higher diversity estimates and a different community structure than the other two libraries from each sample. We hypothesize that a combination of polymerase dissociation, cloning bias and mispriming due to secondary structure accounts for the differences. While this relationship is not linear, it is clear that the smallest amplicon libraries contained more different types of sequences, and accordingly, more diverse members of the community. Because divergent and lower abundant taxa can be more readily detected with smaller amplicons, they may provide better assessments of total community diversity and taxonomic membership than longer amplicons in molecular studies of microbial communities. [source]


    Soil CO2 flux and photoautotrophic community composition in high-elevation, ,barren' soil

    ENVIRONMENTAL MICROBIOLOGY, Issue 3 2009
    Kristen R. Freeman
    Summary Soil-dominated ecosystems, with little or no plant cover (i.e. deserts, polar regions, high-elevation areas and zones of glacial retreat), are often described as ,barren', despite their potential to host photoautotrophic microbial communities. In high-elevation, subnival zone soil (i.e. elevations higher than the zone of continuous vegetation), the structure and function of these photoautotrophic microbial communities remains essentially unknown. We measured soil CO2 flux at three sites (above 3600 m) and used molecular techniques to determine the composition and distribution of soil photoautotrophs in the Colorado Front Range. Soil CO2 flux data from 2002 and 2007 indicate that light-driven CO2 uptake occurred on most dates. A diverse community of Cyanobacteria, Chloroflexi and eukaryotic algae was present in the top 2 cm of the soil, whereas these clades were nearly absent in deeper soils (2,4 cm). Cyanobacterial communities were composed of lineages most closely related to Microcoleus vaginatus and Phormidium murrayi, eukaryotic photoautotrophs were dominated by green algae, and three novel clades of Chloroflexi were also abundant in the surface soil. During the light hours of the 2007 snow-free measurement period, CO2 uptake was conservatively estimated to be 23.7 g C m,2 season,1. Our study reveals that photoautotrophic microbial communities play an important role in the biogeochemical cycling of subnival zone soil. [source]


    Development of a bacterial challenge test for gnotobiotic sea bass (Dicentrarchus labrax) larvae

    ENVIRONMENTAL MICROBIOLOGY, Issue 2 2009
    K. Dierckens
    Summary The use of probiotic microorganisms in aquaculture is gaining a lot of interest. Gnotobiotic model systems are required in order to fully understand the effects and modes-of-action of these microorganisms, as the native microbial communities present in non-sterile animals can lead to false conclusions. In this study, a gnotobiotic sea bass larvae (Dicentrarchus labrax) test system was developed. In order to obtain bacteria-free animals, the eggs were disinfected with glutaraldehyde and subsequently incubated in a solution of rifampicin and ampicillin. Axenity was confirmed using culture-dependent and -independent techniques. The gnotobiotic larvae were fed axenic Artemia sp. from 7 days after hatching onwards. In the challenge test, one of the three opportunistic pathogens, Aeromonas hydrophila, Listonella anguillarum serovar O1 and O2a, was added to the model system via the water and encapsulated in Artemia sp. Only serovar O2a led to increased mortality in the sea bass larvae. The presented gnotobiotic model can be used for research on, among others, reciprocal metabolic effects between microorganisms and the host (e.g. as measured by gene expression), immunostimulants, pharmacological research and the histological development of the gastrointestinal tract and growth of larvae. [source]


    Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Cinegas, Mexico

    ENVIRONMENTAL MICROBIOLOGY, Issue 1 2009
    Mya Breitbart
    Summary Ancient biologically mediated sedimentary carbonate deposits, including stromatolites and other microbialites, provide insight into environmental conditions on early Earth. The primary limitation to interpreting these records is our lack of understanding regarding microbial processes and the preservation of geochemical signatures in contemporary microbialite systems. Using a combination of metagenomic sequencing and isotopic analyses, this study describes the identity, metabolic potential and chemical processes of microbial communities from living microbialites from Cuatro Cinegas, Mexico. Metagenomic sequencing revealed a diverse, redox-dependent microbial community associated with the microbialites. The microbialite community is distinct from other marine and freshwater microbial communities, and demonstrates extensive environmental adaptation. The microbialite metagenomes contain a large number of genes involved in the production of exopolymeric substances and the formation of biofilms, creating a complex, spatially structured environment. In addition to the spatial complexity of the biofilm, microbial activity is tightly controlled by sensory and regulatory systems, which allow for coordination of autotrophic and heterotrophic processes. Isotopic measurements of the intracrystalline organic matter demonstrate the importance of heterotrophic respiration of photoautotrophic biomass in the precipitation of calcium carbonate. The genomic and stable isotopic data presented here significantly enhance our evolving knowledge of contemporary biomineralization processes, and are directly applicable to studies of ancient microbialites. [source]


    Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary

    ENVIRONMENTAL MICROBIOLOGY, Issue 11 2008
    Annika C. Mosier
    Summary Ammonia oxidation in marine and estuarine sediments plays a pivotal role in the cycling and removal of nitrogen. Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems. In this study, we examined the abundance and diversity of ammonia-oxidizing archaea (AOA) and betaproteobacteria (,-AOB) across physicochemical gradients in San Francisco Bay , the largest estuary on the west coast of the USA. In contrast to reports that AOA are far more abundant than ,-AOB in both terrestrial and marine systems, our quantitative PCR estimates indicated that ,-AOB amoA (encoding ammonia monooxygenase subunit A) copy numbers were greater than AOA amoA in most of the estuary. Ammonia-oxidizing archaea were only more pervasive than ,-AOB in the low-salinity region of the estuary. Both AOA and ,-AOB communities exhibited distinct spatial structure within the estuary. AOA amoA sequences from the north part of the estuary formed a large and distinct low-salinity phylogenetic group. The majority of the ,-AOB sequences were closely related to other marine/estuarine Nitrosomonas -like and Nitrosospira -like sequences. Both ammonia-oxidizer community composition and abundance were strongly correlated with salinity. Ammonia-oxidizing enrichment cultures contained AOA and ,-AOB amoA sequences with high similarity to environmental sequences. Overall, this study significantly enhances our understanding of estuarine ammonia-oxidizing microbial communities and highlights the environmental conditions and niches under which different AOA and ,-AOB phylotypes may thrive. [source]


    The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling

    ENVIRONMENTAL MICROBIOLOGY, Issue 11 2008
    Diana R. Nemergut
    Summary Many studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0,5 cm) samples from five control and five long-term N-amended plots established and maintained at the Niwot Ridge Long-term Ecological Research (LTER) site. Samples were bulked by treatment and all analyses were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N-amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N-amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G-lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function. [source]


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

    ENVIRONMENTAL MICROBIOLOGY, Issue 9 2008
    Allison K. Shaw
    Summary The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples. [source]


    Gradients of coastal fish farm effluents and their effect on coral reef microbes

    ENVIRONMENTAL MICROBIOLOGY, Issue 9 2008
    Melissa Garren
    Summary Coastal milkfish (Chanos chanos) farming may be a source of organic matter enrichment for coral reefs in Bolinao, Republic of the Philippines. Interactions among microbial communities associated with the water column, corals and milkfish feces can provide insight into the ecosystem's response to enrichment. Samples were collected at sites along a transect that extended from suspended milkfish pens into the coral reef. Water was characterized by steep gradients in the concentrations of dissolved organic carbon (70,160 ,M), total dissolved nitrogen (7,40 ,M), chlorophyll a (0.25,10 ,g l,1), particulate matter (106,832 ,g l,1), bacteria (5 105,1 106 cells ml,1) and viruses (1,7 107 ml,1) that correlated with distance from the fish cages. Particle-attached bacteria, which were observed by scanning laser confocal microscopy, increased across the gradient from < 0.1% to 5.6% of total bacteria at the fish pens. Analyses of 16S rRNA genes by denaturing gradient gel electrophoresis and environmental clone libraries revealed distinct microbial communities for each sample type. Coral libraries had the greatest number of phyla represented (range: 6,8) while fish feces contained the lowest number (3). Coral libraries also had the greatest number of ,novel' sequences (defined as < 93% similar to any sequence in the NCBI nt database; 29% compared with 3% and 5% in the feces and seawater libraries respectively). Despite the differences in microbial community composition, some 16S rRNA sequences co-occurred across sample types including Acinetobacter sp. and Ralstonia sp. Such patterns raise the question of whether bacteria might be transported from the fish pens to corals or if microenvironments at the fish pens and on the corals select for the same phylotypes. Understanding the underlying mechanisms of effluent,coral interactions will help predict the ability of coral reef ecosystems to resist and rebound from organic matter enrichment. [source]