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Sample records for assess microbial communities

  1. Using Artificial Neural Networks to Assess Changes in Microbial Communities

    SciTech Connect

    Brandt, C.C.; Macnaughton, S.; Palumbo, A.V.; Pfiffner, S.M.; Schryver, J.C.

    1999-04-19

    We evaluated artificial neural networks (ANNs) as a technique for assessing changes in soil microbial communities following exposure to metals. We analyzed signature lipid biomarker (SLB) data collected from two soil microcosm experiments using traditional statistical techniques and ANN. Two phases of data analysis were done; pattern recognition and prediction. In general, the ANNs were better able to detect patterns and relationships in the SLB data than were the traditional statistical techniques.

  2. Ecotoxicological assessment of soil microbial community tolerance to glyphosate.

    PubMed

    Allegrini, Marco; Zabaloy, María Celina; Gómez, Elena del V

    2015-11-15

    Glyphosate is the most used herbicide worldwide. While contrasting results have been observed related with its impact on soil microbial communities, more studies are necessary to elucidate the potential effects of the herbicide. Differences in tolerance detected by Pollution Induced Community Tolerance (PICT) approach could reflect these effects. The objective of the present study was to assess the tolerance to glyphosate (the active ingredient and a commercial formulation) of contrasting soils with (H) and without (NH) history of exposure. The hypothesis of a higher tolerance in H soils due to a sustained selection pressure on community structure was tested through the PICT approach. Results indicated that tolerance to glyphosate is not consistent with previous history of exposure to the herbicide either for the active ingredient or for a commercial formulation. Soils of H and NH sites were also characterized in order to determine to what extent they differ in their functional diversity and structure of microbial communities. Denaturant Gradient Gel Electrophoresis (DGGE) and Quantitative Real Time PCR (Q-PCR) indicated high similarity of Eubacteria profiles as well as no significant differences in abundance, respectively, between H and NH sites. Community level physiological profiling (CLPP) indicated some differences in respiration of specific sources but functional diversity was very similar as reflected by catabolic evenness (E). These results support PICT assay, which ideally requires soils with differences in their exposure to the contaminant but minor differences in other characteristics. This is, to our knowledge, the first report of PICT approach with glyphosate examining tolerance at soil microbial community level. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Assessing the impact of nanomaterials on anaerobic microbial communities.

    PubMed

    Nyberg, Leila; Turco, Ronald F; Nies, Loring

    2008-03-15

    As the technological benefits of nanotechnology begin to rapidly move from laboratory to large-scale industrial application, release of nanomaterials to the environment is inevitable. Little is known about the fate and effects of nanomaterials in nature. Major environmental receptors of nanomaterials will be soil, sediment, and biosolids from wastewater treatment. Analysis of anaerobic microbial activity and communities provides needed information about the effects of nanoparticles in certain environments. In this study, biosolids from anaerobic wastewater treatment sludge were exposed to fullerene (C60) in order to model an environmentally relevant discharge scenario. Activity was assessed by monitoring production of CO2 and CH4. Changes in community structure were monitored by denaturing gradient gel electrophoresis (DGGE), using primer sets targeting the small subunit rRNA genes of Bacteria, Archaea, and Eukarya. Findings suggest that C60 fullerenes have no significant effect on the anaerobic community over an exposure period of a few months. This conclusion is based on the absence of toxicity indicated by no change in methanogenesis relative to untreated reference samples. DGGE results show no evidence of substantial community shifts due to treatment with C60, in any subset of the microbial community.

  4. Using Artificial Neural Networks to Assess Microbial Communities

    SciTech Connect

    Almeida, J.S.; Brand, C.C.; Palumbo, A.V.; Pfiffner, S.M.; Schryver, J.C.

    1998-09-08

    We are evaluating artificial neural networks (ANNs) as tools for assessing changes in soil microbial communities following exposure to metals. We analyzed signature lipid biomarker data collected from two soil microcosm experiments using an autoassociative ANN. In one experiment, the microcosms were exposed to O, 100, or 250 ppm of metals, and in the other experiment the microcosms were exposed to O or 500 ppm of metals. The ANNs were able to distinguish between microcosms exposed and not exposed to metals in both experiments.

  5. Multilevel Samplers to Assess Microbial Community Response to Biostimulation

    NASA Astrophysics Data System (ADS)

    Baldwin, B. R.; McKinley, J. P.; Peacock, A. D.; Park, M.; Ogles, D.; Istok, J. D.; Resch, C. T.; White, D. C.

    2006-05-01

    Passive multilevel samplers (MLS) containing a solid matrix for microbial colonization were used in conjunction with a push-pull biostimulation experiment designed to promote biological U(VI) and Tc(VII) reduction. MLS were deployed at 24 elevations in the injection well and two down gradient wells to investigate the spatial variability in microbial community composition and growth prior to and following biostimulation. The microbial community was characterized by real-time PCR (Q-PCR) quantification of eubacteria, NO3- reducing bacteria (nirS and nirK), δ-proteobacteria, Geobacter sp., and methanogens (mcrA). Pretest cell densities were low overall but varied substantially with significantly greater eubacterial populations detected at circumneutral pH (T-test, α=0.05) suggesting carbon substrate and low pH limitation of microbial activity. Although pretest cell densities were low, denitrifying bacteria were dominant members of the microbial community. Biostimulation with an ethanol amended groundwater resulted in concurrent NO3- and Tc(VII) reduction followed by U(VI) reduction. Q-PCR analysis of MLS revealed significant (1-2 orders of magnitude, T-test, α=0.05) increases in cell densities of eubacteria, denitrifiers, δ- proteobacteria, Geobacter sp., and methanogens in response to biostimulation. Traditionally characterization of sediment samples has been used to investigate the microbial community response to biostimulation, however, collection of sediment samples is expensive and not conducive to deep aquifers or temporal studies. The results presented demonstrate that push-pull tests with passive MLS provide an inexpensive approach to determine the effect of biostimulation on contaminant concentrations, geochemical conditions, and the microbial community composition and function.

  6. Quantitative phylogenetic assessment of microbial communities indiverse environments

    SciTech Connect

    von Mering, C.; Hugenholtz, P.; Raes, J.; Tringe, S.G.; Doerks,T.; Jensen, L.J.; Ward, N.; Bork, P.

    2007-01-01

    The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.

  7. Assessing the Unseen Bacterial Diversity in Microbial Communities

    PubMed Central

    Caro-Quintero, Alejandro; Ochman, Howard

    2015-01-01

    For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria—individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach—termed phyloTAGs—that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations. PMID:26615218

  8. Pyrosequencing-based assessment of microbial community shifts in leachate from animal carcass burial lysimeter.

    PubMed

    Kim, Hyun Young; Seo, Jiyoung; Kim, Tae-Hun; Shim, Bomi; Cha, Seok Mun; Yu, Seungho

    2017-02-26

    This study examined the use of microbial community structure as a bio-indicator of decomposition levels. High-throughput pyrosequencing technology was used to assess the shift in microbial community of leachate from animal carcass lysimeter. The leachate samples were collected monthly for one year and a total of 164,639 pyrosequencing reads were obtained and used in the taxonomic classification and operational taxonomy units (OTUs) distribution analysis based on sequence similarity. Our results show considerable changes in the phylum-level bacterial composition, suggesting that the microbial community is a sensitive parameter affected by the burial environment. The phylum classification results showed that Proteobacteria (Pseudomonas) were the most influential taxa in earlier decomposition stage whereas Firmicutes (Clostridium, Sporanaerobacter, and Peptostreptococcus) were dominant in later stage under anaerobic conditions. The result of this study can provide useful information on a time series of leachate profiles of microbial community structures and suggest patterns of microbial diversity in livestock burial sites. In addition, this result can be applicable to predict the decomposition stages under clay loam based soil conditions of animal livestock.

  9. Why Microbial Communities?

    ScienceCinema

    Fredrickson, Jim (PNNL)

    2016-07-12

    The Microbial Communities Initiative is a 5-year investment by Pacific Northwest National Laboratory that integrates biological/ecological experimentation, analytical chemistry, and simulation modeling. The objective is to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities. Dr. Fredrickson introduces the symposium by defining microbial communities and describing their scientific relevance as they relate to solving problems in energy, climate, and sustainability.

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

    PubMed

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

    2015-10-01

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

  11. Assessing toxic levels of hydrocarbons on microbial degrader communities in vadose zone fill soils

    SciTech Connect

    Schoenberg, T.H.; Long, S.C.

    1995-12-31

    Authentic fill samples were collected from the vadose zone at a highway travel plaza. The contamination at the site is a combination of gasoline, diesel, and waste oil resulting from leaking underground storage tanks. Microbial assessments including plate counts and specific-degrader enumerations were performed to establish the presence of degrader microbial communities, and thus bioremediation potential. Contaminant levels were estimated in samples by quantifying headspace VOCs in collection jars. Physical soil characteristics including soil grain size distribution and moisture content were measured to evaluate the potential ecological variables that would affect implementation of a bioremediation technology. Toxicity screening using the Microtox{trademark} acute toxicity assay was used to compare the level of toxicity present among samples. These analyses were used to assess the potential for using in situ bioventing remediation to clean-up the leaking underground storage tank spill study site. High contaminant levels appear to have exerted a toxic effect and resulted in smaller total microbial community sizes in highly contaminated areas (thousands of ppmv) of the site. Microtox{trademark} EC50 results generally corroborated with the trends of the enumeration experiments. Microbial characterization results indicate that in situ bioremediation would be possible at the study site. Soil heterogeneity appears to pose the greatest challenges to the design and implementation of bioremediation at this site.

  12. Effects of vegetation type on soil microbial community structure and catabolic diversity assessed by polyphasic methods in North China.

    PubMed

    Han, Xue-mei; Wang, Ren-qing; Liu, Jian; Wang, Meng-cheng; Zhou, Juan; Guo, Wei-hua

    2007-01-01

    Soil microbes play a major role in ecological processes and are closely associated with the aboveground plant community. In order to understand the effects of vegetation type on the characteristics of soil microbial communities, the soil microbial communities were assessed by plate counts, phospholipid fatty acid (PLFA) and Biolog microplate techniques in five plant communities, i.e., soybean field (SF), artificial turf (AT), artificial shrub (AS), natural shrub (NS), and maize field (MF) in Jinan, Shandong Province, North China. The results showed that plant diversity had little discernible effect on microbial biomass but a positive impact on the evenness of utilized substrates in Biolog microplate. Legumes could significantly enhance the number of cultural microorganisms, microbial biomass, and community catabolic diversity. Except for SF dominated by legumes, the biomass of fungi and the catabolic diversity of microbial community were higher in less disturbed soil beneath NS than in frequently disturbed soils beneath the other vegetation types. These results confirmed that high number of plant species, legumes, and natural vegetation types tend to support soil microbial communities with higher function. The present study also found a significant correlation between the number of cultured bacteria and catabolic diversity of the bacterial community. Different research methods led to varied results in this study. The combination of several approaches is recommended for accurately describing the characteristics of microbial communities in many respects.

  13. Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants.

    PubMed

    Meerbergen, Ken; Van Geel, Maarten; Waud, Michael; Willems, Kris A; Dewil, Raf; Van Impe, Jan; Appels, Lise; Lievens, Bart

    2017-02-01

    It is assumed that microbial communities involved in the biological treatment of different wastewaters having a different chemical composition harbor different microbial populations which are specifically adapted to the environmental stresses encountered in these systems. Yet, little is known about the composition of these microbial communities. Therefore, the aim of this study was to assess the microbial community composition over two seasons (winter and summer) in activated sludge from well-operating textile wastewater treatment plants (WWTPs) in comparison with municipal WWTPs, and to explain observed differences by environmental variables. 454-pyrosequencing generated 160 archaeal and 1645 bacterial species-level Operational Taxonomic Units (OTUs), with lower observed richness in activated sludge from textile WWTPs compared to municipal WWTPs. The bacterial phyla Planctomycetes, Chloroflexi, Chlorobi, and Acidobacteria were more abundant in activated sludge samples from textile WWTPs, together with archaeal members of Thaumarchaeota. Nonmetric multidimensional scaling analysis of the microbial communities showed that microbial communities from textile and municipal WWTPs were significantly different, with a seasonal effect on archaea. Nitrifying and denitrifying bacteria as well as phosphate-accumulation bacteria were more abundant in municipal WWTPs, while sulfate-reducing bacteria were almost only detected in textile WWTPs. Additionally, microbial communities from textile WWTPs were more dissimilar than those of municipal WWTPs, possibly due to a wider diversity in environmental stresses to which microbial communities in textile WWTPs are subjected to. High salinity, high organic loads, and a higher water temperature were important potential variables driving the microbial community composition in textile WWTPs. This study provides a general view on the composition of microbial communities in activated sludge of textile WWTPs, and may provide novel insights

  14. Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

    NASA Astrophysics Data System (ADS)

    Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

    2015-04-01

    Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5

  15. In-Drift Microbial Communities

    SciTech Connect

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  16. Analysis of Structural and Physiological Profiles To Assess the Effects of Cu on Biofilm Microbial Communities

    PubMed Central

    Massieux, B.; Boivin, M. E. Y.; van den Ende, F. P.; Langenskiöld, J.; Marvan, P.; Barranguet, C.; Admiraal, W.; Laanbroek, H. J.; Zwart, G.

    2004-01-01

    We investigated the effects of copper on the structure and physiology of freshwater biofilm microbial communities. For this purpose, biofilms that were grown during 4 weeks in a shallow, slightly polluted ditch were exposed, in aquaria in our laboratory, to a range of copper concentrations (0, 1, 3, and 10 μM). Denaturing gradient gel electrophoresis (DGGE) revealed changes in the bacterial community in all aquaria. The extent of change was related to the concentration of copper applied, indicating that copper directly or indirectly caused the effects. Concomitantly with these changes in structure, changes in the metabolic potential of the heterotrophic bacterial community were apparent from changes in substrate use profiles as assessed on Biolog plates. The structure of the phototrophic community also changed during the experiment, as observed by microscopic analysis in combination with DGGE analysis of eukaryotic microorganisms and cyanobacteria. However, the extent of community change, as observed by DGGE, was not significantly greater in the copper treatments than in the control. Yet microscopic analysis showed a development toward a greater proportion of cyanobacteria in the treatments with the highest copper concentrations. Furthermore, copper did affect the physiology of the phototrophic community, as evidenced by the fact that a decrease in photosynthetic capacity was detected in the treatment with the highest copper concentration. Therefore, we conclude that copper affected the physiology of the biofilm and had an effect on the structure of the communities composing this biofilm. PMID:15294780

  17. Mathematical modeling as a tool to assess microbial community responses to CO2 injection

    NASA Astrophysics Data System (ADS)

    Vilcaez, J.

    2014-12-01

    The issue of subsurface microbial community responses to the injection of CO2 has great importance not only from a risk assessment point of view but also from the perspective of CO2 recycling to CH4. In this sense, the objective of this study is to develop mathematical models to make a quantitative description of the responses of subsurface indigenous microbial communities to the injection of CO2. For this end, TOUGHREACTV1.2 reactive transport simulator with its module ECO2N is used as the modeling framework. The targeted microbial community is composed of fermentative bacteria (Organic matter → Acetate & H2), acetotrophic methanogens (Acetate → Methane & CO2), acetotrophic Sulfate Reducing Bacteria (SRB) (Acetate → H2S & CO2), hydrogenotrophic methanogens (H2 & CO2 → CH4), and hydrogenotrophic SRB (H2 → H2S). Due to the multiple hydrogeological, geochemical and microbiological factors intervening in both the response of subsurface microbial communities to the injection of CO2 and the chemical and physical fate of CO2 itself, at this stage simulations have been performed in batch mode. That means numerical simulations aimed to track changes in CO2 saturation levels, pH, and concentrations of mineral and aqueous phase species over time at selected initial conditions. Numerical simulation results indicate that the activity of microbes associated with methanogenic processes in geological storage sites of CO2 is governed by the level of CO2 saturation in the pore space as well as by the presence of pH buffering minerals such as calcite. With calcite in the mineral phase attenuating drops in pH below inhibitory levels, for instance it is shown that acetotrophic and hydrogenotrophic SRB outcompete acetotrophic and hydrogenotrophic methanogens for acetate and H2, respectively. During the initial stages of the reaction when the pH level is lowest, the higher tolerance of hydrogenotrophic methanogens to acidic pH levels is reflected by a preferential formation of

  18. GC fractionation enhances microbial community diversity assessment and detection of minority populations of bacteria by denaturing gradient gel electrophoresis.

    PubMed

    Holben, William E; Feris, Kevin P; Kettunen, Anu; Apajalahti, Juha H A

    2004-04-01

    Effectively and accurately assessing total microbial community diversity is one of the primary challenges in modern microbial ecology. This is particularly true with regard to the detection and characterization of unculturable populations and those present only in low abundance. We report a novel strategy, GC fractionation combined with denaturing gradient gel electrophoresis (GC-DGGE), which combines mechanistically different community analysis approaches to enhance assessment of microbial community diversity and detection of minority populations of microbes. This approach employs GC fractionation as an initial step to reduce the complexity of the community in each fraction. This reduced complexity facilitates subsequent detection of diversity in individual fractions. DGGE analysis of individual fractions revealed bands that were undetected or only poorly represented when total bacterial community DNA was analyzed. Also, directed cloning and sequencing of individual bands from DGGE lanes corresponding to individual G+C fractions allowed detection of numerous phylotypes that were not recovered using a traditional random cloning and sequencing approach.

  19. Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.

    PubMed

    Tapio, Ilma; Shingfield, Kevin J; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J; Wallace, R John

    2016-01-01

    Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.

  20. Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community

    PubMed Central

    Tapio, Ilma; Shingfield, Kevin J.; McKain, Nest; Bonin, Aurélie; Fischer, Daniel; Bayat, Ali R.; Vilkki, Johanna; Taberlet, Pierre; Snelling, Timothy J.; Wallace, R. John

    2016-01-01

    Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non-invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint. PMID:26986467

  1. Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms

    USDA-ARS?s Scientific Manuscript database

    Organic farming is a growing field of agriculture that is benign on the environment but there are contradictory reports about the impact of these practices on the soil microbial community, i.e. some studies showed higher microbial diversity in organic farms but others showed no differences in divers...

  2. Temporal and spatial assessment of microbial communities in commercial silages from bunker silos.

    PubMed

    Kraut-Cohen, J; Tripathi, V; Chen, Y; Gatica, J; Volchinski, V; Sela, S; Weinberg, Z; Cytryn, E

    2016-08-01

    Ensiling is a feed preservation method of moist forage crops that generally depends on naturally developing lactic acid bacteria to convert water-soluble carbohydrates into organic acids. While bacterial community dynamics have been previously assessed in bench-scale and pilot ensiling facilities, almost no studies have assessed the microbiomes of large-scale silage facilities. This study analyzed bacterial community composition in mature silage from bunker silos in three commercial production centers as related to pH, organic matter, volatile fatty acid composition, and spatial distribution within the ensiling bunker. It revealed significant physicochemical differences between "preserved" regions situated in the center and along the walls of the silage bunkers that were characterized by high concentrations of lactic acid and other volatiles and pH values below 5, and "spoiled" regions in the corners (shoulders) of the bunkers that had low lactic acid concentrations and high pH values. Preserved silage was dominated (>90 %) by lactic acid bacteria and characterized by high similarity and low taxonomic diversity, whereas spoiled silage had highly diverse microbiomes with low abundances of lactic acid bacteria (<5 %) that were sometimes characterized by high levels of Enterobacteriaceae. Spatial position had a much stronger impact on the microbial community composition than feedstock type, sampling date, or production center location supporting previous studies demonstrating that ecology and not geography is a major driver of environmental microbiomes.

  3. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    EPA Science Inventory

    Devereux, Richard. 2005. Seagrass Rhizosphere Microbial Communities. In: Interactions Between Macro- and Microorganisms in Marine Sediments. E. Kristense, J.E. Kostka and R.H. Haese, Editors. American Geophysical Union, Washington, DC. p199-216. (ERL,GB 1213).

    Seagrasses ...

  4. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    EPA Science Inventory

    Devereux, Richard. 2005. Seagrass Rhizosphere Microbial Communities. In: Interactions Between Macro- and Microorganisms in Marine Sediments. E. Kristense, J.E. Kostka and R.H. Haese, Editors. American Geophysical Union, Washington, DC. p199-216. (ERL,GB 1213).

    Seagrasses ...

  5. Composition of Microbial Communities in Blount Springs, Alabama and Assessment of their Chemolithotrophic Capabilities

    NASA Astrophysics Data System (ADS)

    Morrissey, T.; Aharon, P.; Olson, J.

    2010-12-01

    Microbial assemblages consisting of chemolithotrophic organisms are found in extreme environments and provide clues as to how life forms survived the harsh conditions of early Earth. Diverse microbial communities were observed in a sulfur spring in Blount Springs, Blount Co., Alabama. DNA was extracted from microbial samples and amplified by polymerase chain reaction. Terminal restriction fragment length polymorphism community analysis was performed to determine the diversity of bacterial and fungal communities in the sulfur spring. Cation and anion concentrations within the spring water were also evaluated to determine the potential chemolithotrophic capabilities of the resident microbes. Carbon, hydrogen, and oxygen isotopes were evaluated to determine the carbon flow and the source of the water in the streams.

  6. Effects of pig manure containing copper and zinc on microbial community assessed via phospholipids in soils.

    PubMed

    Zhang, Yan; Luo, Wei; Jia, Junmei; Kong, Peiru; Tong, Xiaojuan; Lu, Yonglong; Xie, Liqiong; Ma, Fulong; Giesy, John P

    2014-08-01

    Pig manure (PM) is widely used as an organic fertilizer to increase yields of crops. Excessive application of compost containing relatively great concentrations of copper (Cu) and zinc (Zn) can change soil quality. To clarify the effects of different rates of application and to determine the optimal rate of fertilization, PM containing 1,115 mg Cu kg(-1), dry mass (dm) and 1,497 mg Zn kg(-1), dm was applied to alkaline soil at rates of 0, 11, 22, 44, 88, and 222 g PM kg(-1), dm. Phospholipid fatty acids (PLFAs) were used to assess soil microbial community composition. Application of PM resulted in greater concentrations of total nitrogen (TN), NH4 (+)-N, NO3 (-)-N, total carbon (TC), soil organic matter (SOM) but lesser pH values. Soils with application rates of 88-222 g PM kg(-1), dm had concentrations of total and EDTA-extractable Cu and Zn significantly greater than those in soil without PM, and concentrations of T-Cu and T-Zn in these amended soils exceeded maximum limits set by standards in china. Except in the soil with a rate of 11 g PM kg(-1), dm, total bacterial and fungal PLFAs were directly proportional to rate of application of PM. Biomasses of bacteria and fungi were significantly greater in soils with application rates of 44-222 g PM kg(-1), dm than in the soil without PM. SOM, TC and EDTA-Zn had the most direct influence on soil microbial communities. To improve fertility of soils and maintain quality of soil, rate of application should be 22-44 g PM kg(-1) dm, soil containing Cu and Zn.

  7. Kinetic modelling and microbial community assessment of anaerobic biphasic fixed film bioreactor treating distillery spent wash.

    PubMed

    Acharya, Bhavik K; Pathak, Hilor; Mohana, Sarayu; Shouche, Yogesh; Singh, Vasdev; Madamwar, Datta

    2011-08-01

    Anaerobic digestion, microbial community structure and kinetics were studied in a biphasic continuously fed, upflow anaerobic fixed film reactor treating high strength distillery wastewater. Treatment efficiency of the bioreactor was investigated at different hydraulic retention times (HRT) and organic loading rates (OLR 5-20 kg COD m⁻³ d⁻¹). Applying the modified Stover-Kincannon model to the reactor, the maximum removal rate constant (U(max)) and saturation value constant (K(B)) were found to be 2 kg m⁻³ d⁻¹ and 1.69 kg m⁻³ d⁻¹ respectively. Bacterial community structures of acidogenic and methanogenic reactors were assessed using culture-independent analyses. Sequencing of 16S rRNA genes exhibited a total of 123 distinct operational taxonomic units (OTUs) comprising 49 from acidogenic reactor and 74 (28 of eubacteria and 46 of archaea) from methanogenic reactor. The findings reveal the role of Lactobacillus sp. (Firmicutes) as dominant acid producing organisms in acidogenic reactor and Methanoculleus sp. (Euryarchaeotes) as foremost methanogens in methanogenic reactor.

  8. Temporal assessment of microbial communities in soils of two contrasting mangroves.

    PubMed

    Rigonato, Janaina; Kent, Angela D; Gumiere, Thiago; Branco, Luiz Henrique Zanini; Andreote, Fernando Dini; Fiore, Marli Fátima

    2017-08-01

    Variations in microbial communities promoted by alterations in environmental conditions are reflected in similarities/differences both at taxonomic and functional levels. Here we used a natural gradient within mangroves from seashore to upland, to contrast the natural variability in bacteria, cyanobacteria and diazotroph assemblages in a pristine area compared to an oil polluted area along a timespan of three years, based on ARISA (bacteria and cyanobacteria) and nifH T-RFLP (diazotrophs) fingerprinting. The data presented herein indicated that changes in all the communities evaluated were mainly driven by the temporal effect in the contaminated area, while local effects were dominant on the pristine mangrove. A positive correlation of community structure between diazotrophs and cyanobacteria was observed, suggesting the functional importance of this phylum as nitrogen fixers in mangroves soils. Different ecological patterns explained the microbial behavior in the pristine and polluted mangroves. Stochastic models in the pristine mangrove indicate that there is not a specific environmental factor that determines the bacterial distribution, while cyanobacteria and diazotrophs better fitted in deterministic model in the same area. For the contaminated mangrove site, deterministic models better represented the variations in the communities, suggesting that the presence of oil might change the microbial ecological structures over time. Mangroves represent a unique environment threatened by global change, and this study contributed to the knowledge of the microbial distribution in such areas and its response on persistent contamination historic events. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  9. Assessing the dynamic of microbial communities during leaf decomposition in a low-order stream by microscopic and molecular techniques.

    PubMed

    Duarte, Sofia; Pascoal, Cláudia; Alves, Artur; Correia, António; Cássio, Fernanda

    2010-07-20

    Although a number of studies have indicated that microbes are key players in nutrient cycling, limitations on how to accurately assess their diversity have constrained further knowledge on the role of microbial diversity in organic matter decomposition in streams. Microbial diversity on leaf litter of Alnus glutinosa was assessed by microscopic analysis of bacterial cells and released fungal conidia, and by the number of operational taxonomic units (OTUs) from denaturing gradient gel electrophoresis using two different primer pairs targeting the rDNA of fungi (ITS2 and 5' end of the 18S region) and bacteria (V3 region and V6-V8 regions). Fingerprints of fungal and bacterial DNA showed a higher diverse microbial community on decomposing leaves than that assessed by microscopy-based techniques. Higher number of OTUs was obtained with primers targeting the ITS2 region of fungi, but the selected primers for bacteria showed similar number of OTUs. A succession of fungal or bacterial taxa throughout leaf decomposition was found, regardless of the chosen primer. These microbial communities ensured a rapid decomposition of submerged leaf litter (k=-0.045 day(-1)). Fungal biomass (up to 58 mg g(-1) AFDM) contributed with more than 98% to the total microbial biomass, supporting a greater role of fungi than bacteria in leaf-litter decomposition in streams. Copyright 2009 Elsevier GmbH. All rights reserved.

  10. Continuous fungal treatment of non-sterile veterinary hospital effluent: pharmaceuticals removal and microbial community assessment.

    PubMed

    Badia-Fabregat, Marina; Lucas, Daniel; Pereira, Maria Alcina; Alves, Madalena; Pennanen, Taina; Fritze, Hannu; Rodríguez-Mozaz, Sara; Barceló, Damià; Vicent, Teresa; Caminal, Glòria

    2016-03-01

    Source point treatment of effluents with a high load of pharmaceutical active compounds (PhACs), such as hospital wastewater, is a matter of discussion among the scientific community. Fungal treatments have been reported to be successful in degrading this type of pollutants and, therefore, the white-rot fungus Trametes versicolor was applied for the removal of PhACs from veterinary hospital wastewater. Sixty-six percent removal was achieved in a non-sterile batch bioreactor inoculated with T. versicolor pellets. On the other hand, the study of microbial communities by means of DGGE and phylogenetic analyses led us to identify some microbial interactions and helped us moving to a continuous process. PhAC removal efficiency achieved in the fungal treatment operated in non-sterile continuous mode was 44 % after adjusting the C/N ratio with respect to the previously calculated one for sterile treatments. Fungal and bacterial communities in the continuous bioreactors were monitored as well.

  11. Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

    PubMed

    Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

    2014-01-01

    The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent

  12. Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

    PubMed Central

    Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

    2014-01-01

    The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent

  13. First Microbial Community Assessment of Borehole Fluids from the Deep Underground Science and Engineering Laboratory (DUSEL)

    NASA Astrophysics Data System (ADS)

    Moser, D. P.; Anderson, C.; Bang, S.; Jones, T. L.; Boutt, D.; Kieft, T.; Sherwood Lollar, B.; Murdoch, L. C.; Pfiffner, S. M.; Bruckner, J.; Fisher, J. C.; Newburn, J.; Wheatley, A.; Onstott, T. C.

    2010-12-01

    Fluid and gas samples were collected from two flowing boreholes at the 4100 (1,250 m) and 4850 ft (1478 m) levels of the former Homestake Gold Mine in Lead, South Dakota. Service- and flood water samples were also collected as comparative benchmarks. With a maximum depth of 8,000 ft, (2,438 m), this mine currently hosts the Sanford Laboratory and is the proposed location for the US Deep Underground Science and Engineering Laboratory (DUSEL). The uncased 4100L hole is a legacy of mining; whereas, the cased 4850 hole was drilled in 2009 in support of large cavity construction. Both were packered or valved to exclude mine air and sampled anaerobically using aseptic technique. Physical measurements, aquatic and dissolved gas chemistry, cell counts, and microbial community assessments (SSU rRNA libraries) were performed on all samples. This study represents the first at Sanford Lab/DUSEL specifically focused on the deep biosphere rather than mine microbiology. Fluids from the two holes differed markedly, with that from 4100L being characterized by NaHCO3 and 4850 by Na2SO4. pH values of 8.2 vs. 7.5, conductivities (μS) of 1790 vs. 7667 and alkalinities (mg/L) of 767 vs. 187 were obtained from 4100L and 4850, respectively. As expected, the deeper 4850L hole had the higher temperature (38 vs. 30 oC). Neither had measureable nitrate, but both had similar dissolved organic C (DOC) concentrations (0.8 vs. 0.9 mg/L). Sulfate was present at 337 vs. 4,470 mg/L in 4100L and 4850L. Major dissolved gases were N2 (91 and 81 vol%), O2 (12 and 16 vol%) and CH4 (0.07 and 3.35 vol%) in 4100L and 4850L. The δ13C of CH4 was -51 and -56.7 permil in 4100L and 4850, respectively. The uncorrected 14C age of DIC was calculated at 25,310 (+/- 220) and 47,700 (+/-3,100) years for the two fluids. Cell counts were 5.9e3 and 2.01e5 in 4100L and 4850. Microbial community structure was diverse in both holes and distinct from that of service water. A large proportion of rRNA library clones were

  14. Assessing microbial communities for a metabolic profile similar to activated sludge.

    PubMed

    Paixão, S M; Sàágua, M C; Tenreiro, R; Anselmo, A M

    2007-05-01

    To search for reliable testing inocula alternatives to activated sludge cultures, several model microbial consortia were compared with activated sludge populations for their functional diversity. The evaluation of the metabolic potential of these mixed inocula was performed using the Biolog EcoPlates and GN and GP MicroPlates (Biolog, Inc., Hayward, California). The community-level physiological profiles (CLPPs) obtained for model communities and activated sludge samples were analyzed by principal component analysis and hierarchic clustering methods, to evaluate the ability of Biolog plates to distinguish among the different microbial communities. The effect of different inocula preparation methodologies on the community structure was also studied. The CLPPs obtained with EcoPlates and GN MicroPlates showed that EcoPlates are suitable to screen communities with a metabolic profile similar to activated sludge. New, well-defined, standardized, and safe inocula presenting the same metabolic community profile as activated sludge were selected and can be tested as surrogate cultures in activated-sludge-based bioassays.

  15. Quantitative assessment of in situ microbial communities affecting nuclear waste disposal

    SciTech Connect

    White, D.C. |

    1996-05-01

    Microbes in the environments surrounding nuclear waste depositories pose several questions regarding the protection of the surrounding communities. microbes can facilitate microbially influenced corrosion (MIC), mobilize and facilitate the transport of nuclides as well as produce gaseous emissions which can compromise containment. We have developed an analysis of the extant microbiota that is independent of quantitative recovery and subsequent growth, based on signature biomarkers analysis (SBA).

  16. Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

    SciTech Connect

    Elias, Dwayne; Schadt, Christopher; Miller, Lance; Phelps, Tommy; Brown, S. D.; Arkin, Adam; Hazen, Terry; Drake, Megin; Yang, Z.K.; Podar, Mircea

    2010-05-17

    One of the largest experimental gaps is between the simplicity of pure cultures and the complexity of open environmental systems, particularly in metal-contaminated areas. These microbial communities form ecosystem foundations, drive biogeochemical processes, and are relevant for biotechnology and bioremediation. A model, metal-reducing microbial community was constructed as either syntrophic or competitive to study microbial cell to cell interactions, cell signaling and competition for resources. The microbial community was comprised of the metal-reducing Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens PCA. Additionally, Methanococcus maripaludis S2 was added to study complete carbon reduction and maintain a low hydrogen partial pressure for syntrophism to occur. Further, considerable work has been published on D. vulgaris and the D. vulgaris/ Mc. maripaludis co-culture both with and without stress. We are extending this work by conducting the same stress conditions on the model community. Additionally, this comprehensive investigation includes physiological and metabolic analyses as well as specially designed mRNA microarrays with the genes for all three organisms on one slide so as to follow gene expression changes in the various cultivation conditions as well as being comparable to the co- and individual cultures. Further, state-of -the-art comprehensive AMT tag proteomics allows for these comparisons at the protein level for a systems biology assessment of a model, metal-reducing microbial community. Preliminary data revealed that lactate oxidation by D. vulgaris was sufficient to support both G. sulfurreducens and M. maripaludis via the excretion of H2 and acetate. Fumarate was utilized by G. sulfurreducens and reduced to succinate since neither of the other two organisms can reduce fumarate. Methane was quantified, suggesting acetate and H2 concentrations were sufficient for M. maripaludis. Steady state community cultivation will allow for

  17. Assessing the bias linked to DNA recovery from biofiltration woodchips for microbial community investigation by fingerprinting.

    PubMed

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2010-01-01

    In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.

  18. Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities.

    PubMed

    Lamendella, Regina; Strutt, Steven; Borglin, Sharon; Chakraborty, Romy; Tas, Neslihan; Mason, Olivia U; Hultman, Jenni; Prestat, Emmanuel; Hazen, Terry C; Jansson, Janet K

    2014-01-01

    One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria) had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252) well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil.

  19. Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

    PubMed Central

    Lamendella, Regina; Strutt, Steven; Borglin, Sharon; Chakraborty, Romy; Tas, Neslihan; Mason, Olivia U.; Hultman, Jenni; Prestat, Emmanuel; Hazen, Terry C.; Jansson, Janet K.

    2014-01-01

    One of the major environmental concerns of the Deepwater Horizon oil spill in the Gulf of Mexico was the ecological impact of the oil that reached shorelines of the Gulf Coast. Here we investigated the impact of the oil on the microbial composition in beach samples collected in June 2010 along a heavily impacted shoreline near Grand Isle, Louisiana. Successional changes in the microbial community structure due to the oil contamination were determined by deep sequencing of 16S rRNA genes. Metatranscriptomics was used to determine expression of functional genes involved in hydrocarbon degradation processes. In addition, potential hydrocarbon-degrading Bacteria were obtained in culture. The 16S data revealed that highly contaminated samples had higher abundances of Alpha- and Gammaproteobacteria sequences. Successional changes in these classes were observed over time, during which the oil was partially degraded. The metatranscriptome data revealed that PAH, n-alkane, and toluene degradation genes were expressed in the contaminated samples, with high homology to genes from Alteromonadales, Rhodobacterales, and Pseudomonales. Notably, Marinobacter (Gammaproteobacteria) had the highest representation of expressed genes in the samples. A Marinobacter isolated from this beach was shown to have potential for transformation of hydrocarbons in incubation experiments with oil obtained from the Mississippi Canyon Block 252 (MC252) well; collected during the Deepwater Horizon spill. The combined data revealed a response of the beach microbial community to oil contaminants, including prevalence of Bacteria endowed with the functional capacity to degrade oil. PMID:24772107

  20. Evaluation of the ISO standard 11063 DNA extraction procedure for assessing soil microbial abundance and community structure.

    PubMed

    Plassart, Pierre; Terrat, Sébastien; Thomson, Bruce; Griffiths, Robert; Dequiedt, Samuel; Lelievre, Mélanie; Regnier, Tiffanie; Nowak, Virginie; Bailey, Mark; Lemanceau, Philippe; Bispo, Antonio; Chabbi, Abad; Maron, Pierre-Alain; Mougel, Christophe; Ranjard, Lionel

    2012-01-01

    Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.

  1. Evaluation of the ISO Standard 11063 DNA Extraction Procedure for Assessing Soil Microbial Abundance and Community Structure

    PubMed Central

    Griffiths, Robert; Dequiedt, Samuel; Lelievre, Mélanie; Regnier, Tiffanie; Nowak, Virginie; Bailey, Mark; Lemanceau, Philippe; Bispo, Antonio; Chabbi, Abad; Maron, Pierre-Alain; Mougel, Christophe; Ranjard, Lionel

    2012-01-01

    Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities. PMID:22984486

  2. Biodiversity of Soil Microbial Communities Following Woody Plant Invasion of Grassland: An Assessment Using Molecular Methods

    NASA Astrophysics Data System (ADS)

    Kantola, I. B.; Gentry, T. J.; Filley, T. R.; Boutton, T. W.

    2012-12-01

    Woody plants have encroached into grasslands, savannas, and other grass-dominated ecosystems throughout the world during the last century. This dramatic vegetation change is likely driven by livestock grazing, altered fire frequencies, elevated atmospheric CO2 concentrations, and/or changes in atmospheric deposition patterns. Woody invasion often results in significant changes in ecosystem function, including alterations in above- and belowground primary productivity, soil C, N, and P storage and turnover, and the size and activity of the soil microbial biomass pool. The purpose of this study was to examine the relationships and interactions between plant communities and soil microbial communities in the Rio Grande Plains region of southern Texas where grasslands have been largely replaced by woodlands. Research was conducted along a successional chronosequence representing the stages of woody plant encroachment from open grassland to closed-canopy woodland. To characterize soil microbial community composition, soil samples (0-7.5 cm) were collected in remnant grasslands (representing time 0) and near the centers of woody plant clusters, groves, and drainage woodlands ranging in age from 10 to 130 yrs. Ages of woody plant stands were determined by dendrochronology. Community DNA was extracted from each soil sample with a MoBio PowerMax Soil DNA isolation kit. The DNA concentrations were quantified on a NanoDrop ND-1000 spectrophotometer and diluted to a standard concentration. Pyrosequencing was performed by the Research and Testing Laboratory (Lubbock, TX) according to Roche 454 Titanium chemistry protocols. Samples were amplified with primers 27F and 519R for bacteria, and primers ITS1F and ITS4 for fungi. Sequences were aligned using BioEdit and the RDP Pipeline and analyzed in MOTHUR. Non-metric multidimensional scaling of the operational taxonomic units identified by pyrosequencing revealed that both bacterial and fungal community composition were

  3. A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

    PubMed Central

    Schloss, Patrick D; Handelsman, Jo

    2008-01-01

    Background The 99% of bacteria in the environment that are recalcitrant to culturing have spurred the development of metagenomics, a culture-independent approach to sample and characterize microbial genomes. Massive datasets of metagenomic sequences have been accumulated, but analysis of these sequences has focused primarily on the descriptive comparison of the relative abundance of proteins that belong to specific functional categories. More robust statistical methods are needed to make inferences from metagenomic data. In this study, we developed and applied a suite of tools to describe and compare the richness, membership, and structure of microbial communities using peptide fragment sequences extracted from metagenomic sequence data. Results Application of these tools to acid mine drainage, soil, and whale fall metagenomic sequence collections revealed groups of peptide fragments with a relatively high abundance and no known function. When combined with analysis of 16S rRNA gene fragments from the same communities these tools enabled us to demonstrate that although there was no overlap in the types of 16S rRNA gene sequence observed, there was a core collection of operational protein families that was shared among the three environments. Conclusion The results of comparisons between the three habitats were surprising considering the relatively low overlap of membership and the distinctively different characteristics of the three habitats. These tools will facilitate the use of metagenomics to pursue statistically sound genome-based ecological analyses. PMID:18215273

  4. Method for Assessing Heterogeneity in Turnover Rates within Microbial Communities

    PubMed Central

    Laws, Edward A.; Jones, David; Karl, David M.

    1986-01-01

    A method is presented for determining both the average turnover rate and the standard deviation of the average turnover rate of the adenine nucleotide (AN) pool within a population of microorganisms. The method requires the calculation of the initial slope and curvature of a plot of AN specific activity versus time following the introduction of [3H]adenine. An analysis of noise-corrupted data indicated that the method is capable of detecting a lack of uniformity in the turnover rate when the coefficient of variation of the turnover rate exceeds 39%. An analysis of field data revealed a significant lack of uniformity in the turnover rates of microbial communities in a marine sediment sample and freshwater pond but no significant nonuniformity in the turnover rates of microbial communities in a seawater sample and in a second freshwater pond. Although the method has been applied only to the analysis of AN turnover rates, it is applicable to any intracellular pool for which a suitable radioactive precursor exists. PMID:16347178

  5. Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria.

    PubMed

    van de Water, Jeroen A J M; Melkonian, Rémy; Voolstra, Christian R; Junca, Howard; Beraud, Eric; Allemand, Denis; Ferrier-Pagès, Christine

    2017-02-01

    Gorgonians are key habitat-forming species of Mediterranean benthic communities, but their populations have suffered from mass mortality events linked to high summer seawater temperatures and microbial disease. However, our knowledge on the diversity, dynamics and function of gorgonian-associated microbial communities is limited. Here, we analysed the spatial variability of the microbiomes of five sympatric gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa, Leptogorgia sarmentosa and Paramuricea clavata), collected from the Mediterranean Sea over a scale of ∼1100 km, using next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all gorgonian species were generally dominated by members of the genus Endozoicomonas, which were at very low abundance in the surrounding seawater. Although the composition of the core microbiome (operational taxonomic units consistently present in a species) was found to be unique for each host species, significant overlap was observed. These spatially consistent associations between gorgonians and their core bacteria suggest intricate symbiotic relationships and regulation of the microbiome composition by the host. At the same time, local variations in microbiome composition were observed. Functional predictive profiling indicated that these differences could be attributed to seawater pollution. Taken together, our data indicate that gorgonian-associated microbiomes are composed of spatially conserved bacteria (core microbiome members) and locally variant members, and that local pollution may influence these local associations, potentially impacting gorgonian health.

  6. Performance Assessment of Full-Scale Wastewater Treatment Plants Based on Seasonal Variability of Microbial Communities via High-Throughput Sequencing

    PubMed Central

    Liu, Tang; Liu, Shufeng; Zheng, Maosheng; Chen, Qian; Ni, Jinren

    2016-01-01

    Microbial communities of activated sludge (AS) play a key role in the performance of wastewater treatment processes. However, seasonal variability of microbial population in varying AS-based processes has been poorly correlated with operation of full-scale wastewater treatment systems (WWTSs). In this paper, significant seasonal variability of AS microbial communities in eight WWTSs located in the city of Guangzhou were revealed in terms of 16S rRNA-based Miseq sequencing. Furthermore, variation redundancy analysis (RDA) demonstrated that the microbial community compositions closely correlated with WWTS operation parameters such as temperature, BOD, NH4+-N and TN. Consequently, support vector regression models which reasonably predicted effluent BOD, SS and TN in WWTSs were established based on microbial community compositions. This work provided an alternative tool for rapid assessment on performance of full-scale wastewater treatment plants. PMID:27049964

  7. Performance Assessment of Full-Scale Wastewater Treatment Plants Based on Seasonal Variability of Microbial Communities via High-Throughput Sequencing.

    PubMed

    Liu, Tang; Liu, Shufeng; Zheng, Maosheng; Chen, Qian; Ni, Jinren

    2016-01-01

    Microbial communities of activated sludge (AS) play a key role in the performance of wastewater treatment processes. However, seasonal variability of microbial population in varying AS-based processes has been poorly correlated with operation of full-scale wastewater treatment systems (WWTSs). In this paper, significant seasonal variability of AS microbial communities in eight WWTSs located in the city of Guangzhou were revealed in terms of 16S rRNA-based Miseq sequencing. Furthermore, variation redundancy analysis (RDA) demonstrated that the microbial community compositions closely correlated with WWTS operation parameters such as temperature, BOD, NH4+-N and TN. Consequently, support vector regression models which reasonably predicted effluent BOD, SS and TN in WWTSs were established based on microbial community compositions. This work provided an alternative tool for rapid assessment on performance of full-scale wastewater treatment plants.

  8. Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry.

    PubMed

    Johnson, David R; Czechowska, Kamila; Chèvre, Nathalie; van der Meer, Jan Roelof

    2009-07-01

    Biocides are widely used for domestic hygiene, agricultural and industrial applications. Their widespread use has resulted in their introduction into the environment and raised concerns about potential deleterious effects on aquatic ecosystems. In this study, the toxicity of the biocides triclosan, penconazole and metalaxyl were evaluated with the freshwater bacterium Caulobacter crescentus and with a freshwater microbial community using a combination of single- and double-stain flow cytometric assays. Growth of C.  crescentus and the freshwater community were repressed by triclosan but not by penconazole or metalaxyl at concentrations up to 250 μM. The repressive effect of triclosan was dependent on culture conditions. Caulobacter crescentus was more sensitive to triclosan when grown with high glucose at high cell density than when grown directly in sterilized lake water at low cell density. This suggests that the use of conventional growth conditions may overestimate biocide toxicity. Additional experiments showed that the freshwater community was more sensitive to triclosan than C.  crescentus, with 10 nM of triclosan being sufficient to repress growth and change the phylogenetic composition of the community. These results demonstrate that isolate-based assays may underestimate biocide toxicity and highlight the importance of assessing toxicity directly on natural microbial communities. Because 10 nM of triclosan is within the range of concentrations observed in freshwater systems, these results also raise concerns about the risk of introducing triclosan into the environment.

  9. Assessment of the microbial community in a constructed wetland that receives acid coal mine drainage

    SciTech Connect

    Nicomrat, D.; Dick, W.A.; Tuovinen, O.H.

    2006-01-15

    Constructed wetlands are used to treat acid drainage from surface or underground coal mines. However, little is known about the microbial communities in the receiving wetland cells. The purpose of this work was to characterize the microbial population present in a wetland that was receiving acid coal mine drainage (AMD). Samples were collected from the oxic sediment zone of a constructed wetland cell in southeastern Ohio that was treating acid drainage from an underground coal mine seep. Samples comprised Fe(Ill) precipitates and were pretreated with ammonium oxalate to remove interfering iron, and the DNA was extracted and purified by agarose gel electrophoresis prior to amplification of portions of the 16S rRNA gene. Amplified products were separated by denaturing gradient gel electrophoresis and DNA from seven distinct bands was excised from the gel and sequenced. The sequences were matched to sequences in the GenBank bacterial 16S rDNA database. The DNA in two of the bands yielded matches with Acidithiobacillus ferrooxidans and the DNA in each of the remaining five bands was consistent with one of the following microorganisms: Acidithiobacillus thiooxidans, strain TRA3-20 (a eubacterium), strain BEN-4 (an arsenite-oxidizing bacterium), an Alcaligenes sp., and a Bordetella sp. Low bacterial diversity in these samples reflects the highly inorganic nature of the oxic sediment layer where high abundance of iron- and sulfur-oxidizing bacteria would be expected. The results we obtained by molecular methods supported our findings, obtained using culture methods, that the dominant microbial species in an acid receiving, oxic wetland are A. thiooxidans and A. ferrooxidans.

  10. Assessment of the microbial community in a constructed wetland that receives acid coal mine drainage.

    PubMed

    Nicomrat, Duongruitai; Dick, Warren A; Tuovinen, Olli H

    2006-01-01

    Constructed wetlands are used to treat acid drainage from surface or underground coal mines. However, little is known about the microbial communities in the receiving wetland cells. The purpose of this work was to characterize the microbial population present in a wetland that was receiving acid coal mine drainage (AMD). Samples were collected from the oxic sediment zone of a constructed wetland cell in southeastern Ohio that was treating acid drainage from an underground coal mine seep. Samples comprised Fe(III) precipitates and were pretreated with ammonium oxalate to remove interfering iron, and the DNA was extracted and purified by agarose gel electrophoresis prior to amplification of portions of the 16S rRNA gene. Amplified products were separated by denaturing gradient gel electrophoresis and DNA from seven distinct bands was excised from the gel and sequenced. The sequences were matched to sequences in the GenBank bacterial 16S rDNA database. The DNA in two of the bands yielded matches with Acidithiobacillus ferrooxidans and the DNA in each of the remaining five bands was consistent with one of the following microorganisms: Acidithiobacillus thiooxidans, strain TRA3-20 (a eubacterium), strain BEN-4 (an arsenite-oxidizing bacterium), an Alcaligenes sp., and a Bordetella sp. Low bacterial diversity in these samples reflects the highly inorganic nature of the oxic sediment layer where high abundance of iron- and sulfur-oxidizing bacteria would be expected. The results we obtained by molecular methods supported our findings, obtained using culture methods, that the dominant microbial species in an acid receiving, oxic wetland are A. thiooxidans and A. ferrooxidans.

  11. Biomass assessment of microbial surface communities by means of hyperspectral remote sensing data.

    PubMed

    Rodríguez-Caballero, Emilio; Paul, Max; Tamm, Alexandra; Caesar, Jennifer; Büdel, Burkhard; Escribano, Paula; Hill, Joachim; Weber, Bettina

    2017-05-15

    Dryland vegetation developed morphological and physiological strategies to cope with drought. However, as aridity increases, vascular plant coverage gets sparse and microbially-dominated surface communities (MSC), comprising cyanobacteria, algae, lichens and bryophytes together with heterotropic bacteria, archaea and fungi, gain relevance. Nevertheless, the relevance of MSC net primary productivity has only rarely been considered in ecosystem scale studies, and detailed information on their contribution to the total photosynthetic biomass reservoir is largely missing. In this study, we mapped the spatial distribution of two different MSC (biological soil crusts and quartz fields hosting hypolithic crusts) at two different sites within the South African Succulent Karoo (Soebatsfontein and Knersvlakte). Then we characterized both types of MSC in terms of chlorophyll content, and combining these data with the biocrust and quartz field maps, we estimated total biomass values of MSCs and their spatial patterns within the two different ecosystems. Our results revealed that MSC are important vegetation components of the South African Karoo biome, revealing clear differences between the two sites. At Soebatsfontein, MSC occurred as biological soil crusts (biocrusts), which covered about one third of the landscape reaching an overall biomass value of ~480gha(-1) of chlorophyll a+b at the landscape scale. In the Knersvlakte, which is characterized by harsher environmental conditions (i.e. higher solar radiation and potential evapotranspiration), MSC occurred as biocrusts, but also formed hypolithic crusts growing on the lower soil-immersed parts of translucent quartz pebbles. Whereas chlorophyll concentrations of biocrusts and hypolithic crusts where insignificantly lower in the Knersvlakte, the overall MSC biomass reservoir was by far larger with ~780gha(-1) of chlorophyll a+b. Thus, the complementary microbially-dominated surface communities promoted biomass formation

  12. Assessment of Changes in Microbial Community Structure during Operation of an Ammonia Biofilter with Molecular Tools

    PubMed Central

    Sakano, Y.; Kerkhof, L.

    1998-01-01

    Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria. PMID:9835577

  13. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools

    NASA Technical Reports Server (NTRS)

    Sakano, Y.; Kerkhof, L.; Janes, H. W. (Principal Investigator)

    1998-01-01

    Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria.

  14. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools

    NASA Technical Reports Server (NTRS)

    Sakano, Y.; Kerkhof, L.; Janes, H. W. (Principal Investigator)

    1998-01-01

    Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria.

  15. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools

    SciTech Connect

    Sakano, Y.; Kerkhof, L.

    1998-12-01

    Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria.

  16. Assessment of changes in the microbial community of constructed wetland mesocosms in response to acid mine drainage exposure.

    PubMed

    Weber, Kela P; Gehder, Matthias; Legge, Raymond L

    2008-01-01

    Changes in the bacterial community in the interstitial water of 5 different constructed wetland mesocosms were studied over a 22-day period following exposure to simulated acid mine drainage (AMD). The community-level physiological profile (CLPP) of each mesocosm was assessed using substrate utilization patterns gathered via BIOLOG ECO plates. Principal component analysis (PCA) of the BIOLOG ECO plate data proved feasible and useful in characterizing the interstitial bacterial community in the constructed wetland mesocosms based on mesocosm characteristics such as fixed biological regime development and plant presence, and was also used to successfully track changes in the interstitial bacterial community in response to AMD exposure. Clustering analysis of the BIOLOG ECO plate data was used to characterize the interstitial bacterial community and to validate the mesocosm groupings observed through PCA ordination. The calculation of substrate-based diversity indices from the BIOLOG ECO plate data was used to assess the robustness and the degree of change shown by the metabolic fingerprint of the interstitial bacterial community within the mesocosms. The interstitial bacterial community in the constructed mesocosms was shown to be significantly affected after exposure to AMD. Exposure to AMD caused similar bacterial species to detach from the fixed biotic regime of the mesocosms. It was also shown that mesocosms planted with Phragmites australis did not experience as great an ecological shift in the microbial ecology of the interstitial water after exposure to AMD as did the unplanted mesocosms. The substrate-based diversity indices for the planted mesocosms were also found to be more stable, after exposure to AMD, than those for the unplanted mesocosms. It is possible that the interaction between the plant root system and the substrate biological regime, collectively called the rhizosphere, may create a more ecologically robust and stable treatment system.

  17. Quantitative microbial risk assessment of Cryptosporidium and Giardia in well water from a native community of Mexico.

    PubMed

    Balderrama-Carmona, Ana Paola; Gortáres-Moroyoqui, Pablo; Álvarez-Valencia, Luis Humberto; Castro-Espinoza, Luciano; Balderas-Cortés, José de Jesús; Mondaca-Fernández, Iram; Chaidez-Quiroz, Cristóbal; Meza-Montenegro, María Mercedes

    2015-01-01

    Cryptosporidium and Giardia are gastrointestinal disease-causing organisms transmitted by the fecal-oral route, zoonotic and prevalent in all socioeconomic segments with greater emphasis in rural communities. The goal of this study was to assess the risk of cryptosporidiosis and giardiasis of Potam dwellers consuming drinking water from communal well water. To achieve the goal, quantitative microbial risk assessment (QMRA) was carried out as follows: (a) identification of Cryptosporidium oocysts and Giardia cysts in well water samples by information collection rule method, (b) assessment of exposure to healthy Potam residents, (c) dose-response modelling, and (d) risk characterization using an exponential model. All well water samples tested were positive for Cryptosporidium and Giardia. The QMRA results indicate a mean of annual risks of 99:100 (0.99) for cryptosporidiosis and 1:1 (1.0) for giardiasis. The outcome of the present study may drive decision-makers to establish an educational and treatment program to reduce the incidence of parasite-borne intestinal infection in the Potam community, and to conduct risk analysis programs in other similar rural communities in Mexico.

  18. Systems biology of Microbial Communities

    SciTech Connect

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  19. Assessment of natural sepiolite on cadmium stabilization, microbial communities, and enzyme activities in acidic soil.

    PubMed

    Sun, Yuebing; Sun, Guohong; Xu, Yingming; Wang, Lin; Liang, Xuefeng; Lin, Dasong; Hu, Fazhi

    2013-05-01

    A pot trial was conducted to assess the efficiency of sepiolite-induced cadmium (Cd) immobilization in ultisoils. Under Cd concentrations of 1.25, 2.5, and 5 mg kg(-1), the available Cd in the soil after the application of 1-10 % sepiolite decreased by a maximum of 44.4, 23.0, and 17.0 %, respectively, compared with no sepiolite treatments. The increase in the values of soil enzyme activities and microbial number proved that a certain metabolic recovery occurred after sepiolite treatment. The dry biomass of spinach (Spinacia oleracea) increased with increasing sepiolite concentration in the soil. However, the concentration (dry weight) of Cd in the spinach shoots decreased with the increase in sepiolite dose, with maximum reduction of 92.2, 90.0, and 84.9 %, respectively, compared with that of unamended soils. Under a Cd level of 1.25 mg kg(-1), the Cd concentration in the edible parts of spinach at 1 % sepiolite amendment was lower than 0.2 mg kg(-1) fresh weight, the maximum permissible concentration (MPC) of Cd in vegetable. Even at higher Cd concentrations (2.5 and 5 mg kg(-1)), safe spinach was produced when the sepiolite treatment was up to 5 %. The results showed that sepiolite-assisted remediation could potentially succeed on a field scale by decreasing Cd entry into the food chain.

  20. Assessment and impact of microbial fecal pollution and human enteric pathogens in a coastal community.

    PubMed

    Lipp, E K; Farrah, S A; Rose, J B

    2001-04-01

    The goals of this study were to assess watersheds impacted by high densities of OSDS (onsite sewage disposal systems) for evidence of fecal contamination and evaluate the occurrence of human pathogens in coastal waters off west Florida. Eleven stations (representing six watersheds) were intensively sampled for microbial indicators of fecal pollution (fecal coliform bacteria, enterococci, Clostridium perfringens and coliphage) and the human enteric pathogens, Cryptosporidium, Giardia, and enteroviruses during the summer rainy season (May-September 1996). Levels of all indicators ranged between < 5 and > 4000 CFU/100 ml. Cryptosporidium and Giardia were detected infrequently (6.8% and 2.3% of samples tested positive, respectively). Conversely, infectious enteroviruses were detected at low levels in 5 of the 6 watersheds sampled. Using cluster analysis, sites were grouped into two categories, high and low risks, based on combined levels of indicators. These results suggest that stations of highest pollution risk were located within areas of high OSDS densities. Furthermore, data indicate a subsurface transport of contaminated water to surface waters. The high prevalence of enteroviruses throughout the study area suggests a chronic pollution problem and potential risk to recreational swimmers in and around Sarasota Bay.

  1. Synthetic networks in microbial communities

    NASA Astrophysics Data System (ADS)

    Suel, Gurol

    2015-03-01

    While bacteria are single celled organisms, they predominantly reside in structured communities known as biofilms. Cells in biofilms are encapsulated and protected by the extracellular matrix (ECM), which also confines cells in space. During biofilm development, microbial cells are organized in space and over time. Little is known regarding the processes that drive the spatio-temporal organization of microbial communities. Here I will present our latest efforts that utilize synthetic biology approaches to uncover the organizational principles that drive biofilm development. I will also discuss the possible implications of our recent findings in terms of the cost and benefit to biofilm cells.

  2. Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

    PubMed Central

    Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

    2014-01-01

    Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683

  3. Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania.

    PubMed

    Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J; Wright, Justin R; Rosenberger, Abigail; McClure, Erin E; Grube, Alyssa M; Peterson, Mark P; Keddache, Mehdi; Mason, Olivia U; Hazen, Terry C; Grant, Christopher J; Lamendella, Regina

    2014-01-01

    Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA- sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems.

  4. Using Phospholipids and Stable Carbon Isotopes to Assess Microbial Community Structures and Carbon Cycle Pathways in Kamchatka Hot Springs

    NASA Astrophysics Data System (ADS)

    Zhao, W.; Romanek, C. S.; Burgess, E. A.; Wiegel, J.; Mills, G.; Zhang, C. L.

    2006-12-01

    Phospholipid fatty acid (PLFA) and stable carbon isotopes were used to assess the microbial community structures in Kamchatka hot springs. Eighteen mats or surface sediments were collected from hot springs having temperatures of 31 to 91°C and pHs of 4.9 to 8.5. These samples were clearly separated into three groups according to the bacterial PLFA: 1) those dominated by terminally branched odd-numbered fatty acids, 2) those dominated by C18:1 and 3) those dominated by C20:1. With support from other minor PLFA components, group 2 may be used as biomarkers for Chloroflexales or other phototrophic bacteria and group 3 for Aquificales, respectively. Among the sampled hot springs, the Arkashin pool represents the simplest microbial structure with members of Aquificales being the dominant primary producers. On the other hand, the Zavarzin pool may represent the most heterogeneous pool that may include members of Chloroflexales and Aquificales as primary producers. Bacterial 16S rDNA clone libraries confirmed the presence of these microbial groups in the two pools. Results of stable carbon isotope fractionation between CO2 source, bulk biomass and total PLFA showed that primary producers in the Arkashin pool primarily used the reductive tricarboxylic acid (rTCA) cycle (e.g., members of Aquificales); whereas the Zavarzin pool may be a mixture of the 3-hydroxypropionate (3-HP) pathway (e.g. members of Chloroflexales) and the rTCA cycle. Bacterial contribution using the Calvin cycle was not significant and may be less important in Kamchatka hot springs.

  5. Syntrophic exchange in synthetic microbial communities

    PubMed Central

    Mee, Michael T.; Collins, James J.; Church, George M.; Wang, Harris H.

    2014-01-01

    Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology. PMID:24778240

  6. Syntrophic exchange in synthetic microbial communities.

    PubMed

    Mee, Michael T; Collins, James J; Church, George M; Wang, Harris H

    2014-05-20

    Metabolic crossfeeding is an important process that can broadly shape microbial communities. However, little is known about specific crossfeeding principles that drive the formation and maintenance of individuals within a mixed population. Here, we devised a series of synthetic syntrophic communities to probe the complex interactions underlying metabolic exchange of amino acids. We experimentally analyzed multimember, multidimensional communities of Escherichia coli of increasing sophistication to assess the outcomes of synergistic crossfeeding. We find that biosynthetically costly amino acids including methionine, lysine, isoleucine, arginine, and aromatics, tend to promote stronger cooperative interactions than amino acids that are cheaper to produce. Furthermore, cells that share common intermediates along branching pathways yielded more synergistic growth, but exhibited many instances of both positive and negative epistasis when these interactions scaled to higher dimensions. In more complex communities, we find certain members exhibiting keystone species-like behavior that drastically impact the community dynamics. Based on comparative genomic analysis of >6,000 sequenced bacteria from diverse environments, we present evidence suggesting that amino acid biosynthesis has been broadly optimized to reduce individual metabolic burden in favor of enhanced crossfeeding to support synergistic growth across the biosphere. These results improve our basic understanding of microbial syntrophy while also highlighting the utility and limitations of current modeling approaches to describe the dynamic complexities underlying microbial ecosystems. This work sets the foundation for future endeavors to resolve key questions in microbial ecology and evolution, and presents a platform to develop better and more robust engineered synthetic communities for industrial biotechnology.

  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.

    PubMed

    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.

  8. Assessing the microbial community and functional genes in a vertical soil profile with long-term arsenic contamination.

    PubMed

    Xiong, Jinbo; He, Zhili; Van Nostrand, Joy D; Luo, Guosheng; Tu, Shuxin; Zhou, Jizhong; Wang, Gejiao

    2012-01-01

    Arsenic (As) contamination in soil and groundwater has become a serious problem to public health. To examine how microbial communities and functional genes respond to long-term arsenic contamination in vertical soil profile, soil samples were collected from the surface to the depth of 4 m (with an interval of 1 m) after 16-year arsenic downward infiltration. Integrating BioLog and functional gene microarray (GeoChip 3.0) technologies, we showed that microbial metabolic potential and diversity substantially decreased, and community structure was markedly distinct along the depth. Variations in microbial community functional genes, including genes responsible for As resistance, carbon and nitrogen cycling, phosphorus utilization and cytochrome c oxidases were detected. In particular, changes in community structures and activities were correlated with the biogeochemical features along the vertical soil profile when using the rbcL and nifH genes as biomarkers, evident for a gradual transition from aerobic to anaerobic lifestyles. The C/N showed marginally significant correlations with arsenic resistance (p = 0.069) and carbon cycling genes (p = 0.073), and significant correlation with nitrogen fixation genes (p = 0.024). The combination of C/N, NO(3) (-) and P showed the highest correlation (r = 0.779, p = 0.062) with the microbial community structure. Contradict to our hypotheses, a long-term arsenic downward infiltration was not the primary factor, while the spatial isolation and nutrient availability were the key forces in shaping the community structure. This study provides new insights about the heterogeneity of microbial community metabolic potential and future biodiversity preservation for arsenic bioremediation management.

  9. Assessment of 10 years of CO2 fumigation on soil microbial communities and function in a sweetgum plantation

    SciTech Connect

    Austin, Emily E; Castro Gonzalez, Hector F; Sides, Katherine E; Schadt, Christopher Warren; Classen, Aimee T

    2009-01-01

    Increased vegetative growth and soil carbon (C) storage under elevated carbon dioxide concentration ([CO2]) has been demonstrated in a number of experiments. However, the ability of ecosystems, either above- or belowground, to maintain increased carbon storage relies on the response of soil processes, such as nitrogen (N) availability, to climatic change. These soil processes are mediated by microbial communities whose activity and structure may also respond to increasing atmospheric [CO2]. We took advantage of a long-term (ca 10 year) CO2 enrichment experiment in a sweetgum plantation located in Tennessee to test the hypothesis that observed increases in root production in elevated relative to ambient CO2 plots would alter microbial community structure, increase microbial activity, and increase soil nutrient cycling. We found that elevated [CO2] had no detectable effect on microbial community structure using 16S rRNA gene cloning libraries, on microbial activity measured with extracellular enzyme activity, or on potential soil N mineralization and nitrification rates. These results are similar to those found at other sites and are consistent with continued C storage in forest ecosystems in the near future.

  10. Microbial Risk Assessment

    NASA Technical Reports Server (NTRS)

    Ott, C. M.; Mena, K. D.; Nickerson, C.A.; Pierson, D. L.

    2009-01-01

    Historically, microbiological spaceflight requirements have been established in a subjective manner based upon expert opinion of both environmental and clinical monitoring results and the incidence of disease. The limited amount of data, especially from long-duration missions, has created very conservative requirements based primarily on the concentration of microorganisms. Periodic reevaluations of new data from later missions have allowed some relaxation of these stringent requirements. However, the requirements remain very conservative and subjective in nature, and the risk of crew illness due to infectious microorganisms is not well defined. The use of modeling techniques for microbial risk has been applied in the food and potable water industries and has exceptional potential for spaceflight applications. From a productivity standpoint, this type of modeling can (1) decrease unnecessary costs and resource usage and (2) prevent inadequate or inappropriate data for health assessment. In addition, a quantitative model has several advantages for risk management and communication. By identifying the variable components of the model and the knowledge associated with each component, this type of modeling can: (1) Systematically identify and close knowledge gaps, (2) Systematically identify acceptable and unacceptable risks, (3) Improve communication with stakeholders as to the reasons for resource use, and (4) Facilitate external scientific approval of the NASA requirements. The modeling of microbial risk involves the evaluation of several key factors including hazard identification, crew exposure assessment, dose-response assessment, and risk characterization. Many of these factors are similar to conditions found on Earth; however, the spaceflight environment is very specialized as the inhabitants live in a small, semi-closed environment that is often dependent on regenerative life support systems. To further complicate modeling efforts, microbial dose

  11. Microbial Risk Assessment

    NASA Technical Reports Server (NTRS)

    Ott, C. M.; Mena, K. D.; Nickerson, C.A.; Pierson, D. L.

    2009-01-01

    Historically, microbiological spaceflight requirements have been established in a subjective manner based upon expert opinion of both environmental and clinical monitoring results and the incidence of disease. The limited amount of data, especially from long-duration missions, has created very conservative requirements based primarily on the concentration of microorganisms. Periodic reevaluations of new data from later missions have allowed some relaxation of these stringent requirements. However, the requirements remain very conservative and subjective in nature, and the risk of crew illness due to infectious microorganisms is not well defined. The use of modeling techniques for microbial risk has been applied in the food and potable water industries and has exceptional potential for spaceflight applications. From a productivity standpoint, this type of modeling can (1) decrease unnecessary costs and resource usage and (2) prevent inadequate or inappropriate data for health assessment. In addition, a quantitative model has several advantages for risk management and communication. By identifying the variable components of the model and the knowledge associated with each component, this type of modeling can: (1) Systematically identify and close knowledge gaps, (2) Systematically identify acceptable and unacceptable risks, (3) Improve communication with stakeholders as to the reasons for resource use, and (4) Facilitate external scientific approval of the NASA requirements. The modeling of microbial risk involves the evaluation of several key factors including hazard identification, crew exposure assessment, dose-response assessment, and risk characterization. Many of these factors are similar to conditions found on Earth; however, the spaceflight environment is very specialized as the inhabitants live in a small, semi-closed environment that is often dependent on regenerative life support systems. To further complicate modeling efforts, microbial dose

  12. Assessing the relative effects of geographic location and soil type on microbial communities associated with straw decomposition.

    PubMed

    Sun, Bo; Wang, Xiaoyue; Wang, Feng; Jiang, Yuji; Zhang, Xue-Xian

    2013-06-01

    Decomposition of plant residues is largely mediated by soil-dwelling microorganisms whose activities are influenced by both climate conditions and properties of the soil. However, a comprehensive understanding of their relative importance remains elusive, mainly because traditional methods, such as soil incubation and environmental surveys, have a limited ability to differentiate between the combined effects of climate and soil. Here, we performed a large-scale reciprocal soil transplantation experiment, whereby microbial communities associated with straw decomposition were examined in three initially identical soils placed in parallel in three climate regions of China (red soil, Chao soil, and black soil, located in midsubtropical, warm-temperate, and cold-temperate zones). Maize straws buried in mesh bags were sampled at 0.5, 1, and 2 years after the burial and subjected to chemical, physical, and microbiological analyses, e.g., phospholipid fatty acid analysis for microbial abundance, community-level physiological profiling, and 16S rRNA gene denaturing gradient gel electrophoresis, respectively, for functional and phylogenic diversity. Results of aggregated boosted tree analysis show that location rather soil is the primary determining factor for the rate of straw decomposition and structures of the associated microbial communities. Principal component analysis indicates that the straw communities are primarily grouped by location at any of the three time points. In contrast, microbial communities in bulk soil remained closely related to one another for each soil. Together, our data suggest that climate (specifically, geographic location) has stronger effects than soil on straw decomposition; moreover, the successive process of microbial communities in soils is slower than those in straw residues in response to climate changes.

  13. Assessing the Relative Effects of Geographic Location and Soil Type on Microbial Communities Associated with Straw Decomposition

    PubMed Central

    Wang, Xiaoyue; Wang, Feng; Jiang, Yuji

    2013-01-01

    Decomposition of plant residues is largely mediated by soil-dwelling microorganisms whose activities are influenced by both climate conditions and properties of the soil. However, a comprehensive understanding of their relative importance remains elusive, mainly because traditional methods, such as soil incubation and environmental surveys, have a limited ability to differentiate between the combined effects of climate and soil. Here, we performed a large-scale reciprocal soil transplantation experiment, whereby microbial communities associated with straw decomposition were examined in three initially identical soils placed in parallel in three climate regions of China (red soil, Chao soil, and black soil, located in midsubtropical, warm-temperate, and cold-temperate zones). Maize straws buried in mesh bags were sampled at 0.5, 1, and 2 years after the burial and subjected to chemical, physical, and microbiological analyses, e.g., phospholipid fatty acid analysis for microbial abundance, community-level physiological profiling, and 16S rRNA gene denaturing gradient gel electrophoresis, respectively, for functional and phylogenic diversity. Results of aggregated boosted tree analysis show that location rather soil is the primary determining factor for the rate of straw decomposition and structures of the associated microbial communities. Principal component analysis indicates that the straw communities are primarily grouped by location at any of the three time points. In contrast, microbial communities in bulk soil remained closely related to one another for each soil. Together, our data suggest that climate (specifically, geographic location) has stronger effects than soil on straw decomposition; moreover, the successive process of microbial communities in soils is slower than those in straw residues in response to climate changes. PMID:23524671

  14. ASSESSING CHANGES IN SOIL MICROBIAL COMMUNITIES AND CARBON MINERALIZATION IN BT AND NON-BT CORN RESIDUE-AMENDED SOILS

    USDA-ARS?s Scientific Manuscript database

    The effects of Bt corn (Zea mays L.) residue on soil microbial communities and rates of C mineralization were investigated. The Bt corn residue had a higher lignin content (12%) and lignin/N (9.9) ratio compared with its non-Bt near-isoline (10% lignin; lignin/N = 8.6). We examined the relationships...

  15. Soil ecotoxicity assessment of glyphosate use under field conditions: microbial activity and community structure of Eubacteria and ammonia-oxidising bacteria.

    PubMed

    Zabaloy, María C; Carné, Ignacio; Viassolo, Rodrigo; Gómez, Marisa A; Gomez, Elena

    2016-04-01

    A plot-scale experiment was conducted to assess the impact of field application rates of glyphosate on soil microbial communities by taking measurements of microbial activity (in terms of substrate-induced respiration and enzyme activity) in parallel with culture-independent approaches to assessing both bacterial abundance and diversity. Two rates of glyphosate, alone or in a mixture with 2,4-dichlorophenoxyacetic acid, were applied directly onto the soil surface, simulating normal use in chemical fallow in no-till systems. No consistent rate-dependent responses were observed in the microbial activity parameters investigated in the field plots that were exposed to glyphosate. Denaturant gradient gel electrophoresis (DGGE) of the overall bacterial community (Eubacteria) and ammonia-oxidising bacteria (AOB) revealed no effects of the high rate of glyphosate on the structure of the communities in comparison with the control. No treatment effects were observed on the abundance of Eubacteria shortly after treatment in 2010, while a small but significant difference between the high rate and the control was detected in the first sampling in 2011. The abundance of AOB was relatively low during the study, and treatment effects were undetectable. The absence of negative effects on soil microbial communities in this study suggests that glyphosate use at recommended rates poses low risk to the microbiota. © 2015 Society of Chemical Industry.

  16. Development and Assessment of Whole-Genome Oligonucleotide Microarrays to Analyze an Anaerobic Microbial Community and its Responses to Oxidative Stress

    SciTech Connect

    Scholten, Johannes C.; Culley, David E.; Nie, Lei; Munn, Kyle J.; Chow, Lely; Brockman, Fred J.; Zhang, Weiwen

    2007-06-29

    The application of DNA microarray technology to investigate multiple-species microbial community presents great challenges. In this study, we reported the design and quality assessment of four whole genome oligonucleotide microarrays for two syntroph bacteria, Desulfovibrio vulgaris and Syntrophobacter fumaroxidans, and two archaeal methanogens, Methanosarcina barkeri and Methanospirillum hungatei, and their application to analyze global gene expression of this four-species microbial community in response to oxidative stress. In order to minimize the possible cross-hybridization, cross-genome comparison was performed to assure all probes unique to each genome so that the microarrays could provide species-level resolution. Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates. Microarray analysis showed that S. fumaroxidans and M. hungatei responded to the stress with up-regulation of several genes known to be involved in ROS detoxification, such as catalase and rubrerythrin in S. fumaroxidans and thioredoxin and heat shock protein Hsp20 in M. hungatei. Consistent with previous study in pure culture, the microarray analysis showed that genes involved in methane production and energy metabolism were down-regulated by oxidative stress in M. barkeri. However, D. vulgaris seemed less sensitive to the oxidative stress when grown in a community, with almost no gene up-regulated. The study demonstrated the successful application of microarray technology to multiple-species microbial community, and our preliminary results indicated that the approach can provide novel insights on the metabolic and regulatory networks within microbial communities.

  17. Ohmic resistance affects microbial community and ...

    EPA Pesticide Factsheets

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MXC to better comprehend anode fundamentals. Microbial community analysis using 16S rRNA illumine sequencing showed that Geobactor genus, one of the most kinetically efficient anode-respiring bacteria (ARB), was abundant (87%) only on the biofilm anode closest to a reference electrode in which current density was the highest among four anodes. In comparison, Geobacter populations were less than 11% for other three anodes more distant from the reference electrode, generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest anode, while EKA was as high as -0.134 V for the farthest anode. Our study clearly proves that ohmic resistance changes anode potential which mainly causes different biofilm communities on individual anodes and consequently influences anode kinetics. This study explored the use of multiple anodes in microelectrochemical cells and the microbial community on these anodes, as a function of the efficiency in producing hydrogen peroxide.

  18. Culture independent assessment of human milk microbial community in lactational mastitis.

    PubMed

    Patel, Shriram H; Vaidya, Yati H; Patel, Reena J; Pandit, Ramesh J; Joshi, Chaitanya G; Kunjadiya, Anju P

    2017-08-10

    Breastfeeding undoubtedly provides important benefits to the mother-infant dyad and should be encouraged. Mastitis, one of the common but major cause of premature weaning among lactating women, is an inflammation of connective tissue within the mammary gland. This study reports the influence of mastitis on human milk microbiota by utilizing 16 S rRNA gene sequencing approach. We sampled and sequenced microbiome from 50 human milk samples, including 16 subacute mastitis (SAM), 16 acute mastitis (AM) and 18 healthy-controls. Compared to controls, SAM and AM microbiota were quite distinct and drastically reduced. Genera including, Aeromonas, Staphylococcus, Ralstonia, Klebsiella, Serratia, Enterococcus and Pseudomonas were significantly enriched in SAM and AM samples, while Acinetobacter, Ruminococcus, Clostridium, Faecalibacterium and Eubacterium were consistently depleted. Further analysis of our samples revealed positive aerotolerant odds ratio, indicating dramatic depletion of obligate anaerobes and enrichment of aerotolerant bacteria during the course of mastitis. In addition, predicted functional metagenomics identified several gene pathways related to bacterial proliferation and colonization (e.g. two-component system, bacterial secretion system and motility proteins) in SAM and AM samples. In conclusion, our study confirmed previous hypothesis that mastitis women have lower microbial diversity, increased abundance of opportunistic pathogens and depletion of commensal obligate anaerobes.

  19. Assessing the influence of farm fertility amendments, field management, and sorghum genotypes on soil microbial communities and grain quality

    USDA-ARS?s Scientific Manuscript database

    Four genotypes of grain sorghum (two commercial hybrids and two open-pollinated cultivars) were assessed for grain production, protein and mineral concentrations, grain physical properties, and starch quality characteristics. Genotypes were also characterized for their influence on soil microbial co...

  20. Comparison of microbial community assays for the assessment of stream biofilm ecology.

    PubMed

    Vinten, A J A; Artz, R R E; Thomas, N; Potts, J M; Avery, L; Langan, S J; Watson, H; Cook, Y; Taylor, C; Abel, C; Reid, E; Singh, B K

    2011-06-01

    We investigated a range of microbiological community assays performed on scrapes of biofilms formed on artificial diffusing substrates deployed in 8 streams in eastern Scotland, with a view to using them to characterize ecological response to stream water quality. The assays considered were: Multiplex Terminal Restriction Fragment Length Polymorphism or M-TRFLP (a molecular method), Phospholipid Fatty Acid or PLFA analysis (a biochemical method) and MICRORESP™ (a physiological method) alongside TDI, diatom species, and chlorophyll a content. Four of the streams were classified as of excellent status (3-6μg/L Soluble Reactive Phosphorus (SRP)) with respect to soluble P content under the EU Water Framework Directive and four were of borderline good/moderate or moderate status (43-577μg/L SRP). At each site, 3 replicates of 3 solute diffusion treatments were deployed in a Latin square design. Solute diffusion treatments were: KCl (as a control solute), N and P (to investigate the effect of nutrient enrichment), or the herbicide isoproturon (as a "high impact" control, which aimed to affect biofilm growth in a way detectable by all assays). Biofilms were sampled after 4weeks deployment in a low flow period of early summer 2006. The chlorophyll a content of biofilms after 4weeks was 2.0±0.29mg/m(2) (mean±se). Dry matter content was 16.0±13.1g/m(2). The M-TRFLP was successfully used for generating community profiles of cyanobacteria, algae and bacteria and was much faster than diatom identification. The PFLA and TDI were successful after an increase in the sample size, due to low counts. The MICRORESP(™) assays were often below or near detection limit. We estimated the per-sample times for the successful assays as follows: M-TRFLP: 20min, PLFA 40min, TDI 90min. Using MANOVA on the first 5 principal co-ordinates, all the assays except MICRORESP(™) showed significant differences between sites, but none of the assays showed a significant effect of either initial

  1. Flat laminated microbial mat communities

    NASA Astrophysics Data System (ADS)

    Franks, Jonathan; Stolz, John F.

    2009-10-01

    Flat laminated microbial mats are complex microbial ecosystems that inhabit a wide range of environments (e.g., caves, iron springs, thermal springs and pools, salt marshes, hypersaline ponds and lagoons, methane and petroleum seeps, sea mounts, deep sea vents, arctic dry valleys). Their community structure is defined by physical (e.g., light quantity and quality, temperature, density and pressure) and chemical (e.g., oxygen, oxidation/reduction potential, salinity, pH, available electron acceptors and donors, chemical species) parameters as well as species interactions. The main primary producers may be photoautotrophs (e.g., cyanobacteria, purple phototrophs, green phototrophs) or chemolithoautophs (e.g., colorless sulfur oxidizing bacteria). Anaerobic phototrophy may predominate in organic rich environments that support high rates of respiration. These communities are dynamic systems exhibiting both spatial and temporal heterogeneity. They are characterized by steep gradients with microenvironments on the submillimeter scale. Diel oscillations in the physical-chemical profile (e.g., oxygen, hydrogen sulfide, pH) and species distribution are typical for phototroph-dominated communities. Flat laminated microbial mats are often sites of robust biogeochemical cycling. In addition to well-established modes of metabolism for phototrophy (oxygenic and non-oxygenic), respiration (both aerobic and anaerobic), and fermentation, novel energetic pathways have been discovered (e.g., nitrate reduction couple to the oxidation of ammonia, sulfur, or arsenite). The application of culture-independent techniques (e.g., 16S rRNA clonal libraries, metagenomics), continue to expand our understanding of species composition and metabolic functions of these complex ecosystems.

  2. Microbial community structure and denitrification in a wetland mitigation bank.

    PubMed

    Peralta, Ariane L; Matthews, Jeffrey W; Kent, Angela D

    2010-07-01

    Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts.

  3. Microbial Community Structure and Denitrification in a Wetland Mitigation Bank▿

    PubMed Central

    Peralta, Ariane L.; Matthews, Jeffrey W.; Kent, Angela D.

    2010-01-01

    Wetland mitigation is implemented to replace ecosystem functions provided by wetlands; however, restoration efforts frequently fail to establish equivalent levels of ecosystem services. Delivery of microbially mediated ecosystem functions, such as denitrification, is influenced by both the structure and activity of the microbial community. The objective of this study was to compare the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial community composition was assessed using terminal restriction fragment length polymorphism targeting the 16S rRNA gene (total bacteria) and the nosZ gene (denitrifiers). Comparisons of microbial function were based on potential denitrification rates. Bacterial community structures differed significantly between restored and reference wetlands; denitrifier community assemblages were similar among reference sites but highly variable among restored sites throughout the mitigation bank. Potential denitrification was highest in the reference wetland sites. These data demonstrate that wetland restoration efforts in this mitigation bank have not successfully restored denitrification and that differences in potential denitrification rates may be due to distinct microbial assemblages observed in restored and reference (natural) wetlands. Further, we have identified gradients in soil moisture and soil fertility that were associated with differences in microbial community structure. Microbial function was influenced by bacterial community composition and soil fertility. Identifying soil factors that are primary ecological drivers of soil bacterial communities, especially denitrifying populations, can potentially aid the development of predictive models for restoration of biogeochemical transformations and enhance the success of wetland restoration efforts. PMID:20453124

  4. Microbial biomass, activity and community composition in constructed wetlands.

    PubMed

    Truu, Marika; Juhanson, Jaanis; Truu, Jaak

    2009-06-15

    The aim of the current article is to give an overview about microbial communities and their functioning but also about factors affecting microbial activity in the three most common types (surface flow and two types of sub-surface flow) of constructed wetlands. The paper reviews the community composition and structural diversity of the microbial biomass, analyzing different aspects of microbial activity with respect to wastewater properties, specific wetland type, and environmental parameters. A brief introduction about the application of different novel molecular techniques for the assessment of microbial communities in constructed wetlands is also given. Microbially mediated processes in constructed wetlands are mainly dependent on hydraulic conditions, wastewater properties, including substrate and nutrient quality and availability, filter material or soil type, plants, and different environmental factors. Microbial biomass is within similar ranges in both horizontal and vertical subsurface flow and surface flow constructed wetlands. Stratification of the biomass but also a stratified structural pattern of the bacterial community can be seen in subsurface flow systems. Microbial biomass C/N ratio is higher in horizontal flow systems compared to vertical flow systems, indicating the structural differences in microbial communities between those two constructed wetland types. The total activity of the microbial community is in the same range, but heterotrophic growth is higher in the subsurface (vertical flow) system compared to the surface flow systems. Available species-specific data about microbial communities in different types of wetlands is scarce and therefore it is impossible make any general conclusions about the dynamics of microbial community structure in wetlands, its relationship to removal processes and operational parameters.

  5. Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Assess Microbial Community Structure in Compost Systems

    NASA Astrophysics Data System (ADS)

    Tiquia, Sonia M.

    Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in composting systems. This analysis is based on the restriction endonuclease digestion of fluorescently end-labeled PCR products. The digested product is mixed with a DNA size standard, itself labeled with a distinct fluorescent dye, and the fragments are then separated by capillary or gel electrophoresis using an automated sequencer. Upon analysis, only the terminal end-labeled restriction fragments are detected. An electropherogram is produced, which shows a profile of compost microbial community as a series of peaks of varying height. This technique has also been effectively used in the exploration of complex microbial environments and in the study of bacterial, archaeal, and eukaryal populations in natural habitats.

  6. Fundamentals of Microbial Community Resistance and Resilience

    PubMed Central

    Shade, Ashley; Peter, Hannes; Allison, Steven D.; Baho, Didier L.; Berga, Mercè; Bürgmann, Helmut; Huber, David H.; Langenheder, Silke; Lennon, Jay T.; Martiny, Jennifer B. H.; Matulich, Kristin L.; Schmidt, Thomas M.; Handelsman, Jo

    2012-01-01

    Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives – informed by meta-omics data – may provide about microbial community stability. PMID:23267351

  7. Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption.

    PubMed

    Stoops, J; Crauwels, S; Waud, M; Claes, J; Lievens, B; Van Campenhout, L

    2016-02-01

    In Western countries, the popularity of edible insects as an alternative animal protein source is increasing. Nevertheless, there is a lack of profound insight into the microbial safety and shelf life of living insects sold for human consumption. The purpose of this study was to characterise the microflora of fresh edible mealworm larvae and grasshoppers in a quantitative and qualitative way. Therefore, culture-dependent analyses (the total viable aerobic count, Enterobacteriaceae, lactic acid bacteria, yeasts and moulds, and bacterial endospores) and next-generation sequencing (454amplicon pyrosequencing) were performed. High microbial counts were obtained for both insect species. Different insect batches resulted in quite similar microbial numbers, except for bacterial endospores. However, the bacterial community composition differed between both insect species. The most abundant operational taxonomic unit in mealworm larvae was Propionibacterium. Also members of the genera Haemophilus, Staphylococcus and Clostridium were found. Grasshoppers were mainly dominated by Weissella, Lactococcus and Yersinia/Rahnella. Overall, a variety of potential spoilage bacteria and food pathogens were characterised. The results of this study suggest that a processing step with a microbiocidal effect is required to avoid or minimize risks involved with the consumption of edible insects.

  8. Hydrolytic microbial communities in terrestrial ecosystems

    NASA Astrophysics Data System (ADS)

    Manucharova, Natalia; Chernov, Timofey; Kolcova, Ekaterina; Zelezova, Alena; Lukacheva, Euhenia; Zenova, Galina

    2014-05-01

    Hydrolytic microbial communities in terrestrial ecosystems Manucharova N.A., Chernov T.I., Kolcova E.M., Zelezova A.D., Lukacheva E.G. Lomonosov Moscow State University, Russia Vertical differentiation of terrestrial biogeocenoses is conditioned by the formation of vertical tiers that differ considerably in the composition and structure of microbial communities. All the three tiers, phylloplane, litter and soil, are united by a single flow of organic matter, and are spatially separated successional stages of decomposition of organic substances. Decomposition of organic matter is mainly due to the activity of microorganisms producing enzymes - hydrolase and lyase - which destroy complex organic compounds. Application of molecular biological techniques (FISH) in environmental studies provides a more complete information concerning the taxonomic diversity and potential hydrolytic activity of microbial complexes of terrestrial ecosystems that exist in a wide range of environmental factors (moisture, temperature, redox potential, organic matter). The combination of two molecular biological techniques (FISH and DGGE-analysis of fragments of gene 16S rRNA total amplificate) enables an informative assessment of the differences in the structure of dominant and minor components of hydrolytic complexes formed in different tiers of terrestrial ecosystems. The functional activity of hydrolytic microbial complexes of terrestrial ecosystems is determined by the activity of dominant and minor components, which also have a high gross enzymatic activity. Degradation of biopolymers in the phylloplane is mainly due to the representatives of the Proteobacteria phylogenetic group (classes alpha and beta). In mineral soil horizons, the role of hydrolytic representatives of Firmicutes and Actinobacteria increases. Among the key environmental parameters that determine the functional activity of the hydrolytic (chitinolytic) complex of soil layer (moisture, nutrient supply, successional

  9. Assessment of microbial communities in mung bean (Vigna radiata) rhizosphere upon exposure to phytotoxic levels of Copper.

    PubMed

    Sharaff, Murali; Archana, G

    2015-11-01

    Pollution of agricultural soils by Cu is of concern as it could bring about alterations in microbial communities, ultimately eliminating certain plant beneficial bacteria thus disturbing soil fertility and plant growth. To understand the response of rhizobacterial communities upon Cu perturbation, mung bean (Vigna radiata) plants were grown in agricultural soil amended with CuSO4 (0-1000 mg kg(-1) ) under laboratory conditions. Culture-independent and -dependent Denaturing Gradient Gel Electrophoresis (CI-DGGE and CD-DGGE) fingerprinting techniques were employed to monitor rhizobacterial community shifts upon Cu amendment. In group specific PCR-DGGE, a negative impact was seen on α-Proteobacteria followed by β-Proteobacteria resulting in a concomitant decrease in diversity indices with increased Cu concentration. No significant changes were observed in Firmicutes and Actinomycetes populations. In CD-DGGE rhizobacterial community shift was observed above 500 mg kg(-1) (CuSO4 ), however certain bands were predominantly present in all treatments. Plants showed toxic effects by reduction in growth and elevated Cu accumulation, with root system being affected prominently. From this study it is evident that above 250 mg kg(-1) , rhizobacterial communities are adversely affected. α-Proteobacteria was found to be a sensitive bio-indicator for Cu toxicity and is of particular significance since this group includes majority of plant growth promoting rhizobacteria.

  10. Molecular Survey of Concrete Biofilm Microbial Communities

    EPA Science Inventory

    Although several studies have shown that bacteria can deteriorate concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different microbial communities associated with concrete biofilms using 16S rRNA g...

  11. Molecular Survey of Concrete Biofilm Microbial Communities

    EPA Science Inventory

    Although several studies have shown that bacteria can deteriorate concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different microbial communities associated with concrete biofilms using 16S rRNA g...

  12. Breastfeeding increases microbial community resilience.

    PubMed

    Carvalho-Ramos, Isabel I; Duarte, Rubens T D; Brandt, Katia; Martinez, Marina B; Taddei, Carla R

    2017-09-05

    Since the present group had already described the composition of the intestinal microbiota of Brazilian infants under low social economic level, the aim of the present study was to analyze the microbial community structure changes in this group of infants during their early life due to external factors. Fecal samples were collected from 11 infants monthly during the first year of life. The infants were followed regarding clinical and diet information and characterized according to breastfeeding practices. DNA was extracted from fecal samples of each child and subjected to denaturing gradient gel electrophoresis analysis. The results revealed a pattern of similarity between the time points for those who were on exclusive breastfeeding or predominant breastfeeding. Although there were changes in intensity and fluctuation of some bands, the denaturing gradient gel electrophoresis patterns in the one-year microbial analysis were stable for breastfeeding children. There was uninterrupted ecological succession despite the influence of external factors, such as complementary feeding and antibiotic administration, suggesting microbiota resilience. This was not observed for those children who had mixed feeding and introduction of solid food before the 5(th) month of life. These results suggested an intestinal microbiota pattern resilient to external forces, due to the probiotic and prebiotic effects of exclusive breastfeeding, reinforcing the importance of exclusive breastfeeding until the 6(th) month of life. Copyright © 2017 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

  13. Development and Use of Integrated Microarray-Based Genomic Technologies for Assessing Microbial Community Composition and Dynamics

    SciTech Connect

    J. Zhou; S.-K. Rhee; C. Schadt; T. Gentry; Z. He; X. Li; X. Liu; J. Liebich; S.C. Chong; L. Wu

    2004-03-17

    different microbial communities and processes at the NABIR-FRC in Oak Ridge, TN. One project involves the monitoring of the development and dynamics of the microbial community of a fluidized bed reactor (FBR) used for reducing nitrate and the other project monitors microbial community responses to stimulation of uranium reducing populations via ethanol donor additions in situ and in a model system. Additionally, we are developing novel strategies for increasing microarray hybridization sensitivity. Finally, great improvements to our methods of probe design were made by the development of a new computer program, CommOligo. CommOligo designs unique and group-specific oligo probes for whole-genomes, metagenomes, and groups of environmental sequences and uses a new global alignment algorithm to design single or multiple probes for each gene or group. We are now using this program to design a more comprehensive functional gene array for environmental studies. Overall, our results indicate that the 50mer-based microarray technology has potential as a specific and quantitative tool to reveal the composition of microbial communities and their dynamics important to processes within contaminated environments.

  14. Development and Use of Integrated Microarray-Based Genomic Technologies for Assessing Microbial Community Composition and Dynamics

    SciTech Connect

    Zhou, J.; Wu, L.; Gentry, T.; Schadt, C.; He, Z.; Li, X.

    2006-04-05

    different microbial communities and processes at the NABIR-FRC in Oak Ridge, TN. One project involves the monitoring of the development and dynamics of the microbial community of a fluidized bed reactor (FBR) used for reducing nitrate and the other project monitors microbial community responses to stimulation of uranium reducing populations via ethanol donor additions in situ and in a model system. Additionally, we are developing novel strategies for increasing microarray hybridization sensitivity. Finally, great improvements to our methods of probe design were made by the development of a new computer program, CommOligo. CommOligo designs unique and group-specific oligo probes for whole-genomes, metagenomes, and groups of environmental sequences and uses a new global alignment algorithm to design single or multiple probes for each gene or group. We are now using this program to design a more comprehensive functional gene array for environmental studies. Overall, our results indicate that the 50mer-based microarray technology has potential as a specific and quantitative tool to reveal the composition of microbial communities and their dynamics important to processes within contaminated environments.

  15. Novel Assay To Assess Permissiveness of a Soil Microbial Community toward Receipt of Mobile Genetic Elements▿ †

    PubMed Central

    Musovic, Sanin; Dechesne, Arnaud; Sørensen, Jan; Smets, Barth F.

    2010-01-01

    There is a wealth of evidence indicating that mobile genetic elements can spread in natural microbial communities. However, little is known regarding the fraction of the community that actually engages in this behavior. Here we report on a new approach to quantify the fraction of a bacterial community that is able to receive and maintain an exogenous conjugal plasmid termed community permissiveness. Conjugal transfer of a broad-host-range plasmid labeled with a zygotically inducible green fluorescent protein (RP4::gfp) from a donor strain (Pseudomonas putida) to a soil bacterial suspension was examined. The mixture of cells was incubated on membrane filters supported by different solid media. Plasmid transfer was scored by in situ visualization of green fluorescent transconjugant microcolonies, and host range was determined by traditional plating or microcolony isolation by using a micromanipulator. Among the conditions tested, the highest plasmid transfer incidence (approximately 1 transfer per 104 soil bacteria) was measured after 48 h of incubation on either a 10% soil extract or a 10-fold diluted R2A medium. Stereomicroscopy combined with image analysis allowed easy examination and enumeration of green fluorescent microcolonies. In all experiments, however, stereomicroscopy consistently underestimated the number of conjugation events (approximately 10-fold) in comparison to confocal laser scanning microscopy. The plasmid host range was broad and included bacteria belonging to the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria classes of proteobacteria. The isolation of transconjugant microcolonies by micromanipulation greatly extended the estimated plasmid host range among soil bacteria. The new approach can be applied to examine the permissiveness of various communities toward receipt of different mobile elements. PMID:20511430

  16. Ammonium removal from high-salinity oilfield-produced water: assessing the microbial community dynamics at increasing salt concentrations.

    PubMed

    Quartaroli, Larissa; Silva, Lívia C Fidélis; Silva, Claudio Mudadu; Lima, Helena Santiago; de Paula, Sergio Oliveira; de Oliveira, Valéria Maia; de Cássia S da Silva, Marliane; Kasuya, Maria Catarina M; de Sousa, Maíra Paula; Torres, Ana Paula R; Souza, Rodrigo Suhett; Bassin, João Paulo; da Silva, Cynthia Canêdo

    2017-01-01

    Water generated during oil exploration is chemically complex and contains high concentrations of ammonium and, in some cases, high salinity. The most common way to remove ammonium from effluent is a biological process, which can be performed by different routes and different groups of microorganisms. However, the presence of salts in the effluents could be an inhibiting factor for biological processes, interfering directly with treatment. This study aimed to evaluate changes in the profile of a microbial community involved in the process of ammonium removal when subjected to a gradual increase of salt (NaCl), in which the complete inhibition of the ammonium removal process occurred at 125 g L(-1) NaCl. During the sludge acclimatization process, samples were collected and submitted to denaturing gradient gel electrophoresis (DGGE) and massive sequencing of the 16S ribosomal RNA (rRNA) genes. As the salt concentration increased in the reactor, a change in the microbial community was observed by the DGGE band profiles. As a result, there was a reduction in the presence of bacterial populations, and an increase in archaeal populations was found. The sequencing data suggested that ammonium removal in the reactor was carried out by different metabolic routes by autotrophic nitrifying bacteria, such as Nitrosococcus, Nitrosomonas, Nitrosovibrio, Nitrospira, and Nitrococcus; ammonium-oxidizing archaea Candidatus nitrosoarchaeum; ANAMMOX microorganisms, such as Candidatus brocadia, Candidatus kuenenia, and Candidatus scalindua; and microorganisms with the potential to be heterotrophic nitrifying, such as Paracoccus spp., Pseudomonas spp., Bacillus spp., Marinobacter sp., and Alcaligenes spp.

  17. Use of Microarray-based Genomic Technologies for Assessing Microbial Community Composition and Dynamics in Contaminated Groundwater

    NASA Astrophysics Data System (ADS)

    Zhou, J.; Schadt, C.; Gentry, T.; He, Z.; Wu, L.; Rhee, S.; Liu, X.; Liebich, J.; Chong, S.; Yang, Z.; Gao, H.

    2004-12-01

    To effectively monitor microbial populations involved in various important processes, a 50-mer-based oligonucleotide microarray was developed based on known genes and pathways involved in: biodegradation, metal resistance and reduction, denitrification, nitrification, nitrogen fixation, methane oxidation, methanogenesis, carbon polymer decomposition, and sulfate reduction. This array contains approx 2000 unique and group-specific probes with <85% similarity to their non-target sequences. Based on artificial probes, our results showed that at hybridization conditions of 50oC and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. Detection limits were about 5-10ng genomic DNA in the absence of background DNA, and 50-100ng ( ˜1.3 ¡A107 cells) in the presence background DNA. Strong linear relationships between signal intensity and target DNA and RNA concentration were observed (r2 = 0.95-0.99). Real-time PCR analysis of 12 representative genes was consistent with microarray-based quantification (r2 = 0.95). Also novel approaches were developed and used to increase microarray detection sensitivity of both DNA and mRNA. Application of these array-based technologies to analyze microbial communities in contaminated groundwaters from the US Department of Energy¡_s Natural and Accelerated Bioremediation Research Program (NABIR) Field Research Center at Oak Ridge, TN, demonstrated that it is feasible to biostimulate the indigenous microbial populations for contaminant remediation but the process could be very complicated due to highly spatial heterogeneous microbial distributions. Based on these results, more comprehensive functional gene arrays containing ˜27,000 probes from the genes important for biogeochemical cycling of C, N, S, P, metal resistance and

  18. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity.

  19. Interactions Among Grassland Plant Species, Microbial Communities, and Soil Processes

    NASA Astrophysics Data System (ADS)

    Eviner, V.; Waldrop, M.; Schwartz, E.; Pett-Ridge, J.; Firestone, M.

    2002-12-01

    Plant-microbial interactions are thought to be an important determinant of ecosystem processes, yet we do not know whether impacts of plant species on soil microbial community composition translate to impacts on function. We established field plots in a California annual grassland of five plant monocultures for two years to determine the effects of different plant species on the composition of the bulk soil microbial community and selected soil processes. Plant species were associated with distinct ecosystem process rates such as net nitrogen mineralization, nitrification, decomposition and soil respiration. Bacterial community substrate utilization profiles differed among different plant species and were related to labile soil C. DNA-based fingerprints of bacterial, ammonia oxidizer, and fungal communities did not generally differ in soils planted to different species; however, these microbial community profiles did strongly correlate to rates of decomposition. Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis of soil microbial communities showed that the lupine community was distinct from the other four plant-associated communities. Phospholipid fatty acid (PLFA) patterns also failed to distinguish differences in the overall microbial communities associated with the five different moncultures. Interestingly, PLFA biomarker 16:1w5, indicative of AM fungi, differed among plant species treatments. This PLFA biomarker and bacterial TRFLP patterns were related to decomposition rates of a common litter. In summary, large functional differences were found between field plots with different plant species and the composition of the microbial communities was closely related to some of the functions assessed, independent of plant species. Only small plant-induced changes in microbial community composition were detected, yet apparently these changes had significant impact on function. Our analyses were not specifically targeted to microsites with high

  20. Glycoside Hydrolases across Environmental Microbial Communities

    PubMed Central

    Berlemont, Renaud

    2016-01-01

    Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities. PMID:27992426

  1. Metaproteomic analysis of Chesapeake Bay microbial communities

    PubMed Central

    Kan, Jinjun; Hanson, Thomas E; Ginter, Joy M; Wang, Kui; Chen, Feng

    2005-01-01

    Background Natural microbial communities are extremely complex and dynamic systems in terms of their population structure and functions. However, little is known about the in situ functions of the microbial communities. Results This study describes the application of proteomic approaches (metaproteomics) to observe expressed protein profiles of natural microbial communities (metaproteomes). The technique was validated using a constructed community and subsequently used to analyze Chesapeake Bay microbial community (0.2 to 3.0 μm) metaproteomes. Chesapeake Bay metaproteomes contained proteins from pI 4–8 with apparent molecular masses between 10–80 kDa. Replicated middle Bay metaproteomes shared ~92% of all detected spots, but only shared 30% and 70% of common protein spots with upper and lower Bay metaproteomes. MALDI-TOF analysis of highly expressed proteins produced no significant matches to known proteins. Three Chesapeake Bay proteins were tentatively identified by LC-MS/MS sequencing coupled with MS-BLAST searching. The proteins identified were of marine microbial origin and correlated with abundant Chesapeake Bay microbial lineages, Bacteroides and α-proteobacteria. Conclusion Our results represent the first metaproteomic study of aquatic microbial assemblages and demonstrate the potential of metaproteomic approaches to link metagenomic data, taxonomic diversity, functional diversity and biological processes in natural environments. PMID:16176596

  2. Two-stage microbial community experimental design

    PubMed Central

    Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, Curtis

    2013-01-01

    Microbial community samples can be efficiently surveyed in high throughput by sequencing markers such as the 16S ribosomal RNA gene. Often, a collection of samples is then selected for subsequent metagenomic, metabolomic or other follow-up. Two-stage study design has long been used in ecology but has not yet been studied in-depth for high-throughput microbial community investigations. To avoid ad hoc sample selection, we developed and validated several purposive sample selection methods for two-stage studies (that is, biological criteria) targeting differing types of microbial communities. These methods select follow-up samples from large community surveys, with criteria including samples typical of the initially surveyed population, targeting specific microbial clades or rare species, maximizing diversity, representing extreme or deviant communities, or identifying communities distinct or discriminating among environment or host phenotypes. The accuracies of each sampling technique and their influences on the characteristics of the resulting selected microbial community were evaluated using both simulated and experimental data. Specifically, all criteria were able to identify samples whose properties were accurately retained in 318 paired 16S amplicon and whole-community metagenomic (follow-up) samples from the Human Microbiome Project. Some selection criteria resulted in follow-up samples that were strongly non-representative of the original survey population; diversity maximization particularly undersampled community configurations. Only selection of intentionally representative samples minimized differences in the selected sample set from the original microbial survey. An implementation is provided as the microPITA (Microbiomes: Picking Interesting Taxa for Analysis) software for two-stage study design of microbial communities. PMID:23949665

  3. Two-stage microbial community experimental design.

    PubMed

    Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, Curtis

    2013-12-01

    Microbial community samples can be efficiently surveyed in high throughput by sequencing markers such as the 16S ribosomal RNA gene. Often, a collection of samples is then selected for subsequent metagenomic, metabolomic or other follow-up. Two-stage study design has long been used in ecology but has not yet been studied in-depth for high-throughput microbial community investigations. To avoid ad hoc sample selection, we developed and validated several purposive sample selection methods for two-stage studies (that is, biological criteria) targeting differing types of microbial communities. These methods select follow-up samples from large community surveys, with criteria including samples typical of the initially surveyed population, targeting specific microbial clades or rare species, maximizing diversity, representing extreme or deviant communities, or identifying communities distinct or discriminating among environment or host phenotypes. The accuracies of each sampling technique and their influences on the characteristics of the resulting selected microbial community were evaluated using both simulated and experimental data. Specifically, all criteria were able to identify samples whose properties were accurately retained in 318 paired 16S amplicon and whole-community metagenomic (follow-up) samples from the Human Microbiome Project. Some selection criteria resulted in follow-up samples that were strongly non-representative of the original survey population; diversity maximization particularly undersampled community configurations. Only selection of intentionally representative samples minimized differences in the selected sample set from the original microbial survey. An implementation is provided as the microPITA (Microbiomes: Picking Interesting Taxa for Analysis) software for two-stage study design of microbial communities.

  4. Microbial community assembly and metabolic function during mammalian corpse decomposition

    SciTech Connect

    Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

    2015-12-10

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  5. Microbial community assembly and metabolic function during mammalian corpse decomposition.

    PubMed

    Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

    2016-01-08

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  6. Microbial community assembly and metabolic function during mammalian corpse decomposition

    USGS Publications Warehouse

    Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

    2016-01-01

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  7. Environmental Regulation of Microbial Community Structure

    NASA Technical Reports Server (NTRS)

    Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

    2002-01-01

    Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.

  8. Environmental Regulation of Microbial Community Structure

    NASA Technical Reports Server (NTRS)

    Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

    2002-01-01

    Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.

  9. Preliminary assessment of microbial communities and biodegradation of chlorinated volatile organic compounds in wetlands at Cluster 13, Lauderick Creek area, Aberdeen Proving Ground, Maryland

    USGS Publications Warehouse

    Lorah, Michelle M.; Voytek, Mary A.; Spencer, Tracey A.

    2003-01-01

    A preliminary assessment of the microbial communities and biodegradation processes for chlorinated volatile organic compounds was con-ducted by the U.S. Geological Survey in wetlands at the Cluster 13, Lauderick Creek area at Aberdeen Proving Ground, Maryland. The U.S. Geological Survey collected wetland sediment samples from 11 sites in the Lauderick Creek area for microbial analyses, and used existing data to evaluate biodegradation processes and rates. The bacterial and methanogen communities in the Lauderick Creek wetland sediments were similar to those observed in a previous U.S. Geological Survey study at the West Branch Canal Creek wet-land area, Aberdeen Proving Ground. Evaluation of the degradation rate of 1,1,2,2-tetrachloroethane and the daughter compounds produced also showed similar results for the two wetlands. How-ever, a vertical profile of contaminant concentra-tions in the wetlands was available at only one site in the Lauderick Creek area, and flow velocities in the wetland sediment are unknown. To better evaluate natural attenuation processes and rates in the wetland sediments at Lauderick Creek, chemi-cal and hydrologic measurements are needed along ground-water flowpaths in the wetland at additional sites and during different seasons. Nat-ural attenuation in the wetlands, enhanced biore-mediation, and constructed wetlands could be feasible remediation methods for the chlorinated volatile organic compounds discharging in the Lauderick Creek area. The similarities in the microbial communities and biodegradation pro-cesses at the Lauderick Creek and West Branch Canal Creek areas indicate that enhanced bioreme-diation techniques currently being developed for the West Branch Canal Creek wetland area would be transferable to this area.

  10. Composition and physiological profiling of sprout-associated microbial communities

    NASA Technical Reports Server (NTRS)

    Matos, Anabelle; Garland, Jay L.; Fett, William F.

    2002-01-01

    The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of

  11. Composition and physiological profiling of sprout-associated microbial communities.

    PubMed

    Matos, Anabelle; Garland, Jay L; Fett, William F

    2002-12-01

    The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of

  12. Signaling in host-associated microbial communities

    PubMed Central

    Fischbach, Michael A.; Segre, Julia A.

    2016-01-01

    Human-associated microbiota form and stabilize communities based on interspecies interactions. We review how these microbe-microbe and microbe-host interactions are communicated to shape communities over a human’s lifespan, including periods of health and disease. Modeling and dissecting signaling in host-associated communities is crucial to understand their function, and will open the door to therapies that prevent or correct microbial community dysfunction to promote health and treat disease. PMID:26967294

  13. High-resolution phylogenetic microbial community profiling

    SciTech Connect

    Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; Bowman, Brett; Bowers, Robert M.; Levy, Asaf; Gies, Esther A.; Cheng, Jan -Fang; Copeland, Alex; Klenk, Hans -Peter; Hallam, Steven; Hugenholtz, Philip; Tringe, Susannah G.; Woyke, Tanja

    2016-02-09

    Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.

  14. High-resolution phylogenetic microbial community profiling

    PubMed Central

    Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; Bowman, Brett; Bowers, Robert M; Levy, Asaf; Gies, Esther A; Cheng, Jan-Fang; Copeland, Alex; Klenk, Hans-Peter; Hallam, Steven J; Hugenholtz, Philip; Tringe, Susannah G; Woyke, Tanja

    2016-01-01

    Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential. PMID:26859772

  15. Surface reflectance degradation by microbial communities

    DOE PAGES

    Cheng, Meng -Dawn; Allman, Steve L.; Graham, David E.; ...

    2015-11-05

    Building envelope, such as a roof, is the interface between a building structure and the environment. Understanding of the physics of microbial interactions with the building envelope is limited. In addition to the natural weathering, microorganisms and airborne particulate matter that attach to a cool roof tend to reduce the roof reflectance over time, compromising the energy efficiency advantages of the reflective coating designs. We applied microbial ecology analysis to identify the natural communities present on the exposed coatings and investigated the reduction kinetics of the surface reflectance upon the introduction of a defined mixture of both photoautotrophic and heterotrophicmore » microorganisms representing the natural communities. The result are (1) reflectance degradation by microbial communities follows a first-order kinetic relationship and (2) more than 50% of degradation from the initial reflectance value can be caused by microbial species alone in much less time than 3 years required by the current standard ENERGY STAR® test methods.« less

  16. Surface reflectance degradation by microbial communities

    SciTech Connect

    Cheng, Meng -Dawn; Allman, Steve L.; Graham, David E.; Cheng, Karen R.; Pfiffner, Susan Marie; Vishnivetskaya, Tatiana A.; Desjarlais, Andre Omer

    2015-11-05

    Building envelope, such as a roof, is the interface between a building structure and the environment. Understanding of the physics of microbial interactions with the building envelope is limited. In addition to the natural weathering, microorganisms and airborne particulate matter that attach to a cool roof tend to reduce the roof reflectance over time, compromising the energy efficiency advantages of the reflective coating designs. We applied microbial ecology analysis to identify the natural communities present on the exposed coatings and investigated the reduction kinetics of the surface reflectance upon the introduction of a defined mixture of both photoautotrophic and heterotrophic microorganisms representing the natural communities. The result are (1) reflectance degradation by microbial communities follows a first-order kinetic relationship and (2) more than 50% of degradation from the initial reflectance value can be caused by microbial species alone in much less time than 3 years required by the current standard ENERGY STAR® test methods.

  17. Soil microbial community of abandoned sand fields.

    PubMed

    Elhottová, D; Szili-Kovács, T; Tríska, J

    2002-01-01

    Microbiological evaluation of sandy grassland soils from two different stages of secondary succession on abandoned fields (4 and 8 years old fallow) was carried out as a part of research focused on restoration of semi-natural vegetation communities in Kiskunság National Park in Hungary. There was an apparent total N and organic C enrichment, stimulation of microbial growth and microbial community structure change on fields abandoned by agricultural practice (small family farm) in comparison with native undisturbed grassland. A successional trend of the microbial community was found after 4 and 8 years of fallow-lying soil. It consisted in a shift of r-survival strategy to more efficient C economy, in a decrease of specific respiration and metabolic activity, forced accumulation of storage bacterial compounds and increased fungal distribution. The composition of microbial phospholipid fatty acids mixture of soils abandoned at various times was significantly different.

  18. Impact of diverse soil microbial communities on crop residues decomposition

    NASA Astrophysics Data System (ADS)

    Mrad, Fida; Bennegadi-Laurent, Nadia; Ailhas, Jérôme; Leblanc, Nathalie; Trinsoutrot-Gattin, Isabelle; Laval, Karine; Gattin, Richard

    2017-04-01

    mineralization, and chemical measures. Physicochemical composition of crop residues was assessed by Fourier transform infrared spectroscopy FTIR technique at 0 and 83 days. The experiment was conducted in microcosms over 83 days for the biological measurements and 175 days for the C mineralization. The first results showed variations in the C & N rates, and the microbial abundances and functions over time, with a peak at 5 days and a decrease at 83 days for most of the measurements. The soil microbial communities' composition (different management practices) highly impacted the crop residues decomposition. The biochemical composition of crop residues influenced less the microbial communities of each soil. Further studies on the valorization of these residues into agro materials will be carried out. References: Andrews SS., Karlen DL., and Cambardella CA. (2004) The soil management assessment framework: a quantitative soil quality evaluation method. Soil Science Society of America, 68: 1945-1962

  19. Anthropogenic perturbations in marine microbial communities.

    PubMed

    Nogales, Balbina; Lanfranconi, Mariana P; Piña-Villalonga, Juana M; Bosch, Rafael

    2011-03-01

    Human activities impact marine ecosystems at a global scale and all levels of complexity of life. Despite their importance as key players in ecosystem processes, the stress caused to microorganisms has been greatly neglected. This fact is aggravated by difficulties in the analysis of microbial communities and their high diversity, making the definition of patterns difficult. In this review, we discuss the effects of nutrient increase, pollution by organic chemicals and heavy metals and the introduction of antibiotics and pathogens into the environment. Microbial communities respond positively to nutrients and chemical pollution by increasing cell numbers. There are also significant changes in community composition, increases in diversity and high temporal variability. These changes, which evidence the modification of the environmental conditions due to anthropogenic stress, usually alter community functionality, although this aspect has not been explored in depth. Altered microbial communities in human-impacted marine environments can in turn have detrimental effects on human health (i.e. spread of pathogens and antibiotic resistance). New threats to marine ecosystems, i.e. related to climate change, could also have an impact on microbial communities. Therefore, an effort dedicated to analyse the microbial compartment in detail should be made when studying the impact of anthropogenic activities on marine ecosystems.

  20. Interspecies Interactions within Oral Microbial Communities

    PubMed Central

    Kuramitsu, Howard K.; He, Xuesong; Lux, Renate; Anderson, Maxwell H.; Shi, Wenyuan

    2007-01-01

    Summary: While reductionism has greatly advanced microbiology in the past 400 years, assembly of smaller pieces just could not explain the whole! Modern microbiologists are learning “system thinking” and “holism.” Such an approach is changing our understanding of microbial physiology and our ability to diagnose/treat microbial infections. This review uses oral microbial communities as a focal point to describe this new trend. With the common name “dental plaque,” oral microbial communities are some of the most complex microbial floras in the human body, consisting of more than 700 different bacterial species. For a very long time, oral microbiologists endeavored to use reductionism to identify the key genes or key pathogens responsible for oral microbial pathogenesis. The limitations of reductionism forced scientists to begin adopting new strategies using emerging concepts such as interspecies interaction, microbial community, biofilms, polymicrobial disease, etc. These new research directions indicate that the whole is much more than the simple sum of its parts, since the interactions between different parts resulted in many new physiological functions which cannot be observed with individual components. This review describes some of these interesting interspecies-interaction scenarios. PMID:18063722

  1. Nutrient Addition Dramatically Accelerates Microbial Community Succession

    PubMed Central

    Knelman, Joseph E.; Schmidt, Steven K.; Lynch, Ryan C.; Darcy, John L.; Castle, Sarah C.; Cleveland, Cory C.; Nemergut, Diana R.

    2014-01-01

    The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients – important drivers of plant succession – affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession. PMID:25050551

  2. Nutrient addition dramatically accelerates microbial community succession.

    PubMed

    Knelman, Joseph E; Schmidt, Steven K; Lynch, Ryan C; Darcy, John L; Castle, Sarah C; Cleveland, Cory C; Nemergut, Diana R

    2014-01-01

    The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients--important drivers of plant succession--affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession.

  3. Assessment of microbial communities associated with fermentative-methanogenic biodegradation of aromatic hydrocarbons in groundwater contaminated with a biodiesel blend (B20).

    PubMed

    Ramos, Débora Toledo; da Silva, Márcio Luís Busi; Nossa, Carlos Wolfgang; Alvarez, Pedro J J; Corseuil, Henry Xavier

    2014-09-01

    A controlled field experiment was conducted to assess the potential for fermentative-methanogenic biostimulation (by ammonium-acetate injection) to enhance biodegradation of benzene, toluene, ethylbenzene and xylenes (BTEX) as well as polycyclic aromatic hydrocarbons (PAHs) in groundwater contaminated with biodiesel B20 (20:80 v/v soybean biodiesel and diesel). Changes in microbial community structure were assessed by pyrosequencing 16S rRNA analyses. BTEX and PAH removal began 0.7 year following the release, concomitantly with the increase in the relative abundance of Desulfitobacterium and Geobacter spp. (from 5 to 52.7 % and 15.8 to 37.3 % of total Bacteria 16S rRNA, respectively), which are known to anaerobically degrade hydrocarbons. The accumulation of anaerobic metabolites acetate and hydrogen that could hinder the thermodynamic feasibility of BTEX and PAH biotransformations under fermentative/methanogenic conditions was apparently alleviated by the growing predominance of Methanosarcina. This suggests the importance of microbial population shifts that enrich microorganisms capable of interacting syntrophically to enhance the feasibility of fermentative-methanogenic bioremediation of biodiesel blend releases.

  4. Chernozems microbial community under anthropogenic impact (Russia)

    NASA Astrophysics Data System (ADS)

    Ivashchenko, Kristina; Ananyeva, Nadezhda; Sushko, Sofia; Vasenev, Viacheslav

    2017-04-01

    Chernozems is important natural resource, which in the last decade under intense influence as a result of plowing and urbanization. The parameters of soil microbial community functioning might be identify some soil deterioration under the impacts. Our research was focused on assessment of microbial community status in different soil layers of virgin steppe, bare fallow and urban ecosystems (Kursk region). In each ecosystem, we chose randomly 3-5 spatially distributed sites, where soil samples were collected by auguring up to 0.5 m depth (each layer 10 cm thickness) and up to 1.5 m depth (0-10, 10-50, 50-100, 100-150 cm layers), totally 127 samples. The bulk density was measured for these soil layers. In all soil samples the microbial biomass carbon content (Cmic) was analyzed by substrate-induced respiration (SIR) method and basal respiration (BR) was assessed by CO2 rate production. The fungi-to-bacteria ratio (selective inhibition technique with antibiotics) was determined and portion of Cmic in soil organic carbon (Corg) content was calculated in topsoil (0-10 cm). The Corg (dichromate oxidation) and pHw (potentiometry) values were measured. The Cmic and BR profile pools were calculated using bulk density and thickness of studied layers. The Cmic (0-10 cm) was varied from 84 to 1954 µg C g-1 soil, in steppe it was on average 3-4 times higher than those in bare fallow and urban. The BR rate was amounted from 0.20 to 1.57 µg CO2-C g-1 soil h-1, however no significant difference between studied ecosystems was found. It was shown the relationship between Cmic, BR and Corg (the linear regression, R2=0.92 and 0.75, respectively, p<0.05). The Cmic / Corg ratio in steppe was on average 3.3%, it was significantly higher those bare fallow and urban (1.6 and 0.7%, respectively). The fungi-to-bacteria ratio was decreased along ecosystems row: virgin steppe>bare fallow>urban, and it was on average 6.0, 5.2 and 1.8, respectively. The Cmic profile pool (0.5 m) of steppe was

  5. Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing "Stress-on-Stress" Responses.

    PubMed

    Azarbad, Hamed; van Gestel, Cornelis A M; Niklińska, Maria; Laskowski, Ryszard; Röling, Wilfred F M; van Straalen, Nico M

    2016-06-14

    Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the "costs" of adaptation to metals affect the responses of metal-tolerant communities to other stress factors ("stress-on-stress"). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors.

  6. Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses

    PubMed Central

    Azarbad, Hamed; van Gestel, Cornelis A. M.; Niklińska, Maria; Laskowski, Ryszard; Röling, Wilfred F. M.; van Straalen, Nico M.

    2016-01-01

    Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination have been shown to maintain their function by developing metal-tolerance mechanisms. In the present work, we review recent experiments, with specific emphasis on studies that have been conducted in polluted areas with a long-term history of contamination that also applied DNA-based approaches. We evaluate how the “costs” of adaptation to metals affect the responses of metal-tolerant communities to other stress factors (“stress-on-stress”). We discuss recent studies on the stability of microbial communities, in terms of resistance and resilience to additional stressors, focusing on metal pollution as the initial stress, and discuss possible factors influencing the functional and structural stability of microbial communities towards secondary stressors. There is increasing evidence that the history of environmental conditions and disturbance regimes play central roles in responses of microbial communities towards secondary stressors. PMID:27314330

  7. Stable microbial community composition on the Greenland Ice Sheet.

    PubMed

    Musilova, Michaela; Tranter, Martyn; Bennett, Sarah A; Wadham, Jemma; Anesio, Alexandre M

    2015-01-01

    The first molecular-based studies of microbes in snow and on glaciers have only recently been performed on the vast Greenland Ice Sheet (GrIS). Aeolian microbial seeding is hypothesized to impact on glacier surface community compositions. Localized melting of glacier debris (cryoconite) into the surface ice forms cryoconite holes, which are considered 'hot spots' for microbial activity on glaciers. To date, few studies have attempted to assess the origin and evolution of cryoconite and cryoconite hole communities throughout a melt season. In this study, a range of experimental approaches was used for the first time to study the inputs, temporal and structural transformations of GrIS microbial communities over the course of a whole ablation season. Small amounts of aeolian (wind and snow) microbes were potentially seeding the stable communities that were already present on the glacier (composed mainly of Proteobacteria, Cyanobacteria, and Actinobacteria). However, the dominant bacterial taxa in the aeolian samples (Firmicutes) did not establish themselves in local glacier surface communities. Cryoconite and cryoconite hole community composition remained stable throughout the ablation season following the fast community turnover, which accompanied the initial snow melt. The presence of stable communities in cryoconite and cryoconite holes on the GrIS will allow future studies to assess glacier surface microbial diversity at individual study sites from sampling intervals of short duration only. Aeolian inputs also had significantly different organic δ(13)C values (-28.0 to -27.0‰) from the glacier surface values (-25.7 to -23.6‰), indicating that in situ microbial processes are important in fixing new organic matter and transforming aeolian organic carbon. The continuous productivity of stable communities over one melt season makes them important contributors to biogeochemical nutrient cycling on glaciers.

  8. Stable microbial community composition on the Greenland Ice Sheet

    PubMed Central

    Musilova, Michaela; Tranter, Martyn; Bennett, Sarah A.; Wadham, Jemma; Anesio, Alexandre M.

    2015-01-01

    The first molecular-based studies of microbes in snow and on glaciers have only recently been performed on the vast Greenland Ice Sheet (GrIS). Aeolian microbial seeding is hypothesized to impact on glacier surface community compositions. Localized melting of glacier debris (cryoconite) into the surface ice forms cryoconite holes, which are considered ‘hot spots’ for microbial activity on glaciers. To date, few studies have attempted to assess the origin and evolution of cryoconite and cryoconite hole communities throughout a melt season. In this study, a range of experimental approaches was used for the first time to study the inputs, temporal and structural transformations of GrIS microbial communities over the course of a whole ablation season. Small amounts of aeolian (wind and snow) microbes were potentially seeding the stable communities that were already present on the glacier (composed mainly of Proteobacteria, Cyanobacteria, and Actinobacteria). However, the dominant bacterial taxa in the aeolian samples (Firmicutes) did not establish themselves in local glacier surface communities. Cryoconite and cryoconite hole community composition remained stable throughout the ablation season following the fast community turnover, which accompanied the initial snow melt. The presence of stable communities in cryoconite and cryoconite holes on the GrIS will allow future studies to assess glacier surface microbial diversity at individual study sites from sampling intervals of short duration only. Aeolian inputs also had significantly different organic δ13C values (-28.0 to -27.0‰) from the glacier surface values (-25.7 to -23.6‰), indicating that in situ microbial processes are important in fixing new organic matter and transforming aeolian organic carbon. The continuous productivity of stable communities over one melt season makes them important contributors to biogeochemical nutrient cycling on glaciers. PMID:25852658

  9. Microbial astronauts: assembling microbial communities for advanced life support systems

    NASA Technical Reports Server (NTRS)

    Roberts, M. S.; Garland, J. L.; Mills, A. L.

    2004-01-01

    Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem

  10. Gut microbial communities of social bees.

    PubMed

    Kwong, Waldan K; Moran, Nancy A

    2016-06-01

    The gut microbiota can have profound effects on hosts, but the study of these relationships in humans is challenging. The specialized gut microbial community of honey bees is similar to the mammalian microbiota, as both are mostly composed of host-adapted, facultatively anaerobic and microaerophilic bacteria. However, the microbial community of the bee gut is far simpler than the mammalian microbiota, being dominated by only nine bacterial species clusters that are specific to bees and that are transmitted through social interactions between individuals. Recent developments, which include the discovery of extensive strain-level variation, evidence of protective and nutritional functions, and reports of eco-physiological or disease-associated perturbations to the microbial community, have drawn attention to the role of the microbiota in bee health and its potential as a model for studying the ecology and evolution of gut symbionts.

  11. Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities.

    PubMed

    Patin, Nastassia V; Schorn, Michelle; Aguinaldo, Kristen; Lincecum, Tommie; Moore, Bradley S; Jensen, Paul R

    2017-02-15

    Marine sediments harbor complex microbial communities that remain poorly studied relative to other biomes such as seawater. Moreover, bacteria in these communities produce antibiotics and other bioactive secondary metabolites, yet little is known about how these compounds affect microbial community structure. In this study, we used next-generation amplicon sequencing to assess native microbial community composition in shallow tropical marine sediments. The results revealed complex communities comprised of largely uncultured taxa, with considerable spatial heterogeneity and known antibiotic producers comprising only a small fraction of the total diversity. Organic extracts from cultured strains of the sediment-dwelling actinomycete genus Salinispora were then used in mesocosm studies to address how secondary metabolites shape sediment community composition. We identified predatory bacteria and other taxa that were consistently reduced in the extract-treated mesocosms, suggesting that they may be the targets of allelopathic interactions. We tested related taxa for extract sensitivity and found general agreement with the culture-independent results. Conversely, several taxa were enriched in the extract-treated mesocosms, suggesting that some bacteria benefited from the interactions. The results provide evidence that bacterial secondary metabolites can have complex and significant effects on sediment microbial communities.

  12. Does iron inhibit cryptoendolithic microbial communities?

    NASA Technical Reports Server (NTRS)

    Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

    1988-01-01

    Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

  13. Does iron inhibit cryptoendolithic microbial communities?

    NASA Technical Reports Server (NTRS)

    Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

    1988-01-01

    Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

  14. Microbial Community Degradation of Widely Used Quaternary Ammonium Disinfectants

    PubMed Central

    Oh, Seungdae; Kurt, Zohre; Tsementzi, Despina; Weigand, Michael R.; Kim, Minjae; Hatt, Janet K.; Tandukar, Madan; Pavlostathis, Spyros G.; Spain, Jim C.

    2014-01-01

    Benzalkonium chlorides (BACs) are disinfectants widely used in a variety of clinical and environmental settings to prevent microbial infections, and they are frequently detected in nontarget environments, such as aquatic and engineered biological systems, even at toxic levels. Therefore, microbial degradation of BACs has important ramifications for alleviating disinfectant toxicity in nontarget environments as well as compromising disinfectant efficacy in target environments. However, how natural microbial communities respond to BAC exposure and what genes underlie BAC biodegradation remain elusive. Our previous metagenomic analysis of a river sediment microbial community revealed that BAC exposure selected for a low-diversity community, dominated by several members of the Pseudomonas genus that quickly degraded BACs. To elucidate the genetic determinants of BAC degradation, we conducted time-series metatranscriptomic analysis of this microbial community during a complete feeding cycle with BACs as the sole carbon and energy source under aerobic conditions. Metatranscriptomic profiles revealed a candidate gene for BAC dealkylation, the first step in BAC biodegradation that results in a product 500 times less toxic. Subsequent biochemical assays and isolate characterization verified that the putative amine oxidase gene product was functionally capable of initiating BAC degradation. Our analysis also revealed cooperative interactions among community members to alleviate BAC toxicity, such as the further degradation of BAC dealkylation by-products by organisms not encoding amine oxidase. Collectively, our results advance the understanding of BAC aerobic biodegradation and provide genetic biomarkers to assess the critical first step of this process in nontarget environments. PMID:24951783

  15. Integrated Environmental Modeling: Quantitative Microbial Risk Assessment

    EPA Science Inventory

    The presentation discusses the need for microbial assessments and presents a road map associated with quantitative microbial risk assessments, through an integrated environmental modeling approach. A brief introduction and the strengths of the current knowledge are illustrated. W...

  16. Integrated Environmental Modeling: Quantitative Microbial Risk Assessment

    EPA Science Inventory

    The presentation discusses the need for microbial assessments and presents a road map associated with quantitative microbial risk assessments, through an integrated environmental modeling approach. A brief introduction and the strengths of the current knowledge are illustrated. W...

  17. Development of a Screening Assay for Microbial Community Profiling

    NASA Astrophysics Data System (ADS)

    Miracle, A. L.; Tilton, F.; Bonheyo, G. T.; McDermott, J.

    2010-12-01

    Remediation of subsurface contaminant plumes has been challenging in the aspects of site characterization, design for treatability, and monitoring of treatment efficacy, to name a few. Characterization of physical and geochemical properties can be achieved through advances in sensor technologies, modeling, and well placement. However, the biotic composition within the subsurface is also an important component that adds an additional biochemical contribution that is not currently being assessed. Changes in the environment have impacts to the composition of microbial communities at this solid/fluid phase interface. The introduction of a remediative treatment may provide an abundant food source for microorganisms in the subsurface and alter the community dynamics. Such changes to the microbial community composition may have dramatic effects on bulk community biochemistry, which in turn may affect the quality of the remediative treatment in terms of effectiveness and transport through alteration of the environment. A screening array is being developed based on DNA sequence information from indigenous microorganisms within target sediments to be used to assess microbial community changes throughout remediative treatments and through time. Integration of physical, chemical, and biotic community information will be assessed to determine efficacy of treatment before, during, and after treatment to assess success of treatment, and measure any post-treatment changes.

  18. High-resolution phylogenetic microbial community profiling

    SciTech Connect

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  19. High-resolution phylogenetic microbial community profiling

    DOE PAGES

    Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; ...

    2016-02-09

    Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

  20. Understanding Microbial Communities: Function, Structure and Dynamics

    DTIC Science & Technology

    2015-02-11

    microbial communities: Function, structure and dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to...dynamics’, at the Isaac Newton Institute, University of Cambridge, United Kingdom, from August to December 2014. The programme involved over 150...Communities: Function, Structure and Dynamics’, at the Isaac Newton Institute, Cambridge University, UK, from 19th August 2014 – 19th December 2014

  1. Method for analyzing microbial communities

    DOEpatents

    Zhou, Jizhong [Oak Ridge, TN; Wu, Liyou [Oak Ridge, TN

    2010-07-20

    The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.

  2. Microbial community profiles and microbial carbon cycling in Orca Basin

    NASA Astrophysics Data System (ADS)

    Hyde, A.; Teske, A.; Joye, S. B.; Montoya, J. P.; Nigro, L.

    2016-12-01

    Orca Basin is the largest seafloor brine pools in the world, covering over 400 km2 and reaching brine layer depths of 200 m. The brine pool contains water 8 times denser than the overlying seawater and is separated from the overlying water column by a sharp pycnocline that prevents vertical mixing. The transition from ambient seawater to brine occurs over 100 m [2150 to 2250 m] and is characterized by distinct changes in temperature, salinity, chemical conditions, oxygen, and organic matter concentration. The sharp brine-seawater interface results in a sharp pycnocline, which serves as a particle trap for sinking marine organic matter. Previous studies have used lipids to show that this organic-rich interface is host to an active microbial community which is potentially involved in deep-sea carbon remineralization and metal-cycling. Additionally, previous work on methane, ethane, and propane concentrations and 13C-isotopic signatures has also implicated the brine pool, as well as the interface, as sources for biogenic low-molecular weight hydrocarbons, resulting from the high concentration of suspended organic matter above and within the brine pool. Here we investigate the profiles of microbial community composition and metabolic potential in Orca Basin, ranging from seawater through the Orca Basin chemocline and into the deep Orca Basin brine. To characterize the microbial community and stratification, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing of filtered water above, within, and below the Orca Basin chemocline. Our sequence data shows that three distinct and unique communities exist in the Orca Basin water column. We also use thermodynamic modeling of hydrocarbon degradation to investigate the favorability of C1-C3 hydrocarbon oxidation at the brine-seawater interface and the potential for Orca Basin to serve as a deep-sea hydrocarbon sink.

  3. Modeling adaptation of carbon use efficiency in microbial communities.

    PubMed

    Allison, Steven D

    2014-01-01

    In new microbial-biogeochemical models, microbial carbon use efficiency (CUE) is often assumed to decline with increasing temperature. Under this assumption, soil carbon losses under warming are small because microbial biomass declines. Yet there is also empirical evidence that CUE may adapt (i.e., become less sensitive) to warming, thereby mitigating negative effects on microbial biomass. To analyze potential mechanisms of CUE adaptation, I used two theoretical models to implement a tradeoff between microbial uptake rate and CUE. This rate-yield tradeoff is based on thermodynamic principles and suggests that microbes with greater investment in resource acquisition should have lower CUE. Microbial communities or individuals could adapt to warming by reducing investment in enzymes and uptake machinery. Consistent with this idea, a simple analytical model predicted that adaptation can offset 50% of the warming-induced decline in CUE. To assess the ecosystem implications of the rate-yield tradeoff, I quantified CUE adaptation in a spatially-structured simulation model with 100 microbial taxa and 12 soil carbon substrates. This model predicted much lower CUE adaptation, likely due to additional physiological and ecological constraints on microbes. In particular, specific resource acquisition traits are needed to maintain stoichiometric balance, and taxa with high CUE and low enzyme investment rely on low-yield, high-enzyme neighbors to catalyze substrate degradation. In contrast to published microbial models, simulations with greater CUE adaptation also showed greater carbon storage under warming. This pattern occurred because microbial communities with stronger CUE adaptation produced fewer degradative enzymes, despite increases in biomass. Thus, the rate-yield tradeoff prevents CUE adaptation from driving ecosystem carbon loss under climate warming.

  4. Trajectories of Microbial Community Function in Response to Accelerated Remediation of Subsurface Metal Contaminants

    SciTech Connect

    Firestone, Mary

    2015-01-14

    Objectives of proposed research were to; Determine if the trajectories of microbial community composition and function following organic carbon amendment can be related to, and predicted by, key environmental determinants; Assess the relative importance of the characteristics of the indigenous microbial community, sediment, groundwater, and concentration of organic carbon amendment as the major determinants of microbial community functional response and bioremediation capacity; and Provide a fundamental understanding of the microbial community ecology underlying subsurface metal remediation requisite to successful application of accelerated remediation and long-term stewardship of DOE-IFC sites.

  5. Role of vermicompost chemical composition, microbial functional diversity, and fungal community structure in their microbial respiratory response to three pesticides.

    PubMed

    Fernández-Gómez, Manuel J; Nogales, Rogelio; Insam, Heribert; Romero, Esperanza; Goberna, Marta

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture.

  6. Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

    PubMed Central

    Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

    2016-01-01

    Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. PMID:27527164

  7. Experimental warming effects on the microbial community of a temperate mountain forest soil.

    PubMed

    Schindlbacher, A; Rodler, A; Kuffner, M; Kitzler, B; Sessitsch, A; Zechmeister-Boltenstern, S

    2011-07-01

    Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO(2) (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.

  8. Experimental warming effects on the microbial community of a temperate mountain forest soil

    PubMed Central

    Schindlbacher, A.; Rodler, A.; Kuffner, M.; Kitzler, B.; Sessitsch, A.; Zechmeister-Boltenstern, S.

    2011-01-01

    Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO2 (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency. PMID:21760644

  9. Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities.

    PubMed

    Castro-Nallar, Eduardo; Shen, Ying; Freishtat, Robert J; Pérez-Losada, Marcos; Manimaran, Solaiappan; Liu, Gang; Johnson, W Evan; Crandall, Keith A

    2015-08-16

    The relationships between infections in early life and asthma are not completely understood. Likewise, the clinical relevance of microbial communities present in the respiratory tract is only partially known. A number of microbiome studies analyzing respiratory tract samples have found increased proportions of gamma-Proteobacteria including Haemophilus influenzae, Moraxella catarrhalis, and Firmicutes such as Streptococcus pneumoniae. The aim of this study was to present a new approach that combines RNA microbial identification with host gene expression to characterize and validate metagenomic taxonomic profiling in individuals with asthma. Using whole metagenomic shotgun RNA sequencing, we characterized and compared the microbial communities of individuals, children and adolescents, with asthma and controls. The resulting data were analyzed by partitioning human and microbial reads. Microbial reads were then used to characterize the microbial diversity of each patient, and potential differences between asthmatic and healthy groups. Human reads were used to assess the expression of known genes involved in the host immune response to specific pathogens and detect potential differences between those with asthma and controls. Microbial communities in the nasal cavities of children differed significantly between asthmatics and controls. After read count normalization, some bacterial species were significantly overrepresented in asthma patients (Wald test, p-value < 0.05), including Escherichia coli and Psychrobacter. Among these, Moraxella catarrhalis exhibited ~14-fold over abundance in asthmatics versus controls. Differential host gene expression analysis confirms that the presence of Moraxella catarrhalis is associated to a specific M. catarrhalis core gene signature expressed by the host. For the first time, we show the power of combining RNA taxonomic profiling and host gene expression signatures for microbial identification. Our approach not only identifies

  10. Wetland Microbial Community Response to Restoration

    NASA Astrophysics Data System (ADS)

    Theroux, S.; Hartman, W.; Tringe, S. G.

    2015-12-01

    Wetland restoration has been proposed as a potential long-term carbon storage solution, with a goal of engineering geochemical dynamics to accelerate peat accretion and encourage greenhouse gas (GHG) sequestration. However, wetland microbial community composition and metabolic rates are poorly understood and their predicted response to wetland restoration is a veritable unknown. In an effort to better understand the underlying factors that shape the balance of carbon flux in wetland soils, we targeted the microbial communities along a salinity gradient ranging from freshwater tidal marshes to hypersaline ponds in the San Francisco Bay-Delta region. Using 16S rRNA gene sequencing and shotgun metagenomics, coupled with greenhouse gas measurements, we sampled sixteen sites capturing a range in salinity and restoration status. Seawater delivers sulfate to wetland ecosystems, encouraging sulfate reduction and discouraging methane production. As expected, we observed the highest rates of methane production in the freshwater wetlands. Recently restored wetlands had significantly higher rates of methane production compared to their historic counterparts that could be attributed to variations in trace metal and organic carbon content in younger wetlands. In contrast, our sequencing results revealed an almost immediate return of the indigenous microbial communities following seasonal flooding and full tidal restoration in saline and hypersaline wetlands and managed ponds. Notably, we found elevated methane production rates in hypersaline ponds, the result of methylotrophic methane production confirmed by sequence data and lab incubations. Our study links belowground microbial communities and their aboveground greenhouse gas production and highlights the inherent complexity in predicting wetland microbial response in the face of both natural and unnatural disturbances.

  11. High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes

    PubMed Central

    Ling, Alison L.; Robertson, Charles E.; Harris, J. Kirk; Frank, Daniel N.; Kotter, Cassandra V.; Stevens, Mark J.; Pace, Norman R.; Hernandez, Mark T.

    2015-01-01

    Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers. PMID:25748024

  12. High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes.

    PubMed

    Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

    2015-01-01

    Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.

  13. From microbial communities to cells

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1985-01-01

    The eukraotic cell, the unit of structure of protoctists, plants, fungi, and animals, is not at all homologous to prokaryotic cells. Instead the eukaryotic cell is homologous to communities of microorganisms such as those of the sulfuretum. This research is based on the hypothesis that at least four different interacting community members entered the original associations that, when stabilized, led to the emergence of eukaryotic cells. These are: (1) host nucleocytoplasm (thermoplasma like archaebacteria); (2) mitochrondria (paracoccus or bdellovibryo like respiring bacteria; and (3) plastids (cyanobacteria) and undulipodia. Tubulin like protein was found in the free living spirochete Spirochaeta bajacaliforniensis and in several other spirochetes. The amino acid sequence was to see if the spirochete protein is homologous to the tubulin of undulipodial and mitotic spindle microtubules.

  14. Can Transgenic Maize Affect Soil Microbial Communities?

    PubMed Central

    Mulder, Christian; Wouterse, Marja; Raubuch, Markus; Roelofs, Willem; Rutgers, Michiel

    2006-01-01

    The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical guilds) and/or a change in numerical abundance of their cells. Litter placement is known for its strong influence on the soil decomposer communities. The effects of the addition of crop residues on respiration and catabolic activities of the bacterial community were examined in microcosm experiments. Four cultivars of Zea mays L. of two different isolines (each one including the conventional crop and its Bacillus thuringiensis cultivar) and one control of bulk soil were included in the experimental design. The growth models suggest a dichotomy between soils amended with either conventional or transgenic maize residues. The Cry1Ab protein appeared to influence the composition of the microbial community. The highly enhanced soil respiration observed during the first 72 h after the addition of Bt-maize residues can be interpreted as being related to the presence of the transgenic crop residues. This result was confirmed by agar plate counting, as the averages of the colony-forming units of soils in conventional treatments were about one-third of those treated with transgenic straw. Furthermore, the addition of Bt-maize appeared to induce increased microbial consumption of carbohydrates in BIOLOG EcoPlates. Three weeks after the addition of maize residues to the soils, no differences between the consumption rate of specific chemical guilds by bacteria in soils amended with transgenic maize and bacteria in soils amended with conventional maize were detectable. Reaped crop residues, comparable to post-harvest maize straw (a common practice in current agriculture), rapidly influence the soil bacterial cells at a functional level. Overall, these data support the existence of short

  15. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

    Treesearch

    Daniela F. Cusack; Whendee L. Silver; Margaret S. Torn; Sarah D. Burton; Mary K. Firestone

    2011-01-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of...

  16. Mass Spectrometry Imaging of Complex Microbial Communities

    PubMed Central

    2016-01-01

    Conspectus In the two decades since mass spectrometry imaging (MSI) was first applied to visualize the distribution of peptides across biological tissues and cells, the technique has become increasingly effective and reliable. MSI excels at providing complementary information to existing methods for molecular analysis—such as genomics, transcriptomics, and metabolomics—and stands apart from other chemical imaging modalities through its capability to generate information that is simultaneously multiplexed and chemically specific. Today a diverse family of MSI approaches are applied throughout the scientific community to study the distribution of proteins, peptides, and small-molecule metabolites across many biological models. The inherent strengths of MSI make the technique valuable for studying microbial systems. Many microbes reside in surface-attached multicellular and multispecies communities, such as biofilms and motile colonies, where they work together to harness surrounding nutrients, fend off hostile organisms, and shield one another from adverse environmental conditions. These processes, as well as many others essential for microbial survival, are mediated through the production and utilization of a diverse assortment of chemicals. Although bacterial cells are generally only a few microns in diameter, the ecologies they influence can encompass entire ecosystems, and the chemical changes that they bring about can occur over time scales ranging from milliseconds to decades. Because of their incredible complexity, our understanding of and influence over microbial systems requires detailed scientific evaluations that yield both chemical and spatial information. MSI is well-positioned to fulfill these requirements. With small adaptations to existing methods, the technique can be applied to study a wide variety of chemical interactions, including those that occur inside single-species microbial communities, between cohabitating microbes, and between microbes

  17. Microbial abundance and community structure in a melting alpine snowpack.

    PubMed

    Lazzaro, Anna; Wismer, Andrea; Schneebeli, Martin; Erny, Isolde; Zeyer, Josef

    2015-05-01

    Snowmelt is a crucial period for alpine soil ecosystems, as it is related to inputs of nutrients, particulate matter and microorganisms to the underlying soil. Although snow-inhabiting microbial communities represent an important inoculum for soils, they have thus far received little attention. The distribution and structure of these microorganisms in the snowpack may be linked to the physical properties of the snowpack at snowmelt. Snow samples were taken from snow profiles at four sites (1930-2519 m a.s.l.) in the catchment of the Tiefengletscher, Canton Uri, Switzerland. Microbial (Archaea, Bacteria and Fungi) communities were investigated through T-RFLP profiling of the 16S and 18S rRNA genes, respectively. In parallel, we assessed physical and chemical parameters relevant to the understanding of melting processes. Along the snow profiles, density increased with depth due to compaction, while other physico-chemical parameters, such as temperature and concentrations of DOC and soluble ions, remained in the same range (e.g. <2 mg DOC L(-1), 5-30 μg NH4 (+)-N L(-1)) in all samples at all sites. Along the snow profiles, no major change was observed either in cell abundance or in bacterial and fungal diversity. No Archaea could be detected in the snow. Microbial communities, however, differed significantly between sites. Our results show that meltwater rearranges soluble ions and microbial communities in the snowpack.

  18. Microbial Forensics: A Scientific Assessment

    SciTech Connect

    Keim, Paul

    2003-02-17

    be accomplished if we understand basic principles that control microbial physiology. Finally, the more precise and refined a microbial forensic system becomes, the more proper guidelines for handling and storage will be defined. Thus, improper dissemination or use of the pathogens will be reduced and inadvertent release will be minimized. An additional outcome of establishing these guidelines or rules is that the legitimate investigator will be protected to pursue research without unnecessary intrusion. Colloquium participants identified a variety of needs and directions in the following areas: sample handling and collection, detection, research direction, data access, QA/QC, and education. General recommendations are provided for direction or insight for the scientific community, law enforcement community, legal community, and the public.

  19. The dynamic genetic repertoire of microbial communities

    PubMed Central

    Wilmes, Paul; Simmons, Sheri L; Denef, Vincent J; Banfield, Jillian F

    2009-01-01

    Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity. PMID:19054116

  20. Multiscale Modeling of Microbial Communities

    NASA Astrophysics Data System (ADS)

    Blanchard, Andrew

    Although bacteria are single-celled organisms, they exist in nature primarily in the form of complex communities, participating in a vast array of social interactions through regulatory gene networks. The social interactions between individual cells drive the emergence of community structures, resulting in an intricate relationship across multiple spatiotemporal scales. Here, I present my work towards developing and applying the tools necessary to model the complex dynamics of bacterial communities. In Chapter 2, I utilize a reaction-diffusion model to determine the population dynamics for a population with two species. One species (CDI+) utilizes contact dependent inhibition to kill the other sensitive species (CDI-). The competition can produce diverse patterns, including extinction, coexistence, and localized aggregation. The emergence, relative abundance, and characteristic features of these patterns are collectively determined by the competitive benefit of CDI and its growth disadvantage for a given rate of population diffusion. The results provide a systematic and statistical view of CDI-based bacterial population competition, expanding the spectrum of our knowledge about CDI systems and possibly facilitating new experimental tests for a deeper understanding of bacterial interactions. In the following chapter, I present a systematic computational survey on the relationship between social interaction types and population structures for two-species communities by developing and utilizing a hybrid computational framework that combines discrete element techniques with reaction-diffusion equations. The impact of deleterious and beneficial interactions on the community are quantified. Deleterious interactions generate an increased variance in relative abundance, a drastic decrease in surviving lineages, and a rough expanding front. In contrast, beneficial interactions contribute to a reduced variance in relative abundance, an enhancement in lineage number, and a

  1. Microbial community dynamics in continuous microbial fuel cells fed with synthetic wastewater and pig slurry.

    PubMed

    Sotres, Ana; Tey, Laura; Bonmatí, August; Viñas, Marc

    2016-10-01

    Two-chambered microbial fuel cells (MFCs) operating with synthetic wastewater and pig slurry were assessed. Additionally, the use of 2-bromoethanesulfonate (BES-Inh) was studied. The synthetic wastewater-fed MFC (MFCSW) showed a maximum power density (PDmax) of 2138mWm(-3), and the addition of BES-Inh (10mM) did not show any improvement in its performance (PDmax=2078mWm(-3)). When pig slurry was used as feed (MFCPS), PDmax increased up to 5623mWm(-3). The microbial community composition was affected by the type of substrate used. While, Pseudomonadaceae and Clostridiaceae were the most representative families within the acetate-based medium, Flavobacteriaceae, Chitinophagaceae, Comamonadaceae and Nitrosomonadaceae were predominant when pig slurry was used as feed. Otherwise, only the Eubacterial microbial community composition was strongly modified when adding BES-Inh, thus leading to an enrichment of the Bacteroidetes phylum. Oppositely, the Archaeal community was less affected by the addition of BES-Inh, and Methanosarcina sp., arose as the predominant family in both situations. Despite all the differences in microbial communities, 6 operational taxonomic units (OTUs) belonging to Bacteroidetes (Porphyromonadaceae and Marinilabiaceae) and Firmicutes (Clostridiales) were found to be common to both MFCs, also for different contents of COD and N-NH4(+), and therefore could be considered as the bioanode core microbiome.

  2. Understanding Bacteriophage Specificity in Natural Microbial Communities

    PubMed Central

    Koskella, Britt; Meaden, Sean

    2013-01-01

    Studying the coevolutionary dynamics between bacteria and the bacteriophage viruses that infect them is critical to understanding both microbial diversity and ecosystem functioning. Phages can play a key role in shaping bacterial population dynamics and can significantly alter both intra- and inter-specific competition among bacterial hosts. Predicting how phages might influence community stability and apparent competition, however, requires an understanding of how bacteria-phage interaction networks evolve as a function of host diversity and community dynamics. Here, we first review the progress that has been made in understanding phage specificity, including the use of experimental evolution, we then introduce a new dataset on natural bacteriophages collected from the phyllosphere of horse chestnut trees, and finally we highlight that bacterial sensitivity to phage is rarely a binary trait and that this variation should be taken into account and reported. We emphasize that there is currently insufficient evidence to make broad generalizations about phage host range in natural populations, the limits of phage adaptation to novel hosts, or the implications of phage specificity in shaping microbial communities. However, the combination of experimental and genomic approaches with the study of natural communities will allow new insight to the evolution and impact of phage specificity within complex bacterial communities. PMID:23478639

  3. Involving communities in community assessment.

    PubMed

    Clark, Mary Jo; Cary, Susan; Diemert, Grover; Ceballos, Rose; Sifuentes, Maria; Atteberry, Irene; Vue, Fu; Trieu, Sandy

    2003-01-01

    Focus groups provide an effective means of incorporating the perspectives of "hidden" populations in assessments of community health needs and assets. A series of focus groups was conducted with specifically targeted segments of a community to develop a comprehensive picture of community health. The authors describe the focus group process, major findings, and the use of focus group results in a highly multicultural community. Despite differences in age, length of residence, and ethnicity, the focus groups were remarkably similar in the issues raised. The majority of participants viewed the multicultural nature of the community as an asset but voiced some of the difficulties of living in a multiethnic and multilanguage environment. Similar areas of concern in the community arose from all of the focus groups, including housing and other environmental issues and problems of access to health care. Focus group findings have been used to initiate activity addressing identified community problems. Focus group participation had the added benefit of increasing community members' participation in other community endeavors.

  4. Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

    PubMed Central

    Rosselli, Riccardo; Romoli, Ottavia; Vitulo, Nicola; Vezzi, Alessandro; Campanaro, Stefano; de Pascale, Fabio; Schiavon, Riccardo; Tiarca, Maurizio; Poletto, Fabio; Concheri, Giuseppe; Valle, Giorgio; Squartini, Andrea

    2016-01-01

    The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies. PMID:27577787

  5. A multi-year assessment of the environmental impact of transgenic Eucalyptus trees harboring a bacterial choline oxidase gene on biomass, precinct vegetation and the microbial community.

    PubMed

    Oguchi, Taichi; Kashimura, Yuko; Mimura, Makiko; Yu, Xiang; Matsunaga, Etsuko; Nanto, Kazuya; Shimada, Teruhisa; Kikuchi, Akira; Watanabe, Kazuo N

    2014-10-01

    A 4-year field trial for the salt tolerant Eucalyptus globulus Labill. harboring the choline oxidase (codA) gene derived from the halobacterium Arthrobacter globiformis was conducted to assess the impact of transgenic versus non-transgenic trees on biomass production, the adjacent soil microbial communities and vegetation by monitoring growth parameters, seasonal changes in soil microbes and the allelopathic activity of leaves. Three independently-derived lines of transgenic E. globulus were compared with three independent non-transgenic lines including two elite clones. No significant differences in biomass production were detected between transgenic lines and non-transgenic controls derived from same seed bulk, while differences were seen compared to two elite clones. Significant differences in the number of soil microbes present were also detected at different sampling times but not between transgenic and non-transgenic lines. The allelopathic activity of leaves from both transgenic and non-transgenic lines also varied significantly with sampling time, but the allelopathic activity of leaves from transgenic lines did not differ significantly from those from non-transgenic lines. These results indicate that, for the observed variables, the impact on the environment of codA-transgenic E. globulus did not differ significantly from that of the non-transformed controls on this field trial.

  6. Microbial community degradation of widely used quaternary ammonium disinfectants.

    PubMed

    Oh, Seungdae; Kurt, Zohre; Tsementzi, Despina; Weigand, Michael R; Kim, Minjae; Hatt, Janet K; Tandukar, Madan; Pavlostathis, Spyros G; Spain, Jim C; Konstantinidis, Konstantinos T

    2014-10-01

    Benzalkonium chlorides (BACs) are disinfectants widely used in a variety of clinical and environmental settings to prevent microbial infections, and they are frequently detected in nontarget environments, such as aquatic and engineered biological systems, even at toxic levels. Therefore, microbial degradation of BACs has important ramifications for alleviating disinfectant toxicity in nontarget environments as well as compromising disinfectant efficacy in target environments. However, how natural microbial communities respond to BAC exposure and what genes underlie BAC biodegradation remain elusive. Our previous metagenomic analysis of a river sediment microbial community revealed that BAC exposure selected for a low-diversity community, dominated by several members of the Pseudomonas genus that quickly degraded BACs. To elucidate the genetic determinants of BAC degradation, we conducted time-series metatranscriptomic analysis of this microbial community during a complete feeding cycle with BACs as the sole carbon and energy source under aerobic conditions. Metatranscriptomic profiles revealed a candidate gene for BAC dealkylation, the first step in BAC biodegradation that results in a product 500 times less toxic. Subsequent biochemical assays and isolate characterization verified that the putative amine oxidase gene product was functionally capable of initiating BAC degradation. Our analysis also revealed cooperative interactions among community members to alleviate BAC toxicity, such as the further degradation of BAC dealkylation by-products by organisms not encoding amine oxidase. Collectively, our results advance the understanding of BAC aerobic biodegradation and provide genetic biomarkers to assess the critical first step of this process in nontarget environments. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  7. Relationship between honeybee nutrition and their microbial communities.

    PubMed

    Saraiva, Miriane Acosta; Zemolin, Ana Paula Pegoraro; Franco, Jeferson Luis; Boldo, Juliano Tomazzoni; Stefenon, Valdir Marcos; Triplett, Eric W; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Wurdig

    2015-04-01

    The microbiota and the functional genes actively involved in the process of breakdown and utilization of pollen grains in beebread and bee guts are not yet understood. The aim of this work was to assess the diversity and community structure of bacteria and archaea in Africanized honeybee guts and beebread as well as to predict the genes involved in the microbial bioprocessing of pollen using state of the art 'post-light' based sequencing technology. A total of 11 bacterial phyla were found within bee guts and 10 bacterial phyla were found within beebread. Although the phylum level comparison shows most phyla in common, a deeper phylogenetic analysis showed greater variation of taxonomic composition. The families Enterobacteriaceae, Ricketsiaceae, Spiroplasmataceae and Bacillaceae, were the main groups responsible for the specificity of the bee gut while the main families responsible for the specificity of the beebread were Neisseriaceae, Flavobacteriaceae, Acetobacteraceae and Lactobacillaceae. In terms of microbial community structure, the analysis showed that the communities from the two environments were quite different from each other with only 7 % of species-level taxa shared between bee gut and beebread. The results indicated the presence of a highly specialized and well-adapted microbiota within each bee gut and beebread. The beebread community included a greater relative abundance of genes related to amino acid, carbohydrate, and lipid metabolism, suggesting that pollen biodegradation predominantly occurs in the beebread. These results suggests a complex and important relationship between honeybee nutrition and their microbial communities.

  8. Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

    PubMed Central

    Maphosa, Farai; Lieten, Shakti H.; Dinkla, Inez; Stams, Alfons J.; Smidt, Hauke; Fennell, Donna E.

    2012-01-01

    Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants. PMID:23060869

  9. Urea transformation of wetland microbial communities.

    PubMed

    Thorén, Ann-Karin

    2007-02-01

    Transformation of urea to ammonium is an important link in the nitrogen cycle in soil and water. Although microbial nitrogen transformations, such as nitrification and denitrification, are well studied in freshwater sediment and epiphytic biofilm in shallow waters, information about urea transformation in these environments is scarce. In this study, urea transformation of sedimentary, planktonic, and epiphytic microbial communities was quantified and urea transformation of epiphytic biofilms associated with three different common wetland macrophyte species is compared. The microbial communities were collected from a constructed wetland in October 2002 and urea transformation was quantified in the laboratory at in situ temperature (12 degrees C) with the use of the 14C-urea tracer method, which measures the release of 14CO2 as a direct result of urease activity. It was found that the urea transformation was 100 times higher in sediment (12-22 mmol urea-N m(-2) day(-1)) compared with the epiphytic activity on the surfaces of the submerged plant Elodea canadensis (0.1-0.2 mmol urea-N m(-2) day(-1)). The epiphytic activity of leaves of Typha latifolia was lower (0.001-0.03 mmol urea-N m(-2) day(-1)), while urea transformation was negligible in the water column and on the submerged leaves of the emergent plant Phragmites australis. However, because this wetland was dominated by dense beds of the submerged macrophyte E. canadensis, this plant provided a large surface area for epiphytic microbial activity-in the range of 23-33 m2 of plant surfaces per square meter of wetland. Thus, in the wetland system scale at the existing plant distribution and density, the submerged plant community had the potential to transform 2-7 mmol urea-N m(-2) day(-1) and was in the same magnitude as the urea transformation in the sediment.

  10. ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS

    EPA Science Inventory

    Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

  11. ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS

    EPA Science Inventory

    Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

  12. Emergent biosynthetic capacity in simple microbial communities.

    PubMed

    Chiu, Hsuan-Chao; Levy, Roie; Borenstein, Elhanan

    2014-07-01

    Microbes have an astonishing capacity to transform their environments. Yet, the metabolic capacity of a single species is limited and the vast majority of microorganisms form complex communities and join forces to exhibit capabilities far exceeding those achieved by any single species. Such enhanced metabolic capacities represent a promising route to many medical, environmental, and industrial applications and call for the development of a predictive, systems-level understanding of synergistic microbial capacity. Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems. We specifically focus on detecting emergent biosynthetic capacity--instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. Using this framework to model a large collection of two-species communities on multiple media, we demonstrate that emergent biosynthetic capacity is highly prevalent. We identify commonly observed emergent metabolites and metabolic reprogramming patterns, characterizing typical mechanisms of emergent capacity. We further find that emergent secretion tends to occur in two waves, the first as soon as the two organisms are introduced, and the second when the medium is depleted and nutrients become limited. Finally, aiming to identify global community determinants of emergent capacity, we find a marked association between the level of emergent biosynthetic capacity and the functional/phylogenetic distance between community members. Specifically, we demonstrate a "Goldilocks" principle, where high levels of emergent capacity are observed when the species comprising the community are functionally neither too close, nor too distant. Taken together, our results

  13. Emergent Biosynthetic Capacity in Simple Microbial Communities

    PubMed Central

    Chiu, Hsuan-Chao; Levy, Roie; Borenstein, Elhanan

    2014-01-01

    Microbes have an astonishing capacity to transform their environments. Yet, the metabolic capacity of a single species is limited and the vast majority of microorganisms form complex communities and join forces to exhibit capabilities far exceeding those achieved by any single species. Such enhanced metabolic capacities represent a promising route to many medical, environmental, and industrial applications and call for the development of a predictive, systems-level understanding of synergistic microbial capacity. Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems. We specifically focus on detecting emergent biosynthetic capacity – instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. Using this framework to model a large collection of two-species communities on multiple media, we demonstrate that emergent biosynthetic capacity is highly prevalent. We identify commonly observed emergent metabolites and metabolic reprogramming patterns, characterizing typical mechanisms of emergent capacity. We further find that emergent secretion tends to occur in two waves, the first as soon as the two organisms are introduced, and the second when the medium is depleted and nutrients become limited. Finally, aiming to identify global community determinants of emergent capacity, we find a marked association between the level of emergent biosynthetic capacity and the functional/phylogenetic distance between community members. Specifically, we demonstrate a “Goldilocks” principle, where high levels of emergent capacity are observed when the species comprising the community are functionally neither too close, nor too distant. Taken together, our results

  14. Agroforestry management in vineyards: effects on soil microbial communities

    NASA Astrophysics Data System (ADS)

    Montagne, Virginie; Nowak, Virginie; Guilland, Charles; Gontier, Laure; Dufourcq, Thierry; Guenser, Josépha; Grimaldi, Juliette; Bourgade, Emilie; Ranjard, Lionel

    2017-04-01

    Some vineyard practices (tillage, chemical weeding or pest management) are generally known to impact the environment with particular negative effects on the diversity and the abundance of soil microorganisms, and cause water and soil pollutions. In an agro-ecological context, innovative cropping systems have been developed to improve ecosystem services. Among them, agroforestry offers strategies of sustainable land management practices. It consists in intercropping trees with annual/perennial/fodder crop on the same plot but it is weakly referenced with grapevine. The present study assesses the effects of intercropped and neighbouring trees on the soil of three agroforestry vineyards, in south-western France regions. More precisely soils of the different plots were sampled and the impact of the distance to the tree or to the neighbouring trees (forest) on soil microbial community has been considered. Indigenous soil microbial communities were characterized by a metagenomic approach that consisted in extracting the molecular microbial biomass, then in calculating the soil fungi/bacteria ratio - obtained by qPCR - and then in characterizing the soil microbial diversity - through Illumina sequencing of 16S and 18S regions. Our results showed a significant difference between the soil of agroforestry vineyards and the soil sampled in the neighbouring forest in terms of microbial abundance and diversity. However, only structure and composition of bacterial community seem to be influenced by the implanted trees in the vine plots. In addition, the comparison of microbial co-occurrence networks between vine and forest plots as well as inside vine plots according to distance to the tree allow revealing a more sensitive impact of agroforestry practices. Altogether, the results we obtained build up the first references for concerning the soil of agroforestry vineyards which will be interpreted in terms of soil quality, functioning and sustainability.

  15. Microbial Communities in Pre-Columbian Coprolites

    PubMed Central

    Santiago-Rodriguez, Tasha M.; Narganes-Storde, Yvonne M.; Chanlatte, Luis; Crespo-Torres, Edwin; Toranzos, Gary A.; Jimenez-Flores, Rafael; Hamrick, Alice; Cano, Raul J.

    2013-01-01

    The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures. PMID:23755194

  16. Native soil organic matter conditions the response of microbial communities to organic inputs with different stability

    NASA Astrophysics Data System (ADS)

    Yanardaǧ, Ibrahim H.; Zornoza, Raúl; Bastida, Felipe; Büyükkiliç-Yanardaǧ, Asuman; Acosta, Jose A.; García, Carlos; Faz, Ángel; Mermut, Ahmet R.

    2017-04-01

    The response of soil microbial communities from soils with different soil organic matter (SOM) content to organic inputs with different stability is still poorly understood. Thus, an incubation experiment was designed to study how the addition of pig slurry (PS), its manure (M) and its biochar (BC) affect soil microbial community and activity in three soils differing in SOM content (Regosol, Luvisol and Kastanozem). The evolution of different C and N fractions, microbial biomass C and N, enzyme activities and microbial community structure by the use of phospholipid fatty acid (PLFA) analysis was assessed for 60 days. Results showed that the different amendments had different effect on microbial properties depending on the soil type. The addition of M caused the highest increase in all microbial properties in the three soils, followed by PS. These changes were more intense in the soil with the lowest SOM (Regosol). The addition of M and PS caused changes in the microbial community structure in all soils, which were more related to the presence of available sources of N than to the labile fractions of C. The addition of BC was followed by increases in the proportions of fungi and Gram positive bacteria in the Regosol, while enhanced the proportion of actinobacteria in all soil types, related to increments in pH and soil C recalcitrance. Thus, native SOM determined the response of microbial communities to external inputs with different stability, soils with low SOM being more prone to increase microbial biomass and activity and change microbial community structure.

  17. Decoding molecular interactions in microbial communities

    PubMed Central

    Abreu, Nicole A.; Taga, Michiko E.

    2016-01-01

    Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia. PMID:27417261

  18. Community Impact Assessment Handbook.

    ERIC Educational Resources Information Center

    Northern Alberta Development Council, Peace River.

    This handbook is intended for communities that wish to undertake their own community impact assessment (CIA). The goal is to enable communities to plan for changes before they occur, so they can cope with changes when they do occur. CIA involves forecasting and evaluating the full range of unintended consequences for the community of development…

  19. The Community Assessment System.

    ERIC Educational Resources Information Center

    Haynes, Alan E.

    The Community Assessment System (CAS) is a research technique designed to probe small, rural community perceptions and attitudes toward planned economic expansion and social development by generating suggestions for general or specific community modifications; ascertaining community attitudes and possible responses to a specific modification;…

  20. Remediation of antimony-rich mine waters: Assessment of antimony removal and shifts in the microbial community of an onsite field-scale bioreactor.

    PubMed

    Sun, Weimin; Xiao, Enzong; Kalin, Margarete; Krumins, Valdis; Dong, Yiran; Ning, Zengping; Liu, Tong; Sun, Min; Zhao, Yanlong; Wu, Shiliang; Mao, Jianzhong; Xiao, Tangfu

    2016-08-01

    An on-site field-scale bioreactor for passive treatment of antimony (Sb) contamination was installed downstream of an active Sb mine in Southwest China, and operated for one year (including a six month monitoring period). This bioreactor consisted of five treatment units, including one pre-aerobic cell, two aerobic cells, and two microaerobic cells. With the aerobic cells inoculated with indigenous mine water microflora, the bioreactor removed more than 90% of total soluble Sb and 80% of soluble antimonite (Sb(III)). An increase in pH and decrease of oxidation-reduction potential (Eh) was also observed along the flow direction. High-throughput sequencing of the small subunit ribosomal RNA (SSU rRNA) gene variable (V4) region revealed that taxonomically diverse microbial communities developed in the bioreactor. Metal (loid)-oxidizing bacteria including Ferrovum, Thiomonas, Gallionella, and Leptospirillum, were highly enriched in the bioreactor cells where the highest total Sb and Sb(III) removal occurred. Canonical correspondence analysis (CCA) indicated that a suite of in situ physicochemical parameters including pH and Eh were substantially correlated with the overall microbial communities. Based on an UPGMA (Unweighted Pair Group Method with Arithmetic Mean) tree and PCoA (Principal Coordinates Analysis), the microbial composition of each cell was distinct, indicating these in situ physicochemical parameters had an effect in shaping the indigenous microbial communities. Overall, this study was the first to employ a field-scale bioreactor to treat Sb-rich mine water onsite and, moreover, the findings suggest the feasibility of the bioreactor in removing elevated Sb from mine waters. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. A Comparison of Microbial Community Structures by Depth and Season Under Switchgrass

    NASA Astrophysics Data System (ADS)

    Fansler, S. J.; Smith, J. L.; Bolton, H.; Bailey, V. L.

    2008-12-01

    As part of a multidisciplinary study of C sequestration in switchgrass production systems, the soil microbial community structure was monitored at 6 different depths (reaching 90 cm) in both spring and autumn. Microbial community structure was assessed using ribosomal intergenic spacer analysis (RISA), and primers were used specific to either bacteria or fungi, generating microbial community fingerprints for each taxonomic group. Diverse microbial communities for both groups were detected throughout the soil profile. It is notable that while community structure clearly changed with depth, there was the deepest soil samples still retained relatively diverse communities. Seasonally, differences are clearly evident within plots at the surface. As the plots were replicated, significant differences in the community fingerprints with depth and season are reported.

  2. Evolutionary limits to cooperation in microbial communities

    PubMed Central

    Oliveira, Nuno M.; Niehus, Rene; Foster, Kevin R.

    2014-01-01

    Microbes produce many compounds that are costly to a focal cell but promote the survival and reproduction of neighboring cells. This observation has led to the suggestion that microbial strains and species will commonly cooperate by exchanging compounds. Here, we examine this idea with an ecoevolutionary model where microbes make multiple secretions, which can be exchanged among genotypes. We show that cooperation between genotypes only evolves under specific demographic regimes characterized by intermediate genetic mixing. The key constraint on cooperative exchanges is a loss of autonomy: strains become reliant on complementary genotypes that may not be reliably encountered. Moreover, the form of cooperation that we observe arises through mutual exploitation that is related to cheating and “Black Queen” evolution for a single secretion. A major corollary is that the evolution of cooperative exchanges reduces community productivity relative to an autonomous strain that makes everything it needs. This prediction finds support in recent work from synthetic communities. Overall, our work suggests that natural selection will often limit cooperative exchanges in microbial communities and that, when exchanges do occur, they can be an inefficient solution to group living. PMID:25453102

  3. Microbial community composition in sediments resists perturbation by nutrient enrichment

    PubMed Central

    Bowen, Jennifer L; Ward, Bess B; Morrison, Hilary G; Hobbie, John E; Valiela, Ivan; Deegan, Linda A; Sogin, Mitchell L

    2011-01-01

    Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply in our sampling locations, despite demonstrable and diverse nutrient-induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. PMID:21412346

  4. Microbial community composition in sediments resists perturbation by nutrient enrichment.

    PubMed

    Bowen, Jennifer L; Ward, Bess B; Morrison, Hilary G; Hobbie, John E; Valiela, Ivan; Deegan, Linda A; Sogin, Mitchell L

    2011-09-01

    Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply in our sampling locations, despite demonstrable and diverse nutrient-induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation.

  5. Responses of soil microbial community to experimental warming and precipitation manipulation

    NASA Astrophysics Data System (ADS)

    Li, G.; Kim, S.; Park, M. J.; Han, S. H.; Lee, J.; Son, Y.

    2015-12-01

    An experimental nursery was established with two-year-old Pinus densiflora seedlings at Korea University to study soil microbial community responses to air warming (+3°C) and precipitation manipulation (-30% and +30%). Soil samplings were collected monthly from July to November, 2014. Substrate utilization profile of microbial community was examined using BIOLOG EcoPlate. Microbial community composition was assessed by high-throughput sequencing technology. The results showed that warming significantly affected the substrate utilization profile of microbial community (P<0.05), which labile substrates were degraded more quickly in warming plots than unwarmed plots. Only significant effects of warming on fungal community richness and abundance were observed (all P<0.05). Compared with unwarmed and precipitation control treatment, fungal community richness in the others were significantly decreased by 1.22%-15.27% (P<0.05), but community diversity in those treatments were slightly increased (P>0.05). In contrast, compared with unwarmed and precipitation control treatment, the bacterial community richness in the others were increased, but community abundance and diversity in those treatments were decreased (all P>0.05). These changes in microbial community structure resulted in the changes in community functional composition, which microbial metabolic functions were higher in warming plots than unwarmed plots. Since microorganisms differ in their susceptibility to stressors, changes in the soil environment affect the microbial community. Therefore, the results indicated that effects of warming and precipitation manipulation on soil microbial community might be related to warming and precipitation manipulation-induced changes in soil moisture. We suggested that shifts in the microbial community may be important implications for soil carbon and nitrogen dynamics in a warmer world. This study was supported by National Research Foundation of Korea (NRF-2013R1A1A2012242).

  6. Microbial community assembly, theory and rare functions.

    PubMed

    Pholchan, Mujalin K; Baptista, Joana de C; Davenport, Russell J; Sloan, William T; Curtis, Thomas P

    2013-01-01

    Views of community assembly have traditionally been based on the contrasting perspectives of the deterministic niche paradigm and stochastic neutral models. This study sought to determine if we could use empirical interventions conceived from a niche and neutral perspective to change the diversity and evenness of the microbial community within a reactor treating wastewater and to see if there was any associated change in the removal of endocrine disrupting compounds (EDCs). The systematic removal of EDCs and micropollutants from biological treatment systems is a major challenge for environmental engineers. We manipulated pairs of bioreactors in an experiment in which "niche" (temporal variation in resource concentration and resource complexity) and "neutral" (community size and immigration) attributes were changed and the effect on the detectable diversity and the removal of steroidal estrogens was evaluated. The effects of manipulations on diversity suggested that both niche and neutral processes are important in community assembly. We found that temporal variation in environmental conditions increased diversity but resource complexity did not. Larger communities had greater diversity but attempting to increase immigration by adding soil had the opposite effect. The effects of the manipulations on EDC removal efficiency were complex. Decreases in diversity, which were associated with a decrease in evenness, were associated with an increase in EDC removal. A simple generalized neutral model (calibrated with parameters typical of wastewater treatment plants) showed that decreases in diversity should lead to the increase in abundance of some ostensibly taxa rare. We conclude that neither niche and neutral perspectives nor the effect of diversity on putative rare functions can be properly understood by naïve qualitative observations. Instead, the relative importance of the key microbial mechanisms must be determined and, ideally, expressed mathematically.

  7. Microbial community assembly, theory and rare functions

    PubMed Central

    Pholchan, Mujalin K.; Baptista, Joana de C.; Davenport, Russell J.; Sloan, William T.; Curtis, Thomas P.

    2013-01-01

    Views of community assembly have traditionally been based on the contrasting perspectives of the deterministic niche paradigm and stochastic neutral models. This study sought to determine if we could use empirical interventions conceived from a niche and neutral perspective to change the diversity and evenness of the microbial community within a reactor treating wastewater and to see if there was any associated change in the removal of endocrine disrupting compounds (EDCs). The systematic removal of EDCs and micropollutants from biological treatment systems is a major challenge for environmental engineers. We manipulated pairs of bioreactors in an experiment in which “niche” (temporal variation in resource concentration and resource complexity) and “neutral” (community size and immigration) attributes were changed and the effect on the detectable diversity and the removal of steroidal estrogens was evaluated. The effects of manipulations on diversity suggested that both niche and neutral processes are important in community assembly. We found that temporal variation in environmental conditions increased diversity but resource complexity did not. Larger communities had greater diversity but attempting to increase immigration by adding soil had the opposite effect. The effects of the manipulations on EDC removal efficiency were complex. Decreases in diversity, which were associated with a decrease in evenness, were associated with an increase in EDC removal. A simple generalized neutral model (calibrated with parameters typical of wastewater treatment plants) showed that decreases in diversity should lead to the increase in abundance of some ostensibly taxa rare. We conclude that neither niche and neutral perspectives nor the effect of diversity on putative rare functions can be properly understood by naïve qualitative observations. Instead, the relative importance of the key microbial mechanisms must be determined and, ideally, expressed mathematically

  8. Quantitative Microbial Risk Assessment Tutorial - Primer

    EPA Science Inventory

    This document provides a Quantitative Microbial Risk Assessment (QMRA) primer that organizes QMRA tutorials. The tutorials describe functionality of a QMRA infrastructure, guide the user through software use and assessment options, provide step-by-step instructions for implementi...

  9. Use of 16S rRNA gene based clone libraries to assess microbial communities potentially involved in anaerobic methane oxidation in a Mediterranean cold seep.

    PubMed

    Heijs, Sander K; Haese, Ralf R; van der Wielen, Paul W J J; Forney, Larry J; van Elsas, Jan Dirk

    2007-04-01

    This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22-34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0-6 cm). Communities in the middle layer (6-22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study.

  10. Use of 16S rRNA Gene Based Clone Libraries to Assess Microbial Communities Potentially Involved in Anaerobic Methane Oxidation in a Mediterranean Cold Seep

    PubMed Central

    Haese, Ralf R.; van der Wielen, Paul W. J. J.; Forney, Larry J.; van Elsas, Jan Dirk

    2007-01-01

    This study provides data on the diversities of bacterial and archaeal communities in an active methane seep at the Kazan mud volcano in the deep Eastern Mediterranean sea. Layers of varying depths in the Kazan sediments were investigated in terms of (1) chemical parameters and (2) DNA-based microbial population structures. The latter was accomplished by analyzing the sequences of directly amplified 16S rRNA genes, resulting in the phylogenetic analysis of the prokaryotic communities. Sequences of organisms potentially associated with processes such as anaerobic methane oxidation and sulfate reduction were thus identified. Overall, the sediment layers revealed the presence of sequences of quite diverse bacterial and archaeal communities, which varied considerably with depth. Dominant types revealed in these communities are known as key organisms involved in the following processes: (1) anaerobic methane oxidation and sulfate reduction, (2) sulfide oxidation, and (3) a range of (aerobic) heterotrophic processes. In the communities in the lowest sediment layer sampled (22–34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic organisms abounded in the top sediment layer (0–6 cm). Communities in the middle layer (6–22 cm) contained organisms that could be linked to either of the aforementioned processes. We discuss how these phylogeny (sequence)-based findings can support the ongoing molecular work aimed at unraveling both the functioning and the functional diversities of the communities under study. PMID:17431711

  11. Sampling microbial communities in the National Ecological Observatory Network

    NASA Astrophysics Data System (ADS)

    Adams, H. E.; Parnell, J.; Powell, H.

    2012-12-01

    The National Ecological Observatory Network (NEON) is a national-scale research platform to enable the community to assess impacts of climate change, land-use change, and invasive species on ecosystem structure and function at regional and continental scales. The NEON Observatory will collect data on aquatic organisms over 30 years in 36 sites across the United States, including Alaska and Puerto Rico as well as terrestrial organisms at 60 sites including Hawaii. Included in the biological measurements are microbial measurements in terrestrial and aquatic environments, including small, wadeable streams and shallow lakes. Microbial sampling in both aquatic and terrestrial habitats is being planned to coincide with biogeochemical sampling due to similarity of time scale and influence of external drivers. Aquatic sampling is geared toward species diversity and function. Terrestrial sampling aims to collect data on diversity, function, and spatial distribution dynamics. We are in the process of prioritizing data products, so that the most dynamic processes such as enzymatic activity will be measured more frequently and more intensive measures such as metagenome sequence data will be measured on a periodic basis. Here we present our initial microbial sampling strategy and invite the community to provide comment on the design and learn about microbial data products from the Observatory.

  12. Microbial community composition and diversity in Caspian Sea sediments.

    PubMed

    Mahmoudi, Nagissa; Robeson, Michael S; Castro, Hector F; Fortney, Julian L; Techtmann, Stephen M; Joyner, Dominique C; Paradis, Charles J; Pfiffner, Susan M; Hazen, Terry C

    2015-01-01

    The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria, specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented.

  13. Microbial community composition and diversity in Caspian Sea sediments

    PubMed Central

    Mahmoudi, Nagissa; Robeson, Michael S.; Castro, Hector F.; Fortney, Julian L.; Techtmann, Stephen M.; Joyner, Dominique C.; Paradis, Charles J.; Pfiffner, Susan M.; Hazen, Terry C.

    2014-01-01

    The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria, specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented. PMID:25764536

  14. Testing the functional significance of microbial community composition.

    Treesearch

    Michael S. Strickland; Christian Lauber; Noah Fierer; Mark A. Bradford

    2009-01-01

    A critical assumption underlying terrestrial ecosystem models is that soil microbial communities, when placed in a common environment, will function in an identical manner regardless of the composition...

  15. Biochar addition impacts soil microbial community in tropical soils

    NASA Astrophysics Data System (ADS)

    Paz-Ferreiro, Jorge; Fu, Shenglei; Méndez, Ana; Gascó, Gabriel

    2014-05-01

    Studies on the effect of biochar on soil microbial activity and community structure in tropical areas are scarce. In this study we report the effect of several types of biochar (sewage sludge biochar, paper mill waste biochar, miscanthus biochar and pinewood biochar) in the soil microbial community of two tropical soils, an Acrisol and an Oxisol. In addition we study the effect of the presence or absence of earthworms in soil microbial community. Soil microbial community was more strongly affected by biochar than by the presence or absence of macrofauna.

  16. Microbial Communities Initiative: Melding Technology, Experimentation, and Theory

    ScienceCinema

    Konopka, Allan

    2016-07-12

    The Microbial Communities Initiative is a 5-year investment by Pacific Northwest National Laboratory that integrates biological/ecological experimentation, analytical chemistry, and simulation modeling. The objective is to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities. Dr. Konopka describes PNNLs Microbial Communities Initiative. The MCI will integrate biological/ecological experimentation, analytical chemistry, and simulation modeling to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities.

  17. Multifactorial diversity sustains microbial community stability.

    PubMed

    Erkus, Oylum; de Jager, Victor C L; Spus, Maciej; van Alen-Boerrigter, Ingrid J; van Rijswijck, Irma M H; Hazelwood, Lucie; Janssen, Patrick W M; van Hijum, Sacha A F T; Kleerebezem, Michiel; Smid, Eddy J

    2013-11-01

    Maintenance of a high degree of biodiversity in homogeneous environments is poorly understood. A complex cheese starter culture with a long history of use was characterized as a model system to study simple microbial communities. Eight distinct genetic lineages were identified, encompassing two species: Lactococcus lactis and Leuconostoc mesenteroides. The genetic lineages were found to be collections of strains with variable plasmid content and phage sensitivities. Kill-the-winner hypothesis explaining the suppression of the fittest strains by density-dependent phage predation was operational at the strain level. This prevents the eradication of entire genetic lineages from the community during propagation regimes (back-slopping), stabilizing the genetic heterogeneity in the starter culture against environmental uncertainty.

  18. Multifactorial diversity sustains microbial community stability

    PubMed Central

    Erkus, Oylum; de Jager, Victor CL; Spus, Maciej; van Alen-Boerrigter, Ingrid J; van Rijswijck, Irma MH; Hazelwood, Lucie; Janssen, Patrick WM; van Hijum, Sacha AFT; Kleerebezem, Michiel; Smid, Eddy J

    2013-01-01

    Maintenance of a high degree of biodiversity in homogeneous environments is poorly understood. A complex cheese starter culture with a long history of use was characterized as a model system to study simple microbial communities. Eight distinct genetic lineages were identified, encompassing two species: Lactococcus lactis and Leuconostoc mesenteroides. The genetic lineages were found to be collections of strains with variable plasmid content and phage sensitivities. Kill-the-winner hypothesis explaining the suppression of the fittest strains by density-dependent phage predation was operational at the strain level. This prevents the eradication of entire genetic lineages from the community during propagation regimes (back-slopping), stabilizing the genetic heterogeneity in the starter culture against environmental uncertainty. PMID:23823494

  19. Metabolic specialization and the assembly of microbial communities.

    PubMed

    Johnson, David R; Goldschmidt, Felix; Lilja, Elin E; Ackermann, Martin

    2012-11-01

    Metabolic specialization is a general biological principle that shapes the assembly of microbial communities. Individual cell types rarely metabolize a wide range of substrates within their environment. Instead, different cell types often specialize at metabolizing only subsets of the available substrates. What is the advantage of metabolizing subsets of the available substrates rather than all of them? In this perspective piece, we argue that biochemical conflicts between different metabolic processes can promote metabolic specialization and that a better understanding of these conflicts is therefore important for revealing the general principles and rules that govern the assembly of microbial communities. We first discuss three types of biochemical conflicts that could promote metabolic specialization. Next, we demonstrate how knowledge about the consequences of biochemical conflicts can be used to predict whether different metabolic processes are likely to be performed by the same cell type or by different cell types. We then discuss the major challenges in identifying and assessing biochemical conflicts between different metabolic processes and propose several approaches for their measurement. Finally, we argue that a deeper understanding of the biochemical causes of metabolic specialization could serve as a foundation for the field of synthetic ecology, where the objective would be to rationally engineer the assembly of a microbial community to perform a desired biotransformation.

  20. Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments

    PubMed Central

    Saarenheimo, Jatta; Aalto, Sanni L.; Rissanen, Antti J.; Tiirola, Marja

    2017-01-01

    Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significant amounts of organic material and nitrogen and even microbes into the receiving water bodies, altering physico-chemical conditions and microbial functions. In this study, we examined how nitrified wastewater affects the microbiology of boreal lake sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene, and a more detailed view on nitrogen transformation processes was gained with qPCR targeting on functional genes (nirS, nirK, nosZI, nosZII, amoAarchaea, and amoAbacteria). In both of the two studied lake sites, the microbial community composition differed significantly between control point and wastewater discharge point, and a gradual shift toward natural community composition was seen downstream following the wastewater gradient. SourceTracker analysis predicted that ∼2% of sediment microbes were of WWTP-origin on the study site where wastewater was freely mixed with the lake water, while when wastewater was specially discharged to the sediment surface, ∼6% of microbes originated from WWTP, but the wastewater-influenced area was more limited. In nitrogen transformation processes, the ratio between nitrifying archaea (AOA) and bacteria (AOB) was affected by wastewater effluent, as the AOA abundance decreased from the control point (AOA:AOB 28:1 in Keuruu, 11:1 in Petäjävesi) to the wastewater-influenced sampling points, where AOB dominated (AOA:AOB 1:2–1:15 in Keuruu, 1:3–1:19 in Petäjävesi). The study showed that wastewater can affect sediment microbial community through importing nutrients and organic material and altering habitat characteristics, but also through bringing wastewater-originated microbes to the sediment, and may thus have significant impact on the freshwater biogeochemistry, especially in the nutrient-poor boreal ecosystems. PMID:28487691

  1. Glyphosate toxicity and the effects of long-term vegetation control on soil microbial communities

    Treesearch

    Matt D. Busse; Alice W. Ratcliff; Carol J. Stestak; Robert F. Powers

    2001-01-01

    We assessed the direct and indirect effect of the herbicide glyphosate on soil microbial communities from soil bioassays at glyphosate concentrations up to 100-fold greater than expected following a single field application. Indirect effects on microbial biomass, respiration, and metabolic diversity (Biolog and catabolic response profile) were compared seasonally after...

  2. Metagenomic analysis of the microbial community in kefir grains.

    PubMed

    Nalbantoglu, Ufuk; Cakar, Atilla; Dogan, Haluk; Abaci, Neslihan; Ustek, Duran; Sayood, Khalid; Can, Handan

    2014-08-01

    Kefir grains as a probiotic have been subject to microbial community identification using culture-dependent and independent methods that target specific strains in the community, or that are based on limited 16S rRNA analysis. We performed whole genome shotgun pyrosequencing using two Turkish Kefir grains. Sequencing generated 3,682,455 high quality reads for a total of ∼1.6 Gbp of data assembled into 6151 contigs with a total length of ∼24 Mbp. Species identification mapped 88.16% and 93.81% of the reads rendering 4 Mpb of assembly that did not show any homology to known bacterial sequences. Identified communities in the two grains showed high concordance where Lactobacillus was the most abundant genus with a mapped abundance of 99.42% and 99.79%. This genus was dominantly represented by three species Lactobacillus kefiranofaciens, Lactobacillus buchneri and Lactobacillus helveticus with a total mapped abundance of 97.63% and 98.74%. We compared and verified our findings with 16S pyrosequencing and model based 16S data analysis. Our results suggest that microbial community profiling using whole genome shotgun data is feasible, can identify novel species data, and has the potential to generate a more accurate and detailed assessment of the underlying bacterial community, especially for low abundance species. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

    SciTech Connect

    Cusack, Daniela F.; Silver, Whendee; Torn, Margaret S.; Burton, Sarah D.; Firestone, Mary

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

  4. Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests.

    PubMed

    Cusack, Daniela F; Silver, Whendee L; Torn, Margaret S; Burton, Sarah D; Firestone, Mary K

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

  5. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    NASA Astrophysics Data System (ADS)

    Dhar, Bipro Ranjan; Ryu, Hodon; Santo Domingo, Jorge W.; Lee, Hyung-Sool

    2016-11-01

    Multi-anode microbial electrochemical cells (MxCs) are considered as one of the most promising configurations for scale-up of MxCs, but understanding of anode kinetics in multiple anodes is limited in the MxCs. In this study we assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MxC to better comprehend anode fundamentals. Microbial community analysis targeting 16S rRNA Illumina sequencing showed that Geobacter genus was abundant (87%) only on the biofilm anode closest to a reference electrode (low ohmic energy loss) in which current density was the highest among three anodes. In comparison, Geobacter populations were less than 1% for biofilms on other two anodes distant from the reference electrode (high ohmic energy loss), generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest biofilm anode to the reference electrode, while EKA was as high as -0.134 V for the farthest anode. Our study proves that electric potential of individual anodes changed by ohmic energy loss shifts biofilm communities on individual anodes and consequently influences electron transfer kinetics on each anode in the multi-anode MxC.

  6. Sheep-urine-induced changes in soil microbial community structure.

    PubMed

    Nunan, Naoise; Singh, Brajesh; Reid, Eileen; Ord, Brian; Papert, Artemis; Squires, Julie; Prosser, Jim I; Wheatley, Ron E; McNicol, Jim; Millard, Peter

    2006-05-01

    Soil microbial communities play an important role in nutrient cycling and nutrient availability, especially in unimproved soils. In grazed pastures, sheep urine causes local changes in nutrient concentration which may be a source of heterogeneity in microbial community structure. In the present study, we investigated the effects of synthetic urine on soil microbial community structure, using physiological (community level physiological profiling, CLPP), biochemical (phospholipid fatty acid analysis, PLFA) and molecular (denaturing gradient gel electrophoresis, DGGE) fingerprinting methods. PLFA data suggested that synthetic urine treatment had no significant effect on total microbial (total PLFA), total bacterial or fungal biomass; however, significant changes in microbial community structure were observed with both PLFA and DGGE data. PLFA data suggested that synthetic urine induced a shift towards communities with higher concentrations of branched fatty acids. DGGE banding patterns derived from control and treated soils differed, due to a higher proportion of DNA sequences migrating only to the upper regions of the gel in synthetic urine-treated samples. The shifts in community structure measured by PLFA and DGGE were significantly correlated with one another, suggesting that both datasets reflected the same changes in microbial communities. Synthetic urine treatment preferentially stimulated the use of rhizosphere-C in sole-carbon-source utilisation profiles. The changes caused by synthetic urine addition accounted for only 10-15% of the total variability in community structure, suggesting that overall microbial community structure was reasonably stable and that changes were confined to a small proportion of the communities.

  7. Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

    NASA Astrophysics Data System (ADS)

    Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

    2016-09-01

    Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

  8. Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

    PubMed

    Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

    2010-08-01

    Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

  9. Microbial communities in the deep subsurface

    NASA Astrophysics Data System (ADS)

    Krumholz, Lee R.

    The diversity of microbial populations and microbial communities within the earth's subsurface is summarized in this review. Scientists are currently exploring the subsurface and addressing questions of microbial diversity, the interactions among microorganisms, and mechanisms for maintenance of subsurface microbial communities. Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain. Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface. Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits. In this review, each of these microbial communities is discussed in detail with specific reference to their energy sources, their observed growth patterns, and their diverse composition. This information is critical to develop further understanding of subsurface

  10. Effect of pesticides on microbial communities in container aquatic habitats

    PubMed Central

    Muturi, Ephantus J.; Donthu, Ravi Kiran; Fields, Christopher J.; Moise, Imelda K.; Kim, Chang-Hyun

    2017-01-01

    Container aquatic habitats support a specialized community of macroinvertebrates (e.g. mosquitoes) that feed on microbial communities associated with decaying organic matter. These aquatic habitats are often embedded within and around agricultural lands and are frequently exposed to pesticides. We used a microcosm approach to examine the single and combined effects of two herbicides (atrazine, glyphosate), and three insecticides (malathion, carbaryl, permethrin) on microbial communities of container aquatic habitats. MiSeq sequencing of the V4 region of both bacterial and archaeal 16S rRNA gene was used to characterize the microbial communities of indoor microcosms that were either exposed to each pesticide alone, a mix of herbicides, a mix of insecticides, or a mix of all five insecticides. Individual insecticides but not herbicides reduced the microbial diversity and richness and two insecticides, carbaryl and permethrin, also altered the microbial community structure. A mixture of herbicides had no effect on microbial diversity or structure but a mixture of insecticides or all five pesticides reduced microbial diversity and altered the community structure. These findings suggest that exposure of aquatic ecosystems to individual pesticides or their mixtures can disrupt aquatic microbial communities and there is need to decipher how these changes affect resident macroinvertebrate communities. PMID:28300212

  11. Effect of pesticides on microbial communities in container aquatic habitats.

    PubMed

    Muturi, Ephantus J; Donthu, Ravi Kiran; Fields, Christopher J; Moise, Imelda K; Kim, Chang-Hyun

    2017-03-16

    Container aquatic habitats support a specialized community of macroinvertebrates (e.g. mosquitoes) that feed on microbial communities associated with decaying organic matter. These aquatic habitats are often embedded within and around agricultural lands and are frequently exposed to pesticides. We used a microcosm approach to examine the single and combined effects of two herbicides (atrazine, glyphosate), and three insecticides (malathion, carbaryl, permethrin) on microbial communities of container aquatic habitats. MiSeq sequencing of the V4 region of both bacterial and archaeal 16S rRNA gene was used to characterize the microbial communities of indoor microcosms that were either exposed to each pesticide alone, a mix of herbicides, a mix of insecticides, or a mix of all five insecticides. Individual insecticides but not herbicides reduced the microbial diversity and richness and two insecticides, carbaryl and permethrin, also altered the microbial community structure. A mixture of herbicides had no effect on microbial diversity or structure but a mixture of insecticides or all five pesticides reduced microbial diversity and altered the community structure. These findings suggest that exposure of aquatic ecosystems to individual pesticides or their mixtures can disrupt aquatic microbial communities and there is need to decipher how these changes affect resident macroinvertebrate communities.

  12. Soil amendments yield persisting changes in the microbial communities

    USDA-ARS?s Scientific Manuscript database

    Soil microbial communities are sensitive to carbon amendments and largely control the decomposition and accumulation of soil organic matter. In this study, we evaluated whether the type of carbon amendment applied to wheat-cropped or fallow soil imparted lasting effects on the microbial community w...

  13. Response of soil microbial communities during changes in land management

    USDA-ARS?s Scientific Manuscript database

    The response of soil microbial communities to restoration following disturbances is poorly understood. We studied the soil microbial communities in a forest disturbance-restoration series comprising a native deciduous forest (DF), conventionally tilled cropland (CT) and mid-succession forest (SF) re...

  14. Community history affects the predictability of microbial ecosystem development.

    PubMed

    Pagaling, Eulyn; Strathdee, Fiona; Spears, Bryan M; Cates, Michael E; Allen, Rosalind J; Free, Andrew

    2014-01-01

    Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community's previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications.

  15. Community history affects the predictability of microbial ecosystem development

    PubMed Central

    Pagaling, Eulyn; Strathdee, Fiona; Spears, Bryan M; Cates, Michael E; Allen, Rosalind J; Free, Andrew

    2014-01-01

    Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community's previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications. PMID:23985743

  16. Assessing the impact of composting and vermicomposting on bacterial community size and structure, and microbial functional diversity of an olive-mill waste.

    PubMed

    Vivas, A; Moreno, B; Garcia-Rodriguez, S; Benitez, E

    2009-02-01

    The aim of this study was to couple biochemical and molecular methodologies for evaluating the impact of two recycling technologies (composting and vermicomposting) on a toxic organic waste. To do this, six enzyme activities controlling the key metabolic pathways of the breakdown of organic matter, real-time PCR assays targeting 16S rRNA genes, and denaturing gradient gel electrophoresis (DGGE) profiling-sequence analysis of PCR-amplified 16S rRNA fragments have been used to determine the functional diversity, bacterial number, and bacterial community structure, respectively, in a mixture of olive waste and sheep manure, and in the derived compost and vermicompost. Both the recycling technologies were effective in activating the microbial parameters of the toxic waste, the vermicomposting being the best process to produce greater bacterial diversity, greater bacterial numbers and greater functional diversity. Although several identical populations were detected in the processed and non-processed materials, each technology modified the original microbial communities of the waste in a diverse way, indicating the different roles of each one in the bacterial selection.

  17. Elevated temperature alters carbon cycling in a model microbial community

    NASA Astrophysics Data System (ADS)

    Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

    2013-12-01

    Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other

  18. Subglacial Microbial Communities and Their Relationship to Bedrock Lithology

    NASA Astrophysics Data System (ADS)

    Skidmore, M. L.; Lanoil, B. D.; Anderson, S. P.; Sharp, M.; Foght, J.; Nealson, K. H.

    2002-12-01

    -blot hybridization on samples taken in 2001/2002 from a range of environments at the two glaciers to assess a) if the microbial populations are stable through time and b) the spatial variability of populations at each glacier. The studies reported here are the first to examine the composition of microbial communities in contrasting glaciated catchments using molecular techniques. The data imply a microbial influence on subglacial geochemical dynamics; a hypothesis that we plan to pursue in future studies.

  19. Microbial diversity during cellulose decomposition in different forest stands: I. microbial communities and environmental conditions.

    PubMed

    Kubartová, Ariana; Moukoumi, Judicaël; Béguiristain, Thierry; Ranger, Jacques; Berthelin, Jacques

    2007-10-01

    We studied the effect of forest tree species on a community of decomposers that colonize cellulose strips. Both fungal and bacterial communities were targeted in a native forest dominated by beech and oak and 30-year-old beech and spruce plantations, growing in similar ecological conditions in the Breuil-Chenue experimental forest site in Morvan (France). Microbial ingrowths from the 3rd to 10th month of strip decomposition (May to December 2004) were studied. Community composition was assessed using temperature gradient gel electrophoresis with universal fungal (ITS1F, ITS2) and bacterial (1401r, 968f) primers. Soil temperature and moisture as well as fungal biomass were also measured to give additional information on decomposition processes. Changing the dominant tree species had no significant influence in the number of decomposer species. However, decomposer community composition was clearly different. If compared to the native forest, where community composition highly differed, young monocultures displayed similar species structure for fungi and bacteria. Both species numbers and community composition evolved during the decay process. Time effect was found to be more important than tree species. Nevertheless, the actual environmental conditions and seasonal effect seemed to be even more determining factors for the development of microbial communities. The course and correlations of the explored variables often differed between tree species, although certain general trends were identified. Fungal biomass was high in summer, despite that species richness (SR) decreased and conversely, that high SR did not necessarily mean high biomass values. It can be concluded that the growth and development of the microbiological communities that colonized a model material in situ depended on the combination of physical and biological factors acting collectively and interdependently at the forest soil microsite.

  20. Cheese Microbial Risk Assessments — A Review

    PubMed Central

    Choi, Kyoung-Hee; Lee, Heeyoung; Lee, Soomin; Kim, Sejeong; Yoon, Yohan

    2016-01-01

    Cheese is generally considered a safe and nutritious food, but foodborne illnesses linked to cheese consumption have occurred in many countries. Several microbial risk assessments related to Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli infections, causing cheese-related foodborne illnesses, have been conducted. Although the assessments of microbial risk in soft and low moisture cheeses such as semi-hard and hard cheeses have been accomplished, it has been more focused on the correlations between pathogenic bacteria and soft cheese, because cheese-associated foodborne illnesses have been attributed to the consumption of soft cheeses. As a part of this microbial risk assessment, predictive models have been developed to describe the relationship between several factors (pH, Aw, starter culture, and time) and the fates of foodborne pathogens in cheese. Predictions from these studies have been used for microbial risk assessment as a part of exposure assessment. These microbial risk assessments have identified that risk increased in cheese with high moisture content, especially for raw milk cheese, but the risk can be reduced by preharvest and postharvest preventions. For accurate quantitative microbial risk assessment, more data including interventions such as curd cooking conditions (temperature and time) and ripening period should be available for predictive models developed with cheese, cheese consumption amounts and cheese intake frequency data as well as more dose-response models. PMID:26950859

  1. Microbial communities in oil-contaminated seawater.

    PubMed

    Harayama, Shigeaki; Kasai, Yuki; Hara, Akihiro

    2004-06-01

    Although diverse bacteria capable of degrading petroleum hydrocarbons have been isolated and characterized, the vast majority of hydrocarbon-degrading bacteria, including anaerobes, could remain undiscovered, as a large fraction of bacteria inhabiting marine environments are uncultivable. Using culture-independent rRNA approaches, changes in the structure of microbial communities have been analyzed in marine environments contaminated by a real oil spill and in micro- or mesocosms that mimic such environments. Alcanivorax and Cycloclasticus of the gamma-Proteobacteria were identified as two key organisms with major roles in the degradation of petroleum hydrocarbons. Alcanivorax is responsible for alkane biodegradation, whereas Cycloclasticus degrades various aromatic hydrocarbons. This information will be useful to develop in situ bioremediation strategies for the clean-up of marine oil spills.

  2. Community Proteomics of a Natural Microbial Biofilm

    SciTech Connect

    Ram, Rachna J.; Verberkmoes, Nathan C; Thelen, Michael P.; Tyson, Gene W.; Baker, Brett J.; Shah, Manesh B; BlakeII, Robert C.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2005-06-01

    Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.

  3. Scope of potential bacterial agents of diarrhoea and microbial assessment of quality of river water sources in rural Venda communities in South Africa.

    PubMed

    Obi, C L; Potgieter, N; Bessong, P O; Matsaung, G

    2003-01-01

    The microbial quality of several, usually untreated, surface domestic water sources, used by rural communities in the Venda Region of South Africa, was assessed to gauge their fitness for human consumption and to highlight the possible impact of waterborne diseases. The water sources studied were six points on the Levubu River and the rivers Mutale, Ngwedi, Tshinane, Makonde, Mutshindudi and Mudaswali. Total and faecal coliform, heterotrophic bacteria, enterococci and coliphage counts were used as indicators/surrogates to estimate the degree of bacterial and viral contamination respectively by standard methods. The presence of potential bacterial agents of diarrhoea such as Salmonella, Shigella, Campylobacter, Plesiomonas, Aeromonas and Vibrio was also determined. Results showed that the ranges of counts with regard to all the water sources investigated were 2.9 x 10(2) - 6.3 x 10(4) CFU/100 mL for faecal coliforms, 6.0 x 10(2) - 3.7 x 10(4) CFU/100 mL for total coliforms, 1.8 x 10(2) - 1.3 x 10(6) CFU/mL for heterotrophic plate count, 1.0 x 10(1) - 3.7 x 10(4) CFU/100 mL for enterococci and 0-13 PFU/100 mL for coliphages. These values are far higher than the acceptable maximum limits prescribed for South Africa by the Dept of Water & Forestry and the Water Research Commission - 0 CFU/100 mL, 5 CFU/100 mL, 1.0 x 10(2) CFU/mL, 0 CFU/100 mL and 1 PFU/100 mL for faecal coliforms, total coliforms, heterotrophic bacteria, enterococci and coliphages respectively. Salmonella, Shigella, Vibrio cholerae, Campylobacter, Aeromonas and Plesiomonas were isolated from several of the water sources investigated. The use of these water sources for drinking and domestic purposes poses a serious threat to the health and well being of the users and calls for urgent government intervention.

  4. Microbial Communities of Continuously Cropped, Irrigated Rice Fields

    PubMed Central

    Reichardt, W.; Mascarina, G.; Padre, B.; Doll, J.

    1997-01-01

    In continuously cropped, irrigated rice fields, soil microbial biomass as measured by total phospholipid fatty acid concentrations declined during the second half of the crop cycle. This decline was also observed in other components of the microbial community assessed by viable counts, including denitrifiers and sporeformers. Simultaneous with total biomass decline was the increase in potential indicators of nutrient stress--such as ratios of cyclopropanol ((Sigma)[cy/(omega)7c]) and trans ((Sigma)[(omega)7t/(omega)7c]) phospholipid fatty acids--in plain crop soil but not in the rhizosphere. Polyhydroxyalkanoate levels were enhanced in the root environment of mature rice. Polyunsaturated eukaryotic biomarkers accounted for only 13 to 16 mol% of the total phospholipids, including 2 mol% of 18:2(omega)6, which is considered a fungal biomarker. Single biomarkers for defined physiological groups of bacteria did not follow the declining trend of total microbial biomass. Signature compounds for gram-positive and gram-negative fermenters (plasmalogen phospholipids), methanogenic bacteria (diether lipids), and methanotrophs (18:1(omega)8c) increased as the crop approached maturity. Methanotrophs were not particularly enriched in the rhizosphere. Methanogenic biomarkers were, however, most abundant in root extracts from mature rice plants. Assuming that soil microbial biomass plays a significant role as a passive nutrient pool, its reduction during the second half of the cropping season suggests a mechanism that may ultimately contribute to declining productivity in irrigated, continuous rice cropping systems. PMID:16535489

  5. Alpine Microbial Community Responses to Summer Warming

    NASA Astrophysics Data System (ADS)

    Osborne, B. B.; Baron, J.; Wallenstein, M. D.

    2011-12-01

    Remote alpine ecosystems of the western US are vulnerable to anthropogenic drivers of change. Atmospheric nitrogen (N) deposition and a changing climate introduce nutrients, alter hydrological processes, and expose soils to novel temperature regimes. We asked whether terrestrial microbes, specifically nitrifiers that may contribute to already high lake and stream NO3- concentrations, may be responding to changes in important controls of community development and activity associated with a changing climate, namely temperature and moisture. In August 2010 we sampled three soils from the Loch Vale Watershed in Rocky Mountain National Park which fell along a gradient of succession commonly represented in deglaciated alpine catchments. These included well-developed meadow soils, poorly vegetated talus substrate, and newly-exposed glacial outwash. Outwash, talus, and meadow samples were all N-rich and contained NH4-N concentrations ~7 times higher than NO3-N. Soils were incubated for 45 days at 2.5, 10, and 25oC and three moisture levels based on initial field conditions. Nitrifier concentrations were greatest in outwash, intermediate in talus, and lowest in meadow samples. Bacterial nitrifier abundance greatly surpassed archaeal nitrifier levels. Net nitrification was also greatest in outwash, followed by meadow and talus respectively. Moisture, rather than temperature, was a dominant control over both nitrifier abundance and activity. Linking the influence of temperature and moisture on alpine microbial communities will provide insight into control thresholds, optima, and synergistic interactions. This research is part of a larger study of controls on headwater stream and lake NO3-. Characterizing microbial NO3- production in the alpine will help us evaluate the importance of biological, as opposed to physical, sources of stream NO3-. It will also inform our ability to forecast and mitigate consequences of anthropogenic drivers of change on these systems.

  6. Controls on soil microbial community stability under climate change

    PubMed Central

    de Vries, Franciska T.; Shade, Ashley

    2013-01-01

    Soil microbial communities are intricately linked to ecosystem functioning because they play important roles in carbon and nitrogen cycling. Still, we know little about how soil microbial communities will be affected by disturbances expected with climate change. This is a significant gap in understanding, as the stability of microbial communities, defined as a community's ability to resist and recover from disturbances, likely has consequences for ecosystem function. Here, we propose a framework for predicting a community's response to climate change, based on specific functional traits present in the community, the relative dominance of r- and K-strategists, and the soil environment. We hypothesize that the relative abundance of r- and K-strategists will inform about a community's resistance and resilience to climate change associated disturbances. We also propose that other factors specific to soils, such as moisture content and the presence of plants, may enhance a community's resilience. For example, recent evidence suggests microbial grazers, resource availability, and plant roots each impact on microbial community stability. We explore these hypotheses by offering three vignettes of published data that we re-analyzed. Our results show that community measures of the relative abundance of r- and K-strategists, as well as environmental properties like resource availability and the abundance and diversity of higher trophic levels, can contribute to explaining the response of microbial community composition to climate change-related disturbances. However, further investigation and experimental validation is necessary to directly test these hypotheses across a wide range of soil ecosystems. PMID:24032030

  7. Microbial community functional change during vertebrate carrion decomposition.

    PubMed

    Pechal, Jennifer L; Crippen, Tawni L; Tarone, Aaron M; Lewis, Andrew J; Tomberlin, Jeffery K; Benbow, M Eric

    2013-01-01

    Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.

  8. Microbial Community Functional Change during Vertebrate Carrion Decomposition

    PubMed Central

    Pechal, Jennifer L.; Crippen, Tawni L.; Tarone, Aaron M.; Lewis, Andrew J.; Tomberlin, Jeffery K.; Benbow, M. Eric

    2013-01-01

    Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition. PMID:24265741

  9. Relationships between sediment microbial communities and pollutants in two California salt marshes.

    PubMed

    Cao, Y; Cherr, G N; Córdova-Kreylos, A L; Fan, T W-M; Green, P G; Higashi, R M; Lamontagne, M G; Scow, K M; Vines, C A; Yuan, J; Holden, P A

    2006-11-01

    Salt marshes are important ecosystems whose plant and microbial communities can alter terrestrially derived pollutants prior to coastal water discharge. However, knowledge regarding relationships between anthropogenic pollutant levels and salt marsh microbial communities is limited, and salt marshes on the West Coast of the United States are rarely examined. In this study, we investigated the relationships between microbial community composition and 24 pollutants (20 metals and 4 organics) in two California salt marshes. Multivariate ordination techniques were used to assess how bacterial community composition, as determined by terminal restriction fragment length polymorphism and phospholipid fatty acid analyses, was related to pollution. Sea urchin embryo toxicity measurements and plant tissue metabolite profiles were considered two other biometrics of pollution. Spatial effects were strongly manifested across marshes and across channel elevations within marshes. Utilizing partial canonical correspondence analysis, an ordination technique new to microbial ecology, we found that several metals were strongly associated with microbial community composition after accounting for spatial effects. The major patterns in plant metabolite profiles were consistent with patterns across microbial community profiles, but sea urchin embryo assays, which are commonly used to evaluate ecological toxicity, had no identifiable relationships with pollution. Whereas salt marshes are generally dynamic and complex habitats, microbial communities in these marshes appear to be relatively sensitive indicators of toxic pollutants.

  10. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

    PubMed Central

    Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

  11. Impact of genetically modified crops on soil- and plant-associated microbial communities.

    PubMed

    Dunfield, Kari E; Germida, James J

    2004-01-01

    Transgenic or genetically modified plants possess novel genes that impart beneficial characteristics such as herbicide resistance. One of the least understood areas in the environmental risk assessment of genetically modified crops is their impact on soil- and plant-associated microbial communities. The potential for interaction between transgenic plants and plant residues and the soil microbial community is not well understood. The recognition that these interactions could change microbial biodiversity and affect ecosystem functioning has initiated a limited number of studies in the area. At this time, studies have shown the possibility that transgenes can be transferred to native soil microorganisms through horizontal gene transfer, although there is not evidence of this occurring in the soil. Furthermore, novel proteins have been shown to be released from transgenic plants into the soil ecosystem, and their presence can influence the biodiversity of the microbial community by selectively stimulating the growth of organisms that can use them. Microbial diversity can be altered when associated with transgenic plants; however, these effects are both variable and transient. Soil- and plant-associated microbial communities are influenced not only by plant species and transgene insertion but also by environmental factors such as field site and sampling date. Minor alterations in the diversity of the microbial community could affect soil health and ecosystem functioning, and therefore, the impact that plant variety may have on the dynamics of the rhizosphere microbial populations and in turn plant growth and health and ecosystem sustainability, requires further study.

  12. Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

    PubMed Central

    Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

    2011-01-01

    Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

  13. Microbial Communities of the Okinawa Backarc Basin Subvent Biosphere

    NASA Astrophysics Data System (ADS)

    Brandt, L. D.; House, C. H.

    2014-12-01

    IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 m. Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 m. Site C0014 is a unique location to study changes in microbial communities with depth, as the hydrothermal system generates a thermally and geochemically restrictive subvent biosphere. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data suggests that Archaea represent a significant proportion of the indigenous community throughout the top 15 m of sediment, where Archaea then abruptly disappear. Furthermore, a deeper classification of Archaeal sequences suggests a transition from a mesophilic community to a potentially thermophilic one, where there is an increasingly stronger signal of Miscellaneous Crenarchaeotic Group (MCG) followed by Terrestrial Hot Spring Crenarchaeotic Group (THSCG). Additionally, there are several horizons in which methanotrophy is likely supported, indicated by peaks in anaerobic methanotrophic Archaea. The cessation of Archaea as well as Chloroflexi, a common marine subsurface bacterial phylum, at approximately 15 meters below seafloor (mbsf) is suggestive of a potential boundary within Site C0014 in which the environmental conditions have become too restrictive

  14. Successive DNA extractions improve characterization of soil microbial communities

    PubMed Central

    de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

    2017-01-01

    Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

  15. Reciprocal influences of microbial community and hydrogeomorphology in sandy streambeds

    NASA Astrophysics Data System (ADS)

    Mendoza-Lera, C.; Federlein, L. L.; Frossard, A.; Gessner, M. O.; Knie, M.; Mutz, M.

    2015-12-01

    Stream hydrogeomorphology is a strong determinant of streambed microbial community activity, which in turn influences stream biogeochemistry. Whether this influence is unidirectional or whether microbial communities can also modulate biogeochemical processes by affecting hydrogeomorphology is an emerging question in research on sediment-water interfaces. Using experimental flumes simulating sandy streams, we tested whether such influences can occur through altered water exchange across the sediment-water interface. Results show that microbial communities in sandy streambeds can indeed affect hydrogeomorphology by producing gas bubbles. Specifically, gas bubbles accumulating in microbial biofilms can alter the water exchange by (i) reducing sediment pore space or (ii) provoking the detachment of the microbial biofilm detachment and thus altering streambed topography. Additionally, results indicate that water exchange is the major for the structure and activity of the microbial community. Our data also indicate that the potential of microbial communities to influence water exchange can be modulated by factors such as light intensity and discharge fluctuations. These biological-physical interactions and their effects on the influence of microbial communities on hydrogeomorphology is a source of spatiotemporal variability in water exchange across the sediment-water interface. Heterogeneity in water exchange is known to increase biogeochemical pathways and, thus, ecosystem functions. These results suggest that a holistic understanding of vertical connectivity in running waters requires consideration of biological-physical interactions at the water-sediment interface.

  16. Substrate-induced changes in microbial community-level physiological profiles and their application to discriminate soil microbial communities.

    PubMed

    Chen, Jian; Xie, Huijun; Zhuang, Xuliangli; Zhuang, Guoqiang; Bai, Zhihui; Zhang, Hongxun

    2008-01-01

    The addition of simple substrates could affect the microbial respiration in soils. This substrate-induced respiration is widely used to estimate the soil microbial biomass, but little attention has been paid to its influence on the changes of community-level physiological profiles. In this study, the process of microbial communities responding to the added substrate using sole-carbon-source utilization (BIOLOG) was investigated. BIOLOG is biased toward fast-growing bacteria; this advantage was taken to detect the prompt response of the active microbial communities to the added substrate. Four soil samples from agricultural fields adjacent to heavy metal mines were amended with L-arginine, citric acid, or D-glucose. Substrate amendments could, generally, not only increase the metabolic activity of the microbial communities, but also change the metabolic diverse patterns compared with no-substrate control. By tracking the process, it was found that the variance between substrate-induced treatment and control fluctuated greatly during the incubation course, and the influences of these three substrates were different. In addition, the application of these induced changes to discriminate soil microbial communities was tested. The distance among all samples was greatly increased, which further showed the functional variance among microbial communities in soils. This can be very useful in the discrimination of microbial communities even with high similarity.

  17. Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment.

    PubMed

    González-Toril, Elena; Santofimia, Esther; Blanco, Yolanda; López-Pamo, Enrique; Gómez, Manuel J; Bobadilla, Miguel; Cruz, Rolando; Palomino, Edwin Julio; Aguilera, Ángeles

    2015-11-01

    The exposure of fresh sulfide-rich lithologies by the retracement of the Nevado Pastoruri glacier (Central Andes, Perú) is increasing the presence of heavy metals in the water as well as decreasing the pH, producing an acid rock drainage (ARD) process in the area. We describe the microbial communities of an extreme ARD site in Huascarán National Park as well as their correlation with the water physicochemistry. Microbial biodiversity was analyzed by FLX 454 sequencing of the 16S rRNA gene. The suggested geomicrobiological model of the area distinguishes three different zones. The proglacial zone is located in the upper part of the valley, where the ARD process is not evident yet. Most of the OTUs detected in this area were related to sequences associated with cold environments (i.e., psychrotolerant species of Cyanobacteria or Bacteroidetes). After the proglacial area, an ARD-influenced zone appeared, characterized by the presence of phylotypes related to acidophiles (Acidiphilium) as well as other species related to acidic and cold environments (i.e., acidophilic species of Chloroflexi, Clostridium and Verrumicrobia). Sulfur- and iron-oxidizing acidophilic bacteria (Acidithiobacillus) were also identified. The post-ARD area was characterized by the presence of OTUs related to microorganisms detected in soils, permafrost, high mountain environments, and deglaciation areas (Sphingomonadales, Caulobacter or Comamonadaceae).

  18. Pharmaceuticals removal and microbial community assessment in a continuous fungal treatment of non-sterile real hospital wastewater after a coagulation-flocculation pretreatment.

    PubMed

    Mir-Tutusaus, J A; Parladé, E; Llorca, M; Villagrasa, M; Barceló, D; Rodriguez-Mozaz, S; Martinez-Alonso, M; Gaju, N; Caminal, G; Sarrà, M

    2017-06-01

    Hospital wastewaters are a main source of pharmaceutical active compounds, which are usually highly recalcitrant and can accumulate in surface and groundwater bodies. Fungal treatments can remove these contaminants prior to discharge, but real wastewater poses a problem to fungal survival due to bacterial competition. This study successfully treated real non-spiked, non-sterile wastewater in a continuous fungal fluidized bed bioreactor coupled to a coagulation-flocculation pretreatment for 56 days. A control bioreactor without the fungus was also operated and the results were compared. A denaturing gradient gel electrophoresis (DGGE) and sequencing approach was used to study the microbial community arisen in both reactors and as a result some bacterial degraders are proposed. The fungal operation successfully removed analgesics and anti-inflammatories, and even the most recalcitrant pharmaceutical families such as antibiotics and psychiatric drugs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Functional Diversity of Microbial Communities in Sludge-Amended Soils

    NASA Astrophysics Data System (ADS)

    Sun, Y. H.; Yang, Z. H.; Zhao, J. J.; Li, Q.

    The BIOLOG method was applied to exploration of functional diversity of soil microbial communities in sludge-amended soils sampled from the Yangtze River Delta. Results indicated that metabolic profile, functional diversity indexes and Kinetic parameters of the soil microbial communities changed following soil amendment with sewage sludge, suggesting that the changes occurred in population of the microbes capable of exploiting carbon substrates and in this capability as well. The kinetic study of the functional diversity revealed that the metabolic profile of the soil microbial communities exhibited non-linear correlation with the incubation time, showing a curse of sigmoid that fits the dynamic model of growth of the soil microbial communities. In all the treatments, except for treatments of coastal fluvo-aquic soil amended with fresh sludge and dried sludge from Hangzhou, kinetic parameters K and r of the functional diversity of the soil microbial communities decreased significantly and parameter S increased. Changes in characteristics of the functional diversity well reflected differences in C utilizing capacity and model of the soil microbial communities in the sludge-amended soils, and changes in functional diversity of the soil microbial communities in a particular eco-environment, like soil amended with sewage sludge.

  20. "LOVE TO HATE" pesticides: felicity or curse for the soil microbial community? An FP7 IAPP Marie Curie project aiming to establish tools for the assessment of the mechanisms controlling the interactions of pesticides with soil microorganisms.

    PubMed

    Karpouzas, D G; Tsiamis, G; Trevisan, M; Ferrari, F; Malandain, C; Sibourg, O; Martin-Laurent, F

    2016-09-01

    Pesticides end up in soil where they interact with soil microorganisms in various ways. On the Yin Side of the interaction, pesticides could exert toxicity on soil microorganisms, while on the Yang side of interaction, pesticides could be used as energy source by a fraction of the soil microbial community. The LOVE TO HATE project is an IAPP Marie Curie project which aims to study these complex interactions of pesticides with soil microorganisms and provide novel tools which will be useful both for pesticide regulatory purposes and agricultural use. On the Yin side of the interactions, a new regulatory scheme for assessing the soil microbial toxicity of pesticides will be proposed based on the use of advanced standardized tools and a well-defined experimental tiered scheme. On the Yang side of the interactions, advanced molecular tools like amplicon sequencing and functional metagenomics will be applied to define microbes that are involved in the rapid transformation of pesticides in soils and isolate novel pesticide biocatalysts. In addition, a functional microarray has been designed to estimate the biodegradation genetic potential of the microbial community of agricultural soils for a range of pesticide groups.

  1. Microbial community structure of a freshwater system receiving wastewater effluent.

    PubMed

    Hladilek, Matthew D; Gaines, Karen F; Novak, James M; Collard, David A; Johnson, Daniel B; Canam, Thomas

    2016-11-01

    Despite our dependency on treatment facilities to condition wastewater for eventual release to the environment, our knowledge regarding the effects of treated water on the local watershed is extremely limited. Responses of lotic systems to the treated wastewater effluent have been traditionally investigated by examining the benthic macroinvertebrate assemblages and community structure; however, these studies do not address the microbial diversity of the water systems. In the present study, planktonic and benthic bacterial community structure were examined at 14 sites (from 60 m upstream to 12,100 m downstream) and at two time points along an aquatic system receiving treated effluent from the Charleston Wastewater Treatment Plant (Charleston, IL). Total bacterial DNA was isolated and 16S rRNA sequences were analyzed using a metagenomics platform. The community structure in planktonic bacterial communities was significantly correlated with dissolved oxygen concentration. Benthic bacterial communities were not correlated with water quality but did have a significant geographic structuring. A local restructuring effect was observed in both planktonic and benthic communities near the treated wastewater effluent, which was characterized by an increase in abundance of sphingobacteria. Sites further downstream from the wastewater facility appeared to be less influenced by the effluent. Overall, the present study demonstrated the utility of targeted high-throughput sequencing as a tool to assess the effects of treated wastewater effluent on a receiving water system, and highlighted the potential for this technology to be used for routine monitoring by wastewater facilities.

  2. Comparative Metagenomics of Freshwater Microbial Communities

    SciTech Connect

    Hemme, Chris; Deng, Ye; Tu, Qichao; Fields, Matthew; Gentry, Terry; Wu, Liyou; Tringe, Susannah; Watson, David; He, Zhili; Hazen, Terry; Tiedje, James; Rubin, Eddy; Zhou, Jizhong

    2010-05-17

    Previous analyses of a microbial metagenome from uranium and nitric-acid contaminated groundwater (FW106) showed significant environmental effects resulting from the rapid introduction of multiple contaminants. Effects include a massive loss of species and strain biodiversity, accumulation of toxin resistant genes in the metagenome and lateral transfer of toxin resistance genes between community members. To better understand these results in an ecological context, a second metagenome from a pristine groundwater system located along the same geological strike was sequenced and analyzed (FW301). It is hypothesized that FW301 approximates the ancestral FW106 community based on phylogenetic profiles and common geological parameters; however, even if is not the case, the datasets still permit comparisons between healthy and stressed groundwater ecosystems. Complex carbohydrate metabolism has been almost entirely lost in the stressed ecosystem. In contrast, the pristine system encodes a wide diversity of complex carbohydrate metabolism systems, suggesting that carbon turnover is very rapid and less leaky in the healthy groundwater system. FW301 encodes many (~;;160+) carbon monoxide dehydrogenase genes while FW106 encodes none. This result suggests that the community is frequently exposed to oxygen from aerated rainwater percolating into the subsurface, with a resulting high rate of carbon metabolism and CO production. When oxygen levels fall, the CO then serves as a major carbon source for the community. FW301 appears to be capable of CO2 fixation via the reductive carboxylase (reverse TCA) cycle and possibly acetogenesis, activities; these activities are lacking in the heterotrophic FW106 system which relies exclusively on respiration of nitrate and/or oxygen for energy production. FW301 encodes a complete set of B12 biosynthesis pathway at high abundance suggesting the use of sodium gradients for energy production in the healthy groundwater community. Overall

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

    PubMed

    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.

  4. Effect of gold nanoparticles and ciprofloxacin on microbial catabolism: a community-based approach.

    PubMed

    Weber, Kela P; Petersen, Elijah J; Bissegger, Sonja; Koch, Iris; Zhang, Jun; Reimer, Kenneth J; Rehmann, Lars; Slawson, Robin M; Legge, Raymond L; O'Carroll, Denis M

    2014-01-01

    The effect of gold nanoparticles (AuNPs) and ciprofloxacin on the catabolism of microbial communities was assessed. This was accomplished through an ex situ methodology designed to give a priori knowledge on the potential for nanoparticles, or other emerging contaminants, to affect the catabolic capabilities of microbial communities in the environment. Microbial communities from a variety of sources were incubated with 31 prespecified carbon sources and either National Institute of Standards and Technology reference material 10-nm AuNPs or ciprofloxacin on 96-well microtiter plates. From the ciprofloxacin study, dose-response curves were generated and exemplified how this method can be used to assess the effect of a toxicant on overall catabolic capabilities of microbial communities. With 10-nm AuNPs at concentrations ranging from 0.01 µg/mL to 0.5 µg/mL, rhizosphere communities from Typha roots were only slightly catabolically inhibited at a single concentration (0.05 µg/mL); no effects were seen on wetland water communities, and a minor positive (i.e., enhanced catabolic capabilities) effect was observed for loamy soil communities. This positive effect might have been because of a thin layer of citrate found on these AuNPs that initiated cometabolism with some of the carbon sources studied. Under the conditions considered, the possible adverse effects of AuNPs on the catabolic capabilities of microbial communities appears to be minimal. © 2013 SETAC.

  5. Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

    PubMed Central

    Dunfield, Kari E.; Germida, James J.

    2003-01-01

    The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified

  6. Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

    PubMed Central

    Song, Hyun-Seob; Renslow, Ryan S.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2015-01-01

    Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community's functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities. PMID:26648912

  7. Mangrove succession enriches the sediment microbial community in South China

    PubMed Central

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-01-01

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession. PMID:27265262

  8. Mangrove succession enriches the sediment microbial community in South China.

    PubMed

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-06-06

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

  9. Mangrove succession enriches the sediment microbial community in South China

    NASA Astrophysics Data System (ADS)

    Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

    2016-06-01

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.

  10. Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities.

    PubMed

    Song, Hyun-Seob; Renslow, Ryan S; Fredrickson, Jim K; Lindemann, Stephen R

    2015-01-01

    Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems that undergo both recoverable and unrecoverable transitions, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community's functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities.

  11. Adaptation of Aquatic Microbial Communities to Hg2+ Stress †

    PubMed Central

    Barkay, Tamar

    1987-01-01

    The mechanism of adaptation to Hg2+ in four aquatic habitats was studied by correlating microbially mediated Hg2+ volatilization with the adaptive state of the exposed communities. Community diversity, heterotrophic activity, and Hg2+ resistance measurements indicated that adaptation of all four communities was stimulated by preexposure to Hg2+. In saline water communities, adaptation was associated with rapid volatilization after an initial lag period. This mechanism, however, did not promote adaptation in a freshwater sample, in which Hg2+ was volatilized slowly, regardless of the resistance level of the microbial community. Distribution of the mer operon among representative colonies of the communities was not related to adaptation to Hg2+. Thus, although volatilization enabled some microbial communities to sustain their functions in Hg2+-stressed environments, it was not mediated by the genes that serve as a model system in molecular studies of bacterial resistance to mercurials. PMID:16347488

  12. A trait-based approach for examining microbial community assembly

    NASA Astrophysics Data System (ADS)

    Prest, T. L.; Nemergut, D.

    2015-12-01

    Microorganisms regulate all of Earth's major biogeochemical cycles and an understanding of how microbial communities assemble is a key part in evaluating controls over many types of ecosystem processes. Rapid advances in technology and bioinformatics have led to a better appreciation for the variation in microbial community structure in time and space. Yet, advances in theory are necessary to make sense of these data and allow us to generate unifying hypotheses about the causes and consequences of patterns in microbial biodiversity and what they mean for ecosystem function. Here, I will present a metaanalysis of microbial community assembly from a variety of successional and post-disturbance systems. Our analysis shows various distinct patterns in community assembly, and the potential importance of nutrients and dispersal in shaping microbial community beta diversity in these systems. We also used a trait-based approach to generate hypotheses about the mechanisms driving patterns of microbial community assembly and the implications for function. Our work reveals the importance of rRNA operon copy number as a community aggregated trait in helping to reconcile differences in community dynamics between distinct types of successional and disturbed systems. Specifically, our results demonstrate that decreases in average copy number can be a common feature of communities across various drivers of ecological succession, supporting a transition from an r-selected to a K-selected community. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, from cells to populations and communities, and has implications for both ecology and evolution. Trait-based approaches are an important next step to generate and test hypotheses about the forces structuring microbial communities and the subsequent consequences for ecosystem function.

  13. Linking pollution induced community tolerance (PICT) and microbial community structure in chronically metal polluted estuarine sediments.

    PubMed

    Ogilvie, Lesley A; Grant, Alistair

    2008-03-01

    We tested the ability of pollution induced community tolerance (PICT) to detect the effects of chronic metal pollution on estuarine sediment microbial communities, along a gradient spanning two orders of magnitude in metal concentrations. In tandem, we investigated the associated microbial community structure using terminal restriction fragment length polymorphism (T-RFLP). Tolerance of microbes to Cu, measured as IC50 (inhibitory concentration 50%), was strongly correlated with pore water Cu concentration (r(2)=0.842). No strong correlation existed for other metals tested, highlighting the ability of PICT to identify the pollutant causing a toxic effect. There was no correlation between microbial community structure and community tolerance to metals tested, but analysis of community structure did provide some information on reasons for observed PICT response. PICT methodology used here provided a greater strength and consistency of association with pollutant concentration compared to microbial community structure and can be recommended as a sensitive indicator of metal pollution on estuarine sediment microbial communities.

  14. Microbial community dynamics alleviate stoichiometric constraints during litter decay

    PubMed Central

    Kaiser, Christina; Franklin, Oskar; Dieckmann, Ulf; Richter, Andreas

    2014-01-01

    Under the current paradigm, organic matter decomposition and nutrient cycling rates are a function of the imbalance between substrate and microbial biomass stoichiometry. Challenging this view, we demonstrate that in an individual-based model, microbial community dynamics alter relative C and N limitation during litter decomposition, leading to a system behaviour not predictable from stoichiometric theory alone. Rather, the dynamics of interacting functional groups lead to an adaptation at the community level, which accelerates nitrogen recycling in litter with high initial C : N ratios and thus alleviates microbial N limitation. This mechanism allows microbial decomposers to overcome large imbalances between resource and biomass stoichiometry without the need to decrease carbon use efficiency (CUE), which is in contrast to predictions of traditional stoichiometric mass balance equations. We conclude that identifying and implementing microbial community-driven mechanisms in biogeochemical models are necessary for accurately predicting terrestrial C fluxes in response to changing environmental conditions. PMID:24628731

  15. Microbial Communities Are Well Adapted to Disturbances in Energy Input

    PubMed Central

    Vallino, Joseph J.

    2016-01-01

    ABSTRACT Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic “unstable” communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and

  16. Microbial Communities Are Well Adapted to Disturbances in Energy Input.

    PubMed

    Fernandez-Gonzalez, Nuria; Huber, Julie A; Vallino, Joseph J

    2016-01-01

    Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating

  17. Microbial communities involved in electricity generation from sulfide oxidation in a microbial fuel cell.

    PubMed

    Sun, Min; Tong, Zhong-Hua; Sheng, Guo-Ping; Chen, Yong-Zhen; Zhang, Feng; Mu, Zhe-Xuan; Wang, Hua-Lin; Zeng, Raymond J; Liu, Xian-Wei; Yu, Han-Qing; Wei, Li; Ma, Fang

    2010-10-15

    Simultaneous electricity generation and sulfide removal can be achieved in a microbial fuel cell (MFC). In electricity harvesting from sulfide oxidation in such an MFC, various microbial communities are involved. It is essential to elucidate the microbial communities and their roles in the sulfide conversion and electricity generation. In this work, an MFC was constructed to enrich a microbial consortium, which could harvest electricity from sulfide oxidation. Electrochemical analysis demonstrated that microbial catalysis was involved in electricity output in the sulfide-fed MFC. The anode-attached and planktonic communities could perform catalysis independently, and synergistic interactions occurred when the two communities worked together. A 16S rRNA clone library analysis was employed to characterize the microbial communities in the MFC. The anode-attached and planktonic communities shared similar richness and diversity, while the LIBSHUFF analysis revealed that the two community structures were significantly different. The exoelectrogenic, sulfur-oxidizing and sulfate-reducing bacteria were found in the MFC anodic chamber. The discovery of these bacteria was consistent with the community characteristics for electricity generation from sulfide oxidation. The exoelectrogenic bacteria were found both on the anode and in the solution. The sulfur-oxidizing bacteria were present in greater abundance on the anode than in the solution, while the sulfate-reducing bacteria preferably lived in the solution.

  18. Microbial community-level toxicity testing of linear alkylbenzene sulfonates in aquatic microcosms.

    PubMed

    Brandt, Kristian K; Jørgensen, Niels O G; Nielsen, Tommy H; Winding, Anne

    2004-08-01

    Complex microbial communities may serve as ideal and ecologically relevant toxicity indicators. We here report an assessment of frequently used methods in microbial ecology for their feasibility to detect toxic effects of the environmentally important surfactant linear alkylbenzene sulfonate (LAS) on microbial communities in lake water and treated waste water. The two microbial communities were evaluated for changes in community structure and function over a period of 7 weeks in replicated aquatic microcosms amended with various levels of LAS (0, 0.1, 1, 10 or 100 mg l(-1)) and inorganic nutrients. In general, the two communities behaved similarly when challenged with LAS. Following lag periods of 1-3 weeks, LAS was degraded to non-toxic substances. Denaturing gradient gel electrophoresis of 16S rRNA gene fragments and [3H]leucine incorporation were the most sensitive assays with effect levels of 0-1 and 1-10 mg LAS l(-1), respectively. Community-level physiological profiles and pollution-induced community tolerance determinations using Biolog microplates demonstrated less sensitivity with effect levels of 10-100 mg LAS l(-1). Total cell counts and net uptake of inorganic N and P were unaffected even at 100 mg LAS l(-1). Interestingly, different microbial communities developed in some replicate microcosms, indicating the importance of stochastic events for community succession. We conclude that microbial community-level toxicity testing holds great promise and suggest a polyphasic approach involving a range of independent methods targeting both the structure and function of the tested microbial communities.

  19. Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells.

    PubMed

    Liu, Qian; Liu, Bingfeng; Li, Wei; Zhao, Xin; Zuo, Wenjing; Xing, Defeng

    2017-01-01

    The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter, which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs.

  20. Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells

    PubMed Central

    Liu, Qian; Liu, Bingfeng; Li, Wei; Zhao, Xin; Zuo, Wenjing; Xing, Defeng

    2017-01-01

    The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter, which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs. PMID:28638368

  1. Cultivation and quantitative proteomic analyses of acidophilic microbial communities

    SciTech Connect

    Belnap, Christopher P.; Pan, Chongle; Verberkmoes, Nathan C; Power, Mary E.; Samatova, Nagiza F; Carver, Rudolf L.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.

  2. Aspects of Diversity Measurement for Microbial Communities

    PubMed Central

    Mills, Aaron L.; Wassel, Raymond A.

    1980-01-01

    A useful measure of diversity was calculated for microbial communities collected from lake water and sediment samples using the Shannon index (H′) and rarefaction [E(S)]. Isolates were clustered by a numerical taxonomy approach in which limited (<20) tests were used so that the groups obtained represented a level of resolution other than species. The numerical value of diversity for each sample was affected by the number of tests used; however, the relative diversity compared among several sampling locations was the same whether 11 or 19 characters were examined. The number of isolates (i.e., sample size) strongly influenced the value of H′ so that unequal sized samples could not be compared. Rarefaction accounts for differences in sample size inherently so that such comparisons are made simple. Due to the type of sampling carried out by microbiologists, H′ is estimated and not determined and therefore requires a statement of error associated with it. Failure to report error provided potentially misleading results. Calculation of the variance of H′ is not a simple matter and may be impossible when handling a large number of samples. With rarefaction, the variance of E(S) is readily determined, facilitating the comparison of many samples. PMID:16345636

  3. Microbial community analysis of a single chamber microbial fuel cell using potato wastewater.

    PubMed

    Li, Zhen; Haynes, Rishika; Sato, Eugene; Shields, Malcolm S; Fujita, Yoshiko; Sato, Chikashi

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bio-electrochemical reactions mediated by microorganisms. This study investigated the diversity of the microbial community in an air cathode single chamber MFC that used potato-process wastewater as substrate. Terminal restriction fragment length polymorphism results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S ribosomal DNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that use potato wastewater.

  4. Microbial Community Analysis of a Single Chamber Microbial Fuel Cell Using Potato Wastewater

    SciTech Connect

    Zhen Li; Rishika Haynes; Eugene Sato; Malcolm Shields; Yoshiko Fujita; Chikashi Sato

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.

  5. Microbial communities as biosensors for monitoring urban environments.

    PubMed

    Ling, Fangqiong

    2017-09-01

    The BE microbiome is a naturally embedded biosensor in urban infrastructure that can be used to monitor environmental quality and human activity. There are many potential opportunities for leveraging BE microbial communities to guide urban design and public health policy. © 2017 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  6. Microbial community structure and biomass in developing drinking water biofilms.

    PubMed

    Keinänen, Minna M; Martikainen, Pertti J; Kontro, Merja H

    2004-03-01

    Traditional techniques to study microbes, such as culturable counts, microbial biomass, or microbial activity, do not give information on the microbial ecology of drinking water systems. The aim of this study was to analyze whether the microbial community structure and biomass differed in biofilms collected from two Finnish drinking water distribution systems (A and B) receiving conventionally treated (coagulation, filtration, disinfection) surface water. Phospholipid fatty acid methyl esters (PLFAs) and lipopolysaccharide 3-hydroxy fatty acid methyl esters (LPS 3-OH-FAs) were analyzed from biofilms as a function of water residence time and development time. The microbial communities were rather stabile through the distribution systems, as water residence time had minor effects on PLFA profiles. In distribution system A, the microbial community structure in biofilms, which had developed in 6 weeks, was more complex than those grown for 23 or 40 weeks. The microbial communities between the studied distribution systems differed, possibly reflecting the differences in raw water, water purification processes, and distribution systems. The viable microbial biomass, estimated on the basis of PLFAs, increased with increasing water residence time in both distribution systems. The quantitative amount of LPS 3-OH-FAs increased with increasing development time of biofilms of distribution system B. In distribution system A, LPS 3-OH-FAs were below the detection limit.

  7. Integrating ecological and engineering concepts of resilience in microbial communities

    SciTech Connect

    Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; Lindemann, Stephen R.

    2015-12-01

    We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the two concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.

  8. Integrating ecological and engineering concepts of resilience in microbial communities

    DOE PAGES

    Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; ...

    2015-12-01

    We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

  9. The Ecology of Microbial Communities Associated with Macrocystis pyrifera

    PubMed Central

    Michelou, Vanessa K.; Caporaso, J. Gregory; Knight, Rob; Palumbi, Stephen R.

    2013-01-01

    Kelp forests are characterized by high biodiversity and productivity, and the cycling of kelp-produced carbon is a vital process in this ecosystem. Although bacteria are assumed to play a major role in kelp forest carbon cycling, knowledge of the composition and diversity of these bacterial communities is lacking. Bacterial communities on the surface of Macrocystis pyrifera and adjacent seawater were sampled at the Hopkins Marine Station in Monterey Bay, CA, and further studied using 454-tag pyrosequencing of 16S RNA genes. Our results suggest that M. pyrifera-dominated kelp forests harbor distinct microbial communities that vary temporally. The distribution of sequence tags assigned to Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the surface of the kelp and the surrounding water. Several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed considerable temporal variation, often with similar trends in the seawater and the surface of the kelp. Bacterial community structure and membership correlated with the kelp surface serving as host, and varied over time. Several kelp-specific taxa were highly similar to other bacteria known to either prevent the colonization of eukaryotic larvae or exhibit antibacterial activities. Some of these kelp-specific bacterial associations might play an important role for M. pyrifera. This study provides the first assessment of the diversity and phylogenetic profile of the bacterial communities associated with M. pyrifera. PMID:23840715

  10. The Ecology of Microbial Communities Associated with Macrocystis pyrifera.

    PubMed

    Michelou, Vanessa K; Caporaso, J Gregory; Knight, Rob; Palumbi, Stephen R

    2013-01-01

    Kelp forests are characterized by high biodiversity and productivity, and the cycling of kelp-produced carbon is a vital process in this ecosystem. Although bacteria are assumed to play a major role in kelp forest carbon cycling, knowledge of the composition and diversity of these bacterial communities is lacking. Bacterial communities on the surface of Macrocystis pyrifera and adjacent seawater were sampled at the Hopkins Marine Station in Monterey Bay, CA, and further studied using 454-tag pyrosequencing of 16S RNA genes. Our results suggest that M. pyrifera-dominated kelp forests harbor distinct microbial communities that vary temporally. The distribution of sequence tags assigned to Gammaproteobacteria, Alphaproteobacteria and Bacteriodetes differed between the surface of the kelp and the surrounding water. Several abundant Rhodobacteraceae, uncultivated Gammaproteobacteria and Bacteriodetes-associated tags displayed considerable temporal variation, often with similar trends in the seawater and the surface of the kelp. Bacterial community structure and membership correlated with the kelp surface serving as host, and varied over time. Several kelp-specific taxa were highly similar to other bacteria known to either prevent the colonization of eukaryotic larvae or exhibit antibacterial activities. Some of these kelp-specific bacterial associations might play an important role for M. pyrifera. This study provides the first assessment of the diversity and phylogenetic profile of the bacterial communities associated with M. pyrifera.

  11. Integration of stable carbon isotope, microbial community, dissolved hydrogen gas, and 2HH2O tracer data to assess bioaugmentation for chlorinated ethene degradation in fractured rocks

    USGS Publications Warehouse

    Révész, Kinga M.; Lollar, Barbara Sherwood; Kirshtein, Julie D.; Tiedeman, Claire R.; Imbrigiotta, Thomas E.; Goode, Daniel J.; Shapiro, Allen M.; Voytek, Mary A.; Lancombe, Pierre J.; Busenberg, Eurybiades

    2014-01-01

    An in situ bioaugmentation (BA) experiment was conducted to understand processes controlling microbial dechlorination of trichloroethene (TCE) in groundwater at the Naval Air Warfare Center (NAWC), West Trenton, NJ. In the BA experiment, an electron donor (emulsified vegetable oil and sodium lactate) and a chloro-respiring microbial consortium were injected into a well in fractured mudstone of Triassic age. Water enriched in 2H was also injected as a tracer of the BA solution, to monitor advective transport processes. The changes in concentration and the δ13C of TCE, cis-dichloroethene (cis-DCE), and vinyl chloride (VC); the δ2H of water; changes in the abundance of the microbial communities; and the concentration of dissolved H2 gas compared to pre- test conditions, provided multiple lines of evidence that enhanced biodegradation occurred in the injection well and in two downgradient wells. For those wells where the biodegradation was stimulated intensively, the sum of the molar chlorinated ethene (CE) concentrations in post-BA water was higher than that of the sum of the pre-BA background molar CE concentrations. The concentration ratios of TCE/(cis-DCE + VC) indicated that the increase in molar CE concentration may result from additional TCE mobilized from the rock matrix in response to the oil injection or due to desorption/diffusion. The stable carbon isotope mass-balance calculations show that the weighted average 13C isotope of the CEs was enriched for around a year compared to the background value in a two year monitoring period, an effective indication that dechlorination of VC was occurring. Insights gained from this study can be applied to efforts to use BA in other fractured rock systems. The study demonstrates that a BA approach can substantially enhance in situ bioremediation not only in fractures connected to the injection well, but also in the rock matrix around the well due to processes such as diffusion and desorption. Because the effect of the

  12. Integration of stable carbon isotope, microbial community, dissolved hydrogen gas, and ²HH₂O tracer data to assess bioaugmentation for chlorinated ethene degradation in fractured rocks.

    PubMed

    Révész, Kinga M; Lollar, Barbara Sherwood; Kirshtein, Julie D; Tiedeman, Claire R; Imbrigiotta, Thomas E; Goode, Daniel J; Shapiro, Allen M; Voytek, Mary A; Lacombe, Pierre J; Busenberg, Eurybiades

    2014-01-01

    An in situ bioaugmentation (BA) experiment was conducted to understand processes controlling microbial dechlorination of trichloroethene (TCE) in groundwater at the Naval Air Warfare Center (NAWC), West Trenton, NJ. In the BA experiment, an electron donor (emulsified vegetable oil and sodium lactate) and a chloro-respiring microbial consortium were injected into a well in fractured mudstone of Triassic age. Water enriched in ²H was also injected as a tracer of the BA solution, to monitor advective transport processes. The changes in concentration and the δ¹³C of TCE, cis-dichloroethene (cis-DCE), and vinyl chloride (VC); the δ²H of water; changes in the abundance of the microbial communities; and the concentration of dissolved H₂ gas compared to pre- test conditions, provided multiple lines of evidence that enhanced biodegradation occurred in the injection well and in two downgradient wells. For those wells where the biodegradation was stimulated intensively, the sum of the molar chlorinated ethene (CE) concentrations in post-BA water was higher than that of the sum of the pre-BA background molar CE concentrations. The concentration ratios of TCE/(cis-DCE+VC) indicated that the increase in molar CE concentration may result from additional TCE mobilized from the rock matrix in response to the oil injection or due to desorption/diffusion. The stable carbon isotope mass-balance calculations show that the weighted average ¹³C isotope of the CEs was enriched for around a year compared to the background value in a two year monitoring period, an effective indication that dechlorination of VC was occurring. Insights gained from this study can be applied to efforts to use BA in other fractured rock systems. The study demonstrates that a BA approach can substantially enhance in situ bioremediation not only in fractures connected to the injection well, but also in the rock matrix around the well due to processes such as diffusion and desorption. Because the effect

  13. Microbial communities respond to experimental warming, but site matters.

    PubMed

    Cregger, Melissa A; Sanders, Nathan J; Dunn, Robert R; Classen, Aimée T

    2014-01-01

    Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems.

  14. A hydrogen-based subsurface microbial community dominated by methanogens

    USGS Publications Warehouse

    Chapelle, F.H.; O'Neil, Kyle; Bradley, P.M.; Methe, B.A.; Ciufo, S.A.; Knobel, L.L.; Lovley, D.R.

    2002-01-01

    The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem1-5. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16s ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

  15. Microbial communities respond to experimental warming, but site matters

    PubMed Central

    Sanders, Nathan J.; Dunn, Robert R.; Classen, Aimée T.

    2014-01-01

    Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems. PMID:24795850

  16. A hydrogen-based subsurface microbial community dominated by methanogens

    NASA Astrophysics Data System (ADS)

    Chapelle, Francis H.; O'Neill, Kathleen; Bradley, Paul M.; Methé, Barbara A.; Ciufo, Stacy A.; Knobel, LeRoy L.; Lovley, Derek R.

    2002-01-01

    The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

  17. A hydrogen-based subsurface microbial community dominated by methanogens.

    PubMed

    Chapelle, Francis H; O'Neill, Kathleen; Bradley, Paul M; Methé, Barbara A; Ciufo, Stacy A; Knobel, LeRoy L; Lovley, Derek R

    2002-01-17

    The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

  18. Differential microbial communities in hot spring mats from Western Thailand.

    PubMed

    Portillo, M C; Sririn, V; Kanoksilapatham, W; Gonzalez, J M

    2009-03-01

    The microbial communities of freshwater hot spring mats from Boekleung (Western Thailand) were studied. Temperatures ranged from over 50 up to 57 degrees C. Green-, red-, and yellow colored mat layers were analyzed. In order to detect the major components of the microbial communities constituting the mat as well as the microorganisms showing significant metabolic activity, samples were analyzed using DNA- and RNA-based molecular techniques, respectively. Microbial community fingerprints, performed by denaturing gradient gel electrophoresis (DGGE), revealed clear differences among mat layers. Thermophilic phototrophic microorganisms, Cyanobacteria and Chloroflexi, constituted the major groups in these communities (on average 65 and 51% from DNA and RNA analyses, respectively). Other bacteria detected in the mat were Bacteroidetes, members of the Candidate Division OP10, Actinobacteria, and Planctomycetes. Differently colored mat layers showed characteristic bacterial communities and the major components of the metabolically active fraction of these communities have been identified.

  19. Microbial community transitions across the deep sediment-basement interface

    NASA Astrophysics Data System (ADS)

    Labonté, J.; Lever, M. A.; Orcutt, B.

    2015-12-01

    Previous studies of microbial abundance and geochemistry in deep marine sediments indicate a stimulation of microbial activity near the sediment-basement interface; yet, the extent to which microbial communities in bottom sediments and underlying crustal habitats interact is unclear. We conducted tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement samples to try to identify patterns in microbial community shifts across sediment-basement interfaces, focusing on samples from the subsurface of the Juan de Fuca Ridge flank (IODP Expedition 327). Our results demonstrate that sediment and the basaltic crust harbor microbial communities that are phylogenetically connected, but the eveness is characteristic of the environment. We will discuss the microbial community transitions that occur horizontally along fluid flow pathways and vertically across the sediment basement interface, as well as the possible implications regarding the controls of microbial community composition along deep sediment-basement interfaces in hydrothermal systems. We will also highlight efforts to overcome sample contamination in crustal subsurface samples.

  20. Metabolically active microbial communities in uranium-contaminated subsurface sediments.

    PubMed

    Akob, Denise M; Mills, Heath J; Kostka, Joel E

    2007-01-01

    In order to develop effective bioremediation strategies for radionuclide contaminants, the composition and metabolic potential of microbial communities need to be better understood, especially in highly contaminated subsurface sediments for which little cultivation-independent information is available. In this study, we characterized metabolically active and total microbial communities associated with uranium-contaminated subsurface sediments along geochemical gradients. DNA and RNA were extracted and amplified from four sediment-depth intervals representing moderately acidic (pH 3.7) to near-neutral (pH 6.7) conditions. Phylotypes related to Proteobacteria (Alpha-, Beta-, Delta- and Gammaproteobacteria), Bacteroidetes, Actinobacteria, Firmicutes and Planctomycetes were detected in DNA- and RNA-derived clone libraries. Diversity and numerical dominance of phylotypes were observed to correspond to changes in sediment geochemistry and rates of microbial activity, suggesting that geochemical conditions have selected for well-adapted taxa. Sequences closely related to nitrate-reducing bacteria represented 28% and 43% of clones from the total and metabolically active fractions of the microbial community, respectively. This study provides the first detailed analysis of total and metabolically active microbial communities in radionuclide-contaminated subsurface sediments. Our microbial community analysis, in conjunction with rates of microbial activity, points to several groups of nitrate-reducers that appear to be well adapted to environmental conditions common to radionuclide-contaminated sites.

  1. Effect of warming and drought on grassland microbial communities.

    PubMed

    Sheik, Cody S; Beasley, William Howard; Elshahed, Mostafa S; Zhou, Xuhui; Luo, Yiqi; Krumholz, Lee R

    2011-10-01

    The soil microbiome is responsible for mediating key ecological processes; however, little is known about its sensitivity to climate change. Observed increases in global temperatures and alteration to rainfall patterns, due to anthropogenic release of greenhouse gases, will likely have a strong influence on soil microbial communities and ultimately the ecosystem services they provide. Therefore, it is vital to understand how soil microbial communities will respond to future climate change scenarios. To this end, we surveyed the abundance, diversity and structure of microbial communities over a 2-year period from a long-term in situ warming experiment that experienced a moderate natural drought. We found the warming treatment and soil water budgets strongly influence bacterial population size and diversity. In normal precipitation years, the warming treatment significantly increased microbial population size 40-150% but decreased diversity and significantly changed the composition of the community when compared with the unwarmed controls. However during drought conditions, the warming treatment significantly reduced soil moisture thereby creating unfavorable growth conditions that led to a 50-80% reduction in the microbial population size when compared with the control. Warmed plots also saw an increase in species richness, diversity and evenness; however, community composition was unaffected suggesting that few phylotypes may be active under these stressful conditions. Our results indicate that under warmed conditions, ecosystem water budget regulates the abundance and diversity of microbial populations and that rainfall timing is critical at the onset of drought for sustaining microbial populations.

  2. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    PubMed

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

  3. Assessing the soil microbial carbon budget: Probing with salt stress

    NASA Astrophysics Data System (ADS)

    Rath, Kristin; Rousk, Johannes

    2014-05-01

    The amount of carbon stored as soil organic matter (SOM) constitutes a pool more than double the size of the atmospheric carbon pool. Soil respiration represents one of the largest fluxes of carbon between terrestrial ecosystems and the atmosphere. A large fraction of the CO2 released by soils is produced by the microbial decomposition of SOM. The microbial carbon budget is characterized by their carbon use efficiency, i.e. the partitioning of substrate into growth and respiration. This will shape the role of the soil as a net source or sink for carbon. One of the canonical factors known to influence microbial processes in soil is pH. In aquatic systems salinity has been found to have a comparably strong influence as pH. However salinity remains understudied in soil, despite its growing relevance due to land use change and agricultural practices. The aim of this project is to understand how microbial carbon dynamics respond to disturbance by changing environmental conditions, using salinity as a reversible stressor. First, we compiled a comparative analysis of the sensitivity of different microbial processes to increasing salt concentrations. Second, we compared different salts to determine whether salt toxicity depended on the identity of the salt. Third, we used samples from a natural salinity gradient to assess if a legacy of salt exposure can influence the microbial response to changing salt concentrations. If salt had an ecologically significant effect in shaping these communities, we would assume that microbial processes would be less sensitive to an increase in salt concentrations. The sensitivity of microbial processes to salt was investigated by establishing inhibition curves in order to estimate EC50 values (the concentration resulting in 50% inhibition). These EC50 values were used to compare bacterial and fungal growth responses, as well as catabolic processes such as respiration and nitrogen mineralisation. Initial results suggest that growth related

  4. Biodegradation of Hydrocarbon Contaminants by Patuxent River Soil Microbial Communities.

    DTIC Science & Technology

    1992-06-01

    Engineering University of North Carolina BIODEGRADATION OF HYDROCARBON CONTAMINANTS BY PATUXENT RIVER SOIL MICROBIAL COMMUNITIES Abstract This study...on those rates and adaptation times. Tests were conducted by adding C-labeled compounds to jet fuel- contaminated soil from the fuel farm at the...BIODEGRADATION OF HYDRO- L CARBON CONTAMINANTS BY PATUXENT PR - RM33E80 RIVER SOIL MICROBIAL COMMUNITI c - N6258349-P-7594 & umu WU - DN668037 Dr. Frederic K

  5. Analysis of oxygen reduction and microbial community of air-diffusion biocathode in microbial fuel cells.

    PubMed

    Wang, Zejie; Zheng, Yue; Xiao, Yong; Wu, Song; Wu, Yicheng; Yang, Zhaohui; Zhao, Feng

    2013-09-01

    Microbes play irreplaceable role in oxygen reduction reaction of biocathode in microbial fuel cells (MFCs). In this study, air-diffusion biocathode MFCs were set up for accelerating oxygen reduction and microbial community analysis. Linear sweep voltammetry and Tafel curve confirmed the function of cathode biofilm to catalyze oxygen reduction. Microbial community analysis revealed higher diversity and richness of community in plankton than in biofilm. Proteobacteria was the shared predominant phylum in both biofilm and plankton (39.9% and 49.8%) followed by Planctomycetes (29.9%) and Bacteroidetes (13.3%) in biofilm, while Bacteroidetes (28.2%) in plankton. Minor fraction (534, 16.4%) of the total operational taxonomic units (3252) was overlapped demonstrating the disproportionation of bacterial distribution in biofilm and plankton. Pseudomonadales, Rhizobiales and Sphingobacteriales were exoelectrogenic orders in the present study. The research obtained deep insight of microbial community and provided more comprehensive information on uncultured rare bacteria.

  6. Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge.

    PubMed

    Dahle, Håkon; Økland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H

    2015-07-01

    Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki's Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition.

  7. Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge

    PubMed Central

    Dahle, Håkon; Økland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H

    2015-01-01

    Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki's Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition. PMID:25575309

  8. Effects of a ciliate protozoa predator on microbial communities in pitcher plant (Sarracenia purpurea) leaves.

    PubMed

    Paisie, Taylor K; Miller, Thomas E; Mason, Olivia U

    2014-01-01

    The aquatic communities found within the water filled leaves of the pitcher plant, Sarracenia purpurea, have a simple trophic structure providing an ideal system to study microscale interactions between protozoan predators and their bacterial prey. In this study, replicate communities were maintained with and without the presence of the bactivorous protozoan, Colpoda steinii, to determine the effects of grazing on microbial communities. Changes in microbial (Archaea and Bacteria) community structure were assessed using iTag sequencing of 16S rRNA genes. The microbial communities were similar with and without the protozoan predator, with>1000 species. Of these species, Archaea were negligible, with Bacteria comprising 99.99% of the microbial community. The Proteobacteria and Bacteroidetes were the most dominant phyla. The addition of a protozoan predator did not have a significant effect on microbial evenness nor richness. However, the presence of the protozoan did cause a significant shift in the relative abundances of a number of bacterial species. This suggested that bactivorous protozoan may target specific bacterial species and/or that certain bacterial species have innate mechanisms by which they evade predators. These findings help to elucidate the effect that trophic structure perturbations have on predator prey interactions in microbial systems.

  9. Human and Environmental Impacts on River Sediment Microbial Communities

    DOE PAGES

    Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; ...

    2014-05-19

    Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUsmore » do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.« less

  10. Human and Environmental Impacts on River Sediment Microbial Communities

    SciTech Connect

    Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; Blackwolf, Frederick; Roundstone, Wayne; Scott, Nicole; Hooker, Jeff; Madsen, Robert; Coleman, Maureen L.; Gilbert, Jack A.

    2014-05-19

    Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (~65,000 microbial ‘species’ identified) and most novel (93% of OTUs do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices.

  11. Human and Environmental Impacts on River Sediment Microbial Communities

    PubMed Central

    Gibbons, Sean M.; Jones, Edwin; Bearquiver, Angelita; Blackwolf, Frederick; Roundstone, Wayne; Scott, Nicole; Hooker, Jeff; Madsen, Robert; Coleman, Maureen L.; Gilbert, Jack A.

    2014-01-01

    Sediment microbial communities are responsible for a majority of the metabolic activity in river and stream ecosystems. Understanding the dynamics in community structure and function across freshwater environments will help us to predict how these ecosystems will change in response to human land-use practices. Here we present a spatiotemporal study of sediments in the Tongue River (Montana, USA), comprising six sites along 134 km of river sampled in both spring and fall for two years. Sequencing of 16S rRNA amplicons and shotgun metagenomes revealed that these sediments are the richest (∼65,000 microbial ‘species’ identified) and most novel (93% of OTUs do not match known microbial diversity) ecosystems analyzed by the Earth Microbiome Project to date, and display more functional diversity than was detected in a recent review of global soil metagenomes. Community structure and functional potential have been significantly altered by anthropogenic drivers, including increased pathogenicity and antibiotic metabolism markers near towns and metabolic signatures of coal and coalbed methane extraction byproducts. The core (OTUs shared across all samples) and the overall microbial community exhibited highly similar structure, and phylogeny was weakly coupled with functional potential. Together, these results suggest that microbial community structure is shaped by environmental drivers and niche filtering, though stochastic assembly processes likely play a role as well. These results indicate that sediment microbial communities are highly complex and sensitive to changes in land use practices. PMID:24841417

  12. Habitat constraints on the functional significance of soil microbial communities

    NASA Astrophysics Data System (ADS)

    Nunan, Naoise; Leloup, Julie; Ruamps, Léo; Pouteau, Valérie; Chenu, Claire

    2017-04-01

    An underlying assumption of most ecosystem models is that soil microbial communities are functionally equivalent; in other words, that microbial activity under given set of conditions is not dependent on the composition or diversity of the communities. Although a number of studies have suggested that this assumption is incorrect, ecosystem models can adequately describe ecosystem processes, such as soil C dynamics, without an explicit description of microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that microbial communities are not always functionally equivalent. The data suggest that when the supply of substrate is restricted, then the functioning of different microbial communities cannot be distinguished, but when the supply is less restricted, the intrinsic functional differences among communities can be expressed. When the supply of C is restricted then C dynamics are related to the properties of the physical and chemical environment of the soil. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments such as the rhizosphere or the litter layer, but are less likely to do so in oligotrophic environments such as the mineral layers of soil.

  13. Soil microbial communities following bush removal in a Namibian savanna

    NASA Astrophysics Data System (ADS)

    Buyer, Jeffrey S.; Schmidt-Küntzel, Anne; Nghikembua, Matti; Maul, Jude E.; Marker, Laurie

    2016-03-01

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

  14. Soil microbial communities following bush removal in a Namibian savanna

    NASA Astrophysics Data System (ADS)

    Buyer, J. S.; Schmidt-Küntzel, A.; Nghikembua, M.; Maul, J. E.; Marker, L.

    2015-12-01

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

  15. Exploring the Microbial Community of Shell Disease in Homarus americanus

    NASA Astrophysics Data System (ADS)

    Unzueta Martinez, A.; Feinman, S. G.; Bowen, J. L.; Tlusty, M. F.

    2016-02-01

    The American lobster, Homarus americanus is an important commercial fishery in New England, and generated nearly half a billion dollars in revenue in 2012. Outbreaks of shell disease among H. americanus populations have caused a great deal of concern regarding its cause and spread. Although shell disease is not usually lethal, afflicted lobsters have an unattractive appearance and are generally unmarketable. Shell disease is hypothesized to be caused by infectious microorganisms, but no etiological agent has been identified. This project characterizes the microbial communities associated with the formation of shell disease in lobsters and how these communities change during the progression of the disease. Microbial samples were collected on lobsters at the site of a new shell disease location, as well as at 0.5, 1, and 1.5 cm away from the site. Microbial DNA was extracted from each sample, the 16S rRNA gene amplified using PCR, and sequenced using high throughput sequencing. The results showed that microbial communities on diseased lobster shells were significantly different spatially, but not temporally. The diversity of microbes was lowest at the site of shell disease, and increased with distance from the site. This work elucidated the microbial community composition of shell disease, tracked this community throughout the progression of disease, and demonstrated a gradual rather than abrupt demarcation in microbial community between symptomatic and asymptomatic shell.

  16. Culturability as an indicator of succession in microbial communities

    NASA Technical Reports Server (NTRS)

    Garland, J. L.; Cook, K. L.; Adams, J. L.; Kerkhof, L.

    2001-01-01

    Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to

  17. Culturability as an indicator of succession in microbial communities

    NASA Technical Reports Server (NTRS)

    Garland, J. L.; Cook, K. L.; Adams, J. L.; Kerkhof, L.

    2001-01-01

    Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to

  18. Culturability as an indicator of succession in microbial communities.

    PubMed

    Garland, J L; Cook, K L; Adams, J L; Kerkhof, L

    2001-08-01

    Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to

  19. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    NASA Astrophysics Data System (ADS)

    Park, J. E.; Lee, B. T.; Son, A.

    2015-12-01

    Heavy metals leached from exhausted mines have been causing severe environmental problems in nearby soils and groundwater. Environmental mitigation was performed based on the heavy metal stabilization using Calcite and steel slag in Korea. Since the soil stabilization only temporarily immobilizes the contaminants to soil matrix, the potential risk of re-leaching heavy metal still exists. Therefore the follow-up management of stabilized soils and the corresponding evaluation methods are required to avoid the consequent contamination from the stabilized soils. In this study, microbial community analysis using pyrosequencing was performed for assessing the potential leaching of the stabilized soils. As a result of rarefaction curve and Chao1 and Shannon indices, the stabilized soil has shown lower richness and diversity as compared to non-contaminated negative control. At the phyla level, as the degree of contamination increases, most of phyla decreased with only exception of increased proteobacteria. Among proteobacteria, gamma-proteobacteria increased against the heavy metal contamination. At the species level, Methylobacter tundripaludum of gamma-proteobacteria showed the highest relative portion of microbial community, indicating that methanotrophs may play an important role in either solubilization or immobilization of heavy metals in stabilized soils.

  20. Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

    PubMed Central

    Yrjälä, Kim; Alakukku, Laura; Palojärvi, Ansa

    2012-01-01

    The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy. PMID:22983972

  1. Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica.

    PubMed

    Herbold, Craig W; Lee, Charles K; McDonald, Ian R; Cary, S Craig

    2014-05-20

    New evidence in aerobiology challenges the assumption that geographical isolation is an effective barrier to microbial transport. However, given the uncertainty with which aerobiological organisms are recruited into existing communities, the ultimate impact of microbial dispersal is difficult to assess. Here we use molecular genetic approaches to examine microbial communities inhabiting fumarolic soils on Mount Erebus, the southernmost geothermal site on Earth, to evaluate the ecological significance of global-scale microbial dispersal. There, hot, fumarolic soils provide an effective environmental filter to test the viability of organisms that have been distributed via aeolian transport over geological time. We find that cosmopolitan thermophiles dominate the surface, whereas endemic Archaea and members of poorly understood Bacterial candidate divisions dominate the immediate subsurface. These results imply that aeolian processes readily disperse viable organisms globally, where they are incorporated into pre-existing complex communities of endemic and cosmopolitan taxa.

  2. Shifts in microbial communities in bioaugmented grease interceptors removing fat, oil, and grease (FOG).

    PubMed

    He, Xia; So, Mark Jason; de Los Reyes, Francis L

    2016-08-01

    To understand the effect of daily bioaugmentation in full-scale grease interceptors (GIs), we compared the microbial communities occurring in two full-scale GIs during bioaugmented and non-bioaugmented cycles. The changes in microbial communities were determined using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene clone library construction. Differences in the microbial community structure between control and bioaugmented cycles were observed in all cases, although the dominant terminal restriction fragments in the biological product were not detected. The addition of bioaugmentation products and changes in the GI microbial ecology were related to differences in GI performance. Understanding the shifts due to bioaugmentation will result in more informed assessments of the benefits of bioadditives on FOG removal in GIs as well as the effects on downstream sewer lines.

  3. A conceptual framework for invasion in microbial communities.

    PubMed

    Kinnunen, Marta; Dechesne, Arnaud; Proctor, Caitlin; Hammes, Frederik; Johnson, David; Quintela-Baluja, Marcos; Graham, David; Daffonchio, Daniele; Fodelianakis, Stilianos; Hahn, Nicole; Boon, Nico; Smets, Barth F

    2016-12-01

    There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process.

  4. Succession in a microbial mat community - A Gaian perspective

    NASA Technical Reports Server (NTRS)

    Stolz, J. F.

    1984-01-01

    The contribution of prokaryotes to Gaian control systems is discussed. The survival of the Microcoleus-dominated stratified microbial community at Laguna Figueroa, after heavy rains flooded the evaporite flat with up to 3 m of water and deposited 5-10 cm of allocthonous sediment, demonstrates the resiliency of these communities to short-term perturbations while the microbial fossil record attests to their persistence over geologic time. It is shown that the great diversity of microbial species and their short generation time make them uniquely suited for Gaian mechanisms.

  5. Phylogenetic approaches to microbial community classification.

    PubMed

    Ning, Jie; Beiko, Robert G

    2015-10-05

    The microbiota from different body sites are dominated by different major groups of microbes, but the variations within a body site such as the mouth can be more subtle. Accurate predictive models can serve as useful tools for distinguishing sub-sites and understanding key organisms and their roles and can highlight deviations from expected distributions of microbes. Good classification depends on choosing the right combination of classifier, feature representation, and learning model. Machine-learning procedures have been used in the past for supervised classification, but increased attention to feature representation and selection may produce better models and predictions. We focused our attention on the classification of nine oral sites and dental plaque in particular, using data collected from the Human Microbiome Project. A key focus of our representations was the use of phylogenetic information, both as the basis for custom kernels and as a way to represent sets of microbes to the classifier. We also used the PICRUSt software, which draws on phylogenetic relationships to predict molecular functions and to generate additional features for the classifier. Custom kernels based on the UniFrac measure of community dissimilarity did not improve performance. However, feature representation was vital to classification accuracy, with microbial clade and function representations providing useful information to the classifier; combining the two types of features did not yield increased prediction accuracy. Many of the best-performing clades and functions had clear associations with oral microflora. The classification of oral microbiota remains a challenging problem; our best accuracy on the plaque dataset was approximately 81 %. Perfect accuracy may be unattainable due to the close proximity of the sites and intra-individual variation. However, further exploration of the space of both classifiers and feature representations is likely to increase the accuracy of

  6. Microbial communities of printing paper machines.

    PubMed

    Väisänen, O M; Weber, A; Bennasar, A; Rainey, F A; Busse, H J; Salkinoja-Salonen, M S

    1998-06-01

    The microbial content of printing paper machines, running at a temperature of 45-50 degrees C and at pH 4.5-5, was studied. Bacteria were prevalent colonizers of the machine wet end and the raw materials. A total of 390 strains of aerobic bacteria were isolated and 86% of these were identified to genus and species by biochemical, chemotaxonomic and phylogenetic methods. The most common bacteria found at the machine wet end were Bacillus coagulans and other Bacillus species, Burkholderia cepacia, Ralstonia pickettii, and in pink slimes, accumulating in the wire area and press section, species of Deinococcus, aureobacterium and Brevibacterium. Paper-making chemicals also contained species of Aureobacterium, B. cereus, B. licheniformis, B. sphaericus, Bordetella, Hydrogenophaga, Klebsiella pneumoniae, Pantoea agglomerans, Pseudomonas stutzeri, Staphylococcus and sometimes other enteric bacteria, but these did not colonize the process water. Yeasts and moulds were not present in significant numbers. A total of 131 strains were tested for their potential to degrade paper-making raw materials; 91 strains were found to have degradative activity, mainly species of Burkholderia and Ralstonia, Sphingomonas and Bacillus, and enterobacteria produced enzymes which degraded paper-making chemicals. Stainless steel adhering strains occurred in slimes and wire water and were identified as Burkholderia cepacia, B. coagulans and Deinococcus geothermalis. Coloured slimes were formed on the machine by species of Deinococcus, Acinetobacter and Methylobacterium (pink), Aureobacterium, Pantoea and Ralstonia (yellowish) and Microbulbifer-related strains (brown). The impact of the strains and species found in the printing paper machine community on the technical quality of paper, machine operation, and as a potential biohazard (Hazard Group 2 bacteria), is discussed.

  7. Effects of community versus single strain inoculants on the biocontrol of Salmonella and microbial community dynamics in alfalfa sprouts.

    PubMed

    Matos, Anabelle; Garland, Jay L

    2005-01-01

    Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that

  8. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    SciTech Connect

    Stegen, James C.; Konopka, Allan; McKinely, Jim; Murray, Christopher J.; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-07-29

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, diversity, and community composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial diversity—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.

  9. [Characteristics of soil microbial community structure in Cunninghamia lanceolata plantation].

    PubMed

    Xia, Zhi-Chao; Kong, Chui-Hua; Wang, Peng; Chen, Long-Chi; Wang, Si-Long

    2012-08-01

    By using dilution plate, fumigation extraction, and phospholipid fatty acid (PLFA) methods, this paper studied the quantities of soil microbial populations and the characteristics of soil microbial community structure in a Chinese fir (Cunninghamia lanceolata) plantation converted from an evergreen broadleaved forest. The results showed that, during the vegetation change from evergreen broadleaved forest to Chinese fir plantation, the microbial biomass carbon and the quantities of culturable bacteria and actinomyces were decreased. The total PLFAs, bacterial PLFAs, and fungi PLFAs in the woodland soil from Chinese fir plantation were decreased by 49.4%, 52.4%, 46.6%, simultaneously. And G+ and G- bacterial PLFAs in Chinese fir plantation were lower than in evergreen broadleaved forest. As compared with those in rhizosphere soil from Chinese fir plantation, the microbial biomass carbon and the quantities of culturable bacteria and actinomyces in bulk soil were decreased. The total PLFAs, bacterial PLFAs, and G+ and G- bacterial PLFAs in the rhizosphere soil were increased, while the ratio of fungal to bacterial PLFAs was lowered. The principal component analysis of the soil microbial community structure indicated that the first principal component (PC1) and the second principal component (PC2) together accounted for 78.2% of total variation of soil microbial community structure. This study showed there were some differences in the soil microbial community structure between evergreen broadleaved forest and Chinese fir plantation.

  10. Characterization of biocarbon-source recovery and microbial community shifts from waste activated sludge by conditioning with cornstover: Assessment of cellulosic compositions

    PubMed Central

    Wen, Kaili; Zhou, Aijuan; Zhang, Jiaguang; Liu, Zhihong; Wang, Guoying; Liu, Wenzong; Wang, Aijie; Yue, Xiuping

    2017-01-01

    Most studies on the production of volatile fatty acids (VFAs) from waste activated sludge (WAS) digestion have focused on operating conditions, pretreatments and characteristic adjustments. Conditioning by extra carbon sources (ECS), normally added in a solid form, has been reported to be an efficient approach. However, this has caused considerable waste of monomeric sugars in the hydrolysate. In this study, the effects of two added forms (pretreated straw (S) and hydrolyzed liquid (L)) of cornstover (CS) on WAS acidification were investigated. To obtain different cellulosic compositions of CS, low-thermal or autoclaved assisted alkaline (TA or AA) pretreatments were conducted. The results showed that AA-L test achieved the highest VFAs value (653 mg COD/g VSS), followed by AA-S (613 mg COD/g VSS). These values were 12% and 28% higher, respectively, than that obtained in the TA-L and TA-S tests. Meanwhile, higher percentages of acetic acid were observed after AA pretreatment (~62% versus ~53% in TA). The added forms of CS played an important role in structuring the innate microbial community in the WAS, as shown by high-throughput sequencing and canonical correspondence analysis. The findings obtained in this work may provide a scientific basis for the potential implementation of co-digesting WAS with ECS simultaneously obtaining energy and high value-added products. PMID:28211495

  11. Characterization of biocarbon-source recovery and microbial community shifts from waste activated sludge by conditioning with cornstover: Assessment of cellulosic compositions

    NASA Astrophysics Data System (ADS)

    Wen, Kaili; Zhou, Aijuan; Zhang, Jiaguang; Liu, Zhihong; Wang, Guoying; Liu, Wenzong; Wang, Aijie; Yue, Xiuping

    2017-02-01

    Most studies on the production of volatile fatty acids (VFAs) from waste activated sludge (WAS) digestion have focused on operating conditions, pretreatments and characteristic adjustments. Conditioning by extra carbon sources (ECS), normally added in a solid form, has been reported to be an efficient approach. However, this has caused considerable waste of monomeric sugars in the hydrolysate. In this study, the effects of two added forms (pretreated straw (S) and hydrolyzed liquid (L)) of cornstover (CS) on WAS acidification were investigated. To obtain different cellulosic compositions of CS, low-thermal or autoclaved assisted alkaline (TA or AA) pretreatments were conducted. The results showed that AA-L test achieved the highest VFAs value (653 mg COD/g VSS), followed by AA-S (613 mg COD/g VSS). These values were 12% and 28% higher, respectively, than that obtained in the TA-L and TA-S tests. Meanwhile, higher percentages of acetic acid were observed after AA pretreatment (~62% versus ~53% in TA). The added forms of CS played an important role in structuring the innate microbial community in the WAS, as shown by high-throughput sequencing and canonical correspondence analysis. The findings obtained in this work may provide a scientific basis for the potential implementation of co-digesting WAS with ECS simultaneously obtaining energy and high value-added products.

  12. Evaluation of dredged sediment co-composted with green waste as plant growing media assessed by eco-toxicological tests, plant growth and microbial community structure.

    PubMed

    Mattei, Paola; Pastorelli, Roberta; Rami, Gabriele; Mocali, Stefano; Giagnoni, Laura; Gonnelli, Cristina; Renella, Giancarlo

    2017-07-05

    Dredged sediments have currently no broad reuse options as compared to other wastes due to their peculiar physico-chemical properties, posing problems for the management of the large volumes of sediments dredged worldwide. In this study we evaluated the performance of sediment (S) co-composted with green waste (GW) as growing medium for ornamental plants. Analysis of the microbial community structure, eco-toxicological tests, were conducted on sediments at 1:1 and 3:1S:GW composting ratios. Sediment-based growing media were then reused to growth the ornamental plant Photina x fraseri in a pilot-scale experiment and plants' physiological and chemical parameters were measured. The results showed that co-composting with green waste increased the diversity of bacteria, fungi and archaea as compared to the untreated sediments, and that both the 1:1 and 3:1 S:GW composted sediments had no substantial eco-toxicological impacts, allowing an excellent plant growth. We concluded that co-composted of sediment with green waste produce a growing medium with suitable properties for growing ornamental plants, and represent a sustainable option for beneficial use of dredged sediments. Copyright © 2017. Published by Elsevier B.V.

  13. Characterization of the microbial community in a lotic environment to assess the effect of pollution on nitrifying and potentially pathogenic bacteria.

    PubMed

    Medeiros, J D; Araújo, L X; da Silva, V L; Diniz, C G; Cesar, D E; Del'Duca, A; Coelho, C M

    2014-08-01

    This study aimed to investigate microbes involved in the nitrogen cycle and potentially pathogenic bacteria from urban and rural sites of the São Pedro stream. Water samples were collected from two sites. A seasonal survey of bacterial abundance was conducted. The dissolved nutrient content was analysed. PCR and FISH analysis were performed to identify and quantify microbes involved in the nitrogen cycle and potentially pathogenic bacteria. The seasonal survey revealed that the bacterial abundance was similar along the year on the rural area but varied on the urban site. Higher concentration of dissolved nutrients in the urban area indicated a eutrophic system. Considering the nitrifying microbes, the genus Nitrobacter was found, especially in the urban area, and may act as the principal bacteria in converting nitrite into nitrate at this site. The molecular markers napA, amoA, and nfrA were more accumulated at the urban site, justifying the higher content of nutrients metabolised by these enzymes. Finally, high intensity of amplicons from Enterococcus, Streptococcus, Bacteroides/Prevotella/Porphyromonas, Salmonella, S. aureus, P. aeruginosa and the diarrheagenic lineages of E. coli were observed at the urban site. These results indicate a change in the structure of the microbial community imposed by anthrophic actions. The incidence of pathogenic bacteria in aquatic environments is of particular importance to public health, emphasising the need for sewage treatment to minimise the environmental impacts associated with urbanisation.

  14. Relating Anaerobic Digestion Microbial Community and Process Function

    PubMed Central

    Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

    2015-01-01

    Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure–function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community–activity relationships or improve engineered bioprocesses. PMID:27127410

  15. Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

    PubMed Central

    Zhou, Jizhong; Liu, Wenzong; Deng, Ye; Jiang, Yi-Huei; Xue, Kai; He, Zhili; Van Nostrand, Joy D.; Wu, Liyou; Yang, Yunfeng; Wang, Aijie

    2013-01-01

    ABSTRACT The processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2 production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management. PMID:23462114

  16. Exploration of community traits as ecological markers in microbial metagenomes.

    PubMed

    Barberán, Albert; Fernández-Guerra, Antoni; Bohannan, Brendan J M; Casamayor, Emilio O

    2012-04-01

    The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait-based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to genomic properties in 53 metagenomic aquatic samples from the Global Ocean Sampling (GOS) expedition. We found significant differences between the community profile derived from the commonly used 16S rRNA gene and from the functional trait set. The traits proved to be valuable ecological markers by discriminating between marine ecosystems (coastal vs. open ocean) and between oceans (Atlantic vs. Indian vs. Pacific). Intertrait relationships were also assessed, and we propose some that could be further used as habitat descriptors or indicators of artefacts during sample processing. Overall, the approach presented here may help to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework. © 2011 Blackwell Publishing Ltd.

  17. Optimized DNA extraction and metagenomic sequencing of airborne microbial communities.

    PubMed

    Jiang, Wenjun; Liang, Peng; Wang, Buying; Fang, Jianhuo; Lang, Jidong; Tian, Geng; Jiang, Jingkun; Zhu, Ting F

    2015-05-01

    Metagenomic sequencing has been widely used for the study of microbial communities from various environments such as soil, ocean, sediment and fresh water. Nonetheless, metagenomic sequencing of microbial communities in the air remains technically challenging, partly owing to the limited mass of collectable atmospheric particulate matter and the low biological content it contains. Here we present an optimized protocol for extracting up to tens of nanograms of airborne microbial genomic DNA from collected particulate matter. With an improved sequencing library preparation protocol, this quantity is sufficient for downstream applications, such as metagenomic sequencing for sampling various genes from the airborne microbial community. The described protocol takes ∼12 h of bench time over 2-3 d, and it can be performed with standard molecular biology equipment in the laboratory. A modified version of this protocol may also be used for genomic DNA extraction from other environmental samples of limited mass or low biological content.

  18. Microbial communities associated with wet flue gas desulfurization systems

    PubMed Central

    Brown, Bryan P.; Brown, Shannon R.; Senko, John M.

    2012-01-01

    Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

  19. Microbial communities associated with wet flue gas desulfurization systems.

    PubMed

    Brown, Bryan P; Brown, Shannon R; Senko, John M

    2012-01-01

    Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.

  20. QUANTITATIVE RISK ASSESSMENT FOR MICROBIAL AGENTS

    EPA Science Inventory

    Compared to chemical risk assessment, the process for microbial agents and infectious disease is more complex because of host factors and the variety of settings in which disease transmission can occur. While the National Academy of Science has established a paradigm for performi...

  1. QUANTITATIVE RISK ASSESSMENT FOR MICROBIAL AGENTS

    EPA Science Inventory

    Compared to chemical risk assessment, the process for microbial agents and infectious disease is more complex because of host factors and the variety of settings in which disease transmission can occur. While the National Academy of Science has established a paradigm for performi...

  2. Soil and plant effects on microbial community structure.

    PubMed

    Buyer, Jeffrey S; Roberts, Daniel P; Russek-Cohen, Estelle

    2002-11-01

    We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.

  3. Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers.

    PubMed

    Kleinsteuber, Sabine; Schleinitz, Kathleen M; Vogt, Carsten

    2012-05-01

    Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.

  4. Sulfur Cycling and Microbial Community Structure in Cave Environment: some geomicrobiological aspects

    NASA Astrophysics Data System (ADS)

    Gulecal, Y.; Temel, M.

    2013-12-01

    In the last decade, cave microbiology has emerged as a growing interdisciplinary field. Because of caves provides a unique subsurface environment for the exploration of microbial life and their roles on biogeochemical cycling under extreme condition. Sulfidic caves form in carbonate rocks where sulfide-rich waters interact with oxygen at the water table or at subterranean springs (1). Terrestrial sulfidic caves and springs are abundant and diverse, as assessed by efforts to characterize cave microbial ecosystems and to understand large scale geochemical processes (2). In this study we examined the geochemical features, microbial community and capacity of sulfur cycling in sulfidic cave ( Kaklik Cave, Turkey ) and its two hot springs. Pyrosequencing were used to understand bacterial diversity and community structure in this study area with contrasting hydrochemial and geological properties. Environmental nucleic acids were extracted, and PCR-directed screens reveal the presence or absence of functional genes, indicating genetic capacity for sulfur cycling. The microbial community displayed a high level of microbial diversity, representing 22 phylum of the Bacteria and 5 phylum of the Archaea. Our results provide a comparative view of the microbial communities and processes involved in sulfur cycling in sulfidic cave environments. 1- Macalady et al. (2007) Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy. Env.Mic. 9(6), 1402-1414 2- Rossmassler et al. Drivers of epsilonproteobacterial community composition in sulfidic caves and springs.

  5. Microbial community structure elucidates performance of Glyceria maxima plant microbial fuel cell.

    PubMed

    Timmers, Ruud A; Rothballer, Michael; Strik, David P B T B; Engel, Marion; Schulz, Stephan; Schloter, Michael; Hartmann, Anton; Hamelers, Bert; Buisman, Cees

    2012-04-01

    The plant microbial fuel cell (PMFC) is a technology in which living plant roots provide electron donor, via rhizodeposition, to a mixed microbial community to generate electricity in a microbial fuel cell. Analysis and localisation of the microbial community is necessary for gaining insight into the competition for electron donor in a PMFC. This paper characterises the anode-rhizosphere bacterial community of a Glyceria maxima (reed mannagrass) PMFC. Electrochemically active bacteria (EAB) were located on the root surfaces, but they were more abundant colonising the graphite granular electrode. Anaerobic cellulolytic bacteria dominated the area where most of the EAB were found, indicating that the current was probably generated via the hydrolysis of cellulose. Due to the presence of oxygen and nitrate, short-chain fatty acid-utilising denitrifiers were the major competitors for the electron donor. Acetate-utilising methanogens played a minor role in the competition for electron donor, probably due to the availability of graphite granules as electron acceptors.

  6. Assets-oriented community assessment.

    PubMed

    Sharpe, P A; Greaney, M L; Lee, P R; Royce, S W

    2000-01-01

    Determining how to promote community health requires that community health workers first assess where the community stands. The authors maintain that Healthy Communities initiatives are better served by assets-oriented assessment methods than by standard "problem-focused" or "needs-based" approaches. An assets orientation allows community members to identify, support, and mobilize existing community resources to create a shared vision of change, and encourages greater creativity when community members do address problems and obstacles.

  7. Assets-oriented community assessment.

    PubMed Central

    Sharpe, P A; Greaney, M L; Lee, P R; Royce, S W

    2000-01-01

    Determining how to promote community health requires that community health workers first assess where the community stands. The authors maintain that Healthy Communities initiatives are better served by assets-oriented assessment methods than by standard "problem-focused" or "needs-based" approaches. An assets orientation allows community members to identify, support, and mobilize existing community resources to create a shared vision of change, and encourages greater creativity when community members do address problems and obstacles. Images p207-a PMID:10968755

  8. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade.

    PubMed

    Hodgson, Douglas M; Smith, Ann; Dahale, Sonal; Stratford, James P; Li, Jia V; Grüning, André; Bushell, Michael E; Marchesi, Julian R; Avignone Rossa, C

    2016-01-01

    Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities.

  9. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade

    PubMed Central

    Hodgson, Douglas M.; Smith, Ann; Dahale, Sonal; Stratford, James P.; Li, Jia V.; Grüning, André; Bushell, Michael E.; Marchesi, Julian R.; Avignone Rossa, C.

    2016-01-01

    Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities. PMID:27242723

  10. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    NASA Astrophysics Data System (ADS)

    Stegen, James C.; Konopka, Allan; McKinley, James P.; Murray, Chris; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-07-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.

  11. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    PubMed Central

    Stegen, James C.; Konopka, Allan; McKinley, James P.; Murray, Chris; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-01-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions. PMID:27469056

  12. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

    2003-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

  13. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies.

    PubMed

    Stegen, James C; Konopka, Allan; McKinley, James P; Murray, Chris; Lin, Xueju; Miller, Micah D; Kennedy, David W; Miller, Erin A; Resch, Charles T; Fredrickson, Jim K

    2016-07-29

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies-oxidized, reduced, and transition-within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness-the number of microbial taxa-was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.

  14. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

    2003-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

  15. Adaptation of aquatic microbial communities to pollutant stress

    SciTech Connect

    Barkay, T.; Pritchard, H.

    1988-01-01

    Adaptation to biodegradation of p-nitrophenol and to volatilization of Hg/sup 2 +/ are examples of the role the process plays in removal of environmental pollutants and in maintaining active microbial communities in impacted ecosystems. A molecular mechanism of adaptation to Hg/sup 2 +/ is suggested by the enrichment of mercury resistance (MER) genes in some communities upon exposure to mercury.

  16. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

    SciTech Connect

    Song, Hyun-Seob; Cannon, William R.; Beliaev, Alex S.; Konopka, Allan

    2014-10-17

    Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.

  17. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    SciTech Connect

    Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.; Tanner, Ralph S.; Green Tringe, Susannah; Bristow, Jim; Suflita, Joseph M.

    2009-09-16

    Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfatereducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptideand amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely injected into reservoirs for oil recovery purposes, are biodegraded and provide biocorrosive microbial communities with an important source of nutrients.

  18. Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities.

    PubMed

    Duncan, Kathleen E; Gieg, Lisa M; Parisi, Victoria A; Tanner, Ralph S; Tringe, Susannah Green; Bristow, Jim; Suflita, Joseph M

    2009-10-15

    Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfate-reducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptide- and amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria, and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely reinjected into reservoirs for oil recovery purposes, are biodegraded and can provide biocorrosive microbial communities with an important source of nutrients.

  19. Hyporheic microbial community development is a sensitive indicator of metal contamination.

    PubMed

    Feris, Kevin P; Ramsey, Philip W; Gibbons, Sean M; Frazar, Chris; Rillig, Matthias C; Moore, Johnnie N; Gannon, James E; Holben, William E

    2009-08-15

    Accurate natural resource damage assessment necessitates monitoring organisms or communities that respond most sensitively to contaminants. Observational studies have demonstrated a correlation between fluvial heavy metal deposition and hyporheic microbial community structure. To establish a causal relationship between sediment metal content and the structure of colonizing bacterial communities, we performed a controlled field experiment River sediments of 1.75-2.36 mm in diameter with five different contaminant concentrations were collected from an environmental metal contamination gradient. Sediments were sterilized and then recolonized by incubation in the hyporheic zone of an uncontaminated river (i.e., a common garden experiment was performed). A significant correlation between hyporheic microbial community structure and heavy metal contamination (R2 = 0.81) was observed. The abundance of two phylogenetic groups was highly correlated with the level of heavy metal contamination (Group I, R2 = 0.96; Group III, R2 = 0.96, most closely affiliated with the alpha- and gamma-proteobacteria, respectively). Microbial community structural responses were detected at metal concentrations an order of magnitude lower than those previously reported to impact benthic macroinvertebrate communities. We conclude that hyporheic microbial communities could offer the most sensitive method for assessing natural resource damage in lotic ecosystems in response to fluvial heavy metal deposition.

  20. Response of a salt marsh microbial community to metal contamination

    NASA Astrophysics Data System (ADS)

    Mucha, Ana P.; Teixeira, Catarina; Reis, Izabela; Magalhães, Catarina; Bordalo, Adriano A.; Almeida, C. Marisa R.

    2013-09-01

    Salt marshes are important sinks for contaminants, namely metals that tend to accumulate around plant roots and could eventually be taken up in a process known as phytoremediation. On the other hand, microbial communities display important roles in the salt marsh ecosystems, such as recycling of nutrients and/or degradation of organic contaminants. Thus, plants can benefit from the microbial activity in the phytoremediation process. Nevertheless, above certain levels, metals are known to be toxic to microorganisms, fact that can eventually compromise their ecological functions. In this vein, the aim of present study was to investigate, in the laboratory, the effect of selected metals (Cd, Cu and Pb) on the microbial communities associated to the roots of two salt marsh plants. Sediments colonized by Juncus maritimus and Phragmites australis were collected in the River Lima estuary (NW Portugal), and spiked with each of the metals at three different Effects Range-Median (ERM) concentrations (1, 10×, 50×), being ERM the sediment quality guideline that indicates the concentration above which adverse biological effects may frequently occur. Spiked sediments were incubated with a nutritive saline solution, being left in the dark under constant agitation for 7 days. The results showed that, despite the initial sediments colonized by J. maritimus and P. australis displayed significant (p < 0.05) differences in terms of microbial community structure (evaluated by ARISA), they presented similar microbial abundances (estimated by DAPI). Also, in terms of microbial abundance, both sediments showed a similar response to metal addition, with a decrease in number of cells only observed for the higher addition of Cu. Nevertheless, both Cu and Pb, at intermediate metals levels promote a shift in the microbial community structure, with possibly effect on the ecological function of these microbial communities in salt marshes. These changes may affect plants phytoremediation

  1. Population dynamics of electrogenic microbial communities in microbial fuel cells started with three different inoculum sources.

    PubMed

    Ishii, Shun'ichi; Suzuki, Shino; Yamanaka, Yuko; Wu, Angela; Nealson, Kenneth H; Bretschger, Orianna

    2017-10-01

    Microbial fuel cells (MFCs) are one of the bioelectrochemical systems that exploit microorganisms as biocatalysts to degrade organic matters and recover energy as electric power. Here, we explored how the established electrogenic microbial communities were influenced by three different inoculum sources; anaerobic sludge of the wastewater plant, rice paddy field soil, and coastal lagoon sediment. We periodically characterized both electricity generation with sucrose consumption and 16S rRNA-basis microbial community composition. The electrochemical features of MFCs were slightly different among three inocula, and the lagoon sediment-inoculated MFC showed the highest performance in terms of the treatment time. Meanwhile, although the inoculated microbial communities were highly diverse and quite different, only twelve genera affiliated with δ-Proteobacteria, γ-Proteobacteria, Bacilli, Clostridia/Negativicutes or Bacteroidetes were abundantly enriched in all MFC anode communities. Within them, several fermentative genera were clearly different due to the inocula, while the inocula-specific phylotypes were identified in an electrogenic genus Geobacter. The relative abundances of phylotypes closely-related to Geobacter metallireducens were increased in later stages of all the sucrose-fed MFCs. These results indicate that key microbial members for the functional electrogenic community widely exist in natural ecosystems, but the community members presenting in inoculum sources affected the MFC performances. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Fecal microbial communities of healthy adult dogs fed raw meat-based diets with or without inulin or yeast cell wall extracts as assessed by 454 pyrosequencing.

    PubMed

    Beloshapka, Alison N; Dowd, Scot E; Suchodolski, Jan S; Steiner, Jörg M; Duclos, Laura; Swanson, Kelly S

    2013-06-01

    Our objective was to determine the effects of feeding raw meat-based diets with or without inulin or yeast cell wall extract (YCW) on fecal microbial communities of dogs using 454 pyrosequencing. Six healthy female adult beagles (5.5 ± 0.5 years; 8.5 ± 0.5 kg) were randomly assigned to six test diets using a Latin square design: (1) beef control; (2) beef + 1.4% inulin; (3) beef + 1.4% YCW; (4) chicken control; (5) chicken + 1.4% inulin; and (6) chicken + 1.4% YCW. Following 14 days of adaptation, fresh fecal samples were collected on day 15 or day 16 of each period. Fecal genomic DNA was extracted and used to create 16S rRNA gene amplicons, which were subjected to 454 pyrosequencing and qPCR. Predominant fecal bacterial phyla included Fusobacteria, Firmicutes, Bacteroidetes, and Proteobacteria. Beef-based diets increased (P < 0.05) Escherichia, but decreased (P < 0.05) Anaerobiospirillum vs. chicken-based diets. Inulin decreased (P < 0.05) Enterobacteriaceae. Inulin increased (P < 0.05) Megamonas vs. control. Inulin also decreased (P < 0.05) Escherichia vs. YCW. qPCR data showed that YCW increased (P < 0.05) Bifidobacterium vs. inulin and control and inulin increased (P < 0.05) Lactobacillus vs. YCW. Although a few changes in fecal microbiota were observed with inulin or YCW consumption, a strong prebiotic effect was not observed.

  3. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

    DOE PAGES

    Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; ...

    2015-06-28

    Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

  4. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

    SciTech Connect

    Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; Susilawati, Endang; Jackson, Randall D.; Balser, Teresa C.; Tiedje, James M.

    2015-06-28

    Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipid analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.

  5. Microbial communities inhabiting hypersaline microbial mats from the Abu Dhabi sabkha

    NASA Astrophysics Data System (ADS)

    Andrade, Luiza; Dutton, Kirsten; Paul, Andreas; van der Land, Cees; Sherry, Angela; Lokier, Stephen; Head, Ian

    2017-04-01

    Microbial mats are organo-sedimentary structures that are typically found in areas with extreme environmental conditions. Since these ecosystems are considered to be representative of the oldest forms of life on Earth, the study of microbial mats can inform our understanding of the development of life early in the history of our planet. In this study, we used hypersaline microbial mats from the Abu Dhabi sabkha (coastal salt flats). Cores of microbial mats (ca. 90 mm depth) were collected within an intertidal region. The cores were sliced into layers 2-3 mm thick and genomic DNA was extracted from each layer. A fragment of the 16S rRNA encoding gene was amplified in all DNA extracts, using barcoded primers, and the amplicons sequenced with the Ion Torrent platform to investigate the composition of the microbial communities down the depth of the cores. Preliminary results revealed a high proportion of Archaea (15.5-40.8% abundance) in all layers, with Halobacteria appearing to be more significant in the first 40 mm (0.4-10.3% of the total microbial community). Members of the Deltaproteobacteria were dominant in almost all layers of the microbial mat (≤ 48.6% relative abundance); however this dominance was not reflected in the first 8 mm, where the abundance was less than 2%. Chloroflexi and Anaerolinea, representing 93% of bacterial abundance, dominated the first 8 mm depth and decreased at greater depth (≤ 3% relative abundance). Cyanobacteria were found only in the top 10 mm, with unexpected low abundance (≤ 3% of the total number of reads). These results show a vertical zonation of microbial communities and processes in the microbial mats. Further analyses are underway to investigate if these patterns are repeated at other sites along a transect of the sabkha, and to relate the microbial composition to the physical-chemical conditions of the sites.

  6. Spatial heterogeneity of eukaryotic microbial communities in an unstudied geothermal diatomaceous biological soil crust: Yellowstone National Park, WY, USA.

    PubMed

    Meadow, James F; Zabinski, Catherine A

    2012-10-01

    Knowledge of microbial communities and their inherent heterogeneity has dramatically increased with the widespread use of high-throughput sequencing technologies, and we are learning more about the ecological processes that structure microbial communities across a wide range of environments, as well as the relative scales of importance for describing bacterial communities in natural systems. Little work has been carried out to assess fine-scale eukaryotic microbial heterogeneity in soils. Here, we present findings from a bar-coded 18S rRNA survey of the eukaryotic microbial communities in a previously unstudied geothermal diatomaceous biological soil crust in Yellowstone National Park, WY, USA, in which we explicitly compare microbial community heterogeneity at the particle scale within soil cores. Multivariate analysis of community composition showed that while subsamples from within the same soil core clustered together, community dissimilarity between particles in the same core was high. This study describes a novel soil microbial environment and also adds to our growing understanding of microbial heterogeneity and the scales relevant to the study of soil microbial communities.

  7. ADAPTATION OF AQUIFER MICROBIAL COMMUNITIES TO THE BIODEGRADATION OF XENOBIOTIC COMPOUNDS: INFLUENCE OF SUBSTRATE CONCENTRATION AND PREEXPOSURE

    EPA Science Inventory

    Studies were conducted to examine the adaptation response of aquifer microbial communities to xenobiotic compounds and the influence of chemical preexposure in the laboratory and in situ on adaptation. Adaptation and biodegradation were assessed as mineralization and cellular inc...

  8. ADAPTATION OF AQUIFER MICROBIAL COMMUNITIES TO THE BIODEGRADATION OF XENOBIOTIC COMPOUNDS: INFLUENCE OF SUBSTRATE CONCENTRATION AND PREEXPOSURE

    EPA Science Inventory

    Studies were conducted to examine the adaptation response of aquifer microbial communities to xenobiotic compounds and the influence of chemical preexposure in the laboratory and in situ on adaptation. Adaptation and biodegradation were assessed as mineralization and cellular inc...

  9. Microbial communities and soil fertility in flood irrigated orchards under different management systems in eastern spain

    NASA Astrophysics Data System (ADS)

    Morugán-Coronado, Alicia; García-Orenes, Fuensanta; Caravaca, Fuensanta; Roldán, Antonio

    2016-04-01

    Unsuitable land management such as the excessive use of herbicides can lead to a loss of soil fertility and a drastic reduction in the abundance of microbial populations and their functions related to nutrient cycling. Microbial communities are the most sensitive and rapid indicators of perturbations in agroecosystems. A field experiment was performed in an orange-trees orchard (Citrus sinensis) to assess the long-term effect of three different management systems on the soil microbial community biomass, structure and composition (phospholipid fatty acids (PLFAs) total, pattern, and abundance). The three agricultural systems assayed were established 30 years ago: herbicides (Glyphosate (N-(phosphonomethyl)glycine) with inorganic fertilizers (H), intensive ploughing and inorganic fertilizers (NPK 15%) (P) and organic farming (chipped pruned branches and weeds, manure from sheep and goats) (O). Nine soil samples were taken from each system. The results showed that the management practices including herbicides and intensive ploughing had similar results on soil microbial properties, while organic fertilization significantly increased microbial biomass, shifted the structure and composition of the soil microbial community, and stimulated microbial activity, when compared to inorganic fertilization systems; thus, enhancing the sustainability of this agroecosystem under semiarid conditions.

  10. Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

    PubMed Central

    2013-01-01

    The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research. PMID:23957006

  11. Microbial inoculants and their impact on soil microbial communities: a review.

    PubMed

    Trabelsi, Darine; Mhamdi, Ridha

    2013-01-01

    The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research.

  12. Ecofunctional enzymes of microbial communities in ground water.

    PubMed

    Fliermans, C B; Franck, M M; Hazen, T C; Gorden, R W

    1997-07-01

    Biolog technology was initially developed as a rapid, broad spectrum method for the biochemical identification of clinical microorganisms. Demand and creative application of this technology has resulted in the development of Biolog plates for Gram-negative and Gram-positive bacteria, for yeast and Lactobacillus sp. Microbial ecologists have extended the use of these plates from the identification of pure culture isolates to a tool for quantifying the metabolic patterns of mixed cultures, consortia and entire microbial communities. Patterns that develop on Biolog microplates are a result of the oxidation of the substrates by microorganisms in the inoculum and the subsequent reduction of the tetrazolium dye to form a color in response to detectable reactions. Depending upon the functional enzymes present in the isolate or community one of a possible 4 x 10(28) patterns can be expressed. The patterns were used to distinguish the physiological ecology of various microbial communities present in remediated groundwater. The data indicate that one can observe differences in the microbial community among treatments of bioventing, 1% and 4% methane injection, and pulse injection of air, methane and nutrients both between and among wells. The investigation indicates that Biolog technology is a useful parameter to measure the physiological response of the microbial community to perturbation and allows one to design enhancement techniques to further the degradation of selected recalcitrant and toxic chemicals. Further it allows one to evaluate the recovery of the microbial subsurface ecosystem after the perturbations have ceased. We propose the term 'ecofunctional enzymes' (EFE) as the most descriptive and useful term for the Biolog plate patterns generated by microbial communities. We offer this designation and provide ecological application in an attempt to standardize the terminology for this relatively new and unique technology.

  13. Microbial communities within saltmarsh sediments: Composition, abundance and pollution constraints

    NASA Astrophysics Data System (ADS)

    Machado, Ana; Magalhães, Catarina; Mucha, Ana P.; Almeida, C. Marisa R.; Bordalo, Adriano A.

    2012-03-01

    The influence of the saltmarsh plant Halimione portucaloides and the level of sediment metal contamination on the distribution of microbial communities were investigated in two Portuguese estuarine systems with different degrees of metal contamination: the Cavado (41.5 N; 8.7 W) and Sado estuaries. In the Sado, two saltmarshes were studied: Lisnave (38.4 N; 8.7 W) and Comporta (38.4 N; 8.8 W). A PCR rDNA-DGGE approach and direct microscopic counts of DAPI-stained cells were applied to study the biodiversity and abundance of prokaryotic communities. Sediment characteristics and metal concentrations (Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) were also evaluated to identify possible environmental pollution constraints on spatial and temporal microbial dynamics. Redundancy analysis (RDA) revealed that the Lisnave saltmarsh microbial community was usually associated with a higher degree of metal contamination, especially the metal Pb. In clear contrast, the Cavado estuary microbial assemblage composition was associated with low metal concentrations but higher organic matter content. The Comporta saltmarsh bacterial community clustered in a separate branch, and was associated with higher levels of different metals, such as Ni, Cr and Zn. Additionally, the microbial community structure of the Lisnave and Cavado showed a seasonal pattern. Moreover, microbial abundance correlated negatively with metal concentrations, being higher at the Cavado estuarine site and with general higher counts in the rhizosediment. These findings suggest that increased metal concentrations negatively affect the abundance of prokaryotic cells and that saltmarsh plants may have a pivotal role in shaping the microbial community structure.

  14. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

  15. Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities.

    PubMed

    Waldrop, Mark P; Firestone, Mary K

    2004-01-01

    Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four (13)C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the (13)C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-(13)C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by (13)C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram+ biomarkers showed more incorporation of SOM-C than did Gram- biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More (13)C (from both simple and recalcitrant sources) was incorporated into the Gram- biomarkers than Gram+ biomarkers despite the fact that the Gram+ group generally comprised a greater portion of the bacterial biomass than did markers for the Gram- group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles

  16. The Bio-Community Perl toolkit for microbial ecology

    PubMed Central

    Angly, Florent E.; Fields, Christopher J.; Tyson, Gene W.

    2014-01-01

    Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. Contact: f.angly@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics online PMID:24618462

  17. The Bio-Community Perl toolkit for microbial ecology.

    PubMed

    Angly, Florent E; Fields, Christopher J; Tyson, Gene W

    2014-07-01

    The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. © The Author 2014. Published by Oxford University Press.

  18. Community-Level Assessment of the Effects of the Broad-Spectrum Antimicrobial Chlorhexidine on the Outcome of River Microbial Biofilm Development▿

    PubMed Central

    Lawrence, J. R.; Zhu, B.; Swerhone, G. D. W.; Topp, E.; Roy, J.; Wassenaar, L. I.; Rema, T.; Korber, D. R.

    2008-01-01

    Chlorhexidine is a common-use antibacterial agent found in a range of personal-care products. We used rotating annular reactors to cultivate river biofilms under the influence of chlorhexidine or its molar equivalent in nutrients. Studies of the degradation of [14C]chlorhexidine demonstrated that no mineralization of the compound occurred. During studies with 100 μg liter−1 chlorhexidine, significant changes were observed in the protozoan and micrometazoan populations, the algal and cyanobacterial biomass, the bacterial biomass, and carbon utilization. Denaturing gradient gel electrophoresis (DGGE) in combination with statistical analyses showed that the communities developing under control and 100 μg liter−1 chlorhexidine were significantly different. At 10 μg liter−1 chlorhexidine, there was significantly increased algal and cyanobacterial biomass while the bacterial biomass was not significantly affected (P < 0.05). No significant effects on protozoan or metazoan grazing were detected at the 10-μg liter−1 chlorhexidine level. Fluorescent in situ hybridization indicated a significant reduction in the abundance of betaproteobacteria and gammaproteobacteria (P < 0.05). Archaeal cell counts were significantly reduced by both chlorhexidine and nutrient treatments. DGGE and statistical analyses indicated that 10 μg liter−1 chlorhexidine and molar equivalent nutrient treatments were significantly different from control communities. In contrast to community level observations, toxicological testing with a panel of cyanobacteria, algae, and protozoa indicated no detectable effects at 10, 50, and 100 μg liter−1 chlorhexidine. Thus, community level assessment indicated a risk of low levels of chlorhexidine in aquatic habitats while conventional approaches did not. PMID:18378652

  19. Microbial communities play important roles in modulating paddy soil fertility

    NASA Astrophysics Data System (ADS)

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-02-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production.

  20. Microbial communities play important roles in modulating paddy soil fertility

    PubMed Central

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-01-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production. PMID:26841839

  1. Microbial communities play important roles in modulating paddy soil fertility.

    PubMed

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-02-04

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production.

  2. Structures of Microbial Communities in Alpine Soils: Seasonal and Elevational Effects.

    PubMed

    Lazzaro, Anna; Hilfiker, Daniela; Zeyer, Josef

    2015-01-01

    Microbial communities in alpine environments are exposed to several environmental factors related to elevation and local site conditions and to extreme seasonal variations. However, little is known on the combined impact of such factors on microbial community structure. We assessed the effects of seasonal variations on soil fungal and bacterial communities along an elevational gradient (from alpine meadows to a glacier forefield, 1930-2519 m a.s.l.) over 14 months. Samples were taken during all four seasons, even under the winter snowpack and at snowmelt. Microbial community structures and abundances were investigated using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR (qPCR) of the 16S and 18S rRNA genes. Illumina sequencing was performed to identify key bacterial groups in selected samples. We found that the soil properties varied significantly with the seasons and along the elevational gradient. For example, concentrations of soluble nutrients (e.g., [Formula: see text], [Formula: see text], [Formula: see text]) significantly increased in October but decreased drastically under the winter snowpack. At all times, the alpine meadows showed higher soluble nutrient concentrations than the glacier forefield. Microbial community structures at the different sites were strongly affected by seasonal variations. Under winter snowpack, bacterial communities were dominated by ubiquitous groups (i.e., beta-Proteobacteria, which made up to 25.7% of the total reads in the glacier forefield). In the snow-free seasons, other groups (i.e., Cyanobacteria) became more abundant (from 1% under winter snow in the glacier forefield samples to 8.1% in summer). In summary, elevation had a significant effect on soil properties, whereas season influenced soil properties as well as microbial community structure. Vegetation had a minor impact on microbial communities. At every elevation analyzed, bacterial, and fungal community structures exhibited a

  3. Structures of Microbial Communities in Alpine Soils: Seasonal and Elevational Effects

    PubMed Central

    Lazzaro, Anna; Hilfiker, Daniela; Zeyer, Josef

    2015-01-01

    Microbial communities in alpine environments are exposed to several environmental factors related to elevation and local site conditions and to extreme seasonal variations. However, little is known on the combined impact of such factors on microbial community structure. We assessed the effects of seasonal variations on soil fungal and bacterial communities along an elevational gradient (from alpine meadows to a glacier forefield, 1930–2519 m a.s.l.) over 14 months. Samples were taken during all four seasons, even under the winter snowpack and at snowmelt. Microbial community structures and abundances were investigated using Terminal Restriction Fragment Length Polymorphism (T-RFLP) and quantitative PCR (qPCR) of the 16S and 18S rRNA genes. Illumina sequencing was performed to identify key bacterial groups in selected samples. We found that the soil properties varied significantly with the seasons and along the elevational gradient. For example, concentrations of soluble nutrients (e.g., NH4+-N, SO42−-S, PO43−-P) significantly increased in October but decreased drastically under the winter snowpack. At all times, the alpine meadows showed higher soluble nutrient concentrations than the glacier forefield. Microbial community structures at the different sites were strongly affected by seasonal variations. Under winter snowpack, bacterial communities were dominated by ubiquitous groups (i.e., beta-Proteobacteria, which made up to 25.7% of the total reads in the glacier forefield). In the snow-free seasons, other groups (i.e., Cyanobacteria) became more abundant (from 1% under winter snow in the glacier forefield samples to 8.1% in summer). In summary, elevation had a significant effect on soil properties, whereas season influenced soil properties as well as microbial community structure. Vegetation had a minor impact on microbial communities. At every elevation analyzed, bacterial, and fungal community structures exhibited a pronounced annual cycle. PMID:26635785

  4. Warm-adapted microbial communities enhance their carbon-use efficiency in warmed soils

    NASA Astrophysics Data System (ADS)

    Rousk, Johannes; Frey, Serita

    2017-04-01

    Ecosystem models predict that climate warming will stimulate microbial decomposition of soil carbon (C), resulting in a positive feedback to increasing temperatures. The current generation of models assume that the temperature sensitivities of microbial processes do not respond to warming. However, recent studies have suggested that the ability of microbial communities to adapt to warming can lead both strengthened and weakened feedbacks. A further complication is that the balance between microbial C used for growth to that used for respiration - the microbial carbon-use efficiency (CUE) - also has been shown through both modelling and empirical study to respond to warming. In our study, we set out to assess how chronic warming (+5°C over ambient during 9 years) of a temperate hardwood forest floor (Harvard Forest LTER, USA) affected temperature sensitivities of microbial processes in soil. To do this, we first determined the temperature relationships for bacterial growth, fungal growth, and respiration in plots exposed to warmed or ambient conditions. Secondly, we parametrised the established temperature functions microbial growth and respiration with plot-specific measured soil temperature data at a hourly time-resolution over the course of 3 years to estimate the real-time variation of in situ microbial C production and respiration. To estimate the microbial CUE, we also divided the microbial C production with the sum of microbial C production and respiration as a proxy for substrate use. We found that warm-adapted bacterial and fungal communities both shifted their temperature relationships to grow at higher rates in warm conditions which coincided with reduced rates at cool conditions. As such, their optimal temperature (Topt), minimum temperature (Tmin) and temperature sensitivity (Q10) were all increased. The temperature relationship for temperature, in contrast, was only marginally shifted in the same direction, but at a much smaller effect size, with

  5. Functional diversity of the microbial community in healthy subjects and periodontitis patients based on sole carbon source utilization.

    PubMed

    Zhang, Yifei; Zheng, Yunfei; Hu, Jianwei; Du, Ning; Chen, Feng

    2014-01-01

    Chronic periodontitis is one of the most common forms of biofilm-induced diseases. Most of the recent studies were focus on the dental plaque microbial diversity and microbiomes. However, analyzing bacterial diversity at the taxonomic level alone limits deeper comprehension of the ecological relevance of the community. In this study, we compared the metabolic functional diversity of the microbial community in healthy subjects and periodontitis patients in a creative way--to assess the sole carbon source utilization using Biolog assay, which was first applied on oral micro-ecology assessment. Pattern analyses of 95-sole carbon sources catabolism provide a community-level phenotypic profile of the microbial community from different habitats. We found that the microbial community in the periodontitis group had greater metabolic activity compared to the microbial community in the healthy group. Differences in the metabolism of specific carbohydrates (e.g. β-methyl-D-glucoside, stachyose, maltose, D-mannose, β-methyl-D-glucoside and pyruvic acid) were observed between the healthy and periodontitis groups. Subjects from the healthy and periodontitis groups could be well distinguished by cluster and principle component analyses according to the utilization of discriminate carbon sources. Our results indicate significant difference in microbial functional diversity between healthy subjects and periodontitis patients. We also found Biolog technology is effective to further our understanding of community structure as a composite of functional abilities, and it enables the identification of ecologically relevant functional differences among oral microbial communities.

  6. Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

    PubMed Central

    Ben Maamar, Sarah; Aquilina, Luc; Quaiser, Achim; Pauwels, Hélène; Michon-Coudouel, Sophie; Vergnaud-Ayraud, Virginie; Labasque, Thierry; Roques, Clément; Abbott, Benjamin W.; Dufresne, Alexis

    2015-01-01

    This study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities. PMID:26733990

  7. Water management history affects GHG kinetics and microbial communities composition of an Italian rice paddy

    NASA Astrophysics Data System (ADS)

    Lagomarsino, Alessandra; Agnelli, Allessandroelio; Pastorelli, Roberta; Pallara, Grazia; Rasse, Daniel; Silvennoinen, Hanna

    2015-04-01

    The water management system of cultivated soils is one of the most important factors affecting the respective magnitudes of CH4 and N2O emissions. We hypothesized an effect of past management on soil microbial communities and greenhouse gas (GHG) production potential The objective of this study were to i) assess the influence of water management history on GHG production potential and microbial community structure, ii) relate GHGs fluxes to the microbial communities involved in CH4 and N2O production inhabiting the different soils. Moreover, the influence of different soil conditioning procedures on GHG potential fluxes was determined. To reach this aim, four soils with different history of water management were compared, using dried and sieved, pre-incubated and fresh soils. Soil conditioning procedures strongly affected GHG emissions potential: drying and sieving determined the highest emission rates and the largest differences among soil types, probably through the release of labile substrates. Conversely, soil pre-incubation tended to homogenize and level out the differences among soils. Microbial communities composition drove GHG emissions potential and was affected by past management. The water management history strongly affected microbial communities structure and the specific microbial pattern of each soil was strictly linked to the gas (CH4 or N2O) emitted. Aerobic soil stimulated N2O peaks, given a possible major contribution of coupled nitrification/denitrification process. As expected, CH4 was lower in aerobic soil, which showed a less abundant archeal community. This work added evidences to support the hypothesis of an adaptation of microbial communities to past land management that reflected in the potential GHG fluxes.

  8. Microbial diversity and interactions in subgingival biofilm communities.

    PubMed

    Diaz, Patricia I

    2012-01-01

    The human subgingival environment is a complex environmental niche where microorganisms from the three domains of life meet to form diverse biofilm communities that exist in close proximity to the host. Bacteria constitute the most abundant, diverse and ultimately well-studied component of these communities with about 500 bacterial taxa reported to occur in this niche. Cultivation and molecular approaches are revealing the breadth and depth of subgingival biofilm diversity as part of an effort to understand the subgingival microbiome, the collection of microorganisms that inhabit the gingival crevices. Although these investigations are constructing a pretty detailed taxonomical census of subgingival microbial communities, including inter-subject and temporal variability in community structure, as well as differences according to periodontal health status, we are still at the front steps in terms of understanding community function. Clinical studies that evaluate community structure need to be coupled with biologically relevant models that allow evaluation of the ecological determinants of subgingival biofilm maturation. Functional characteristics of subgingival biofilm communities that still need to be clarified include main metabolic processes that support microbial communities, identification of keystone species, microbial interactions and signaling events that lead to community maturation and the relationship of different communities with the host. This manuscript presents a summary of our current understanding of subgingival microbial diversity and an overview of experimental models used to dissect the functional characteristics of subgingival communities. Future coupling of 'omics'-based approaches with such models will facilitate a better understanding of subgingival ecology opening opportunities for community manipulation. Copyright © 2012 S. Karger AG, Basel.

  9. Control of Boreal Forest Soil Microbial Communities and Processes by Plant Secondary Compounds

    NASA Astrophysics Data System (ADS)

    Leewis, M. C.; Leigh, M. B.

    2016-12-01

    Plants release an array of secondary plant metabolites (SPMEs), which vary widely between plant species/progenies and may drive shifts in soil microbial community structure and function. We hypothesize that SPMEs released through litterfall and root turnover in the boreal forest control ecosystem carbon cycling by inhibiting microbial decomposition processes, which are overcome partially by increased aromatic biodegradation of microbial communities that also fortuitously prime soils for accelerated biodegradation of contaminants. Soils and litter (stems, roots, senescing leaves) were collected from 3 different birch progenies from Iceland, Finland, and Siberia that have been reported to contain different SPME content (low, medium, high, respectively) due to differences in herbivory pressure over their natural history, as well as black spruce, all growing in a long-term common tree garden at the Kevo Subarctic Field Research Institute, Finland. We characterized the SPME content of these plant progenies and used a variety of traditional microbiological techniques (e.g., enzyme assays, litter decomposition and contaminant biodegradation rates) and molecular techniques (e.g., high-throughput amplicon sequencing for bacteria and fungi) to assess how different levels of SPMEs may correlate to shifts in microbial community structure and function. Microbial communities (bacterial and fungal) significantly varied in composition as well as leaf litter and diesel biodegradation rates, in accordance with the phytochemistry of the trees present. This study offers novel, fundamental information about phytochemical controls on ecosystem processes, resilience to contaminants, and microbial decomposition processes.

  10. Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community.

    PubMed

    Zhou, Jizhong; Liu, Wenzong; Deng, Ye; Jiang, Yi-Huei; Xue, Kai; He, Zhili; Van Nostrand, Joy D; Wu, Liyou; Yang, Yunfeng; Wang, Aijie

    2013-03-05

    ABSTRACT The processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2 production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management. IMPORTANCE Microorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of

  11. Microbial communities associated with house dust.

    PubMed

    Rintala, Helena; Pitkäranta, Miia; Täubel, Martin

    2012-01-01

    House dust is a complex mixture of inorganic and organic material with microbes in abundance. Few microbial species are actually able to grow and proliferate in dust and only if enough moisture is provided. Hence, most of the microbial content originates from sources other than the dust itself. The most important sources of microbes in house dust are outdoor air and other outdoor material tracked into the buildings, occupants of the buildings including pets and microbial growth on moist construction materials. Based on numerous cultivation studies, Penicillium, Aspergillus, Cladosporium, and about 20 other fungal genera are the most commonly isolated genera from house dust. The cultivable bacterial flora is dominated by Gram-positive genera, such as Staplylococcus, Corynebacterium, and Lactococcus. Culture-independent studies have shown that both the fungal and the bacterial flora are far more diverse, with estimates of up to 500-1000 different species being present in house dust. Concentrations of microbes in house dust vary from nondetectable to 10(9) cells g(-1) dust, depending on the dust type, detection method, type of the indoor environment and season, among other factors. Microbial assemblages in different house dust types usually share the same core species; however, alterations in the composition are caused by differing sources of microbes for different dust types. For example, mattress dust is dominated by species originating from the user of the mattress, whereas floor dust reflects rather outdoor sources. Farming homes contain higher microbial load than urban homes and according to a recent study, temperate climate zones show higher dust microbial diversity than tropical zones.

  12. Anodic and cathodic microbial communities in single chamber microbial fuel cells.

    PubMed

    Daghio, Matteo; Gandolfi, Isabella; Bestetti, Giuseppina; Franzetti, Andrea; Guerrini, Edoardo; Cristiani, Pierangela

    2015-01-25

    Microbial fuel cells (MFCs) are a rapidly growing technology for energy production from wastewater and biomasses. In a MFC, a microbial biofilm oxidizes organic matter and transfers electrons from reduced compounds to an anode as the electron acceptor by extracellular electron transfer (EET). The aim of this work was to characterize the microbial communities operating in a Single Chamber Microbial Fuel Cell (SCMFC) fed with acetate and inoculated with a biogas digestate in order to gain more insight into anodic and cathodic EET. Taxonomic characterization of the communities was carried out by Illumina sequencing of a fragment of the 16S rRNA gene. Microorganisms belonging to Geovibrio genus and purple non-sulfur (PNS) bacteria were found to be dominant in the anodic biofilm. The alkaliphilic genus Nitrincola and anaerobic microorganisms belonging to Porphyromonadaceae family were the most abundant bacteria in the cathodic biofilm.

  13. Next generation barcode tagged sequencing for monitoring microbial community dynamics.

    PubMed

    Breakwell, Katy; Tetu, Sasha G; Elbourne, Liam D H

    2014-01-01

    Microbial identification using 16S rDNA variable regions has become increasingly popular over the past decade. The application of next-generation amplicon sequencing to these regions allows microbial communities to be sequenced in far greater depth than previous techniques, as well as allowing for the identification of unculturable or rare organisms within a sample. Multiplexing can be used to sequence multiple samples in tandem through the use of sample-specific identification sequences which are attached to each amplicon, making this a cost-effective method for large-scale microbial identification experiments.

  14. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    EPA Science Inventory

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial communi...

  15. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    EPA Science Inventory

    Multi-anode microbial electrochemical cells (MXCs) are considered as one of the most promising configurations for scale-up of MXCs, but fundamental understanding of anode kinetics governing current density is limited in the MXCs. In this study we first assessed microbial communi...

  16. Using a trait-based approach to link microbial community composition and functioning to soil salinity

    NASA Astrophysics Data System (ADS)

    Rath, Kristin; Fierer, Noah; Rousk, Johannes

    2017-04-01

    Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared

  17. Measurements of Microbial Community Activities in Individual Soil Macroaggregates

    SciTech Connect

    Bailey, Vanessa L.; Bilskis, Christina L.; Fansler, Sarah J.; McCue, Lee Ann; Smith, Jeff L.; Konopka, Allan

    2012-05-01

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for {beta}-glucosidase, N-acetyl-{beta}-D-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual aggregates (250-1000 {mu}m diameter). Across all enzymes, the smallest aggregates had the greatest activity and the range of enzyme activities observed in all aggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and {beta}-glucosidase on the same aggregates suggest the presence of both extracellular {beta}-glucosidase functioning in aggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low {beta}-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.

  18. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    SciTech Connect

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  19. Microbial ecology of ocean biogeochemistry: a community perspective.

    PubMed

    Strom, Suzanne L

    2008-05-23

    The oceans harbor a tremendous diversity of marine microbes. Different functional groups of bacteria, archaea, and protists arise from this diversity to dominate various habitats and drive globally important biogeochemical cycles. Explanations for the distribution of microbial taxa and their associated activity often focus on resource availability and abiotic conditions. However, the continual reshaping of communities by mortality, allelopathy, symbiosis, and other processes shows that community interactions exert strong selective pressure on marine microbes. Deeper exploration of microbial interactions is now possible via molecular prospecting and taxon-specific experimental approaches. A holistic outlook that encompasses the full array of selective pressures on individuals will help elucidate the maintenance of microbial diversity and the regulation of biogeochemical reactions by planktonic communities.

  20. Evolutionary relationships of wild hominids recapitulated by gut microbial communities.

    PubMed

    Ochman, Howard; Worobey, Michael; Kuo, Chih-Horng; Ndjango, Jean-Bosco N; Peeters, Martine; Hahn, Beatrice H; Hugenholtz, Philip

    2010-11-16

    Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence the microbial communities within the primate gut. To determine the source of variation in the composition of the microbiota within and among species, we investigated the distal gut microbial communities harbored by great apes, as present in fecal samples recovered within their native ranges. We found that the branching order of host-species phylogenies based on the composition of these microbial communities is completely congruent with the known relationships of the hosts. Although the gut is initially and continuously seeded by bacteria that are acquired from external sources, we establish that over evolutionary timescales, the composition of the gut microbiota among great ape species is phylogenetically conserved and has diverged in a manner consistent with vertical inheritance.

  1. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

    PubMed Central

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

    2016-01-01

    Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures—imposed by sediment and porewater physicochemistry—integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning. PMID:28123379

  2. Linking Microbial Community Structure to Function in Representative Simulated Systems

    PubMed Central

    Marcus, Ian M.; Wilder, Hailey A.; Quazi, Shanin J.

    2013-01-01

    Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present. PMID:23396331

  3. The Relationship between Microbial Community Evenness and Function in Slow Sand Filters

    PubMed Central

    Quince, Christopher; Davies, Robert L.; Dorea, Caetano C.; Collins, Gavin

    2015-01-01

    ABSTRACT Two full-scale slow sand filters (SSFs) were sampled periodically from April until November 2011 to study the spatial and temporal structures of the bacterial communities found in the filters. To monitor global changes in the microbial communities, DNA from sand samples taken at different depths and locations within the SSFs and at different filters ages was used for Illumina 16S rRNA gene sequencing. Additionally, 15 water quality parameters were monitored to assess filter performance, with functionally relevant microbial members being identified by using multivariate statistics. The bacterial diversity in the SSFs was found to be much larger than previously documented, with community composition being shaped by the characteristics of the SSFs (filter age and depth) and sampling characteristics (month, side, and distance from the influent and effluent pipes). We found that several key genera (Acidovorax, Halomonas, Sphingobium, and Sphingomonas) were associated with filter performance. In addition, at the whole-community level, a strong positive correlation was found between species evenness and filter performance. This study is the first to comprehensively characterize the microbial community of SSFs and link specific microbes to water quality parameters. In doing so, we reveal key patterns in microbial community structure that relate to overall community function. PMID:26463159

  4. Non-destructive sampling of rock-dwelling microbial communities using sterile adhesive tape.

    PubMed

    Cutler, Nick A; Oliver, Anna E; Viles, Heather A; Whiteley, Andrew S

    2012-12-01

    Building stone provides a habitat for an array of microorganisms, many of which have been demonstrated to have a deleterious effect on the appearance and/or structural integrity of stone masonry. It is essential to understand the composition and structure of stone-dwelling (lithobiontic) microbial communities if successful stone conservation strategies are to be applied, particularly in the face of global environmental change. Ideally, the techniques used to sample such assemblages should be non-destructive due to the sensitive conservation status of many stone buildings. This paper quantitatively assesses the performance of sterile adhesive tape as a non-destructive sampling technique and compares the results of tape sampling with an alternative, destructive, sampling method. We used DNA fingerprinting (TRFLP) to characterise the algal, fungal and bacterial communities living on a stone slab. Our results demonstrate that tape sampling may be used to collect viable quantities of microbial DNA from environmental samples. This technique is ideally suited to the sampling of microbial biofilms, particularly when these communities are dominated by green algae. It provides a good approximation of total community diversity (i.e. the aggregate diversity of epilithic and endolithic communities). Tape sampling is straightforward, rapid and cost effective. When combined with molecular analytical techniques, this sampling method has the potential to make a major contribution to efforts to understand the structure of lithobiontic microbial communities and our ability to predict the response of such communities to future environmental change.

  5. Neotropical Andes hot springs harbor diverse and distinct planktonic microbial communities.

    PubMed

    Delgado-Serrano, Luisa; López, Gina; Bohorquez, Laura C; Bustos, José R; Rubiano, Carolina; Osorio-Forero, César; Junca, Howard; Baena, Sandra; Zambrano, María M

    2014-07-01

    Microbial explorations of hot springs have led to remarkable discoveries and improved our understanding of life under extreme conditions. The Andean Mountains harbor diverse habitats, including an extensive chain of geothermal heated water sources. In this study, we describe and compare the planktonic microbial communities present in five high-mountain hot springs with distinct geochemical characteristics, at varying altitudes and geographical locations in the Colombian Andes. The diversity and structure of the microbial communities were assessed by pyrosequencing the V5 - V6 region of the 16S rRNA gene. The planktonic communities varied in terms of diversity indexes and were dominated by the bacterial phyla Proteobacteria, Aquificae, Chloroflexi, Cyanobacteria, Firmicutes, Nitrospirae, and Thermotogae, with site-specific bacterial taxa also observed in some cases. Statistical analyses showed that these microbial communities were distinct from one another and that they clustered in a manner consistent with physicochemical parameters of the environment sampled. Multivariate analysis suggested that pH and sulfate were among the main variables influencing population structure and diversity. The results show that despite their geographical proximity and some shared geochemical characteristics, there were few shared operational taxonomic units (OTUs) and that community structure was influenced mainly by environmental factors that have resulted in different microbial populations. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  6. Microbial Communities Model Parameter Calculation for TSPA/SR

    SciTech Connect

    D. Jolley

    2001-07-16

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M&O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M&O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow {Delta}G (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M&O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed.

  7. Assessment of the living and total biomass of microbial communities in the background chestnut soil and in the paleosols under burial mounds

    NASA Astrophysics Data System (ADS)

    Khomutova, T. E.; Kashirskaya, N. N.; Demkin, V. A.

    2011-12-01

    The contents of phospholipids and carbon of the total microbial biomass were determined in the modern chestnut soil and in the paleosols buried under mounds of the Bronze and Early Iron Ages (5000-1800 years ago) in the dry steppe of the Lower Volga River basin. Judging from data on the ratio between the contents of phospholipids and organic carbon in the microbial cells, the carbon content of the living microbial biomass was calculated and compared with the total microbial biomass and total organic carbon in the studied soils. In the background chestnut soil, the content of phospholipids in the A1, B1, and B2 horizons amounted to 452, 205, and 189 nmol/g, respectively; in the paleosols, it was 28-130% of the present-day level. The maximum content was measured in the paleosols buried 5000 and 2000 years ago, in the periods with an increased humidity of the climate. In the background chestnut soil, the total microbial biomass was estimated at 5680 (the A1 horizon), 3380 (B1), and 4250 (B2) μg C/g; in the paleosols, it was by 2.5-7.0 times lower. In the upper horizons of the background soil, the portion of the living microbial biomass in the total biomass was much less than that in the paleosols under the burial mounds; it varied within 8.5-15.3% and 15-81%, respectively. The portion of living microbial biomass in the total organic carbon content of the background chestnut soil was about 4-8%. In the paleosols buried in the Early Iron Age (2000 and 1800 years ago), this value did not exceed 3-8%; in the paleosols of the Bronze Age (5000-4000 years ago), it reached 40% of the total organic carbon.

  8. Seasonal variation in an acid mine drainage microbial community.

    PubMed

    Auld, Ryan R; Mykytczuk, Nadia C S; Leduc, Leo G; Merritt, Thomas J S

    2017-02-01

    Environmental oxidation and microbial metabolism drive production of acid mine drainage (AMD). Understanding changes in the microbial community, due to geochemical and seasonal characteristics, is fundamental to AMD monitoring and remediation. Using direct sequencing of the 16S and 18S rRNA genes to identify bacterial, archaeal, and eukaryotic members of the microbial community at an AMD site in Northern Ontario, Canada, we found a dynamic community varying significantly across winter and summer sampling times. Community composition was correlated with physical and chemical properties, including water temperature, pH, conductivity, winter ice thickness, and metal concentrations. Within Bacteria, Acidithiobacillus was the dominant genus during winter (11%-57% of sequences) but Acidiphilium was dominant during summer (47%-87%). Within Eukarya, Chrysophyceae (1.5%-94%) and Microbotrymycetes (8%-92%) dominated the winter community, and LKM11 (4%-62%) and Chrysophyceae (25%-87%) the summer. There was less diversity and variability within the Archaea, with similar summer and winter communities mainly comprising Thermoplasmata (33%-64%) and Thermoprotei (5%-20%) classes but also including a large portion of unclassified reads (∼40%). Overall, the active AMD community varied significantly between winter and summer, with changing community profiles closely correlated to specific differences in AMD geochemical and physical properties, including pH, water temperature, ice thickness, and sulfate and metal concentrations.

  9. Taxonomical and functional microbial community selection in soybean rhizosphere.

    PubMed

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-08-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors.

  10. Taxonomical and functional microbial community selection in soybean rhizosphere

    PubMed Central

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-01-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

  11. The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil.

    PubMed

    Griffiths, B S; Kuan, H L; Ritz, K; Glover, L A; McCaig, A E; Fenwick, C

    2004-01-01

    Soil collected from an upland pasture was manipulated experimentally in ways shown previously to alter microbial community structure. One set of soil was subjected to chloroform fumigation for 0, 0.5, 2, or 24 h and the other was sterilised by gamma-irradiation and inoculated with a 10(-2), 10(-4), 10(-6), or 10(-8) dilution of a soil suspension prepared from unsterilized soil. Following incubation for 8 months, to allow for the stabilization of microbial biomass and activity, the resulting microbial community structure (determined by PCR-DGGE of bacterial specific amplification products of total soil DNA) was assessed. In addition, the functional stability (defined here as the resistance and resilience of short-term decomposition of plant residues to a transient heat or a persistent copper perturbation) was determined. Changes in the active bacterial population following perturbation (determined by RT-PCR-DGGE of total soil RNA) were also monitored. The manipulations resulted in distinct shifts in microbial community structure as shown by PCR-DGGE profiles, but no significant decreases in the number of bands. These shifts in microbial community structure were associated with a reduction in functional stability. The clear correlation between altered microbial community structure and functional stability observed in this upland pasture soil was not evident when the same protocols were applied to soils in other studies. RT-PCR-DGGE profiles only detected a shift in the active bacterial population following heat, but not copper, perturbation. We conclude that the functional stability of decomposition is related to specific components of the microbial community.

  12. Manipulating soil microbial communities in extensive green roof substrates.

    PubMed

    Molineux, Chloe J; Connop, Stuart P; Gange, Alan C

    2014-09-15

    There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Microbial community structure and diversity as indicators for evaluating soil quality

    USDA-ARS?s Scientific Manuscript database

    This review addresses two critical questions regarding soil quality: (1) which soil microbial properties, in particular diversity and community structure, most effectively characterize soil quality and should be used as indicators, and (2) how can soil quality assessed by such indicators be improved...

  14. Effects of management, soil attributes and region on soil microbial communities in vineyards (Napa, California, USA)

    USDA-ARS?s Scientific Manuscript database

    Soil microorganisms play an important role in soil health. However, little is known about the relationship between soil microbial community composition and diversity and commercially significant aspects of soil health. The purpose of this study is to: (1) assess the impact of management practices on...

  15. Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration

    NASA Astrophysics Data System (ADS)

    Alster, Charlotte J.; Koyama, Akihiro; Johnson, Nels G.; Wallenstein, Matthew D.; von Fischer, Joseph C.

    2016-06-01

    There is compelling evidence that microbial communities vary widely in their temperature sensitivity and may adapt to warming through time. To date, this sensitivity has been largely characterized using a range of models relying on versions of the Arrhenius equation, which predicts an exponential increase in reaction rate with temperature. However, there is growing evidence from laboratory and field studies that observe nonmonotonic responses of reaction rates to variation in temperature, indicating that Arrhenius is not an appropriate model for quantitatively characterizing temperature sensitivity. Recently, Hobbs et al. (2013) developed macromolecular rate theory (MMRT), which incorporates thermodynamic temperature optima as arising from heat capacity differences between isoenzymes. We applied MMRT to measurements of respiration from soils incubated at different temperatures. These soils were collected from three grassland sites across the U.S. Great Plains and reciprocally transplanted, allowing us to isolate the effects of microbial community type from edaphic factors. We found that microbial community type explained roughly 30% of the variation in the CO2 production rate from the labile C pool but that temperature and soil type were most important in explaining variation in labile and recalcitrant C pool size. For six out of the nine soil × inoculum combinations, MMRT was superior to Arrhenius. The MMRT analysis revealed that microbial communities have distinct heat capacity values and temperature sensitivities sometimes independent of soil type. These results challenge the current paradigm for modeling temperature sensitivity of soil C pools and understanding of microbial enzyme dynamics.

  16. Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

    USGS Publications Warehouse

    Waldrop, M.P.; Firestone, M.K.

    2006-01-01

    Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling

  17. Effects of Nutrient Enrichment on Microbial Communities and Carbon Cycling in Wetland Soils

    NASA Astrophysics Data System (ADS)

    Hartman, W.; Neubauer, S. C.; Richardson, C. J.

    2013-12-01

    Soil microbial communities are responsible for catalyzing biogeochemical transformations underlying critical wetland functions, including cycling of carbon (C) and nutrients, and emissions of greenhouse gasses (GHG). Alteration of nutrient availability in wetland soils may commonly occur as the result of anthropogenic impacts including runoff from human land uses in uplands, alteration of hydrology, and atmospheric deposition. However, the impacts of altered nutrient availability on microbial communities and carbon cycling in wetland soils are poorly understood. To assess these impacts, soil microbial communities and carbon cycling were determined in replicate experimental nutrient addition plots (control, +N, +P, +NP) across several wetland types, including pocosin peat bogs (NC), freshwater tidal marshes (GA), and tidal salt marshes (SC). Microbial communities were determined by pyrosequencing (Roche 454) extracted soil DNA, targeting both bacteria (16S rDNA) and fungi (LSU) at a depth of ca. 1000 sequences per plot. Wetland carbon cycling was evaluated using static chambers to determine soil GHG fluxes, and plant inclusion chambers were used to determine ecosystem C cycling. Soil bacterial communities responded to nutrient addition treatments in freshwater and tidal marshes, while fungal communities did not respond to treatments in any of our sites. We also compared microbial communities to continuous biogeochemical variables in soil, and found that bacterial community composition was correlated only with the content and availability of soil phosphorus, while fungi responded to phosphorus stoichiometry and soil pH. Surprisingly, we did not find a significant effect of our nutrient addition treatments on most metrics of carbon cycling. However, we did find that several metrics of soil carbon cycling appeared much more related to soil phosphorus than to nitrogen or soil carbon pools. Finally, while overall microbial community composition was weakly correlated with

  18. Ecological restoration alters microbial communities in mine tailings profiles.

    PubMed

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-29

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

  19. Cooperation in microbial communities and their biotechnological applications

    PubMed Central

    Cavaliere, Matteo; Feng, Song; Soyer, Orkun S.

    2017-01-01

    Summary Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross‐feeding, which can be understood in the general framework of ecological and evolutionary (eco‐evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of ‘cheating’ cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications. PMID:28447371

  20. Life in the "plastisphere": microbial communities on plastic marine debris.

    PubMed

    Zettler, Erik R; Mincer, Tracy J; Amaral-Zettler, Linda A

    2013-07-02

    Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean.

  1. Ecological restoration alters microbial communities in mine tailings profiles

    NASA Astrophysics Data System (ADS)

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

  2. [Soil microbial community composition and diversity in Panax quinquefolius rhizosphere].

    PubMed

    Qi, Jianjun; Zhao, Xiaomeng; Zhou, Lilii; Sun, Peng; Zhang, Xuesong; Li, Xianen

    2010-09-01

    The objective of this work was to analyze the soil microbial community diversity and structure in Panax quinquefolius rhizosphere and elucidated the rules of the ecology shift. Two community-based microbiological measurements, community level physiological profiling (CLPP) using Biolog sole C source utilization tests and phospholipid ester-linked fatty acid (PLFA) profiles, were used to evaluate soil microbial community function and composition of different Panax quinquefolius cropping soils. The properties, pH, N, P, K and organic matter were analyzed also. There were many differences in soil properties such as lower pH (5.82) in Jilin soil but higher pH (8.27) in Beijing soil and there were significant higher content of organic matter, available N, P, K in Jilin soil than those in Beijing soil. The analysis of soil microbial ecology showed a similar result in AWCD, Biolog and PLFA pattern. According to the PC1 score in principal analysis of Biolog and PLFA, the soils in 2, 3 and 4 years cultivated P. quinquefolius rhizophere were distinguished from the control and 1 year soils. The result indicated that the metabolism function reduced and the structure shifted in rhizophere soil microbial community after P. quinquefolius cropping. These may be the primary reason of the disease occur severely in P. quinquefolius field.

  3. Quantitative tracking of isotope flows in proteomes of microbial communities

    SciTech Connect

    Fisher, Curt; Hyatt, Philip Douglas; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2011-01-01

    Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic stable isotope probing (SIP) method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, {approx}50%, and {approx}98%. The method was then used to monitor incorporation of 15N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established into regrowing communities and provides insight into metabolism during biofilm formation. The SIP-proteomics method can be extended to many systems to track fluxes of 13C or 15N in microbial communities.

  4. Ecological restoration alters microbial communities in mine tailings profiles

    PubMed Central

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-01-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings. PMID:27126064

  5. Links between plant community composition, soil organic matter quality and microbial communities in contrasting tundra habitats.

    PubMed

    Eskelinen, Anu; Stark, Sari; Männistö, Minna

    2009-08-01

    Plant communities, soil organic matter and microbial communities are predicted to be interlinked and to exhibit concordant patterns along major environmental gradients. We investigated the relationships between plant functional type composition, soil organic matter quality and decomposer community composition, and how these are related to major environmental variation in non-acid and acid soils derived from calcareous versus siliceous bedrocks, respectively. We analysed vegetation, organic matter and microbial community compositions from five non-acidic and five acidic heath sites in alpine tundra in northern Europe. Sequential organic matter fractionation was used to characterize organic matter quality and phospholipid fatty acid analysis to detect major variation in decomposer communities. Non-acidic and acidic heaths differed substantially in vegetation composition, and these disparities were associated with congruent shifts in soil organic matter and microbial communities. A high proportion of forbs in the vegetation was positively associated with low C:N and high soluble N:phenolics ratios in soil organic matter, and a high proportion of bacteria in the microbial community. On the contrary, dwarf shrub-rich vegetation was associated with high C:N and low soluble N:phenolics ratios, and a high proportion of fungi in the microbial community. Our study demonstrates a strong link between the plant community composition, soil organic matter quality, and microbial community composition, and that differences in one compartment are paralleled by changes in others. Variation in the forb-shrub gradient of vegetation may largely dictate variations in the chemical quality of organic matter and decomposer communities in tundra ecosystems. Soil pH, through its direct and indirect effects on plant and microbial communities, seems to function as an ultimate environmental driver that gives rise to and amplifies the interactions between above- and belowground systems.

  6. Simulation modeling for microbial risk assessment.

    PubMed

    Cassin, M H; Paoli, G M; Lammerding, A M

    1998-11-01

    Quantitative microbial risk assessment implies an estimation of the probability and impact of adverse health outcomes due to microbial hazards. In the case of food safety, the probability of human illness is a complex function of the variability of many parameters that influence the microbial environment, from the production to the consumption of a food. The analytical integration required to estimate the probability of foodborne illness is intractable in all but the simplest of models. Monte Carlo simulation is an alternative to computing analytical solutions. In some cases, a risk assessment may be commissioned to serve a larger purpose than simply the estimation of risk. A Monte Carlo simulation can provide insights into complex processes that are invaluable, and otherwise unavailable, to those charged with the task of risk management. Using examples from a farm-to-fork model of the fate of Escherichia coli O157:H7 in ground beef hamburgers, this paper describes specifically how such goals as research prioritization, risk-based characterization of control points, and risk-based comparison of intervention strategies can be objectively achieved using Monte Carlo simulation.

  7. The social structure of microbial community involved in colonization resistance

    PubMed Central

    He, Xuesong; McLean, Jeffrey S; Guo, Lihong; Lux, Renate; Shi, Wenyuan

    2014-01-01

    It is well established that host-associated microbial communities can interfere with the colonization and establishment of microbes of foreign origins, a phenomenon often referred to as bacterial interference or colonization resistance. However, due to the complexity of the indigenous microbiota, it has been extremely difficult to elucidate the community colonization resistance mechanisms and identify the bacterial species involved. In a recent study, we have established an in vitro mice oral microbial community (O-mix) and demonstrated its colonization resistance against an Escherichia coli strain of mice gut origin. In this study, we further analyzed the community structure of the O-mix by using a dilution/regrowth approach and identified the bacterial species involved in colonization resistance against E. coli. Our results revealed that, within the O-mix there were three different types of bacterial species forming unique social structure. They act as ‘Sensor', ‘Mediator' and ‘Killer', respectively, and have coordinated roles in initiating the antagonistic action and preventing the integration of E. coli. The functional role of each identified bacterial species was further confirmed by E. coli-specific responsiveness of the synthetic communities composed of different combination of the identified players. The study reveals for the first time the sophisticated structural and functional organization of a colonization resistance pathway within a microbial community. Furthermore, our results emphasize the importance of ‘Facilitation' or positive interactions in the development of community-level functions, such as colonization resistance. PMID:24088624

  8. Stochastic and Deterministic Assembly Processes in Subsurface Microbial Communities

    SciTech Connect

    Stegen, James C.; Lin, Xueju; Konopka, Allan; Fredrickson, Jim K.

    2012-03-29

    A major goal of microbial community ecology is to understand the forces that structure community composition. Deterministic selection by specific environmental factors is sometimes important, but in other cases stochastic or ecologically neutral processes dominate. Lacking is a unified conceptual framework aiming to understand why deterministic processes dominate in some contexts but not others. Here we work towards such a framework. By testing predictions derived from general ecological theory we aim to uncover factors that govern the relative influences of deterministic and stochastic processes. We couple spatiotemporal data on subsurface microbial communities and environmental parameters with metrics and null models of within and between community phylogenetic composition. Testing for phylogenetic signal in organismal niches showed that more closely related taxa have more similar habitat associations. Community phylogenetic analyses further showed that ecologically similar taxa coexist to a greater degree than expected by chance. Environmental filtering thus deterministically governs subsurface microbial community composition. More importantly, the influence of deterministic environmental filtering relative to stochastic factors was maximized at both ends of an environmental variation gradient. A stronger role of stochastic factors was, however, supported through analyses of phylogenetic temporal turnover. While phylogenetic turnover was on average faster than expected, most pairwise comparisons were not themselves significantly non-random. The relative influence of deterministic environmental filtering over community dynamics was elevated, however, in the most temporally and spatially variable environments. Our results point to general rules governing the relative influences of stochastic and deterministic processes across micro- and macro-organisms.

  9. Horizontal gene transfer in an acid mine drainage microbial community.

    PubMed

    Guo, Jiangtao; Wang, Qi; Wang, Xiaoqi; Wang, Fumeng; Yao, Jinxian; Zhu, Huaiqiu

    2015-07-04

    Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance. Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT. Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.

  10. Long-Term Effects of Multiwalled Carbon Nanotubes and Graphene on Microbial Communities in Dry Soil.

    PubMed

    Ge, Yuan; Priester, John H; Mortimer, Monika; Chang, Chong Hyun; Ji, Zhaoxia; Schimel, Joshua P; Holden, Patricia A

    2016-04-05

    Little is known about the long-term effects of engineered carbonaceous nanomaterials (ECNMs) on soil microbial communities, especially when compared to possible effects of natural or industrial carbonaceous materials. To address these issues, we exposed dry grassland soil for 1 year to 1 mg g(-1) of either natural nanostructured material (biochar), industrial carbon black, three types of multiwalled carbon nanotubes (MWCNTs), or graphene. Soil microbial biomass was assessed by substrate induced respiration and by extractable DNA. Bacterial and fungal communities were examined by terminal restriction fragment length polymorphism (T-RFLP). Microbial activity was assessed by soil basal respiration. At day 0, there was no treatment effect on soil DNA or T-RFLP profiles, indicating negligible interference between the amended materials and the methods for DNA extraction, quantification, and community analysis. After a 1-year exposure, compared to the no amendment control, some treatments reduced soil DNA (e.g., biochar, all three MWCNT types, and graphene; P < 0.05) and altered bacterial communities (e.g., biochar, carbon black, narrow MWCNTs, and graphene); however, there were no significant differences across the amended treatments. These findings suggest that ECNMs may moderately affect dry soil microbial communities but that the effects are similar to those from natural and industrial carbonaceous materials, even after 1-year exposure.

  11. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

    PubMed Central

    Gontang, Erin A.; Aylward, Frank O.; Carlos, Camila; Glavina del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A.; Tringe, Susannah G.; Currie, Cameron R.; Kolter, Roberto

    2017-01-01

    Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach’s food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans. PMID:28545131

  12. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

    PubMed

    Gontang, Erin A; Aylward, Frank O; Carlos, Camila; Glavina Del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A; Tringe, Susannah G; Currie, Cameron R; Kolter, Roberto

    2017-01-01

    Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

  13. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre

    DOE PAGES

    Fontanez, Kristina M.; Eppley, John M.; Samo, Ty J.; ...

    2015-05-19

    Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similaritiesmore » with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transport and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. In conclusion, these data indicate the central role of eukaryotic taxa in structuring sinking particle microbial assemblages, as

  14. Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre

    SciTech Connect

    Fontanez, Kristina M.; Eppley, John M.; Samo, Ty J.; Karl, David M.; DeLong, Edward F.

    2015-05-19

    Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean's interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) to assess the nature of particle-associated microbial communities collected at a variety of depths in the North Pacific Subtropical Gyre. Comparative metagenomics was used to assess differences in microbial taxa and functional gene repertoires in PITs containing a preservative (poisoned traps) compared to preservative-free traps where growth was allowed to continue in situ (live traps). Live trap microbial communities shared taxonomic and functional similarities with bacteria previously reported to be enriched in dissolved organic matter (DOM) microcosms (e.g., Alteromonas and Methylophaga), in addition to other particle and eukaryote-associated bacteria (e.g., Flavobacteriales and Pseudoalteromonas). Poisoned trap microbial assemblages were enriched in Vibrio and Campylobacterales likely associated with eukaryotic surfaces and intestinal tracts as symbionts, pathogens, or saprophytes. The functional gene content of microbial assemblages in poisoned traps included a variety of genes involved in virulence, anaerobic metabolism, attachment to chitinaceaous surfaces, and chitin degradation. The presence of chitinaceaous surfaces was also accompanied by the co-existence of bacteria which encoded the capacity to attach to, transport and metabolize chitin and its derivatives. Distinctly different microbial assemblages predominated in live traps, which were largely represented by copiotrophs and eukaryote-associated bacterial communities. Predominant sediment trap-assocaited eukaryotic phyla included Dinoflagellata, Metazoa (mostly copepods), Protalveolata, Retaria, and Stramenopiles. In concl