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Sample records for microbial communities significantly

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

    Science.gov (United States)

    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.

  2. Significance of Microbial Communities and Interactions in Safeguarding Reactive Mine Tailings by Ecological Engineering▿†

    Science.gov (United States)

    N̆ancucheo, Ivan; Johnson, D. Barrie

    2011-01-01

    Pyritic mine tailings (mineral waste generated by metal mining) pose significant risk to the environment as point sources of acidic, metal-rich effluents (acid mine drainage [AMD]). While the accelerated oxidative dissolution of pyrite and other sulfide minerals in tailings by acidophilic chemolithotrophic prokaryotes has been widely reported, other acidophiles (heterotrophic bacteria that catalyze the dissimilatory reduction of iron and sulfur) can reverse the reactions involved in AMD genesis, and these have been implicated in the “natural attenuation” of mine waters. We have investigated whether by manipulating microbial communities in tailings (inoculating with iron- and sulfur-reducing acidophilic bacteria and phototrophic acidophilic microalgae) it is possible to mitigate the impact of the acid-generating and metal-mobilizing chemolithotrophic prokaryotes that are indigenous to tailing deposits. Sixty tailings mesocosms were set up, using five different microbial inoculation variants, and analyzed at regular intervals for changes in physicochemical and microbiological parameters for up to 1 year. Differences between treatment protocols were most apparent between tailings that had been inoculated with acidophilic algae in addition to aerobic and anaerobic heterotrophic bacteria and those that had been inoculated with only pyrite-oxidizing chemolithotrophs; these differences included higher pH values, lower redox potentials, and smaller concentrations of soluble copper and zinc. The results suggest that empirical ecological engineering of tailing lagoons to promote the growth and activities of iron- and sulfate-reducing bacteria could minimize their risk of AMD production and that the heterotrophic populations could be sustained by facilitating the growth of microalgae to provide continuous inputs of organic carbon. PMID:21965397

  3. SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree

    OpenAIRE

    Stevens, John R.; Jones, Todd R.; Lefevre, Michael; Ganesan, Balasubramanian; Weimer, Bart C.

    2017-01-01

    Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significan...

  4. Systems biology of Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

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

    2015-07-01

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

  6. Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

    Directory of Open Access Journals (Sweden)

    Ren Bai

    2017-05-01

    Full Text Available Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2 techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai, an Oxisol (Leizhou, and an Ultisol (Taoyuan along four profile depths (up to 70 cm in depth in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and

  7. Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

    Science.gov (United States)

    Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

    2017-01-01

    Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and

  8. Laboratory simulation reveals significant impacts of ocean acidification on microbial community composition and host-pathogen interactions between the blood clam and Vibrio harveyi.

    Science.gov (United States)

    Zha, Shanjie; Liu, Saixi; Su, Wenhao; Shi, Wei; Xiao, Guoqiang; Yan, Maocang; Liu, Guangxu

    2017-12-01

    It has been suggested that climate change may promote the outbreaks of diseases in the sea through altering the host susceptibility, the pathogen virulence, and the host-pathogen interaction. However, the impacts of ocean acidification (OA) on the pathogen components of bacterial community and the host-pathogen interaction of marine bivalves are still poorly understood. Therefore, 16S rRNA high-throughput sequencing and host-pathogen interaction analysis between blood clam (Tegillarca granosa) and Vibrio harveyi were conducted in the present study to gain a better understanding of the ecological impacts of ocean acidification. The results obtained revealed a significant impact of ocean acidification on the composition of microbial community at laboratory scale. Notably, the abundance of Vibrio, a major group of pathogens to many marine organisms, was significantly increased under ocean acidification condition. In addition, the survival rate and haemolytic activity of V. harveyi were significantly higher in the presence of haemolymph of OA treated T. granosa, indicating a compromised immunity of the clam and enhanced virulence of V. harveyi under future ocean acidification scenarios. Conclusively, the results obtained in this study suggest that future ocean acidification may increase the risk of Vibrio pathogen infection for marine bivalve species, such as blood clams. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. What is microbial community ecology?

    Science.gov (United States)

    Konopka, Allan

    2009-11-01

    The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

  10. In-Drift Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. In-Drift Microbial Communities

    International Nuclear Information System (INIS)

    Jolley, D.

    2000-01-01

    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

  12. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

    OpenAIRE

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.

    2010-01-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remedi...

  13. Microbial communities in blueberry soils

    Science.gov (United States)

    Microbial communities thrive in the soil of the plant root zone and it is clear that these communities play a role in plant health. Although blueberry fields can be productive for decades, yields are sometimes below expectations and fields that are replanted sometimes underperform and/or take too lo...

  14. Seasonality in ocean microbial communities.

    Science.gov (United States)

    Giovannoni, Stephen J; Vergin, Kevin L

    2012-02-10

    Ocean warming occurs every year in seasonal cycles that can help us to understand long-term responses of plankton to climate change. Rhythmic seasonal patterns of microbial community turnover are revealed when high-resolution measurements of microbial plankton diversity are applied to samples collected in lengthy time series. Seasonal cycles in microbial plankton are complex, but the expansion of fixed ocean stations monitoring long-term change and the development of automated instrumentation are providing the time-series data needed to understand how these cycles vary across broad geographical scales. By accumulating data and using predictive modeling, we gain insights into changes that will occur as the ocean surface continues to warm and as the extent and duration of ocean stratification increase. These developments will enable marine scientists to predict changes in geochemical cycles mediated by microbial communities and to gauge their broader impacts.

  15. Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach▿ †

    Science.gov (United States)

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K.; Jardine, Philip M.; Zhou, Jizhong; Criddle, Craig S.; Marsh, Terence L.; Tiedje, James M.

    2010-01-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared. PMID:20729318

  16. Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.

    Science.gov (United States)

    Cardenas, Erick; Wu, Wei-Min; Leigh, Mary Beth; Carley, Jack; Carroll, Sue; Gentry, Terry; Luo, Jian; Watson, David; Gu, Baohua; Ginder-Vogel, Matthew; Kitanidis, Peter K; Jardine, Philip M; Zhou, Jizhong; Criddle, Craig S; Marsh, Terence L; Tiedje, James M

    2010-10-01

    Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.

  17. [Characterization and microbial community shifts of rice strawdegrading microbial consortia].

    Science.gov (United States)

    Wang, Chunfang; Ma, Shichun; Huang, Yan; Liu, Laiyan; Fan, Hui; Deng, Yu

    2016-12-04

    To study the relationship between microbial community and degradation rate of rice straw, we compared and analyzed cellulose-decomposing ability, microbial community structures and shifts of microbial consortia F1 and F2. We determined exoglucanase activity by 3, 5-dinitrosalicylic acid colorimetry. We determined content of cellulose, hemicellulose and lignin in rice straw by Van Soest method, and calculated degradation rates of rice straw by the weight changes before and after a 10-day incubation. We analyzed and compared the microbial communities and functional microbiology shifts by clone libraries, Miseq analysis and real time-PCR based on the 16S rRNA gene and cel48 genes. Total degradation rate, cellulose, and hemicellulose degradation rate of microbial consortia F1 were significantly higher than that of F2. The variation trend of exoglucanase activity in both microbial consortia F1 and F2 was consistent with that of cel48 gene copies. Microbial diversity of F1 was complex with aerobic bacteria as dominant species, whereas that of F2 was simple with a high proportion of anaerobic cellulose decomposing bacteria in the later stage of incubation. In the first 4 days, unclassified Bacillales and Bacillus were dominant in both F1 and F2. The dominant species and abundance became different after 4-day incubation, Bacteroidetes and Firmicutes were dominant phyla of F1 and F2, respectively. Although Petrimonas and Pusillimonas were common dominant species in F1 and F2, abundance of Petrimonas in F2 (38.30%) was significantly higher than that in F1 (9.47%), and the abundance of Clostridiales OPB54 in F2 increased to 14.85% after 8-day incubation. The abundance of cel48 gene related with cellulose degradation rate and exoglucanase activity, and cel48 gene has the potential as a molecular marker to monitor the process of cellulose degradation. Microbial community structure has a remarkable impact on the degradation efficiency of straw cellulose, and Petrimonas

  18. Community genomics among stratified microbial assemblages in the ocean's interior

    DEFF Research Database (Denmark)

    DeLong, Edward F; Preston, Christina M; Mincer, Tracy

    2006-01-01

    Microbial life predominates in the ocean, yet little is known about its genomic variability, especially along the depth continuum. We report here genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near-sea floor depths. Sequence......, and host-viral interactions. Comparative genomic analyses of stratified microbial communities have the potential to provide significant insight into higher-order community organization and dynamics....

  19. Screening of complex thermophilic microbial community and ...

    African Journals Online (AJOL)

    Screening of complex thermophilic microbial community and application during municipal solid waste aerobic composting. ... African Journal of Biotechnology ... Complex microbial community HP83 and HC181 were applied during municipal solid waste aerobic composting that was carried out in a composting reactor under ...

  20. Invasion in microbial communities: Role of community composition and assembly processes

    DEFF Research Database (Denmark)

    Kinnunen, Marta

    of microbial community assembly. Biotic factors include interactions between different microbial groups as well as the community response to alien species – invaders. Microbial invasions can have significant effects on the composition and functioning of resident communities. There is, however, lack......Microbes contribute to all biogeochemical cycles on earth and are responsible for key biological processes that support the survival of plants and animals. There is increased interest in controlling and managing microbial communities in different ecosystems in order to make targeted microbiological...... processes more effective. In order to manage microbial communities, it is essential to understand the factors that shape and influence microbial community composition. In addition to abiotic factors, such as environmental conditions and resource availability, biotic factors also shape the dynamics...

  1. Effects of biochar blends on microbial community composition in two coastal plain soils

    Science.gov (United States)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

  2. Resistance and Resilience of Soil Microbial Communities Exposed to Petroleum-Derived Compounds

    DEFF Research Database (Denmark)

    Modrzynski, Jakub Jan

    Functioning of soil microbial communities is generally considered resilient to disturbance, including chemical stress. Activities of soil microbial communities are often sustained in polluted environments due to exceptional plasticity of microbial communities and functional redundancy. Pollution......-induced community tolerance (PICT) often develops following chemical stress. Nonetheless, environmental pollution may severely disturb functioning of soil microbial communities, thereby threatening provision of important ecosystem services provided by microorganisms. Pollution with petroleum and petroleum......-derived compounds (PDCs) is a significant environmental problem on a global scale. Research addressing interactions between microorganisms and PDC pollution is dominated by studies of biodegradation, with less emphasis on microbial ecotoxicology. Soil microbial communities are generally considered highly resilient...

  3. Standard filtration practices may significantly distort planktonic microbial diversity estimates

    Directory of Open Access Journals (Sweden)

    Cory Cruz Padilla

    2015-06-01

    Full Text Available Fractionation of biomass by filtration is a standard method for sampling planktonic microbes. It is unclear how the taxonomic composition of filtered biomass changes depending on sample volume. Using seawater from a marine oxygen minimum zone, we quantified the 16S rRNA gene composition of biomass on a prefilter (1.6 μm pore-size and a downstream 0.2 μm filter over sample volumes from 0.05 to 5 L. Significant community shifts occurred in both filter fractions, and were most dramatic in the prefilter community. Sequences matching Vibrionales decreased from ~40-60% of prefilter datasets at low volumes (0.05-0.5 L to less than 5% at higher volumes, while groups such at the Chromatiales and Thiohalorhabdales followed opposite trends, increasing from minor representation to become the dominant taxa at higher volumes. Groups often associated with marine particles, including members of the Deltaproteobacteria, Planctomycetes and Bacteroidetes, were among those showing the greatest increase with volume (4 to 27-fold. Taxon richness (97% similarity clusters also varied significantly with volume, and in opposing directions depending on filter fraction, highlighting potential biases in community complexity estimates. These data raise concerns for studies using filter fractionation for quantitative comparisons of aquatic microbial diversity, for example between free-living and particle-associated communities.

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

    Science.gov (United States)

    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.

  5. Soil microbial community successional patterns during forest ecosystem restoration.

    Science.gov (United States)

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

    2011-09-01

    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.

  6. Glycoside Hydrolases across Environmental Microbial Communities.

    Directory of Open Access Journals (Sweden)

    Renaud Berlemont

    2016-12-01

    Full Text Available 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.

  7. Exocellular electron transfer in anaerobic microbial communities

    NARCIS (Netherlands)

    Stams, A.J.M.; Bok, de F.A.M.; Plugge, C.M.; Eekert, van M.H.A.; Dolfing, J.; Schraa, G.

    2006-01-01

    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory

  8. DNA metabarcoding of microbial communities for healthcare

    Directory of Open Access Journals (Sweden)

    Zaets I. Ye.

    2016-02-01

    Full Text Available High-throughput sequencing allows obtaining DNA barcodes of multiple species of microorganisms from single environmental samples. Next Generation Sequencing (NGS-based profiling provides new opportunities to evaluate the human health effect of microbial community members affiliated to probiotics. The DNA metabarcoding may serve to a quality control of microbial communities, comprising complex probiotics and other fermented foods. A detailed inventory of complex communities is a pre-requisite of understanding their functionality as whole entities that makes it possible to design more effective bio-products by precise replacement of one community member by others. The present paper illustrates how the NGS-based DNA metabarcoding aims at the profiling of both wild and hybrid multi-microbial communities with the example of kombucha probiotic beverage fermented by yeast-bacterial partners.

  9. Dynamics of culturable soil microbial communities during ...

    African Journals Online (AJOL)

    Ecological zones impacted significantly (P < 0.05) on bacterial proliferation, but not on fungal growth. Sampling period significantly (P < 0.05) affected microbial density and the semi-arid agroecozone was more supportive of microbial proliferation than the arid zone. A total of nine predominant fungal species belonging to ...

  10. Chernozems microbial community under anthropogenic impact (Russia)

    Science.gov (United States)

    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, pecosystems 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 reached up on average 206 g C m-2, and it was 2.0 and 2.5 times higher those bare fallow and urban, respectively. The BR profile pool (0.5 m) in steppe and bare fallow was reached up 5.9 and 5

  11. Does iron inhibit cryptoendolithic microbial communities?

    Science.gov (United States)

    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.

  12. High-resolution phylogenetic microbial community profiling

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    NARCIS (Netherlands)

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    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

  14. Land use type significantly affects microbial gene transcription in soil.

    Science.gov (United States)

    Nacke, Heiko; Fischer, Christiane; Thürmer, Andrea; Meinicke, Peter; Daniel, Rolf

    2014-05-01

    Soil microorganisms play an essential role in sustaining biogeochemical processes and cycling of nutrients across different land use types. To gain insights into microbial gene transcription in forest and grassland soil, we isolated mRNA from 32 sampling sites. After sequencing of generated complementary DNA (cDNA), a total of 5,824,229 sequences could be further analyzed. We were able to assign nonribosomal cDNA sequences to all three domains of life. A dominance of bacterial sequences, which were affiliated to 25 different phyla, was found. Bacterial groups capable of aromatic compound degradation such as Phenylobacterium and Burkholderia were detected in significantly higher relative abundance in forest soil than in grassland soil. Accordingly, KEGG pathway categories related to degradation of aromatic ring-containing molecules (e.g., benzoate degradation) were identified in high abundance within forest soil-derived metatranscriptomic datasets. The impact of land use type forest on community composition and activity is evidently to a high degree caused by the presence of wood breakdown products. Correspondingly, bacterial groups known to be involved in lignin degradation and containing ligninolytic genes such as Burkholderia, Bradyrhizobium, and Azospirillum exhibited increased transcriptional activity in forest soil. Higher solar radiation in grassland presumably induced increased transcription of photosynthesis-related genes within this land use type. This is in accordance with high abundance of photosynthetic organisms and plant-infecting viruses in grassland.

  15. Metagenomic analysis of microbial communities and beyond

    DEFF Research Database (Denmark)

    Schreiber, Lars

    2014-01-01

    From small clone libraries to large next-generation sequencing datasets – the field of community genomics or metagenomics has developed tremendously within the last years. This chapter will summarize some of these developments and will also highlight pitfalls of current metagenomic analyses...... heterologous expression of metagenomic DNA fragments to discover novel metabolic functions. Lastly, the chapter will shortly discuss the meta-analysis of gene expression of microbial communities, more precisely metatranscriptomics and metaproteomics....

  16. Soil microbial community of abandoned sand fields

    Czech Academy of Sciences Publication Activity Database

    Elhottová, Dana; Szili-Kovács, T.; Tříska, Jan

    2002-01-01

    Roč. 47, č. 4 (2002), s. 435-440 ISSN 0015-5632 R&D Projects: GA ČR GA526/99/P033 Grant - others:OTKA(HU) T25739 Institutional research plan: CEZ:AV0Z6066911 Keywords : microbial community * abandoned fields Subject RIV: EH - Ecology, Behaviour Impact factor: 0.979, year: 2002

  17. Effects of heavy metals on soil microbial community

    Science.gov (United States)

    Chu, Dian

    2018-02-01

    Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

  18. Engineering chemical interactions in microbial communities.

    Science.gov (United States)

    Kenny, Douglas J; Balskus, Emily P

    2018-03-05

    Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.

  19. Termites and flooding affect microbial communities in decomposing wood

    Science.gov (United States)

    Michael D. Ulyshen; Susan V. Diehl; Dragica Jeremic

    2016-01-01

    Wood properties and microbial community characteristics were compared between loblolly pine (Pinus taeda L.) logs protected or unprotected from termites (Blattodea: Rhinotermitidae: Reticulitermes spp.) and other arthropods for two years in seasonally flooded and unflooded forests in the southeastern United States. Significant compositional differences were observed...

  20. Ecological restoration alters microbial communities in mine tailings profiles.

    Science.gov (United States)

    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.

  1. Ecological restoration alters microbial communities in mine tailings profiles

    Science.gov (United States)

    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. Comparative Metagenomics of Freshwater Microbial Communities

    International Nuclear Information System (INIS)

    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

    2010-01-01

    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 community structure elucidates performance of Glyceria maxima plant microbial fuel cell

    OpenAIRE

    Timmers, R.A.; Rothballer, M.; Strik, D.P.B.T.B.; Engel, M.; Schulz, M.; Hartmann, A.; Hamelers, H.V.M.; Buisman, C.J.N.

    2012-01-01

    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) w...

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

    OpenAIRE

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

    2012-01-01

    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) w...

  5. Mapping the ecological networks of microbial communities.

    Science.gov (United States)

    Xiao, Yandong; Angulo, Marco Tulio; Friedman, Jonathan; Waldor, Matthew K; Weiss, Scott T; Liu, Yang-Yu

    2017-12-11

    Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka-Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world microbial communities, such as the human gut microbiota.

  6. Multiscale Modeling of Microbial Communities

    Science.gov (United States)

    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

  7. Microbial Community Structure of an Alluvial Aquifer Treated to Encourage Microbial Induced Calcite Precipitation

    Science.gov (United States)

    Ohan, J.; Saneiyan, S.; Lee, J.; Ntarlagiannis, D.; Burns, S.; Colwell, F. S.

    2017-12-01

    An oligotrophic aquifer in the Colorado River floodplain (Rifle, CO) was treated with molasses and urea to encourage microbial induced calcite precipitation (MICP). This would stabilize the soil mass by reducing porosity and strengthening the mineral fabric. Over the course of a 15-day treatment period, microbial biomass was collected from monitoring well groundwater for DNA extraction and sequencing. Bromide, a conservative tracer, was co-injected and subsequently detected in downgradient wells, confirming effective nutrient delivery. Conductivity increased during the injection regime and an overall decrease in pH was observed. Groundwater chemistry showed a marked increase in ammonia, suggesting urea hydrolysis - a process catalyzed by the enzyme urease - the primary enzyme implicated in MICP. Additionally, soluble iron was detected, suggesting a general increase in microbial activity; possibly as iron-reducing bacteria changed insoluble ferric oxide to soluble ferrous hydroxide in the anoxic aquifer. DNA sequencing of the 16S rRNA gene confirmed the presence of iron reducing bacteria, including Shewanella and Desulfuromonadales. Generally, a decrease in microbial community diversity was observed when pre-injection community taxa were compared with post-injection community taxa. Phyla indicative of anoxic aquifers were represented in accordance with previous literature at the Rifle site. Linear discriminant analysis showed significant differences in representative phyla over the course of the injection series. Geophysical monitoring of the site further suggested changes that could be due to MICP. Induced polarization increased the phase shift in the primary treated area, in agreement with laboratory experiments. Cross-hole seismic testing confirmed that the shear wave velocities increased in the treated soil mass, implying the soil matrix became more stable. Future investigations will help elucidate the viability and efficacy of MICP treatment in changing

  8. Horizontal gene transfer in an acid mine drainage microbial community.

    Science.gov (United States)

    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.

  9. The potential significance of microbial activity in radioactive waste disposal

    International Nuclear Information System (INIS)

    McCabe, A.M.

    1987-12-01

    The aim of this report is to assess the potential significance of microbial activity in radioactive waste disposal. It outlines the major factors which need to be considered in order to evaluate the importance of microbiological action. These include water and nutritional sources (particularly carbon) hostile conditions (particularly the effects of radiation and pH), the establishment of pH micro-environments and the degradative effect of microbial metabolic by-products on the disposed waste forms. Before an active microbial population can develop there are certain basic requirements for life. These are outlined and the possibility of colonisation occurring within the chemical, radiological and nutritional constraints of a repository are considered. Once colonisation is assumed, the effect of microbial activity is discussed under five headings, i.e. (i) direct attack, (ii) physical disruption (which includes consideration of fissuring processes and void formation), (iii) gas generation (which may be of particular importance), (iv) radionuclide uptake and finally (v) alteration of groundwater chemistry. Particular attention is paid to the possibility of environments becoming established both within the waste form itself (allowing microbes to attack from the inside of the repository outward) or attack on the encapsulant materials (microbes attacking from the outside inward). (author)

  10. Microbial community composition affects soil fungistasis.

    Science.gov (United States)

    de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

    2003-02-01

    Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

  11. Exocellular electron transfer in anaerobic microbial communities.

    Science.gov (United States)

    Stams, Alfons J M; de Bok, Frank A M; Plugge, Caroline M; van Eekert, Miriam H A; Dolfing, Jan; Schraa, Gosse

    2006-03-01

    Exocellular electron transfer plays an important role in anaerobic microbial communities that degrade organic matter. Interspecies hydrogen transfer between microorganisms is the driving force for complete biodegradation in methanogenic environments. Many organic compounds are degraded by obligatory syntrophic consortia of proton-reducing acetogenic bacteria and hydrogen-consuming methanogenic archaea. Anaerobic microorganisms that use insoluble electron acceptors for growth, such as iron- and manganese-oxide as well as inert graphite electrodes in microbial fuel cells, also transfer electrons exocellularly. Soluble compounds, like humic substances, quinones, phenazines and riboflavin, can function as exocellular electron mediators enhancing this type of anaerobic respiration. However, direct electron transfer by cell-cell contact is important as well. This review addresses the mechanisms of exocellular electron transfer in anaerobic microbial communities. There are fundamental differences but also similarities between electron transfer to another microorganism or to an insoluble electron acceptor. The physical separation of the electron donor and electron acceptor metabolism allows energy conservation in compounds as methane and hydrogen or as electricity. Furthermore, this separation is essential in the donation or acceptance of electrons in some environmental technological processes, e.g. soil remediation, wastewater purification and corrosion.

  12. The electric picnic: synergistic requirements for exoelectrogenic microbial communities

    KAUST Repository

    Kiely, Patrick D; Regan, John M; Logan, Bruce E

    2011-01-01

    (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation

  13. Emergent biosynthetic capacity in simple microbial communities.

    Directory of Open Access Journals (Sweden)

    Hsuan-Chao Chiu

    2014-07-01

    Full Text Available 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

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

    Science.gov (United States)

    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...

  15. Exogenous Nitrogen Addition Reduced the Temperature Sensitivity of Microbial Respiration without Altering the Microbial Community Composition

    Directory of Open Access Journals (Sweden)

    Hui Wei

    2017-12-01

    Full Text Available Atmospheric nitrogen (N deposition is changing in both load quantity and chemical composition. The load effects have been studied extensively, whereas the composition effects remain poorly understood. We conducted a microcosm experiment to study how N chemistry affected the soil microbial community composition characterized by phospholipid fatty acids (PLFAs and activity indicated by microbial CO2 release. Surface and subsurface soils collected from an old-growth subtropical forest were supplemented with three N-containing materials (ammonium, nitrate, and urea at the current regional deposition load (50 kg ha-1 yr-1 and incubated at three temperatures (10, 20, and 30°C to detect the interactive effects of N deposition and temperature. The results showed that the additions of N, regardless of form, did not alter the microbial PLFAs at any of the three temperatures. However, the addition of urea significantly stimulated soil CO2 release in the early incubation stage. Compared with the control, N addition consistently reduced the temperature dependency of microbial respiration, implying that N deposition could potentially weaken the positive feedback of the warming-stimulated soil CO2 release to the atmosphere. The consistent N effects for the surface and subsurface soils suggest that the effects of N on soil microbial communities may be independent of soil chemical contents and stoichiometry.

  16. Microbial Resources and Enological Significance: Opportunities and Benefits

    Directory of Open Access Journals (Sweden)

    Leonardo Petruzzi

    2017-06-01

    Full Text Available Among the innovative trends in the wine sector, the continuous exploration of enological properties associated with wine microbial resources represents a cornerstone driver of quality improvement. Since the advent of starter cultures technology, the attention has been focused on intraspecific biodiversity within the primary species responsible for alcoholic fermentation (Saccharomyces cerevisiae and, subsequently, for the so-called ‘malolactic fermentation’ (Oenococcus oeni. However, in the last decade, a relevant number of studies proposed the enological exploitation of an increasing number of species (e.g., non-Saccharomyces yeasts associated with spontaneous fermentation in wine. These new species/strains may provide technological solutions to specific problems and/or improve sensory characteristics, such as complexity, mouth-feel and flavors. This review offers an overview of the available information on the enological/protechnological significance of microbial resources associated with winemaking, summarizing the opportunities and the benefits associated with the enological exploitation of this microbial potential. We discuss proposed solutions to improve quality and safety of wines (e.g., alternative starter cultures, multistrains starter cultures and future perspectives.

  17. Microbial Resources and Enological Significance: Opportunities and Benefits

    Science.gov (United States)

    Petruzzi, Leonardo; Capozzi, Vittorio; Berbegal, Carmen; Corbo, Maria R.; Bevilacqua, Antonio; Spano, Giuseppe; Sinigaglia, Milena

    2017-01-01

    Among the innovative trends in the wine sector, the continuous exploration of enological properties associated with wine microbial resources represents a cornerstone driver of quality improvement. Since the advent of starter cultures technology, the attention has been focused on intraspecific biodiversity within the primary species responsible for alcoholic fermentation (Saccharomyces cerevisiae) and, subsequently, for the so-called ‘malolactic fermentation’ (Oenococcus oeni). However, in the last decade, a relevant number of studies proposed the enological exploitation of an increasing number of species (e.g., non-Saccharomyces yeasts) associated with spontaneous fermentation in wine. These new species/strains may provide technological solutions to specific problems and/or improve sensory characteristics, such as complexity, mouth-feel and flavors. This review offers an overview of the available information on the enological/protechnological significance of microbial resources associated with winemaking, summarizing the opportunities and the benefits associated with the enological exploitation of this microbial potential. We discuss proposed solutions to improve quality and safety of wines (e.g., alternative starter cultures, multistrains starter cultures) and future perspectives. PMID:28642742

  18. Metabarcoding of the kombucha microbial community grown in different microenvironments.

    Science.gov (United States)

    Reva, Oleg N; Zaets, Iryna E; Ovcharenko, Leonid P; Kukharenko, Olga E; Shpylova, Switlana P; Podolich, Olga V; de Vera, Jean-Pierre; Kozyrovska, Natalia O

    2015-12-01

    Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions. Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture (KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the KMC under different conditions revealed the core part of the community which included acetobacteria of two genera Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas spp., which previously had not been described in KMC, were found to be minor but permanent members of the community. The community composition was dependent on the growth conditions. The bacterial component of KMC was relatively stable, but may include additional member-lactobacilli. The yeast species composition was significantly variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink. As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community composition should be provided by using DNA metabarcoding.

  19. Permissiveness of soil microbial communities towards broad host range plasmids

    DEFF Research Database (Denmark)

    Klümper, Uli

    . Plasmids are implicated in the rapid spread of antibiotic resistance and the emergence of multi-resistant pathogenic bacteria, making it crucial to be able to quantify, understand, and, ideally, control plasmid transfer in mixed microbial communities. The fate of plasmids in microbial communities...... of microbial communities may be directly interconnected through transfer of BHR plasmids at a so far unrecognized level. The developed method furthermore enabled me to explore how agronomic practices may affect gene transfer in soil microbial communities. I compared bacterial communities extracted from plots...

  20. Perturbation metatranscriptomics for studying complex microbial communities

    DEFF Research Database (Denmark)

    Williams, Rohan B.H.; Kirkegaard, Rasmus Hansen; Arumugam, Krithika

    Studying the functional state of natural or engineered microbial communities presents substantial challenges due to both the complexities of field sampling, and, in the laboratory context, the inability of culture or reactor systems to maintain community composition ex situ over long periods. Here...... correlation between orthologous genes (Pearson r=0.4). We also used these data to annotate uncharacterized genes in the Ca. nitrospira defluvii genome: finding clear evidence for several previously unrecognized denitrification related genes, using a combination of expression profiles and protein domain data...... are associated with the transition from anoxic to aerobic conditions, and are observable at a whole community level and 3) these data provide a means of identifying unannotated genes in reference genomes that are likely to be associated with specific functional processes. More broadly, our approach permits...

  1. Environmental Drivers of Differences in Microbial Community Structure in Crude Oil Reservoirs across a Methanogenic Gradient

    OpenAIRE

    Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

    2016-01-01

    Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, a...

  2. Response of soil microbial communities and microbial interactions to long-term heavy metal contamination.

    Science.gov (United States)

    Li, Xiaoqi; Meng, Delong; Li, Juan; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan; Cheng, Cheng; Xiao, Yunhua; Liu, Zhenghua; Yan, Mingli

    2017-12-01

    Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    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.

  4. The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

    Science.gov (United States)

    Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

    2011-12-01

    communities, while the quality of available organic matter may have played a significant role in supporting high performing microbial communities.

  5. Evolving Microbial Communities in Cellulose-Fed Microbial Fuel Cell

    Directory of Open Access Journals (Sweden)

    Renata Toczyłowska-Mamińska

    2018-01-01

    Full Text Available The abundance of cellulosic wastes make them attractive source of energy for producing electricity in microbial fuel cells (MFCs. However, electricity production from cellulose requires obligate anaerobes that can degrade cellulose and transfer electrons to the electrode (exoelectrogens, and thus most previous MFC studies have been conducted using two-chamber systems to avoid oxygen contamination of the anode. Single-chamber, air-cathode MFCs typically produce higher power densities than aqueous catholyte MFCs and avoid energy input for the cathodic reaction. To better understand the bacterial communities that evolve in single-chamber air-cathode MFCs fed cellulose, we examined the changes in the bacterial consortium in an MFC fed cellulose over time. The most predominant bacteria shown to be capable electron generation was Firmicutes, with the fermenters decomposing cellulose Bacteroidetes. The main genera developed after extended operation of the cellulose-fed MFC were cellulolytic strains, fermenters and electrogens that included: Parabacteroides, Proteiniphilum, Catonella and Clostridium. These results demonstrate that different communities evolve in air-cathode MFCs fed cellulose than the previous two-chamber reactors.

  6. Cultivation Of Deep Subsurface Microbial Communities

    Science.gov (United States)

    Obrzut, Natalia; Casar, Caitlin; Osburn, Magdalena R.

    2018-01-01

    The potential habitability of surface environments on other planets in our solar system is limited by exposure to extreme radiation and desiccation. In contrast, subsurface environments may offer protection from these stressors and are potential reservoirs for liquid water and energy that support microbial life (Michalski et al., 2013) and are thus of interest to the astrobiology community. The samples used in this project were extracted from the Deep Mine Microbial Observatory (DeMMO) in the former Homestake Mine at depths of 800 to 2000 feet underground (Osburn et al., 2014). Phylogenetic data from these sites indicates the lack of cultured representatives within the community. We used geochemical data to guide media design to cultivate and isolate organisms from the DeMMO communities. Media used for cultivation varied from heterotrophic with oxygen, nitrate or sulfate to autotrophic media with ammonia or ferrous iron. Environmental fluid was used as inoculum in batch cultivation and strains were isolated via serial transfers or dilution to extinction. These methods resulted in isolating aerobic heterotrophs, nitrate reducers, sulfate reducers, ammonia oxidizers, and ferric iron reducers. DNA sequencing of these strains is underway to confirm which species they belong to. This project is part of the NASA Astrobiology Institute Life Underground initiative to detect and characterize subsurface microbial life; by characterizing the intraterrestrials, the life living deep within Earth’s crust, we aim to understand the controls on how and where life survives in subsurface settings. Cultivation of terrestrial deep subsurface microbes will provide insight into the survival mechanisms of intraterrestrials guiding the search for these life forms on other planets.

  7. Environmental controls on microbial communities in continental serpentinite fluids

    Directory of Open Access Journals (Sweden)

    Melitza eCrespo-Medina

    2014-11-01

    Full Text Available Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate and formate, with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the three month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

  8. Spatial Distribution of Viruses Associated with Planktonic and Attached Microbial Communities in Hydrothermal Environments

    Science.gov (United States)

    Nunoura, Takuro; Kazama, Hiromi; Noguchi, Takuroh; Inoue, Kazuhiro; Akashi, Hironori; Yamanaka, Toshiro; Toki, Tomohiro; Yamamoto, Masahiro; Furushima, Yasuo; Ueno, Yuichiro; Yamamoto, Hiroyuki; Takai, Ken

    2012-01-01

    Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments. PMID:22210205

  9. Soil microbial community response to land use and various soil ...

    African Journals Online (AJOL)

    Soil microbial community response to land use and various soil elements in a city landscape of north China. ... African Journal of Biotechnology ... Legumes played an important role in stimulating the growth and reproduction of various soil microbial populations, accordingly promoting the microbial catabolic activity.

  10. Copper removal and microbial community analysis in single-chamber microbial fuel cell.

    Science.gov (United States)

    Wu, Yining; Zhao, Xin; Jin, Min; Li, Yan; Li, Shuai; Kong, Fanying; Nan, Jun; Wang, Aijie

    2018-04-01

    In this study, copper removal and electricity generation were investigated in a single-chamber microbial fuel cell (MFC). Result showed that copper was efficiently removed in the membrane-less MFC with removal efficiency of 98.3% at the tolerable Cu 2+ concentration of 12.5 mg L -1 , the corresponding open circuit voltage and maximum power density were 0.78 V and 10.2 W m -3 , respectively. The mechanism analysis demonstrated that microbial electrochemical reduction contributed to the copper removal with the products of Cu and Cu 2 O deposited at biocathode. Moreover, the microbial community analysis indicated that microbial communities changed with different copper concentrations. The dominant phyla were Proteobacteria and Bacteroidetes which could play key roles in electricity generation, while Actinobacteria and Acidobacteria were also observed which were responsible for Cu-resistant and copper removal. It will be of important guiding significance for the recovery of copper from low concentration wastewater through single-chamber MFC with simultaneous energy recovery. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Microbial communities in the deep subsurface

    Science.gov (United States)

    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

  12. Significance and Biological Importance of Pyrimidine in the Microbial World

    Directory of Open Access Journals (Sweden)

    Vinita Sharma

    2014-01-01

    Full Text Available Microbes are unique creatures that adapt to varying lifestyles and environment resistance in extreme or adverse conditions. The genetic architecture of microbe may bear a significant signature not only in the sequences position, but also in the lifestyle to which it is adapted. It becomes a challenge for the society to find new chemical entities which can treat microbial infections. The present review aims to focus on account of important chemical moiety, that is, pyrimidine and its various derivatives as antimicrobial agents. In the current studies we represent more than 200 pyrimidines as antimicrobial agents with different mono-, di-, tri-, and tetrasubstituted classes along with in vitro antimicrobial activities of pyrimidines derivatives which can facilitate the development of more potent and effective antimicrobial agents.

  13. Impact of (+/-)-catechin on soil microbial communities.

    Science.gov (United States)

    Inderjit; Kaur, Rajwant; Kaur, Surinder; Callaway, Ragan M

    2009-01-01

    Catechin is a highly studied but controversial allelochemical reported as a component of the root exudates of Centaurea maculosa. Initial reports of high and consistent exudation rates and soil concentrations have been shown to be highly inaccurate, but the chemical has been found in root exudates at and much less frequently in soil but sporadically at high concentrations. Part of the problem of detection and measuring phytotoxicity in natural soils may be due to the confounding effect of soil microbes, and little is known about interactions between catechin and soil microbes. Here we tested the effect of catechin on soil microbial communities and the feedback of these effects to two plant species. We found that catechin inhibits microbial activity in the soil we tested, and by doing so appears to promote plant growth in the microbe-free environment. This is in striking contrast to other in vitro studies, emphasizing the highly conditional effects of the chemical and suggesting that the phytotoxic effects of catechin may be exerted through the microbes in some soils.

  14. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

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

    Science.gov (United States)

    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

  16. Evidence for the functional significance of diazotroph community structure in soil.

    Science.gov (United States)

    Hsu, Shi-Fang; Buckley, Daniel H

    2009-01-01

    Microbial ecologists continue to seek a greater understanding of the factors that govern the ecological significance of microbial community structure. Changes in community structure have been shown to have functional significance for processes that are mediated by a narrow spectrum of organisms, such as nitrification and denitrification, but in some cases, functional redundancy in the community seems to buffer microbial ecosystem processes. The functional significance of microbial community structure is frequently obscured by environmental variation and is hard to detect in short-term experiments. We examine the functional significance of free-living diazotrophs in a replicated long-term tillage experiment in which extraneous variation is minimized and N-fixation rates can be related to soil characteristics and diazotroph community structure. Soil characteristics were found to be primarily impacted by tillage management, whereas N-fixation rates and diazotroph community structure were impacted by both biomass management practices and interactions between tillage and biomass management. The data suggest that the variation in diazotroph community structure has a greater impact on N-fixation rates than do soil characteristics at the site. N-fixation rates displayed a saturating response to increases in diazotroph community diversity. These results show that the changes in the community structure of free-living diazotrophs in soils can have ecological significance and suggest that this response is related to a change in community diversity.

  17. Microbial community composition of transiently wetted Antarctic Dry Valley soils.

    Science.gov (United States)

    Niederberger, Thomas D; Sohm, Jill A; Gunderson, Troy E; Parker, Alexander E; Tirindelli, Joëlle; Capone, Douglas G; Carpenter, Edward J; Cary, Stephen C

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm(3) for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.

  18. Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity

    Directory of Open Access Journals (Sweden)

    Binu M Tripathi

    2016-04-01

    Full Text Available There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

  19. Microbial community functional change during vertebrate carrion decomposition.

    Directory of Open Access Journals (Sweden)

    Jennifer L Pechal

    Full Text Available 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.

  20. Boom clay pore water, home of a diverse microbial community

    International Nuclear Information System (INIS)

    Wouters, Katinka; Moors, Hugo; Leys, Natalie

    2012-01-01

    structure and phylogeny of the bacterial population, without however any visual conformation or indication of in situ activity. In a second approach therefore, microbial presence, activity and metabolic capacity in BCPW samples was assessed by respectively scanning electron microscopy (SEM), analysis of intracellular adenosine triphosphate (ATP) and cultivation in relevant, anaerobic media by most probable number technique (MPN). Microbial presence was confirmed to be abundant, up to an average of 108 cultivable cells per mL and 10 7 metabolically active cells per mL. To evaluate specific properties of these cultivated subpopulations, individual microbial strains were isolated and identified in a third approach. Fifteen different bacterial genera were identified, belonging to the Proteobacteria (5), Actinobacteria (5), Firmicutes (2) and Bacteroidetes (3). The isolates are very similar to commonly found environmental strains with relevant capacities for survival in the stringent conditions of Boom clay, like sulphide dependence, sporulation, (facultative) anaerobic metabolism or oligo-trophy. Comparison with the OTU-based analysis reveals that the isolates covered the population surprisingly well in terms of bacterial phyla. Most importantly, their significance in the community could be estimated in terms of relative abundance and omnipresence. Combining these results, a representative BCPW microbial community composition was characterized. In fulfilment of the first aim, a combination of three BCPW piezometer filters (Morpheus F6-F9-F23) was selected to serve as representative microbial community sample for future lab scale experiments. As for the second aim, the omnipresence of such a diverse and in situ active microbial community is surprising. Microbial contamination during piezometer installation and survival of introduced species during several years in stringent conditions are therefore considered quite credible. On the other hand, the indicated diversity of

  1. Boom clay pore water, home of a diverse microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Wouters, Katinka; Moors, Hugo; Leys, Natalie [SCK.CEN, Environment, Health and Safety Institute, B-2400 Mol (Belgium)

    2012-10-15

    structure and phylogeny of the bacterial population, without however any visual conformation or indication of in situ activity. In a second approach therefore, microbial presence, activity and metabolic capacity in BCPW samples was assessed by respectively scanning electron microscopy (SEM), analysis of intracellular adenosine triphosphate (ATP) and cultivation in relevant, anaerobic media by most probable number technique (MPN). Microbial presence was confirmed to be abundant, up to an average of 108 cultivable cells per mL and 10{sup 7} metabolically active cells per mL. To evaluate specific properties of these cultivated subpopulations, individual microbial strains were isolated and identified in a third approach. Fifteen different bacterial genera were identified, belonging to the Proteobacteria (5), Actinobacteria (5), Firmicutes (2) and Bacteroidetes (3). The isolates are very similar to commonly found environmental strains with relevant capacities for survival in the stringent conditions of Boom clay, like sulphide dependence, sporulation, (facultative) anaerobic metabolism or oligo-trophy. Comparison with the OTU-based analysis reveals that the isolates covered the population surprisingly well in terms of bacterial phyla. Most importantly, their significance in the community could be estimated in terms of relative abundance and omnipresence. Combining these results, a representative BCPW microbial community composition was characterized. In fulfilment of the first aim, a combination of three BCPW piezometer filters (Morpheus F6-F9-F23) was selected to serve as representative microbial community sample for future lab scale experiments. As for the second aim, the omnipresence of such a diverse and in situ active microbial community is surprising. Microbial contamination during piezometer installation and survival of introduced species during several years in stringent conditions are therefore considered quite credible. On the other hand, the indicated diversity of

  2. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    International Nuclear Information System (INIS)

    Widenfalk, Anneli; Bertilsson, Stefan; Sundh, Ingvar; Goedkoop, Willem

    2008-01-01

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points

  3. Effects of pesticides on community composition and activity of sediment microbes - responses at various levels of microbial community organization

    Energy Technology Data Exchange (ETDEWEB)

    Widenfalk, Anneli [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)], E-mail: anneli.widenfalk@kemi.se; Bertilsson, Stefan [Limnology/Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvaegen 20, SE-752 36 Uppsala (Sweden); Sundh, Ingvar [Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, SE-750 07 Uppsala (Sweden); Goedkoop, Willem [Department of Environmental Assessment, Swedish University of Agricultural Sciences, P.O. Box 7050, SE-750 07 Uppsala (Sweden)

    2008-04-15

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology. - Molecular techniques revealed pesticide-induced changes at lower levels of microbial community organization that were not detected by community-level end points.

  4. The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

    Science.gov (United States)

    Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

    2016-01-01

    Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

  5. Research Progress on the Relationship Between Oral Microbial Community and Tumor

    Directory of Open Access Journals (Sweden)

    Ma Shujun

    2016-03-01

    Full Text Available Significant progress was observed in studies of the relationship between oral Helicobacter pylori and gastric cancer and tumors. Based on three distinct and close relationships, namely, the relationship between oral H. pylori and gastric cancer, between oral microbial communities and oral squamous cell carcinoma, and between oral microbial communities of human immunodeficiency virus-infected patients and tumors, this work reviews the relationship between oral microbial communities and tumors. This research also provides reference for further analysis of the relationship between oral microorganisms and tumors to realize early diagnosis of tumor patients through detecting oral microorganisms under adjuvant therapy.

  6. Mapping and determinism of soil microbial community distribution across an agricultural landscape.

    Science.gov (United States)

    Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

    2015-06-01

    Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  7. Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

    Directory of Open Access Journals (Sweden)

    Zhuofei Xu

    Full Text Available As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.

  8. In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities

    Energy Technology Data Exchange (ETDEWEB)

    Bohn, Paul W. [Univ. of Notre Dame, IN (United States); Shrout, J. D. [Univ. of Notre Dame, IN (United States); Sweedler, J. V. [Univ. of Illinois, Urbana-Champaign, IL (United States); Farrand, S. [Univ. of Illinois, Urbana-Champaign, IL (United States)

    2016-01-25

    This document constitutes the final technical report for DE-SC0006642, In Situ Correlated Molecular Imaging of Chemically Communicating Microbial Communities, a project carried out collaboratively by investigators at Notre Dame and UIUC. The work carried out under DOE support in this project produced advances in two areas: development of new highly sophisticated correlated imaging approaches and the application of these new tools to the growth and differentiation of microbial communities under a variety of environmental conditions. A significant effort involved the creation of technical enhancements and sampling approaches to allow us to advance heterocorrelated mass spectrometry imaging (MSI) and correlated Raman microscopy (CRM) from bacterial cultures and biofilms. We then exploited these measurement advances in heterocorrelated MS/CRM imaging to determine relationship of signaling molecules and excreted signaling molecules produced by P. aeruginosa to conditions relevant to the rhizosphere. In particular, we: (1) developed a laboratory testbed mimic for the rhizosphere to enable microbial growth on slides under controlled conditions; (2) integrated specific measurements of (a) rhamnolipids, (b) quinolone/quinolones, and (c) phenazines specific to P. aeruginosa; and (3) utilized the imaging tools to probe how messenger secretion, quorum sensing and swarming behavior are correlated with behavior.

  9. Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

    Science.gov (United States)

    Guo, Xue; Zhou, Xishu; Hale, Lauren; Yuan, Mengting; Feng, Jiajie; Ning, Daliang; Shi, Zhou; Qin, Yujia; Liu, Feifei; Wu, Liyou; He, Zhili; Van Nostrand, Joy D.; Liu, Xueduan; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong

    2018-01-01

    Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices. PMID:29904372

  10. Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

    Directory of Open Access Journals (Sweden)

    Jenna L Shelton

    2016-09-01

    Full Text Available Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow up-dip wells was different than the 17 deeper, down-dip wells, and that

  11. Microbial Communities of the Okinawa Backarc Basin Subvent Biosphere

    Science.gov (United States)

    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

  12. Effects of application of corn straw on soil microbial community structure during the maize growing season.

    Science.gov (United States)

    Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

    2015-01-01

    This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Oral microbial community assembly under the influence of periodontitis.

    Science.gov (United States)

    Chen, Hongju; Peng, Shuting; Dai, Lin; Zou, Quan; Yi, Bin; Yang, Xianghong; Ma, Zhanshan Sam

    2017-01-01

    Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23%) passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports). This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly), it does not seem to cause the 'mutation' of the 'genotype" (mechanism) of community assembly. We argue that the 'phenotypic

  14. Oral microbial community assembly under the influence of periodontitis.

    Directory of Open Access Journals (Sweden)

    Hongju Chen

    Full Text Available Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis. Here we reanalyze the dataset from Abusleme et al.'s comparative study of the oral microbial communities from periodontitis patients and healthy individuals. Our study demonstrates that 14 out of 61 communities (23% passed the neutrality test, a percentage significantly higher than the previous reported neutrality rate of 1% in human microbiome (Li & Ma 2016, Scientific Reports. This suggests that, while the niche selection may play a predominant role in the assembly and diversity maintenance in oral microbiome, the effect of neutral dynamics may not be ignored. However, no statistically significant differences in the neutrality passing rates were detected between the periodontitis and healthy treatments with Fisher's exact probability test and multiple testing corrections, suggesting that the mechanism of community assembly is robust against disturbances such as periodontitis. In addition, our study confirmed previous finding that periodontitis patients exhibited higher biodiversity. These findings suggest that while periodontitis may significantly change the community composition measured by diversity (i.e., the exhibition or 'phenotype' of community assembly, it does not seem to cause the 'mutation' of the 'genotype" (mechanism of community assembly. We argue that the

  15. Metagenomics meets time series analysis: unraveling microbial community dynamics

    NARCIS (Netherlands)

    Faust, K.; Lahti, L.M.; Gonze, D.; Vos, de W.M.; Raes, J.

    2015-01-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic

  16. Microbial community dynamics in diesel waste biodegradation using ...

    African Journals Online (AJOL)

    Microbial community dynamics in diesel waste biodegradation using sequencing batch bioreactor operation mode (SBR) ... African Journal of Biotechnology ... Oxygen uptake rate (OUR) indicated increases in microbial activity from cycle one to cycle two (124.9 to 252.9 mgO2/L/h) and decreases in cycles three and four ...

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

    Science.gov (United States)

    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

  18. Halotolerant PGPRs Prevent Major Shifts in Indigenous Microbial Community Structure Under Salinity Stress.

    Science.gov (United States)

    Bharti, Nidhi; Barnawal, Deepti; Maji, Deepamala; Kalra, Alok

    2015-07-01

    The resilience of soil microbial populations and processes to environmental perturbation is of increasing interest as alteration in rhizosphere microbial community dynamics impacts the combined functions of plant-microbe interactions. The present study was conducted to investigate the effect of inoculation with halotolerant rhizobacteria Bacillus pumilus (STR2), Halomonas desiderata (STR8), and Exiguobacterium oxidotolerans (STR36) on the indigenous root-associated microbial (bacterial and fungal) communities in maize under non-saline and salinity stress. Plants inoculated with halotolerant rhizobacteria recorded improved growth as illustrated by significantly higher shoot and root dry weight and elongation in comparison to un-inoculated control plants under both non-saline and saline conditions. Additive main effect and multiplicative interaction ordination analysis revealed that plant growth promoting rhizobacteria (PGPR) inoculations as well as salinity are major drivers of microbial community shift in maize rhizosphere. Salinity negatively impacts microbial community as analysed through diversity indices; among the PGPR-inoculated plants, STR2-inoculated plants recorded higher values of diversity indices. As observed in the terminal-restriction fragment length polymorphism analysis, the inoculation of halotolerant rhizobacteria prevents major shift of the microbial community structure, thus enhancing the resilience capacity of the microbial communities.

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

    Science.gov (United States)

    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

  20. Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

    Science.gov (United States)

    Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

    2017-12-01

    Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

  1. Shift in soil microbial communities with shrub encroachment in Inner Mongolia grasslands, China

    Science.gov (United States)

    Shen, H.; Li, H.; Zhang, J.; Hu, H.; Chen, L.; Zhu, Y.; Fang, J.

    2017-12-01

    The ongoing expansion of shrub encroachment into grasslands represents a unique form of land cover change. How this process affects soil microbial communities is poorly understood. In this study, we aim to assess the effects of shrub encroachment on soil microbial biomass, abundance and composition by comparing data between shrub patches and neighboring herb patches in shrub-encroached grasslands (SEGs) in Inner Mongolia, China. Fourteen SEG sites from two ecosystem types (typical and desert grasslands) were investigated. The phospholipid fatty acid (PLFA) method was used to analyze the composition and biomass of the soil microbial community. Our results showed that the top-soil microbial biomass and abundances of gram-negative bacteria, arbuscular mycorrhizal fungi, and actinomycetes were significantly higher in shrub patches than in herb patches in both typical and desert grasslands (P fungi to bacteria ratio was significantly higher in shrub patches than in herb patches in desert grassland (P soil microbial communities, which makes the microbial communities toward a fresh organic carbon-based structure. This study highlights the importance of edaphic and climate factors in microbial community shifts in SEGs.

  2. Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

    Science.gov (United States)

    Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

    2016-04-26

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

  3. Soil Microbial Community Contribution to Small Headwater Stream Metabolism.

    Science.gov (United States)

    Clapcott, J. E.; Gooderham, J. P.; Barmuta, L. A.; Davies, P. E.

    2005-05-01

    The temporal dynamics of sediment respiration were examined in seven small headwater streams in forested catchments in 2004. A strong seasonal response was observed with higher respiration rates in depositional zones than in gravel runs. The data were also examined in the context of proportional habitat distributions that highlighted the importance of high flow events in shaping whole stream metabolic budgets. This study specifically examines the question of terrestrial soil respiration contribution to whole stream metabolism by the controlled inundation of terrestrial soils. The experiment included six experimentally inundated terrestrial zones, six terrestrial controls, and six in-stream depositional zones. Sediment bacterial respiration was measured using 14C leucine incorporation and cotton strip bioassays were also employed to provide an indicative measure of sediment microbial activity. Despite high variability and exhibiting significantly lower bacterial activity than in-stream sediments, modelling using flow data and habitat mapping illustrated the important contribution of terrestrial soil respiration to the whole stream metabolic budgets of small headwater streams. In addition, microbial community composition examined using phospholipid fatty acid analysis clearly differentiated between terrestrial and aquatic communities. Freshly inundated terrestrial communities remained similar to un-inundated controls after 28 days.

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

    Science.gov (United States)

    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.

  5. Soil microbial community response to aboveground vegetation and ...

    African Journals Online (AJOL)

    lenovo

    2011-11-21

    Nov 21, 2011 ... magnitude, activity, structure and function of soil microbial community may .... CaO were quantified by inductively coupled plasmaatomic emission spectroscopy ...... Validation of signature polarlipid fatty acid biomarkers for ...

  6. Elimination of pyraclostrobin by simultaneous microbial degradation coupled with the Fenton process in microbial fuel cells and the microbial community.

    Science.gov (United States)

    Zhao, Huanhuan; Kong, Chui-Hua

    2018-06-01

    The elimination of pyraclostrobin by simultaneous microbial degradation and Fenton oxidation was achieved in a microbial fuel cell (MFC) system. After 12 h of incubation, the removal rate of pyraclostrobin was 1.4 mg/L/h at the anode and 1.7 mg/L/h at the cathode. The pyraclostrobin concentration was less than the detection limit (0.1 mg/L) after 72 h at the anode and 24 h at the cathode. The air flow rate, temperature, and pH of the catholyte had significant effects on the generation of H 2 O 2 . The maximum production of H 2 O 2 was 1.2 mg/L after reaction for 20 h during the Fenton process. Microbial community analysis indicated that functional bacteria in the genera Chryseobacterium, Stenotrophomonas, Arcobacter, and Comamonas were predominant in the anodic biofilm. In conclusion, the MFC-Fenton system provides an effective approach for treating environmental contaminants. Copyright © 2018 Elsevier Ltd. All rights reserved.

  7. A conceptual framework for invasion in microbial communities

    DEFF Research Database (Denmark)

    Kinnunen, Marta; Dechesne, Arnaud; Proctor, Caitlin

    2016-01-01

    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...

  8. Relating Anaerobic Digestion Microbial Community and Process Function.

    Science.gov (United States)

    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.

  9. Long-term oil contamination causes similar changes in microbial communities of two distinct soils.

    Science.gov (United States)

    Liao, Jingqiu; Wang, Jie; Jiang, Dalin; Wang, Michael Cai; Huang, Yi

    2015-12-01

    Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of

  10. Variations in soil microbial community structure induced by the conversion from paddy fields to upland fields

    Science.gov (United States)

    Dai, X.

    2015-12-01

    Land-use conversion is an important factor influencing the carbon and nitrogen gas exchange between land and atmosphere, and soil microorganisms is main driver of soil carbon and nitrogen gas production. Understanding the effect of land-use conversion on soil microbial communities and its influencing factor is important for greenhouse gas emission reduction and soil organic carbon and nitrogen sequestration and stability. The influence of land use conversion on soil process was undergoing a dynamic change, but little research has been done to understand the effect on soil microbial communities during the initial years after land conversion. In the study, the influences of land-use conversion from double rice cropping (RR) to maize-maize (MM) and soybean-peanut (SP) double cropping systems on soil physical and chemical properties, and microbial community structure was studied after two years of the conversion in southern China. The results showed that land use conversion significantly changed soil properties, microbial communities and biomass. Soil pH significantly decreased by 0.50 and 0.52 after conversion to MM and SP, respectively. Soil TN and NH4-N also significantly decreased by 9%-15% and 60% after conversion to upland fields, respectively. The total PLFAs, bacterial, gram-positive bacterial (G+), gram-negative bacterial (G-) and actinomycetic PLFAs decreased significantly. The ng g-1 soil concentration of monounsaturated chain PLFAs 16:1ω7c and 18:1ω9t were significantly higher at paddy fields than at upland fields. No significant differences in soil properties, microbial communities and biomass were found between conversed MM and SP. Our results indicated that land use conversion, not crop type conversed had a significant effects on soil properties and microbial communities at the initial of land conversion. And soil pH was the key factor regulating the variations in soil microbial community structure after land use conversion from paddy to upland fields.

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

    Directory of Open Access Journals (Sweden)

    Taylor K Paisie

    Full Text Available 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.

  12. The electric picnic: synergistic requirements for exoelectrogenic microbial communities

    KAUST Repository

    Kiely, Patrick D

    2011-06-01

    Characterization of the various microbial populations present in exoelectrogenic biofilms provides insight into the processes required to convert complex organic matter in wastewater streams into electrical current in bioelectrochemical systems (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation end products by exoelectrogens (typically Geobacter species) relieves feedback inhibition for the fermentative consortia, allowing for rapid metabolism of organics. Identification of specific syntrophic processes and the communities characteristic of these anodic biofilms will be a valuable aid in improving the performance of BESs. © 2011 Elsevier Ltd.

  13. Influence of soil zinc concentrations on zinc sensitivity and functional diversity of microbial communities

    International Nuclear Information System (INIS)

    Lock, K.; Janssen, C.R.

    2005-01-01

    Pollution induced community tolerance (PICT) is based on the phenomenon that toxic effects reduce survival of the most sensitive organisms, thus increasing community tolerance. Community tolerance for a contaminant is thus a strong indicator for the presence of that contaminant at the level of adverse concentrations. Here we assessed PICT in 11 soils contaminated with zinc runoff from galvanised electricity pylons and 11 reference soils sampled at 10 m distance from these pylons. Using PICT, the influence of background concentration and bioavailability of zinc on zinc sensitivity and functional diversity of microbial communities was assessed. Zinc sensitivity of microbial communities decreased significantly with increasing zinc concentrations in pore water and calcium chloride extracted fraction while no significant relationship was found with total zinc concentration in the soil. It was also found that functional diversity of microbial communities decreased with increasing zinc concentrations, indicating that increased tolerance is indeed an undesirable phenomenon when environmental quality is considered. The hypothesis that zinc sensitivity of microbial communities is related to background zinc concentration in pore water could not be confirmed. - Zinc sensitivity of microbial communities and functional diversity decrease with increasing zinc concentration in the pore water

  14. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with

  15. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Science.gov (United States)

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

  16. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    Directory of Open Access Journals (Sweden)

    Thomas H A Haverkamp

    Full Text Available Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm sediment communities are affected by local conditions within the sediment.

  17. A conceptual framework for invasion in microbial communities

    KAUST Repository

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

    2016-01-01

    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.

  18. A conceptual framework for invasion in microbial communities

    Science.gov (United States)

    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

    2016-01-01

    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. PMID:27137125

  19. A conceptual framework for invasion in microbial communities

    KAUST Repository

    Kinnunen, Marta

    2016-05-03

    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.

  20. Convergent development of anodic bacterial communities in microbial fuel cells.

    KAUST Repository

    Yates, Matthew D

    2012-05-10

    Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m(-2)). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    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.

  3. Microbial community analysis of ambient temperature anaerobic digesters

    Energy Technology Data Exchange (ETDEWEB)

    Ciotola, R. [Ohio State Univ., Columbus, OH (United States). Dept. of Food, Agriculture and Biological Engineering

    2010-07-01

    This paper reported on a study in which designs for Chinese and Indian fixed-dome anaerobic digesters were modified in an effort to produce smaller and more affordable digesters. While these types of systems are common in tropical regions of developing countries, they have not been used in colder climates because of the low biogas yield during the winter months. Although there is evidence that sufficient biogas production can be maintained in colder temperatures through design and operational changes, there is a lack of knowledge about the seasonal changes in the composition of the microbial communities in ambient temperature digesters. More knowledge is needed to design and operate systems for maximum biogas yield in temperate climates. The purpose of this study was to cultivate a microbial community that maximizes biogas production at psychrophilic temperatures. The study was conducted on a 300 gallon experimental anaerobic digester on the campus of Ohio State University. Culture-independent methods were used on weekly samples collected from the digester in order to examine microbial community response to changes in ambient temperature. Microbial community profiles were established using universal bacterial and archaeal primers that targeted the 16S rRNA gene. In addition to the methanogenic archaea, this analysis also targeted some of the other numerically and functionally important microbial taxa in anaerobic digesters, such as hydrolytic, fermentative, acetogenic and sulfate reducing bacteria. According to preliminary results, the composition of the microbial community shifts with changes in seasonal temperature.

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

    Science.gov (United States)

    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.

  5. Soil Microbial Community Structure Evolution along Halophyte Succession in Bohai Bay Wetland

    Directory of Open Access Journals (Sweden)

    Mingyang Cong

    2014-01-01

    Full Text Available It is urgent to recover Bohai Bay costal wetland ecosystem because of covering a large area of severe saline-alkali soil. To explore the relationship between halophyte herbaceous succession and microbial community structure, we chose four local communities which played an important role in improving soil microenvironment. We performed phospholipid fatty acid analysis, measured soil parameters, and evaluated shifts of microbial community structure. Results showed that microbial community structure changed significantly along succession and bacteria community was dominant. Total phospholipid fatty acid content increased in different successional stages but decreased with depth, with similar variations in bacterial and fungal biomass. Soil organic carbon and especially total nitrogen were positively correlated with microbial biomass. Colonization of pioneering salt-tolerant plants Suaeda glauca in saline-alkali bare land changed total soil microorganism content and composition. These results showed that belowground processes were strongly related with aboveground halophyte succession. Fungal/bacterial ratio, Gram-negative/Gram-positive bacteria ratio, total microbial biomass, and fungi and bacteria content could indicate the degree of succession stages in Bohai Bay wetland ecosystem. And also these findings demonstrated that microbial community biomass and composition evolved along with vegetation succession environmental variables.

  6. Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

    Science.gov (United States)

    Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

    2017-12-01

    New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

  7. Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau.

    Science.gov (United States)

    Zhang, Yuguang; Lu, Zhenmei; Liu, Shanshan; Yang, Yunfeng; He, Zhili; Ren, Zuohua; Zhou, Jizhong; Li, Diqiang

    2013-03-29

    GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes. High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were

  8. Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment

    Directory of Open Access Journals (Sweden)

    Ziming Yang

    2017-09-01

    Full Text Available Microbial decomposition of soil organic carbon (SOC in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05 associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol, methane and CO2 production, and Fe(III reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.

  9. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    Science.gov (United States)

    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.

  10. Influence of seawater intrusion on microbial communities in groundwater.

    Science.gov (United States)

    Unno, Tatsuya; Kim, Jungman; Kim, Yumi; Nguyen, Son G; Guevarra, Robin B; Kim, Gee Pyo; Lee, Ji-Hoon; Sadowsky, Michael J

    2015-11-01

    Groundwater is the sole source of potable water on Jeju Island in the Republic of (South) Korea. Groundwater is also used for irrigation and industrial purposes, and it is severely impacted by seawater intrusion in coastal areas. Consequently, monitoring the intrusion of seawater into groundwater on Jeju is very important for health and environmental reasons. A number of studies have used hydrological models to predict the deterioration of groundwater quality caused by seawater intrusion. However, there is conflicting evidence of intrusion due to complicated environmental influences on groundwater quality. Here we investigated the use of next generation sequencing (NGS)-based microbial community analysis as a way to monitor groundwater quality and detect seawater intrusion. Pristine groundwater, groundwater from three coastal areas, and seawater were compared. Analysis of the distribution of bacterial species clearly indicated that the high and low salinity groundwater differed significantly with respect to microbial composition. While members of the family Parvularculaceae were only identified in high salinity water samples, a greater percentage of the phylum Actinobacteria was predominantly observed in pristine groundwater. In addition, we identified 48 shared operational taxonomic units (OTUs) with seawater, among which the high salinity groundwater sample shared a greater number of bacterial species with seawater (6.7%). In contrast, other groundwater samples shared less than 0.5%. Our results suggest that NGS-based microbial community analysis of groundwater may be a useful tool for monitoring groundwater quality and detect seawater intrusion. This technology may also provide additional insights in understanding hydrological dynamics. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Microbial Herd Protection Mediated by Antagonistic Interaction in Polymicrobial Communities

    Science.gov (United States)

    Wong, Megan J. Q.; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian

    2016-01-01

    ABSTRACT In host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist, despite significant antagonistic interactions between species, are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through the delivery of toxic effectors. It is well established that intraspecies protection is conferred by immunity proteins that neutralize effector toxicities. In contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS-active antagonistic bacterial species, Aeromonas hydrophila and Vibrio cholerae, to demonstrate that interspecies protection is dependent on effectors. A. hydrophila and V. cholerae do not share conserved immunity genes but could coexist equally in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the competing wild-type strain. Time-lapse microscopic analyses showed that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interactions inside each cluster and restricting the interactions to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulated our experimental observations. These results provide mechanistic insights regarding the general role of microbial weapons in determining the structures of complex multispecies communities. IMPORTANCE Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in

  12. Microbial herd protection mediated by antagonistic interaction in polymicrobial communities.

    Science.gov (United States)

    Wong, Megan; Liang, Xiaoye; Smart, Matt; Tang, Le; Moore, Richard; Ingalls, Brian; Dong, Tao G

    2016-09-16

    In the host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist - despite significant antagonistic interactions between species - are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through delivery of toxic effectors. It is well established that intra-species protection is conferred by immunity proteins that neutralize effector toxicities. By contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS active antagonistic bacteria, Aeromonas hydrophila (AH) and Vibrio cholerae (VC), to demonstrate that interspecies protection is dependent on effectors. AH and VC do not share conserved immunity genes but could equally co-exist in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the other competing wild type. Time-lapse microscopy analyses show that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interaction inside each cluster and restricting it to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulate our experimental observation. These results provide mechanistic insights for the general role of microbial weapons in determining the structures of complex multispecies communities. Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in determining community structures and exchange of genetic materials

  13. Stochastic Community Assembly: Does It Matter in Microbial Ecology?

    Science.gov (United States)

    Zhou, Jizhong; Ning, Daliang

    2017-12-01

    Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research. Copyright © 2017 American Society for Microbiology.

  14. Differences in microbial community composition between injection and production water samples of water flooding petroleum reservoirs

    Directory of Open Access Journals (Sweden)

    P. K. Gao

    2015-06-01

    Full Text Available Microbial communities in injected water are expected to have significant influence on those of reservoir strata in long-term water flooding petroleum reservoirs. To investigate the similarities and differences in microbial communities in injected water and reservoir strata, high-throughput sequencing of microbial partial 16S rRNA of the water samples collected from the wellhead and downhole of injection wells, and from production wells in a homogeneous sandstone reservoir and a heterogeneous conglomerate reservoir were performed. The results indicate that a small number of microbial populations are shared between the water samples from the injection and production wells in the sandstone reservoir, whereas a large number of microbial populations are shared in the conglomerate reservoir. The bacterial and archaeal communities in the reservoir strata have high concentrations, which are similar to those in the injected water. However, microbial population abundance exhibited large differences between the water samples from the injection and production wells. The number of shared populations reflects the influence of microbial communities in injected water on those in reservoir strata to some extent, and show strong association with the unique variation of reservoir environments.

  15. Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

    Directory of Open Access Journals (Sweden)

    Darine Trabelsi

    2013-01-01

    Full Text Available 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.

  16. The role of macrobiota in structuring microbial communities along rocky shores

    Directory of Open Access Journals (Sweden)

    Catherine A. Pfister

    2014-10-01

    Full Text Available Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.

  17. Cellular content of biomolecules in sub-seafloor microbial communities

    DEFF Research Database (Denmark)

    Braun, Stefan; Morono, Yuki; Becker, Kevin W.

    2016-01-01

    the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density...... content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates......Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than...

  18. Discovery of enzymes for toluene synthesis from anoxic microbial communities

    DEFF Research Database (Denmark)

    Beller, Harry R.; Rodrigues, Andria V.; Zargar, Kamrun

    2018-01-01

    Microbial toluene biosynthesis was reported in anoxic lake sediments more than three decades ago, but the enzyme catalyzing this biochemically challenging reaction has never been identified. Here we report the toluene-producing enzyme PhdB, a glycyl radical enzyme of bacterial origin that catalyzes...... phenylacetate decarboxylation, and its cognate activating enzyme PhdA, a radical S-adenosylmethionine enzyme, discovered in two distinct anoxic microbial communities that produce toluene. The unconventional process of enzyme discovery from a complex microbial community (>300,000 genes), rather than from...... a microbial isolate, involved metagenomics- and metaproteomics-enabled biochemistry, as well as in vitro confirmation of activity with recombinant enzymes. This work expands the known catalytic range of glycyl radical enzymes (only seven reaction types had been characterized previously) and aromatic...

  19. Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

    Science.gov (United States)

    Li, Ping; Wang, Yanhong; Dai, Xinyue; Zhang, Rui; Jiang, Zhou; Jiang, Dawei; Wang, Shang; Jiang, Hongchen; Wang, Yanxin; Dong, Hailiang

    2015-01-01

    A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater) and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes) in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs). Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-), SO4(2-)/total sulfur ratio, and Fe(2+) were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

  20. Microbial community in high arsenic shallow groundwater aquifers in Hetao Basin of Inner Mongolia, China.

    Directory of Open Access Journals (Sweden)

    Ping Li

    Full Text Available A survey was carried out on the microbial community of 20 groundwater samples (4 low and 16 high arsenic groundwater and 19 sediments from three boreholes (two high arsenic and one low arsenic boreholes in a high arsenic groundwater system located in Hetao Basin, Inner Mongolia, using the 454 pyrosequencing approach. A total of 233,704 sequence reads were obtained and classified into 12-267 operational taxonomic units (OTUs. Groundwater and sediment samples were divided into low and high arsenic groups based on measured geochemical parameters and microbial communities, by hierarchical clustering and principal coordinates analysis. Richness and diversity of the microbial communities in high arsenic sediments are higher than those in high arsenic groundwater. Microbial community structure was significantly different either between low and high arsenic samples or between groundwater and sediments. Acinetobacter, Pseudomonas, Psychrobacter and Alishewanella were the top four genera in high arsenic groundwater, while Thiobacillus, Pseudomonas, Hydrogenophaga, Enterobacteriaceae, Sulfuricurvum and Arthrobacter dominated high arsenic sediments. Archaeal sequences in high arsenic groundwater were mostly related to methanogens. Biota-environment matching and co-inertia analyses showed that arsenic, total organic carbon, SO4(2-, SO4(2-/total sulfur ratio, and Fe(2+ were important environmental factors shaping the observed microbial communities. The results of this study expand our current understanding of microbial ecology in high arsenic groundwater aquifers and emphasize the potential importance of microbes in arsenic transformation in the Hetao Basin, Inner Mongolia.

  1. Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

    Science.gov (United States)

    Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

    2016-03-22

    Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

  2. The significance of microbial processes in hydrogeology and geochemistry

    Science.gov (United States)

    Chapelle, Francis H.

    Microbial processes affect the chemical composition of groundwater and the hydraulic properties of aquifers in both contaminated and pristine groundwater systems. The patterns of water-chemistry changes that occur depend upon the relative abundance of electron donors and electron acceptors. In many pristine aquifers, where microbial metabolism is limited by the availability of electron donors (usually organic matter), dissolved inorganic carbon (DIC) accumulates slowly along aquifer flow paths and available electron acceptors are consumed sequentially in the order dissolved oxygen >nitrate>Fe(III)>sulfate>CO2 (methanogenesis). In aquifers contaminated by anthropogenic contaminants, an excess of available organic carbon often exists, and microbial metabolism is limited by the availability of electron acceptors. In addition to changes in groundwater chemistry, the solid matrix of the aquifer is affected by microbial processes. The production of carbon dioxide and organic acids can lead to increased mineral solubility, which can lead to the development of secondary porosity and permeability. Conversely, microbial production of carbonate, ferrous iron, and sulfide can result in the precipitation of secondary calcite or pyrite cements that reduce primary porosity and permeability in groundwater systems. Les processus microbiologiques peuvent affecter la composition chimique de l'eau souterraine et les propriétés hydrauliques des nappes aussi bien dans les systèmes aquifères pollués que dans les systèmes indemnes de pollution. Les changements de chimisme des eaux qui se produisent dépendent de l'abondance relative des donneurs et des accepteurs d'électrons. Dans les aquifères non contaminés, où le métabolisme microbien est limité par la disponibilité des donneurs d'électrons (en général la matière organique), le carbone minéral dissous (CMD) s'accumule lentement le long des axes d'écoulement souterrain et les accepteurs d'électrons disponibles sont

  3. Microbial community dynamics and transformation of vascular plant detritus in two wetland ecosystems

    International Nuclear Information System (INIS)

    Moran, M.A.

    1987-01-01

    The microbial ecology of two wetland ecosystems in southeastern Georgia, USA, was studied with respect to microbial community dynamics and microbially-mediated transformations of vascular plant detritus. In the Okefenokee Swamp, biomass of microorganisms in the water column and sediments was generally lower in winter months and higher during spring and summer. Biomass and activity (measured as 14 C-lignocellulose mineralization) differed significantly among five habitats within the Okefenokee, and also among locations within each habitat. Significant heterogeneity in the structure of Okefenokee microbial communities was found at scales from 30 cm to 150 m. In field and laboratory studies of vascular plant decomposition in the Okefenokee and a salt marsh on Sapelo Island, the mathematical model which best describes decomposition kinetics is the decaying coefficient model

  4. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    Energy Technology Data Exchange (ETDEWEB)

    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.

  5. Quantifying electron fluxes in methanogenic microbial communities

    NARCIS (Netherlands)

    Junicke, H.

    2015-01-01

    Anaerobic digestion is a widely applied process in which close interactions between different microbial groups result in the formation of renewable energy in the form of biogas. Nevertheless, the regulatory mechanisms of the electron transfer between acetogenic bacteria and methanogenic archaea in

  6. Microbial communities in a High Arctic polar desert landscape

    Directory of Open Access Journals (Sweden)

    Clare M McCann

    2016-03-01

    Full Text Available The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the α- and β-diversity of polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla consistently dominated the soils and accounted for 95 % of all sequences, with Proteobacteria, Actinobacteria and Chloroflexi being the dominant lineages. In contrast to previous investigations of Arctic soils, Acidobacterial relative abundances were low as were the Archaea throughout the Kongsfjorden polar desert landscape. Lower Acidobacterial abundances were attributed to the circumneutral soil pH in this region which has resulted from the weathering of the underlying carbonate geology. In addition, we correlated previously measured geochemical variables to determine potential controls on the communities. Soil phosphorus, pH, nitrogen and calcium significantly correlated with β-diversity indicating a landscape scale lithological control of soil nutrients which in turn influenced community composition. In addition, soil phosphorus and pH significantly correlated with α- diversity, specifically the Shannon diversity and Chao 1 richness indices.

  7. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    Science.gov (United States)

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-06-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  8. Mineralogic control on abundance and diversity of surface-adherent microbial communities

    Science.gov (United States)

    Mauck, Brena S.; Roberts, Jennifer A.

    2007-01-01

    In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

  9. Significance, mechanisms and environmental implications of microbial bio-mineralization

    International Nuclear Information System (INIS)

    Benzerara, K.; Miot, J.; Morin, G.; Ona-Nguema, G.; Skouri-Panet, F.; Ferard, C.

    2011-01-01

    Microorganisms can mediate the formation of minerals by a process called bio-mineralization. This process offers an efficient way to sequester inorganic pollutants within relatively stable solid phases. Here we review some of the main mechanisms involved in the mediation of mineral precipitation by microorganisms. This includes supersaturation caused by metabolic activity, the triggering of nucleation by production of more or less specific organic molecules, and the impact of mineral growth. While these processes have been widely studied in the laboratory, assessment of their importance in the environment is more difficult. We illustrate this difficulty using a case study on an As-contaminated acid mine drainage located in the South of France (Carnoules, Gard). In particular, we explore the potential relationships that might exist between microbial diversity and mineral precipitation. The present review, far from being exhaustive, highlights some recent advances in the field of bio-mineralogy and provides non-specialists an introduction to some of the main approaches and some questions that remain unanswered. (authors)

  10. Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

    Science.gov (United States)

    Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

    2014-11-01

    Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

  11. Genome-reconstruction for eukaryotes from complex natural microbial communities.

    Science.gov (United States)

    West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

    2018-04-01

    Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

  12. In-Well Sediment Incubators to Evaluate Microbial Community Stability and Dynamics following Bioimmobilization of Uranium

    International Nuclear Information System (INIS)

    Baldwin, Brett R.; Peacock, Aaron D.; Gan, M.; Resch, Charles T.; Arntzen, Evan V.; Smithgall, A.N.; Pfiffner, S.; Freifeld, Barry M.; White, D.C.; Long, Philip E.

    2009-01-01

    An in-situ incubation device (ISI) was developed in order to investigate the stability and dynamics of sediment associated microbial communities to prevailing subsurface oxidizing or reducing conditions. Here we describe the use of these devices at the Old Rifle Uranium Mill Tailings Remedial Action (UMTRA) site. During the 7 month deployment oxidized Rifle aquifer background sediments (RABS) were deployed in previously biostimulated wells under iron reducing conditions, cell densities of known iron reducing bacteria including Geobacteraceae increased significantly showing the microbial community response to local subsurface conditions. PLFA profiles of RABS following in situ deployment were strikingly similar to those of adjacent sediment cores suggesting ISI results could be extrapolated to the native material of the test plots. Results for ISI deployed reduced sediments showed only slight changes in community composition and pointed toward the ability of the ISIs to monitor microbial community stability and response to subsurface conditions.

  13. Microbial Communities Model Parameter Calculation for TSPA/SR

    International Nuclear Information System (INIS)

    D. Jolley

    2001-01-01

    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 and 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 and 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 ΔG (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 and 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 and O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed

  14. Modeling adaptation of carbon use efficiency in microbial communities

    Directory of Open Access Journals (Sweden)

    Steven D Allison

    2014-10-01

    Full Text Available 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.

  15. Manipulating soil microbial communities in extensive green roof substrates.

    Science.gov (United States)

    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.

  16. A Mosaic of Geothermal and Marine Features Shapes Microbial Community Structure on Deception Island Volcano, Antarctica

    Directory of Open Access Journals (Sweden)

    Amanda G. Bendia

    2018-05-01

    Full Text Available Active volcanoes in Antarctica contrast with their predominantly cold surroundings, resulting in environmental conditions capable of selecting for versatile and extremely diverse microbial communities. This is especially true on Deception Island, where geothermal, marine, and polar environments combine to create an extraordinary range of environmental conditions. Our main goal in this study was to understand how microbial community structure is shaped by gradients of temperature, salinity, and geochemistry in polar marine volcanoes. Thereby, we collected surface sediment samples associated with fumaroles and glaciers at two sites on Deception, with temperatures ranging from 0 to 98°C. Sequencing of the 16S rRNA gene was performed to assess the composition and diversity of Bacteria and Archaea. Our results revealed that Deception harbors a combination of taxonomic groups commonly found both in cold and geothermal environments of continental Antarctica, and also groups normally identified at deep and shallow-sea hydrothermal vents, such as hyperthermophilic archaea. We observed a clear separation in microbial community structure across environmental gradients, suggesting that microbial community structure is strongly niche driven on Deception. Bacterial community structure was significantly associated with temperature, pH, salinity, and chemical composition; in contrast, archaeal community structure was strongly associated only with temperature. Our work suggests that Deception represents a peculiar “open-air” laboratory to elucidate central questions regarding molecular adaptability, microbial evolution, and biogeography of extremophiles in polar regions.

  17. Epigeic earthworms exert a bottleneck effect on microbial communities through gut associated processes.

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    María Gómez-Brandón

    Full Text Available BACKGROUND: Earthworms play a critical role in organic matter decomposition because of the interactions they establish with microorganisms. The ingestion, digestion, assimilation of organic material in the gut and then casting is the first step in earthworm-microorganism interactions. The current knowledge of these direct effects is still limited for epigeic earthworm species, mainly those living in man-made environments. Here we tested whether and to what extent the earthworm Eisenia andrei is capable of altering the microbiological properties of fresh organic matter through gut associated processes; and if these direct effects are related to the earthworm diet. METHODOLOGY: To address these questions we determined the microbial community structure (phospholipid fatty acid profiles and microbial activity (fluorescein diacetate hydrolysis in the earthworm casts derived from three types of animal manure (cow, horse and pig manure, which differed in microbial composition. PRINCIPAL FINDINGS: The passage of the organic material through the gut of E. andrei reduced the total microbial biomass irrespective of the type of manure, and resulted in a decrease in bacterial biomass in all the manures; whilst leaving the fungi unaffected in the egested materials. However, unlike the microbial biomass, no such reduction was detected in the total microbial activity of cast samples derived from the pig manure. Moreover, no differences were found between cast samples derived from the different types of manure with regards to microbial community structure, which provides strong evidence for a bottleneck effect of worm digestion on microbial populations of the original material consumed. CONCLUSIONS/SIGNIFICANCE: Our data reveal that earthworm gut is a major shaper of microbial communities, thereby favouring the existence of a reduced but more active microbial population in the egested materials, which is of great importance to understand how biotic interactions

  18. The impact of zero-valent iron nanoparticles upon soil microbial communities is context dependent.

    Science.gov (United States)

    Pawlett, Mark; Ritz, Karl; Dorey, Robert A; Rocks, Sophie; Ramsden, Jeremy; Harris, Jim A

    2013-02-01

    Nanosized zero-valent iron (nZVI) is an effective land remediation tool, but there remains little information regarding its impact upon and interactions with the soil microbial community. nZVI stabilised with sodium carboxymethyl cellulose was applied to soils of three contrasting textures and organic matter contents to determine impacts on soil microbial biomass, phenotypic (phospholipid fatty acid (PLFA)), and functional (multiple substrate-induced respiration (MSIR)) profiles. The nZVI significantly reduced microbial biomass by 29 % but only where soil was amended with 5 % straw. Effects of nZVI on MSIR profiles were only evident in the clay soils and were independent of organic matter content. PLFA profiling indicated that the soil microbial community structure in sandy soils were apparently the most, and clay soils the least, vulnerable to nZVI suggesting a protective effect imparted by clays. Evidence of nZVI bactericidal effects on Gram-negative bacteria and a potential reduction of arbuscular mycorrhizal fungi are presented. Data imply that the impact of nZVI on soil microbial communities is dependent on organic matter content and soil mineral type. Thereby, evaluations of nZVI toxicity on soil microbial communities should consider context. The reduction of AM fungi following nZVI application may have implications for land remediation.

  19. Acclimation of subsurface microbial communities to mercury

    DEFF Research Database (Denmark)

    de Lipthay, Julia R; Rasmussen, Lasse D; Øregaard, Gunnar

    2008-01-01

    of mercury tolerance and functional versatility of bacterial communities in contaminated soils initially were higher for surface soil, compared with the deeper soils. However, following new mercury exposure, no differences between bacterial communities were observed, which indicates a high adaptive potential......We studied the acclimation to mercury of bacterial communities of different depths from contaminated and noncontaminated floodplain soils. The level of mercury tolerance of the bacterial communities from the contaminated site was higher than those of the reference site. Furthermore, the level...... of the subsurface communities, possibly due to differences in the availability of mercury. IncP-1 trfA genes were detected in extracted community DNA from all soil depths of the contaminated site, and this finding was correlated to the isolation of four different mercury-resistance plasmids, all belonging...

  20. Life in the "plastisphere": microbial communities on plastic marine debris.

    Science.gov (United States)

    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. Anode microbial communities produced by changing from microbial fuel cell to microbial electrolysis cell operation using two different wastewaters

    KAUST Repository

    Kiely, Patrick D.; Cusick, Roland; Call, Douglas F.; Selembo, Priscilla A.; Regan, John M.; Logan, Bruce E.

    2011-01-01

    Conditions in microbial fuel cells (MFCs) differ from those in microbial electrolysis cells (MECs) due to the intrusion of oxygen through the cathode and the release of H2 gas into solution. Based on 16S rRNA gene clone libraries, anode communities in reactors fed acetic acid decreased in species richness and diversity, and increased in numbers of Geobacter sulfurreducens, when reactors were shifted from MFCs to MECs. With a complex source of organic matter (potato wastewater), the proportion of Geobacteraceae remained constant when MFCs were converted into MECs, but the percentage of clones belonging to G. sulfurreducens decreased and the percentage of G. metallireducens clones increased. A dairy manure wastewater-fed MFC produced little power, and had more diverse microbial communities, but did not generate current in an MEC. These results show changes in Geobacter species in response to the MEC environment and that higher species diversity is not correlated with current. © 2010 Elsevier Ltd.

  2. Effects of lead and cadmium nitrate on biomass and substrate utilization pattern of soil microbial communities.

    Science.gov (United States)

    Muhammad, Akmal; Xu, Jianming; Li, Zhaojun; Wang, Haizhen; Yao, Huaiying

    2005-07-01

    A study was conducted to evaluate the effects of different concentrations of lead (Pb) and cadmium (Cd) applied as their nitrates on soil microbial biomass carbon (C(mic)) and nitrogen (N(mic)), and substrate utilization pattern of soil microbial communities. The C(mic) and N(mic) contents were determined at 0, 14, 28, 42 and 56 days after heavy metal application (DAA). The results showed a significant decline in the C(mic) for all Pb and Cd amended soils from the start to 28 DAA. From 28 to 56 DAA, C(mic) contents changed non-significantly for all other treatments except for 600 mgkg(-1) Pb and 100 mgkg(-1) Cd in which it declined significantly from 42 to 56 DAA. The N(mic) contents also decreased significantly from start to 28 DAA for all other Pb and Cd treatments except for 200 mgkg(-1) Pb which did not show significant difference from the control. Control and 200 mgkg(-1) Pb had significantly lower soil microbial biomass C:N ratio as compared with other Pb treatments from 14 to 42 DAA, however at 56 DAA, only 1000 mgkg(-1) Pb showed significantly higher C:N ratio compared with other treatments. No significant difference in C:N ratio for all Cd treated soils was seen from start to 28 DAA, however from 42 to 56 DAA, 100 mgkg(-1) Pb showed significantly higher C:N ratio compared with other treatments. On 56 DAA, substrate utilization pattern of soil microbial communities was determined by inoculating Biolog ECO plates. The results indicated that Pb and Cd addition inhibited the functional activity of soil microbial communities as indicated by the intensity of average well color development (AWCD) during 168 h of incubation. Multivariate analysis of sole carbon source utilization pattern demonstrated that higher levels of heavy metal application had significantly affected soil microbial community structure.

  3. Sediment Microbial Communities Influenced by Cool Hydrothermal Fluid Migration

    Directory of Open Access Journals (Sweden)

    Laura A. Zinke

    2018-06-01

    Full Text Available Cool hydrothermal systems (CHSs are prevalent across the seafloor and discharge fluid volumes that rival oceanic input from rivers, yet the microbial ecology of these systems are poorly constrained. The Dorado Outcrop on the ridge flank of the Cocos Plate in the northeastern tropical Pacific Ocean is the first confirmed CHS, discharging minimally altered <15°C fluid from the shallow lithosphere through diffuse venting and seepage. In this paper, we characterize the resident sediment microbial communities influenced by cool hydrothermal advection, which is evident from nitrate and oxygen concentrations. 16S rRNA gene sequencing revealed that Thaumarchaea, Proteobacteria, and Planctomycetes were the most abundant phyla in all sediments across the system regardless of influence from seepage. Members of the Thaumarchaeota (Marine Group I, Alphaproteobacteria (Rhodospirillales, Nitrospirae, Nitrospina, Acidobacteria, and Gemmatimonadetes were enriched in the sediments influenced by CHS advection. Of the various geochemical parameters investigated, nitrate concentrations correlated best with microbial community structure, indicating structuring based on seepage of nitrate-rich fluids. A comparison of microbial communities from hydrothermal sediments, seafloor basalts, and local seawater at Dorado Outcrop showed differences that highlight the distinct niche space in CHS. Sediment microbial communities from Dorado Outcrop differ from those at previously characterized, warmer CHS sediment, but are similar to deep-sea sediment habitats with surficial ferromanganese nodules, such as the Clarion Clipperton Zone. We conclude that cool hydrothermal venting at seafloor outcrops can alter the local sedimentary oxidation–reduction pathways, which in turn influences the microbial communities within the fluid discharge affected sediment.

  4. Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

    2005-01-01

    Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P < 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P < 0.05). There were also significant decreases (P < 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

  5. Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

    Science.gov (United States)

    Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

  6. The microbial community of the cystic fibrosis airway is disrupted in early life.

    Directory of Open Access Journals (Sweden)

    Julie Renwick

    Full Text Available Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF.Bronchoalveolar lavage (BAL fluid and paired oropharyngeal swabs from clinically stable children with CF (n = 13 and BAL from children without CF (n = 9 were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed.A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p = 0.001; t test and Principle coordinate analysis (p = 0.01; Adonis test. Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu.The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF.

  7. Two distinct microbial communities revealed in the sponge Cinachyrella

    Science.gov (United States)

    Cuvelier, Marie L.; Blake, Emily; Mulheron, Rebecca; McCarthy, Peter J.; Blackwelder, Patricia; Thurber, Rebecca L. Vega; Lopez, Jose V.

    2014-01-01

    Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters. PMID:25408689

  8. Two distinct microbial communities revealed in the sponge Cinachyrella

    Directory of Open Access Journals (Sweden)

    Marie Laure Cuvelier

    2014-11-01

    Full Text Available Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes, which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rDNA tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1 with low diversity (Shannon-Weiner index: 3.73 ± 0.22 and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25. Hosts’ 28S rDNA sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences present in low abundance or below detection limits (<0.07% in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5% and 22.4% of SG1 and SG2’s total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters.

  9. High taxonomic variability despite stable functional structure across microbial communities.

    Science.gov (United States)

    Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

    2016-12-05

    Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

  10. Microbial communities and exopolysaccharides from Polynesian mats.

    Science.gov (United States)

    Rougeaux, H; Guezennec, M; Che, L M; Payri, C; Deslandes, E; Guezennec, J

    2001-03-01

    Microbial mats present in two shallow atolls of French Polynesia were characterized by high amounts of exopolysaccharides associated with cyanobacteria as the predominating species. Cyanobacteria were found in the first centimeters of the gelatinous mats, whereas deeper layers showing the occurrence of the sulfate reducers Desulfovibrio and Desulfobacter species as determined by the presence of specific biomarkers. Exopolysaccharides were extracted from these mats and partially characterized. All fractions contained both neutral sugars and uronic acids with a predominance of the former. The large diversity in monosaccharides can be interpreted as the result of exopolymer biosynthesis by either different or unidentified cyanobacterial species.

  11. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    Science.gov (United States)

    di Meo, C. A.; Giovannoni, S.; Fisk, M.

    2002-12-01

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the

  12. Microbial community analysis of fouled reverse osmosis membranes used in water recycling

    KAUST Repository

    Ayache, C.; Manes, Carmem Lara De O; Pidou, Marc; Croue, Jean-Philippe; Gernjak, Wolfgang

    2013-01-01

    Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

  13. Microbial community analysis of fouled reverse osmosis membranes used in water recycling

    KAUST Repository

    Ayache, C.

    2013-06-01

    Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

  14. Micro-Food Web Structure Shapes Rhizosphere Microbial Communities and Growth in Oak

    Directory of Open Access Journals (Sweden)

    Hazel R. Maboreke

    2018-03-01

    Full Text Available The multitrophic interactions in the rhizosphere impose significant impacts on microbial community structure and function, affecting nutrient mineralisation and consequently plant performance. However, particularly for long-lived plants such as forest trees, the mechanisms by which trophic structure of the micro-food web governs rhizosphere microorganisms are still poorly understood. This study addresses the role of nematodes, as a major component of the soil micro-food web, in influencing the microbial abundance and community structure as well as tree growth. In a greenhouse experiment with Pedunculate Oak seedlings were grown in soil, where the nematode trophic structure was manipulated by altering the proportion of functional groups (i.e., bacterial, fungal, and plant feeders in a full factorial design. The influence on the rhizosphere microbial community, the ectomycorrhizal symbiont Piloderma croceum, and oak growth, was assessed. Soil phospholipid fatty acids were employed to determine changes in the microbial communities. Increased density of singular nematode functional groups showed minor impact by increasing the biomass of single microbial groups (e.g., plant feeders that of Gram-negative bacteria, except fungal feeders, which resulted in a decline of all microorganisms in the soil. In contrast, inoculation of two or three nematode groups promoted microbial biomass and altered the community structure in favour of bacteria, thereby counteracting negative impact of single groups. These findings highlight that the collective action of trophic groups in the soil micro-food web can result in microbial community changes promoting the fitness of the tree, thereby alleviating the negative effects of individual functional groups.

  15. Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem.

    Science.gov (United States)

    Smith, Chris R; Blair, Peter L; Boyd, Charlie; Cody, Brianne; Hazel, Alexander; Hedrick, Ashley; Kathuria, Hitesh; Khurana, Parul; Kramer, Brent; Muterspaw, Kristin; Peck, Charles; Sells, Emily; Skinner, Jessica; Tegeler, Cara; Wolfe, Zoe

    2016-11-01

    The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no-till, had a much greater impact on nearly everything measured compared to the crop planted. No-till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no-till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff-both of which have ecosystem-level effects and both direct and indirect effects on humans and other organisms.

  16. Microbial activities and communities in oil sands tailings ponds

    Energy Technology Data Exchange (ETDEWEB)

    Gieg, Lisa; Ramos, Esther; Clothier, Lindsay; Bordenave, Sylvain; Lin, Shiping; Voordouw, Gerrit; Dong, Xiaoli; Sensen, Christoph [University of Calgary (Canada)

    2011-07-01

    This paper discusses how the microbial communities and their activity play a vital role in tailings ponds. The ponds contain microorganisms along with metals, hydrocarbon diluent, naphthenic acid and others. The ponds play an important role in mining operations because they store bitumen extraction waste and also allow water to be re-used in the bitumen extraction process. Pond management presents a few challenges that include, among others, gas emissions and the presence of toxic and corrosive acids. Microbial activities and communities help in managing these ponds. Microbial activity measurement in active and inactive ponds is described and analyzed and the results are presented. The conditions for reducing sulfate, nitrate and iron are also presented. From the results it can be concluded that naphthenic acids can potentially serve as substrates for anaerobic populations in tailings ponds.

  17. Microbial degradation and impact of Bracken toxin ptaquiloside on microbial communities in soil

    DEFF Research Database (Denmark)

    Engel, Pernille; Brandt, Kristian Koefoed; Rasmussen, Lars Holm

    2007-01-01

    ), but not in the NZ soil (weak acid loamy Entisol). In the DK soil PTA turnover was predominantly due to microbial degradation (biodegradation); chemical hydrolysis was occurring mainly in the uppermost A horizon where pH was very low (3.4). Microbial activity (basal respiration) and growth ([3H]leucine incorporation...... assay) increased after PTA exposure, indicating that the Bracken toxin served as a C substrate for the organotrophic microorganisms. On the other hand, there was no apparent impact of PTA on community size as measured by substrate-induced respiration or composition as indicated by community......-level physiological profiles. Our results demonstrate that PTA stimulates microbial activity and that microorganisms play a predominant role for rapid PTA degradation in Bracken-impacted soils....

  18. Effect of pesticides on soil microbial community.

    Science.gov (United States)

    Lo, Chi-Chu

    2010-07-01

    According to guidelines for the approval of pesticides, information about effects of pesticides on soil microorganisms and soil fertility are required, but the relationships of different structures of pesticides on the growth of various groups of soil microorganisms are not easily predicted. Some pesticides stimulate the growth of microorganisms, but other pesticides have depressive effects or no effects on microorganisms. For examples, carbofuran stimulated the population of Azospirillum and other anaerobic nitrogen fixers in flooded and non-flooded soil, but butachlor reduced the population of Azospirillum and aerobic nitrogen fixers in non-flooded soil. Diuron and chlorotoluron showed no difference between treated and nontreated soil, and linuron showed a strong difference. Phosphorus(P)-contains herbicides glyphosate and insecticide methamidophos stimulated soil microbial growth, but other P-containing insecticide fenamiphos was detrimental to nitrification bacteria. Therefore, the following review presents some data of research carried out during the last 20 years. The effects of twenty-one pesticides on the soil microorganisms associated with nutrient and cycling processes are presented in section 1, and the applications of denaturing gradient gel electrophoresis (DGGE) for studying microbial diversity are discussed in section 2.

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

    NARCIS (Netherlands)

    Maphosa, F.; Lieten, S.; Dinkla, I.; Stams, A.J.M.; Fennel, D.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

  20. Investigation of the microbial communities colonizing prepainted steel used for roofing and walling.

    Science.gov (United States)

    Huynh, Tran T; Jamil, Ili; Pianegonda, Nicole A; Blanksby, Stephen J; Barker, Philip J; Manefield, Mike; Rice, Scott A

    2017-04-01

    Microbial colonization of prepainted steel, commonly used in roofing applications, impacts their aesthetics, durability, and functionality. Understanding the relevant organisms and the mechanisms by which colonization occurs would provide valuable information that can be subsequently used to design fouling prevention strategies. Here, next-generation sequencing and microbial community finger printing (T-RFLP) were used to study the community composition of microbes colonizing prepainted steel roofing materials at Burrawang, Australia and Kapar, Malaysia over a 52-week period. Community diversity was low and was dominated by Bacillus spp., cyanobacteria, actinobacteria, Cladosporium sp., Epicoccum nigrum, and Teratosphaeriaceae sp. Cultivation-based methods isolated approximately 20 different fungi and bacteria, some of which, such as E. nigrum and Cladosporium sp., were represented in the community sequence data. Fluorescence in situ hybridization imaging showed that fungi were the most dominant organisms present. Analysis of the sequence and T-RFLP data indicated that the microbial communities differed significantly between locations and changed significantly over time. The study demonstrates the utility of molecular ecology tools to identify and characterize microbial communities associated with the fouling of painted steel surfaces and ultimately can enable the targeted development of control strategies based on the dominant species responsible for fouling. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  1. Evaluation of soil microbial communities as influenced by crude oil ...

    African Journals Online (AJOL)

    Impact of petroleum pollution in a vulnerable Niger Delta ecosystem was investigated to assess interactions in a first-generation phytoremediation site of a crude oil freshly-spilled agricultural soil. Community-level approach for assessing patterns of sole carbon-source utilization by mixed microbial samples was employed to ...

  2. Impacts of chemical gradients on microbial community structure

    DEFF Research Database (Denmark)

    Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E

    2017-01-01

    Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox ...... Journal advance online publication, 17 January 2017; doi:10.1038/ismej.2016.175....

  3. Effects of PAH-Contaminated Soil on Rhizosphere Microbial Communities

    DEFF Research Database (Denmark)

    Pritchina, Olga; Ely, Cairn; Smets, Barth F.

    2011-01-01

    Bacterial associations with plant roots are thought to contribute to the success of phytoremediation. We tested the effect of addition of a polycyclic aromatic hydrocarbon contaminated soil on the structure of the rhizosphere microbial communities of wheat (Triticum aestivum), lettuce (Lactuca...

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

    Science.gov (United States)

    Mosquitoes develop in a variety of aquatic habitats and 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 agricultural chemicals. We used a microcosm approach to examine ...

  5. Vertically distinct microbial communities in the Mariana and Kermadec trenches

    Science.gov (United States)

    Donaldson, Sierra; Osuntokun, Oladayo; Xia, Qing; Nelson, Alex; Blanton, Jessica; Allen, Eric E.; Church, Matthew J.; Bartlett, Douglas H.

    2018-01-01

    Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct microbial communities compared to those at shallower depths due to high hydrostatic pressures, topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of the communities present in the bottom waters of the Kermadec and Mariana trenches. Estimates of microbial protein production indicate active populations under in situ hydrostatic pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and size fraction are important drivers of microbial community structure. Many putative hadal bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter, are similar to members identified in other trenches. Most of the differences between the two trench microbiomes consists of taxa belonging to the Gammaproteobacteria whose distributions extend throughout the water column. Growth and survival estimates of representative isolates of these taxa under deep-sea conditions suggest that some members may descend from shallower depths and exist as a potentially inactive fraction of the hadal zone. We conclude that the distinct pelagic communities residing in these two trenches, and perhaps by extension other trenches, reflect both cosmopolitan hadal bathytypes and ubiquitous genera found throughout the water column. PMID:29621268

  6. Effect of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil.

    Science.gov (United States)

    Kim, Seong-Hye; Han, Hyo-Yeol; Lee, You-Jin; Kim, Chul Woong; Yang, Ji-Won

    2010-07-15

    Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. Copyright 2010 Elsevier B.V. All rights reserved.

  7. Evaluation of methyl bromide alternatives efficacy against soil-borne pathogens, nematodes and soil microbial community.

    Directory of Open Access Journals (Sweden)

    Hongwei Xie

    Full Text Available Methyl bromide (MB and other alternatives were evaluated for suppression of Fusarium spp., Phytophthora spp., and Meloidogyne spp. and their influence on soil microbial communities. Both Fusarium spp. and Phytophthora spp. were significantly reduced by the MB (30.74 mg kg-1, methyl iodide (MI: 45.58 mg kg-1, metham sodium (MS: 53.92 mg kg-1 treatments. MS exhibited comparable effectiveness to MB in controlling Meloidogyne spp. and total nematodes, followed by MI at the tested rate. By contrast, sulfuryl fluoride (SF: 33.04 mg kg-1 and chloroform (CF: 23.68 mg kg-1 showed low efficacy in controlling Fusarium spp., Phytophthora spp., and Meloidogyne spp. MB, MI and MS significantly lowered the abundance of different microbial populations and microbial biomass in soil, whereas SF and CF had limited influence on them compared with the control. Diversity indices in Biolog studies decreased in response to fumigation, but no significant difference was found among treatments in PLFA studies. Principal component and cluster analyses of Biolog and PLFA data sets revealed that MB and MI treatments greatly influenced the soil microbial community functional and structural diversity compared with SF treatment. These results suggest that fumigants with high effectiveness in suppressing soil-borne disease could significantly influence soil microbial community.

  8. Characterization of fatty acid-producing wastewater microbial communities using next generation sequencing technologies

    Science.gov (United States)

    While wastewater represents a viable source of bacterial biodiesel production, very little is known on the composition of these microbial communities. We studied the taxonomic diversity and succession of microbial communities in bioreactors accumulating fatty acids using 454-pyro...

  9. Membrane biofouling characterization: effects of sample preparation procedures on biofilm structure and the microbial community

    KAUST Repository

    Xue, Zheng

    2014-07-15

    Ensuring the quality and reproducibility of results from biofilm structure and microbial community analysis is essential to membrane biofouling studies. This study evaluated the impacts of three sample preparation factors (ie number of buffer rinses, storage time at 4°C, and DNA extraction method) on the downstream analysis of nitrifying biofilms grown on ultrafiltration membranes. Both rinse and storage affected biofilm structure, as suggested by their strong correlation with total biovolume, biofilm thickness, roughness and the spatial distribution of EPS. Significant variations in DNA yields and microbial community diversity were also observed among samples treated by different rinses, storage and DNA extraction methods. For the tested biofilms, two rinses, no storage and DNA extraction with both mechanical and chemical cell lysis from attached biofilm were the optimal sample preparation procedures for obtaining accurate information about biofilm structure, EPS distribution and the microbial community. © 2014 © 2014 Taylor & Francis.

  10. Impact of long-term diesel contamination on soil microbial community structure

    DEFF Research Database (Denmark)

    Sutton, Nora; Maphosa, Farai; Morillo, Jose

    2013-01-01

    Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical...... properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean...... observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific...

  11. Monitoring of microbial communities in anaerobic digestion sludge for biogas optimisation.

    Science.gov (United States)

    Lim, Jun Wei; Ge, Tianshu; Tong, Yen Wah

    2018-01-01

    This study characterised and compared the microbial communities of anaerobic digestion (AD) sludge using three different methods - (1) Clone library; (2) Pyrosequencing; and (3) Terminal restriction fragment length polymorphism (T-RFLP). Although high-throughput sequencing techniques are becoming increasingly popular and affordable, the reliance of such techniques for frequent monitoring of microbial communities may be a financial burden for some. Furthermore, the depth of microbial analysis revealed by high-throughput sequencing may not be required for monitoring purposes. This study aims to develop a rapid, reliable and economical approach for the monitoring of microbial communities in AD sludge. A combined approach where genetic information of sequences from clone library was used to assign phylogeny to T-RFs determined experimentally was developed in this study. In order to assess the effectiveness of the combined approach, microbial communities determined by the combined approach was compared to that characterised by pyrosequencing. Results showed that both pyrosequencing and clone library methods determined the dominant bacteria phyla to be Proteobacteria, Firmicutes, Bacteroidetes, and Thermotogae. Both methods also found that sludge A and B were predominantly dominated by acetogenic methanogens followed by hydrogenotrophic methanogens. The number of OTUs detected by T-RFLP was significantly lesser than that detected by the clone library. In this study, T-RFLP analysis identified majority of the dominant species of the archaeal consortia. However, many of the more highly diverse bacteria consortia were missed. Nevertheless, the combined approach developed in this study where clone sequences from the clone library were used to assign phylogeny to T-RFs determined experimentally managed to accurately predict the same dominant microbial groups for both sludge A and sludge B, as compared to the pyrosequencing results. Results showed that the combined approach of

  12. Generation of Electricity and Analysis of Microbial Communities in Wheat Straw Biomass-Powered Microbial Fuel Cells

    DEFF Research Database (Denmark)

    Zhang, Yifeng; Min, Booki; Huang, L.

    2009-01-01

    Electricity generation from wheat straw hydrolysate and the microbial ecology of electricity producing microbial communities developed in two chamber microbial fuel cells (MFCs) were investigated. Power density reached 123 mW/m2 with an initial hydrolysate concentration of 1000 mg-COD/L while...

  13. Assessment of microbial communities in PM1 and PM10 of Urumqi during winter

    International Nuclear Information System (INIS)

    Gou, Huange; Lu, Jianjiang; Li, Shanman; Tong, Yanbin; Xie, Chunbin; Zheng, Xiaowu

    2016-01-01

    Recently, inhalable particulate matter has been reported to carry microorganisms responsible for human allergy and respiratory disease. The unique geographical environment and adverse weather conditions of Urumqi cause double pollution of dust and smog, but research on the microbial content of the atmosphere has not been commenced. In this study, 16S and 18S rRNA gene sequencing were conducted to investigate the microbial composition of Urumqi's PM 1 and PM 10 pollutants in winter. Results showed that the bacterial community is mainly composed of Proteobacteria, Firmicutes and Actinobacteria, Proteobacteria accounted for the most proportion which was significant difference in some aforementioned studies. Ascomycota and Basidiomycota constitute the main part of the fungal microbial community. The difference of bacterial relative abundance in sample point is greater than in particle sizes. The sequences of several pathogenic bacteria and opportunistic pathogens were also detected, such as Acinetobacter, Delftia, Serratia, Chryseobacterium, which may impact on immunocompromised populations (elderly, children and postoperative convalescence patients), and some fungal genera may cause several plant diseases. Our findings may serve an important reference value in the global air microbial propagation and air microbial research in desert. - Highlights: • Using 16 s rDNA double variable region (V3 + V4) sequencing to elucidate the bacterial communities. • Several potential microbial allergens and pathogens present in PM 1 and PM 10 were found. • Providing a great supplement to environmental science and human health assessment.

  14. Which Members of the Microbial Communities Are Active? Microarrays

    Science.gov (United States)

    Morris, Brandon E. L.

    only at the early stages of understanding the microbial processes that occur in petroliferous formations and the surrounding subterranean environment. Important first steps in characterising the microbiology of oilfield systems involve identifying the microbial community structure and determining how population diversity changes are affected by the overall geochemical and biological parameters of the system. This is relatively easy to do today by using general 16S rRNA primers for PCR and building clone libraries. For example, previous studies using molecular methods characterised many dominant prokaryotes in petroleum reservoirs (Orphan et al., 2000) and in two Alaskan North Slope oil facilities (Duncan et al., 2009; Pham et al., 2009). However, the problem is that more traditional molecular biology approaches, such as 16S clone libraries, fail to detect large portions of the community perhaps missing up to half of the biodiversity (see Hong et al., 2009) and require significant laboratory time to construct large libraries necessary to increase the probability of detecting the majority of even bacterial biodiversity. In the energy sector, the overarching desire would be to quickly assess the extent of in situ hydrocarbon biodegradation or to disrupt detrimental processes such as biofouling, and in these cases it may not be necessary to identify specific microbial species. Rather, it would be more critical to evaluate metabolic processes or monitor gene products that are implicated in the specific activity of interest. Research goals such as these are well suited for a tailored application of microarray technology.

  15. Challenges in microbial ecology: Building predictive understanding of community function and dynamics

    DEFF Research Database (Denmark)

    Widder, Stefanie; Allen, Rosalind J.; Pfeiffer, Thomas

    2016-01-01

    The importance of microbial communities (MCs) cannot be overstated. MCs underpin the biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform ecosystem functions that impact plants, animals and humans. Yet our ability to predict and manage the function of these highly...... complex, dynamically changing communities is limited. Building predictive models that link MC composition to function is a key emerging challenge in microbial ecology. Here, we argue that addressing this challenge requires close coordination of experimental data collection and method development...... is needed to achieve significant progress in our understanding of MC dynamics and function, and we make specific practical suggestions as to how this could be achieved....

  16. How microbial community composition regulates coral disease development.

    Directory of Open Access Journals (Sweden)

    Justin Mao-Jones

    2010-03-01

    Full Text Available Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.

  17. How microbial community composition regulates coral disease development.

    Science.gov (United States)

    Mao-Jones, Justin; Ritchie, Kim B; Jones, Laura E; Ellner, Stephen P

    2010-03-30

    Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts) and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.

  18. Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis

    Directory of Open Access Journals (Sweden)

    Obed Hernández-Gómez

    2017-07-01

    Full Text Available Multicellular hosts maintain complex associations with microbial communities. While microbial communities often serve important functional roles for their hosts, our understanding of the local and regional processes that structure these communities remains limited. Metacommunity analyses provide a promising tool for investigating mechanisms shaping microbiome heterogeneity, which is essential for predicting functional variation between hosts. Using a metacommunity framework, we examined heterogeneity in the skin microbiome of the eastern hellbender (Cryptobranchus alleganiensis alleganiensis. Hellbenders are broadly distributed throughout river systems in the eastern United States, but are present in specific environmental locations throughout their range. The large range of the species and history of population fragmentation suggest that local and regional processes contribute to the distribution of cutaneous symbiont diversity. Therefore, we characterized the skin and environmental bacterial communities at eight rivers throughout the range of the species. We observed variation among hellbender populations in skin microbial community diversity and proportion of shared operational taxonomic units (OTUs between animal and river water communities. Among populations sampled, we noted significant clumped OTU turnover (i.e., Clementsian structure resulting in unique cutaneous communities. In addition, we observed a significant positive correlation between skin community divergence and hellbender population genetic divergence. Host-population skin community dissimilarity did not correlate strongly with distance between sampling locations, indicating a weak spatial effect on the distribution of symbionts. These results suggest that species sorting mechanisms (i.e., local processes structure local skin microbial communities in hellbenders. The variation in skin community composition observed among host populations foreshadows a similar pattern in

  19. Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

    Science.gov (United States)

    Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

    2017-12-28

    The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

  20. Utilization of Alternate Chirality Enantiomers in Microbial Communities

    Science.gov (United States)

    Pikuta, Elena V.; Hoover, Richard B.

    2010-01-01

    Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

  1. Application of biocathode in microbial fuel cells: cell performance and microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Guo-Wei, Chen [Pusan National Univ. (Korea). Dept. of Environmental Engineering; Hefei Univ. of Technology (China). School of Civil Engineering; Choi, Soo-Jung; Lee, Tae-Ho; Lee, Gil-Young; Cha, Jae-Hwan; Kim, Chang-Won [Pusan National Univ. (Korea). Dept. of Environmental Engineering

    2008-06-15

    Instead of the utilization of artificial redox mediators or other catalysts, a biocathode has been applied in a two-chamber microbial fuel cell in this study, and the cell performance and microbial community were analyzed. After a 2-month startup, the microorganisms of each compartment in microbial fuel cell were well developed, and the output of microbial fuel cell increased and became stable gradually, in terms of electricity generation. At 20 ml/min flow rate of the cathodic influent, the maximum power density reached 19.53 W/m{sup 3}, while the corresponding current and cell voltage were 15.36 mA and 223 mV at an external resistor of 14.9 {omega}, respectively. With the development of microorganisms in both compartments, the internal resistance decreased from initial 40.2 to 14.0 {omega}, too. Microbial community analysis demonstrated that five major groups of the clones were categorized among those 26 clone types derived from the cathode microorganisms. Betaproteobacteria was the most abundant division with 50.0% (37 of 74) of the sequenced clones in the cathode compartment, followed by 21.6% (16 of 74) Bacteroidetes, 9.5% (7 of 74) Alphaproteobacteria, 8.1% (6 of 74) Chlorobi, 4.1% (3 of 74) Deltaproteobacteria, 4.1% (3 of 74) Actinobacteria, and 2.6% (2 of 74) Gammaproteobacteria. (orig.)

  2. Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay.

    Science.gov (United States)

    Zhang, Yan; Chen, Lujun; Sun, Renhua; Dai, Tianjiao; Tian, Jinping; Zheng, Wei; Wen, Donghui

    2016-06-01

    Anthropogenic activities usually contaminate water environments, and have led to the eutrophication of many estuaries and shifts in microbial communities. In this study, the temporal and spatial changes of the microbial community in an industrial effluent receiving area in Hangzhou Bay were investigated by 454 pyrosequencing. The bacterial community showed higher richness and biodiversity than the archaeal community in all sediments. Proteobacteria dominated in the bacterial communities of all the samples; Marine_Group_I and Methanomicrobia were the two dominant archaeal classes in the effluent receiving area. PCoA and AMOVA revealed strong seasonal but minor spatial changes in both bacterial and archaeal communities in the sediments. The seasonal changes of the bacterial community were less significant than those of the archaeal community, which mainly consisted of fluctuations in abundance of a large proportion of longstanding species rather than the appearance and disappearance of major archaeal species. Temperature was found to positively correlate with the dominant bacteria, Betaproteobacteria, and negatively correlate with the dominant archaea, Marine_Group_I; and might be the primary driving force for the seasonal variation of the microbial community. Copyright © 2016. Published by Elsevier B.V.

  3. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Science.gov (United States)

    Zhang, Yuguang; Cong, Jing; Lu, Hui; Yang, Caiyun; Yang, Yunfeng; Zhou, Jizhong; Li, Diqiang

    2014-01-01

    Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (PThe regression analysis showed that a strong positive (Pthe soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (Pthe relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

  4. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

    Directory of Open Access Journals (Sweden)

    Erin A Gontang

    Full Text Available 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.

  5. Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

    Science.gov (United States)

    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.

  6. Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

    Science.gov (United States)

    Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

    2012-07-01

    Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.

  7. Contrasting effects of biochar versus manure on soil microbial communities and enzyme activities in an Aridisol.

    Science.gov (United States)

    Elzobair, Khalid A; Stromberger, Mary E; Ippolito, James A; Lentz, Rodrick D

    2016-01-01

    Biochar can increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be abundant and inexpensive if locally available, and thus can be applied to fields at greater rates than biochar. In a field study comparing biochar and manure, a fast pyrolysis hardwood biochar (22.4 Mg ha(-1)), dairy manure (42 Mg ha(-1) dry wt), a combination of biochar and manure at the aforementioned rates, or no amendment (control) was applied to an Aridisol (n=3) in fall 2008. Plots were annually cropped to corn (Zea maize L.). Surface soils (0-30 cm) were sampled directly under corn plants in late June 2009 and early August 2012, and assayed for microbial community fatty acid methyl ester (FAME) profiles and six extracellular enzyme activities involved in soil C, N, and P cycling. Arbuscular mycorrhizal (AM) fungal colonization was assayed in corn roots in 2012. Biochar had no effect on microbial biomass, community structure, extracellular enzyme activities, or AM fungi root colonization of corn. In the short-term, manure amendment increased microbial biomass, altered microbial community structure, and significantly reduced the relative concentration of the AM fungal biomass in soil. Manure also reduced the percent root colonization of corn by AM fungi in the longer-term. Thus, biochar and manure had contrasting short-term effects on soil microbial communities, perhaps because of the relatively low application rate of biochar. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  9. Nitrogen amendment of green waste impacts microbial community, enzyme secretion and potential for lignocellulose decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Chaowei; Harrold, Duff R.; Claypool, Joshua T.; Simmons, Blake A.; Singer, Steven W.; Simmons, Christopher W.; VanderGheynst, Jean S.

    2017-01-01

    Microorganisms involved in biomass deconstruction are an important resource for organic waste recycling and enzymes for lignocellulose bioconversion. The goals of this paper were to examine the impact of nitrogen amendment on microbial community restructuring, secretion of xylanases and endoglucanases, and potential for biomass deconstruction. Communities were cultivated aerobically at 55 °C on green waste (GW) amended with varying levels of NH4Cl. Bacterial and fungal communities were determined using 16S rRNA and ITS region gene sequencing and PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was applied to predict relative abundance of genes involved in lignocellulose hydrolysis. Nitrogen amendment significantly increased secretion of xylanases and endoglucanases, and microbial activity; enzyme activities and cumulative respiration were greatest when nitrogen level in GW was between 4.13–4.56 wt% (g/g), but decreased with higher nitrogen levels. The microbial community shifted to one with increasing potential to decompose complex polymers as nitrogen increased with peak potential occurring between 3.79–4.45 wt% (g/g) nitrogen amendment. Finally, the results will aid in informing the management of nitrogen level to foster microbial communities capable of secreting enzymes that hydrolyze recalcitrant polymers in lignocellulose and yield rapid decomposition of green waste.

  10. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

    2016-12-16

    Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

  11. Shift in the microbial community composition of surface water and sediment along an urban river.

    Science.gov (United States)

    Wang, Lan; Zhang, Jing; Li, Huilin; Yang, Hong; Peng, Chao; Peng, Zhengsong; Lu, Lu

    2018-06-15

    Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan

    Directory of Open Access Journals (Sweden)

    Satoshi Hiraoka

    2017-08-01

    Full Text Available The presence of microbes in the atmosphere and their transport over long distances across the Earth's surface was recently shown. Precipitation is likely a major path by which aerial microbes fall to the ground surface, affecting its microbial ecosystems and introducing pathogenic microbes. Understanding microbial communities in precipitation is of multidisciplinary interest from the perspectives of microbial ecology and public health; however, community-wide and seasonal analyses have not been conducted. Here, we carried out 16S rRNA amplicon sequencing of 30 precipitation samples that were aseptically collected over 1 year in the Greater Tokyo Area, Japan. The precipitation microbial communities were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria and were overall consistent with those previously reported in atmospheric aerosols and cloud water. Seasonal variations in composition were observed; specifically, Proteobacteria abundance significantly decreased from summer to winter. Notably, estimated ordinary habitats of precipitation microbes were dominated by animal-associated, soil-related, and marine-related environments, and reasonably consistent with estimated air mass backward trajectories. To our knowledge, this is the first amplicon-sequencing study investigating precipitation microbial communities involving sampling over the duration of a year.

  13. Bar-coded pyrosequencing reveals the responses of PBDE-degrading microbial communities to electron donor amendments.

    Directory of Open Access Journals (Sweden)

    Meiying Xu

    Full Text Available Polybrominated diphenyl ethers (PBDEs can be reductively degraded by microorganisms under anaerobic conditions. However, little is known about the effect of electron donors on microbial communities involved in PBDEs degradation. Here we employed 454 Titanium pyrosequencing to examine the phylogenetic diversity, composition, structure and dynamics of microbial communities from microcosms under the conditions of different electron donor amendments. The community structures in each of the five alternate electron donor enrichments were significantly shifted in comparison with those of the control microcosm. Commonly existing OTUs between the treatment and control consortia increased from 5 to 17 and more than 50% of OTUs increased around 13.7 to 186 times at least in one of the microcosms after 90-days enrichment. Although the microbial communities at different taxonomic levels were significantly changed by different environmental variable groups in redundancy analysis, significant correlations were observed between the microbial communities and PBDE congener profiles. The lesser-brominated PBDE congeners, tri-BDE congener (BDE-32 and hexa-BDE, were identified as the key factors shaping the microbial community structures at OTU level. Some rare populations, including the known dechlorinating bacterium, Dehalobacter, showed significant positive-correlation with the amounts of PBDE congeners in the consortia. The same results were also observed on some unclassified bacteria. These results suggest that PBDEs-degrading microbial communities can be successfully enriched, and their structures and compositions can be manipulated through adjusting the environmental parameters.

  14. Molecular isotopic tracing of carbon flow and trophic relationships in a methane supported microbial community

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Werne, J.; Baas, B.

    2002-01-01

    A molecular isotopic study in cold-seep sediments from Kazan mud volcano in the eastern Mediterranean Sea indicates that a significant proportion of methane released in this environment is incorporated into biomass in methane-supported chemosynthetic microbial communities. Furthermore, extremely

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

    Science.gov (United States)

    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

  16. Response of soil microbial activities and microbial community structure to vanadium stress.

    Science.gov (United States)

    Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

    2017-08-01

    High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Timmers, Ruud A.; Strik, David P.B.T.B.; Hamelers, Bert; Buisman, Cees [Wageningen Univ. (Netherlands). Sub-dept. of Environmental Technology; Rothballer, Michael; Hartmann, Anton [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Microbe-Plant Interactions; Engel, Marion; Schulz, Stephan; Schloter, Michael [Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg (Germany). Dept. Terrestrial Ecogenetics

    2012-04-15

    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. (orig.)

  18. Quantitative phylogenetic assessment of microbial communities indiverse environments

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    Science.gov (United States)

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  20. Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

    Science.gov (United States)

    Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

    2017-05-01

    Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. Cathodic microbial community adaptation to the removal of chlorinated herbicide in soil microbial fuel cells.

    Science.gov (United States)

    Li, Yue; Li, Xiaojing; Sun, Yang; Zhao, Xiaodong; Li, Yongtao

    2018-04-05

    The microbial fuel cell (MFC) that uses a solid electrode as the inexhaustible electron acceptor is an innovative remediation technology that simultaneously generates bioelectricity. Chlorinated pollutants are better metabolized by reductive dechlorination in proximity to the cathode. Here, the removal efficiency of the herbicide metolachlor (ML) increased by 262 and 176% in soil MFCs that were spiked with 10 (C10) and 20 mg/kg (C20) of ML, respectively, relative to the non-electrode controls. The bioelectricity output of the C10 and C20 increased by over two- and eightfold, respectively, compared to that of the non-ML control, with maximum current densities of 49.6 ± 2.5 (C10) and 78.9 ± 0.6 mA/m 2 (C20). Based on correlations between ML concentrations and species abundances in the MFCs, it was inferred that Azohydromonas sp., Sphingomonas sp., and Pontibacter sp. play a major role in ML removal around the cathode, with peak removal efficiencies of 56 ± 1% (C10) and 58 ± 1% (C20). Moreover, Clostridium sp., Geobacter sp., Bacillus sp., Romboutsia sp., and Terrisporobacter sp. may be electricigens or closely related microbes due to the significant positive correlation between the bioelectricity generation levels and their abundances around the anode. This study suggests that a directional adaptation of the microbial community has taken place to increase both the removal of chlorinated herbicides around the cathode and the generation of bioelectricity around the anode in bioelectrochemical remediation systems.

  2. Extreme CO2 disturbance and the resilience of soil microbial communities

    Science.gov (United States)

    McFarland, Jack W.; Waldrop, Mark P.; Haw, Monica

    2013-01-01

    Carbon capture and storage (CSS) technology has the potential to inadvertently release large quantities of CO2 through geologic substrates and into surrounding soils and ecosystems. Such a disturbance has the potential to not only alter the structure and function of plant and animal communities, but also soils, soil microbial communities, and the biogeochemical processes they mediate. At Mammoth Mountain, we assessed the soil microbial community response to CO2 disturbance (derived from volcanic ‘cold’ CO2) that resulted in localized tree kill; soil CO2 concentrations in our study area ranged from 0.6% to 60%. Our objectives were to examine how microbial communities and their activities are restructured by extreme CO2 disturbance, and assess the response of major microbial taxa to the reintroduction of limited plant communities following an extensive period (15–20 years) with no plants. We found that CO2-induced tree kill reduced soil carbon (C) availability along our sampling transect. In response, soil microbial biomass decreased by an order of magnitude from healthy forest to impacted areas. Soil microorganisms were most sensitive to changes in soil organic C, which explained almost 60% of the variation for microbial biomass C (MBC) along the CO2gradient. We employed phospholipid fatty acid analysis and quantitative PCR (qPCR) to determine compositional changes among microbial communities in affected areas and found substantial reductions in microbial biomass linked to the loss of soil fungi. In contrast, archaeal populations responded positively to the CO2 disturbance, presumably due to reduced competition of bacteria and fungi, and perhaps unique adaptations to energy stress. Enzyme activities important in the cycling of soil C, nitrogen (N), and phosphorus (P) declined with increasing CO2, though specific activities (per unit MBC) remained stable or increased suggesting functional redundancy among restructured communities. We conclude that both the

  3. Different substrates and starter inocula govern microbial community structures in biogas reactors.

    Science.gov (United States)

    Satpathy, Preseela; Steinigeweg, Sven; Cypionka, Heribert; Engelen, Bert

    2016-01-01

    The influence of different starter inocula on the microbial communities in biogas batch reactors fed with fresh maize and maize silage as substrates was investigated. Molecular biological analysis by Denaturing Gradient Gel Electrophoresis (DGGE) of 16S rRNA gene fragments showed that each inoculum bore specific microbial communities with varying predominant phylotypes. Both, bacterial and archaeal DGGE profiles displayed three distinct communities that developed depending on the type of inoculum. Although maize and silage are similar substrates, different communities dominated the lactate-rich silage compared to lactate-free fresh maize. Cluster analysis of DGGE gels showed the communities of the same substrates to be stable with their respective inoculum. Bacteria-specific DGGE analysis revealed a rich diversity with Firmicutes being predominant. The other abundant phylotypes were Bacteroidetes and Synergistetes. Archaea-specific DGGE analysis displayed less diverse community structures, identifying members of the Methanosarcinales as the dominant methanogens present in all the three biogas digesters. In general, the source of inoculum played a significant role in shaping microbial communities. Adaptability of the inoculum to the substrates fed also influenced community compositions which further impacted the rates of biogas production.

  4. Marine snow microbial communities: scaling of abundances with aggregate size

    DEFF Research Database (Denmark)

    Kiørboe, Thomas

    2003-01-01

    Marine aggregates are inhabited by diverse microbial communities, and the concentration of attached microbes typically exceeds concentrations in the ambient water by orders of magnitude. An extension of the classical Lotka-Volterra model, which includes 3 trophic levels (bacteria, flagellates...... are controlled by flagellate grazing, while flagellate and ciliate populations are governed by colonization and detachment. The model also suggests that microbial populations are turned over rapidly (1 to 20 times d-1) due to continued colonization and detachment. The model overpredicts somewhat the scaling...... of microbial abundances with aggregate size observed in field-collected aggregates. This may be because it disregards the aggregation/disaggregation dynamics of aggregates, as well as interspecific interactions between bacteria....

  5. Microbial communities of the deep unfrozen: Do microbes in taliks increase permafrost carbon vulnerability? (Invited)

    Science.gov (United States)

    Waldrop, M. P.; Blazewicz, S.; Jones, M.; Mcfarland, J. W.; Harden, J. W.; Euskirchen, E. S.; Turetsky, M.; Hultman, J.; Jansson, J.

    2013-12-01

    The vast frozen terrain of northern latitude ecosystems is typically thought of as being nearly biologically inert for the winter period. Yet deep within the frozen ground of northern latitude soils reside microbial communities that can remain active during the winter months. As we have shown previously, microbial communities may remain active in permafrost soils just below the freezing point of water. Though perhaps more importantly, microbial communities persist in unfrozen areas of water, soil, and sediment beneath water bodies the entire year. Microbial activity in taliks may have significant impacts on biogeochemical cycling in northern latitude ecosystems because their activity is not limited by the winter months. Here we present compositional and functional data, including long term incubation data, for microbial communities within permafrost landscapes, in permafrost and taliks, and the implications of these activities on permafrost carbon decomposition and the flux of CO2 and CH4. Our experiment was conducted at the Alaska Peatland Experiment (APEX) within the Bonanza Creek LTER in interior Alaska. Our site consists of a black spruce forest on permafrost that has degraded into thermokarst bogs at various times over the last five hundred years. We assume the parent substrate of the deep (1-1.5m) thermokarst peat was similar to the nearby forest soil and permafrost C before thaw. At this site, flux tower and autochamber data show that the thermokarst bog is a sink of CO2 , but a significant source of CH4. Yet this does not tell the whole story as these data do not fully capture microbial activity within the deep unfrozen talik layer. There is published evidence that within thermokarst bogs, relatively rapid decomposition of old forest floor material may be occurring. There are several possible mechanisms for this pattern; one possible mechanism for accelerated decomposition is the overwintering activities of microbial communities in taliks of thermokarst

  6. Microbial Diversity of a Heavily Polluted Microbial Mat and Its Community Changes following Degradation of Petroleum Compounds

    Science.gov (United States)

    Abed, Raeid M. M.; Safi, Nimer M. D.; Köster, Jürgen; de Beer, Dirk; El-Nahhal, Yasser; Rullkötter, Jürgen; Garcia-Pichel, Ferran

    2002-01-01

    We studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (Wadi Gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. Phormidium- and Oscillatoria-like cyanobacterial morphotypes were dominant in the field. Bacteria belonging to different groups, mainly the Cytophaga-Flavobacterium-Bacteriodes group, the γ and β subclasses of the class Proteobacteria, and the green nonsulfur bacteria, were also detected. In slurry experiments, these communities efficiently degraded phenanthrene and dibenzothiophene completely in 7 days both in the light and in the dark. n-Octadecane and pristane were degraded to 25 and 34% of their original levels, respectively, within 7 days, but there was no further degradation until 40 days. Both cyanobacterial and bacterial communities exhibited noticeable changes concomitant with degradation of the compounds. The populations enriched by exposure to petroleum compounds included a cyanobacterium affiliated phylogenetically with Halomicronema. Bacteria enriched both in the light and in the dark, but not bacteria enriched in any of the controls, belonged to the newly described Holophaga-Geothrix-Acidobacterium phylum. In addition, another bacterial population, found to be a member of green nonsulfur bacteria, was detected only in the bacteria treated in the light. All or some of the populations may play a significant role in metabolizing the petroleum compounds. We concluded that the microbial mats from Wadi Gaza are rich in microorganisms with high biodegradative potential. PMID:11916684

  7. Common hydraulic fracturing fluid additives alter the structure and function of anaerobic microbial communities

    Science.gov (United States)

    Mumford, Adam C.; Akob, Denise M.; Klinges, J. Grace; Cozzarelli, Isabelle M.

    2018-01-01

    The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C3H6BrNO4). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills.

  8. Effects of Biochar Blends on Microbial Community Composition in Two Coastal Plain Soils

    Directory of Open Access Journals (Sweden)

    Thomas F. Ducey

    2015-11-01

    Full Text Available The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure. These impacts are modulated not only by the biochar composition, but also on the soil’s physicochemical characteristics. This indicates that soil characteristics must be considered prior to biochar amendment. A significant portion of the soils of the southeastern coastal plain are severely degraded and, therefore, candidates for biochar amendment to strengthen soil fertility. In this study we focused on two common soil series in the southeastern coastal plain, utilizing feedstocks endemic to the area. We chose feedstocks in four ratios (100% pine chip; 80:20 mixture of pine chip to poultry litter; 50:50 mixture of pine chip to poultry litter; 100% poultry litter prior to pyrolysis and soil amendment as a biochar product. Soil was analyzed for bioavailable nutrients via Mehlich-1 extractions, as well as microbial community composition using phospholipid fatty acid analysis (PLFA. Our results demonstrated significant shifts in microbial community composition in response to biochar amendment, the effects of which were greatest with 100% poultry litter biochar. Strong relationships between PLFAs and several Mehlich-1 extractable nutrients (Al, Cu, Fe, and P were observed.

  9. The veterinary antibiotic oxytetracycline and Cu influence functional diversity of the soil microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Kong, W -D [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China); Zhu, Y -G [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China); Fu, B -J [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China); Marschner, P [Soil and Land Systems, School of Earth and Environmental Sciences, University of Adelaide, DP 636, 5005 (Australia); He, J -Z [Research Center for Eco-Environmental Sciences, Soil Environment of Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Beijing 100085 (China)

    2006-09-15

    There are increasing concerns over the effects of veterinary antibiotics and heavy metals in agricultural soils. The widely used veterinary antibiotic oxytetracycline (OTC), Cu and their combination on soil microbial community function were assessed with the Biolog method. The microbial community was extracted from the soil and exposed to a 0.85% sodium chloride solution containing OTC (0, 1, 5, 11, 43, 109 and 217 {mu}M), or Cu (0, 10, 20, 100 and 300 {mu}M), or combination of the two pollutants (OTC 0, 5, 11 {mu}M and Cu 0, 20 {mu}M). Functional diversity, evenness, average well color development (AWCD) and substrate utilization decreased significantly with increasing concentrations of OTC or Cu (p < 0.005). The critical concentrations were 11 {mu}M for OTC and 20 {mu}M for Cu. The combination of OTC and Cu significantly decreased Shannon's diversity, evenness and utilization of carbohydrates and carboxylic acids compared to individual one of the contaminants. The antibiotic OTC and Cu had significant negative effects on soil microbial community function, particularly when both pollutants were present. - Oxytetracycline reduces the functional diversity of soil microbial community, and the combination of Cu and oxytetracycline leads to a further reduction.

  10. The veterinary antibiotic oxytetracycline and Cu influence functional diversity of the soil microbial community

    International Nuclear Information System (INIS)

    Kong, W.-D.; Zhu, Y.-G.; Fu, B.-J.; Marschner, P.; He, J.-Z.

    2006-01-01

    There are increasing concerns over the effects of veterinary antibiotics and heavy metals in agricultural soils. The widely used veterinary antibiotic oxytetracycline (OTC), Cu and their combination on soil microbial community function were assessed with the Biolog method. The microbial community was extracted from the soil and exposed to a 0.85% sodium chloride solution containing OTC (0, 1, 5, 11, 43, 109 and 217 μM), or Cu (0, 10, 20, 100 and 300 μM), or combination of the two pollutants (OTC 0, 5, 11 μM and Cu 0, 20 μM). Functional diversity, evenness, average well color development (AWCD) and substrate utilization decreased significantly with increasing concentrations of OTC or Cu (p < 0.005). The critical concentrations were 11 μM for OTC and 20 μM for Cu. The combination of OTC and Cu significantly decreased Shannon's diversity, evenness and utilization of carbohydrates and carboxylic acids compared to individual one of the contaminants. The antibiotic OTC and Cu had significant negative effects on soil microbial community function, particularly when both pollutants were present. - Oxytetracycline reduces the functional diversity of soil microbial community, and the combination of Cu and oxytetracycline leads to a further reduction

  11. Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

    Science.gov (United States)

    Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

    2015-12-01

    Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

  12. Deep Subsurface Microbial Communities Shaped by the Chicxulub Impactor

    Science.gov (United States)

    Cockell, C. S.; Coolen, M.; Schaefer, B.; Grice, K.; Gulick, S. P. S.; Morgan, J. V.; Kring, D. A.; Osinski, G.

    2017-12-01

    Fresh core material was obtained by drilling of the Chicxulub impact crater during IODP-ICDP Expedition 364 to assess the present-day biosphere in the crater structure. Cell enumerations through the core show that beneath the post-impact sedimentary rock there is a region of enhanced cell abundance that corresponds to the upper impact suevite layer (Units 1G/2A). We also observed a peak in cell numbers in samples at the bottom of suevite Unit 2C and between the suevitic and grainitoid interface (Unit 3/4). These patterns may reflect preferential movement of fluid and/or availability of nutrients and energy at interfaces. 16S rDNA analysis allows us to rule out contamination of the suevite material since no taxa associated with the drilling mud were observed. Two hundred and fifty microbial enrichments were established using diverse culture media for heterotrophs, autotrophs and chemolithotrophs at temperatures consistent with measured core temperatures. Six yielded growth in the breccia, lower breccia and upper granitoid layer and they affiliated with Acidiphilium, Thermoanaerobacteracea and Desulfohalbiaceae. The latter exhibited visible microbial sulfate-reduction. By contrast, the granitoid material exhibited low cell abundances, most samples were below direct cell detection. DNA extraction revealed pervasive low level contamination by drilling mud taxa, consistent with the highly fractured, high porosity of the impact-shocked granitoids. Few taxa can be attributed to an indigenous biota and no enrichments (at 60 and 70°C) yielded growth. These data show that even with a porosity approximately an order of magnitude greater than most unshocked granites, the uplifted granites have not experienced sufficient fluid flow to establish a significant deep biosphere. Paleosterilisation of the material during impact may have re-set colonisation and the material may have originally been below the depth at which temperatures exceeded the upper temperature limit for life

  13. Bacterial community profiles in low microbial abundance sponges

    KAUST Repository

    Giles, Emily

    2012-09-04

    It has long been recognized that sponges differ in the abundance of associated microorganisms, and they are therefore termed either \\'low microbial abundance\\' (LMA) or \\'high microbial abundance\\' (HMA) sponges. Many previous studies concentrated on the dense microbial communities in HMA sponges, whereas little is known about microorganisms in LMA sponges. Here, two LMA sponges from the Red Sea, two from the Caribbean and one from the South Pacific were investigated. With up to only five bacterial phyla per sponge, all LMA sponges showed lower phylum-level diversity than typical HMA sponges. Interestingly, each LMA sponge was dominated by a large clade within either Cyanobacteria or different classes of Proteobacteria. The overall similarity of bacterial communities among LMA sponges determined by operational taxonomic unit and UniFrac analysis was low. Also the number of sponge-specific clusters, which indicate bacteria specifically associated with sponges and which are numerous in HMA sponges, was low. A biogeographical or host-dependent distribution pattern was not observed. In conclusion, bacterial community profiles of LMA sponges are clearly different from profiles of HMA sponges and, remarkably, each LMA sponge seems to harbour its own unique bacterial community. © 2012 Federation of European Microbiological Societies.

  14. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

    Science.gov (United States)

    Fierer, Noah; Lauber, Christian L; Ramirez, Kelly S; Zaneveld, Jesse; Bradford, Mark A; Knight, Rob

    2012-05-01

    Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.

  15. Impact of treated wastewater for irrigation on soil microbial communities.

    Science.gov (United States)

    Ibekwe, A M; Gonzalez-Rubio, A; Suarez, D L

    2018-05-01

    The use of treated wastewater (TWW) for irrigation has been suggested as an alternative to use of fresh water because of the increasing scarcity of fresh water in arid and semiarid regions of the world. However, significant barriers exist to widespread adoption due to some potential contaminants that may have adverse effects on soil quality and or public health. In this study, we investigated the abundance and diversity of bacterial communities and the presence of potential pathogenic bacterial sequences in TWW in comparison to synthetic fresh water (SFW) using pyrosequencing. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity and abundance of different bacterial groups in TWW irrigated soils to soils treated with SFW. Shannon diversity index values (H') suggest that microbial diversity was not significantly different (P<0.086) between soils with TWW and SFW. Pyrosequencing detected sequences of 17 bacterial phyla with Proteobacteria (32.1%) followed by Firmicutes (26.5%) and Actinobacteria (14.3%). Most of the sequences associated with nitrifying bacteria, nitrogen-fixing bacteria, carbon degraders, denitrifying bacteria, potential pathogens, and fecal indicator bacteria were more abundant in TWW than in SFW. Therefore, TWW effluent may contain bacterial that may be very active in many soil functions as well as some potential pathogens. Published by Elsevier B.V.

  16. Microbial Community Structure of Casing Soil During Mushroom Growth

    Institute of Scientific and Technical Information of China (English)

    CAI Wei-Ming; YAO Huai-Ying; FENG Wei-Lin; JIN Qun-Li; LIU Yue-Yan; LI Nan-Yi; ZHENG Zhong

    2009-01-01

    The culturable bacterial population and phospholipid fatty acid (PLFA)profile of casing soil were investigated at different mushroom (Agaricus bisporusI cropping stages.The change in soil bacterial PLFAs was always accompanied by a change in the soil culturable bacterial population in the first flush.Comparatively higher culturable bacterial population and bacterial PLFAs were found in the casing soil at the primordia formation stage of the first flush.There was a significant increase in the ratio of fungal to bacterial PLFAs during mushroom growth.Multivariate analysis of PLFA data demonstrated that the mushroom cropping stage could considerably affect the microbial community structure of the casing soil.The bacterial population increased significantly from casing soil application to the primordia formation stage of the first flush.Casing soil application resulted in an increase in the ratio of gram-negative bacterial PLFAs to gram-positive bacterial PLFAs,suggesting that some gram-negative bacteria might play an important role in mushroom sporophore initiation.

  17. From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

    Science.gov (United States)

    Li, Xiaofang; Bond, Philip L.; Van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

    2015-01-01

    Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

  18. Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China.

    Science.gov (United States)

    Briggs, Brandon R; Brodie, Eoin L; Tom, Lauren M; Dong, Hailiang; Jiang, Hongchen; Huang, Qiuyuan; Wang, Shang; Hou, Weiguo; Wu, Geng; Huang, Liuquin; Hedlund, Brian P; Zhang, Chuanlun; Dijkstra, Paul; Hungate, Bruce A

    2014-06-01

    Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

    Energy Technology Data Exchange (ETDEWEB)

    Firestone, Mary [Univ. of California, Berkeley, CA (United States)

    2015-03-31

    It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbon decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.

  20. Comparison of the active and resident community of a coastal microbial mat

    OpenAIRE

    Cardoso, Daniela Clara; Sandionigi, Anna; Cretoiu, Mariana Silvia; Casiraghi, Maurizio; Stal, Lucas; Bolhuis, Henk

    2017-01-01

    Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fractio...

  1. Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

    OpenAIRE

    Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

    2012-01-01

    Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysi...

  2. Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau.

    Science.gov (United States)

    Guo, Guangxia; Kong, Weidong; Liu, Jinbo; Zhao, Jingxue; Du, Haodong; Zhang, Xianzhou; Xia, Pinhua

    2015-10-01

    Soil microbial autotrophs play a significant role in CO2 fixation in terrestrial ecosystem, particularly in vegetation-constrained ecosystems with environmental stresses, such as the Tibetan Plateau characterized by low temperature and high UV. However, soil microbial autotrophic communities and their driving factors remain less appreciated. We investigated the structure and shift of microbial autotrophic communities and their driving factors along an elevation gradient (4400-5100 m above sea level) in alpine grassland soils on the Tibetan Plateau. The autotrophic microbial communities were characterized by quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning/sequencing of cbbL genes, encoding the large subunit for the CO2 fixation protein ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). High cbbL gene abundance and high RubisCO enzyme activity were observed and both significantly increased with increasing elevations. Path analysis identified that soil RubisCO enzyme causally originated from microbial autotrophs, and its activity was indirectly driven by soil water content, temperature, and NH4 (+) content. Soil autotrophic microbial community structure dramatically shifted along the elevation and was jointly driven by soil temperature, water content, nutrients, and plant types. The autotrophic microbial communities were dominated by bacterial autotrophs, which were affiliated with Rhizobiales, Burkholderiales, and Actinomycetales. These autotrophs have been well documented to degrade organic matters; thus, metabolic versatility could be a key strategy for microbial autotrophs to survive in the harsh environments. Our results demonstrated high abundance of microbial autotrophs and high CO2 fixation potential in alpine grassland soils and provided a novel model to identify dominant drivers of soil microbial communities and their ecological functions.

  3. Temporal Microbial Community Dynamics in Microbial Electrolysis Cells – Influence of Acetate and Propionate Concentration

    KAUST Repository

    Rao, Hari Ananda

    2017-07-20

    Microbial electrolysis cells (MECs) are widely considered as a next generation wastewater treatment system. However, fundamental insight on the temporal dynamics of microbial communities associated with MEC performance under different organic types with varied loading concentrations is still unknown, nevertheless this knowledge is essential for optimizing this technology for real-scale applications. Here, the temporal dynamics of anodic microbial communities associated with MEC performance was examined at low (0.5 g COD/L) and high (4 g COD/L) concentrations of acetate or propionate, which are important intermediates of fermentation of municipal wastewaters and sludge. The results showed that acetate-fed reactors exhibited higher performance in terms of maximum current density (I: 4.25 ± 0.23 A/m), coulombic efficiency (CE: 95 ± 8%), and substrate degradation rate (98.8 ± 1.2%) than propionate-fed reactors (I: 2.7 ± 0.28 A/m; CE: 68 ± 9.5%; substrate degradation rate: 84 ± 13%) irrespective of the concentrations tested. Despite of the repeated sampling of the anodic biofilm over time, the high-concentration reactors demonstrated lower and stable performance in terms of current density (I: 1.1 ± 0.14 to 4.2 ± 0.21 A/m), coulombic efficiency (CE: 44 ± 4.1 to 103 ± 7.2%) and substrate degradation rate (64.9 ± 6.3 to 99.7 ± 0.5%), while the low-concentration reactors produced higher and dynamic performance (I: 1.1 ± 0.12 to 4.6 ± 0.1 A/m; CE: 52 ± 2.5 to 105 ± 2.7%; substrate degradation rate: 87.2 ± 0.2 to 99.9 ± 0.06%) with the different substrates tested. Correlating reactor\\'s performance with temporal dynamics of microbial communities showed that relatively similar anodic microbial community composition but with varying relative abundances was observed in all the reactors despite differences in the substrate and concentrations tested. Particularly, Geobacter was the predominant bacteria on the anode biofilm of all MECs over time suggesting its

  4. The skin microbiome: Associations between altered microbial communities and disease.

    Science.gov (United States)

    Weyrich, Laura S; Dixit, Shreya; Farrer, Andrew G; Cooper, Alan J; Cooper, Alan J

    2015-11-01

    A single square centimetre of the human skin can contain up to one billion microorganisms. These diverse communities of bacteria, fungi, mites and viruses can provide protection against disease, but can also exacerbate skin lesions, promote disease and delay wound healing. This review addresses the current knowledge surrounding the healthy skin microbiome and examines how different alterations to the skin microbial communities can contribute to disease. Current methodologies are considered, changes in microbial diversity and colonisation by specific microorganisms are discussed in the context of atopic dermatitis, psoriasis, acne vulgaris and chronic wounds. The recent impact of modern Westernised lifestyles on the human skin microbiome is also examined, as well as the potential benefits and pitfalls of novel therapeutic strategies. Further analysis of the human skin microbiome, and its interactions with the host immune system and other commensal microorganisms, will undoubtedly elucidate molecular mechanisms for disease and reveal gateways for novel therapeutic treatment strategies. © 2015 The Australasian College of Dermatologists.

  5. Effects of uranium concentration on microbial community structure and functional potential.

    Science.gov (United States)

    Sutcliffe, Brodie; Chariton, Anthony A; Harford, Andrew J; Hose, Grant C; Greenfield, Paul; Elbourne, Liam D H; Oytam, Yalchin; Stephenson, Sarah; Midgley, David J; Paulsen, Ian T

    2017-08-01

    Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg -1 ), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg -1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg -1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Structural and metabolic responses of microbial community to sewage-borne chlorpyrifos in constructed wetlands.

    Science.gov (United States)

    Zhang, Dan; Wang, Chuan; Zhang, Liping; Xu, Dong; Liu, Biyun; Zhou, Qiaohong; Wu, Zhenbin

    2016-06-01

    Long-term use of chlorpyrifos poses a potential threat to the environment that cannot be ignored, yet little is known about the succession of substrate microbial communities in constructed wetlands (CWs) under chlorpyrifos stress. Six pilot-scale CW systems receiving artificial wastewater containing 1mg/L chlorpyrifos were established to investigate the effects of chlorpyrifos and wetland vegetation on the microbial metabolism pattern of carbon sources and community structure, using BIOLOG and denaturing gradient gel electrophoresis (DGGE) approaches. Based on our samples, BIOLOG showed that Shannon diversity (H') and richness (S) values distinctly increased after 30days when chlorpyrifos was added. At the same time, differences between the vegetated and the non-vegetated systems disappeared. DGGE profiles indicated that H' and S had no significant differences among four different treatments. The effect of chlorpyrifos on the microbial community was mainly reflected at the physiological level. Principal component analysis (PCA) of both BIOLOG and DGGE showed that added chlorpyrifos made a difference on test results. Meanwhile, there was no difference between the vegetation and no-vegetation treatments after addition of chlorpyrifos at the physiological level. Moreover, the vegetation had no significant effect on the microbial community at the genetic level. Comparisons were made between bacteria in this experiment and other known chlorpyrifos-degrading bacteria. The potential chlorpyrifos-degrading ability of bacteria in situ may be considerable. Copyright © 2016. Published by Elsevier B.V.

  7. Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment.

    Science.gov (United States)

    Bai, Yaohui; Huo, Yang; Liao, Kailingli; Qu, Jiuhui

    2017-10-01

    Traditional wastewater treatments based on activated sludge often encounter the problems of bulking and foaming, as well as malodor. To solve these problems, new treatment technologies have emerged in recent decades, including the ecological wastewater treatment process, which introduces selected local plants into the treatment system. With a focus on the underlying mechanisms of the ecological treatment process, we explored the microbial community biomass, composition, and function in the treatment system to understand the microbial growth in this system and its role in pollutant removal. Flow cytometry analysis revealed that ecological treatment significantly decreased influent bacterial quantity, with around 80% removal. 16S rRNA gene sequencing showed that the ecological treatment also altered the bacterial community structure of the wastewater, leading to a significant change in Comamonadaceae in the effluent. In the internal ecological system, because most of microbes aggregate in the plant rhizosphere and the sludge under plant roots, we selected two plant species (Nerium oleander and Arundo donax) to study the characteristics of rhizosphere and sludge microbes. Metagenomic results showed that the microbial community composition and function differed between the two species, and the microbial communities of A. donax were more sensitive to seasonal effects. Combined with their greater biomass and abundance of metabolic genes, microbes associated with N. oleander showed a greater contribution to pollutant removal. Further, the biodegradation pathways of some micropollutants, e.g., atrazine, were estimated.

  8. Functional characteristics and influence factors of microbial community in sewage sludge composting with inorganic bulking agent.

    Science.gov (United States)

    Wang, Ke; Mao, Hailong; Li, Xiangkun

    2018-02-01

    The metabolic function of microbial community dominated organics and nutrients transformation in aerobic composting process. In this study, the metabolic characteristics of bacterial and fungal communities were evaluated in 60 days composting of sludge and pumice by using FUNGuild and PICRUSt, respectively. The results showed that microbial community structure and metabolic characteristics were distinctively different at four composting periods. Bacterial genes related to carbohydrate metabolisms decreased during the first 30 days, but bacterial sequences associated with oxidative phosphorylation and fatty acids synthesis were enhanced in curing phase. Most of fungal animal pathogen and plant pathogen disappeared after treatment, and the abundance of saprotroph fungi increased from 44.3% to 97.8%. Oxidation reduction potential (ORP) significantly increased from -28 to 175 mV through incubation. RDA analysis showed that ORP was a crucial factor on the succession of both bacterial and fungal communities in sludge composting system. Copyright © 2017. Published by Elsevier Ltd.

  9. Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

    Directory of Open Access Journals (Sweden)

    Nam-Il Won

    2017-01-01

    Full Text Available The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA. However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene, we analyzed and compared seawater and sediment communities between sand mining and control (natural sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.

  10. Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

    Science.gov (United States)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  12. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  13. Soil microbial community responses to acid exposure and neutralization treatment.

    Science.gov (United States)

    Shin, Doyun; Lee, Yunho; Park, Jeonghyun; Moon, Hee Sun; Hyun, Sung Pil

    2017-12-15

    Changes in microbial community induced by acid shock were studied in the context of potential release of acids to the environment due to chemical accidents. The responses of microbial communities in three different soils to the exposure to sulfuric or hydrofluoric acid and to the subsequent neutralization treatment were investigated as functions of acid concentration and exposure time by using 16S-rRNA gene based pyrosequencing and DGGE (Denaturing Gradient Gel Electrophoresis). Measurements of soil pH and dissolved ion concentrations revealed that the added acids were neutralized to different degrees, depending on the mineral composition and soil texture. Hydrofluoric acid was more effectively neutralized by the soils, compared with sulfuric acid at the same normality. Gram-negative ß-Proteobacteria were shown to be the most acid-sensitive bacterial strains, while spore-forming Gram-positive Bacilli were the most acid-tolerant. The results of this study suggest that the Gram-positive to Gram-negative bacterial ratio may serve as an effective bio-indicator in assessing the impact of the acid shock on the microbial community. Neutralization treatments helped recover the ratio closer to their original values. The findings of this study show that microbial community changes as well as geochemical changes such as pH and dissolved ion concentrations need to be considered in estimating the impact of an acid spill, in selecting an optimal remediation strategy, and in deciding when to end remedial actions at the acid spill impacted site. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Bacteria and archaea communities in full-scale thermophilic and mesophilic anaerobic digesters treating food wastewater: Key process parameters and microbial indicators of process instability.

    Science.gov (United States)

    Lee, Joonyeob; Shin, Seung Gu; Han, Gyuseong; Koo, Taewoan; Hwang, Seokhwan

    2017-12-01

    In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M. thermophilus, and Methanobacterium beijingense were revealed as dominant methanogens. Bacterial community structures were clearly differentiated by digesters; archaeal community structures of each digester were dominated by one or two methanogen species. Temperature, ammonia, propionate, Na + , and acetate in the digester were significant factors shaping microbial community structures. The total microbial populations, microbial diversity, and specific bacteria genera showed potential as indicators of process instability in the anaerobic digestion of FWW. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils

    Science.gov (United States)

    Romdhane, Sana; Devers-Lamrani, Marion; Barthelmebs, Lise; Calvayrac, Christophe; Bertrand, Cédric; Cooper, Jean-François; Dayan, Franck E.; Martin-Laurent, Fabrice

    2016-01-01

    The ecotoxicological impact of leptospermone, a β-triketone bioherbicide, on the bacterial community of two arable soils was investigated. Soil microcosms were exposed to 0 × (control), 1 × or 10 × recommended dose of leptospermone. The β-triketone was moderately adsorbed to both soils (i.e.,: Kfa ~ 1.2 and Koc ~ 140 mL g−1). Its dissipation was lower in sterilized than in unsterilized soils suggesting that it was mainly influenced by biotic factors. Within 45 days, leptospermone disappeared almost entirely from one of the two soils (i.e., DT50 < 10 days), while 25% remained in the other. The composition of the microbial community assessed by qPCR targeting 11 microbial groups was found to be significantly modified in soil microcosms exposed to leptospermone. Pyrosequencing of 16S rRNA gene amplicons showed a shift in the bacterial community structure and a significant impact of leptospermone on the diversity of the soil bacterial community. Changes in the composition, and in the α- and β-diversity of microbial community were transient in the soil able to fully dissipate the leptospermone, but were persistent in the soil where β-triketone remained. To conclude the bacterial community of the two soils was sensitive to leptospermone and its resilience was observed only when leptospermone was fully dissipated. PMID:27252691

  16. Degradation and impact of phthalate plasticizers on soil microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Cartwright, C.D.; Thompson, I.P.; Burns, R.G.

    2000-05-01

    To assess the impact of phthalates on soil microorganisms and to supplement the environmental risk assessment for these xenobiotics, soil was treated with diethyl phthalate (DEP) or di (2-ethyl hexyl) phthalate (DEHP) at 0.1 to 100 mg/g. Bioavailability and membrane disruption were proposed as the characteristics responsible for the observed fate and toxicity of both compounds. Diethyl phthalate was biodegraded rapidly in soil with a half-life of 0.75 d at 20 C, and was not expected to persist in the environment. The DEHP, although biodegradable in aqueous solution, was recalcitrant in soil, because of poor bioavailability and was predicted to account for the majority of phthalate contamination in the environment. Addition of DEP or DEHP to soil at a concentration similar to that detected in nonindustrial environments had no impact on the structural diversity or functional diversity (BIOLOG) of the microbial community. At concentrations representative of a phthalate spill, DEP reduced numbers of both total culturable bacteria and pseudomonads within 1 d. This was due to disruption of membrane fluidity by the lipophilic phthalate, a mechanism not previously attributed to phthalates. However, DEHP had no effect on the microbial community or membrane fluidity, even at 100 mg/g, and was predicted to have no impact on microbial communities in the environment.

  17. Survival of a microbial soil community under Martian conditions

    Science.gov (United States)

    Hansen, A. A.; Noernberg, P.; Merrison, J.; Lomstein, B. Aa.; Finster, K. W.

    2003-04-01

    Because of the similarities between Earth and Mars early history the hypothesis was forwarded that Mars is a site where extraterrestrial life might have and/or may still occur(red). Sample-return missions are planned by NASA and ESA to test this hypothesis. The enormous economic costs and the logistic challenges of these missions make earth-based model facilities inevitable. The Mars simulation system at University of Aarhus, Denmark allows microbiological experiments under Mars analogue conditions. Thus detailed studies on the effect of Mars environmental conditions on the survival and the activity of a natural microbial soil community were carried out. Changes in the soil community were determined with a suite of different approaches: 1) total microbial respiration activity was investigated with 14C-glucose, 2) the physiological profile was investigated by the EcoLog-system, 3) colony forming units were determined by plate counts and 4) the microbial diversity on the molecular level was accessed with Denaturing Gradient Gel Electrophoresis. The simulation experiments showed that a part of the bacterial community survived Martian conditions corresponding to 9 Sol. These and future simulation experiments will contribute to our understanding of the possibility for extraterrestrial and terrestrial life on Mars.

  18. Lineage-specific responses of microbial communities to environmental change.

    Science.gov (United States)

    Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

    2013-01-01

    A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-03-15

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

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

    International Nuclear Information System (INIS)

    Xiao Shengmu; Xie Xuehui; Liu Jianshe

    2009-01-01

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

  1. Effects of forest conversion on soil microbial communities depend on soil layer on the eastern Tibetan Plateau of China.

    Directory of Open Access Journals (Sweden)

    Ruoyang He

    Full Text Available Forest land-use changes have long been suggested to profoundly affect soil microbial communities. However, how forest type conversion influences soil microbial properties remains unclear in Tibetan boreal forests. The aim of this study was to explore variations of soil microbial profiles in the surface organic layer and subsurface mineral soil among three contrasting forests (natural coniferous forest, NF; secondary birch forest, SF and spruce plantation, PT. Soil microbial biomass, activity and community structure of the two layers were investigated by chloroform fumigation, substrate respiration and phospholipid fatty acid analysis (PLFA, respectively. In the organic layer, both NF and SF exhibited higher soil nutrient levels (carbon, nitrogen and phosphorus, microbial biomass carbon and nitrogen, microbial respiration, PLFA contents as compared to PT. However, the measured parameters in the mineral soils often did not differ following forest type conversion. Irrespective of forest types, the microbial indexes generally were greater in the organic layer than in the mineral soil. PLFAs biomarkers were significantly correlated with soil substrate pools. Taken together, forest land-use change remarkably altered microbial community in the organic layer but often did not affect them in the mineral soil. The microbial responses to forest land-use change depend on soil layer, with organic horizons being more sensitive to forest conversion.

  2. Control of Clostridium difficile infection by defined microbial communities

    Science.gov (United States)

    Collins, James

    2017-01-01

    Summary Each year in the United States, billions of dollars are spent combating almost half a million Clostridium difficile infections (CDI) and trying to reduce the ~29,000 patient deaths where C. difficile has an attributed role (1). In Europe, disease prevalence varies by country and level of surveillance, though yearly costs are estimated at €3 billion (2). One factor contributing to the significant healthcare burden of C. difficile is the relatively high frequency of recurrent C. difficile infections(3). Recurrent C. difficile infection (rCDI), i.e., a second episode of symptomatic CDI occurring within eight weeks of successful initial CDI treatment, occurs in ~25% of patients with 35-65% of these patients experiencing multiple episodes of recurrent disease(4, 5). Using microbial communities to treat rCDI, either as whole fecal transplants or as defined consortia of bacterial isolates have shown great success (in the case of fecal transplants) or potential promise (in the case of defined consortia of isolates). This review will briefly summarize the epidemiology and physiology of C. difficile infection, describe our current understanding of how fecal microbiota transplants treat recurrent CDI, and outline potential ways through which that knowledge can be used to rationally-design and test alternative microbe-based therapeutics. PMID:28936948

  3. Common Hydraulic Fracturing Fluid Additives Alter the Structure and Function of Anaerobic Microbial Communities.

    Science.gov (United States)

    Mumford, Adam C; Akob, Denise M; Klinges, J Grace; Cozzarelli, Isabelle M

    2018-04-15

    The development of unconventional oil and gas (UOG) resources results in the production of large volumes of wastewater containing a complex mixture of hydraulic fracturing chemical additives and components from the formation. The release of these wastewaters into the environment poses potential risks that are poorly understood. Microbial communities in stream sediments form the base of the food chain and may serve as sentinels for changes in stream health. Iron-reducing organisms have been shown to play a role in the biodegradation of a wide range of organic compounds, and so to evaluate their response to UOG wastewater, we enriched anaerobic microbial communities from sediments collected upstream (background) and downstream (impacted) of an UOG wastewater injection disposal facility in the presence of hydraulic fracturing fluid (HFF) additives: guar gum, ethylene glycol, and two biocides, 2,2-dibromo-3-nitrilopropionamide (DBNPA) and bronopol (C 3 H 6 BrNO 4 ). Iron reduction was significantly inhibited early in the incubations with the addition of biocides, whereas amendment with guar gum and ethylene glycol stimulated iron reduction relative to levels in the unamended controls. Changes in the microbial community structure were observed across all treatments, indicating the potential for even small amounts of UOG wastewater components to influence natural microbial processes. The microbial community structure differed between enrichments with background and impacted sediments, suggesting that impacted sediments may have been preconditioned by exposure to wastewater. These experiments demonstrated the potential for biocides to significantly decrease iron reduction rates immediately following a spill and demonstrated how microbial communities previously exposed to UOG wastewater may be more resilient to additional spills. IMPORTANCE Organic components of UOG wastewater can alter microbial communities and biogeochemical processes, which could alter the rates of

  4. Electricity generation and microbial community analysis of alcohol powered microbial fuel cells.

    Science.gov (United States)

    Kim, Jung Rae; Jung, Sok Hee; Regan, John M; Logan, Bruce E

    2007-09-01

    Two different microbial fuel cell (MFC) configurations were investigated for electricity production from ethanol and methanol: a two-chambered, aqueous-cathode MFC; and a single-chamber direct-air cathode MFC. Electricity was generated in the two-chamber system at a maximum power density typical of this system (40+/-2 mW/m2) and a Coulombic efficiency (CE) ranging from 42% to 61% using ethanol. When bacteria were transferred into a single-chamber MFC known to produce higher power densities with different substrates, the maximum power density increased to 488+/-12 mW/m2 (CE = 10%) with ethanol. The voltage generated exhibited saturation kinetics as a function of ethanol concentration in the two-chambered MFC, with a half-saturation constant (Ks) of 4.86 mM. Methanol was also examined as a possible substrate, but it did not result in appreciable electricity generation. Analysis of the anode biofilm and suspension from a two-chamber MFC with ethanol using 16S rDNA-based techniques indicated that bacteria with sequences similar to Proteobacterium Core-1 (33.3% of clone library sequences), Azoarcus sp. (17.4%), and Desulfuromonas sp. M76 (15.9%) were significant members of the anode chamber community. These results indicate that ethanol can be used for sustained electricity generation at room temperature using bacteria on the anode in a MFC.

  5. Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

    Science.gov (United States)

    Kim, M.; Gyeong, H. R.; Lee, Y. K.

    2017-12-01

    Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

  6. Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard

    Directory of Open Access Journals (Sweden)

    P. Kotas

    2018-03-01

    Full Text Available The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS, and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs. We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects, mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.

  7. Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)

    Science.gov (United States)

    Kotas, Petr; Šantrůčková, Hana; Elster, Josef; Kaštovská, Eva

    2018-03-01

    The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS), and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level) were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs). We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects), mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.

  8. Seasonal variations of microbial community in a full scale oil field produced water treatment plant

    Directory of Open Access Journals (Sweden)

    Q. Xie

    2016-01-01

    Full Text Available This study investigated the microbial community in a full scale anaerobic baffled reactor and sequencing batch reactor system for oil-produced water treatment in summer and winter. The community structures of fungi and bacteria were analyzed through polymerase chain reaction–denaturing gradient gel electrophoresis and Illumina high-throughput sequencing, respectively. Chemical oxygen demand effluent concentration achieved lower than 50 mg/L level after the system in both summer and winter, however, chemical oxygen demand removal rates after anaerobic baffled reactor treatment system were significant higher in summer than that in winter, which conformed to the microbial community diversity. Saccharomycotina, Fusarium, and Aspergillus were detected in both anaerobic baffled reactor and sequencing batch reactor during summer and winter. The fungal communities in anaerobic baffled reactor and sequencing batch reactor were shaped by seasons and treatment units, while there was no correlation between abundance of fungi and chemical oxygen demand removal rates. Compared to summer, the total amount of the dominant hydrocarbon degrading bacteria decreased by 10.2% in anaerobic baffled reactor, resulting in only around 23% of chemical oxygen demand was removed in winter. Although microbial community significantly varied in the three parallel sulfide reducing bacteria, the performance of these bioreactors had no significant difference between summer and winter.

  9. Seasonal variations of microbial community in a full scale oil field produced water treatment plant

    International Nuclear Information System (INIS)

    Xie, Q.; Bai, S.; Li, Y.; Liu, L.; Wang, S.; Xi, J.

    2016-01-01

    This study investigated the microbial community in a full scale anaerobic baffled reactor and sequencing batch reactor system for oil-produced water treatment in summer and winter. The community structures of fungi and bacteria were analyzed through polymerase chain reaction–denaturing gradient gel electrophoresis and Illumina high throughput sequencing, respectively. Chemical oxygen demand effluent concentration achieved lower than 50 mg/L level after the system in both summer and winter, however, chemical oxygen demand removal rates after anaerobic baffled reactor treatment system were significant higher in summer than that in winter, which conformed to the microbial community diversity. Saccharomycotina, Fusarium, and Aspergillus were detected in both anaerobic baffled reactor and sequencing batch reactor during summer and winter. The fungal communities in anaerobic baffled reactor and sequencing batch reactor were shaped by seasons and treatment units, while there was no correlation between abundance of fungi and chemical oxygen demand removal rates. Compared to summer, the total amount of the dominant hydrocarbon degrading bacteria decreased by 10.2% in anaerobic baffled reactor, resulting in only around 23% of chemical oxygen demand was removed in winter. Although microbial community significantly varied in the three parallel sulfide reducing bacteria, the performance of these bioreactors had no significant difference between summer and winter.

  10. Dynamics in microbial communities: Unraveling mechanisms to identify principles

    Energy Technology Data Exchange (ETDEWEB)

    Konopka, Allan; Lindemann, Stephen R.; Fredrickson, Jim K.

    2015-07-01

    Diversity begets higher order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions, and it is this “system” that is the basis for higher order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

  11. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories

    DEFF Research Database (Denmark)

    Wigneswaran, Vinoth; Amador Hierro, Cristina Isabel; Jelsbak, Lotte

    2016-01-01

    Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial co...

  12. Bioinformatics for whole-genome shotgun sequencing of microbial communities.

    Directory of Open Access Journals (Sweden)

    Kevin Chen

    2005-07-01

    Full Text Available The application of whole-genome shotgun sequencing to microbial communities represents a major development in metagenomics, the study of uncultured microbes via the tools of modern genomic analysis. In the past year, whole-genome shotgun sequencing projects of prokaryotic communities from an acid mine biofilm, the Sargasso Sea, Minnesota farm soil, three deep-sea whale falls, and deep-sea sediments have been reported, adding to previously published work on viral communities from marine and fecal samples. The interpretation of this new kind of data poses a wide variety of exciting and difficult bioinformatics problems. The aim of this review is to introduce the bioinformatics community to this emerging field by surveying existing techniques and promising new approaches for several of the most interesting of these computational problems.

  13. Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought.

    Science.gov (United States)

    Mark Ibekwe, A; Ors, Selda; Ferreira, Jorge F S; Liu, Xuan; Suarez, Donald L

    2017-02-01

    Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects of irrigation-induced salinity on soil chemical and physical properties and plant growth are well documented. In this study, we examined the effects of salinity, temperature, and temporal variability on soil and rhizosphere microbial communities in sand tanks irrigated with prepared solutions designed to simulate saline wastewater. Three sets of experiments with spinach (Spinacia oleracea L., cv. Racoon) were conducted under saline water during different time periods (early winter, late spring, and early summer). Bacterial 16S V4 rDNA region was amplified utilizing fusion primers designed against the surrounding conserved regions using MiSeq® Illumina sequencing platform. Across the two sample types, bacteria were relatively dominant among three phyla-the Proteobacteria, Cyanobacteria, and Bacteroidetes-accounted for 77.1% of taxa detected in the rhizosphere, while Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific bacterial groups in soil and rhizosphere samples. Permutational analysis of variance (PERMANOVA) analysis showed that soil temperature (P=0.001), rhizosphere temperature (P=0.001), rhizosphere salinity (P=0.032), and evapotranspiration (P=0.002) significantly affected beta diversity of soil and rhizosphere microbial communities. Furthermore, salinity had marginal effects (P=0.078) on soil beta diversity. However, temporal variability differentially affected rhizosphere microbial communities irrigated with saline wastewater. Therefore, microbial communities in

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

    Science.gov (United States)

    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 (pbased 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 alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

  15. Effects of Misgurnus anguillicaudatus and Cipangopaludina cathayensis on Pollutant Removal and Microbial Community in Constructed Wetlands

    Directory of Open Access Journals (Sweden)

    Pengfei Li

    2015-05-01

    Full Text Available Aquatic animals play an important role in the energy flow and matter cycling in the wetland ecosystem. However, little is known about their effects on pollutant removal performance and microbial community in constructed wetlands. This work presents an initial attempt to investigate the effects of Misgurnus anguillicaudatus (loach and Cipangopaludina cathayensis (snail on nutrient removal performance and microbial community of constructed wetlands (CWs. Compared with a control group, CW microcosms with aquatic animals exhibited better pollutant removal performance. The removal efficiencies of total phosphorus (TP in the loach group were 13.1% higher than in the control group, and snails increased the ammonium removal most effectively. Moreover, the concentration of total organic carbon (TOC and TP in sediment significantly reduced with the addition of loaches and snails (p < 0.05, whereas the concentration of total nitrogen (TN showed an obvious increase with the addition of loaches. High-throughput sequencing showed a microbial community structure change. Loaches and snails in wetlands changed the microbial diversity, especially in the Proteobacteria and denitrifying community. Results suggested that benthic aquatic animals might play an important role in CW ecosystems.

  16. Seasonal Changes in Microbial Community Structure in Freshwater Stream Sediment in a North Carolina River Basin

    Directory of Open Access Journals (Sweden)

    John P. Bucci

    2014-01-01

    Full Text Available This study examined seasonal differences in microbial community structure in the sediment of three streams in North Carolina’s Neuse River Basin. Microbes that reside in sediment are at the base of the food chain and have a profound influence on the health of freshwater stream environments. Terminal-Restriction Fragment Length Polymorphism (T-RFLP, molecular fingerprint analysis of 16S rRNA genes was used to examine the diversity of bacterial species in stream sediment. Sediment was sampled in both wet and dry seasons from an agricultural (Bear, mixed urban (Crabtree and forested (Marks Creek, and the microbiota examined. Gamma, Alpha and Beta proteobacteria were prevalent species of microbial taxa represented among all sites. Actinobacteria was the next most prevalent species observed, with greater occurrence in dry compared to the wet season. Discernable clustering was observed of Marks and Bear Creek samples collected during the wetter period (September–April, which corresponded with a period of higher precipitation and cooler surface water temperatures. Although not statistically significant, microbial community structure appeared different between season (ANOSIM, R = 0.60; p < 0.10. Principal components analysis confirmed this pattern and showed that the bacterial groups were separated by wet and dry seasonal periods. These results suggest seasonal differences among the microbial community structure in sediment of freshwater streams and that these communities may respond to changes in precipitation during wetter periods.

  17. [Microbial Community Structure on the Root Surface of Patients with Periodontitis.

    Science.gov (United States)

    Zhang, Ju-Mei; Zhou, Jian-Ye; Bo, Lei; Hu, Xiao-Pan; Jiao, Kang-Li; Li, Zhi-Jie; Li, Yue-Hong; Li, Zhi-Qiang

    2016-11-01

    To study the microbial community structure on the root surface of patients with periodontitis. Bacterial plaque and tissues from the root neck (RN group),root middle (RM group) and root tine (RT group) of six teeth with mobility 3 in one patient with periodontitis were sampled.The V3V4 region of 16S rRNA was sequenced on the Illumina MiSeq platform.The microbial community structure was analyzed by Mothur,Qiime and SPSS software. The principal component analysis (PCoA) results indicated that the RM samples had a similar microbial community structure as that of the RT samples,which was significant different from that of the RN samples.Thirteen phyla were detected in the three groups of samples,which included 7 dominant phyla.29 dominant genera were detected in 184 genera.The abundance of Bacteroidetes _[G-6] and Peptostre ptococcaceae _[XI][G-4] had a positive correlation with the depth of the collection site of samples ( P microbial community structure on the root surface of patients with periodontitis.

  18. Growth and element flux at fine taxonomic resolution in natural microbial communities

    Science.gov (United States)

    Hungate, Bruce; Mau, Rebecca; Schwartz, Egbert; Caporaso, J. Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J.; Liu, Cindy M.; McHugh, Theresa; Marks, Jane C.; Morrissey, Ember; Price, Lance B.

    2015-04-01

    Microorganisms are the engines of global biogeochemical cycles, driving half of all photosynthesis and nearly all decomposition. Yet, quantifying the rates at which uncultured microbial taxa grow and transform elements in intact and highly diverse natural communities in the environment remains among the most pressing challenges in microbial ecology today. Here, we show how shifts in the density of DNA caused by stable isotope incorporation can be used to estimate the growth rates of individual bacterial taxa in intact soil communities. We found that the distribution of growth rates followed the familiar lognormal distribution observed for the abundances, biomasses, and traits of many organisms. Growth rates of most bacterial taxa increased in response to glucose amendment, though the increase in growth observed for many taxa was larger than could be explained by direct utilization of the added glucose for growth, illustrating that glucose addition indirectly stimulated the utilization of other substrates. Variation in growth rates and phylogenetic distances were quantitatively related, connecting evolutionary history and biogeochemical function in intact soil microbial communities. Our approach has the potential to identify biogeochemically significant taxa in the microbial community and quantify their contributions to element transformations and ecosystem processes.

  19. Long-Term Effects of Multiwalled Carbon Nanotubes and Graphene on Microbial Communities in Dry Soil.

    Science.gov (United States)

    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 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.

  20. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon

    Directory of Open Access Journals (Sweden)

    Wei Hui Xu

    2015-09-01

    Full Text Available The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN and microbial biomass phosphorus (MBP were significantly increased, and the ratio of MBC/MBN was decreased (P<0.05. Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P<0.05. The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.

  1. Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

    KAUST Repository

    Li, D.

    2012-07-13

    This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

  2. Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

    KAUST Repository

    Li, D.; Sharp, J. O.; Saikaly, Pascal; Ali, Shahjahan; Alidina, M.; Alarawi, M. S.; Keller, S.; Hoppe-Jones, C.; Drewes, J. E.

    2012-01-01

    This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

  3. Quantitative comparison of the in situ microbial communities in different biomes

    Energy Technology Data Exchange (ETDEWEB)

    White, D.C. [Tennessee Univ., Knoxville, TN (United States)]|[Oak Ridge National Lab., TN (United States); Ringelberg, D.B.; Palmer, R.J. [Tennessee Univ., Knoxville, TN (United States). Center for Environmental Biotechnology

    1995-12-31

    A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedly documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography/

  4. Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems.

    Science.gov (United States)

    Li, Dong; Sharp, Jonathan O; Saikaly, Pascal E; Ali, Shahjahan; Alidina, Mazahirali; Alarawi, Mohammed S; Keller, Stephanie; Hoppe-Jones, Christiane; Drewes, Jörg E

    2012-10-01

    This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

  5. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2017-06-01

    Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

  6. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

    Directory of Open Access Journals (Sweden)

    Gemma Henderson

    Full Text Available Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However

  7. Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

    Directory of Open Access Journals (Sweden)

    Chris L Dupont

    Full Text Available Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

  8. Microbial community dynamics in the rhizosphere of a cadmium hyper-accumulator

    Science.gov (United States)

    Wood, J. L.; Zhang, C.; Mathews, E. R.; Tang, C.; Franks, A. E.

    2016-11-01

    Phytoextraction is influenced by the indigenous soil microbial communities during the remediation of heavy metal contaminated soils. Soil microbial communities can affect plant growth, metal availability and the performance of phytoextraction-assisting inocula. Understanding the basic ecology of indigenous soil communities associated with the phytoextraction process, including the interplay between selective pressures upon the communities, is an important step towards phytoextraction optimization. This study investigated the impact of cadmium (Cd), and the presence of a Cd-accumulating plant, Carpobrotus rossii (Haw.) Schwantes, on the structure of soil-bacterial and fungal communities using automated ribosomal intergenic spacer analysis (ARISA) and quantitative PCR (qPCR). Whilst Cd had no detectable influence upon fungal communities, bacterial communities underwent significant structural changes with no reduction in 16S rRNA copy number. The presence of C. rossii influenced the structure of all communities and increased ITS copy number. Suites of operational taxonomic units (OTUs) changed in abundance in response to either Cd or C. rossii, however we found little evidence to suggest that the two selective pressures were acting synergistically. The Cd-induced turnover in bacterial OTUs suggests that Cd alters competition dynamics within the community. Further work to understand how competition is altered could provide a deeper understanding of the microbiome-plant-environment and aid phytoextraction optimization.

  9. Microbial communities in riparian soils of a settling pond for mine drainage treatment.

    Science.gov (United States)

    Fan, Miaochun; Lin, Yanbing; Huo, Haibo; Liu, Yang; Zhao, Liang; Wang, Entao; Chen, Weimin; Wei, Gehong

    2016-06-01

    Mine drainage leads to serious contamination of soil. To assess the effects of mine drainage on microbial communities in riparian soils, we used an Illumina MiSeq platform to explore the soil microbial composition and diversity along a settling pond used for mine drainage treatment. Non-metric multidimensional scaling analysis showed that the microbial communities differed significantly among the four sampling zones (influent, upstream, downstream and effluent), but not seasonally. Constrained analysis of principal coordinates indicated heavy metals (zinc, lead and copper), total sulphur, pH and available potassium significantly influenced the microbial community compositions. Heavy metals were the key determinants separating the influent zone from the other three zones. Lower diversity indices were observed in the influent zone. However, more potential indicator species, related to sulphur and organic matter metabolism were found there, such as the sulphur-oxidizing genera Acidiferrobacter, Thermithiobacillus, Limnobacter, Thioprofundum and Thiovirga, and the sulphur-reducing genera Desulfotomaculum and Desulfobulbus; the organic matter degrading genera, Porphyrobacter and Paucimonas, were also identified. The results indicated that more microorganisms related to sulphur- and carbon-cycles may exist in soils heavily contaminated by mine drainage. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN HUMAN FECAL MICROBIAL COMMUNITIES

    Science.gov (United States)

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for mo...

  11. Microbial community composition is unaffected by anode potential

    KAUST Repository

    Zhu, Xiuping

    2014-01-21

    There is great controversy on how different set anode potentials affect the performance of a bioelectrochemical system (BES). It is often reported that more positive potentials improve acclimation and performance of exoelectrogenic biofilms, and alter microbial community structure, while in other studies relatively more negative potentials were needed to achieve higher current densities. To address this issue, the biomass, electroactivity, and community structure of anodic biofilms were examined over a wide range of set anode potentials (-0.25, -0.09, 0.21, 0.51, and 0.81 V vs a standard hydrogen electrode, SHE) in single-chamber microbial electrolysis cells. Maximum currents produced using a wastewater inoculum increased with anode potentials in the range of -0.25 to 0.21 V, but decreased at 0.51 and 0.81 V. The maximum currents were positively correlated with increasing biofilm biomass. Pyrosequencing indicated biofilm communities were all similar and dominated by bacteria most similar to Geobacter sulfurreducens. Differences in anode performance with various set potentials suggest that the exoelectrogenic communities self-regulate their exocellular electron transfer pathways to adapt to different anode potentials. © 2013 American Chemical Society.

  12. Microbial community composition is unaffected by anode potential

    KAUST Repository

    Zhu, Xiuping; Yates, Matthew D.; Hatzell, Marta C.; Rao, Hari Ananda; Saikaly, Pascal; Logan, Bruce E.

    2014-01-01

    There is great controversy on how different set anode potentials affect the performance of a bioelectrochemical system (BES). It is often reported that more positive potentials improve acclimation and performance of exoelectrogenic biofilms, and alter microbial community structure, while in other studies relatively more negative potentials were needed to achieve higher current densities. To address this issue, the biomass, electroactivity, and community structure of anodic biofilms were examined over a wide range of set anode potentials (-0.25, -0.09, 0.21, 0.51, and 0.81 V vs a standard hydrogen electrode, SHE) in single-chamber microbial electrolysis cells. Maximum currents produced using a wastewater inoculum increased with anode potentials in the range of -0.25 to 0.21 V, but decreased at 0.51 and 0.81 V. The maximum currents were positively correlated with increasing biofilm biomass. Pyrosequencing indicated biofilm communities were all similar and dominated by bacteria most similar to Geobacter sulfurreducens. Differences in anode performance with various set potentials suggest that the exoelectrogenic communities self-regulate their exocellular electron transfer pathways to adapt to different anode potentials. © 2013 American Chemical Society.

  13. Assessment of microbial communities in PM1 and PM10 of Urumqi during winter.

    Science.gov (United States)

    Gou, Huange; Lu, Jianjiang; Li, Shanman; Tong, Yanbin; Xie, Chunbin; Zheng, Xiaowu

    2016-07-01

    Recently, inhalable particulate matter has been reported to carry microorganisms responsible for human allergy and respiratory disease. The unique geographical environment and adverse weather conditions of Urumqi cause double pollution of dust and smog, but research on the microbial content of the atmosphere has not been commenced. In this study, 16S and 18S rRNA gene sequencing were conducted to investigate the microbial composition of Urumqi's PM1 and PM10 pollutants in winter. Results showed that the bacterial community is mainly composed of Proteobacteria, Firmicutes and Actinobacteria, Proteobacteria accounted for the most proportion which was significant difference in some aforementioned studies. Ascomycota and Basidiomycota constitute the main part of the fungal microbial community. The difference of bacterial relative abundance in sample point is greater than in particle sizes. The sequences of several pathogenic bacteria and opportunistic pathogens were also detected, such as Acinetobacter, Delftia, Serratia, Chryseobacterium, which may impact on immunocompromised populations (elderly, children and postoperative convalescence patients), and some fungal genera may cause several plant diseases. Our findings may serve an important reference value in the global air microbial propagation and air microbial research in desert. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    Science.gov (United States)

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    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 (pPCoA) 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 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 sequencing techniques to microbial community studies.

  16. Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

    Directory of Open Access Journals (Sweden)

    Michael F. Graw

    2018-04-01

    Full Text Available The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

  17. Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea

    Science.gov (United States)

    Graw, Michael F.; D'Angelo, Grace; Borchers, Matthew; Thurber, Andrew R.; Johnson, Joel E.; Zhang, Chuanlun; Liu, Haodong; Colwell, Frederick S.

    2018-01-01

    The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics. PMID:29696012

  18. Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

    Science.gov (United States)

    Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

    2001-12-01

    Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.

  19. Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Fan; Zhang, Xiao-Tao; Hou, Du-Jie [China Univ. of Geosciences, Beijing (China). The Key Lab. of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism; She, Yue-Hui [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology; Li, Hua-Min [Beijing Bioscience Research Center (China); Shu, Fu-Chang; Wang, Zheng-Liang [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Yu, Long-Jiang [Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology

    2012-08-15

    Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes. (orig.)

  20. Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

    Science.gov (United States)

    Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

    2012-08-01

    Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

  1. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories.

    Science.gov (United States)

    Wigneswaran, Vinoth; Amador, Cristina Isabel; Jelsbak, Lotte; Sternberg, Claus; Jelsbak, Lars

    2016-01-01

    Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology.

  2. Soil biochar amendment shapes the composition of N_2O-reducing microbial communities

    International Nuclear Information System (INIS)

    Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H.; Kappler, Andreas; Behrens, Sebastian

    2016-01-01

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N_2O) emissions. N_2O is a potent greenhouse gas. The main sources of N_2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N_2O emission mitigation and the abundance and activity of N_2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N_2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N_2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N_2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N_2O-reducing microbial taxa. • Taxonomic shifts among N_2O-reducing microbes might explain lower N_2O emissions.

  3. Soil biochar amendment shapes the composition of N{sub 2}O-reducing microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Harter, Johannes; Weigold, Pascal [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); El-Hadidi, Mohamed; Huson, Daniel H. [Algorithms in Bioinformatics, Center for Bioinformatics, University of Tuebingen, Sand 14, 72076 Tuebingen (Germany); Kappler, Andreas [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Behrens, Sebastian, E-mail: sbehrens@umn.edu [Geomicrobiology & Microbial Ecology, Center for Applied Geosciences, University of Tuebingen, Sigwartstr. 10, 72076 Tuebingen (Germany); Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, 500 Pillsbury Drive S.E., Minneapolis, MN 55455-0116 (United States); BioTechnology Institute, 140 Gortner Labs, 1479 Gortner Avenue, St. Paul, MN 55108-6106 (United States)

    2016-08-15

    Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N{sub 2}O) emissions. N{sub 2}O is a potent greenhouse gas. The main sources of N{sub 2}O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N{sub 2}O emission mitigation and the abundance and activity of N{sub 2}O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described ‘atypical’ nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N{sub 2}O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N{sub 2}O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N{sub 2}O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. - Highlights: • Biochar promoted anaerobic, alkalinity-adapted, and polymer-degrading microbial taxa. • Biochar fostered the development of distinct N{sub 2}O-reducing microbial taxa. • Taxonomic shifts among N{sub 2}O-reducing microbes

  4. Long-term exposure to benzalkonium chloride disinfectants results in change of microbial community structure and increased antimicrobial resistance.

    Science.gov (United States)

    Tandukar, Madan; Oh, Seungdae; Tezel, Ulas; Konstantinidis, Konstantinos T; Pavlostathis, Spyros G

    2013-09-03

    The effect of benzalkonium chlorides (BACs), a widely used class of quaternary ammonium disinfectants, on microbial community structure and antimicrobial resistance was investigated using three aerobic microbial communities: BACs-unexposed (DP, fed a mixture of dextrin/peptone), BACs-exposed (DPB, fed a mixture of dextrin/peptone and BACs), and BACs-enriched (B, fed only BACs). Long-term exposure to BACs reduced community diversity and resulted in the enrichment of BAC-resistant species, predominantly Pseudomonas species. Exposure of the two microbial communities to BACs significantly decreased their susceptibility to BACs as well as three clinically relevant antibiotics (penicillin G, tetracycline, ciprofloxacin). Increased resistance to BACs and penicillin G of the two BACs-exposed communities is predominantly attributed to degradation or transformation of these compounds, whereas resistance to tetracycline and ciprofloxacin is largely due to the activity of efflux pumps. Quantification of several key multidrug resistance genes showed a much higher number of copies of these genes in the DPB and B microbial communities compared to the DP community. Collectively, our findings indicate that exposure of a microbial community to BACs results in increased antibiotic resistance, which has important implications for both human and environmental health.

  5. Studies on potential effects of fumaric acid on rumen microbial fermentation, methane production and microbial community.

    Science.gov (United States)

    Riede, Susanne; Boguhn, Jeannette; Breves, Gerhard

    2013-01-01

    The greenhouse gas methane (CH4) contributes substantially to global climate change. As a potential approach to decrease ruminal methanogenesis, the effects of different dosages of fumaric acid (FA) on ruminal microbial metabolism and on the microbial community (archaea, bacteria) were studied using a rumen simulation technique (RUSITEC). FA acts as alternative hydrogen acceptor diverting 2H from methanogenesis of archaea towards propionate formation of bacteria. Three identical trials were conducted with 12 fermentation vessels over a period of 14 days. In each trial, four fermentation vessels were assigned to one of the three treatment groups differing in FA dosage: low fumaric acid (LFA), high fumaric acid (HFA) and without FA (control). FA was continuously infused with the buffer. Grass silage and concentrate served as substrate. FA led to decreases in pH and to higher production rates of total short chain fatty acids (SCFA) mediated by increases in propionate for LFA of 1.69 mmol d(-1) and in propionate and acetate production for HFA of 4.49 and 1.10 mmol d(-1), respectively. Concentrations of NH3-N, microbial crude protein synthesis, their efficiency, degradation of crude nutrients and detergent fibre fraction were unchanged. Total gas and CH4 production were not affected by FA. Effects of FA on structure of microbial community by means of single strand conformation polymorphism (SSCP) analyses could not be detected. Given the observed increase in propionate production and the unaffected CH4 production it can be supposed that the availability of reduction equivalents like 2H was not limited by the addition of FA in this study. It has to be concluded from the present study that the application of FA is not an appropriate approach to decrease the ruminal CH4 production.

  6. Nanomodification of the electrodes in microbial fuel cell: impact of nanoparticle density on electricity production and microbial community

    DEFF Research Database (Denmark)

    Al Atraktchi, Fatima Al-Zahraa; Zhang, Yifeng; Angelidaki, Irini

    2014-01-01

    The nano-decoration of electrode with nanoparticles is one effective way to enhance power output of microbial fuel cells (MFCs). However, the amount of nanoparticles used for decoration has not been optimized yet, and how it affects the microbial community is still unknown. In this study, differe...

  7. Microbial community structures in algae cultivation ponds for bioconversion of agricultural wastes from livestock industry for feed production

    Science.gov (United States)

    Dynamics of seasonal microbial community compositions in algae cultivation ponds are complex. There is very limited knowledge on community compositions that may play significant roles in the bioconversion of manure nu¬trients to animal feed. Algae production is an alternative where land area for pro...

  8. Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica.

    Science.gov (United States)

    Teixeira, Lia C R S; Yeargeau, Etienne; Balieiro, Fabiano C; Piccolo, Marisa C; Peixoto, Raquel S; Greer, Charles W; Rosado, Alexandre S

    2013-01-01

    Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.

  9. Plant and bird presence strongly influences the microbial communities in soils of Admiralty Bay, Maritime Antarctica.

    Directory of Open Access Journals (Sweden)

    Lia C R S Teixeira

    Full Text Available Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies, Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.

  10. Plant and Bird Presence Strongly Influences the Microbial Communities in Soils of Admiralty Bay, Maritime Antarctica

    Science.gov (United States)

    Teixeira, Lia C. R. S.; Yeargeau, Etienne; Balieiro, Fabiano C.; Piccolo, Marisa C.; Peixoto, Raquel S.; Greer, Charles W.; Rosado, Alexandre S.

    2013-01-01

    Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing relatively large changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific. PMID:23840411

  11. Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata.

    Science.gov (United States)

    Kamutando, Casper N; Vikram, Surendra; Kamgan-Nkuekam, Gilbert; Makhalanyane, Thulani P; Greve, Michelle; Roux, Johannes J Le; Richardson, David M; Cowan, Don; Valverde, Angel

    2017-07-26

    Invasiveness and the impacts of introduced plants are known to be mediated by plant-microbe interactions. Yet, the microbial communities associated with invasive plants are generally poorly understood. Here we report on the first comprehensive investigation of the bacterial and fungal communities inhabiting the rhizosphere and the surrounding bulk soil of a widespread invasive tree, Acacia dealbata. Amplicon sequencing data indicated that rhizospheric microbial communities differed significantly in structure and composition from those of the bulk soil. Two bacterial (Alphaproteobacteria and Gammaproteobacteria) and two fungal (Pezizomycetes and Agaricomycetes) classes were enriched in the rhizosphere compared with bulk soils. Changes in nutritional status, possibly induced by A. dealbata, primarily shaped rhizosphere soil communities. Despite a high degree of geographic variability in the diversity and composition of microbial communities, invasive A. dealbata populations shared a core of bacterial and fungal taxa, some of which are known to be involved in N and P cycling, while others are regarded as plant pathogens. Shotgun metagenomic analysis also showed that several functional genes related to plant growth promotion were overrepresented in the rhizospheres of A. dealbata. Overall, results suggest that rhizosphere microbes may contribute to the widespread success of this invader in novel environments.

  12. Metagenomic insights into evolution of heavy metal-contaminated groundwater microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Hemme, C.L.; Deng, Y.; Gentry, T.J.; Fields, M.W.; Wu, L.; Barua, S.; Barry, K.; Green-Tringe, S.; Watson, D.B.; He, Z.; Hazen, T.C.; Tiedje, J.M.; Rubin, E.M.; Zhou, J.

    2010-07-01

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ({approx}50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying {gamma}- and {beta}-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  13. Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.; Fields, Matthew W.; Wu, Liyou; Barua, Soumitra; Barry, Kerrie; Tringe, Susannah G.; Watson, David B.; He, Zhili; Hazen, Terry C.; Tiedje, James M.; Rubin, Edward M.; Zhou, Jizhong

    2010-02-15

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  14. Change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light

    KAUST Repository

    Xing, Defeng

    2009-09-01

    Power densities produced by microbial fuel cells (MFCs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. When MFCs with brush anodes were exposed to light (4000 lx), power densities increased by 8-10% for glucose-fed reactors, and 34% for acetate-fed reactors. Denaturing gradient gel electrophoresis (DGGE) profiles based on the 16S rRNA gene showed that exposure to high light levels changed the microbial communities on the anodes. Based on 16S rRNA gene clone libraries of light-exposed systems the anode communities using glucose were also significantly different than those fed acetate. Dominant bacteria that are known exoelectrogens were identified in the anode biofilm, including a purple nonsulfur (PNS) photosynthetic bacterium, Rhodopseudomonas palustris, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS photosynthetic bacteria increased power production when exposed to high light intensities (4000 lx). These results demonstrate that power production and community composition are affected by light conditions as well as electron donors in single-chamber air-cathode MFCs. © 2009 Elsevier B.V. All rights reserved.

  15. Change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light

    KAUST Repository

    Xing, Defeng; Cheng, Shaoan; Regan, John M.; Logan, Bruce E.

    2009-01-01

    Power densities produced by microbial fuel cells (MFCs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. When MFCs with brush anodes were exposed to light (4000 lx), power densities increased by 8-10% for glucose-fed reactors, and 34% for acetate-fed reactors. Denaturing gradient gel electrophoresis (DGGE) profiles based on the 16S rRNA gene showed that exposure to high light levels changed the microbial communities on the anodes. Based on 16S rRNA gene clone libraries of light-exposed systems the anode communities using glucose were also significantly different than those fed acetate. Dominant bacteria that are known exoelectrogens were identified in the anode biofilm, including a purple nonsulfur (PNS) photosynthetic bacterium, Rhodopseudomonas palustris, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS photosynthetic bacteria increased power production when exposed to high light intensities (4000 lx). These results demonstrate that power production and community composition are affected by light conditions as well as electron donors in single-chamber air-cathode MFCs. © 2009 Elsevier B.V. All rights reserved.

  16. Responses of microbial community to pH stress in bioleaching of low grade copper sulfide.

    Science.gov (United States)

    Wang, Yuguang; Li, Kai; Chen, Xinhua; Zhou, Hongbo

    2018-02-01

    The microbial diversity and dynamics in the leachates and on the ore surfaces of different depth of the column were analyzed during bioleaching of low grade copper sulfide at different pH, after inoculation with the same inoculum containing mesophiles and moderate thermophiles. The results indicate that low pH was beneficial to enhance copper extraction. The highest copper extraction (86%) was obtained when pH was controlled at 1.0-1.5. The microbial structures on the ore surfaces were independent of community structures in the leachate, even at the top portion of column. Microbial richness and evenness increased with decreasing pH during bioleaching. pH had significant effects on microbial community structure in the leachate and on the mineral surface of different depth of the column. Leptospirillum ferriphilum accounted for the highest proportions of the community at most times when pH was operated during bioleaching, especially at the end of run. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.

    Science.gov (United States)

    Ren, Ge; Ma, Anzhou; Zhang, Yanfen; Deng, Ye; Zheng, Guodong; Zhuang, Xuliang; Zhuang, Guoqiang; Fortin, Danielle

    2018-04-06

    Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane-cycling microbes and their partners being observed in the iron/sulfate-rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane-rich environments. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  18. Interactions between selected PAHs and the microbial community in rhizosphere of a paddy soil.

    Science.gov (United States)

    Su, Yu H; Yang, Xue Y

    2009-01-15

    This study investigated the interaction of three polycyclic aromatic hydrocarbons (PAHs), i.e., naphthalene (NAP), phenanthrene (PHN), and pyrene (PYR), with the microbial community in the rhizosphere of a paddy soil and the influence of the rice (Oryza sativa) rhizosphere on the microbial community structure. A range of initial NAP, PHN and PYR levels in soil (50-200, 18-72, and 6.6-26.6 mg kg(-1), respectively) were prepared and the soil samples were then aged for 4 months (to yield PAH concentrations at 1.02-1.42, 1.32-4.77, and 2.98-18.5 mg kg(-)(1), respectively) before the soil samples were planted with rice seedlings. The microbial phospholipid-fatty-acid (PLFA) patterns in PAH-contaminated soils were analyzed to elucidate the changes of the microbial biomass and community composition. Results indicated that at the applied concentrations the PAHs were not toxic to rice seedlings, as evidenced by no growth inhibition during the 8-week planting period. However, the microbial biomass, as revealed by PLFAs, decreased significantly with increasing PAH concentration in both rhizospheric and non-rhizospheric soils. The PAHs in soils were obviously toxic to microorganisms, and the toxicity of PHN was greater than PYR due likely to the higher PHN bioavailability. Total PLFAs in rhizospheric soils were profoundly higher than those in non-rhizospheric soils, suggesting that the inhibitive effect of PAHs on microbial activities was alleviated by the rice roots. The principal component analysis (PCA) of the PLFA signatures revealed pronounced changes in PLFA pattern in rhizospheric and non-rhizospheric soils with or without spiked PAHs. Using the PLFA patterns as a biomarker, it was found that Gram-positive bacteria were more sensitive to PAHs than Gram-negative bacteria, and the rhizosphere of rice roots stimulated the growth of aerobic bacteria.

  19. Resistance of Terrestrial Microbial Communities to Impack of Physical Conditinos of Subsurface Layers of Martian Regolith

    Science.gov (United States)

    Cheptsov, V. S.; Vorobyova, E. A.

    2017-05-01

    Currently, astrobiology is focused on Mars as one of the most perspective objects in the Solar System to search for microbial life. It was assumed that the putative biosphere of Mars could be cryopreserved and had been stored for billions of years in anabiotic state like microbial communities of Arctic and Antarctic permafrost deposits have been preserved till now for millions of years. In this case microbial cells should be not able to repair the damages or these processes have to be significantly depressed, and the main factor causing cell's death should be ionizing radiation. In a series of experiments we simulated the effects of combination of physical factors known as characteristics of the Martian regolith (and close to the space environment) on the natural microbial communities inhabiting xerophytic harsh habitats with extreme temperature conditions: polar permafrost and desert soils. The aim of the study was to examine the cumulative effect of factors (gamma radiation, low temperature, low pressure) to assess the possibility of metabolic reactions, and to find limits of the viability of natural microbial communities after exposure to the given conditions. It was found that microbial biomarkers could be reliably detected in soil samples after radiation dose accumulation up to 1 MGy (not further investigated) in combination with exposure to low temperature and low pressure. Resistance to extremely high doses of radiation in simulated conditions proves that if there was an Earth-like biosphere on the early Mars microorganisms could survive in the surface or subsurface layers of the Martian regolith for more than tens of millions of years after climate change. The study gives also some new grounds for the approval of transfer of viable microorganisms in space.

  20. Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

    Science.gov (United States)

    Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

    2015-09-01

    Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

  1. Microbial quality of water in rural communities of Trinidad

    Directory of Open Access Journals (Sweden)

    Pedro Welch

    2000-09-01

    Full Text Available A cross-sectional study was conducted in four rural communities of northeastern Trinidad to determine the microbial quality of water supply to households and that quality's relationship to source and storage device. Of the 167 household water samples tested, total coliforms were detected in 132 of the samples (79.0%, fecal coliforms in 102 (61.1%, and E. coli in 111 (66.5%. There were significant differences among the towns in the proportion of the samples contaminated with coliforms (P < 0.001 and E. coli (P < 0.001. Of 253 strains of E. coli studied, 4 (1.6% were mucoid, 9 (3.6% were hemolytic, and 37 (14.6% were nonsorbitol fermenters. Of 69 isolates of E. coli tested, 10 (14.5% were verocytotoxigenic. Twenty-eight (14.0% of 200 E. coli isolates tested belonged to enteropathogenic serogroups. Standpipe, the most common water source, was utilized by 57 (34.1% of the 167 households. Treated water (pipeborne in homes, standpipes, or truckborne was supplied to 119 households (71.3%, while 48 households (28.7% used water from untreated sources (rain, river/stream, or well as their primary water supply. The type of household storage device was associated with coli-form contamination. Water stored in drums, barrels, or buckets was more likely to harbor fecal coliforms (74.2% of samples than was water stored in tanks (53.3% of samples, even after controlling for water source (P = 0.04. Compared with water from other sources, water piped into homes was significantly less likely to be contaminated with total coliforms (56.9% versus 88.8%, P < 0.001 and fecal coliforms (41.2% versus 69.8%, P < 0.01, even when the type of storage device was taken into account. However, fecal contamination was not associated with whether the water came from a treated or untreated source. We concluded that the drinking water in rural communities in Trinidad was grossly unfit for human consumption, due both to contamination of various water sources and during household

  2. Microbial quality of water in rural communities of Trinidad

    Directory of Open Access Journals (Sweden)

    Welch Pedro

    2000-01-01

    Full Text Available A cross-sectional study was conducted in four rural communities of northeastern Trinidad to determine the microbial quality of water supply to households and that quality's relationship to source and storage device. Of the 167 household water samples tested, total coliforms were detected in 132 of the samples (79.0%, fecal coliforms in 102 (61.1%, and E. coli in 111 (66.5%. There were significant differences among the towns in the proportion of the samples contaminated with coliforms (P < 0.001 and E. coli (P < 0.001. Of 253 strains of E. coli studied, 4 (1.6% were mucoid, 9 (3.6% were hemolytic, and 37 (14.6% were nonsorbitol fermenters. Of 69 isolates of E. coli tested, 10 (14.5% were verocytotoxigenic. Twenty-eight (14.0% of 200 E. coli isolates tested belonged to enteropathogenic serogroups. Standpipe, the most common water source, was utilized by 57 (34.1% of the 167 households. Treated water (pipeborne in homes, standpipes, or truckborne was supplied to 119 households (71.3%, while 48 households (28.7% used water from untreated sources (rain, river/stream, or well as their primary water supply. The type of household storage device was associated with coli-form contamination. Water stored in drums, barrels, or buckets was more likely to harbor fecal coliforms (74.2% of samples than was water stored in tanks (53.3% of samples, even after controlling for water source (P = 0.04. Compared with water from other sources, water piped into homes was significantly less likely to be contaminated with total coliforms (56.9% versus 88.8%, P < 0.001 and fecal coliforms (41.2% versus 69.8%, P < 0.01, even when the type of storage device was taken into account. However, fecal contamination was not associated with whether the water came from a treated or untreated source. We concluded that the drinking water in rural communities in Trinidad was grossly unfit for human consumption, due both to contamination of various water sources and during household

  3. Set anode potentials affect the electron fluxes and microbial community structure in propionate-fed microbial electrolysis cells

    KAUST Repository

    Rao, Hari Ananda; Katuri, Krishna; Logan, Bruce E.; Saikaly, Pascal

    2016-01-01

    , but their relative abundance varied among the tested SAPs. Microbial community analysis implies that complete degradation of propionate in all the tested SAPs was facilitated by syntrophic interactions between fermenters and Geobacter at the anode and ferementers

  4. [Influence of Different Straws Returning with Landfill on Soil Microbial Community Structure Under Dry and Water Farming].

    Science.gov (United States)

    Lan, Mu-ling; Gao, Ming

    2015-11-01

    Based on rice, wheat, corn straw and rape, broad bean green stalk as the research object, using phospholipid fatty acid (PLFA) method, combining principal component analysis method to study the soil microbial quantity, distribution of flora, community structure characteristics under dry and water farming as two different cultivated land use types. The PLFA analysis results showed that: under dry farming, total PLFA quantity ranged 8.35-25.15 nmol x g(-1), showed rape > broad bean > corn > rice > wheat, rape and broad bean significantly increased total PLFA quantity by 1.18 and 1.08 times compared to the treatment without straw; PLFA quantity of bacterial flora in treatments with straws was higher than that without straw, and fungal biomass was significantly increased, so was the species richness of microbial community. Under water faming, the treatments of different straws returning with landfill have improved the PLFA quantity of total soil microbial and flora comparing with the treatment without straw, fungi significantly increased, and species richness of microbial communities value also increased significantly. Total PLFA quantity ranged 4.04-22.19 nmol x g(-1), showed rice > corn > wheat > broad bean > rape, which in rape and broad bean treatments were lower than the treatment without straw; fungal PLFA amount in 5 kinds of straw except broad bean treatment was significantly higher than that of the treatment without straw, bacteria and total PLFA quantity in broad bean processing were significantly lower than those of other treatments, actinomycetes, G+, G- had no significant difference between all treatments; rice, wheat, corn, rape could significantly increase the soil microbial species richness index and dominance index under water faming. The results of principal component analysis showed that broad bean green stalk had the greatest impact on the microbial community structure in the dry soil, rape green stalk and wheat straw had the biggest influence on

  5. Rumen microbial communities influence metabolic phenotypes in lambs

    Directory of Open Access Journals (Sweden)

    Diego P. Morgavi

    2015-10-01

    Full Text Available The rumen microbiota is an essential part of ruminants forging their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.

  6. Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming in Alabama

    Directory of Open Access Journals (Sweden)

    Zachary Senwo

    2011-07-01

    Full Text Available Evaluation of the soil rhizosphere has been limited by the lack of robust assessments that can explore the vast complex structure and diversity of soil microbial communities. Our objective was to combine fatty acid methyl ester (FAME and pyrosequencing techniques to evaluate soil microbial community structure and diversity. In addition, we evaluated biogeochemical functionality of the microbial communities via enzymatic activities of nutrient cycling. Samples were taken from a silt loam at 0–10 and 10–20 cm in an organic farm under lettuce (Lactuca sativa, potato (Solanum tuberosum, onion (Allium cepa L, broccoli (Brassica oleracea var. botrytis and Tall fescue pasture grass (Festuca arundinacea. Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, 10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c varied among the crop rhizospheres. FAME profiles of the soil microbial community under pasture showed a higher fungal:bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Soil under potato showed higher sum of fungal FAME indicators compared to broccoli, onion and lettuce. Microbial biomass C and enzyme activities associated with pasture and potato were higher than the other rhizospheres. The lowest soil microbial biomass C and enzyme activities were found under onion. Pyrosequencing revealed significant differences regarding the maximum operational taxonomic units (OTU at 3% dissimilarity level (roughly corresponding to the bacterial species level at 0–10 cm (581.7–770.0 compared to 10–20 cm (563.3–727.7 soil depths. The lowest OTUs detected at 0–10 cm were under broccoli (581.7; whereas the lowest OTUs found at 10–20 cm were under potato (563.3. The predominant phyla (85% in this soil at both depths were Bacteroidetes (i.e., Flavobacteria, Sphingobacteria, and Proteobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more

  7. Coexistence facilitates interspecific biofilm formation in complex microbial communities

    DEFF Research Database (Denmark)

    Madsen, Jonas Stenløkke; Røder, Henriette Lyng; Russel, Jakob

    2016-01-01

    Social interactions in which bacteria respond to one another by modifying their phenotype are central determinants of microbial communities. It is known that interspecific interactions influence the biofilm phenotype of bacteria; a phenotype that is central to the fitness of bacteria. However......, the underlying role of fundamental ecological factors, specifically coexistence and phylogenetic history, in biofilm formation remains unclear. This study examines how social interactions affect biofilm formation in multi-species co-cultures from five diverse environments. We found prevalence of increased...

  8. The Effect of Long Term Mercury Pollution on the Soil Microbial Community

    DEFF Research Database (Denmark)

    Müller, A.K.; Westergaard, K.; Christensen, Søren

    2001-01-01

    The effect of long-term exposure to mercury on the soil microbial community was investigated in soil from three different sites along a pollution gradient. The amount of total and bioavailable mercury was negatively correlated to the distance from the center of contamination. The size...... of the bacterial and protozoan populations was reduced in the most contaminated soil, whereas there was no significant difference in fungal biomass measured as chitinase activity. Based on the number of colony morphotypes, moreover, the culturable bacterial population was structurally less diverse and contained...... of the number and abundance of bands. The functional potential of the microbial population measured as sole carbon source utilization by Ecoplates® differed between the soils, but there was no change in the number of substrates utilized. The observed changes in the different soil microbial populations...

  9. Influence of attapulgite addition on the biological performance and microbial communities of submerged dynamic membrane bioreactor

    Directory of Open Access Journals (Sweden)

    Wensong Duan

    2017-12-01

    Full Text Available A submerged dynamic membrane bioreactor (sDMBR was developed to test the influence of attapulgite (AT addition on the treatment performances and the microbial community structure and function. The batch experimental results displayed the highest UV254 and dissolved organic carbon (DOC removal efficiencies with 5% AT/mixed liquid suspended solids addition dosage. The continuous sDMBR results showed that the removal efficiencies of chemical oxygen demand, NH4+-N, total nitrogen and total phosphorus significantly increased in the AT added sDMBR. Excitation emission matrix analysis demonstrated that the protein-like peaks and fulvic acid-like peaks were significantly decreased in both in the mixed liquid and the effluent of the AT added reactor. The obligate anaerobes were observed in the sDMBR with AT addition, such as Bacteroidetes and Gamma proteobacterium in the dynamic membrane, which played an important role in the process of sludge granulation. Bacterial community richness significantly increased after AT addition with predominated phyla of Proteobacteria and Bacteroidetes. Similarly, species abundance significantly increased in the AT added sDMBR. Further investigations with cluster proved that AT was a favorite biological carrier for the microbial ecology, which enriched microbial abundance and community diversity of the sDMBR.

  10. Investigation of microbial community structure in constructed mangrove microcosms receiving wastewater-borne polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenyl ethers (PBDEs)

    International Nuclear Information System (INIS)

    Wang, Ya-fen; Wu, Yan; Pi, Na; Tam, Nora Fung-yee

    2014-01-01

    The study aims to examine relationships between microbial community structure and mixed pollutants of polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenyl ethers (PBDEs) in constructed wetland microcosms, planted with Excoecaria agallocha or Kandelia obovata, two common mangrove plant species, and under two tidal regimes, everyday tidal (Te) and no tidal flooding (Tn). Results showed both microbial community structure and the retained amounts of pollutants were significantly determined by tidal regime, while the effect of plant species was small. Higher amounts of PAHs but lower amounts of PBDEs were always retained in sediments under Te than Tn regimes. Accordingly, temporal and vertical distributions of microbial community structure differed greatly between the two tidal regimes. Redundancy analysis further revealed significant correlation between a subgroup of the mixed PAHs and PBDEs with variation in microbial community structure. The findings will help to propose specific strategies to improve the bioremediation efficiency of constructed wetland. - Highlights: • We found synchronous degradation of PAHs and PBDEs in constructed mangrove microcosms. • Retained amounts of PAHs and PBDEs were determined mainly by tidal regime. • Tidal regime in turn significantly determined microbial community structure. • Variations of microbial EL-FAME profiles were more affected by PBDEs than PAHs. • Bap and BDE-154 were two most influential pollutants on microbial community structure. - Sedimentary microbial community structure was significantly determined by tidal regime, which in turn determined retained amounts of PAHs and PBDEs in constructed mangrove microcosms

  11. Methane-oxidizing seawater microbial communities from an Arctic shelf

    Science.gov (United States)

    Uhlig, Christiane; Kirkpatrick, John B.; D'Hondt, Steven; Loose, Brice

    2018-06-01

    Marine microbial communities can consume dissolved methane before it can escape to the atmosphere and contribute to global warming. Seawater over the shallow Arctic shelf is characterized by excess methane compared to atmospheric equilibrium. This methane originates in sediment, permafrost, and hydrate. Particularly high concentrations are found beneath sea ice. We studied the structure and methane oxidation potential of the microbial communities from seawater collected close to Utqiagvik, Alaska, in April 2016. The in situ methane concentrations were 16.3 ± 7.2 nmol L-1, approximately 4.8 times oversaturated relative to atmospheric equilibrium. The group of methane-oxidizing bacteria (MOB) in the natural seawater and incubated seawater was > 97 % dominated by Methylococcales (γ-Proteobacteria). Incubations of seawater under a range of methane concentrations led to loss of diversity in the bacterial community. The abundance of MOB was low with maximal fractions of 2.5 % at 200 times elevated methane concentration, while sequence reads of non-MOB methylotrophs were 4 times more abundant than MOB in most incubations. The abundances of MOB as well as non-MOB methylotroph sequences correlated tightly with the rate constant (kox) for methane oxidation, indicating that non-MOB methylotrophs might be coupled to MOB and involved in community methane oxidation. In sea ice, where methane concentrations of 82 ± 35.8 nmol kg-1 were found, Methylobacterium (α-Proteobacteria) was the dominant MOB with a relative abundance of 80 %. Total MOB abundances were very low in sea ice, with maximal fractions found at the ice-snow interface (0.1 %), while non-MOB methylotrophs were present in abundances similar to natural seawater communities. The dissimilarities in MOB taxa, methane concentrations, and stable isotope ratios between the sea ice and water column point toward different methane dynamics in the two environments.

  12. Toxicity of vapor phase petroleum contaminants to microbial degrader communities

    International Nuclear Information System (INIS)

    Long, S.C.; Davey, C.A.

    1994-01-01

    Petroleum products constitute the largest quantity of synthetic organic chemical products produced in the US. They are comprised of mostly hydrocarbon constituents from many different chemical classes including alkenes, cycloalkanes, aromatic compounds, and polyaromatic hydrocarbons. Many petroleum constituents are classified as volatile organic compounds or VOCs. Petroleum products also constitute a major portion of environmental pollution. One emerging technology, with promise for applications to VOCs in subsurface soil environments, is bioventing coupled with soil vapor extraction. These technologies involve volatilization of contaminants into the soil gas phase by injection and withdrawal of air. This air movement causes enhancement of the aerobic microbial degradation of the mobilized vapors by the indigenous populations. This study investigated the effects of exposure of mixed, subsurface microbial communities to vapor phase petroleum constituents or vapors of petroleum mixtures. Soil slurries were prepared and plated onto mineral salts agar plates and exposed to vapor phase contaminants at equilibrium with pure product. Representative n-alkane, branched alkane, cycloalkane, and aromatic compounds were tested as well as petroleum product mixtures. Vapor exposure altered the numbers and morphologies of the colonies enumerated when compared to controls. However, even at high, equilibrium vapor concentrations, microbial degrader populations were not completely inhibited

  13. Response of the soil microbial community to imazethapyr application in a soybean field.

    Science.gov (United States)

    Xu, Jun; Guo, Liqun; Dong, Fengshou; Liu, Xingang; Wu, Xiaohu; Sheng, Yu; Zhang, Ying; Zheng, Yongquan

    2013-01-01

    The objective of this study was to determine the effects of imazethapyr on soil microbial communities combined with its effect on soybean growth. A short-term field experiment was conducted, and imazethapyr was applied to the soil at three different doses [1-fold, 10-fold, and 50-fold of the recommended field rate (H1, H10, H50)] during the soybean seedling period (with two leaves). Soil sampling was performed after 1, 7, 30, 60, 90, and 120 days of application to determine the imazethapyr concentration and microbial community structure by investigating phospholipid fatty acids (PLFA) and microbial biomass carbon (MBC). The half-lives of the imazethapyr in the field soil varied from 30.1 to 43.3 days. Imazethapyr at H1 was innocuous to soybean plants, but imazethapyr at H10 and H50 led to a significant inhibition in soybean plant height and leaf number. The soil MBC, total PLFA, and bacterial PLFA were decreased by the application of imazethapyr during the initial period and could recover by the end of the experiment. The ratio of Gram-negative/Gram-positive (GN/GP) bacteria during the three treatments went through increases and decreases, and then recovered at the end of the experiment. The fungal PLFA of all three treatments increased during the initial period and then declined, and only the fungal PLFA at H50 recovered by the end of the treatment. A principal component analysis (PCA) of the PLFA clearly separated the treatments and sampling times, and the results demonstrate that imazethapyr alters the microbial community structure. This is the first systemic study reporting the effects of imazethapyr on the soil microbial community structure under soybean field conditions.

  14. The effect of alum addition on microbial communities in poultry litter.

    Science.gov (United States)

    Rothrock, M J; Cook, K L; Warren, J G; Sistani, K

    2008-08-01

    Alum [Al(2)(SO(4))(3).14H(2)O] is a common poultry litter amendment used to decrease water-soluble phosphorus or reduce ammonia volatilization, or both. Although the physiochemical effects of alum addition have been well researched, little attention has been given to the poultry litter microbial communities. The goal of this study was to use molecular biological methods [denaturing gradient gel electrophoresis (DGGE), community cloning, and quantitative real-time PCR] to characterize general, group-specific and pathogenic microbial communities in alum (10% wt/wt) and non-alum-treated litter. According to quantitative real-time PCR analyses, alum addition to the poultry litter resulted in significant reductions in both Campylobacter jejuni and Escherichia coli concentrations by the end of the first month of the experiment (3 log and 2 log, respectively). The concentrations of Salmonella spp. were below detection (Eubacterium and low %GC gram-positive groups in the alum-treated litters by the end of the first month, with no bands detectable for either group after 8 wk of incubation. Conversely, minimal effects of alum addition were observed in the Actinomycetes community. The most significant shift in the microbial community (based on DGGE analyses) occurred in the fungal population, with a large increase in diversity and abundance within 1 mo of alum addition (1 dominant band on d 0 to 9 dominant bands at 4 wk). Specifically, the incidence of Aspergillus spp. increased from 0 to 50% of the sequences in fungal clone libraries (n = 80) over the course of the experiment. This suggests that the addition of alum to poultry litter potentially shifts the microbial populations from bacterially dominated to dominated by fungi. The ramifications of this shift in dominance are still unknown, and future work will be aimed at characterizing these fungi and elucidating their role in the acidified litter environment.

  15. Simultaneous efficient removal of oxyfluorfen with electricity generation in a microbial fuel cell and its microbial community analysis.

    Science.gov (United States)

    Zhang, Qinghua; Zhang, Lei; Wang, Han; Jiang, Qinrui; Zhu, Xiaoyu

    2018-02-01

    The performance of a microbial fuel cell (MFC) to degrade oxyfluorfen was investigated. Approximately 77% of 50 mg/L oxyfluorfen was degraded within 24 h by anodic biofilm. The temperature, pH, and initial oxyfluorfen concentration had a significant effect on oxyfluorfen degrading, and a maximum degradation rate of 94.95% could theoretically be achieved at 31.96 °C, a pH of 7.65, and an initial oxyfluorfen concentration of 120.05 mg/L. Oxyfluorfen was further catabolized through various microbial metabolism pathways. Moreover, the anodic biofilm exhibited multiple catabolic capacities to 4-nitrophenol, chloramphenicol, pyraclostrobin, and sulfamethoxazole. Microbial community analysis indicated that functional bacteria Arcobacter, Acinetobacter, Azospirillum, Azonexus, and Comamonas were the predominant genera in the anodic biofilm. In terms of the efficient removal of various organic compounds and energy recovery, the MFC seemed to be a promising approach for the treatment of environmental contaminants. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. The influence of e-waste recycling on the molecular ecological network of soil microbial communities in Pakistan and China.

    Science.gov (United States)

    Jiang, Longfei; Cheng, Zhineng; Zhang, Dayi; Song, Mengke; Wang, Yujie; Luo, Chunling; Yin, Hua; Li, Jun; Zhang, Gan

    2017-12-01

    Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e.g., Cu, Zn, and Pb). The geographical distance showed limited impacts on microbial communities compared with geochemical factors. The constructed ecological network of soil microbial communities illustrated microbial co-occurrence, competition and antagonism across soils, revealing the response of microbes to soil properties and pollutants. Two of the three main modules constructed with core operational taxonomic units (OTUs) were sensitive to nutrition (total organic carbon and total nitrogen) and pollutants. Five key OTUs assigned to Acidobacteria, Proteobacteria, and Nitrospirae in ecological network were identified. This is the first study to report the effects of e-waste pollutants on soil microbial network, providing a deeper understanding of the ecological influence of crude e-waste recycling activities on soil ecological functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

    KAUST Repository

    Qian, Peiyuan

    2010-07-29

    The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea. © 2011 International Society for Microbial Ecology All rights reserved.

  18. Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

    KAUST Repository

    Qian, Peiyuan; Wang, Yong; Lee, Onon; Lau, Chunkwan; Yang, Jiangke; Lafi, Feras Fawzi; Al-Suwailem, Abdulaziz M.; Wong, Tim

    2010-01-01

    The ecosystems of the Red Sea are among the least-explored microbial habitats in the marine environment. In this study, we investigated the microbial communities in the water column overlying the Atlantis II Deep and Discovery Deep in the Red Sea. Taxonomic classification of pyrosequencing reads of the 16S rRNA gene amplicons showed vertical stratification of microbial diversity from the surface water to 1500 m below the surface. Significant differences in both bacterial and archaeal diversity were observed in the upper (2 and 50 m) and deeper layers (200 and 1500 m). There were no obvious differences in community structure at the same depth for the two sampling stations. The bacterial community in the upper layer was dominated by Cyanobacteria whereas the deeper layer harbored a large proportion of Proteobacteria. Among Archaea, Euryarchaeota, especially Halobacteriales, were dominant in the upper layer but diminished drastically in the deeper layer where Desulfurococcales belonging to Crenarchaeota became the dominant group. The results of our study indicate that the microbial communities sampled in this study are different from those identified in water column in other parts of the world. The depth-wise compositional variation in the microbial communities is attributable to their adaptations to the various environments in the Red Sea. © 2011 International Society for Microbial Ecology All rights reserved.

  19. Silver nanoparticles uptake by salt marsh plants - Implications for phytoremediation processes and effects in microbial community dynamics.

    Science.gov (United States)

    Fernandes, Joana P; Mucha, Ana P; Francisco, Telmo; Gomes, Carlos Rocha; Almeida, C Marisa R

    2017-06-15

    This study investigated the uptake of silver nanoparticles (AgNPs) by a salt marsh plant, Phragmites australis, as well as AgNPs effects on rhizospheric microbial community, evaluating the implications for phytoremediation processes. Experiments were carried out with elutriate solution doped with Ag, either in ionic form or in NP form. Metal uptake was evaluated in plant tissues, elutriate solutions and sediments (by AAS) and microbial community was characterized in terms of bacterial community structure (evaluated by ARISA). Results showed Ag accumulation but only in plant belowground tissues and only in the absence of rhizosediment, the presence of sediment reducing Ag availability. But in plant roots Ag accumulation was higher when Ag was in NP form. Multivariate analysis of ARISA profiles showed significant effect of the absence/presence of Ag either in ionic or NP form on microbial community structure, although without significant differences among bacterial richness and diversity. Overall, P. australis can be useful for phytoremediation of medium contaminated with Ag, including with AgNPs. However, the presence of Ag in either forms affected the microbial community structure, which may cause disturbances in ecosystems function and compromise phytoremediation processes. Such considerations need to be address regarding environmental management strategies applied to the very important estuarine areas. The form in which the metal was added affected metal uptake by Phragmites australis and rhizosediment microbial community structure, which can affect phytoremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Microbial Community Assessment in Wetlands for Water Pollution Control: Past, Present, and Future Outlook

    Directory of Open Access Journals (Sweden)

    Kela P. Weber

    2016-11-01

    Full Text Available The field of treatment wetlands (TWs is rapidly expanding and, arguably, is tasked with studying and understanding one of the most complex water treatment systems available. Microbial communities are generally considered to be responsible for the majority of wastewater constituent degradation in TWs. However, they are also known to be spatially heterogeneous, temporally dynamic, as well as structurally and functionally diverse. Presented here is a meta-analysis of all peer reviewed TW journal articles which utilized a microbial community assessment methodology over the period of 1988 to July 2016. A total of 1101 papers were reviewed, 512 from 1988 to 2012, 215 of which included a microbial community assessment aspect and were subsequently classified as representing past research, and 589 from 2013 to July 2016, 196 of which were classified as representing current TW microbial community research. In general, TW microbial community research has increased over time, with a marked surge in the past four years. Microbial community structure is currently the most commonly used methodological type followed by activity, enumeration and function, respectively. Areas of research focus included nitrogen transformations (156, organic degradation (33, and emerging contaminants (32, with general characterization studies also accounting for a significant proportion (243. Microbial communities from a range of TW systems have been investigated over the last four years with meso-scale (10–1000 L being the most commonly studied system size followed by large-scale (>100,000 L, micro-scale (<10 L, and pilot-scale (1000–100,000 L. Free water surface flow (SF, horizontal subsurface flow (HF, and vertical flow (VF systems are being studied in approximately equal proportions with the majority of studies focused on gaining fixed media/biofilm samples for analysis (rather than from the rhizosphere or interstitial water. Looking at efforts from a regional perspective

  1. Crosstalk Regulates the Capacity for Robust Collective Decision Making in Heterogeneous Microbial Communities

    Science.gov (United States)

    Yusufaly, Tahir; Boedicker, James

    Microbial communities frequently communicate via quorum sensing (QS), where cells produce, secrete, and respond to a threshold level of an autoinducer (AI) molecule, thereby modulating density-dependent gene expression. However, the biology of QS remains incompletely understood in heterogeneous communities, where crosstalk between distinct QS systems leads to novel effects. Such knowledge is necessary both for understanding signaling in real microbial communities, and for the rational design of synthetic communities with designer properties. As a step towards this goal, we investigate the effects of crosstalk between Gram-negative bacteria communicating via LuxI/LuxR-type QS systems, with acyl-homoserine lactone (AHL) AI molecules. After mapping QS in a heterogeneous community onto an artificial neural network model, we systematically analyze how heterogeneity regulates the community's capability for stable yet flexible decision making. We find that there are preferred distributions of interactions which provide optimal tradeoffs between capacity, or the number of different decisions a population can make, and robustness, or the tolerance of the community to disturbances. We compare our results to inferences made from experimental data, and critically discuss implications for the biological significance of crosstalk.

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

    Science.gov (United States)

    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.

  3. Perturbation of an arctic soil microbial community by metal nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Niraj [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Shah, Vishal [Department of Biology, Dowling College, Oakdale, NY 11769 (United States); Walker, Virginia K., E-mail: walkervk@queensu.ca [Department of Biology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada); Department of Biology, School of Environmental Studies and Department of Microbiology and Immunology, Queen' s University, Kingston, Ontario K7L 3N6 (Canada)

    2011-06-15

    Highlights: {yields} Silver, copper and silica nanoparticles had an impact on arctic soil {yields} A microbial community toxicity indicator was developed {yields} Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity {yields} Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78{sup o}N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

  4. Perturbation of an arctic soil microbial community by metal nanoparticles

    International Nuclear Information System (INIS)

    Kumar, Niraj; Shah, Vishal; Walker, Virginia K.

    2011-01-01

    Highlights: → Silver, copper and silica nanoparticles had an impact on arctic soil → A microbial community toxicity indicator was developed → Community surveys using pyrosequencing confirmed a shift in bacterial biodiversity → Troublingly, silver nanoparticles were highly toxic to a plant beneficial bacterium - Abstract: Technological advances allowing routine nanoparticle (NP) manufacture have enabled their use in electronic equipment, foods, clothing and medical devices. Although some NPs have antibacterial activity, little is known about their environmental impact and there is no information on the influence of NPs on soil in the possibly vulnerable ecosystems of polar regions. The potential toxicity of 0.066% silver, copper or silica NPs on a high latitude (>78 o N) soil was determined using community level physiological profiles (CLPP), fatty acid methyl ester (FAME) assays and DNA analysis, including sequencing and denaturing gradient gel electrophoresis (DGGE). The results of these different investigations were amalgamated in order to develop a community toxicity indicator, which revealed that of the three NPs examined, silver NPs could be classified as highly toxic to these arctic consortia. Subsequent culture-based studies confirmed that one of the community-identified plant-associating bacteria, Bradyrhizobium canariense, appeared to have a marked sensitivity to silver NPs. Thus, NP contamination of arctic soils particularly by silver NPs is a concern and procedures for mitigation and remediation of such pollution should be a priority for investigation.

  5. Estimating and mapping ecological processes influencing microbial community assembly.

    Science.gov (United States)

    Stegen, James C; Lin, Xueju; Fredrickson, Jim K; Konopka, Allan E

    2015-01-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.

  6. Estimating and Mapping Ecological Processes Influencing Microbial Community Assembly

    Directory of Open Access Journals (Sweden)

    James C Stegen

    2015-05-01

    Full Text Available Ecological community assembly is governed by a combination of (i selection resulting from among-taxa differences in performance; (ii dispersal resulting from organismal movement; and (iii ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.

  7. Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experiments

    Science.gov (United States)

    Shi, Y.; Zwolinski, M. D.; Schreiber, M. E.; Bahr, J. M.; Sewell, G. W.; Hickey, W. J.

    1999-01-01

    This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantly Bacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65% of the Bacteria community was no longer identifiable by the phylum or subclass probes used. The latter result suggested that toluene exposure fostered the proliferation of phylotype(s) that were otherwise minor constituents of the

  8. Enterotypes in the landscape of gut microbial community composition

    DEFF Research Database (Denmark)

    Costea, Paul I.; Hildebrand, Falk; Manimozhiyan, Arumugam

    2017-01-01

    Population stratification is a useful approach for a better understanding of complex biological problems in human health and wellbeing. The proposal that such stratification applies to the human gut microbiome, in the form of distinct community composition types termed enterotypes, has been met...... with both excitement and controversy. In view of accumulated data and re-analyses since the original work, we revisit the concept of enterotypes, discuss different methods of dividing up the landscape of possible microbiome configurations, and put these concepts into functional, ecological and medical...... contexts. As enterotypes are of use in describing the gut microbial community landscape and may become relevant in clinical practice, we aim to reconcile differing views and encourage a balanced application of the concept....

  9. Microbial communities of the Lemon Creek Glacier show subtle structural variation yet stable phylogenetic composition over space and time

    Directory of Open Access Journals (Sweden)

    Cody Springer Sheik

    2015-05-01

    Full Text Available Glaciers are geologically important yet transient ecosystems that support diverse, biogeochemically significant microbial communities. During the melt season glaciers undergo dramatic physical, geochemical and biological changes that exert great influence on downstream biogeochemical cycles. Thus, we sought to understand the temporal melt-season dynamics of microbial communities and associated geochemistry at the terminus of Lemon Creek Glacier (LCG in coastal southern Alaska. Due to late season snowfall, sampling of LCG occurred in three interconnected areas: proglacial Lake Thomas, the lower glacial outflow stream and the glacier’s terminus. LCG associated microbial communities were phylogenetically diverse and varied by sampling location. However, Betaproteobacteria, Alphaproteobacteria and Bacteroidetes dominated communities at all sampling locations. Strict anaerobic groups such as methanogens, SR1, and OP11 were also recovered from glacier outflows, indicating anoxic conditions in at least some portions of the LCG subglacial environment. Microbial community structure was significantly correlated with sampling location and sodium concentrations. Microbial communities sampled from terminus outflow waters exhibited day-to-day fluctuation in taxonomy and phylogenetic similarity. However, these communities were not significantly different from randomly constructed communities from all three sites. These results indicate that glacial outflows share a large proportion of phylogenetic overlap with downstream environments and that the observed significant shifts in community structure are driven by changes in relative abundance of different taxa, and not complete restructuring of communities. We conclude that LCG glacial discharge hosts a diverse and relatively stable microbiome that shifts at fine taxonomic scales in response to geochemistry and likely water residence time.

  10. Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

    Science.gov (United States)

    Xiao, Yunhua; Liu, Xueduan; Ma, Liyuan; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Zhang, Xian; Hao, Xiaodong; Dong, Weiling; She, Siyuan; Yin, Huaqun

    2016-08-01

    The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

  11. In-Drift Microbial Communities Model Validation Calculations

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Jolley

    2001-09-24

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  12. In-Drift Microbial Communities Model Validation Calculation

    Energy Technology Data Exchange (ETDEWEB)

    D. M. Jolley

    2001-10-31

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  13. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    Energy Technology Data Exchange (ETDEWEB)

    D.M. Jolley

    2001-12-18

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data.

  14. In-Drift Microbial Communities Model Validation Calculations

    International Nuclear Information System (INIS)

    Jolley, D.M.

    2001-01-01

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS MandO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS MandO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS MandO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS MandO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data

  15. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    International Nuclear Information System (INIS)

    D.M. Jolley

    2001-01-01

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M andO 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M andO 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M andO 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M andO (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data

  16. Iron Homeostasis in Yellowstone National Park Hot Spring Microbial Communities

    Science.gov (United States)

    Brown, I.; Tringe, S. G.; Franklin, H.; Bryant, D. A.; Klatt, C. G.; Sarkisova, S. A.; Guevara, M.

    2010-01-01

    It has been postulated that life may have originated on Earth, and possibly on Mars, in association with hydrothermal activity and high concentrations of ferrous iron. However, it is not clear how an iron-rich thermal hydrosphere could be hospitable to microbes, since reduced iron appears to stimulate oxidative stress in all domains of life and particularly in oxygenic phototrophs. Therefore, the study of microbial diversity in iron-depositing hot springs (IDHS) and the mechanisms of iron homeostasis and suppression of oxidative stress may help elucidate how Precambrian organisms could withstand the extremely high concentrations of reactive oxygen species (ROS) produced by interaction between environmental Fe(2+) and O2. Proteins and clusters of orthologous groups (COGs) involved in the maintenance of Fe homeostasis found in cyanobacteria (CB) inhabiting environments with high and low [Fe] were main target of this analysis. Preliminary results of the analysis suggest that the Chocolate Pots (CP) microbial community is heavily dominated by phototrophs from the cyanobacteria (CB), Chloroflexi and Chlorobi phyla, while the Mushroom Spring (MS) effluent channel harbors a more diverse community in which Chloroflexi are the dominant phototrophs. It is speculated that CB inhabiting IDHS have an increased tolerance to both high concentrations of Fe(2+) and ROS produced in the Fenton reaction. This hypothesis was explored via a comparative analysis of the diversity of proteins and COGs involved in Fe and redox homeostasis in the CP and MS microbiomes.

  17. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    Science.gov (United States)

    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.

  18. Similar microbial communities found on two distant seafloor basalts

    Directory of Open Access Journals (Sweden)

    Esther eSinger

    2015-12-01

    Full Text Available The oceanic crust forms two thirds of the Earth’s surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō’ihi Seamount, Hawai’i, and the East Pacific Rise (EPR (9˚N. Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō’ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy.

  19. Microbial community analysis of anaerobic reactors treating soft drink wastewater.

    Directory of Open Access Journals (Sweden)

    Takashi Narihiro

    Full Text Available The anaerobic packed-bed (AP and hybrid packed-bed (HP reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95% after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs. Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR.

  20. Impact of fomesafen on the soil microbial communities in soybean fields in Northeastern China.

    Science.gov (United States)

    Wu, Xiao-Hu; Zhang, Ying; Du, Peng-Qiang; Xu, Jun; Dong, Feng-Shou; Liu, Xin-Gang; Zheng, Yong-Quan

    2018-02-01

    Fomesafen, a widely adopted residual herbicide, is used throughout the soybean region of northern China for the spring planting. However, the ecological risks of using fomesafen in soil remain unknown. The aim of this work was to evaluate the impact of fomesafen on the microbial community structure of soil using laboratory and field experiments. Under laboratory conditions, the application of fomesafen at concentrations of 3.75 and 37.5mg/kg decreased the basal respiration (R B ) and microbial biomass carbon (MBC). In contrast, treatment with 375mg/kg of fomesafen resulted in a significant decrease in the R B , MBC, abundance of both Gram+ and Gram- bacteria, and fungal biomass. Analysis of variance showed that the treatment accounted for most of the variance (38.3%) observed in the soil microbial communities. Furthermore, the field experiment showed that long-term fomesafen application in continuously cropped soybean fields affected the soil bacterial community composition by increasing the relative average abundance of Proteobacteria and Actinobacteria species and decreasing the abundance of Verrucomicrobia species. In addition, Acidobacteria and Chloroflexi species showed a pattern of activation-inhibition. Taken together, our results suggest that the application of fomesafen can affect the community structure of soil bacteria in the spring planting soybean region of northern China. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon.

    Science.gov (United States)

    Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

    2015-01-01

    The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.

  2. Influence of cotton crop development and level of irrigation of microbial community structure

    Science.gov (United States)

    Soil microbial population densities can easily reach one billion cells per gram of soil;and soil microbial diversity has been shown to exceed fifty thousand individual species per gram of soil. Soil type and underlying soil structure are considered primary determinants of microbial community structu...

  3. Impact of simulated acid rain on soil microbial community function in Masson pine seedlings

    Directory of Open Access Journals (Sweden)

    Lin Wang

    2014-09-01

    Conclusion: The results obtained indicated that the higher acid load decreased the soil microbial activity and no effects on soil microbial diversity assessed by Biolog of potted Masson pine seedlings. Simulated acid rain also changed the metabolic capability of the soil microbial community.

  4. Effect of monospecific and mixed sea-buckthorn (Hippophae rhamnoides plantations on the structure and activity of soil microbial communities.

    Directory of Open Access Journals (Sweden)

    Xuan Yu

    Full Text Available This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC, H. rhamnoides and Pinus tabulaeformis (SY, and H. rhamnoides and Platycladus orientalis (SB. Results showed that total organic carbon (TOC, total nitrogen, and ammonium (NH4(+ contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4(+ content, nitrate content (NH3(-, and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations.

  5. Microbial community evolution during simulated managed aquifer recharge in response to different biodegradable dissolved organic carbon (BDOC) concentrations

    KAUST Repository

    Li, Dong

    2013-05-01

    This study investigates the evolution of the microbial community in laboratory-scale soil columns simulating the infiltration zone of managed aquifer recharge (MAR) systems and analogous natural aquifer sediment ecosystems. Parallel systems were supplemented with either moderate (1.1 mg/L) or low (0.5 mg/L) biodegradable dissolved organic carbon (BDOC) for a period of six months during which time, spatial (1 cm, 30 cm, 60 cm, 90 cm, and 120 cm) and temporal (monthly) analyses of sediment-associated microbial community structure were analyzed. Total microbial biomass associated with sediments was positively correlated with BDOC concentration where a significant decline in BDOC was observed along the column length. Analysis of 16S rRNA genes indicated dominance by Bacteria with Archaea comprising less than 1 percent of the total community. Proteobacteria was found to be the major phylum in samples from all column depths with contributions from Betaproteobacteria, Alphaproteobacteria and Gammaproteobacteria. Microbial community structure at all the phylum, class and genus levels differed significantly at 1 cm between columns receiving moderate and low BDOC concentrations; in contrast strong similarities were observed both between parallel column systems and across samples from 30 to 120 cm depths. Samples from 1 cm depth of the low BDOC columns exhibited higher microbial diversity (expressed as Shannon Index) than those at 1 cm of moderate BDOC columns, and both increased from 5.4 to 5.9 at 1 cm depth to 6.7-8.3 at 30-120 cm depths. The microbial community structure reached steady state after 3-4 months since the initiation of the experiment, which also resulted in an improved DOC removal during the same time period. This study suggested that BDOC could significantly influence microbial community structure regarding both composition and diversity of artificial MAR systems and analogous natural aquifer sediment ecosystems. © 2013 Elsevier Ltd.

  6. Increasing atmospheric deposition nitrogen and ammonium reduced microbial activity and changed the bacterial community composition of red paddy soil.

    Science.gov (United States)

    Zhou, Fengwu; Cui, Jian; Zhou, Jing; Yang, John; Li, Yong; Leng, Qiangmei; Wang, Yangqing; He, Dongyi; Song, Liyan; Gao, Min; Zeng, Jun; Chan, Andy

    2018-03-27

    Atmospheric deposition nitrogen (ADN) increases the N content in soil and subsequently impacts microbial activity of soil. However, the effects of ADN on paddy soil microbial activity have not been well characterized. In this study, we studied how red paddy soil microbial activity responses to different contents of ADN through a 10-months ADN simulation on well managed pot experiments. Results showed that all tested contents of ADN fluxes (27, 55, and 82kgNha -1 when its ratio of NH 4 + /NO 3 - -N (R N ) was 2:1) enhanced the soil enzyme activity and microbial biomass carbon and nitrogen and 27kgNha -1 ADN had maximum effects while comparing with the fertilizer treatment. Generally, increasing of both ADN flux and R N (1:2, 1:1 and 2:1 with the ADN flux of 55kgNha -1 ) had similar reduced effects on microbial activity. Furthermore, both ADN flux and R N significantly reduced soil bacterial alpha diversity (pADN flux and R N were the main drivers in shaping paddy soil bacteria community. Overall, the results have indicated that increasing ADN flux and ammonium reduced soil microbial activity and changed the soil bacterial community. The finding highlights how paddy soil microbial community response to ADN and provides information for N management in paddy soil. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

    Science.gov (United States)

    Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

    2013-10-15

    It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the

  8. Evaluating the use of diversity indices to distinguish between microbial communities with different traits.

    Science.gov (United States)

    Feranchuk, Sergey; Belkova, Natalia; Potapova, Ulyana; Kuzmin, Dmitry; Belikov, Sergei

    2018-05-23

    Several measures of biodiversity are commonly used to describe microbial communities, analyzed using 16S gene sequencing. A wide range of available experiments on 16S gene sequencing allows us to present a framework for a comparison of various diversity indices. The criterion for the comparison is the statistical significance of the difference in index values for microbial communities with different traits, within the same experiment. The results of the evaluation indicate that Shannon diversity is the most effective measure among the commonly used diversity indices. The results also indicate that, within the present framework, the Gini coefficient as a diversity index is comparable to Shannon diversity, despite the fact that the Gini coefficient, as a diversity estimator, is far less popular in microbiology than several other measures. Copyright © 2018 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  9. Metals other than uranium affected microbial community composition in a historical uranium-mining site.

    Science.gov (United States)

    Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

    2015-12-01

    To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

  10. Microbial communities associated with the larval gut and eggs of the Western corn rootworm.

    Directory of Open Access Journals (Sweden)

    Flavia Dematheis

    Full Text Available BACKGROUND: The western corn rootworm (WCR is one of the economically most important pests of maize. A better understanding of microbial communities associated with guts and eggs of the WCR is required in order to develop new pest control strategies, and to assess the potential role of the WCR in the dissemination of microorganisms, e.g., mycotoxin-producing fungi. METHODOLOGY/PRINCIPAL FINDINGS: Total community (TC DNA was extracted from maize rhizosphere, WCR eggs, and guts of larvae feeding on maize roots grown in three different soil types. Denaturing gradient gel electrophoresis (DGGE and sequencing of 16S rRNA gene and ITS fragments, PCR-amplified from TC DNA, were used to investigate the fungal and bacterial communities, respectively. Microorganisms in the WCR gut were not influenced by the soil type. Dominant fungal populations in the gut were affiliated to Fusarium spp., while Wolbachia was the most abundant bacterial genus. Identical ribosomal sequences from gut and egg samples confirmed a transovarial transmission of Wolbachia sp. Betaproteobacterial DGGE indicated a stable association of Herbaspirillum sp. with the WCR gut. Dominant egg-associated microorganisms were the bacterium Wolbachia sp. and the fungus Mortierella gamsii. CONCLUSION/SIGNIFICANCE: The soil type-independent composition of the microbial communities in the WCR gut and the dominance of only a few microbial populations suggested either a highly selective environment in the gut lumen or a high abundance of intracellular microorganisms in the gut epithelium. The dominance of Fusarium species in the guts indicated WCR larvae as vectors of mycotoxin-producing fungi. The stable association of Herbaspirillum sp. with WCR gut systems and the absence of corresponding sequences in WCR eggs suggested that this bacterium was postnatally acquired from the environment. The present study provided new insights into the microbial communities associated with larval guts and eggs of

  11. Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea

    KAUST Repository

    Ziegler, Maren; Roik, Anna Krystyna; Porter, Adam; Zubier, Khalid; Mudarris, Mohammed S.; Ormond, Rupert; Voolstra, Christian R.

    2016-01-01

    Coral-associated bacteria play an increasingly recognized part in coral health. We investigated the effect of local anthropogenic impacts on coral microbial communities on reefs near Jeddah, the largest city on the Saudi Arabian coast of the central Red Sea. We analyzed the bacterial community structure of water and corals (Pocillopora verrucosa and Acropora hemprichii) at sites that were relatively unimpacted, exposed to sedimentation & local sewage, or in the discharge area of municipal wastewaters. Coral microbial communities were significantly different at impacted sites: in both corals the main symbiotic taxon decreased in abundance. In contrast, opportunistic bacterial families, such as e.g. Vibrionaceae and Rhodobacteraceae, were more abundant in corals at impacted sites. In conclusion, microbial community response revealed a measurable footprint of anthropogenic impacts to coral ecosystems close to Jeddah, even though the corals appeared visually healthy.

  12. Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea

    KAUST Repository

    Ziegler, Maren

    2016-01-04

    Coral-associated bacteria play an increasingly recognized part in coral health. We investigated the effect of local anthropogenic impacts on coral microbial communities on reefs near Jeddah, the largest city on the Saudi Arabian coast of the central Red Sea. We analyzed the bacterial community structure of water and corals (Pocillopora verrucosa and Acropora hemprichii) at sites that were relatively unimpacted, exposed to sedimentation & local sewage, or in the discharge area of municipal wastewaters. Coral microbial communities were significantly different at impacted sites: in both corals the main symbiotic taxon decreased in abundance. In contrast, opportunistic bacterial families, such as e.g. Vibrionaceae and Rhodobacteraceae, were more abundant in corals at impacted sites. In conclusion, microbial community response revealed a measurable footprint of anthropogenic impacts to coral ecosystems close to Jeddah, even though the corals appeared visually healthy.

  13. Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters

    International Nuclear Information System (INIS)

    Mosher, Jennifer J.; Drake, Meghan M.; Carroll, Susan L.; Yang, Zamin K.; Schadt, Christopher W.; Brown, Stephen D.; Podar, Mircea; Hazen, Terry C.; Arkin, Adam P.; Phelps, Tommy J.; Palumbo, Anthony V.; Faybishenko, Boris A.; Elias, Dwayne A.

    2010-01-01

    The Department of Energy site at Hanford, WA, has been historically impacted by U and Cr from the nuclear weapons industry. In an attempt to stimulate microbial remediation of these metals, in-situ lactate enrichment experiments are ongoing. In order to bridge the gap from the laboratory to the field, we inoculated triplicate anaerobic, continuous-flow glass reactors with groundwater collected from well Hanford 100-H in order to obtain a stable, enriched community while selecting for metal-reducing bacteria. Each reactor was fed from a single carboy containing defined media with 30 mM lactate at a rate of 0.223 ml/min under continuous nitrogen flow at 9 ml/min. Cell counts, organic acids, gDNA (for qPCR and pyrosequencing) and gases were sampled during the experiment. Cell counts remained low (less than 1x107 cells/ml) during the first two weeks of the experiment, but by day 20, had reached a density greater than 1x108 cells/ml. Metabolite analysis showed a decrease in the lactate concentrations over time. Pyruvate concentrations ranged from 20-40 uM the first week of the experiment then was undetectable after day 10. Likewise, formate appeared in the reactors during the first week with concentrations of 1.48-1.65 mM at day 7 then the concentrations decreased to 0.69-0.95 on day 10 and were undetectable on day 15. Acetate was present in low amounts on day 3 (0.15-0.33 mM) and steadily increased to 3.35-5.22 mM over time. Similarly, carbon dioxide was present in low concentrations early on and increased to 0.28-0.35 mM as the experiment progressed. We also were able to detect low amounts of methane (10-20 uM) during the first week of the experiment, but by day 10 the methane was undetectable. From these results and pyrosequencing analysis, we conclude that a shift in the microbial community dynamics occurred over time to eventually form a stable and enriched microbial community. Comprehensive investigations such as these allow for the examination of not only which

  14. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

    Directory of Open Access Journals (Sweden)

    Stéphane Uroz

    Full Text Available In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France. The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource

  15. Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient.

    Science.gov (United States)

    Mondav, Rhiannon; McCalley, Carmody K; Hodgkins, Suzanne B; Frolking, Steve; Saleska, Scott R; Rich, Virginia I; Chanton, Jeff P; Crill, Patrick M

    2017-08-01

    Biogenic production and release of methane (CH 4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

    Science.gov (United States)

    Vega Thurber, Rebecca; Burkepile, Deron E.; Correa, Adrienne M. S.; Thurber, Andrew R.; Shantz, Andrew A.; Welsh, Rory; Pritchard, Catharine; Rosales, Stephanie

    2012-01-01

    With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs. PMID:22957055

  17. Macroalgae decrease growth and alter microbial community structure of the reef-building coral, Porites astreoides.

    Directory of Open Access Journals (Sweden)

    Rebecca Vega Thurber

    Full Text Available With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1 increases or 2 decreases in microbial taxa already present in corals, 3 establishment of new taxa to the coral microbiome, and 4 vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs.

  18. Microbially influenced corrosion communities associated with fuel-grade ethanol environments.

    Science.gov (United States)

    Williamson, Charles H D; Jain, Luke A; Mishra, Brajendra; Olson, David L; Spear, John R

    2015-08-01

    Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these "newer fuels" as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion.

  19. Influence of black carbon addition on phenanthrene dissipation and microbial community structure in soil

    International Nuclear Information System (INIS)

    Wang Ping; Wang Haizhen; Wu Laosheng; Di Hongjie; He Yan; Xu Jianming

    2012-01-01

    Biodegradation processes and changes in microbial community structure were investigated in black carbon (BC) amended soils in a laboratory experiment using two soils (black soil and red soil). We applied different percentages of charcoal as BC (0%, 0.5% and 1% by weight) with 100 mg kg −1 of phenanthrene. Soil samples were collected at different incubation times (0, 7, 15, 30, 60, 120 d). The amendment with BC caused a marked decrease in the dissipation (ascribed to mainly degradation and/or sequestration) of phenanthrene residues from soil. Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil, 0.5% BC amendments were higher. There were significant changes in the PLFA pattern in phenanthrene-spiked soils with time but BC had little effect on the microbial community structure of phenanthrene-spiked soils, as indicated by principal component analysis (PCA) of the PLFA signatures. - Highlights: ► Extracted phenanthrene increased substantially as the BC amount increased. ► Extracted phenanthrene in black soil with 1% BC were higher, oppositely in red soil. ► BC caused a marked decrease in the dissipation of phenanthrene from soil. ► PLFA pattern in phenanthrene-spiked soils with time had significant changes. - BC amendments on phenanthrene extraction were different for two soils and time was a more effective factor in microbial community changes.

  20. Microbial community changes in hydraulic fracturing fluids and produced water from shale gas extraction.

    Science.gov (United States)

    Murali Mohan, Arvind; Hartsock, Angela; Bibby, Kyle J; Hammack, Richard W; Vidic, Radisav D; Gregory, Kelvin B

    2013-11-19

    Microbial communities associated with produced water from hydraulic fracturing are not well understood, and their deleterious activity can lead to significant increases in production costs and adverse environmental impacts. In this study, we compared the microbial ecology in prefracturing fluids (fracturing source water and fracturing fluid) and produced water at multiple time points from a natural gas well in southwestern Pennsylvania using 16S rRNA gene-based clone libraries, pyrosequencing, and quantitative PCR. The majority of the bacterial community in prefracturing fluids constituted aerobic species affiliated with the class Alphaproteobacteria. However, their relative abundance decreased in produced water with an increase in halotolerant, anaerobic/facultative anaerobic species affiliated with the classes Clostridia, Bacilli, Gammaproteobacteria, Epsilonproteobacteria, Bacteroidia, and Fusobacteria. Produced water collected at the last time point (day 187) consisted almost entirely of sequences similar to Clostridia and showed a decrease in bacterial abundance by 3 orders of magnitude compared to the prefracturing fluids and produced water samplesfrom earlier time points. Geochemical analysis showed that produced water contained higher concentrations of salts and total radioactivity compared to prefracturing fluids. This study provides evidence of long-term subsurface selection of the microbial community introduced through hydraulic fracturing, which may include significant implications for disinfection as well as reuse of produced water in future fracturing operations.

  1. Effects of microcystins contamination on soil enzyme activities and microbial community in two typical lakeside soils.

    Science.gov (United States)

    Cao, Qing; Steinman, Alan D; Su, Xiaomei; Xie, Liqiang

    2017-12-01

    A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L -1 ) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application. In contrast, dehydrogenase activity was stimulated in the 1000 μg treatment, and a stimulatory effect also occurred with soil respiration in contaminated soil. The metabolic profiles of the microbial communities indicated that overall carbon metabolic activity in the soils treated with high microcystin concentrations was inhibited, and high concentrations of microcystin also led to different patterns of potential carbon utilization. High microcystin concentrations (100, 1000 μg eq. MC-LR L -1 in Soil A; 10, 100 1000 μg eq. MC-LR L -1 in Soil B) significantly decreased soil potential nitrification rate. Furthermore, the decrease in soil potential nitrification rate was positively correlated with the decrease of the amoA gene abundance, which corresponds to the ammonia-oxidizing bacterial community. We conclude that application of microcystin-enriched irrigation water can significantly impact soil microbial community structure and function. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Profiling of dynamic changes in the microbial community during the soy sauce fermentation process.

    Science.gov (United States)

    Wei, Quanzeng; Wang, Hongbin; Chen, Zhixin; Lv, Zhijia; Xie, Yufeng; Lu, Fuping

    2013-10-01

    Soy sauce is a traditional condiment manufactured by natural inoculation and mixed culture fermentation. As is well known, it is the microbial community that plays an important role in the formation of its flavors. However, to date, its dynamic changes during the long period of fermentation process are still unclear, intensively constraining the improvement and control of the soy sauce quality. In this work, we revealed the dynamic changes of the microbial community by combining a cultured dependent method and a cultured independent method of polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis. Results indicated that the two methods verified and complemented each other in profiling microbial community, and that significant dynamics of the microbial community existed during the fermentation process, especially the strong inhibition of the growth of most of the microbes when entering into the mash stage from the koji stage. In the analysis of bacterial community, Staphylococcus and Bacillus were found to be the dominant bacteria and detected in the whole fermentation process. Kurthia and Klebsiella began to appear in the koji stage and then fade away in the early stage of the mash fermentation. In the analysis of fungal community, Aspergillus sojae and Zygosaccharomyces rouxii were found to be the dominant fungi in the koji and mash fermentation, respectively. It was clearly shown that when A. sojae decreased and disappeared in the middle stage of the mash fermentation, Z. rouxii appeared and increased at the meantime. Aspergillus parasiticus, Trichosporon ovoides and Trichosporon asahii also appeared in the koji and the early period of the mash fermentation and disappeared thereafter. Similar to Z. rouxii, Millerozyma farinosa and Peronospora farinosa were also found spontaneously which appeared in the mid-late period of the mash fermentation. The principal component analysis suggested that the microbial community underwent significant changes in

  3. Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar

    OpenAIRE

    Bletz, Molly C.; Archer, Holly; Harris, Reid N.; McKenzie, Valerie J.; Rabemananjara, Falitiana C. E.; Rakotoarison, Andolalao; Vences, Miguel

    2017-01-01

    Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Usin...

  4. Mechanisms of pollution induced community tolerance in a soil microbial community exposed to Cu

    International Nuclear Information System (INIS)

    Wakelin, Steven; Gerard, Emily; Black, Amanda; Hamonts, Kelly; Condron, Leo; Yuan, Tong; Nostrand, Joy van; Zhou, Jizhong; O'Callaghan, Maureen

    2014-01-01

    Pollution induced community tolerance (PICT) to Cu 2+ , and co-tolerance to nanoparticulate Cu, ionic silver (Ag + ), and vancomycin were measured in field soils treated with Cu 2+ 15 years previously. EC 50 values were determined using substrate induced respiration and correlations made against soil physicochemical properties, microbial community structure, physiological status (qCO 2 ; metabolic quotient), and abundances of genes associated with metal and antibiotic resistance. Previous level of exposure to copper was directly (P  2+ , and also of nanoparticle Cu. However, Cu-exposed communities had no co-tolerance to Ag + and had increased susceptibly to vancomycin. Increased tolerance to both Cu correlated (P  + or vancomycin. • Tolerance not due to shifts in community composition or resistance genes. - Pollution induced community tolerance to Cu was linked with increased metabolic quotient but not changes in community composition or abundance of metal resistance genes in a field soil

  5. Effects of Pheretima Guillelmi Cultivation Time on Microbial Community Diversity and Characteristics of Carbon Metabolism in Vegetable Soil

    Directory of Open Access Journals (Sweden)

    ZHENG Xian-qing

    2015-12-01

    Full Text Available In order to study the effect of different biological tillage time (Pheretima guillelmi on soil microbial community metabolic functions in different soil depths, we set a location test in vegetable field at Chongming Island in Shanghai to analyze the changes of soil microbial community and carbon utilization abilities (Average well- color development, AWCD by using biolog eco-plate method. The three-year results showed that: Bio-tillage significantly improved microbial community activity, and with the increase of tillage years, biological tillage could make the average AWCD 3 to 7 times higher. The Simpson index and Shannon index of the biological tillage treatments were significantly higher than that of the control. The cumulative increase of 0~5 cm soil layer was 49 and 6.28 respectively, and the cumulative increase of 5~20 cm soil layer was 31 and 2.55 respectively. Earthworm bio-tillage significantly increased the soil microbial metabolic ability of 6 kinds of carbon sources, and increased the carbohydrate metabolism activity. In this study, earthworm bio-tillage is an effective way to increase the microbial activity of microbial soil.

  6. Passive warming effect on soil microbial community and humic substance degradation in maritime Antarctic region.

    Science.gov (United States)

    Kim, Dockyu; Park, Ha Ju; Kim, Jung Ho; Youn, Ui Joung; Yang, Yung Hun; Casanova-Katny, Angélica; Vargas, Cristina Muñoz; Venegas, Erick Zagal; Park, Hyun; Hong, Soon Gyu

    2018-06-01

    Although the maritime Antarctic has undergone rapid warming, the effects on indigenous soil-inhabiting microorganisms are not well known. Passive warming experiments using open-top chamber (OTC) have been performed on the Fildes Peninsula in the maritime Antarctic since 2008. When the soil temperature was measured at a depth of 2-5 cm during the 2013-2015 summer seasons, the mean temperature inside OTC (OTC-In) increased by approximately 0.8 °C compared with outside OTC (OTC-Out), while soil chemical and physical characteristics did not change. Soils (2015 summer) from OTC-In and OTC-Out were subjected to analysis for change in microbial community and degradation rate of humic substances (HS, the largest pool of recalcitrant organic carbon in soil). Archaeal and bacterial communities in OTC-In were minimally affected by warming compared with those in OTC-Out, with archaeal methanogenic Thermoplasmata slightly increased in abundance. The abundance of heterotrophic fungi Ascomycota was significantly altered in OTC-In. Total bacterial and fungal biomass in OTC-In increased by 20% compared to OTC-Out, indicating that this may be due to increased microbial degradation activity for soil organic matter (SOM) including HS, which would result in the release of more low-molecular-weight growth substrates from SOM. Despite the effects of warming on the microbial community over the 8-years-experiments warming did not induce any detectable change in content or structure of polymeric HS. These results suggest that increased temperature may have significant and direct effects on soil microbial communities inhabiting maritime Antarctic and that soil microbes would subsequently provide more available carbon sources for other indigenous microbes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Characterization and identification of microbial communities in bovine necrotic vulvovaginitis.

    Science.gov (United States)

    Shpigel, N Y; Adler-Ashkenazy, L; Scheinin, S; Goshen, T; Arazi, A; Pasternak, Z; Gottlieb, Y

    2017-01-01

    Bovine necrotic vulvovaginitis (BNVV) is a severe and potentially fatal disease of post-partum cows that emerged in Israel after large dairy herds were merged. While post-partum cows are commonly affected by mild vulvovaginitis (BVV), in BNVV these benign mucosal abrasions develop into progressive deep necrotic lesions leading to sepsis and death if untreated. The etiology of BNVV is still unknown and a single pathogenic agent has not been found. We hypothesized that BNVV is a polymicrobial disease where the normally benign vaginal microbiome is remodeled and affects the local immune response. To this end, we compared the histopathological changes and the microbial communities using 16S rDNA metagenetic technique in biopsies taken from vaginal lesions in post-partum cows affected by BVV and BNVV. The hallmark of BNVV was the formation of complex polymicrobial communities in the submucosal fascia and abrogation of neutrophil recruitment in these lesions. Additionally, there was a marked difference in the composition of bacterial communities in the BNVV lesions in comparison to the benign BVV lesions. This difference was characterized by the abundance of Bacteroidetes and lower total community membership in BNVV. Indicator taxa for BNVV were Parvimonas, Porphyromonas, unclassified Veillonellaceae, Mycoplasma and Bacteroidetes, whereas unclassified Clostridiales was an indicator for BVV. The results support a polymicrobial etiology for BNVV. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Ananke: temporal clustering reveals ecological dynamics of microbial communities

    Directory of Open Access Journals (Sweden)

    Michael W. Hall

    2017-09-01

    Full Text Available Taxonomic markers such as the 16S ribosomal RNA gene are widely used in microbial community analysis. A common first step in marker-gene analysis is grouping genes into clusters to reduce data sets to a more manageable size and potentially mitigate the effects of sequencing error. Instead of clustering based on sequence identity, marker-gene data sets collected over time can be clustered based on temporal correlation to reveal ecologically meaningful associations. We present Ananke, a free and open-source algorithm and software package that complements existing sequence-identity-based clustering approaches by clustering marker-gene data based on time-series profiles and provides interactive visualization of clusters, including highlighting of internal OTU inconsistencies. Ananke is able to cluster distinct temporal patterns from simulations of multiple ecological patterns, such as periodic seasonal dynamics and organism appearances/disappearances. We apply our algorithm to two longitudinal marker gene data sets: faecal communities from the human gut of an individual sampled over one year, and communities from a freshwater lake sampled over eleven years. Within the gut, the segregation of the bacterial community around a food-poisoning event was immediately clear. In the freshwater lake, we found that high sequence identity between marker genes does not guarantee similar temporal dynamics, and Ananke time-series clusters revealed patterns obscured by clustering based on sequence identity or taxonomy. Ananke is free and open-source software available at https://github.com/beiko-lab/ananke.

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

    Science.gov (United States)

    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.

  10. Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems.

    Science.gov (United States)

    Potter, Caitlin; Freeman, Chris; Golyshin, Peter N; Ackermann, Gail; Fenner, Nathalie; McDonald, James E; Ehbair, Abdassalam; Jones, Timothy G; Murphy, Loretta M; Creer, Simon

    2017-09-12

    Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat 'mesocosm cores' taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. 'Drought-responsive' OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.

  11. [Oxidation of sulfur-containing substrates by aboriginal and experimentally designed microbial communities].

    Science.gov (United States)

    Pivovarova, T A; Bulaev, A G; Roshchupko, P V; Belyĭ, A V; Kondrat'eva, T F

    2012-01-01

    Aboriginal and experimental (constructed of pure microbial cultures) communities of acidophilic chemolithotrophs have been studied. The oxidation of elemental sulfur, sodium thiosulfate, and potassium tetrathionate as sole sources of energy has been monitored. The oxidation rate of the experimental community is higher as compared to the aboriginal community isolated from a flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore. The degree of oxidation of the mentioned S substrates amounts to 17.91, 68.30, and 93.94% for the experimental microbial community and to 10.71, 56.03, and 79.50% for the aboriginal community, respectively. The degree of oxidation of sulfur sulfide forms in the ore flotation concentrate is 59.15% by the aboriginal microbial community and 49.40% by the experimental microbial community. Despite a higher rate of oxidation of S substrates as a sole source of energy by the experimental microbial community, the aboriginal community oxidizes S substrates at a higher rate in the flotation concentrate of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ore, from which it was isolated. Bacterial-chemical oxidation of the flotation concentrate by the aboriginal microbial community allows for the extraction of an additional 32.3% of gold from sulfide minerals, which is by 5.7% larger compared to the yield obtained by the experimental microbial community.

  12. Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

    Science.gov (United States)

    Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

    2015-01-01

    Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils.

    Science.gov (United States)

    Espenberg, Mikk; Truu, Marika; Mander, Ülo; Kasak, Kuno; Nõlvak, Hiie; Ligi, Teele; Oopkaup, Kristjan; Maddison, Martin; Truu, Jaak

    2018-03-16

    Tropical peatlands, which play a crucial role in the maintenance of different ecosystem services, are increasingly drained for agriculture, forestry, peat extraction and human settlement purposes. The present study investigated the differences between natural and drained sites of a tropical peatland in the community structure of soil bacteria and archaea and their potential to perform nitrogen transformation processes. The results indicate significant dissimilarities in the structure of soil bacterial and archaeal communities as well as nirK, nirS, nosZ, nifH and archaeal amoA gene-possessing microbial communities. The reduced denitrification and N 2 -fixing potential was detected in the drained tropical peatland soil. In undisturbed peatland soil, the N 2 O emission was primarily related to nirS-type denitrifiers and dissimilatory nitrate reduction to ammonium, while the conversion of N 2 O to N 2 was controlled by microbes possessing nosZ clade I genes. The denitrifying microbial community of the drained site differed significantly from the natural site community. The main reducers of N 2 O were microbes harbouring nosZ clade II genes in the drained site. Additionally, the importance of DNRA process as one of the controlling mechanisms of N 2 O fluxes in the natural peatlands of the tropics revealed from the results of the study.

  14. Systematic evaluation of bias in microbial community profiles induced by whole genome amplification.

    NARCIS (Netherlands)

    Direito, S.; Zaura, E.; Little, M.; Ehrenfreund, P.; Roling, W.F.M.

    2014-01-01

    Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement

  15. Systematic evaluation of bias in microbial community profiles induced by whole genome amplification

    NARCIS (Netherlands)

    Direito, S.O.L.; Zaura, E.; Little, M.; Ehrenfreund, P.; Röling, W.F.M.

    2014-01-01

    Whole genome amplification methods facilitate the detection and characterization of microbial communities in low biomass environments. We examined the extent to which the actual community structure is reliably revealed and factors contributing to bias. One widely used [multiple displacement

  16. Garlic mustard and its effects on soil microbial communities in a sandy pine forest in central Illinois

    Science.gov (United States)

    Alexander B. Faulkner; Brittany E. Pham; Truc-Quynh D. Nguyen; Kenneth E. Kitchell; Daniel S. O' Keefe; Kelly D. McConnaughay; Sherri J. Morris

    2014-01-01

    This study evaluated the impacts of garlic mustard (Alliaria petiolata), an invasive species, on soil microbial community dynamics in a pine plantation on sandy soils in central Illinois. In situ soil carbon dioxide efflux was significantly greater in invaded sites. Similarly, in vitro carbon mineralization was significantly greater for soils...

  17. Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities.

    Science.gov (United States)

    Legay, N; Baxendale, C; Grigulis, K; Krainer, U; Kastl, E; Schloter, M; Bardgett, R D; Arnoldi, C; Bahn, M; Dumont, M; Poly, F; Pommier, T; Clément, J C; Lavorel, S

    2014-10-01

    Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals

    Directory of Open Access Journals (Sweden)

    Jennifer M. Lang

    2016-01-01

    Full Text Available Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses and epilithic (biofilms on unglazed ceramic tiles communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context.

  19. Response of soil microbial communities to roxarsone pollution along a concentration gradient.

    Science.gov (United States)

    Liu, Yaci; Zhang, Zhaoji; Li, Yasong; Wen, Yi; Fei, Yuhong

    2017-07-29

    The extensive use of roxarsone (3-nitro-4-hydroxyphenylarsonic acid) as a feed additive in the broiler poultry industry can lead to environmental arsenic contamination. This study was conducted to reveal the response of soil microbial communities to roxarsone pollution along a concentration gradient. To explore the degradation process and degradation kinetics of roxarsone concentration gradients in soil, the concentration shift of roxarsone at initial concentrations of 0, 50, 100, and 200 mg/kg, as well as that of the arsenic derivatives, was detected. The soil microbial community composition and structure accompanying roxarsone degradation were investigated by high-throughput sequencing. The results showed that roxarsone degradation was inhibited by a biological inhibitor, confirming that soil microbes were absolutely essential to its degradation. Moreover, soil microbes had considerable potential to degrade roxarsone, as a high initial concentration of roxarsone resulted in a substantially increased degradation rate. The concentrations of the degradation products HAPA (3-amino-4-hydroxyphenylarsonic acid), AS(III), and AS(V) in soils were significantly positively correlated. The soil microbial community composition and structure changed significantly across the roxarsone contamination gradient, and the addition of roxarsone decreased the microbial diversity. Some bacteria tended to be inhibited by roxarsone, while Bacillus, Paenibacillus, Arthrobacter, Lysobacter, and Alkaliphilus played important roles in roxarsone degradation. Moreover, HAPA, AS(III), and AS(V) were significantly positively correlated with Symbiobacterium, which dominated soils containing roxarsone, and their abundance increased with increasing initial roxarsone concentration. Accordingly, Symbiobacterium could serve as indicator of arsenic derivatives released by roxarsone as well as the initial roxarsone concentration. This is the first investigation of microbes closely related to roxarsone

  20. Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors

    Science.gov (United States)

    Williams, Thomas R.

    2014-01-01

    ABSTRACT The aerial surfaces of plants, or phyllosphere, are microbial habitats important to plant and human health. In order to accurately investigate microbial interactions in the phyllosphere under laboratory conditions, the composition of the phyllosphere microbiota should be representative of the diversity of microorganisms residing on plants in nature. We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown plants was also significantly lower and contained relatively higher proportions of Betaproteobacteria as opposed to the Gammaproteobacteria-enriched communities on field lettuce. Incubation of field-grown Romaine lettuce plants in environmental growth chambers for 2 weeks resulted in bacterial cell densities and taxa similar to those on plants in the field but with less diverse bacterial populations overall. In comparison, the inoculation of laboratory-grown Romaine lettuce plants with either freshly collected or cryopreserved microorganisms recovered from field lettuce resulted in the development of a field-like microbiota on the lettuce within 2 days of application. The survival of an inoculated strain of Escherichia coli O157:H7 was unchanged by microbial community transfer; however, the inoculation of E. coli O157:H7 onto those plants resulted in significant shifts in the abundance of certain taxa. This finding was strictly dependent on the presence of a field-associated as opposed to a laboratory-associated microbiota on the plants. Phyllosphere microbiota transplantation in the laboratory will be useful for elucidating microbial interactions on plants that are important to agriculture and microbial food safety. PMID:25118240

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

    OpenAIRE

    Dahle, H?kon; ?kland, 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 f...

  2. Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

    Science.gov (United States)

    Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

    2008-08-01

    Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

  3. Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells.

    Science.gov (United States)

    Rago, Laura; Cristiani, Pierangela; Villa, Federica; Zecchin, Sarah; Colombo, Alessandra; Cavalca, Lucia; Schievano, Andrea

    2017-08-01

    Dissolved oxygen (DO) at cathodic interface is a critical factor influencing microbial fuel cells (MFC) performance. In this work, three MFCs were operated with cathode under different DO conditions: i) air-breathing (A-MFC); ii) water-submerged (W-MFC) and iii) assisted by photosynthetic microorganisms (P-MFC). A plateau of maximum current was reached at 1.06±0.03mA, 1.48±0.06mA and 1.66±0.04mA, increasing respectively for W-MFC, P-MFC and A-MFC. Electrochemical and microbiological tools (Illumina sequencing, confocal microscopy and biofilm cryosectioning) were used to explore anodic and cathodic biofilm in each MFC type. In all cases, biocathodes improved oxygen reduction reaction (ORR) as compared to abiotic condition and A-MFC was the best performing system. Photosynthetic cultures in the cathodic chamber supplied high DO level, up to 16mg O2 L -1 , which sustained aerobic microbial community in P-MFC biocathode. Halomonas, Pseudomonas and other microaerophilic genera reached >50% of the total OTUs. The presence of sulfur reducing bacteria (Desulfuromonas) and purple non-sulfur bacteria in A-MFC biocathode suggested that the recirculation of sulfur compounds could shuttle electrons to sustain the reduction of oxygen as final electron acceptor. The low DO concentration limited the cathode in W-MFC. A model of two different possible microbial mechanisms is proposed which can drive predominantly cathodic ORR. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Microbial community responses in forest mineral soil to compaction, organic matter removal, and vegetation control

    Science.gov (United States)

    Matt D. Busse; Samual E. Beattie; Robert F. Powers; Filpe G. Sanchez; Allan E. Tiarks

    2006-01-01

    We tested three disturbance hypotheses in young conifer plantations: H1: soil compaction and removal of surface organic matter produces sustained changes in microbial community size, activity, and structure in mineral soil; H2: microbial community characteristics in mineral soil are linked to the recovery of plant diversity...

  5. Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

    Science.gov (United States)

    Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

    2016-05-01

    The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.

  6. Impact of long-term Diesel Contamination on Soil Microbial Community Structure

    NARCIS (Netherlands)

    Sutton, N.B.; Maphosa, F.; Morillo, J.A.; Abu Al-Soud, W.; Langenhoff, A.A.M.; Grotenhuis, J.T.C.; Rijnaarts, H.H.M.; Smidt, H.

    2013-01-01

    Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical

  7. Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

    NARCIS (Netherlands)

    Kraigher, Barbara; Stres, Blaz; Hacin, Janez; Ausec, Luka; Mahne, Ivan; van Elsas, Jan D.; Mandic-Mulec, Ines

    Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled

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

    Science.gov (United States)

    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...

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

    OpenAIRE

    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 mini...

  10. Microbial community analysis in rice paddy soils irrigated by acid mine drainage contaminated water.

    Science.gov (United States)

    Sun, Min; Xiao, Tangfu; Ning, Zengping; Xiao, Enzong; Sun, Weimin

    2015-03-01

    Five rice paddy soils located in southwest China were selected for geochemical and microbial community analysis. These rice fields were irrigated with river water which was contaminated by Fe-S-rich acid mine drainage. Microbial communities were characterized by high-throughput sequencing, which showed 39 different phyla/groups in these samples. Among these phyla/groups, Proteobacteria was the most abundant phylum in all samples. Chloroflexi, Acidobacteria, Nitrospirae, and Bacteroidetes exhibited higher relative abundances than other phyla. A number of rare and candidate phyla were also detected. Moreover, canonical correspondence analysis suggested that pH, sulfate, and nitrate were significant factors that shaped the microbial community structure. In addition, a wide diversity of Fe- and S-related bacteria, such as GOUTA19, Shewanella, Geobacter, Desulfobacca, Thiobacillus, Desulfobacterium, and Anaeromyxobacter, might be responsible for biogeochemical Fe and S cycles in the tested rice paddy soils. Among the dominant genera, GOUTA19 and Shewanella were seldom detected in rice paddy soils.

  11. Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

    KAUST Repository

    Bougouffa, Salim; Yang, J. K.; Lee, O. O.; Wang, Y.; Batang, Zenon B.; Al-Suwailem, Abdulaziz M.; Qian, P. Y.

    2013-01-01

    Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

  12. Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns

    KAUST Repository

    Bougouffa, Salim

    2013-03-29

    Atlantis II and Discovery are two hydrothermal and hypersaline deep-sea pools in the Red Sea rift that are characterized by strong thermohalo-stratification and temperatures steadily peaking near the bottom. We conducted comprehensive vertical profiling of the microbial populations in both pools and highlighted the influential environmental factors. Pyrosequencing of the 16S rRNA genes revealed shifts in community structures vis-à-vis depth. High diversity and low abundance were features of the deepest convective layers despite the low cell density. Surprisingly, the brine interfaces had significantly higher cell counts than the overlying deep-sea water, yet they were lowest in diversity. Vertical stratification of the bacterial populations was apparent as we moved from the Alphaproteobacteria-dominated deep sea to the Planctomycetaceae- or Deferribacteres-dominated interfaces to the Gammaproteobacteria-dominated brine layers. Archaeal marine group I was dominant in the deep-sea water and interfaces, while several euryarchaeotic groups increased in the brine. Across sites, microbial phylotypes and abundances varied substantially in the brine interface of Discovery compared with Atlantis II, despite the near-identical populations in the overlying deep-sea waters. The lowest convective layers harbored interestingly similar microbial communities, even though temperature and heavy metal concentrations were very different. Multivariate analysis indicated that temperature and salinity were the major influences shaping the communities. The harsh conditions and the low-abundance phylotypes could explain the observed correlation in the brine pools.

  13. Characteristics of microbial community functional structure of a biological coking wastewater treatment system.

    Science.gov (United States)

    Joshi, Dev Raj; Zhang, Yu; Zhang, Hong; Gao, Yingxin; Yang, Min

    2018-01-01

    Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina HiSeq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run (500days) bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, GeoChip 5.0 detected almost all key functional gene (average 61,940 genes) categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2diox; one ring2,3diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina HiSeq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes- nbzA (nitro-aromatics), tdnB (aniline), and scnABC (thiocyanate) were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, HiSeq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants; hence it will be useful in optimization strategies for biological treatment of coking wastewater. Copyright © 2017. Published by Elsevier B.V.

  14. Microbial community dynamics in the forefield of glaciers.

    Science.gov (United States)

    Bradley, James A; Singarayer, Joy S; Anesio, Alexandre M

    2014-11-22

    Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.

  15. Impact of (±)-catechin on soil microbial communities

    Science.gov (United States)

    Kaur, Rajwant; Kaur, Surinder

    2009-01-01

    Catechin is a highly studied but controversial allelochemical reported as a component of the root exudates of Centaurea maculosa. Initial reports of high and consistent exudation rates and soil concentrations have been shown to be highly inaccurate, but the chemical has been found in root exudates at and much less frequently in soil but sporadically at high concentrations. Part of the problem of detection and measuring phytotoxicity in natural soils may be due to the confounding effect of soil microbes, and little is known about interactions between catechin and soil microbes. Here we tested the effect of catechin on soil microbial communities and the feedback of these effects to two plant species. We found that catechin inhibits microbial activity in the soil we tested, and by doing so appears to promote plant growth in the microbe-free environment. This is in striking contrast to other in vitro studies, emphasizing the highly conditional effects of the chemical and suggesting that the phytotoxic effects of catechin may be exerted through the microbes in some soils. PMID:19704908

  16. Hot spring microbial community composition, morphology, and carbon fixation: implications for interpreting the ancient rock record

    Science.gov (United States)

    Schuler, Caleb G.; Havig, Jeff R.; Hamilton, Trinity L.

    2017-11-01

    Microbial communities in hydrothermal systems exist in a range of macroscopic morphologies including stromatolites, mats, and filaments. The architects of these structures are typically autotrophic, serving as primary producers. Structures attributed to microbial life have been documented in the rock record dating back to the Archean including recent reports of microbially-related structures in terrestrial hot springs that date back as far as 3.5 Ga. Microbial structures exhibit a range of complexity from filaments to more complex mats and stromatolites and the complexity impacts preservation potential. As a result, interpretation of these structures in the rock record relies on isotopic signatures in combination with overall morphology and paleoenvironmental setting. However, the relationships between morphology, microbial community composition, and primary productivity remain poorly constrained. To begin to address this gap, we examined community composition and carbon fixation in filaments, mats, and stromatolites from the Greater Obsidian Pool Area (GOPA) of the Mud Volcano Area, Yellowstone National Park, WY. We targeted morphologies dominated by bacterial phototrophs located in close proximity within the same pool which are exposed to similar geochemistry as well as bacterial mat, algal filament and chemotrophic filaments from nearby springs. Our results indicate i) natural abundance δ13C values of biomass from these features (-11.0 to -24.3 ‰) are similar to those found in the rock record; ii) carbon uptake rates of photoautotrophic communities is greater than chemoautotrophic; iii) oxygenic photosynthesis, anoxygenic photosynthesis, and chemoautotrophy often contribute to carbon fixation within the same morphology; and iv) increasing phototrophic biofilm complexity corresponds to a significant decrease in rates of carbon fixation—filaments had the highest uptake rates whereas carbon fixation by stromatolites was significantly lower. Our data highlight

  17. Hot Spring Microbial Community Composition, Morphology, and Carbon Fixation: Implications for Interpreting the Ancient Rock Record

    Directory of Open Access Journals (Sweden)

    Caleb G. Schuler

    2017-11-01

    Full Text Available Microbial communities in hydrothermal systems exist in a range of macroscopic morphologies including stromatolites, mats, and filaments. The architects of these structures are typically autotrophic, serving as primary producers. Structures attributed to microbial life have been documented in the rock record dating back to the Archean including recent reports of microbially-related structures in terrestrial hot springs that date back as far as 3.5 Ga. Microbial structures exhibit a range of complexity from filaments to more complex mats and stromatolites and the complexity impacts preservation potential. As a result, interpretation of these structures in the rock record relies on isotopic signatures in combination with overall morphology and paleoenvironmental setting. However, the relationships between morphology, microbial community composition, and primary productivity remain poorly constrained. To begin to address this gap, we examined community composition and carbon fixation in filaments, mats, and stromatolites from the Greater Obsidian Pool Area (GOPA of the Mud Volcano Area, Yellowstone National Park, WY. We targeted morphologies dominated by bacterial phototrophs located in close proximity within the same pool which are exposed to similar geochemistry as well as bacterial mat, algal filament and chemotrophic filaments from nearby springs. Our results indicate (i natural abundance δ13C values of biomass from these features (−11.0 to −24.3‰ are similar to those found in the rock record; (ii carbon uptake rates of photoautotrophic communities is greater than chemoautotrophic; (iii oxygenic photosynthesis, anoxygenic photosynthesis, and chemoautotrophy often contribute to carbon fixation within the same morphology; and (iv increasing phototrophic biofilm complexity corresponds to a significant decrease in rates of carbon fixation—filaments had the highest uptake rates whereas carbon fixation by stromatolites was significantly lower

  18. Succession of the functional microbial communities and the metabolic functions in maize straw composting process.

    Science.gov (United States)

    Wei, Huawei; Wang, Liuhong; Hassan, Muhammad; Xie, Bing

    2018-05-01

    Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were applied to study the dynamic changes and effects of microbial community structures as well as the metabolic function of bacterial community in maize straw composting process. Results showed that humic acid contents in loosely combined humus (HA1) and stably combined humus (HA2) increased after composting and Staphylococcus, Cellulosimicrobium and Ochrobactrum possibly participated in the transformation of the process. The bacterial communities differed in different stages of the composting. Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were reported the dominant phyla throughout the process and the relative abundance of the dominant phyla varied significantly (p composting. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Colonization patterns of soil microbial communities in the Atacama Desert.

    Science.gov (United States)

    Crits-Christoph, Alexander; Robinson, Courtney K; Barnum, Tyler; Fricke, W Florian; Davila, Alfonso F; Jedynak, Bruno; McKay, Christopher P; Diruggiero, Jocelyne

    2013-11-20

    The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life. Analyses of high throughput DNA sequence data revealed that bacterial communities from six geographic locations in the hyper-arid core and along a North-South moisture gradient were structurally and phylogenetically distinct (ANOVA test for observed operating taxonomic units at 97% similarity (OTU0.03), P microbial communities' diversity metrics (least squares linear regression for observed OTU0.03 and air RH and soil conductivity, P PCoA Spearman's correlation for air RH and soil conductivity, P <0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples, with increased rates in soils from the southern locations. Our results suggest that microorganisms in the driest soils of the Atacama Desert are in a state of stasis for most of the time, but can potentially metabolize if presented with liquid water for a sufficient duration. Over geological time, rare rain events and physicochemical factors potentially played a major role in selecting micro-organisms that are most adapted to extreme desiccating conditions.

  20. Methanobacterium Dominates Biocathodic Archaeal Communities in Methanogenic Microbial Electrolysis Cells

    KAUST Repository

    Siegert, Michael

    2015-07-06

    © 2015 American Chemical Society. Methane is the primary end product from cathodic current in microbial electrolysis cells (MECs) in the absence of methanogenic inhibitors, but little is known about the archaeal communities that develop in these systems. MECs containing cathodes made from different materials (carbon brushes, or plain graphite blocks or blocks coated with carbon black and platinum, stainless steel, nickel, ferrihydrite, magnetite, iron sulfide, or molybdenum disulfide) were inoculated with anaerobic digester sludge and acclimated at a set potential of -600 mV (versus a standard hydrogen electrode). The archaeal communities on all cathodes, except those coated with platinum, were predominated by Methanobacterium (median 97% of archaea). Cathodes with platinum contained mainly archaea most similar to Methanobrevibacter. Neither of these methanogens were abundant (<0.1% of archaea) in the inoculum, and therefore their high abundance on the cathode resulted from selective enrichment. In contrast, bacterial communities on the cathode were more diverse, containing primarily δ-Proteobacteria (41% of bacteria). The lack of a consistent bacterial genus on the cathodes indicated that there was no similarly selective enrichment of bacteria on the cathode. These results suggest that the genus Methanobacterium was primarily responsible for methane production in MECs when cathodes lack efficient catalysts for hydrogen gas evolution. (Figure Presented).

  1. Quantifying the strength of quorum sensing crosstalk within microbial communities.

    Directory of Open Access Journals (Sweden)

    Kalinga Pavan T Silva

    2017-10-01

    Full Text Available In multispecies microbial communities, the exchange of signals such as acyl-homoserine lactones (AHL enables communication within and between species of Gram-negative bacteria. This process, commonly known as quorum sensing, aids in the regulation of genes crucial for the survival of species within heterogeneous populations of microbes. Although signal exchange was studied extensively in well-mixed environments, less is known about the consequences of crosstalk in spatially distributed mixtures of species. Here, signaling dynamics were measured in a spatially distributed system containing multiple strains utilizing homologous signaling systems. Crosstalk between strains containing the lux, las and rhl AHL-receptor circuits was quantified. In a distributed population of microbes, the impact of community composition on spatio-temporal dynamics was characterized and compared to simulation results using a modified reaction-diffusion model. After introducing a single term to account for crosstalk between each pair of signals, the model was able to reproduce the activation patterns observed in experiments. We quantified the robustness of signal propagation in the presence of interacting signals, finding that signaling dynamics are largely robust to interference. The ability of several wild isolates to participate in AHL-mediated signaling was investigated, revealing distinct signatures of crosstalk for each species. Our results present a route to characterize crosstalk between species and predict systems-level signaling dynamics in multispecies communities.

  2. Microbial communities, processes and functions in acid mine drainage ecosystems.

    Science.gov (United States)

    Chen, Lin-xing; Huang, Li-nan; Méndez-García, Celia; Kuang, Jia-liang; Hua, Zheng-shuang; Liu, Jun; Shu, Wen-sheng

    2016-04-01

    Acid mine drainage (AMD) is generated from the oxidative dissolution of metal sulfides when water and oxygen are available largely due to human mining activities. This process can be accelerated by indigenous microorganisms. In the last several decades, culture-dependent researches have uncovered and validated the roles of AMD microorganisms in metal sulfides oxidation and acid generation processes, and culture-independent studies have largely revealed the diversity and metabolic potentials and activities of AMD communities, leading towards a full understanding of the microbial diversity, functions and interactions in AMD ecosystems. This review describes the diversity of microorganisms and their functions in AMD ecosystems, and discusses their biotechnological applications in biomining and AMD bioremediation according to their capabilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. A metagenomic framework for the study of airborne microbial communities.

    Science.gov (United States)

    Yooseph, Shibu; Andrews-Pfannkoch, Cynthia; Tenney, Aaron; McQuaid, Jeff; Williamson, Shannon; Thiagarajan, Mathangi; Brami, Daniel; Zeigler-Allen, Lisa; Hoffman, Jeff; Goll, Johannes B; Fadrosh, Douglas; Glass, John; Adams, Mark D; Friedman, Robert; Venter, J Craig

    2013-01-01

    Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.

  4. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    Energy Technology Data Exchange (ETDEWEB)

    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 methan