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Sample records for microbial communities potentially

  1. Microbial community composition is unaffected by anode potential.

    PubMed

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

    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.

  2. Hydrocarbon-degrading potential of microbial communities from Arctic plants.

    PubMed

    Ferrera-Rodríguez, O; Greer, C W; Juck, D; Consaul, L L; Martínez-Romero, E; Whyte, L G

    2013-01-01

    To explore rhizospheric microbial communities from Arctic native plant species evaluating their bacterial hydrocarbon-degrading capacities. Eriophorum scheuchzeri, Potentilla cf. rubricaulis, Oxyria digyna, Salix arctica and Puccinellia angustata plant species were collected at Eureka (Canadian high Arctic) along with their rhizospheric soil samples. Their bacterial community fingerprints (16S rRNA gene, DGGE) were distinctive encompassing members from the phyla: Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria. Isolated diesel-degrading bacteria belonged to the phyla Actinobacteria and Proteobacteria. Strains of Mycobacterium, Nocardia, Rhodococcus, Intrasporangiaceae, Leifsoni and Arthrobacter possessed alkB and Pseudomonas possessed both ndoB and xylE gene sequences. Two Rhodococcus strains mineralized [1-(14) C] hexadecane at 5 and -5°C. From the rhizosphere of P. angustata, larger numbers of hydrocarbon-degrading bacteria were isolated than from other plant rhizosphere samples and all three genes alkB (from Actinobacteria), ndoB and xylE (from Pseudomonas) were detected by PCR. (i) Arctic plants have unique rhizospheric bacterial communities. (ii) P. angustata has potential for phytoremediation research at high Arctic soils. (iii) Isolated bacteria mineralized hydrocarbons at ambient low temperatures. To the best of our knowledge, this is the first rhizospheric exploration examining the phytoremediation potential of five Arctic plants and evaluating their microbial hydrocarbon-degrading capacities. © 2012 The Society for Applied Microbiology.

  3. Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

    PubMed Central

    Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C.; Mackie, Roderick I.

    2014-01-01

    Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds. PMID:25383887

  4. Functional potential of soil microbial communities in the maize rhizosphere.

    PubMed

    Li, Xiangzhen; Rui, Junpeng; Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C; Mackie, Roderick I

    2014-01-01

    Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds.

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

    PubMed Central

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

    2015-01-01

    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 < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in 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. PMID:25943705

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    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 < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in 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.

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

    PubMed

    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 < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in 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.

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

    PubMed

    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.

  9. Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species.

    PubMed

    Meiners, Scott J; Phipps, Kelsey K; Pendergast, Thomas H; Canam, Thomas; Carson, Walter P

    2017-04-01

    While both plant-soil feedbacks and allelochemical interactions are key drivers of plant community dynamics, the potential for these two drivers to interact with each other remains largely unexplored. If soil microbes influence allelochemical production, this would represent a novel dimension of heterogeneity in plant-soil feedbacks. To explore the linkage between soil microbial communities and plant chemistry, we experimentally generated soil microbial communities and evaluated their impact on leaf chemical composition and allelopathic potential. Four native perennial old-field species (two each of Aster and Solidago) were grown in pairwise combination with each species' soil microbial community as well as a sterilized inoculum. We demonstrated unequivocally that variation in soil microbial communities altered leaf chemical fingerprints for all focal plant species and also changed their allelopathic potential. Soil microbes reduced allelopathic potential in bioassays by increasing germination 25-54% relative to sterile control soils in all four species. Plants grown with their own microbial communities had the lowest allelopathic potential, suggesting that allelochemical production may be lessened when growing with microbes from conspecifics. The allelopathic potential of plants grown in congener and confamilial soils was indistinguishable from each other, indicating an equivalent response to all non-conspecific microbial communities within these closely related genera. Our results clearly demonstrated that soil microbial communities cause changes in leaf tissue chemistry that altered their allelopathic properties. These findings represent a new mechanism of plant-soil feedbacks that may structure perennial plant communities over very small spatial scales that must be explored in much more detail.

  10. Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types.

    PubMed

    Urbanová, Zuzana; Bárta, Jiří

    2014-12-01

    It is not well understood how the ecological status and microbial community composition of spruce swamp forests (SSF) relate to those found in bogs and fens. To clarify this, we investigated biogeochemical parameters and microbial community composition in a bog, a fen and two SSF using high throughput barcoded sequencing of the small ribosomal subunit (SSU) variable region V4. The results demonstrated that the microbial community of SSF is positioned between those of bogs and fens, and this was confirmed by in silico predicted metabolic potentials. This corresponds well with the position of SSF on the trophic gradient and reflects distinct responses of microbial communities to environmental variables. Species richness and microbial diversity increased significantly from bog to fen, with SSF in between, reflecting the variation in pH, nutrient availability and peat decomposability. The archaeal community, dominated by hydrogenotrophic methanogens, was more similar in SSF and the bog compared with the fen. The composition of the bacterial community of SSF was intermediate between those of bog and fen. However, the production of CO2 (an indicator of peat decomposability) did not differ between SSF and bog, suggesting the limiting effect of low pH and poor litter quality on the functioning of the bacterial community in SSF. These results help to clarify the transitional position of SSF between bogs and fens and showed the strong effect of environmental conditions on microbial community composition and functioning.

  11. Cellulolytic potential under environmental changes in microbial communities from grassland litter

    SciTech Connect

    Berlemont, Renaud; Allison, Steven D.; Weihe, Claudia; Lu, Ying; Brodie, Eoin L.; Martiny, Jennifer B. H.; Martiny, Adam C.

    2014-11-25

    We report that in many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.

  12. Cellulolytic potential under environmental changes in microbial communities from grassland litter

    DOE PAGES

    Berlemont, Renaud; Allison, Steven D.; Weihe, Claudia; ...

    2014-11-25

    We report that in many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of naturalmore » variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.« less

  13. Cellulolytic potential under environmental changes in microbial communities from grassland litter

    PubMed Central

    Berlemont, Renaud; Allison, Steven D.; Weihe, Claudia; Lu, Ying; Brodie, Eoin L.; Martiny, Jennifer B. H.; Martiny, Adam C.

    2014-01-01

    In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction. PMID:25505459

  14. The Potential of Hyperspectral Patterns of Winter Wheat to Detect Changes in Soil Microbial Community Composition

    PubMed Central

    Carvalho, Sabrina; van der Putten, Wim H.; Hol, W. H. G.

    2016-01-01

    Reliable information on soil status and crop health is crucial for detecting and mitigating disasters like pollution or minimizing impact from soil-borne diseases. While infestation with an aggressive soil pathogen can be detected via reflected light spectra, it is unknown to what extent hyperspectral reflectance could be used to detect overall changes in soil biodiversity. We tested the hypotheses that spectra can be used to (1) separate plants growing with microbial communities from different farms; (2) to separate plants growing in different microbial communities due to different land use; and (3) separate plants according to microbial species loss. We measured hyperspectral reflectance patterns of winter wheat plants growing in sterilized soils inoculated with microbial suspensions under controlled conditions. Microbial communities varied due to geographical distance, land use and microbial species loss caused by serial dilution. After 3 months of growth in the presence of microbes from the two different farms plant hyperspectral reflectance patterns differed significantly from each other, while within farms the effects of land use via microbes on plant reflectance spectra were weak. Species loss via dilution on the other hand affected a number of spectral indices for some of the soils. Spectral reflectance can be indicative of differences in microbial communities, with the Renormalized Difference Vegetation Index the most common responding index. Also, a positive correlation was found between the Normalized Difference Vegetation Index and the bacterial species richness, which suggests that plants perform better with higher microbial diversity. There is considerable variation between the soil origins and currently it is not possible yet to make sufficient reliable predictions about the soil microbial community based on the spectral reflectance. We conclude that measuring plant hyperspectral reflectance has potential for detecting changes in microbial

  15. Microbial communities in karst groundwater and their potential use for biomonitoring

    NASA Astrophysics Data System (ADS)

    Pronk, Michiel; Goldscheider, Nico; Zopfi, Jakob

    2009-02-01

    The structure, diversity and dynamics of microbial communities from a swallow hole draining agricultural land and two connected karst springs (Switzerland) were studied using molecular microbiological methods and related to hydrological and physicochemical parameters. Storm responses and an annual hydrological cycle were monitored to determine the short- and long-term variability, respectively, of bacterial communities. Statistical analysis of bacterial genetic fingerprints (16S rDNA PCR-DGGE) of spring water samples revealed several clusters that corresponded well with different levels of the allochthonous swallow hole contribution. Microbial communities in spring water samples highly affected by the swallow hole showed low similarities among them, reflecting the high temporal variability of the bacterial communities infiltrating at the swallow hole. Conversely, high similarities among samples with low allochthonous contribution provided evidence for a stable autochthonous endokarst microbial community. Three spring samples, representative for low, medium and high swallow hole contribution, were analysed by cloning/sequencing in order to identify the major bacterial groups in the communities. The autochthonous endokarst microbial community was mainly characterized of δ-Proteobacteria, Acidobacteria and Nitrospira species. A high percentage of unknown sequences suggested further that many karst aquifer bacteria are still undiscovered. Finally, the potential use of groundwater biomonitoring using microbial communities is discussed.

  16. Microbial Community Functional Potential and Composition Are Shaped by Hydrologic Connectivity in Riverine Floodplain Soils.

    PubMed

    Argiroff, William A; Zak, Donald R; Lanser, Christine M; Wiley, Michael J

    2017-04-01

    Riverine floodplains are ecologically and economically valuable ecosystems that are heavily threatened by anthropogenic stressors. Microbial communities in floodplain soils mediate critical biogeochemical processes, yet we understand little about the relationship between these communities and variation in hydrologic connectivity related to land management or topography. Here, we present metagenomic evidence that differences among microbial communities in three floodplain soils correspond to a long-term gradient of hydrologic connectivity. Specifically, all strictly anaerobic taxa and metabolic pathways were positively associated with increased hydrologic connectivity and flooding frequency. In contrast, most aerobic taxa and all strictly aerobic pathways were negatively related to hydrologic connectivity and flooding frequency. Furthermore, the genetic potential to metabolize organic compounds tended to decrease as hydrologic connectivity increased, which may reflect either the observed concomitant decline of soil organic matter or the parallel increase in both anaerobic taxa and pathways. A decline in soil N, accompanied by an increased genetic potential for oligotrophic N acquisition subsystems, suggests that soil nutrients also shape microbial communities in these soils. We conclude that differences among floodplain soil microbial communities can be conceptualized along a gradient of hydrologic connectivity. Additionally, we show that these differences are likely due to connectivity-related variation in flooding frequency, soil organic matter, and soil N. Our findings are particularly relevant to the restoration and management of microbially mediated biogeochemical processes in riverine floodplain wetlands.

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

    SciTech Connect

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

    2016-11-09

    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.

  18. Effects of constant or dynamic low anode potentials on microbial community development in bioelectrochemical systems.

    PubMed

    Yan, Hengjing; Yates, Matthew D; Regan, John M

    2015-11-01

    In bioelectrochemical systems, exoelectrogenic bacteria respire with anode electrodes as their extracellular electron acceptor; therefore, lower anode potentials can reduce the energy gain to each microbe and select against ones that are not able to respire at a lower potential range. Often fully developed anode communities are compared across bioelectrochemical systems with set anode potentials or fixed external resistances as different operational conditions. However, the comparative effect of the resulting constantly low versus dynamically low anode potentials on the development of anode microbial communities as well as the final cathode microbial communities has not been directly demonstrated. In this study, we used a low fixed anode potential of -250 mV and a higher-current control potential of -119 mV vs. Standard Hydrogen Electrode to approximately correspond with the negative peak anode potential values obtained from microbial fuel cells operated with fixed external resistances of 1 kΩ and 47 Ω, respectively. Pyrosequencing data from a 2-month time series show that a lower set anode potential resulted in a more diverse community than the higher- and variable-potential systems, likely due to the hindered enrichment of a Geobacter-dominated community with limited energy gain at this set potential. In this case, it appears that the selective pressure caused by the low set potential was counteracted by the low energy gain over a 2-month time scale. The air cathode microbial community with constant low anode potentials showed delayed enrichment of denitrifiers or perchlorate-reducing bacteria compared to the fixed external resistance condition.

  19. The functional gene composition and metabolic potential of coral-associated microbial communities

    PubMed Central

    Zhang, Yanying; Ling, Juan; Yang, Qingsong; Wen, Chongqing; Yan, Qingyun; Sun, Hongyan; Van Nostrand, Joy D.; Shi, Zhou; Zhou, Jizhong; Dong, Junde

    2015-01-01

    The phylogenetic diversity of coral-associated microbes has been extensively examined, but some contention remains regarding whether coral-associated microbial communities are species-specific or site-specific. It is suggested that corals may associate with microbes in terms of function, although little is known about the differences in coral-associated microbial functional gene composition and metabolic potential among coral species. Here, 16S rRNA Illumina sequencing and functional gene array (GeoChip 5.0) were used to assess coral-associated microbial communities. Our results indicate that both host species and environmental variables significantly correlate with shifts in the microbial community structure and functional potential. Functional genes related to key biogeochemical cycles including carbon, nitrogen, sulfur and phosphorus cycling, metal homeostasis, organic remediation, antibiotic resistance and secondary metabolism were shown to significantly vary between and among the four study corals (Galaxea astreata, Porites lutea, Porites andrewsi and Pavona decussata). Genes specific for anammox were also detected for the first time in the coral holobiont and positively correlated with ammonium. This study reveals that variability in the functional potential of coral-associated microbial communities is largely driven by changes in environmental factors and further demonstrates the importance of linking environmental parameters with genomic data in complex environmental systems. PMID:26536917

  20. An Integrated Study to Analyze Soil Microbial Community Structure and Metabolic Potential in Two Forest Types

    PubMed Central

    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 (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the 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 (P<0.05) to the 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

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

    PubMed

    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 (P<0.05) at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05) correlation was existed between the 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 (P<0.05) to the 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

  2. Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

    PubMed

    Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

    2017-10-15

    Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO4(2-), NH4(+) or CH4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO4(2-), NH4(+), oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO4(2-), ORP, and high NH4(+), as well as SO4(2-) and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    PubMed

    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.

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

    PubMed Central

    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. PMID:27446035

  5. Potential drivers of microbial community structure and function in Arctic spring snow.

    PubMed

    Maccario, Lorrie; Vogel, Timothy M; Larose, Catherine

    2014-01-01

    The Arctic seasonal snowpack can extend at times over a third of the Earth's land surface. This chemically dynamic environment interacts constantly with different environmental compartments such as atmosphere, soil and meltwater, and thus, strongly influences the entire biosphere. However, the microbial community associated with this habitat remains poorly understood. Our objective was to investigate the functional capacities, diversity and dynamics of the microorganisms in snow and to test the hypothesis that their functional signature reflects the snow environment. We applied a metagenomic approach to nine snow samples taken over 2 months during the spring season. Fungi, Bacteroidetes, and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season. Functional data that strongly correlated with chemical parameters like mercury or nitrogen species supported that this variation could be explained by fluctuations in environmental conditions. Through inter-environmental comparisons we examined potential drivers of snowpack microbial community functioning. Known cold adaptations were detected in all compared environments without any apparent differences in their relative abundance, implying that adaptive mechanisms related to environmental factors other than temperature may play a role in defining the snow microbial community. Photochemical reactions and oxidative stress seem to be decisive parameters in structuring microbial communities inside Arctic snowpacks.

  6. Potential drivers of microbial community structure and function in Arctic spring snow

    PubMed Central

    Maccario, Lorrie; Vogel, Timothy M.; Larose, Catherine

    2014-01-01

    The Arctic seasonal snowpack can extend at times over a third of the Earth’s land surface. This chemically dynamic environment interacts constantly with different environmental compartments such as atmosphere, soil and meltwater, and thus, strongly influences the entire biosphere. However, the microbial community associated with this habitat remains poorly understood. Our objective was to investigate the functional capacities, diversity and dynamics of the microorganisms in snow and to test the hypothesis that their functional signature reflects the snow environment. We applied a metagenomic approach to nine snow samples taken over 2 months during the spring season. Fungi, Bacteroidetes, and Proteobacteria were predominant in metagenomic datasets and changes in community structure were apparent throughout the field season. Functional data that strongly correlated with chemical parameters like mercury or nitrogen species supported that this variation could be explained by fluctuations in environmental conditions. Through inter-environmental comparisons we examined potential drivers of snowpack microbial community functioning. Known cold adaptations were detected in all compared environments without any apparent differences in their relative abundance, implying that adaptive mechanisms related to environmental factors other than temperature may play a role in defining the snow microbial community. Photochemical reactions and oxidative stress seem to be decisive parameters in structuring microbial communities inside Arctic snowpacks. PMID:25147550

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

    PubMed

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

    2016-12-09

    Anode potential has been shown to be a critical factor in the rate of acetate removal in microbial electrolysis cells (MECs), but studies with fermentable substrates and set potentials are lacking. Here, we examined the impact of three different set anode potentials (SAPs; -0.25, 0, and 0.25 V vs. standard hydrogen electrode) on the electrochemical performance, electron flux to various sinks, and anodic microbial community structure in two-chambered MECs fed with propionate. Electrical current (49-71%) and CH4 (22.9-41%) were the largest electron sinks regardless of the potentials tested. Among the three SAPs tested, 0 V showed the highest electron flux to electrical current (71 ± 5%) and the lowest flux to CH4 (22.9 ± 1.2%). In contrast, the SAP of -0.25 V had the lowest electron flux to current (49 ± 6%) and the highest flux to CH4 (41.1 ± 2%). The most dominant genera detected on the anode of all three SAPs based on 16S rRNA gene sequencing were Geobacter, Smithella and Syntrophobacter, 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 and hydrogenotrophic methanogens in suspension.

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

    PubMed Central

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

    2016-01-01

    Anode potential has been shown to be a critical factor in the rate of acetate removal in microbial electrolysis cells (MECs), but studies with fermentable substrates and set potentials are lacking. Here, we examined the impact of three different set anode potentials (SAPs; −0.25, 0, and 0.25 V vs. standard hydrogen electrode) on the electrochemical performance, electron flux to various sinks, and anodic microbial community structure in two-chambered MECs fed with propionate. Electrical current (49–71%) and CH4 (22.9–41%) were the largest electron sinks regardless of the potentials tested. Among the three SAPs tested, 0 V showed the highest electron flux to electrical current (71 ± 5%) and the lowest flux to CH4 (22.9 ± 1.2%). In contrast, the SAP of −0.25 V had the lowest electron flux to current (49 ± 6%) and the highest flux to CH4 (41.1 ± 2%). The most dominant genera detected on the anode of all three SAPs based on 16S rRNA gene sequencing were Geobacter, Smithella and Syntrophobacter, 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 and hydrogenotrophic methanogens in suspension. PMID:27934925

  9. Microbial community responses to temperature increase the potential for soil carbon losses under climate change.

    NASA Astrophysics Data System (ADS)

    Hartley, Iain; Karhu, Kristiina; Auffret, Marc; Hopkins, David; Prosser, Jim; Singh, Brajesh; Subke, Jens-Arne; Wookey, Philip; Ågren, Göran

    2014-05-01

    There are concerns that global warming may stimulate decomposition rates in soils, with the extra CO2 released representing a positive feedback to climate change. However, there is growing recognition that adaptation of soil microbial communities to temperature changes may alter the potential rate of carbon release. Critically, recent studies have produced conflicting results in terms of whether the medium-term soil microbial community response to temperature reduces (compensatory thermal adaptation) or enhances (enhancing thermal adaptation) the instantaneous direct positive effects of temperature on microbial activity. This lack of understanding adds considerably to uncertainty in predictions of the magnitude and direction of carbon-cycle feedbacks to climate change. In this talk, I present results from one of the most extensive investigations ever undertaken into the role that microbial adaptation plays in controlling the temperature sensitivity of decomposition. Soils were collected from a range of ecosystem types, representing a thermal gradient from the Arctic to the Amazon. Our novel soil-cooling approach minimises issues associated with substrate depletion in warming studies, but still tests whether adaptation enhances or reduces the direct impact of temperature changes on microbial activity. We also investigated the mechanisms underlying changes in microbial respiration by quantifying changes in microbial community composition, microbial biomass, mass-specific activity, carbon-use efficiency, and enzyme activities. Our results indicate that enhancing responses are much more common than compensatory thermal acclimation, with the latter being observed in less than 10% of cases. However, identifying the mechanisms underlying enhancing and compensatory adaptation remained elusive. No consistent changes were observed in terms of mass-specific activity, biomass or enzyme activity, indicating that current theory is inadequate in explaining observed patterns

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

    PubMed

    Wang, Yu; Zhang, Rui; He, Zhili; Van Nostrand, Joy D; Zheng, Qiang; Zhou, Jizhong; Jiao, Nianzhi

    2017-01-01

    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 with salinity

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

    PubMed Central

    Wang, Yu; Zhang, Rui; He, Zhili; Van Nostrand, Joy D.; Zheng, Qiang; Zhou, Jizhong; Jiao, Nianzhi

    2017-01-01

    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 with

  12. Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu.

    PubMed

    İnceoğlu, Özgul; Llirós, Marc; Crowe, Sean A; García-Armisen, Tamara; Morana, Cedric; Darchambeau, François; Borges, Alberto V; Descy, Jean-Pierre; Servais, Pierre

    2015-10-01

    The microbial community composition in meromictic Lake Kivu, with one of the largest CH4 reservoirs, was studied using 16S rDNA and ribosomal RNA (rRNA) pyrosequencing during the dry and rainy seasons. Highly abundant taxa were shared in a high percentage between bulk (DNA-based) and active (RNA-based) bacterial communities, whereas a high proportion of rare species was detected only in either an active or bulk community, indicating the existence of a potentially active rare biosphere and the possible underestimation of diversity detected when using only one nucleic acid pool. Most taxa identified as generalists were abundant, and those identified as specialists were more likely to be rare in the bulk community. The overall number of environmental parameters that could explain the variation was higher for abundant taxa in comparison to rare taxa. Clustering analysis based on operational taxonomic units (OTUs at 0.03 cutoff) level revealed significant and systematic microbial community composition shifts with depth. In the oxic zone, Actinobacteria were found highly dominant in the bulk community but not in the metabolically active community. In the oxic-anoxic transition zone, highly abundant potentially active Nitrospira and Methylococcales were observed. The co-occurrence of potentially active sulfur-oxidizing and sulfate-reducing bacteria in the anoxic zone may suggest the presence of an active yet cryptic sulfur cycle.

  13. Microbial communities acclimate to recurring changes in soil redox potential status

    SciTech Connect

    DeAngelis, Kristen M.; Silver, Whendee; Thompson, Andrew; Firestone, Mary K.

    2010-12-03

    Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA-based) and active (RNA-based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO{sub 2} respiration, methanogenesis, N{sub 2}O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4-day redox potential fluctuations did not. Using RNA: DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbialcommunity adapted to fluctuating redox potential.

  14. Microbial communities may modify how litter quality affects potential decomposition rates as tree species migrate

    Treesearch

    Ashley D. Keiser; Jennifer D. Knoepp; Mark A. Bradford

    2013-01-01

    Background and aims Climate change alters regional plant species distributions, creating new combinations of litter species and soil communities. Biogeographic patterns in microbial communities relate to dissimilarity in microbial community function, meaning novel litters to communities may decompose differently than predicted from their chemical composition. Therefore...

  15. Skin microbiota: Microbial community structure and its potential association with health and disease

    PubMed Central

    Rosenthal, Mariana; Goldberg, Deborah; Aiello, Allison; Larson, Elaine; Foxman, Betsy

    2011-01-01

    Skin, the largest human organ, is a complex and dynamic ecosystem inhabited by a multitude of microorganisms. Host demographics and genetics, human behavior, local and regional environmental characteristics, and transmission events may all potentially drive human skin microbiota variability, resulting in an alteration of microbial community structure. This alteration may have important consequences regarding health and disease outcomes among individuals. More specifically, certain diversity patterns of human microbiota may be predictive or diagnostic of disease. The purpose of this review is to briefly describe the skin microbiota, outline the potential determining factors driving its variability, posit the likelihood of an association between the resulting microbial community structure on the skin with disease outcomes among individuals, and finally, to present some challenges and implications for studying the skin microbiota. PMID:21463709

  16. Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals

    PubMed Central

    Lang, Jennifer M.; Erb, Racheal; Pechal, Jennifer L.; Wallace, John R.; McEwan, Ryan W.; Benbow, Mark Eric

    2016-01-01

    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. PMID:27681897

  17. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

    USGS Publications Warehouse

    Chun, Chan Lan; Peller, Julie R.; Shively, Dawn; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J.

    2017-01-01

    Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90 days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24 h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (< 0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

  18. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes.

    PubMed

    Chun, Chan Lan; Peller, Julie R; Shively, Dawn; Byappanahalli, Muruleedhara N; Whitman, Richard L; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J

    2017-01-01

    Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (<0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

  19. Potential of the microbial community present in an unimpacted beach sediment to remediate petroleum hydrocarbons.

    PubMed

    Almeida, C Marisa R; Reis, Izabela; Couto, M Nazaré; Bordalo, Adriano A; Mucha, Ana P

    2013-05-01

    The potential of the microbial communities present in the intertidal zone of an unimpacted beach (a beach that did not suffer any significant oil spill) to degrade hydrocarbons was investigated. For that, laboratory-based microcosms (50-ml flasks) were set up with sandy beach sediment spiked with crude oil and incubated with local seawater for 15 days in the dark. Three bioremediation treatments were tested (biostimulation (BS), autochthonous bioaugmentation (AB), and combined treatment of biostimulation + bioaugmentation (BS + AB)) and the results were compared with natural attenuation (NA). Visual inspection showed clearly an oil solubility increase (confirmed by a higher hydrocarbons concentration in supernatant solutions) for all tested treatments when compared to NA. Significant degradation of the oil, shown by different profiles of petroleum hydrocarbons, was also observed for the different treatments particularly for BS + AB. Therefore, the microbial community of this unimpacted beach sediment could respond to an oil spill, degrading hydrocarbons. But to increase the natural attenuation pace, obtained results indicated that BS + AB is an appropriate approach for the bioremediation of beaches recently impacted by an oil spill. The autochthonous microbial cultures can be obtained "before" or "after" the contamination of the target site, being inoculated into the site right after it contamination.

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

    PubMed

    Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

    2016-01-01

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

  1. Microbial communities in low permeability, high pH uranium mine tailings: characterization and potential effects.

    PubMed

    Bondici, V F; Lawrence, J R; Khan, N H; Hill, J E; Yergeau, E; Wolfaardt, G M; Warner, J; Korber, D R

    2013-06-01

    To describe the diversity and metabolic potential of microbial communities in uranium mine tailings characterized by high pH, high metal concentration and low permeability. To assess microbial diversity and their potential to influence the geochemistry of uranium mine tailings using aerobic and anaerobic culture-based methods, in conjunction with next generation sequencing and clone library sequencing targeting two universal bacterial markers (the 16S rRNA and cpn60 genes). Growth assays revealed that 69% of the 59 distinct culturable isolates evaluated were multiple-metal resistant, with 15% exhibiting dual-metal hypertolerance. There was a moderately positive correlation coefficient (R = 0·43, P < 0·05) between multiple-metal resistance of the isolates and their enzyme expression profile. Of the isolates tested, 17 reduced amorphous iron, 22 reduced molybdate and seven oxidized arsenite. Based on next generation sequencing, tailings depth was shown to influence bacterial community composition, with the difference in the microbial diversity of the upper (0-20 m) and middle (20-40 m) tailings zones being highly significant (P < 0·01) from the lower zone (40-60 m) and the difference in diversity of the upper and middle tailings zone being significant (P < 0·05). Phylotypes closely related to well-known sulfate-reducing and iron-reducing bacteria were identified with low abundance, yet relatively high diversity. The presence of a population of metabolically-diverse, metal-resistant micro-organisms within the tailings environment, along with their demonstrated capacity for transforming metal elements, suggests that these organisms have the potential to influence the long-term geochemistry of the tailings. This study is the first investigation of the diversity and functional potential of micro-organisms present in low permeability, high pH uranium mine tailings. © 2013 The Society for Applied Microbiology.

  2. Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

    PubMed Central

    Nagpal, Sunil; Haque, Mohammed Monzoorul; Mande, Sharmila S.

    2016-01-01

    Background The overall metabolic/functional potential of any given environmental niche is a function of the sum total of genes/proteins/enzymes that are encoded and expressed by various interacting microbes residing in that niche. Consequently, prior (collated) information pertaining to genes, enzymes encoded by the resident microbes can aid in indirectly (re)constructing/ inferring the metabolic/ functional potential of a given microbial community (given its taxonomic abundance profile). In this study, we present Vikodak—a multi-modular package that is based on the above assumption and automates inferring and/ or comparing the functional characteristics of an environment using taxonomic abundance generated from one or more environmental sample datasets. With the underlying assumptions of co-metabolism and independent contributions of different microbes in a community, a concerted effort has been made to accommodate microbial co-existence patterns in various modules incorporated in Vikodak. Results Validation experiments on over 1400 metagenomic samples have confirmed the utility of Vikodak in (a) deciphering enzyme abundance profiles of any KEGG metabolic pathway, (b) functional resolution of distinct metagenomic environments, (c) inferring patterns of functional interaction between resident microbes, and (d) automating statistical comparison of functional features of studied microbiomes. Novel features incorporated in Vikodak also facilitate automatic removal of false positives and spurious functional predictions. Conclusions With novel provisions for comprehensive functional analysis, inclusion of microbial co-existence pattern based algorithms, automated inter-environment comparisons; in-depth analysis of individual metabolic pathways and greater flexibilities at the user end, Vikodak is expected to be an important value addition to the family of existing tools for 16S based function prediction. Availability and Implementation A web implementation of Vikodak

  3. Why Microbial Communities?

    ScienceCinema

    Fredrickson, Jim (PNNL)

    2016-07-12

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

  4. Microbial community in the potential gas hydrate area Kaoping Canyon bearing sediment at offshore SW Taiwan

    NASA Astrophysics Data System (ADS)

    Wu, S. Y.; Hung, C. C.; Lai, S. J.; Ding, J. Y.; Lai, M. C.

    2015-12-01

    The deep sub-seafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass plays a potentially important role in long-term controls of global biogeochemical cycles. The research team from Taiwan, supported by the Central Geological Survey (CGS), has been demonstrated at SW offshore Taiwan that indicated this area is potential gas hydrate region. Therefore, the Gas Hydrate Master Program (GHMP) was brought in the National Energy Program-Phase II (NEP-II) to continue research and development. In this study, the microbial community structure of potential gas hydrate bearing sediments of giant piston core MD-178-10-3291 (KP12N) from the Kaoping Canyon offshore SW of Taiwan were investigated. This core was found many empty spaces and filling huge methane gas (>99.9 %) that might dissociate from solid gas hydrate. 16S rRNA gene clone libraries and phylogenetic analysis showed that the dominant members of Archaea were ANME (13 %), SAGMEG (31 %) and DSAG (20 %), and those of Bacteria were Chloroflexi (13 %), Candidate division JS1 (40 %) and Planctomycetes (15 %). Among them, ANME-3 is only distributed at the sulfate-methane interface (SMI) of 750 cmbsf, and sharing similarity with the Hydrate Ridge clone HydBeg92. ANME-1 and SAGMEG distributed below 750 cmbsf. In addition, DSAG and Candidate division JS1 are most dominant and distributed vertically at all tested depths from 150-3600 cmbsf. Combine the geochemical data and microbial phylotype distribution suggests the potential of gas hydrate bearing sediments at core MD-178-10-3291 (KP12N) from the Kaoping Canyon offshore SW of Taiwan.

  5. Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions.

    PubMed

    Johnson, Jamie M; Wawrik, Boris; Isom, Catherine; Boling, Wilford B; Callaghan, Amy V

    2015-02-01

    Based on the transient exposure of Chesapeake Bay sediments to hydrocarbons and the metabolic versatility of known anaerobic alkane-degrading microorganisms, it was hypothesized that distinct Bay sediment communities, governed by geochemical gradients, would have intrinsic alkane-utilizing potential under sulfate-reducing and/or methanogenic conditions. Sediment cores were collected along a transect of the Bay. Community DNA was interrogated via pyrosequencing of 16S rRNA genes, PCR of anaerobic hydrocarbon activation genes, and qPCR of 16S rRNA genes and genes involved in sulfate reduction/methanogenesis. Site sediments were used to establish microcosms amended with n-hexadecane under sulfate-reducing and methanogenic conditions. Sequencing of 16S rRNA genes indicated that sediments associated with hypoxic water columns contained significantly greater proportions of Bacteria and Archaea consistent with syntrophic degradation of organic matter and methanogenesis compared to less reduced sediments. Microbial taxa frequently associated with hydrocarbon-degrading communities were found throughout the Bay, and the genetic potential for hydrocarbon metabolism was demonstrated via the detection of benzyl-(bssA) and alkylsuccinate synthase (assA) genes. Although microcosm studies did not indicate sulfidogenic alkane degradation, the data suggested that methanogenic conversion of alkanes was occurring. These findings highlight the potential role that anaerobic microorganisms could play in the bioremediation of hydrocarbons in the Bay.

  6. Potential contribution of microbial communities in technical ceramics for the improvement of rheological properties

    NASA Astrophysics Data System (ADS)

    Moreira, Bernardino; Miller, Ana Z.; Santos, Ricardo; Monteiro, Sílvia; Dias, Diamantino; Neves, Orquídia; Dionísio, Amélia; Saiz-Jimenez, Cesareo

    2014-05-01

    Several bacterial and fungal species naturally occurring in ceramic raw materials used in construction, such as Aspergillus, Penicillium and Aureobasidium, are known to produce exopolysaccharides (EPS). These polymers excreted by the cells are of widespread occurrence and may confer unique and potentially interesting properties with potential industrial uses, such as viscosity control, gelation, and flocculation, during ceramic manufacturing. In this study, the microbial communities present in clay raw materials were identified by both cultural methods and DNA-based molecular techniques in order to appraise their potential contribution to enhance the performance of technical ceramics through the use of EPS. Mineralogical identification by X- Ray Diffraction (XRD) and Fourier Transform Infrared (FTIR) spectroscopy of the clay raw materials, as well as characterization of rheological properties of ceramic slips were also performed. Microbial EPS production and its introduction into ceramic slips will be then carried out in order to evaluate their effects on the rheological properties of the ceramic slips, powders and conformed bodies. Some positive aspects related to the use of EPS are: reduction of the environmental impact caused by synthetic organic additives, reduction of production costs, as well as the costs related with operator protection systems, gaseous effluent treatments, complex landfill, among others.

  7. Biogeography and Metabolic Potential of Soil Microbial Communities Across Local Environmental Gradients Illuminated Through Metagenomics

    NASA Astrophysics Data System (ADS)

    Sharrar, A.; Diamond, S.; Butterfield, C.; Starr, E.; Thomas, B. C.; Banfield, J. F.

    2016-12-01

    Soils are extremely heterogeneous and diverse microbial habitats. The distribution of microbes and their metabolic functions in soil is important for carbon and nitrogen cycling and overall ecosystem functioning. Little is known about biogeographical patterns of microbes in soil and how they relate to different environmental gradients. To address this topic, we have obtained metagenomes from 86 soil samples taken at the Eel River Critical Zone Observatory and a nearby meadow in the northern California Angelo Coast Range Reserve over a period of two years. These samples span a variety of environmental parameters, including depth, relief, time since last rainfall, and proximity to root carbon inputs. Phylogenetic diversity and community overlap between these samples was analyzed using ribosomal protein sequence identity and scaffold coverage. Independent of genomic bins, de-replicated ribosomal protein sequences were used to identify thousands of unique organisms between datasets. Despite environmental differences, a subset of these organisms were found in every sample. The dominant phyla in this cosmopolitan subset were Proteobacteria, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Acidobacteria, and Rokubacteria. Archaea and Nitrospirae were particularly prevalent at depths below 30cm. Patterns of ribosomal protein scaffold coverage across samples was used to compare the similarity of the microbial communities. We found that location was the greatest predictor of community similarity, followed by depth. In a subset of 60 samples taken in the same meadow, sampling plot was a greater predictor of community similarity than time since last rainfall in the same year. In addition, genome-independent analyses revealed differences in the metabolic potential for functions involved in nitrogen and carbon metabolism across environmental gradients. This study will further our understanding of soil biogeography and its relationship to overall biogeochemical cycling.

  8. Shifts in Microbial Community Structure with Changes in Cathodic Potential in Marine Sediment Microcosms

    NASA Astrophysics Data System (ADS)

    Lam, B. R.; Rowe, A. R.; Nealson, K. H.

    2014-12-01

    Microorganisms comprise more than 90% of the biomass of the ocean. Their ability to thrive and survive in a wide range of environments from oligotrophic waters to the deep subsurface stems from the great metabolic versatility that exists among them. This metabolic versatility has further expanded with the discovery of extracellular electron transport (EET). EET is the capability of microorganisms to transfer electrons to and from insoluble substrates outside of the cell. Much of what is known about EET comes from studies of model metal reducing microorganisms in the groups Shewanellaceae and Geobacteraceae. However, EET is not limited to these metal reducing microorganisms, and may play a large role in the biogeochemical cycling of several elements. We have developed an electrochemical culturing technique designed to target microorganisms with EET ability and tested these methods in marine sediments. The use of electrodes allows for greater control and quantification of electrons flowing to insoluble substrates as opposed to insoluble substrates such as minerals that are often difficult to measure. We have recently shown that poising electrodes at different redox potentials will enrich for different microbial groups and thus possible metabolisms. In marine sediment microcosms, triplicate electrodes were poised at different cathodic (electron donating) potentials (-300, -400, -500 and -600 mV) and incubated for eight weeks. Community analysis of the 16S rRNA revealed that at lower negative potentials (-500 and -600 mV), more sulfate reducing bacteria in the class Deltaproteobacteria were enriched in comparison to the communities at -300 and -400 mV being dominated by microorganisms within Alphaproteobacteria, Gammaproteobacteria, and Clostridia. This can be explained by sulfate (abundant in seawater) becoming a more energetically favorable electron acceptor with lower applied potentials. In addition, communities at higher potentials showed greater enrichment of the

  9. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill

    PubMed Central

    Kappell, Anthony D.; Wei, Yin; Newton, Ryan J.; Van Nostrand, Joy D.; Zhou, Jizhong; McLellan, Sandra L.; Hristova, Krassimira R.

    2014-01-01

    The Deepwater Horizon (DWH) blowout resulted in oil transport, including polycyclic aromatic hydrocarbons (PAHs) to the Gulf of Mexico shoreline. The microbial communities of these shorelines are thought to be responsible for the intrinsic degradation of PAHs. To investigate the Gulf Coast beach microbial community response to hydrocarbon exposure, we examined the functional gene diversity, bacterial community composition, and PAH degradation capacity of a heavily oiled and non-oiled beach following the oil exposure. With a non-expression functional gene microarray targeting 539 gene families, we detected 28,748 coding sequences. Of these sequences, 10% were uniquely associated with the severely oil-contaminated beach and 6.0% with the non-oiled beach. There was little variation in the functional genes detected between the two beaches; however the relative abundance of functional genes involved in oil degradation pathways, including polycyclic aromatic hydrocarbons (PAHs), were greater in the oiled beach. The microbial PAH degradation potentials of both beaches, were tested in mesocosms. Mesocosms were constructed in glass columns using sands with native microbial communities, circulated with artificial sea water and challenged with a mixture of PAHs. The low-molecular weight PAHs, fluorene and naphthalene, showed rapid depletion in all mesocosms while the high-molecular weight benzo[α]pyrene was not degraded by either microbial community. Both the heavily oiled and the non-impacted coastal communities showed little variation in their biodegradation ability for low molecular weight PAHs. Massively-parallel sequencing of 16S rRNA genes from mesocosm DNA showed that known PAH degraders and genera frequently associated with oil hydrocarbon degradation represented a major portion of the bacterial community. The observed similar response by microbial communities from beaches with a different recent history of oil exposure suggests that Gulf Coast beach communities are

  10. The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill.

    PubMed

    Kappell, Anthony D; Wei, Yin; Newton, Ryan J; Van Nostrand, Joy D; Zhou, Jizhong; McLellan, Sandra L; Hristova, Krassimira R

    2014-01-01

    The Deepwater Horizon (DWH) blowout resulted in oil transport, including polycyclic aromatic hydrocarbons (PAHs) to the Gulf of Mexico shoreline. The microbial communities of these shorelines are thought to be responsible for the intrinsic degradation of PAHs. To investigate the Gulf Coast beach microbial community response to hydrocarbon exposure, we examined the functional gene diversity, bacterial community composition, and PAH degradation capacity of a heavily oiled and non-oiled beach following the oil exposure. With a non-expression functional gene microarray targeting 539 gene families, we detected 28,748 coding sequences. Of these sequences, 10% were uniquely associated with the severely oil-contaminated beach and 6.0% with the non-oiled beach. There was little variation in the functional genes detected between the two beaches; however the relative abundance of functional genes involved in oil degradation pathways, including polycyclic aromatic hydrocarbons (PAHs), were greater in the oiled beach. The microbial PAH degradation potentials of both beaches, were tested in mesocosms. Mesocosms were constructed in glass columns using sands with native microbial communities, circulated with artificial sea water and challenged with a mixture of PAHs. The low-molecular weight PAHs, fluorene and naphthalene, showed rapid depletion in all mesocosms while the high-molecular weight benzo[α]pyrene was not degraded by either microbial community. Both the heavily oiled and the non-impacted coastal communities showed little variation in their biodegradation ability for low molecular weight PAHs. Massively-parallel sequencing of 16S rRNA genes from mesocosm DNA showed that known PAH degraders and genera frequently associated with oil hydrocarbon degradation represented a major portion of the bacterial community. The observed similar response by microbial communities from beaches with a different recent history of oil exposure suggests that Gulf Coast beach communities are

  11. Transitioning from Microbiome Composition to Microbial Community Interactions: The Potential of the Metaorganism Hydra as an Experimental Model

    PubMed Central

    Deines, Peter; Bosch, Thomas C. G.

    2016-01-01

    Animals are home to complex microbial communities, which are shaped through interactions within the community, interactions with the host, and through environmental factors. The advent of high-throughput sequencing methods has led to novel insights in changing patterns of community composition and structure. However, deciphering the different types of interactions among community members, with their hosts and their interplay with their environment is still a challenge of major proportion. The emerging fields of synthetic microbial ecology and community systems biology have the potential to decrypt these complex relationships. Studying host-associated microbiota across multiple spatial and temporal scales will bridge the gap between individual microorganism studies and large-scale whole community surveys. Here, we discuss the unique potential of Hydra as an emerging experimental model in microbiome research. Through in vivo, in vitro, and in silico approaches the interaction structure of host-associated microbial communities and the effects of the host on the microbiota and its interactions can be disentangled. Research in the model system Hydra can unify disciplines from molecular genetics to ecology, opening up the opportunity to discover fundamental rules that govern microbiome community stability. PMID:27790207

  12. Degradation potential and microbial community structure of heavy oil-enriched microbial consortia from mangrove sediments in Okinawa, Japan.

    PubMed

    Bacosa, Hernando P; Suto, Koichi; Inoue, Chihiro

    2013-01-01

    Mangroves constitute valuable coastal resources that are vulnerable to oil pollution. One of the major processes to remove oil from contaminated mangrove sediment is microbial degradation. A study on heavy oil- and hydrocarbon-degrading bacterial consortia from mangrove sediments in Okinawa, Japan was performed to evaluate their capacity to biodegrade and their microbial community composition. Surface sediment samples were obtained from mangrove sites in Okinawa (Teima, Oura, and Okukubi) and enriched with heavy oil as the sole carbon and energy source. The results revealed that all enriched microbial consortia degraded more than 20% of heavy oil in 21 days. The K1 consortium from Okukubi site showed the most extensive degradative capacity after 7 and 21 days. All consortia degraded more than 50% of hexadecane but had little ability to degrade polycyclic aromatic hydrocarbons (PAHs). The consortia were dominated by Pseudomonas or Burkholderia. When incubated in the presence of hydrocarbon compounds, the active bacterial community shifted to favor the dominance of Pseudomonas. The K1 consortium was a superior degrader, demonstrating the highest ability to degrade aliphatic and aromatic hydrocarbon compounds; it was even able to degrade heavy oil at a concentration of 15%(w/v). The dominance and turn-over of Pseudomonas and Burkholderia in the consortia suggest an important ecological role for and relationship between these two genera in the mangrove sediments of Okinawa.

  13. Radiochemically-Supported Microbial Communities: A Potential Mechanism for Biocolloid Production of Importance to Actinide Transport

    SciTech Connect

    Moser, Duane P.; Hamilton-Brehm, Scott D.; Fisher, Jenny C.; Bruckner, James C.; Kruger, Brittany; Sackett, Joshua; Russell, Charles E.; Onstott, Tullis C.; Czerwinski, Ken; Zavarin, Mavrik; Campbell, James H.

    2014-06-01

    Due to the legacy of Cold War nuclear weapons testing, the Nevada National Security Site (NNSS, formerly known as the Nevada Test Site (NTS)) contains millions of Curies of radioactive contamination. Presented here is a summary of the results of the first comprehensive study of subsurface microbial communities of radioactive and nonradioactive aquifers at this site. To achieve the objectives of this project, cooperative actions between the Desert Research Institute (DRI), the Nevada Field Office of the National Nuclear Security Administration (NNSA), the Underground Test Area Activity (UGTA), and contractors such as Navarro-Interra (NI), were required. Ultimately, fluids from 17 boreholes and two water-filled tunnels were sampled (sometimes on multiple occasions and from multiple depths) from the NNSS, the adjacent Nevada Test and Training Range (NTTR), and a reference hole in the Amargosa Valley near Death Valley. The sites sampled ranged from highly-radioactive nuclear device test cavities to uncontaminated perched and regional aquifers. Specific areas sampled included recharge, intermediate, and discharge zones of a 100,000-km2 internally-draining province, known as the Death Valley Regional Flow System (DVRFS), which encompasses the entirety of the NNSS/NTTR and surrounding areas. Specific geological features sampled included: West Pahute and Ranier Mesas (recharge zone), Yucca and Frenchman Flats (transitional zone), and the Western edge of the Amargosa Valley near Death Valley (discharge zone). The original overarching question underlying the proposal supporting this work was stated as: Can radiochemically-produced substrates support indigenous microbial communities and subsequently stimulate biocolloid formation that can affect radionuclides in NNSS subsurface nuclear test/detonation sites? Radioactive and non-radioactive groundwater samples were thus characterized for physical parameters, aqueous geochemistry, and microbial communities using both DNA- and

  14. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

    NASA Astrophysics Data System (ADS)

    Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; van Nostrand, Joy D.; Zhou, Jizhong

    2015-03-01

    Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

  15. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

    PubMed

    Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

    2015-03-20

    Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

  16. Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

    PubMed Central

    Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D.; Zhou, Jizhong

    2015-01-01

    Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems. PMID:25791904

  17. In-Drift Microbial Communities

    SciTech Connect

    D. Jolley

    2000-11-09

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

  18. Exploring the Metabolic Potential of Microbial Communities in Ultra-basic Reducing Spring at The Cedars, CA: Evidence of Microbial Methanogenesis and Heterotrophic Acetogenesis

    NASA Astrophysics Data System (ADS)

    Kohl, L.; Cummings, E.; Cox, A.; Suzuki, S.; Morrrissey, L.; Lang, S. Q.; Richter, A.; Nealson, K. H.; Morrill, P. L.

    2015-12-01

    The Cedars is a complex of ultra-basic, reducing springs located in the Coastal Range Ophiolite (CA, USA), a site of present day serpentinization. Similar to other serpentinization-associated fluids, the groundwaters discharging at The Cedars contain elevated concentrations of C1-C6 alkanes and volatile organic acids (VOAs) which may originate from abiotic or thermogenic processes but can also be produced, consumed, or transformed by microbial activity. In contrast to other continental sites of serpentinization, geochemical indicators (δ13CCH4, δ2HCH4, CH4/C2-C6 alkanes) are consistent with a partial microbial origin of methane at The Cedars. These indicators, however, can provide only indirect evidence of microbial methanogenesis. To further explore the metabolic potential of the indigenous microbial communities at The Cedars, we conducted a series of microcosm experiments in which fluids and sediments collected at The Cedars were incubated with 13C labeled substrates (formate, acetate, bicarbonate, methanol) under anaerobic conditions. 13C from all amended substrates was incorporated into CH4 demonstrating that these microbial communities can convert both organic and inorganic substrates to CH4. The apparent fractionation of 13C between methane and potential substrates indicated that carbonate reduction was the dominant pathway of methanogenesis, and 16S rDNA based community profiling revealed the presence of an OTU closest related to Methanobacterium sp., an autotrophic (CO2/H2) methanogen. Concentrations of C1-C4 VOAs increased 5-fold over the course of the experiment indicating the microbial production of VOAs. This acetogenesis occurred heterotrophically as autotrophic acetogenesis can be excluded because (a) δ13C values of acetate were similar to those of inorganic carbon (inconsistent with the strong discrimination against 13C observed in autotrophic acetogenesis) and (b) no incorporation of 13C from labeled bicarbonate was into acetate was observed.

  19. Phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale wastewater treatment plants.

    PubMed

    Yang, Chao; Zhang, Wei; Liu, Ruihua; Li, Qiang; Li, Baobin; Wang, Shufang; Song, Cunjiang; Qiao, Chuanling; Mulchandani, Ashok

    2011-09-01

    The activated sludge process is an essential process for treating domestic and industrial wastewaters in most wastewater treatment plants (WWTPs). This process consists of a mixture of general and special microorganisms in a form of a complex enrichment population. Thus, the exploration of activated sludge microbial communities is crucial to improve the performance of activated sludge process. In this study, we investigated the phylogenetic diversity and metabolic potential of activated sludge microbial communities in full-scale WWTPs. Four 16S rRNA gene clone libraries were constructed from activated sludge samples. In all samples, Proteobacteria was the most abundant phylogenetic group, followed by Bacteroidetes and Firmicutes. The dominance of Proteobacteria was further demonstrated by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP). Some specific genera, e.g., Nitrosomonas, Thauera, and Dechloromonas, which significantly correlate with the functions and performance of wastewater treatment, were abundant in all samples. A large number of unclassified sequences were found in the library, suggesting that a wide variety of novel species may inhabit complex activated sludge communities. The structures of the bacterial community did not differ significantly among samples. All samples utilized the vast majority of 31 carbon sources of an EcoPlate (Biolog), suggesting that activated sludge microbial communities possess high metabolic potential and equivalent functions required for wastewater treatment.

  20. Polyhydroxyalkanoate (PHA) accumulation potential and PHA-accumulating microbial communities in various activated sludge processes of municipal wastewater treatment plants.

    PubMed

    Sakai, K; Miyake, S; Iwama, K; Inoue, D; Soda, S; Ike, M

    2015-01-01

    To clarify the polyhydroxyalkanoate (PHA) accumulation potential and the PHA-accumulating microbial community structure in activated sludge in municipal wastewater treatment plants (WWTPs) and to identify their influential factors. Nine activated sludge samples were collected from municipal WWTPs employing various biological treatment processes. In acetate-fed 24-h batch experiments under aerobic and nitrogen- and phosphorus-limited conditions, polyhydroxybutyrate (PHB) content of activated sludge increased from 0-1·3 wt% to 7·9-24 wt%, with PHB yields of 0·22-0·50 C-mol 3-hydroxybutyrate (C-mol acetate)(-1). Microbial community analyses found that activated sludge samples that accumulated >20 wt% of PHB after 24-h PHA accumulation experiments had >5·0 × 10(8) copies g(-1)-mixed liquor-suspended solid of phaC genes. Results indicated that (i) activated sludge in municipal WWTPs can accumulate up to approx. 20 wt% of PHA without enrichment processes, (ii) PHA accumulation potential of activated sludge varied depending on the operational conditions (treatment processes) of WWTPs, and (iii) phaC gene number can provide a simple indication of PHA accumulation potential. This is the first study to compare the PHA accumulation potential and PHA-accumulating microbial communities in activated sludge of various treatment processes. Our findings may be useful for enhancing the resource recovery potential of wastewater treatment systems. © 2014 The Society for Applied Microbiology.

  1. Persistence of microbial communities including Pseudomonas aeruginosa in a hospital environment: a potential health hazard

    PubMed Central

    2014-01-01

    Background The persistence of microbial communities and how they change in indoor environments is of immense interest to public health. Moreover, hospital acquired infections are significant contributors to morbidity and mortality. Evidence suggests that, in hospital environments agent transfer between surfaces causes healthcare associated infections in humans, and that surfaces are an important transmission route and may act as a reservoir for some of the pathogens. This study aimed to evaluate the diversity of microorganisms that persist on noncritical equipment and surfaces in a main hospital in Portugal, and are able to grow in selective media for Pseudomonas, and relate them with the presence of Pseudomonas aeruginosa. Results During 2 years, a total of 290 environmental samples were analyzed, in 3 different wards. The percentage of equipment in each ward that showed low contamination level varied between 22% and 38%, and more than 50% of the equipment sampled was highly contaminated. P. aeruginosa was repeatedly isolated from sinks (10 times), from the taps’ biofilm (16 times), and from the showers and bedside tables (two times). Two ERIC clones were isolated more than once. The contamination level of the different taps analyzed showed correlation with the contamination level of the hand gels support, soaps and sinks. Ten different bacteria genera were frequently isolated in the selective media for Pseudomonas. Organisms usually associated with nosocomial infections as Stenotrophomonas maltophilia, Enterococcus feacalis, Serratia nematodiphila were also repeatedly isolated on the same equipment. Conclusions The environment may act as a reservoir for at least some of the pathogens implicated in nosocomial infections. The bacterial contamination level was related to the presence of humidity on the surfaces, and tap water (biofilm) was a point of dispersion of bacterial species, including potentially pathogenic organisms. The materials of the equipment

  2. Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis

    NASA Astrophysics Data System (ADS)

    Kohl, Lukas; Cumming, Emily; Cox, Alison; Rietze, Amanda; Morrissey, Liam; Lang, Susan Q.; Richter, Andreas; Suzuki, Shino; Nealson, Kenneth H.; Morrill, Penny L.

    2016-04-01

    Present-day serpentinization generates groundwaters with conditions (pH > 11, Eh < -550 mV) favorable for the microbial and abiotic production of organic compounds from inorganic precursors. Elevated concentrations of methane, C2-C6 alkanes, acetate, and formate have been detected at these sites, but the microbial or abiotic origin of these compounds remains unclear. While geochemical data indicate that methane at most sites of present-day serpentinization is abiogenic, the stable carbon, hydrogen, and clumped isotope data as well as the hydrocarbon gas composition from The Cedars, CA, USA, are consistent with a microbial origin for methane. However, there is no direct evidence of methanogenesis at this site of serpentinization. We report on laboratory experiments in which the microbial communities in fluids and sediments from The Cedars were incubated with 13C labeled substrates. Increasing methane concentrations and the incorporation of 13C into methane in live experiments, but not in killed controls, demonstrated that methanogens converted methanol, formate, acetate (methyl group), and bicarbonate to methane. The apparent fractionation between methane and potential substrates (α13CCH4-CO2(g) = 1.059 to 1.105, α13CCH4-acetate = 1.042 to 1.119) indicated that methanogenesis was dominated by the carbonate reduction pathway. Increasing concentrations of volatile organic acid anions indicated microbial acetogenesis. α13CCO2(g)-acetate values (0.999 to 1.000), however, were inconsistent with autotrophic acetogenesis, thus suggesting that acetate was produced through fermentation. This is the first study to show direct evidence of microbial methanogenesis and acetogenesis by the native microbial community at a site of present-day serpentinization.

  3. Potential application of ribosomal intergenic spacer analysis to the microbial community analysis of agronomic products.

    PubMed

    Ikeda, Seishi; Fujimura, Tatsuhito; Ytow, Nozomi

    2005-07-13

    Ribosomal intergenic spacer analysis (RISA) has been applied to the microbial community analysis of agronomic products in combination with a simple and rapid DNA extraction method, consisting of a one-step extraction and two-step purification, for a variety of agronomic products. RISA appears to be a useful tool for the study of the community structures of food-associated microbes and their use as a unique fingerprinting signature for each agronomic product. Sequencing analyses of amplicons generated from RISA suggest that this method can detect conventional microbes. In the case of RISA of wasabi paste DNA, the sequences of the amplicons showed high similarity to the plant pathogen Xanthomonas campestris and the soil bacterium Bacillus subtilis, whereas several food-associated bacteria (Lactococcus lactis, Lactococcus raffinolactis, and Lactococcus sakei) were detected using this technique in sausage DNA. Unexpectedly, the sequencing analyses also revealed the presence of several microbes that possessed high similarity to human bacterial pathogens such as Weissella confusa and Yersinia pestis. The results suggest that RISA will be a useful method for routine microbial community analysis in agronomic products.

  4. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    EPA Science Inventory

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

    Seagrasses ...

  5. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    EPA Science Inventory

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

    Seagrasses ...

  6. Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder.

    PubMed

    Lin, Ping; Ding, Bingyu; Feng, Chunyan; Yin, Shuwei; Zhang, Ting; Qi, Xin; Lv, Huiying; Guo, Xiaokui; Dong, Ke; Zhu, Yongzhang; Li, Qingtian

    2017-01-01

    The diagnosis of major depression disorder (MDD) and other mental disorders were depended on some subjective survey scales. There are confirmed relationship between the gut flora and the mental states of MDD patients. The V3-V4 region of the 16S rRNA gene was extracted from the fecal microbial communities in MDD patients, PCR amplified and sequenced on the Illumina Miseq platform. More phylum Firmicutes, less Bacteroidetes, and more genus Prevotella, Klebsiella, Streptococcus and Clostridium XI were found in MDD patients. The changes of the proportion of Prevotella and Klebsiella were consistent with Hamilton depression rating scale. The conclusion was limited by small sample sizes and potential uncontrollable influence factors on fecal microbiota. Prevotella and Klebsiella proportion in fecal microbial communities should be concerned in the diagnosis and therapeutic monitoring of MDD in future. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Microbial communities associated with human decomposition and their potential use as postmortem clocks.

    PubMed

    Finley, Sheree J; Benbow, M Eric; Javan, Gulnaz T

    2015-05-01

    Most forensic research that is used to better understand how to estimate the postmortem interval (PMI) entails the study of the physiochemical characteristics of decomposition and the effects that environmental factors have on the decomposition process. Forensic entomology exploits the life cycles of arthropods like Diptera (blow flies or flesh flies) and Coleoptera (beetles) deposited on the decaying carcass to determine PMI. Forensic taphonomy, from the Greek word taphos meaning burial, studies the creation of the fossils of decomposed cadavers to ascertain information as to the nature and time of death. Compared to other areas of taphonomy, there have been relatively few forensic science studies that have investigated the impact of human decomposition on the microbial changes occurring on or in a corpse or in the soil communities underneath a body. Such research may facilitate the critical determination of PMI. Therefore, the scope of this review is to provide a concise summary of the current progress in the newly emerging field of microbial diversity and the next-generation metagenomic sequencing approaches for assessing these communities in humans and in the soil beneath decomposing human.

  8. Radiochemically-supported microbial communities. A potential mechanism for biocolloid production of importance to actinide transport

    SciTech Connect

    Moser, Duane P.; Hamilton-Brehm, Scott D.; Fisher, Jenny C.; Bruckner, James C.; Kruger, Brittany; Sackett, Joshua; Russell, Charles E.; Onstott, Tullis C.; Czerwinski, Ken; Zavarin, Mavrik; Campbell, James H.

    2015-03-20

    The work described here revealed the presence of diverse microbial communities located across 19 subsurface sites at the NNSS/NTTR and nearby locations. Overall, the diversity of microorganisms was high for subsurface habitats and variable between sites. As of this writing, preparations are being made to combine the Illumina sequences and 16S rRNA clone libraries with other non-NNSS/NTTR well sites of Southern Nevada Regional Flow System for a publication manuscript describing our very broad landscape scale survey of subsurface microbial diversity. Isolates DRI-13 and DRI-14 remain to be fully characterized and named in accordance with the conventions established by Bergey's Manual of Systematic Bacteriology. In preparation to be published, these microorganisms will be submitted to the American Type Culture Collection (ATCC) and the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ).It is anticipated that the data resulting from this study in combination with other data sets that will allow us to produce a number of publications that will be impactful to the subsurface microbiology community.

  9. Connecting Metabolic Potential with Thermodynamic Reality: Lithotrophic Microbial Communities of the Frasassi Cave System

    NASA Astrophysics Data System (ADS)

    McCauley, R. L.; Macalady, J. L.; Schaperdoth, I.

    2013-12-01

    If Martian life evolved during the Noachian period, it likely would have retreated to liquid water refuges where redox chemistry provided metabolically viable substrates. Present-day Mars appears to have such a refuge with data suggesting that liquid water may persist in the subsurface, however limited data is available with regards to subsurface Martian geochemistry and hydrogeology. On Earth, we find microbial communities thriving in subsurface environments utilizing a multitude of lithoautotrophic metabolisms. The Frasassi cave system in Italy hosts many such lithotrophic microbial communities, which are isolated from surface carbon, sunlight, and oxygen similar to possible Martian microbial populations. By studying the community structure, geochemistry and thermodynamics of the system, as well as the metabolic capabilities using metagenomics, we hope to discover microbes are capable of thriving in so-called 'energy-limited' environments and inform the search for life in the solar system. Two subsurface cave lakes in the Frasassi cave system, Lago Infinito and Lago dell'Orsa, have anoxic waters that host rope-like biofilm communities dominated by Deltaproteobacteria, Chloroflexi, and Planctomycetes clades. Thermodynamic calculations based on in situ geochemistry of waters surrounding the biofilms suggest very few metabolisms are energetically-feasible including: 1) anaerobic oxidation of methane (AOM) coupled with sulfate reduction 2) anaerobic ammonia oxidation (anammox) coupled with sulfate reduction 3) methanogenesis (Lago dell'Orsa only) 4) chemotrophic sulfate reduction AOM and anammox were only recently discovered and appear to have low energy yields associated with slow growth rates. AOM coupled with sulfate reduction has been shown to occur in a syntrophy between sulfate-reducing bacteria (SRB) and methanotrophic Archaea. However, these rope-like biofilms have a small (<10%) Archaeal population, which are not closely related to the syntrophic

  10. HIV-associated changes in the enteric microbial community: potential role in loss of homeostasis and development of systemic inflammation

    PubMed Central

    Gootenberg, David B.; Paer, Jeffrey M.; Luevano, Jesus-Mario; Kwon, Douglas S.

    2017-01-01

    Purpose of review Despite HIV therapy advances, average life expectancy in HIV-infected individuals on effective treatment is significantly decreased relative to uninfected persons, largely because of increased incidence of inflammation-related diseases, such as cardiovascular disease and renal dysfunction. The enteric microbial community could potentially cause this inflammation, as HIV-driven destruction of gastrointestinal CD4+ T cells may disturb the microbiota–mucosal immune system balance, disrupting the stable gut microbiome and leading to further deleterious host outcomes. Recent findings Varied enteric microbiome changes have been reported during HIV infection, but unifying patterns have emerged. Community diversity is decreased, similar to pathologies such as inflammatory bowel disease, obesity, and Clostridium difficile infection. Many taxa frequently enriched in HIV-infected individuals, such as Enterobacteriaceae and Erysipelotrichaceae, have pathogenic potential, whereas depleted taxa, such as Bacteroidaceae and Ruminococcaceae, are more linked with anti-inflammatory properties and maintenance of gut homeostasis. The gut viral community in HIV has been found to contain a greater abundance of pathogenesis-associated Adenoviridae and Anelloviridae. These bacterial and viral changes correlate with increased systemic inflammatory markers, such as serum sCD14, sCD163, and IL-6. Summary Enteric microbial community changes may contribute to chronic HIV pathogenesis, but more investigation is necessary, especially in the developing world population with the greatest HIV burden (Video, Supplemental Digital Content 1, which includes the authors’ summary of the importance of the work). PMID:27922852

  11. The microbial communities and potential greenhouse gas production in boreal acid sulphate, non-acid sulphate, and reedy sulphidic soils.

    PubMed

    Šimek, Miloslav; Virtanen, Seija; Simojoki, Asko; Chroňáková, Alica; Elhottová, Dana; Krištůfek, Václav; Yli-Halla, Markku

    2014-01-01

    Acid sulphate (AS) soils along the Baltic coasts contain significant amounts of organic carbon and nitrogen in their subsoils. The abundance, composition, and activity of microbial communities throughout the AS soil profile were analysed. The data from a drained AS soil were compared with those from a drained non-AS soil and a pristine wetland soil from the same region. Moreover, the potential production of methane, carbon dioxide, and nitrous oxide from the soils was determined under laboratory conditions. Direct microscopic counting, glucose-induced respiration (GIR), whole cell hybridisation, and extended phospholipid fatty acid (PLFA) analysis confirmed the presence of abundant microbial communities in the topsoil and also in the deepest Cg2 horizon of the AS soil. The patterns of microbial counts, biomass and activity in the profile of the AS soil and partly also in the non-AS soil therefore differed from the general tendency of gradual decreases in soil profiles. High respiration in the deepest Cg2 horizon of the AS soil (5.66 μg Cg(-1)h(-1), as compared to 2.71 μg Cg(-1)h(-1) in a top Ap horizon) is unusual but reasonable given the large amount of organic carbon in this horizon. Nitrous oxide production peaked in the BCgc horizon of the AS and in the BC horizon of the non-AS soil, but the peak value was ten-fold higher in the AS soil than in the non-AS soil (82.3 vs. 8.6 ng Ng(-1)d(-1)). The data suggest that boreal AS soils on the Baltic coast contain high microbial abundance and activity. This, together with the abundant carbon and total and mineral nitrogen in the deep layers of AS soils, may result in substantial gas production. Consequently, high GHG emissions could occur, for example, when the generally high water table is lowered because of arable farming.

  12. GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage▿ †

    PubMed Central

    Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

    2011-01-01

    Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602

  13. Glycoside Hydrolases across Environmental Microbial Communities

    PubMed Central

    Berlemont, Renaud

    2016-01-01

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

  14. Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield

    PubMed Central

    Brankatschk, Robert; Töwe, Stefanie; Kleineidam, Kristina; Schloter, Michael; Zeyer, Josef

    2011-01-01

    Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions. PMID:21124490

  15. Abundances and potential activities of nitrogen cycling microbial communities along a chronosequence of a glacier forefield.

    PubMed

    Brankatschk, Robert; Töwe, Stefanie; Kleineidam, Kristina; Schloter, Michael; Zeyer, Josef

    2011-06-01

    Glacier forefields are ideal ecosystems to study the development of nutrient cycles as well as single turnover processes during soil development. In this study, we examined the ecology of the microbial nitrogen (N) cycle in bulk soil samples from a chronosequence of the Damma glacier, Switzerland. Major processes of the N cycle were reconstructed on the genetic as well as the potential enzyme activity level at sites of the chronosequence that have been ice-free for 10, 50, 70, 120 and 2000 years. In our study, we focused on N fixation, mineralization (chitinolysis and proteolysis), nitrification and denitrification. Our results suggest that mineralization, mainly the decomposition of deposited organic material, was the main driver for N turnover in initial soils, that is, ice-free for 10 years. Transient soils being ice-free for 50 and 70 years were characterized by a high abundance of N fixing microorganisms. In developed soils, ice-free for 120 and 2000 years, significant rates of nitrification and denitrification were measured. Surprisingly, copy numbers of the respective functional genes encoding the corresponding enzymes were already high in the initial phase of soil development. This clearly indicates that the genetic potential is not the driver for certain functional traits in the initial phase of soil formation but rather a well-balanced expression of the respective genes coding for selected functions.

  16. The effect of storage conditions on microbial community composition and biomethane potential in a biogas starter culture.

    PubMed

    Hagen, Live Heldal; Vivekanand, Vivekanand; Pope, Phillip B; Eijsink, Vincent G H; Horn, Svein J

    2015-07-01

    A new biogas process is initiated by adding a microbial community, typically in the form of a sample collected from a functional biogas plant. This inoculum has considerable impact on the initial performance of a biogas reactor, affecting parameters such as stability, biogas production yields and the overall efficiency of the anaerobic digestion process. In this study, we have analyzed changes in the microbial composition and performance of an inoculum during storage using barcoded pyrosequencing of bacterial and archaeal 16S ribosomal RNA (rRNA) genes, and determination of the biomethane potential, respectively. The inoculum was stored at room temperature, 4 and -20 °C for up to 11 months and cellulose was used as a standard substrate to test the biomethane potential. Storage up to 1 month resulted in similar final methane yields, but the rate of methane production was reduced by storage at -20 °C. Longer storage times resulted in reduced methane yields and slower production kinetics for all storage conditions, with room temperature and frozen samples consistently giving the best and worst performance, respectively. Both storage time and temperature affected the microbial community composition and methanogenic activity. In particular, fluctuations in the relative abundance of Bacteroidetes were observed. Interestingly, a shift from hydrogenotrophic methanogens to methanogens with the capacity to perform acetoclastic methanogensis was observed upon prolonged storage. In conclusion, this study suggests that biogas inocula may be stored up to 1 month with low loss of methanogenic activity, and identifies bacterial and archaeal species that are affected by the storage.

  17. Electrochemical response of a biofilm community to changes in electron-acceptor redox potential elucidated using microbial fuel cells

    NASA Astrophysics Data System (ADS)

    Arbour, T.; Wrighton, K. C.; Mullin, S. W.; Luef, B.; Gilbert, B.; Banfield, J. F.

    2012-12-01

    Currently, we have limited insight into how mineral properties affect dissimilatory metal-reducing bacteria (DMRB) or the microbial communities that contain them. Advances in our understanding of DMRB metabolism have been achieved using microbial fuel cells (MFCs), which exploit the ability of these organisms to transfer electrons extracellularly. By replacing the mineral electron acceptor with a conductive electrode under potentiostat control, the activity of microorganisms capable of interfacial electron transfer can be quantified by the current flowing through the electrode and related to the thermodynamics of respiration. We seek to understand how communities and their individual members respond to changes in mineralogy, and expect mineral redox potential to be a primary control. The ability to precisely control the redox potential of the electron-accepting anodic electrode is our primary motivation for using MFCs. We inoculated duplicate MFCs containing 10 mM acetate in phosphate buffered media with a slurry of subsurface sediment and groundwater obtained from the Integrated Field-Scale Research Challenge Site at Rifle, CO. Electroactive biofilms were established on graphite anodes poised at a favorable potential (0.0 V vs. SHE) before poising at -0.2 V—a potential representative of natural iron reduction. The current was stable across both anodes over more than 100 days of operation, and the percentage of the electrons in acetate recovered as current ("Coulombic efficiency") was typically 70 to >90%. Current density reached 0.4 A/m2 at -0.2 V, to a max of over 1.0 A/m2 at or above ~0.0 V (based on geometric electrode surface area). Media exchanges and biofilm cyclic voltammetry (CV) experiments indicate that electrode-attached microbial communities were responsible for primary electron transfer. Cryo-electron and confocal fluorescence microscopies of the biofilm reveal numerous morphologies of viable microorganisms that are currently being characterized

  18. Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring.

    PubMed

    Lay, Chih-Ying; Mykytczuk, Nadia C S; Yergeau, Étienne; Lamarche-Gagnon, Guillaume; Greer, Charles W; Whyte, Lyle G

    2013-06-01

    The Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (-5°C), hypersalinity (salinity, 24%), and reducing (≈-165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day(-1)). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related to Cyanobacteria (19.7%), Bacteroidetes (13.3%), and Proteobacteria (6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonas spp.), sulfate reducers (Desulfobulbus spp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments.

  19. Defining the Functional Potential and Active Community Members of a Sediment Microbial Community in a High-Arctic Hypersaline Subzero Spring

    PubMed Central

    Lay, Chih-Ying; Mykytczuk, Nadia C. S.; Yergeau, Étienne; Lamarche-Gagnon, Guillaume; Greer, Charles W.

    2013-01-01

    The Lost Hammer (LH) Spring is the coldest and saltiest terrestrial spring discovered to date and is characterized by perennial discharges at subzero temperatures (−5°C), hypersalinity (salinity, 24%), and reducing (≈−165 mV), microoxic, and oligotrophic conditions. It is rich in sulfates (10.0%, wt/wt), dissolved H2S/sulfides (up to 25 ppm), ammonia (≈381 μM), and methane (11.1 g day−1). To determine its total functional and genetic potential and to identify its active microbial components, we performed metagenomic analyses of the LH Spring outlet microbial community and pyrosequencing analyses of the cDNA of its 16S rRNA genes. Reads related to Cyanobacteria (19.7%), Bacteroidetes (13.3%), and Proteobacteria (6.6%) represented the dominant phyla identified among the classified sequences. Reconstruction of the enzyme pathways responsible for bacterial nitrification/denitrification/ammonification and sulfate reduction appeared nearly complete in the metagenomic data set. In the cDNA profile of the LH Spring active community, ammonia oxidizers (Thaumarchaeota), denitrifiers (Pseudomonas spp.), sulfate reducers (Desulfobulbus spp.), and other sulfur oxidizers (Thermoprotei) were present, highlighting their involvement in nitrogen and sulfur cycling. Stress response genes for adapting to cold, osmotic stress, and oxidative stress were also abundant in the metagenome. Comparison of the composition of the functional community of the LH Spring to metagenomes from other saline/subzero environments revealed a close association between the LH Spring and another Canadian high-Arctic permafrost environment, particularly in genes related to sulfur metabolism and dormancy. Overall, this study provides insights into the metabolic potential and the active microbial populations that exist in this hypersaline cryoenvironment and contributes to our understanding of microbial ecology in extreme environments. PMID:23563939

  20. Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes

    PubMed Central

    Obi, Chioma C.; Adebusoye, Sunday A.; Ugoji, Esther O.; Ilori, Mathew O.; Amund, Olukayode O.; Hickey, William J.

    2016-01-01

    Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa’s largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH

  1. Microbial Communities in Sediments of Lagos Lagoon, Nigeria: Elucidation of Community Structure and Potential Impacts of Contamination by Municipal and Industrial Wastes.

    PubMed

    Obi, Chioma C; Adebusoye, Sunday A; Ugoji, Esther O; Ilori, Mathew O; Amund, Olukayode O; Hickey, William J

    2016-01-01

    Estuarine sediments are significant repositories of anthropogenic contaminants, and thus knowledge of the impacts of pollution upon microbial communities in these environments is important to understand potential effects on estuaries as a whole. The Lagos lagoon (Nigeria) is one of Africa's largest estuarine ecosystems, and is impacted by hydrocarbon pollutants and other industrial and municipal wastes. The goal of this study was to elucidate microbial community structure in Lagos lagoon sediments to identify groups that may be adversely affected by pollution, and those that may serve as degraders of environmental contaminants, especially polycyclic aromatic hydrocarbons (PAHs). Sediment samples were collected from sites that ranged in types and levels of anthropogenic impacts. The sediments were characterized for a range of physicochemical properties, and microbial community structure was determined by Illumina sequencing of the 16S rRNA genes. Microbial diversity (species richness and evenness) in the Apapa and Eledu sediments was reduced compared to that of the Ofin site, and communities of both of the former two were dominated by a single operational taxonomic unit (OTU) assigned to the family Helicobacteraceae (Epsilonproteobacteria). In the Ofin community, Epsilonproteobacteria were minor constituents, while the major groups were Cyanobacteria, Bacteroidetes, and Firmicutes, which were all minor in the Apapa and Eledu sediments. Sediment oxygen demand (SOD), a broad indicator of contamination, was identified by multivariate analyses as strongly correlated with variation in alpha diversity. Environmental variables that explained beta diversity patterns included SOD, as well as levels of naphthalene, acenaphthylene, cobalt, cadmium, total organic matter, or nitrate. Of 582 OTU identified, abundance of 167 was significantly correlated (false discovery rate q≤ 0.05) to environmental variables. The largest group of OTU correlated with PAH levels were PAH

  2. Potential for horizontal gene transfer in microbial communities of the terrestrial subsurface.

    PubMed

    Coombs, Jonna M

    2009-01-01

    The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse communities of viable organisms, which have provided evidence of low but detectable metabolic activity. Although much of the terrestrial subsurface may be considered to be distant and isolated, the concept of horizontal gene transfer (HGT) in this environment has far-reaching implications for bioremediation efforts and groundwater quality, industrial harvesting of subsurface natural resources such as petroleum, and accurate assessment of the risks associated with DNA release and transport from genetically modified organisms. This chapter will explore what is known about some of the major mechanisms of HGT, and how the information gained from surface organisms might apply to conditions in the terrestrial subsurface. Evidence for the presence of mobile elements in subsurface bacteria and limited retrospective studies examining genetic signatures of potential past gene transfer events will be discussed.

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

    PubMed Central

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

    2016-01-01

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

  4. Methane potentials of wastewater generated from hydrothermal liquefaction of rice straw: focusing on the wastewater characteristics and microbial community compositions.

    PubMed

    Chen, Huihui; Zhang, Cheng; Rao, Yue; Jing, Yuhang; Luo, Gang; Zhang, Shicheng

    2017-01-01

    Hydrothermal liquefaction (HTL) has been well studied for the bio-oil production from biomass. However, a large amount of wastewater with high organic content is also produced during the HTL process. Therefore, the present study investigated the methane potentials of hydrothermal liquefaction wastewater (HTLWW) obtained from HTL of rice straw at different temperatures (170-320 °C) and residence times (0.5-4 h). The characteristics (e.g., total organic content, organic species, molecular size distribution, etc.) of the HTLWW were studied, and at the same time, microbial community compositions involved in AD of HTLWW were analyzed. The highest methane yield of 314 mL CH4/g COD was obtained from the sample 200 °C-0.5 h (HTL temperature at 200 °C for 0.5 h), while the lowest methane yield 217 mL CH4/g COD was obtained from the sample 320 °C-0.5 h. These results were consistent with the higher amounts of hard biodegradable organics (furans, phenols, etc.) and lower amounts of easily biodegradable organics (sugars and volatile fatty acids) present in sample 320 °C-0.5 h compared to sample 200 °C-0.5 h. Size distribution analysis showed that sample 320 °C-0.5 h contained more organics with molecular size less than 1 kDa (79.5%) compared to sample 200 °C-0.5 h (66.2%). Further studies showed that hard biodegradable organics were present in the organics with molecular size higher than 1 kDa for sample 200 °C-0.5 h. In contrast, those organics were present in both the organics with molecular size higher and less than 1 kDa for sample 320 °C-0.5 h. Microbial community analysis showed that different microbial community compositions were established during the AD with different HTLWW samples due to the different organic compositions. For instance, Petrimonas, which could degrade sugars, had higher abundance in the AD of sample 200 °C-0.5 h (20%) compared to sample 320 °C-0.5 h (7%). The higher abundance of Petrimonas was consistent with

  5. Flat laminated microbial mat communities

    NASA Astrophysics Data System (ADS)

    Franks, Jonathan; Stolz, John F.

    2009-10-01

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

  6. Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei▿

    PubMed Central

    Bowers, Robert M.; Lauber, Christian L.; Wiedinmyer, Christine; Hamady, Micah; Hallar, Anna G.; Fall, Ray; Knight, Rob; Fierer, Noah

    2009-01-01

    Bacteria and fungi are ubiquitous in the atmosphere. The diversity and abundance of airborne microbes may be strongly influenced by atmospheric conditions or even influence atmospheric conditions themselves by acting as ice nucleators. However, few comprehensive studies have described the diversity and dynamics of airborne bacteria and fungi based on culture-independent techniques. We document atmospheric microbial abundance, community composition, and ice nucleation at a high-elevation site in northwestern Colorado. We used a standard small-subunit rRNA gene Sanger sequencing approach for total microbial community analysis and a bacteria-specific 16S rRNA bar-coded pyrosequencing approach (4,864 sequences total). During the 2-week collection period, total microbial abundances were relatively constant, ranging from 9.6 × 105 to 6.6 × 106 cells m−3 of air, and the diversity and composition of the airborne microbial communities were also relatively static. Bacteria and fungi were nearly equivalent, and members of the proteobacterial groups Burkholderiales and Moraxellaceae (particularly the genus Psychrobacter) were dominant. These taxa were not always the most abundant in freshly fallen snow samples collected at this site. Although there was minimal variability in microbial abundances and composition within the atmosphere, the number of biological ice nuclei increased significantly during periods of high relative humidity. However, these changes in ice nuclei numbers were not associated with changes in the relative abundances of the most commonly studied ice-nucleating bacteria. PMID:19502432

  7. Nitrous oxide reduction genetic potential from the microbial community of an intermittently aerated partial nitritation SBR treating mature landfill leachate.

    PubMed

    Gabarró, J; Hernández-Del Amo, E; Gich, F; Ruscalleda, M; Balaguer, M D; Colprim, J

    2013-12-01

    This study investigates the microbial community dynamics in an intermittently aerated partial nitritation (PN) SBR treating landfill leachate, with emphasis to the nosZ encoding gene. PN was successfully achieved and high effluent stability and suitability for a later anammox reactor was ensured. Anoxic feedings allowed denitrifying activity in the reactor. The influent composition influenced the mixed liquor suspended solids concentration leading to variations of specific operational rates. The bacterial community was low diverse due to the stringent conditions in the reactor, and was mostly enriched by members of Betaproteobacteria and Bacteroidetes as determined by 16S rRNA sequencing from excised DGGE melting types. The qPCR analysis for nitrogen cycle-related enzymes (amoA, nirS, nirK and nosZ) demonstrated high amoA enrichment but being nirS the most relatively abundant gene. nosZ was also enriched from the seed sludge. Linear correlation was found mostly between nirS and the organic specific rates. Finally, Bacteroidetes sequenced in this study by 16S rRNA DGGE were not sequenced for nosZ DGGE, indicating that not all denitrifiers deal with complete denitrification. However, nosZ encoding gene bacteria was found during the whole experiment indicating the genetic potential to reduce N2O.

  8. Characterization of the microbial community and polyketide biosynthetic potential in the palmerolide-producing tunicate Synoicum adareanum.

    PubMed

    Riesenfeld, Christian S; Murray, Alison E; Baker, Bill J

    2008-11-01

    Palmerolide A (1) is a macrolide isolated from the Antarctic tunicate Synoicum adareanum that is of interest due to its potential as an antimelanoma drug. Biosynthesis is predicted to occur via a hybrid PKS-NRPS pathway within S. adareanum, but the identity of the palmerolide-producing organism (host or putative host-associated microorganism) has not been established. Microscopic observation revealed a dense microbial community inside the tunicate, and evidence from 16S rRNA gene DGGE profiles and clone library sequences suggests that the bacterial community has moderate phylogenetic complexity. The alpha and gamma classes of Proteobacteria account for ∼75% of the cloned 16S rRNA genes, and the majority of these sequences are affiliated with the genera Pseudovibrio and Microbulbifer. DNA sequences encoding type I PKS ketosynthase (KS) domains were detected by PCR. The S. adareanum KS sequences, which affiliate with the trans-AT clade, are similar to portions of PKS proteins that lack integrated acyltransferase domains in pathways for generating bioactive polyketide compounds, including bryostatin, leinamycin, and pederin.

  9. Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential.

    PubMed

    Pommier, Thomas; Merroune, Asmaa; Bettarel, Yvan; Got, Patrice; Janeau, Jean-Louis; Jouquet, Pascal; Thu, Thuy D; Toan, Tran D; Rochelle-Newall, Emma

    2014-12-01

    While considered as sustainable and low-cost agricultural amendments, the impacts of organic fertilizers on downstream aquatic microbial communities remain poorly documented. We investigated the quantity and quality of the dissolved organic matter leaching from agricultural soil amended with compost, vermicompost or biochar and assessed their effects on lake microbial communities, in terms of viral and bacterial abundances, community structure and metabolic potential. The addition of compost and vermicompost significantly increased the amount of dissolved organic carbon in the leachate compared with soil alone. Leachates from these additions, either with or without biochar, were highly bioavailable to aquatic microbial communities, although reducing the metabolic potential of the community and harbouring more specific communities. Although not affecting bacterial richness or taxonomic distributions, the specific addition of biochar affected the original lake bacterial communities, resulting in a strongly different community. This could be partly explained by viral burst and converging bacterial abundances throughout the samples. These results underline the necessity to include off-site impacts of agricultural amendments when considering their cascading effect on downstream aquatic ecosystems.

  10. Metaproteomic analysis of Chesapeake Bay microbial communities

    PubMed Central

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

    2005-01-01

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

  11. Environmental Regulation of Microbial Community Structure

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  12. Environmental Regulation of Microbial Community Structure

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  13. Metal concentrations in stream biofilm and sediments and their potential to explain biofilm microbial community structure.

    PubMed

    Ancion, Pierre-Yves; Lear, Gavin; Dopheide, Andrew; Lewis, Gillian D

    2013-02-01

    Concentrations of metals associated with sediments have traditionally been analysed to assess the extent of heavy metal contamination in freshwater environments. Stream biofilms present an alternative medium for this assessment which may be more relevant to the risk incurred by stream ecosystems as they are intensively grazed by aquatic organisms at a higher trophic level. Therefore, we investigated zinc, copper and lead concentrations in biofilms and sediments of 23 stream sites variously impacted by urbanisation. Simultaneously, biofilm bacterial and ciliate protozoan community structure was analysed by Automated Ribosomal Intergenic Spacer Analysis and Terminal Restriction Fragment Length Polymorphism, respectively. Statistical analysis revealed that biofilm associated metals explained a greater proportion of the variations observed in bacterial and ciliate communities than did sediment associated-metals. This study suggests that the analysis of metal concentrations in biofilms provide a good assessment of detrimental effects of metal contaminants on aquatic biota.

  14. High-resolution phylogenetic microbial community profiling

    SciTech Connect

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

    2016-02-09

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

  15. High-resolution phylogenetic microbial community profiling

    PubMed Central

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

    2016-01-01

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

  16. The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink

    PubMed Central

    Jones, Christopher M; Graf, Daniel RH; Bru, David; Philippot, Laurent; Hallin, Sara

    2013-01-01

    Nitrous oxide (N2O) is a major radiative forcing and stratospheric ozone-depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to nitrogen gas (N2) by bacteria and archaea harboring the N2O reductase (N2OR), which is the only known N2O sink in the biosphere. Despite its crucial role in mitigating N2O emissions, knowledge of the N2OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N2OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N2O-reducing communities. Examination of N2OR structural elements not considered in the phylogeny revealed that the two clades differ in their signal peptides, indicating differences in the translocation pathway of the N2OR across the membrane. Sequencing of environmental clones of the previously undetected nosZ lineage in various environments showed that it is widespread and diverse. Using quantitative PCR, we demonstrate that this clade was most often at least as abundant as the other, thereby more than doubling the known extent of the overall N2O-reducing community in the environment. Furthermore, we observed that the relative abundance of nosZ from either clade varied among habitat types and environmental conditions. Our results indicate a physiological dichotomy in the diversity of N2O-reducing microorganisms, which might be of importance for understanding the relationship between the diversity of N2O-reducing microorganisms and N2O reduction in different ecosystems. PMID:23151640

  17. Microbial Community-Level Physiological Profiles (CLPP) and herbicide mineralization potential in groundwater affected by agricultural land use

    NASA Astrophysics Data System (ADS)

    Janniche, Gry Sander; Spliid, Henrik; Albrechtsen, Hans-Jørgen

    2012-10-01

    Diffuse groundwater pollution from agricultural land use may impact the microbial groundwater community, which was investigated as Community-Level Physiological Profiles (CLPP) using EcoPlate™. Water was sampled from seven piezometers and a spring in a small agricultural catchment with diffuse herbicide and nitrate pollution. Based on the Shannon-Wiener and Simpson's diversity indices the diversity in the microbial communities was high. The response from the EcoPlates™ showed which substrates support groundwater bacteria, and all 31 carbon sources were utilized by organisms from at least one water sample. However, only nine carbon sources were utilized by all water samples: D-Mannitol, N-acetyl-D-glucosamine, putrescine, D-galacturonic acid, itaconic acid, 4-hydroxy benzoic acid, tween 40, tween 80, and L-asparagine. In all water samples the microorganisms preferred D-mannitol, D-galacturonic acid, tween 40, and 4-hydroxy benzoic acid as substrates, whereas none preferred 2-hydroxy benzoic acid, α-D-lactose, D,L-α-glycerol phosphate, α-ketobutyric acid, L-threonine and glycyl-L-glutamic acid. Principal Component Analysis of the CLPP's clustered the most agriculturally affected groundwater samples, indicating that the agricultural land use affects the groundwater microbial communities. Furthermore, the ability to mineralize atrazine and isoproturon, which have been used in the catchment, was also associated with this cluster.

  18. Metagenomic analysis of an ecological wastewater treatment plant’s microbial communities and their potential to metabolize pharmaceuticals

    PubMed Central

    Balcom, Ian N.; Driscoll, Heather; Vincent, James; Leduc, Meagan

    2016-01-01

    Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm. PMID:27610223

  19. Investigation into the potential toxicity of zero-valent iron nanoparticles to a trichloroethylene-degrading groundwater microbial community

    NASA Astrophysics Data System (ADS)

    Zabetakis, Kara M.

    The microbiological impact of zero-valent iron remediation of groundwater was investigated by exposing a trichloroethylene-degrading anaerobic microbial community to bare and coated iron nanoparticles. Changes in population numbers and metabolic activity were analyzed using qPCR and were compared to those of a blank, negative, and positive control to assess for microbial toxicity. Additionally, these results were compared to those of samples exposed to an equal concentration of iron filings in an attempt to discern the source of toxicity. Statistical analysis revealed that the three iron treatments were equally toxic to total Bacteria and Archaea populations, as compared with the controls. Therefore, toxicity appears to result either from the release of iron ions and the generation of reactive oxygen species, or from alteration of the redox system and the disruption of microbial metabolisms. There does not appear to be a unique nanoparticle-based toxicity.

  20. Systems biology of Microbial Communities

    SciTech Connect

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

    2008-04-11

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

  1. Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments

    NASA Technical Reports Server (NTRS)

    Franklin, R. B.; Garland, J. L.; Bolster, C. H.; Mills, A. L.

    2001-01-01

    A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

  2. Impact of dilution on microbial community structure and functional potential: comparison of numerical simulations and batch culture experiments

    NASA Technical Reports Server (NTRS)

    Franklin, R. B.; Garland, J. L.; Bolster, C. H.; Mills, A. L.

    2001-01-01

    A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted-low-dilution communities and the communities regrown from the very dilute (more than 10(-4)) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10(-1)) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function.

  3. Impact of Dilution on Microbial Community Structure and Functional Potential: Comparison of Numerical Simulations and Batch Culture Experiments

    PubMed Central

    Franklin, Rima B.; Garland, Jay L.; Bolster, Carl H.; Mills, Aaron L.

    2001-01-01

    A series of microcosm experiments was performed using serial dilutions of a sewage microbial community to inoculate a set of batch cultures in sterile sewage. After inoculation, the dilution-defined communities were allowed to regrow for several days and a number of community attributes were measured in the regrown assemblages. Based upon a set of numerical simulations, community structure was expected to differ along the dilution gradient; the greatest differences in structure were anticipated between the undiluted–low-dilution communities and the communities regrown from the very dilute (more than 10−4) inocula. Furthermore, some differences were expected among the lower-dilution treatments (e.g., between undiluted and 10−1) depending upon the evenness of the original community. In general, each of the procedures used to examine the experimental community structures separated the communities into at least two, often three, distinct groups. The groupings were consistent with the simulated dilution of a mixture of organisms with a very uneven distribution. Significant differences in community structure were detected with genetic (amplified fragment length polymorphism and terminal restriction fragment length polymorphism), physiological (community level physiological profiling), and culture-based (colony morphology on R2A agar) measurements. Along with differences in community structure, differences in community size (acridine orange direct counting), composition (ratio of sewage medium counts to R2A counts, monitoring of each colony morphology across the treatments), and metabolic redundancy (i.e., generalist versus specialist) were also observed, suggesting that the differences in structure and diversity of communities maintained in the same environment can be manifested as differences in community organization and function. PMID:11157234

  4. Utilization of microbial community potential for removal of chlorpyrifos: a review.

    PubMed

    Yadav, Maya; Shukla, Awadhesh Kumar; Srivastva, Navnita; Upadhyay, Siddh Nath; Dubey, Suresh Kumar

    2016-08-01

    Chlorpyrifos (CP) is the most commonly used pesticide in agricultural fields worldwide. Exposure to CP and its metabolites creates severe neuron-disorders in human beings. Improper handling and uncontrolled application of CP by farmers have lead to the contamination of surface and ground water bodies. Biodegradation offers an efficient and cost effective method for the removal of CP and other toxic organophosphorus pesticides from the contaminated environment. The degradation of CP by various microorganisms has been investigated by several researchers over the past few years. This review presents a critical summary of the recent published results on the biodegradation of CP. A diverse range of bacterial species such as Agrobacterium sp., Alcaligenes faecalis, Enterobacter sp. Arthrobacter sp. Bacillus pumilus, Pseudomonas sp. etc., fungal species like Trichoderma viridae, Aspergillus niger, Verticillium sp., Acremonium sp. Cladosporium cladosporiodes, etc. and certain algal species viz. Chlorella vulgaris, Spirulina platensis, Synechocystis sp., etc., have been shown to degrade CP. The efficacy of these communities for CP degradation in batch and continuous modes has also been discussed but more studies are required on continuous reactors. Also, the available published information on kinetics of biodegradation of CP along with the available results on molecular biological approaches are discussed in this work.

  5. Synthetic networks in microbial communities

    NASA Astrophysics Data System (ADS)

    Suel, Gurol

    2015-03-01

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

  6. Gut microbial communities of social bees.

    PubMed

    Kwong, Waldan K; Moran, Nancy A

    2016-06-01

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

  7. Health care workers' mobile phones: a potential cause of microbial cross-contamination between hospitals and community.

    PubMed

    Ustun, Cemal; Cihangiroglu, Mustafa

    2012-01-01

    This study evaluated the microbial contamination of health care workers' (HCWs) mobile phones. The study was conducted at a secondary referral hospital in July 2010. Samples were taken from all surfaces of the mobile phones using a sterile swab, and incubated on Brain Heart Infusion agar at 37.5°C for 24 hr. Any isolated microorganisms were grown aerobically on 5% sheep blood agar and eosin methylene-blue agar medium at 37.5°C for 24-48 hr. The Sceptor microdilution system was used to identify the microorganisms, together with conventional methods. The oxacillin disc diffusion test and double-disc synergy test were used to identify methicillin-resistant Staphylococcus aureus (MRSA) and expanded-spectrum beta-lactamase (ESBL)-producing Gram-negative bacilli, respectively. The mobile phones were also categorized according to whether the HCWs used them in the intensive care unit (ICU). Overall, 183 mobile phones were screened: 94 (51.4%) from nurses, 32 (17.5%) from laboratory workers, and 57 (31.1%) from health care staff. In total, 179 (97.8%) culture-positive specimens were isolated from the 183 mobile phones, including 17 (9.5%) MRSA and 20 (11.2%) ESBL-producing Escherichia coli, which can cause nosocomial infections. No statistical difference was observed in the recovery of MRSA (p = 0.3) and ESBL-producing E. coli (p = 0.6) between the HCW groups. Forty-four (24.6%) of the 179 specimens were isolated from mobile phones of ICU workers, including two MRSA and nine ESBL-producing E. coli. A significant (p = 0.02) difference was detected in the isolation of ESBL-producing E. coli between ICU workers and non-ICU workers. HCWs' mobile phones are potential vectors for transferring nosocomial pathogens between HCWs, patients, and the community.

  8. A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products.

    PubMed

    Marfil-Santana, Miguel David; O'Connor-Sánchez, Aileen; Ramírez-Prado, Jorge Humberto; De Los Santos-Briones, Cesar; López-Aguiar; Lluvia, Korynthia; Rojas-Herrera, Rafael; Lago-Lestón, Asunción; Prieto-Davó, Alejandra

    2016-11-01

    The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.

  9. High-resolution phylogenetic microbial community profiling

    SciTech Connect

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

    2014-03-17

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

  10. Ohmic resistance affects microbial community and ...

    EPA Pesticide Factsheets

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

  11. High-resolution phylogenetic microbial community profiling

    DOE PAGES

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

    2016-02-09

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

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

    NASA Technical Reports Server (NTRS)

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

    2004-01-01

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

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

    PubMed

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

    2010-07-01

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

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

    PubMed Central

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

    2010-01-01

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

  15. Metagenomic Investigation of the Microbial Community Structure and Diversity for Sentinel Coral Reefs and Urbanized Coastal Waters in Southeast Florida, and Molecular Microbial Source Tracking to Characterize Potential LBSP Microbial Contaminant Influences

    NASA Astrophysics Data System (ADS)

    Sinigalliano, C. D.

    2016-02-01

    Coral reefs and recreational beaches provide critical ecosystem services. However, coastal waters of the Southeast Florida region receive anthropogenic discharges from highly urbanized watersheds via runoff, canals, coastal inlets, and treated wastewater outfalls. There is concern regarding the biological contaminants that enter the coastal zone from land-based sources, especially for viable pathogens and genetic elements that could confer virulence or resistance. Targeted molecular microbial source tracking (MST) by quantitative PCR allows the measurement of specific microbial contaminants such as host-specific fecal indicators. These fecal source markers can help track specific fecal contamination of public health concern in the coastal zone and may also help track exposure of coral reefs to such contamination. A range of pathogens associated with sewage/septic contamination have shown detrimental impact to coral communities, including changes to the biodiversity of coral microbiomes. High-throughput Next-Generation-Sequencing (NGS) and community genomic analysis can provide a comprehensive, culture-independent approach to investigate microbial community diversity in complex environmental samples. The combination of host-specific microbial source tracking by qPCR and metagenomic NGS can provide substantial enhancement to traditional methods of water quality assessment to better protect both environmental biodiversity and human health. Reported here is a multifaceted water quality assessment study of three coastal inlets, two treated wastewater outfalls, and four sentinel coral reef communities in the Southeast Florida coastal zone offshore of Miami-Dade and Broward Counties. This study utilized a combination of bi-monthly sampling for nutrients, fecal indicator bacteria, and human-source molecular source tracking to measure specific contaminants of ecosystem and public health concern. In addition, 16S metagenomic analysis using Illumina Next-Generation Sequencing

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  17. Impact of soil matric potential on the fine-scale spatial distribution and activity of specific microbial degrader communities.

    PubMed

    Monard, Cécile; Mchergui, Chokri; Nunan, Naoise; Martin-Laurent, Fabrice; Vieublé-Gonod, Laure

    2012-09-01

    The impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of (13) C-glucose and (13) C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials (-0.001, -0.01 and -0.316 MPa) in 6 × 6 × 6 mm(3) cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales.

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

    PubMed

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

    2007-04-01

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

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

    PubMed Central

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

    2007-01-01

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

  20. Molecular-based approaches to characterize coastal microbial community and their potential relation to the trophic state of Red Sea

    PubMed Central

    Ansari, Mohd Ikram; Harb, Moustapha; Jones, Burton; Hong, Pei-Ying

    2015-01-01

    Molecular-based approaches were used to characterize the coastal microbiota and to elucidate the trophic state of Red Sea. Nutrient content and enterococci numbers were monitored, and used to correlate with the abundance of microbial markers. Microbial source tracking revealed the presence of >1 human-associated Bacteroides spp. at some of the near-shore sampling sites and at a heavily frequented beach. Water samples collected from the beaches had occasional exceedances in enterococci numbers, higher total organic carbon (TOC, 1.48–2.18 mg/L) and nitrogen (TN, 0.15–0.27 mg/L) than that detected in the near-shore waters. Enterococci abundances obtained from next-generation sequencing did not correlate well with the cultured enterococci numbers. The abundance of certain genera, for example Arcobacter, Pseudomonas and unclassified Campylobacterales, was observed to exhibit slight correlation with TOC and TN. Low abundance of functional genes accounting for up to 41 copies/L of each Pseudomonas aeruginosa and Campylobacter coli were detected. Arcobacter butzleri was also detected in abundance ranging from 111 to 238 copies/L. Operational taxonomic units (OTUs) associated with cyanobacteria, Prochlorococcus, Ostreococcus spp. and Gramella were more prevalent in waters that were likely impacted by urban runoffs and recreational activities. These OTUs could potentially serve as quantifiable markers indicative of the water quality. PMID:25758166

  1. Molecular-based approaches to characterize coastal microbial community and their potential relation to the trophic state of Red Sea.

    PubMed

    Ansari, Mohd Ikram; Harb, Moustapha; Jones, Burton; Hong, Pei-Ying

    2015-03-11

    Molecular-based approaches were used to characterize the coastal microbiota and to elucidate the trophic state of Red Sea. Nutrient content and enterococci numbers were monitored, and used to correlate with the abundance of microbial markers. Microbial source tracking revealed the presence of >1 human-associated Bacteroides spp. at some of the near-shore sampling sites and at a heavily frequented beach. Water samples collected from the beaches had occasional exceedances in enterococci numbers, higher total organic carbon (TOC, 1.48-2.18 mg/L) and nitrogen (TN, 0.15-0.27 mg/L) than that detected in the near-shore waters. Enterococci abundances obtained from next-generation sequencing did not correlate well with the cultured enterococci numbers. The abundance of certain genera, for example Arcobacter, Pseudomonas and unclassified Campylobacterales, was observed to exhibit slight correlation with TOC and TN. Low abundance of functional genes accounting for up to 41 copies/L of each Pseudomonas aeruginosa and Campylobacter coli were detected. Arcobacter butzleri was also detected in abundance ranging from 111 to 238 copies/L. Operational taxonomic units (OTUs) associated with cyanobacteria, Prochlorococcus, Ostreococcus spp. and Gramella were more prevalent in waters that were likely impacted by urban runoffs and recreational activities. These OTUs could potentially serve as quantifiable markers indicative of the water quality.

  2. Wetland Microbial Community Response to Restoration

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  3. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.

    PubMed

    Sibley, Christopher D; Peirano, Gisele; Church, Deirdre L

    2012-04-01

    Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.

  4. Mass Spectrometry Imaging of Complex Microbial Communities

    PubMed Central

    2016-01-01

    and their hosts. In recognition of this potential for scientific advancement, researchers have adapted MSI methodologies for the specific needs of the microbiology research community. As a result, workflows exist for imaging microbial systems with many of the common MSI ionization methods. Despite this progress, there is substantial room for improvements in instrumentation, sample preparation, and data interpretation. This Account provides a brief overview of the state of technology in microbial MSI, illuminates selected applications that demonstrate the potential of the technique, and highlights a series of development challenges that are needed to move the field forward. In the coming years, as microbial MSI becomes easier to use and more universally applicable, the technique will evolve into a fundamental tool widely applied throughout many divisions of science, medicine, and industry. PMID:28001363

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

    PubMed

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

    2014-01-01

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

  6. Community history affects the predictability of microbial ecosystem development

    PubMed Central

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

    2014-01-01

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

  7. Fundamentals of Microbial Community Resistance and Resilience

    PubMed Central

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

    2012-01-01

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

  8. Hydrolytic microbial communities in terrestrial ecosystems

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  9. Potential and optimization of two-phase anaerobic digestion of oil refinery waste activated sludge and microbial community study

    PubMed Central

    Wang, Qinghong; Liang, Ying; Zhao, Peng; Li, Qing X.; Guo, Shaohui; Chen, Chunmao

    2016-01-01

    Oil refinery waste activated sludge produced from oil wastewater biological treatment is a major industrial sludge. Two-phase anaerobic digestion of oil refinery waste activated sludge was studied for the first time. Thermal pretreatment under 170 °C is effective on sludge solubilization. At the optimum hydrolytic-acidogenic condition which was pH of 6.5, temperature of 55 °C and HRT of 2 days, 2754 mg/L volatile fatty acids (VFAs) were produced and acetic acid and butyric acid were the key components. Comparative studies of single-phase and two-phase anaerobic digestion in terms of organic removal, biogas production and methane concentration were conducted. The cumulative methane production and soluble COD (SCOD) removal efficiency in the two-phase system were 228 mL/g COD added and 77.8%, respectively, which were 1.6 and 2.1 times higher than those in single-phase anaerobic digestion. Such improved performance is attributed to intensification of dominant microbial population in separated reactors. Caloramator, Ureibacillus, Dechloromonas, Petrobacter, and T78 played important roles in hydrolytic-acidification and oil-organics degradation. Syntrophic bacteria in the family Porphyromonadaceae and the genus Anaerobranca provide acetate for methanogen. The results demonstrated the potential and operating condition of two-phase anaerobic digestion in treatment of oil refinery waste activated sludge. PMID:27905538

  10. Potential and optimization of two-phase anaerobic digestion of oil refinery waste activated sludge and microbial community study.

    PubMed

    Wang, Qinghong; Liang, Ying; Zhao, Peng; Li, Qing X; Guo, Shaohui; Chen, Chunmao

    2016-12-01

    Oil refinery waste activated sludge produced from oil wastewater biological treatment is a major industrial sludge. Two-phase anaerobic digestion of oil refinery waste activated sludge was studied for the first time. Thermal pretreatment under 170 °C is effective on sludge solubilization. At the optimum hydrolytic-acidogenic condition which was pH of 6.5, temperature of 55 °C and HRT of 2 days, 2754 mg/L volatile fatty acids (VFAs) were produced and acetic acid and butyric acid were the key components. Comparative studies of single-phase and two-phase anaerobic digestion in terms of organic removal, biogas production and methane concentration were conducted. The cumulative methane production and soluble COD (SCOD) removal efficiency in the two-phase system were 228 mL/g COD added and 77.8%, respectively, which were 1.6 and 2.1 times higher than those in single-phase anaerobic digestion. Such improved performance is attributed to intensification of dominant microbial population in separated reactors. Caloramator, Ureibacillus, Dechloromonas, Petrobacter, and T78 played important roles in hydrolytic-acidification and oil-organics degradation. Syntrophic bacteria in the family Porphyromonadaceae and the genus Anaerobranca provide acetate for methanogen. The results demonstrated the potential and operating condition of two-phase anaerobic digestion in treatment of oil refinery waste activated sludge.

  11. Potential and optimization of two-phase anaerobic digestion of oil refinery waste activated sludge and microbial community study

    NASA Astrophysics Data System (ADS)

    Wang, Qinghong; Liang, Ying; Zhao, Peng; Li, Qing X.; Guo, Shaohui; Chen, Chunmao

    2016-12-01

    Oil refinery waste activated sludge produced from oil wastewater biological treatment is a major industrial sludge. Two-phase anaerobic digestion of oil refinery waste activated sludge was studied for the first time. Thermal pretreatment under 170 °C is effective on sludge solubilization. At the optimum hydrolytic-acidogenic condition which was pH of 6.5, temperature of 55 °C and HRT of 2 days, 2754 mg/L volatile fatty acids (VFAs) were produced and acetic acid and butyric acid were the key components. Comparative studies of single-phase and two-phase anaerobic digestion in terms of organic removal, biogas production and methane concentration were conducted. The cumulative methane production and soluble COD (SCOD) removal efficiency in the two-phase system were 228 mL/g COD added and 77.8%, respectively, which were 1.6 and 2.1 times higher than those in single-phase anaerobic digestion. Such improved performance is attributed to intensification of dominant microbial population in separated reactors. Caloramator, Ureibacillus, Dechloromonas, Petrobacter, and T78 played important roles in hydrolytic-acidification and oil-organics degradation. Syntrophic bacteria in the family Porphyromonadaceae and the genus Anaerobranca provide acetate for methanogen. The results demonstrated the potential and operating condition of two-phase anaerobic digestion in treatment of oil refinery waste activated sludge.

  12. Microbial communities as biosensors for monitoring urban environments.

    PubMed

    Ling, Fangqiong

    2017-09-01

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

  13. Molecular Survey of Concrete Biofilm Microbial Communities

    EPA Science Inventory

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

  14. Molecular Survey of Concrete Biofilm Microbial Communities

    EPA Science Inventory

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  16. The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

    PubMed

    Mohan, Arvind Murali; Bibby, Kyle J; Lipus, Daniel; Hammack, Richard W; Gregory, Kelvin B

    2014-01-01

    Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

  17. The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

    DOE PAGES

    Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; ...

    2014-10-22

    Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsiblemore » for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.« less

  18. The Functional Potential of Microbial Communities in Hydraulic Fracturing Source Water and Produced Water from Natural Gas Extraction Characterized by Metagenomic Sequencing

    PubMed Central

    Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.

    2014-01-01

    Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection. PMID:25338024

  19. Breastfeeding increases microbial community resilience.

    PubMed

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

    2017-09-05

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

  20. Urea transformation of wetland microbial communities.

    PubMed

    Thorén, Ann-Karin

    2007-02-01

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

  1. Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

    USGS Publications Warehouse

    Waldrop, M.P.; Firestone, M.K.

    2006-01-01

    Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling

  2. Emergent biosynthetic capacity in simple microbial communities.

    PubMed

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

    2014-07-01

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

  3. Emergent Biosynthetic Capacity in Simple Microbial Communities

    PubMed Central

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

    2014-01-01

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

  4. Methane Potential and Microbial Community Dynamics in Anaerobic Digestion of Silage and Dry Cornstalks: a Substrate Exchange Study.

    PubMed

    Zhao, Ye; Yuan, Xufeng; Wen, Boting; Wang, Xiaofen; Zhu, Wanbin; Cui, Zongjun

    2017-01-01

    Silage and dry are the two typical cornstalk forms. Either form could be used as substrate in biogas plants and might be replaced by another when shortage occurred. This study focused on the feeding sequence of these two kinds of feedstocks, aiming to discuss their specific methane potential (SMP). A 15-day hydraulic retention time was chosen for semi-continuous experiments based on the batch test results. In semi-continuous experiments, before and after feedstocks were exchanged, the significantly decreased and comparable SMPs of silage and dry cornstalks indicated that a basis of unstable digestion would result in incomplete methane release from the subsequent digestion. A higher similarity of bacterial community structure and greater quantity of bacteria were shown in acidified silage cornstalk digestion through band similarity analysis. Methanosaetaceae and methanomicrobiales were the predominant methanogens, and aceticlastic methanogenesis was the main route for methane production. The different feeding sequences affected the hydrolysis course and further influenced the methanogenic proliferation. Our work suggests that silage cornstalk digestion should be conducted before dry cornstalk digestion.

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

    NASA Astrophysics Data System (ADS)

    Prest, T. L.; Nemergut, D.

    2015-12-01

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

  6. Human and Environmental Impacts on River Sediment Microbial Communities

    DOE PAGES

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

    2014-05-19

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

  7. Human and Environmental Impacts on River Sediment Microbial Communities

    SciTech Connect

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

    2014-05-19

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

  8. Human and Environmental Impacts on River Sediment Microbial Communities

    PubMed Central

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

    2014-01-01

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

  9. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

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

    2008-10-01

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

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

    PubMed

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

    2007-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

    activity (such as rhizosphere soil) and our DNA and PLFA-based analyses included a potentially huge "dormant" community of soil microorganisms. While our analyses could detect little impact of plant species on overall microbial community profiles, a smaller active-fraction of the soil microbial community may have been more significantly affected.

  13. Two-stage microbial community experimental design

    PubMed Central

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

    2013-01-01

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

  14. Two-stage microbial community experimental design.

    PubMed

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

    2013-12-01

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

  15. The Role of Shipyard Pollutants in Structuring Coral Reef Microbial Communities: Monitoring Environmental Change and the Potential Causes of Coral Disease

    DTIC Science & Technology

    2006-06-01

    communities composed of 3 to 7 unique types of bacteria. Conversely , the less-impacted sites of SB and PH have 75% of their microbial communities made up...glucosamine (Table 2), and appeared to contain significant quantities of the alcohol sugar inositol, which had not been detected in mucus before. The...tissues was used to determine differences in the relative proportion of autotrophic (Symbiodinium) versus heterotrophic modes of coral nutrition and

  16. A conceptual framework for invasion in microbial communities.

    PubMed

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

    2016-12-01

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

  17. Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area.

    PubMed

    Gandolfi, Isabella; Canedoli, Claudia; Imperato, Valeria; Tagliaferri, Ilario; Gkorezis, Panagiotis; Vangronsveld, Jaco; Padoa Schioppa, Emilio; Papacchini, Maddalena; Bestetti, Giuseppina; Franzetti, Andrea

    2017-01-01

    Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.g. tree species, leaf age and physiology, environmental conditions. In this work, bacterial communities hosted by urban Platanus x acerifolia leaves were taxonomically characterized using high throughput sequencing of 16S rRNA gene, and their temporal and spatial variability was assessed by comparing samples collected from different locations in the city of Milan (Italy) and in different months. The diversity of alkane hydroxylase (alkB) phylotypes harboured by phyllospheric bacteria associated to urban Platanus trees was also evaluated. Results revealed that temporal changes, which are related to seasonality, acted as a stronger driver both on Platanus phyllospheric community structure and on alkB phylotype diversity than sampling location. Biodiversity of bacterial communities decreased along the growing season, leading to a strong dominance by the genus Stenotrophomonas. On the contrary, diversity of hydrocarbon-degrading populations increased over the months, although it resulted lower than that reported for other habitats. It was therefore hypothesized that atmospheric hydrocarbons might play a key role in the selection of phyllospheric populations in urban areas. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Signaling in host-associated microbial communities

    PubMed Central

    Fischbach, Michael A.; Segre, Julia A.

    2016-01-01

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

  19. Surface reflectance degradation by microbial communities

    DOE PAGES

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

    2015-11-05

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

  20. Surface reflectance degradation by microbial communities

    SciTech Connect

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

    2015-11-05

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

  1. Soil microbial community of abandoned sand fields.

    PubMed

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

    2002-01-01

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

  2. Diversity of cloacal microbial community in migratory shorebirds that use the Tagus estuary as stopover habitat and their potential to harbor and disperse pathogenic microorganisms.

    PubMed

    Santos, Susana S; Pardal, Sara; Proença, Diogo N; Lopes, Ricardo J; Ramos, Jaime A; Mendes, Luísa; Morais, Paula V

    2012-10-01

    The diversity of the cloacal microbial community in migratory shorebirds, caught at the Tagus estuary, Portugal, was assessed by cultivation (R2A and Nutrient Agar media) and denaturing gradient gel electrophoresis profiling (DGGE) to provide a better understanding of the birds' potential to harbor and disperse pathogens. Three different bird species belonging to four different populations were studied: common redshank (Tringa totanus), black-winged stilt (Himantopus himantopus) and nominate and Icelandic populations of black-tailed godwit (Limosa limosa). DGGE profiling and partial 16S RNA gene sequences of 240 isolates, and 26 DGGE bands resulting in 58 clones, were analyzed. Most isolates were members of the phylum Firmicutes and Actinobacteria and only a small portion belonged to the Proteobacteria and Deinococcus-Thermus phyla. Potentially pathogenic strains carried by the birds were found such as Helicobacter and Staphylococcus in all bird species, and Clostridium, Mycobacterium, Rhodococcus, Legionella and Corynebacterium in black-winged stilts. Unexpectedly, bacteria from the phylum Deinococcus-Thermus were isolated in shorebirds and were present in all the bird species studied.

  3. Population abundance of potentially pathogenic organisms in intestinal microbiome of jungle crow (Corvus macrorhynchos) shown with 16S rRNA gene-based microbial community analysis.

    PubMed

    Maeda, Isamu; Siddiki, Mohammad Shohel Rana; Nozawa-Takeda, Tsutomu; Tsukahara, Naoki; Tani, Yuri; Naito, Taki; Sugita, Shoei

    2013-01-01

    Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

  4. Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos) Shown with 16S rRNA Gene-Based Microbial Community Analysis

    PubMed Central

    Maeda, Isamu; Siddiki, Mohammad Shohel Rana; Nozawa-Takeda, Tsutomu; Tsukahara, Naoki; Tani, Yuri; Naito, Taki; Sugita, Shoei

    2013-01-01

    Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms. PMID:24058905

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

    PubMed

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

    2014-08-01

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

  6. Measurements of Microbial Community Activities in Individual Soil Macroaggregates

    SciTech Connect

    Bailey, Vanessa L.; Bilskis, Christina L.; Fansler, Sarah J.; McCue, Lee Ann; Smith, Jeff L.; Konopka, Allan

    2012-05-01

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for {beta}-glucosidase, N-acetyl-{beta}-D-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual aggregates (250-1000 {mu}m diameter). Across all enzymes, the smallest aggregates had the greatest activity and the range of enzyme activities observed in all aggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and {beta}-glucosidase on the same aggregates suggest the presence of both extracellular {beta}-glucosidase functioning in aggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low {beta}-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.

  7. Microbial communities associated with wet flue gas desulfurization systems

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-01-01

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

  9. The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing

    SciTech Connect

    Mohan, Arvind Murali; Bibby, Kyle J.; Lipus, Daniel; Hammack, Richard W.; Gregory, Kelvin B.; Forster, Robert J.

    2014-10-22

    Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. Thus, the metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

  10. Anthropogenic perturbations in marine microbial communities.

    PubMed

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

    2011-03-01

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

  11. Interspecies Interactions within Oral Microbial Communities

    PubMed Central

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

    2007-01-01

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

  12. Nutrient Addition Dramatically Accelerates Microbial Community Succession

    PubMed Central

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

    2014-01-01

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

  13. Nutrient addition dramatically accelerates microbial community succession.

    PubMed

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

    2014-01-01

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

  14. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

    SciTech Connect

    Song, Hyun-Seob; Cannon, William R.; Beliaev, Alex S.; Konopka, Allan

    2014-10-17

    Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

    Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities. PMID:27242723

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

    PubMed Central

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

    2016-01-01

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

  18. Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities

    PubMed Central

    Oberding, Lisa; Gieg, Lisa M.

    2016-01-01

    Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs) related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data. PMID:27681901

  19. Syntrophic exchange in synthetic microbial communities

    PubMed Central

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

    2014-01-01

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

  20. Syntrophic exchange in synthetic microbial communities.

    PubMed

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

    2014-05-20

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

  1. Response of a salt marsh microbial community to metal contamination

    NASA Astrophysics Data System (ADS)

    Mucha, Ana P.; Teixeira, Catarina; Reis, Izabela; Magalhães, Catarina; Bordalo, Adriano A.; Almeida, C. Marisa R.

    2013-09-01

    Salt marshes are important sinks for contaminants, namely metals that tend to accumulate around plant roots and could eventually be taken up in a process known as phytoremediation. On the other hand, microbial communities display important roles in the salt marsh ecosystems, such as recycling of nutrients and/or degradation of organic contaminants. Thus, plants can benefit from the microbial activity in the phytoremediation process. Nevertheless, above certain levels, metals are known to be toxic to microorganisms, fact that can eventually compromise their ecological functions. In this vein, the aim of present study was to investigate, in the laboratory, the effect of selected metals (Cd, Cu and Pb) on the microbial communities associated to the roots of two salt marsh plants. Sediments colonized by Juncus maritimus and Phragmites australis were collected in the River Lima estuary (NW Portugal), and spiked with each of the metals at three different Effects Range-Median (ERM) concentrations (1, 10×, 50×), being ERM the sediment quality guideline that indicates the concentration above which adverse biological effects may frequently occur. Spiked sediments were incubated with a nutritive saline solution, being left in the dark under constant agitation for 7 days. The results showed that, despite the initial sediments colonized by J. maritimus and P. australis displayed significant (p < 0.05) differences in terms of microbial community structure (evaluated by ARISA), they presented similar microbial abundances (estimated by DAPI). Also, in terms of microbial abundance, both sediments showed a similar response to metal addition, with a decrease in number of cells only observed for the higher addition of Cu. Nevertheless, both Cu and Pb, at intermediate metals levels promote a shift in the microbial community structure, with possibly effect on the ecological function of these microbial communities in salt marshes. These changes may affect plants phytoremediation

  2. Does iron inhibit cryptoendolithic microbial communities?

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  3. Does iron inhibit cryptoendolithic microbial communities?

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  4. Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities.

    PubMed

    Jay, Z J; Rusch, D B; Tringe, S G; Bailey, C; Jennings, R M; Inskeep, W P

    2014-01-01

    High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.

  5. Predominant Acidilobus-Like Populations from Geothermal Environments in Yellowstone National Park Exhibit Similar Metabolic Potential in Different Hypoxic Microbial Communities

    PubMed Central

    Jay, Z. J.; Rusch, D. B.; Tringe, S. G.; Bailey, C.; Jennings, R. M.

    2014-01-01

    High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems. PMID:24162572

  6. Microbial Communities Model Parameter Calculation for TSPA/SR

    SciTech Connect

    D. Jolley

    2001-07-16

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M&O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M&O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow {Delta}G (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M&O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed.

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

    PubMed

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

    2015-01-01

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

  8. Stable microbial community composition on the Greenland Ice Sheet

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2013-06-01

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

  10. Understanding Microbial Communities: Function, Structure and Dynamics

    DTIC Science & Technology

    2015-02-11

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

  11. Method for analyzing microbial communities

    DOEpatents

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

    2010-07-20

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

  12. [Potential Carbon Fixation Capability of Non-photosynthetic Microbial Community at Different Depth of the South China Sea and Its Response to Different Electron Donors].

    PubMed

    Fang, Feng; Wang, Lei; Xi, Xue-fei; Hu, Jia-jun; Fu, Xiao-hua; Lu, Bing; Xu, Dian-sheng

    2015-05-01

    The seawater samples collected from many different areas with different depth in the South China Sea were cultivated using different electron donors respectively. And the variation in the potential carbon fixation capability ( PCFC ) of non-photosynthetic microbial community (NPMC) in seawater with different depth was determined after a cycle of cultivation through the statistic analysis. In addition, the cause for the variation was clarified through analyzing key gene abundance regarding CO2 fixation and characteristics of seawater with different depth. The result showed that the PCFCs of NPMC in seawater with different depth were generally low and had no significant difference when using NaNO2 as the electron donor. The PCFC of NPMC in surface seawater was higher than that in deep seawater when using H2 as the electron donor, on the contrary, the PCFC of NPMC in deep seawater was higher than that in surface seawater when using Na2S2O3 as the electron donor. The abundance of the main CO2 fixation gene cbbL in surface seawater was higher than that in deep seawater while the cbbM gene abundance in deep seawater was higher than that in surface seawater. Most hydrogen-oxidizing bacteria had the cbbL gene, and most sulfur bacteria had the cbbM gene. The tendency of seawater cbbL/cbbM gene abundance with the change of depth revealed that there were different kinds of bacteria accounting for the majority in NPMC fixing CO2 at different depth of ocean, which led to different response of PCFC of NPMC at different depth of the sea to different electron donors. The distributions of dissolved oxygen and inorganic carbon concentration with the change of the depth of the sea might be an important reason leading to the difference of NPMC structure and even the difference of PCFC at different depth of the sea.

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

    PubMed

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

    2015-08-16

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

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

    PubMed

    Allison, Steven D

    2014-01-01

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

  15. From microbial communities to cells

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1985-01-01

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

  16. Can Transgenic Maize Affect Soil Microbial Communities?

    PubMed Central

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

    2006-01-01

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

  17. Aspects of Diversity Measurement for Microbial Communities

    PubMed Central

    Mills, Aaron L.; Wassel, Raymond A.

    1980-01-01

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

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

    PubMed

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

    2003-01-01

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

  19. Microbial Community Structure in the Rhizosphere of Rice Plants

    PubMed Central

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  20. Modeled carbon respiration of microbial communities with explicit enzyme representation

    NASA Astrophysics Data System (ADS)

    Todd-Brown, K. E.; Allison, S. D.

    2009-12-01

    Most carbon cycling models do not represent microbial biomass and extracellular enzymes directly. We previously introduced a partial differential equation and agent-based model to investigate dynamics of microbial decomposers and carbon respiration. In this model we explored the respiration rate of a microbial community comprised of producers (microbes that secrete foraging enzymes) and cheaters (microbes that do not secrete enzymes but benefit from them) The inclusion of cheaters reduced the producer population, which in turn reduced the amount of enzyme in the system and slowed the conversion of substrate into product. This limited the overall biomass and reduced the amount of CO2 released by the system. Here we introduce an analogous ordinary differential equation model for well-mixed systems, such as chemostats and aquatic or marine environments. We tested this model against experimental data from communities of Pseudomonas bacteria that produce protease enzymes. We found that the new model matches the experimental data and hypothesize that diffusion would reduce the expected respiration rate in diffusion-limited systems, such as soils or agar plates,. Our models suggest that enzyme producers grow more slowly due to the added energetic burden of enzyme production. Furthermore, mixed cheater/producer communities are less efficient at mineralizing carbon substrates than pure producer populations. Diffusion of enzymes through the system plays a key role in reducing the overall respiration rate. These results have potential implications for soil and aquatic carbon models, suggesting that both microbial biomass and community composition should be explicitly represented. If community composition is ignored, then there could be a systematic overestimation of the carbon respired from the system. Our results emphasize that mechanistic modeling of microbial communities can improve prediction of carbon cycling under varying environmental conditions.

  1. A Comparison of Microbial Communities from Deep Igneous Crust

    NASA Astrophysics Data System (ADS)

    Smith, A. R.; Flores, G. E.; Fisk, M. R.; Colwell, F. S.; Thurber, A. R.; Mason, O. U.; Popa, R.

    2013-12-01

    Recent investigations of life in Earth's crust have revealed common themes in organism function, taxonomy, and diversity. Capacities for hydrogen oxidation, carbon fixation, methanogenesis and methanotrophy, iron and sulfur metabolisms, and hydrocarbon degradation often predominate in deep life communities, and crustal mineralogy has been hypothesized as a driving force for determining deep life community assemblages. Recently, we found that minerals characteristic of the igneous crust harbored unique communities when incubated in the Juan de Fuca Ridge flank borehole IODP 1301A. Here we present attached mineral biofilm morphologies and a comparison of our mineral communities to those from a variety of locations, contamination states, and igneous crustal or mineralogical types. We found that differences in borehole mineral communities were reflected in biofilm morphologies. Olivine biofilms were thick, carbon-rich films with embedded cells of uniform size and shape and often contained secondary minerals. Encrusted cells, spherical and rod-shaped cells, and tubes were indicative of glass surfaces. We also found that the attached communities from incubated borehole minerals were taxonomically more similar to native, attached communities from marine and continental crust than to communities from the aquifer water that seeded it. Our findings further support the hypothesis that mineralogy selects for microbial communities that have distinct phylogenetic, morphological, and potentially functional, signatures. This has important implications for resolving ecosystem function and microbial distributions in igneous crust, the largest deep habitat on Earth.

  2. The dynamic genetic repertoire of microbial communities

    PubMed Central

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

    2009-01-01

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

  3. Multiscale Modeling of Microbial Communities

    NASA Astrophysics Data System (ADS)

    Blanchard, Andrew

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

  4. Effectiveness of ecological rescue for altered soil microbial communities and functions.

    PubMed

    Calderón, Kadiya; Spor, Aymé; Breuil, Marie-Christine; Bru, David; Bizouard, Florian; Violle, Cyrille; Barnard, Romain L; Philippot, Laurent

    2017-01-01

    Soil ecosystems worldwide are subjected to marked modifications caused by anthropogenic disturbances and global climate change, resulting in microbial diversity loss and alteration of ecosystem functions. Despite the paucity of studies, restoration ecology provides an appropriate framework for testing the potential of manipulating soil microbial communities for the recovery of ecosystem functioning. We used a reciprocal transplant design in experimentally altered microbial communities to investigate the effectiveness of introducing microbial communities in degraded soil ecosystems to restore N-cycle functioning. Microbial diversity loss resulted in alternative compositional states associated with impaired N-cycle functioning. Here, the addition of complex microbial communities to these altered communities revealed a pivotal role of deterministic community assembly processes. The diversity of some alternative compositional states was successfully increased but without significant restoration of soil N-cycle functioning. However, in the most degraded alternative state, the introduction of new microbial communities caused an overall decrease in phylogenetic diversity and richness. The successful soil colonization by newly introduced species for some compositional states indicates that priority effects could be overridden when attempting to manipulate microbial communities for soil restoration. Altogether, our result showed consistent patterns within restoration treatments with minor idiosyncratic effects. This suggests the predominance of deterministic processes and the predictability of restoration trajectories, which could be used to guide the effective management of microbial community assemblages for ecological restoration of soils.

  5. Investigating the Response of Microbial Communities to Cyclodextrin

    NASA Astrophysics Data System (ADS)

    Szponar, N.; Slater, G.; Smith, J.

    2009-05-01

    Recent studies have found applications of hydroxypropyl-β-cyclodextrin (HPβCD) to be highly effective in removing DDT from soils in situ. However, the persistence of HPβCD within the soil and its impact on soil microbial communities is still unclear. It has been suggested that cyclodextrin might provide a substrate for microbial communities resulting in changes in the ongoing effectiveness of remediation and/or soil hydraulic properties. The potential exists that stimulation of the soil microbial community may contribute to removal of DDT, along with the solubilization effects normally associated with cyclodextrin treatment. This study investigated the response of soil microbial communities from a site undergoing remediation of DDT with HPβCD through microcosm and bench scale column studies. Phospholipid fatty acid (PLFA) analysis and their natural abundance 13C signatures can be used to identify in situ microbial metabolism of HPβCD. Heterotrophic organisms have PLFA with 13C signatures 3 to 6‰ depleted from their carbon source. Cyclodextrin was found to have a δ13C of -16‰ resulting from its formation via enzymatic degradation of cornstarch. In contrast, soil organic matter, had a predominantly C3 plant derived signature and a δ13C of -25‰. Incorporation of HPβCD by soil microbial communities would therefore cause a shift to a more enriched isotopic value. While microcosm studies demonstrated no noticeable change in biomass and few changes in PLFA distribution, column studies treated with a 10% solution of HPβCD demonstrated an approximate doubling of microbial biomass after 6 weeks of application based on PLFA concentrations. Concurrent changes in PLFA distribution further indicated a response to cyclodextrin. Changes in PLFA concentration and distribution were concurrent with isotopic enrichment of PLFA in treated columns. This isotopic enrichment provided direct evidence for microbial consumption of cyclodextrin. Incorporation of 13C enriched

  6. Understanding Bacteriophage Specificity in Natural Microbial Communities

    PubMed Central

    Koskella, Britt; Meaden, Sean

    2013-01-01

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

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

    PubMed

    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.

  8. Microbial communities of printing paper machines.

    PubMed

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

    1998-06-01

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

  9. Environmental microarray analyses of Antarctic soil microbial communities.

    PubMed

    Yergeau, Etienne; Schoondermark-Stolk, Sung A; Brodie, Eoin L; Déjean, Sébastien; DeSantis, Todd Z; Gonçalves, Olivier; Piceno, Yvette M; Andersen, Gary L; Kowalchuk, George A

    2009-03-01

    Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also experiencing unequalled effects of global warming. Owing to their uniqueness and the potential impact of global warming on these pristine systems, there is considerable interest in determining the structure and function of microbial communities in the Antarctic. We therefore utilized a recently designed 16S rRNA gene microarray, the PhyloChip, which targets 8741 bacterial and archaeal taxa, to interrogate microbial communities inhabiting densely vegetated and bare fell-field soils along a latitudinal gradient ranging from 51 degrees S (Falkland Islands) to 72 degrees S (Coal Nunatak). Results indicated a clear decrease in diversity with increasing latitude, with the two southernmost sites harboring the most distinct Bacterial and Archaeal communities. The microarray approach proved more sensitive in detecting the breadth of microbial diversity than polymerase chain reaction-based bacterial 16S rRNA gene libraries of modest size ( approximately 190 clones per library). Furthermore, the relative signal intensities summed for phyla and families on the PhyloChip were significantly correlated with the relative occurrence of these taxa in clone libraries. PhyloChip data were also compared with functional gene microarray data obtained earlier, highlighting numerous significant relationships and providing evidence for a strong link between community composition and functional gene distribution in Antarctic soils. Integration of these PhyloChip data with other complementary methods provides an unprecedented understanding of the microbial diversity and community structure of terrestrial Antarctic habitats.

  10. Microbial communities on Australian modified atmosphere packaged Atlantic salmon.

    PubMed

    Powell, S M; Tamplin, M L

    2012-05-01

    The role of specific spoilage organisms (SSO) in products such as Atlantic salmon has been well documented. However, little is known about what other micro-organisms are present and these organisms may indirectly influence spoilage by their interactions with the SS0. We used a combination of culture-based and DNA-based methods to explore the microbial communities found on Atlantic salmon fillets packed in a modified atmosphere of carbon dioxide and nitrogen. After 15 days the communities were dominated by Shewanella spp. or Carnobacterium spp. and a variety of other genera were present in smaller numbers. Variability in the microbial community composition in packages processed on the same day was also observed. This was mostly due to differences in the presence of minor members of the community including species from genera such as Iodobacter, Serratia, Morganella and Yersinia. The combination of culture-based and culture-independent methods provided greater insight into the development of microbial communities on Atlantic salmon than would have been possible using only one method. This work highlights the potential importance of lactic acid bacteria (LAB) in fresh Atlantic salmon stored under modified atmosphere conditions. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

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

    EPA Science Inventory

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

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

    EPA Science Inventory

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

  13. Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips

    SciTech Connect

    van der Lelie, D.; Taghavi, S.; McCorkle, S. M.; Li, L. L.; Malfatti, S. A.; Monteleone, D.; Donohoe, B. S.; Ding, S. Y.; Adney, W. S.; Himmel, M. E.; Tringe, S. G.

    2012-05-01

    This study describes the composition and metabolic potential of a lignocellulosic biomass degrading community that decays poplar wood chips under anaerobic conditions. We examined the community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material. The composition of this community contrasts in important ways with biomass-degrading communities associated with higher organisms, which have evolved over millions of years into a symbiotic relationship. Both mammalian and insect hosts provide partial size reduction, chemical treatments (low or high pH environments), and complex enzymatic 'secretomes' that improve microbial access to cell wall polymers. We hypothesized that in order to efficiently degrade coarse untreated biomass, a spontaneously assembled free-living community must both employ alternative strategies, such as enzymatic lignin depolymerization, for accessing hemicellulose and cellulose and have a much broader metabolic potential than host-associated communities. This would suggest that such a community would make a valuable resource for finding new catalytic functions involved in biomass decomposition and gaining new insight into the poorly understood process of anaerobic lignin depolymerization. Therefore, in addition to determining the major players in this community, our work specifically aimed at identifying functions potentially involved in the depolymerization of cellulose, hemicelluloses, and lignin, and to assign specific roles to the prevalent community members in the collaborative process of biomass decomposition. A bacterium similar to Magnetospirillum was identified among the dominant community members, which could play a key role in the anaerobic breakdown of aromatic compounds. We suggest that these compounds are released from the lignin fraction in poplar hardwood during the decay process, which would point to

  14. Microbial Communities in Pre-Columbian Coprolites

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial

  16. Response of microbial community composition and function to soil climate change

    USGS Publications Warehouse

    Waldrop, M.P.; Firestone, M.K.

    2006-01-01

    Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

  17. Decoding molecular interactions in microbial communities

    PubMed Central

    Abreu, Nicole A.; Taga, Michiko E.

    2016-01-01

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

  18. Electricity generation and microbial community changes in microbial fuel cells packed with different anodic materials.

    PubMed

    Sun, Yanmei; Wei, Jincheng; Liang, Peng; Huang, Xia

    2011-12-01

    Four materials, carbon felt cube (CFC), granular graphite (GG), granular activated carbon (GAC) and granular semicoke (GS) were tested as packed anodic materials to seek a potentially practical material for microbial fuel cells (MFCs). The microbial community and its correlation with the electricity generation performance of MFCs were explored. The maximum power density was found in GAC, followed by CFC, GG and GS. In GAC and CFC packed MFCs, Geobacter was the dominating genus, while Azospira was the most populous group in GG. Results further indicated that GAC was the most favorable for Geobacter adherence and growth, and the maximum power densities had positive correlation with the total biomass and the relative abundance of Geobacter, but without apparent correlation with the microbial diversity. Due to the low content of Geobacter in GS, power generated in this system may be attributed to other microorganisms such as Synergistes, Bacteroidetes and Castellaniella.

  19. Effects of low-shear modeled microgravity on a microbial community filtered through a 0.2-μm filter and its potential application in screening for novel microorganisms.

    PubMed

    Aoyagi, Hideki; Kuroda, Akiha

    2012-07-01

    The effects of low-shear modeled microgravity (LSMMG) on a microbial community filtered through a 0.2-μm filter were investigated, and the potential application of LSMMG in the screening of microorganisms was evaluated. Pond water was passed through a 0.2-μm filter and the filtrate inoculated into two kinds of media (Schneider's insect medium, and ten-times-diluted Schneider's insect [0.1-Sch] medium). The cultures were incubated under LSMMG and normal-gravity and the microbial cell growth rates compared. Cell growth rates, final cell concentrations, and substrate consumption rates were higher in the LSMMG culture than in the normal-gravity culture. The microbial communities obtained under the various culture conditions were subjected to denaturing gradient gel electrophoresis (DGGE), revealing three different groups of microorganisms: (i) microorganisms whose growth rates were increased by LSMMG; (ii) microorganisms whose growth rates were suppressed or inhibited by LSMMG; and (iii) microorganisms whose growth rates were not affected by LSMMG. Sequence analysis of the microorganisms whose growth rates were increased by LSMMG showed that some had high similarity with unculturable microorganisms. When these microorganisms that displayed similarity with unculturable microorganisms were cultivated on agar plates, some of the DGGE bands present in the LSMMG culture were also present. We show that it is possible to isolate and cultivate uncultured microorganisms by using combinations of LSMMG, normal-gravity, and agar plate culturing techniques.

  20. Anodic microbial community diversity as a predictor of the power output of microbial fuel cells.

    PubMed

    Stratford, James P; Beecroft, Nelli J; Slade, Robert C T; Grüning, André; Avignone-Rossa, Claudio

    2014-03-01

    The relationship between the diversity of mixed-species microbial consortia and their electrogenic potential in the anodes of microbial fuel cells was examined using different diversity measures as predictors. Identical microbial fuel cells were sampled at multiple time-points. Biofilm and suspension communities were analysed by denaturing gradient gel electrophoresis to calculate the number and relative abundance of species. Shannon and Simpson indices and richness were examined for association with power using bivariate and multiple linear regression, with biofilm DNA as an additional variable. In simple bivariate regressions, the correlation of Shannon diversity of the biofilm and power is stronger (r=0.65, p=0.001) than between power and richness (r=0.39, p=0.076), or between power and the Simpson index (r=0.5, p=0.018). Using Shannon diversity and biofilm DNA as predictors of power, a regression model can be constructed (r=0.73, p<0.001). Ecological parameters such as the Shannon index are predictive of the electrogenic potential of microbial communities.

  1. Evolutionary limits to cooperation in microbial communities

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-09-01

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

  4. Fluvial network imprints on microbial diversity and community network topology

    NASA Astrophysics Data System (ADS)

    Battin, T. J.; Besemer, K.; Widder, S.; Singer, G. A.; Ceola, S.; Bertuzzo, E.; Quince, C.; Sloan, W. T.; Rinaldo, A.

    2013-12-01

    Streams and rivers sculpt continental landscapes and the networks they form carry universal signatures of spatial organization. Biodiversity in fluvial networks ranks among the highest on Earth and microorganisms therein, often enclosed in biofilms, fulfill critical ecosystem functions even with repercussions on the global carbon cycle. We extensively used 454 pyrosequencing on biofilm samples from more than 100 streams from a 5th-order catchment, derived alpha and beta diversity patterns and, using co-occurrence analyses, we studied community network organization. Contrary to current theory and to animal diversity studies, we found microbial alpha diversity in biofilms to decrease downstream with confluences likely acting as filters to biodiversity as it propagates from the smallest headwaters to larger rivers. Along with higher beta diversity in the headwaters, these findings highlight headwaters as critical reservoirs of microbial diversity for entire fluvial networks. Co-occurrence analyses revealed a lower level of fragmentation of community networks in headwaters than in larger rivers downstream and further identified gatekeepers (at family level) as potential architects of the observed network topology. Similarly, fragmentation was higher downstream than upstream of confluences. Consistent with current network theory, simple model simulations suggest that fragmentation patterns are linked to persistence against perturbations. We further explore the role of perturbation for community network topology in the context of fluvial network hydrology. Our findings have deep implications for restoration and conservation. They portrait the imprint of fluvial networks on microbial community networks and thereby expand our knowledge on biodiversity and ecosystem persistence.

  5. Microbial community assembly, theory and rare functions.

    PubMed

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

    2013-01-01

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

  6. Microbial community assembly, theory and rare functions

    PubMed Central

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

    2013-01-01

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

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

    PubMed

    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.

  8. Metaproteomics of complex microbial communities in biogas plants

    PubMed Central

    Heyer, Robert; Kohrs, Fabian; Reichl, Udo; Benndorf, Dirk

    2015-01-01

    Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed. PMID:25874383

  9. The succession pattern of soil microbial communities and its relationship with tobacco bacterial wilt.

    PubMed

    Niu, Jiaojiao; Rang, Zhongwen; Zhang, Chao; Chen, Wu; Tian, Feng; Yin, Huaqun; Dai, Linjian

    2016-10-06

    The interaction mechanism between crop and soil microbial communities is a key issue in both agriculture and soil ecology. However, how soil microbial communities respond to crop planting and ultimately affect crop health still remain unclear. In this research, we explored how soil microbial communities shifted during tobacco cultivation under different rotation systems (control, maize rotation, lily rotation and turnip rotation). Our analyses showed that soil microbial communities had a general response pattern to tobacco planting, as the abundances of Proteobacteria and Planctomycetes increased while Acidobacteria and Verrucomicrobia decreased during tobacco cultivation, no matter which rotation system was adopted. Notably, tobacco decreased the diversity and co-occurrence of soil microorganisms, but maize rotation might suppress tobacco bacterial wilt by alleviating the decrease in biodiversity and co-occurrence. Molecular ecological network analysis indicated that there was stronger competition between potential disease suppressive (e.g., Acidobacteria) and inducible bacteria (e.g., Chloroflexi) in maize rotation systems. Both soil properties (e.g., pH, Ca content) and microbial communities of tobacco mature period depended on their counterparts of fallow period, and all these factors shaped tobacco disease comprehensively. Both soil microbial communities of fallow stage and tobacco selection shaped the communities of tobacco mature stage. And effective rotation crop (maize) could decrease the incidence of tobacco bacterial wilt by alleviating the decrease in diversity and co-occurrences of microbial populations. This study would deepen our understanding about succession mechanism of soil microbial communities during crop cultivation and their relationship with crop health.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  11. Testing the functional significance of microbial community composition.

    Treesearch

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

    2009-01-01

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

  12. Biochar addition impacts soil microbial community in tropical soils

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    ScienceCinema

    Konopka, Allan

    2016-07-12

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

  14. Antibiotic effects on microbial community characteristics in soils under conservation management practices

    USDA-ARS?s Scientific Manuscript database

    Veterinary antibiotics (VAs) administered to livestock are introduced to agroecosystems via land application of manure, posing a potential human and environmental health risk. These Antibiotics may adversely affect soil microbial communities. The objectives of this research were to investigate poten...

  15. Do gut microbial communities differ in pediatric IBS and health?

    PubMed Central

    Shankar, Vijay; Agans, Richard; Holmes, Benjamin; Raymer, Michael; Paliy, Oleg

    2013-01-01

    Human gastrointestinal microbial communities are recognized as important determinants of the host health and disease status. We have recently examined the distal gut microbiota of two groups of children: healthy adolescents and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS). We have revealed the common core of phylotypes shared among all children, identified genera differentially abundant between two groups and surveyed possible relationships among intestinal microbial genera and phylotypes. In this article we explored the use of supervised and unsupervised ordination and classification methods to separate and classify child fecal samples based on their quantitative microbial profile. We observed sample separation according to the participant health status, and this separation could often be attributed to the abundance levels of several specific microbial genera. We also extended our original correlation network analysis of the relative abundances of bacterial genera across samples and determined possible association networks separately for healthy and IBS groups. Interestingly, the number of significant genus abundance associations was drastically lower among the IBS samples, which can potentially be attributed to the existence of multiple routes to microbiota disbalance in IBS or to the loss of microbial interactions during IBS development. PMID:23674073

  16. Do gut microbial communities differ in pediatric IBS and health?

    PubMed

    Shankar, Vijay; Agans, Richard; Holmes, Benjamin; Raymer, Michael; Paliy, Oleg

    2013-01-01

    Human gastrointestinal microbial communities are recognized as important determinants of the host health and disease status. We have recently examined the distal gut microbiota of two groups of children: healthy adolescents and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS). We have revealed the common core of phylotypes shared among all children, identified genera differentially abundant between two groups and surveyed possible relationships among intestinal microbial genera and phylotypes. In this article we explored the use of supervised and unsupervised ordination and classification methods to separate and classify child fecal samples based on their quantitative microbial profile. We observed sample separation according to the participant health status, and this separation could often be attributed to the abundance levels of several specific microbial genera. We also extended our original correlation network analysis of the relative abundances of bacterial genera across samples and determined possible association networks separately for healthy and IBS groups. Interestingly, the number of significant genus abundance associations was drastically lower among the IBS samples, which can potentially be attributed to the existence of multiple routes to microbiota disbalance in IBS or to the loss of microbial interactions during IBS development.

  17. Multifactorial diversity sustains microbial community stability.

    PubMed

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

    2013-11-01

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

  18. Multifactorial diversity sustains microbial community stability

    PubMed Central

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

    2013-01-01

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

  19. Microbial Communities Associated with Phosphorite-bearing Sediments

    NASA Astrophysics Data System (ADS)

    Zoss, R.; Bailey, J.; Flood, B.; Jones, D. S.

    2016-12-01

    Phosphorus is a limiting nutrient in the environment and is an important component of many biological molecules. Calcium phosphate mineral deposits known as phosphorites, are also the primary source of P for agriculture. Understanding phosphorite formation may improve management of P resources. However, the processes that mediate calcium phosphate mineral precipitation in certain marine pore waters remain poorly understood. Phosphogenesis occurs in sediments beneath some oceanic upwelling zones that harbor polyphosphate-accumulating giant sulfur bacteria (GSB). These bacteria may concentrate phosphate in sediment pore waters - creating supersaturated conditions with respect to apatite. However, the relationship between microbes and phosphogenesis is not fully resolved. To further study this relationship, we examined microbial communities from two sources: sediment cores recovered from the shelf of the Benguela region, and DNA extracted from washed phosphorites recovered from those same sediments. We used itag and clone library sequencing of the 16S rRNA gene to examine the microbial communities and their relationship with the environment. We found that many of our sediments shared large numbers of phylotypes with one another, and that the same metabolic guilds were represented at localities across the shelf. Sulfur-reducing bacteria and sulfur-oxidizing bacteria were abundant in our datasets. Phylotypes that are known to carry out nitrification and/or anammox (anaerobic ammonia oxidation) were also well-represented. Our phosphorite extraction, however, contained a distinct microbial community from those observed in the modern sediments. We observed both an enrichment of certain common microbial classes and a complete absence of others. These results could represent an ancient microbial assemblage that was present when the apatite precipitated. While these taxa may or may not have contributed to apatite precipitation, several groups represented in the phosphorite

  20. Dominance of candidate Saccharibacteria in a membrane bioreactor treating medium age landfill leachate: Effects of organic load on microbial communities, hydrolytic potential and extracellular polymeric substances.

    PubMed

    Remmas, Nikolaos; Melidis, Paraschos; Zerva, Ioanna; Kristoffersen, Jon Bent; Nikolaki, Sofia; Tsiamis, George; Ntougias, Spyridon

    2017-08-01

    A membrane bioreactor (MBR), accomplishing high nitrogen removal efficiencies, was evaluated under various landfill leachate concentrations (50, 75 and 100% v/v). Proteinous and carbohydrate extracellular polymeric substances (EPS) and soluble microbial product (SMP) were strongly correlated (p<0.01) with organic load, salinity and NH4(+)-N. Exceptionally high β-glucosidase activities (6700-10,100Ug(-1)) were determined during MBR operation with 50% v/v leachate, as a result of the low organic carbon availability that extendedly induced β-glucosidases to breakdown the least biodegradable organic fraction. Illumina sequencing revealed that candidate Saccharibacteria were dominant, independently of the leachate concentration applied, whereas other microbiota (21.2% of total reads) disappeared when undiluted leachate was used. Fungal taxa shifted from a Saccharomyces- to a newly-described Cryptomycota-based community with increasing leachate concentration. Indeed, this is the first report on the dominance of candidate Saccharibacteria and on the examination of their metabolic behavior in a bioreactor treating real wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Culture-independent methods for identifying microbial communities in cheese.

    PubMed

    Jany, Jean-Luc; Barbier, Georges

    2008-10-01

    This review focuses on the culture-independent methods available for the description of both bacterial and fungal communities in cheese. Important steps of the culture-independent strategy, which relies on bulk DNA extraction from cheese and polymerase chain reaction (PCR) amplification of selected sequences, are discussed. We critically evaluate the identification techniques already used for monitoring microbial communities in cheese, including PCR-denaturing gradient gel electrophoresis (PCR-DGGE), PCR-temporal temperature gradient gel electrophoresis (PCR-TTGE) or single-strand conformation polymorphism-PCR (SSCP-PCR) as well as some other techniques that remain to be adapted to the study of cheese communities. Further, our analysis draws attention to the lack of data available on suitable DNA sequences for identifying fungal communities in cheese and proposes some potential DNA targets.

  2. Determinants of the distribution of nitrogen-cycling microbial communities at the landscape scale.

    PubMed

    Bru, D; Ramette, A; Saby, N P A; Dequiedt, S; Ranjard, L; Jolivet, C; Arrouays, D; Philippot, L

    2011-03-01

    Little information is available regarding the landscape-scale distribution of microbial communities and its environmental determinants. However, a landscape perspective is needed to understand the relative importance of local and regional factors and land management for the microbial communities and the ecosystem services they provide. In the most comprehensive analysis of spatial patterns of microbial communities to date, we investigated the distribution of functional microbial communities involved in N-cycling and of the total bacterial and crenarchaeal communities over 107 sites in Burgundy, a 31,500 km(2) region of France, using a 16 × 16 km(2) sampling grid. At each sampling site, the abundance of total bacteria, crenarchaea, nitrate reducers, denitrifiers- and ammonia oxidizers were estimated by quantitative PCR and 42 soil physico-chemical properties were measured. The relative contributions of land use, spatial distance, climatic conditions, time, and soil physico-chemical properties to the spatial distribution of the different communities were analyzed by canonical variation partitioning. Our results indicate that 43-85% of the spatial variation in community abundances could be explained by the measured environmental parameters, with soil chemical properties (mostly pH) being the main driver. We found spatial autocorrelation up to 739 km and used geostatistical modelling to generate predictive maps of the distribution of microbial communities at the landscape scale. The present study highlights the potential of a spatially explicit approach for microbial ecology to identify the overarching factors driving the spatial heterogeneity of microbial communities even at the landscape scale.

  3. Short-term effect of capping on microbial communities in freshwater sediments.

    PubMed

    Wang, Qi; Kassem, Issmat I; Sigler, Von; Gruden, Cyndee

    2009-04-01

    Because biogas bubbles can influence cap integrity, the effect of capping and cap material on the ebullition potential in sediments must be studied. The goal of this comprehensive study was to determine the short-term effect of capping regime on the activity, metabolic potential, and community structure of sediment microorganisms. To evaluate the effect of capping (sand, synthetic aggregate, and no cap) on microbial communities (i.e., nitrifiers and methanogens), sediments were collected from the Anacostia River (Washington, D.C.). Microbial communities in sand-capped sediments exhibited the highest activity (tetrazolium redox dye, fluorescein diacetate hydrolysis assay, and biogas production), while communities in uncapped sediments exhibited the highest metabolic diversity. Substantial changes in microbial community structure (denaturing gradient gel electrophoresis) did not occur as a result of capping. Our data showed that the nature and magnitude of the effect that capping can have on microbial activity (biogas production) will likely be dependent on the capping materials chosen.

  4. The influence of human exploration on the microbial community structure and ammonia oxidizing potential of the Su Bentu limestone cave in Sardinia, Italy

    PubMed Central

    Koskinen, Kaisa; Sanna, Laura; D’Angeli, Ilenia M.; De Waele, Jo; Marcia, Paolo; Moissl-Eichinger, Christine; Rettberg, Petra

    2017-01-01

    The bacterial diversity in the Su Bentu Cave in Sardinia was investigated by means of 16S rRNA gene-based analysis. This 15 km long cave, carved in Jurassic limestone, hosts a variety of calcite speleothems, and a long succession of subterranean lakes with mixed granite and carbonate sands. The lower level is occasionally flooded by a rising groundwater level, but with only scarce input of organic remains (leaves and charcoal fragments). On the quiet cave pools there are visible calcite rafts, whereas walls are locally coated with manganese deposits. In the drier upper levels, where organic input is much more subdued, moonmilk—a hydrated calcium-magnesium carbonate speleothem—can be found. Relative humidity approaches 100% and the measured mean annual cave air temperature is 14.8°C. Samples were obtained in 2014 from calcite rafts, moonmilk, manganese oxide deposits and soil (limestone and granite grains). Microclimatic conditions in the cave near the sampling sites, sample properties, physico-chemical parameters of water, and sediment composition were determined. The microbial community of this system is predominately composed of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Nitrospirae, and Firmicutes. Sampling sites near the entrance of the cave and in close proximity of the underground campsite–located 500 meters deep into the cave—revealed the highest diversity as well as the highest number of human associated microorganisms. Two samples obtained in very close proximity of each other near the campsite, indicate that the human impact is localized and is not distributed freely within the system. Analysis of the abundance of bacterial and archaeal amoA genes revealed a far greater abundance of archaeal amoA genes compared to bacterial representatives. The results of this study highlight that human impact is confined to locations that are utilized as campsites and that exploration leaves little microbial trails. Furthermore, we uncovered a

  5. The influence of human exploration on the microbial community structure and ammonia oxidizing potential of the Su Bentu limestone cave in Sardinia, Italy.

    PubMed

    Leuko, Stefan; Koskinen, Kaisa; Sanna, Laura; D'Angeli, Ilenia M; De Waele, Jo; Marcia, Paolo; Moissl-Eichinger, Christine; Rettberg, Petra

    2017-01-01

    The bacterial diversity in the Su Bentu Cave in Sardinia was investigated by means of 16S rRNA gene-based analysis. This 15 km long cave, carved in Jurassic limestone, hosts a variety of calcite speleothems, and a long succession of subterranean lakes with mixed granite and carbonate sands. The lower level is occasionally flooded by a rising groundwater level, but with only scarce input of organic remains (leaves and charcoal fragments). On the quiet cave pools there are visible calcite rafts, whereas walls are locally coated with manganese deposits. In the drier upper levels, where organic input is much more subdued, moonmilk-a hydrated calcium-magnesium carbonate speleothem-can be found. Relative humidity approaches 100% and the measured mean annual cave air temperature is 14.8°C. Samples were obtained in 2014 from calcite rafts, moonmilk, manganese oxide deposits and soil (limestone and granite grains). Microclimatic conditions in the cave near the sampling sites, sample properties, physico-chemical parameters of water, and sediment composition were determined. The microbial community of this system is predominately composed of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Nitrospirae, and Firmicutes. Sampling sites near the entrance of the cave and in close proximity of the underground campsite-located 500 meters deep into the cave-revealed the highest diversity as well as the highest number of human associated microorganisms. Two samples obtained in very close proximity of each other near the campsite, indicate that the human impact is localized and is not distributed freely within the system. Analysis of the abundance of bacterial and archaeal amoA genes revealed a far greater abundance of archaeal amoA genes compared to bacterial representatives. The results of this study highlight that human impact is confined to locations that are utilized as campsites and that exploration leaves little microbial trails. Furthermore, we uncovered a highly

  6. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

    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 drill hole ~16°C), where petrographic evidence suggested the presence of microbial alteration. Archaeal 16S rRNA genes were amplified, cloned, and twelve clones representing the most abundant groups were sequenced. Eleven out of the twelve clones were 97 to 99% similar to Group I marine Crenarchaeota, while the remaining clone was 95% similar to Euryarchaeota, based on BLAST searches of the GenBank database. Our community-level approach to studying microbes living in volcanic glasses has provided a greater understanding of the microbial communities that potentially alter these materials.

  7. Perfluoroalkyl Acids Shift Microbial Community Structure Across Experimental Scales

    NASA Astrophysics Data System (ADS)

    Weathers, T. S.; Sharp, J.

    2016-12-01

    Perfluoroalkyl acids (PFAAs) are contaminants of emerging concern that have increasingly been found in groundwater and drinking water systems. Previously, we demonstrated that PFAAs significantly alter the abundance of specific microbial clades in batch reductive dechlorinating systems, resulting in decreased chlorinated solvent attenuation capabilities. To further understand the impacts of PFAA exposure on subsurface microbial processes and PFAA transport, we investigated changes in microbial community structure as a function of PFAA presence in flow-through columns simulating aquifer transport. Phylogenetic analysis using high throughput, next generation sequencing performed after exposure to 250 pore volumes of source zone concentrations of PFAAs (10 mg/L each of 11 analytes including PFOS and PFOA) resulted in patterns that mirrored those observed in batch systems, demonstrating a conservation of community dynamics across experimental scales. Of the nine clades observed in both batch and flow-through systems, six were similarly impacted as a function of PFAA exposure, regardless of the experimental differences in transport and redox state. Specifically, the presence of PFAAs enhanced the relative abundance of Archaea, Bacteroidetes (phylum), and the family Veillonellaceae in both systems. Repressed clades include the genus Sedimentibacter, Ruminococcaceae (family), and the Anaerolineales, which contains Dehalococcoides, a genus known for its ability to fully dechlorinate TCE. As PFAAs are often co-located with TCE and BTEX, changes in microbial community structure can result in hindered bioremediation of these co-contaminants. Consideration of community shifts and corresponding changes in behavior, such as repressed reductive dechlorination or increased biofilm formation, will aid in the development of conceptual site models that account for co-contaminant bioremediation potential and PFAA transport.

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

    PubMed

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

    2006-05-01

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

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

    PubMed

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

    2015-11-15

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

  10. Microbial lectins and their prospective mitogenic potential.

    PubMed

    Singh, Ram Sarup; Walia, Amandeep K

    2014-11-01

    The binding of mitogenic lectins to the glycoconjugates on cell surface receptor triggers multitude of reactions involving different signal transduction pathways which ultimately results in cell proliferation. Since 1960 after the chance discovery of mitogenic property of lectins by Nowell, it has attracted more attention. The property of stimulation of mature lymphocytes aided the immunological investigations to study and analyse the mechanism of cell stimulation and division. Plant lectins are extensively studied for mitogenic activity and their widespread applications are also reported. During the past two decades, the study of biological properties of microbial lectins has increased tremendously. Their biological activities including mitogenic potential are equally applicable as that of plant lectins. The review mainly focuses on mitogenic potential of microbial lectins. It will provide a comprehensive view regarding distribution of this remarkable property among microbes including algae, fungi and bacteria, mechanisms and models of mitogenic stimulation, and also assays being employed to detect the mitogenic activity.

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

    PubMed

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

    2014-08-01

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

  12. Microbial Communities of the Okinawa Backarc Basin Subvent Biosphere

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed Central

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

    2016-01-01

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

  14. Microbial communities in the deep subsurface

    NASA Astrophysics Data System (ADS)

    Krumholz, Lee R.

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-03-16

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

  17. Soil amendments yield persisting changes in the microbial communities

    USDA-ARS?s Scientific Manuscript database

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

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

    USDA-ARS?s Scientific Manuscript database

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

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

    PubMed

    Truu, Marika; Juhanson, Jaanis; Truu, Jaak

    2009-06-15

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

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

    PubMed

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

    2010-08-01

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

  1. Chernozems microbial community under anthropogenic impact (Russia)

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    PubMed Central

    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. PMID:27798702

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

    PubMed

    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.

  4. Microbial communities in oil-contaminated seawater.

    PubMed

    Harayama, Shigeaki; Kasai, Yuki; Hara, Akihiro

    2004-06-01

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

  5. Community Proteomics of a Natural Microbial Biofilm

    SciTech Connect

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

    2005-06-01

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

  6. Identifying the microbial communities and operational conditions for optimized wastewater treatment in microbial fuel cells.

    PubMed

    Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Wu, Angela; Yamanaka, Yuko; Nealson, Kenneth H; Bretschger, Orianna

    2013-12-01

    Microbial fuel cells (MFCs) are devices that exploit microorganisms as "biocatalysts" to recover energy from organic matter in the form of electricity. MFCs have been explored as possible energy neutral wastewater treatment systems; however, fundamental knowledge is still required about how MFC-associated microbial communities are affected by different operational conditions and can be optimized for accelerated wastewater treatment rates. In this study, we explored how electricity-generating microbial biofilms were established at MFC anodes and responded to three different operational conditions during wastewater treatment: 1) MFC operation using a 750 Ω external resistor (0.3 mA current production); 2) set-potential (SP) operation with the anode electrode potentiostatically controlled to +100 mV vs SHE (4.0 mA current production); and 3) open circuit (OC) operation (zero current generation). For all reactors, primary clarifier effluent collected from a municipal wastewater plant was used as the sole carbon and microbial source. Batch operation demonstrated nearly complete organic matter consumption after a residence time of 8-12 days for the MFC condition, 4-6 days for the SP condition, and 15-20 days for the OC condition. These results indicate that higher current generation accelerates organic matter degradation during MFC wastewater treatment. The microbial community analysis was conducted for the three reactors using 16S rRNA gene sequencing. Although the inoculated wastewater was dominated by members of Epsilonproteobacteria, Gammaproteobacteria, and Bacteroidetes species, the electricity-generating biofilms in MFC and SP reactors were dominated by Deltaproteobacteria and Bacteroidetes. Within Deltaproteobacteria, phylotypes classified to family Desulfobulbaceae and Geobacteraceae increased significantly under the SP condition with higher current generation; however those phylotypes were not found in the OC reactor. These analyses suggest that species

  7. Alpine Microbial Community Responses to Summer Warming

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  8. Controls on soil microbial community stability under climate change

    PubMed Central

    de Vries, Franciska T.; Shade, Ashley

    2013-01-01

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

  9. Microbial community functional change during vertebrate carrion decomposition.

    PubMed

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

    2013-01-01

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

  10. Microbial Community Functional Change during Vertebrate Carrion Decomposition

    PubMed Central

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

    2013-01-01

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

  11. Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe.

    PubMed

    Purahong, Witoon; Schloter, Michael; Pecyna, Marek J; Kapturska, Danuta; Däumlich, Veronika; Mital, Sanchit; Buscot, François; Hofrichter, Martin; Gutknecht, Jessica L M; Krüger, Dirk

    2014-11-12

    The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

  12. Microbial Communities of Continuously Cropped, Irrigated Rice Fields

    PubMed Central

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

    1997-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  14. Effects of octahedral molecular sieve on treatment performance, microbial metabolism, and microbial community in expanded granular sludge bed reactor.

    PubMed

    Pan, Fei; Xu, Aihua; Xia, Dongsheng; Yu, Yang; Chen, Guo; Meyer, Melissa; Zhao, Dongye; Huang, Ching-Hua; Wu, Qihang; Fu, Jie

    2015-12-15

    This study evaluated the effects of synthesized octahedral molecular sieve (OMS-2) nanoparticles on the anaerobic microbial community in a model digester, expanded granular sludge bed (EGSB) reactor. The addition of OMS-2 (0.025 g/L) in the EGSB reactors resulted in an enhanced operational performance, i.e., COD removal and biogas production increased by 4% and 11% respectively, and effluent volatile fatty acid (VFA) decreased by 11% relative to the control group. The Biolog EcoPlate™ test was employed to investigate microbial metabolism in the EGSB reactors. Results showed that OMS-2 not only increased the microbial metabolic level but also significantly changed the community level physiological profiling of the microorganisms. The Illumina MiSeq high-throughput sequencing of 16S rRNA gene indicated OMS-2 enhanced the microbial diversity and altered the community structure. The largest bacterial genus Lactococcus, a lactic acid bacterium, reduced from 29.3% to 20.4% by abundance in the presence of 0.25 g/L OMS-2, which may be conducive to decreasing the VFA production and increasing the microbial diversity. OMS-2 also increased the quantities of acetogenic bacteria and Archaea, and promoted the acetogenesis and methanogenesis. The X-ray photoelectron spectroscopy illustrated that Mn(IV)/Mn(III) with high redox potential in OMS-2 were reduced to Mn(II) in the EGSB reactors; this in turn affected the microbial community. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Microbial community structure characteristics associated membrane fouling in A/O-MBR system.

    PubMed

    Gao, Da-Wen; Wen, Zhi-Dan; Li, Bao; Liang, Hong

    2014-02-01

    The study demonstrated the potential relationship between microbial community structure and membrane fouling in an anoxic-oxic membrane bioreactor (A/O-MBR). The results showed that the microbial community structure in biocake was different with aerobic mixture, and the dominant populations were out of sync during the fouling process. Based on microbial community structure and metabolites analysis, the results showed that the succession of microbial community might be the leading factor to the variation of metabolites, and it might be the primary cause of membrane fouling. The rise of Shannon diversity index (H) of the microbial community in A/O-MBR went with the gradually serious membrane fouling. Pareto-Lorenz curve was used to describe the evenness of microbial distribution in A/O-MBR, and the result indicated when community evenness was low, the membrane fouling took place smoothly or slightly, otherwise, high evenness of microbial community would lead to more seriously membrane fouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Response of a salt marsh microbial community to antibiotic contamination.

    PubMed

    Fernandes, Joana P; Almeida, C Marisa R; Basto, M Clara P; Mucha, Ana P

    2015-11-01

    Salt marsh plants and associated microorganisms can have an important role in contaminant removal from estuaries, through bioremediation processes. Nevertheless, the interaction between emerging contaminants, namely antibiotics, and plant-microorganism associations in estuarine environment are still scarcely known. In this vein, the aim of the present study was to evaluate, in controlled conditions, the response of a salt marsh plant-microorganism association to a contamination with a veterinary antibiotic. For that a salt marsh plant (Phragmites australis) and its respective rhizosediment were collected in a temperate estuary (Lima estuary, NW Portugal) and exposed for 7 days to enrofloxacin (ENR) under different nutritional conditions in sediment elutriates. Response was evaluated in terms of ENR removal and changes in microbial community structure (evaluated by ARISA) and abundance (estimated by DAPI). In general, no significant changes were observed in microbial abundance. Changes in bacterial richness and diversity were observed but only in unplanted systems. However, multivariate analysis of ARISA profiles showed significant effect of both the presence of plant and type of treatment on the microbial community structure, with significant differences among all treatment groups. In addition, plants and associated microorganisms presented a potential for antibiotic removal that, although highly dependent on their nutritional status, can be a valuable asset to recover impacted areas such as estuarine ones.

  17. Bioinformatic Approaches Reveal Metagenomic Characterization of Soil Microbial Community

    PubMed Central

    Xu, Zhuofei; Hansen, Martin Asser; Hansen, Lars H.; Jacquiod, Samuel; Sørensen, Søren J.

    2014-01-01

    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. PMID:24691166

  18. Microbial diversity and potential pathogens in ornamental fish aquarium water.

    PubMed

    Smith, Katherine F; Schmidt, Victor; Rosen, Gail E; Amaral-Zettler, Linda

    2012-01-01

    Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.). The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus) and Chinese algae eaters (Gyrinocheilus aymonieri) purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%), Bacteroidetes (18%) and Planctomycetes (6%), with the top four phyla representing >80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species.

  19. Microbial Diversity and Potential Pathogens in Ornamental Fish Aquarium Water

    PubMed Central

    Smith, Katherine F.; Schmidt, Victor; Rosen, Gail E.; Amaral-Zettler, Linda

    2012-01-01

    Ornamental fishes are among the most popular and fastest growing categories of pets in the United States (U.S.). The global scope and scale of the ornamental fish trade and growing popularity of pet fish in the U.S. are strong indicators of the myriad economic and social benefits the pet industry provides. Relatively little is known about the microbial communities associated with these ornamental fishes or the aquarium water in which they are transported and housed. Using conventional molecular approaches and next generation high-throughput amplicon sequencing of 16S ribosomal RNA gene hypervariable regions, we characterized the bacterial community of aquarium water containing common goldfish (Carassius auratus) and Chinese algae eaters (Gyrinocheilus aymonieri) purchased from seven pet/aquarium shops in Rhode Island and identified the presence of potential pathogens. Our survey identified a total of 30 phyla, the most common being Proteobacteria (52%), Bacteroidetes (18%) and Planctomycetes (6%), with the top four phyla representing >80% of all sequences. Sequences from our water samples were most closely related to eleven bacterial species that have the potential to cause disease in fishes, humans and other species: Coxiella burnetii, Flavobacterium columnare, Legionella birminghamensis, L. pneumophila, Vibrio cholerae, V. mimicus. V. vulnificus, Aeromonas schubertii, A. veronii, A. hydrophila and Plesiomonas shigelloides. Our results, combined with evidence from the literature, suggest aquarium tank water harboring ornamental fish are an understudied source for novel microbial communities and pathogens that pose potential risks to the pet industry, fishes in trade, humans and other species. PMID:22970112

  20. Successive DNA extractions improve characterization of soil microbial communities

    PubMed Central

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

    2017-01-01

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

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

    PubMed

    Dunfield, Kari E; Germida, James J

    2004-01-01

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

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

    PubMed

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

    2008-01-01

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

  3. Proteogenomic approaches for the molecular characterization of natural microbial communities.

    PubMed

    Banfield, Jillian F; Verberkmoes, Nathan C; Hettich, Robert L; Thelen, Michael P

    2005-01-01

    genetic potential of the associated populations. Thus, it is necessary to develop bioinformatics approaches to generate relatively comprehensive gene inventories for each organism type. These inventories are critical for expression and functional analyses. In proteomic studies, for example, peptides that differ from those predicted from gene sequences can be measured, but they generally cannot be identified by database matching, even if the difference is only a single amino acid residue. Furthermore, many of the identified proteins have no known function. We propose that these challenges can be addressed by development of proteogenomic, biochemical, and geochemical methods that will be initially deployed in a simple, natural model ecosystem. The resulting approach should be broadly applicable and will enhance the utility and significance of genomic data from isolates and consortia for study of organisms in many habitats. Solutions draining pyrite-rich deposits are referred to as acid mine drainage (AMD). AMD is a very prevalent, international environmental problem associated with energy and metal resources. The biological-mineralogical interactions that define these systems can be harnessed for energy-efficient metal recovery and removal of sulfur from coal. The detailed understanding of microbial ecology and ecosystem dynamics resulting from the proposed work will provide a scientific foundation for dealing with the environmental challenges and technological opportunities, and yield new methods for analysis of more complex natural communities.

  4. Electrosynthesis of Commodity Chemicals by an Autotrophic Microbial Community

    PubMed Central

    Marshall, Christopher W.; Ross, Daniel E.; Fichot, Erin B.; Norman, R. Sean

    2012-01-01

    A microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at −590 mV versus the standard hydrogen electrode (SHE) with CO2 as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariant Archaea population of Methanobacterium spp. and a shifting Bacteria population. Acetobacterium spp. were the most abundant Bacteria on the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from <1 to 7 mM day−1 (per cathode liquid volume) and was concomitantly produced with acetate and hydrogen. Acetogenesis increased to >4 mM day−1 (accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to >11 mM day−1 (versus 0.045 mM day−1 abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of −460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility. PMID:23001672

  5. Electrosynthesis of commodity chemicals by an autotrophic microbial community.

    PubMed

    Marshall, Christopher W; Ross, Daniel E; Fichot, Erin B; Norman, R Sean; May, Harold D

    2012-12-01

    A microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at -590 mV versus the standard hydrogen electrode (SHE) with CO(2) as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariant Archaea population of Methanobacterium spp. and a shifting Bacteria population. Acetobacterium spp. were the most abundant Bacteria on the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from <1 to 7 mM day(-1) (per cathode liquid volume) and was concomitantly produced with acetate and hydrogen. Acetogenesis increased to >4 mM day(-1) (accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to >11 mM day(-1) (versus 0.045 mM day(-1) abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of -460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility.

  6. Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia).

    PubMed

    Rozanov, Alexey S; Bryanskaya, Alla V; Malup, Tatiana K; Meshcheryakova, Irina A; Lazareva, Elena V; Taran, Oksana P; Ivanisenko, Timofey V; Ivanisenko, Vladimir A; Zhmodik, Sergey M; Kolchanov, Nikolay A; Peltek, Sergey E

    2014-01-01

    Geothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental questions, as well as those with practical benefits. Uzon caldera is located in the Uzon-Geyser depression that is situated in the centre of the Karym-Semyachin region of the East Kamchatka graben-synclinorium. The microbial communities of Zavarzin spring are well studied; however, its benthic microbial mat has not been previously described. Pyrosequencing of the V3 region of the 16S rRNA gene was used to study the benthic microbial community of the Zavarzin thermal spring (Uzon Caldera, Kamchatka). The community is dominated by bacteria (>95% of all sequences), including thermophilic, chemoorganotrophic Caldiserica (33.0%) and Dictyoglomi (24.8%). The benthic community and the previously examined planktonic community of Zavarzin spring have qualitatively similar, but quantitatively different, compositions. In this study, we performed a metagenomic analysis of the benthic microbial mat of Zavarzin spring. We compared this benthic community to microbial communities found in the water and of an integral probe consisting of water and bottom sediments. Various phylogenetic groups of microorganisms, including potentially new ones, represent the full-fledged trophic system of Zavarzin. A thorough geochemical study of the spring was performed.

  7. Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia)

    PubMed Central

    2014-01-01

    Background Geothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental questions, as well as those with practical benefits. Uzon caldera is located in the Uzon-Geyser depression that is situated in the centre of the Karym-Semyachin region of the East Kamchatka graben-synclinorium. The microbial communities of Zavarzin spring are well studied; however, its benthic microbial mat has not been previously described. Results Pyrosequencing of the V3 region of the 16S rRNA gene was used to study the benthic microbial community of the Zavarzin thermal spring (Uzon Caldera, Kamchatka). The community is dominated by bacteria (>95% of all sequences), including thermophilic, chemoorganotrophic Caldiserica (33.0%) and Dictyoglomi (24.8%). The benthic community and the previously examined planktonic community of Zavarzin spring have qualitatively similar, but quantitatively different, compositions. Conclusions In this study, we performed a metagenomic analysis of the benthic microbial mat of Zavarzin spring. We compared this benthic community to microbial communities found in the water and of an integral probe consisting of water and bottom sediments. Various phylogenetic groups of microorganisms, including potentially new ones, represent the full-fledged trophic system of Zavarzin. A thorough geochemical study of the spring was performed. PMID:25563397

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

    NASA Astrophysics Data System (ADS)

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

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

  9. Microbial community changes along the active seepage site of one cold seep in the Red Sea.

    PubMed

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep.

  10. Microbial community changes along the active seepage site of one cold seep in the Red Sea

    PubMed Central

    Cao, Huiluo; Zhang, Weipeng; Wang, Yong; Qian, Pei-Yuan

    2015-01-01

    The active seepage of the marine cold seeps could be a critical process for the exchange of energy between the submerged geosphere and the sea floor environment through organic-rich fluids, potentially even affecting surrounding microbial habitats. However, few studies have investigated the associated microbial community changes. In the present study, 16S rRNA genes were pyrosequenced to decipher changes in the microbial communities from the Thuwal seepage point in the Red Sea to nearby marine sediments in the brine pool, normal marine sediments and water, and benthic microbial mats. An unexpected number of reads from unclassified groups were detected in these habitats; however, the ecological functions of these groups remain unresolved. Furthermore, ammonia-oxidizing archaeal community structures were investigated using the ammonia monooxygenase subunit A (amoA) gene. Analysis of amoA showed that planktonic marine habitats, including seeps and marine water, hosted archaeal ammonia oxidizers that differed from those in microbial mats and marine sediments, suggesting modifications of the ammonia oxidizing archaeal (AOA) communities along the environmental gradient from active seepage sites to peripheral areas. Changes in the microbial community structure of AOA in different habitats (water vs. sediment) potentially correlated with changes in salinity and oxygen concentrations. Overall, the present results revealed for the first time unanticipated novel microbial groups and changes in the ammonia-oxidizing archaea in response to environmental gradients near the active seepages of a cold seep. PMID:26284035

  11. Microbial communities associated with the invasive Hawaiian sponge Mycale armata.

    PubMed

    Wang, Guangyi; Yoon, Sang-Hwal; Lefait, Emilie

    2009-03-01

    Microbial symbionts are fundamentally important to their host ecology, but microbial communities of invasive marine species remain largely unexplored. Clone libraries and Denaturing gradient gel electrophoresis analyses revealed diverse microbial phylotypes in the invasive marine sponge Mycale armata. Phylotypes were related to eight phyla: Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Acidobacteria, Chloroflexi, Crenarchaeota and Firmicutes, with predominant alphaproteobacterial sequences (>58%). Three Bacterial Phylotype Groups (BPG1--associated only with sequence from marine sponges; BPG2--associated with sponges and other marine organisms and BPG3--potential new phylotypes) were identified in M. armata. The operational taxonomic units (OTU) of cluster BPG2-B, belonging to Rhodobacteraceae, are dominant sequences of two clone libraries of M. armata, but constitute only a small fraction of sequences from the non-invasive sponge Dysidea sp. Six OTUs from M. armata were potential new phylotypes because of their low sequence identity with their reference sequences. Our results suggest that M. armata harbors both sponge-specific phylotypes and bacterial phylotypes from other marine organisms.

  12. Comparative Metagenomics of Freshwater Microbial Communities

    SciTech Connect

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

    2010-05-17

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

  13. Electrical potential source mechanisms in microbial induced sulfate reducing environments

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Slater, L.; Ntarlagiannis, D.; Singh, K.; Doherty, R.

    2007-12-01

    In order to compare self-potential (SP) signals resulting from possible 'geobattery' effects with electrodic potential signals based on a known galvanic cell (GC) effect in the presence of sulfide, we designed a column experiment using dual sensor Ag-AgCl electrodes. Water from the Langan River (Belfast, UK), known to contain a sulfate reducing microbial community, was obtained. Two experimental columns were packed with fine-grained glass beads. One column continuously circulated (closed loop) with autoclaved river water as a control, while the other retained biologically active natural river water. Six Ag-AgCl electrodes equally spaced along one side of each column, and three Ag-AgCl self potential electrodes (where the metal is in electrolytic contact with the column via a sterilized 1M KCl agar gel), were placed on the other side of each column. Electrical potential signals were continuously recorded with both sensor types. Induced polarization, electrical resistivity, temperature and aqueous geochemistry measurements (pH, Eh, and conductivity) were taken once daily. Over the 20 day experiment duration, darkening of the circulating fluid, biofilm formation and a sulfurous smell were observed in the biologically active column whereas no such color change (or smell) was observed for the control column. In the active column electrodic potential readings approached 570 mV whereas stable and small electrodic potential values (~8 mV) were detected in the control column.. Self potential signals were consistently only 1-8 mV in both columns. The experiment shows although electrodic potentials (at the electrode) are diagnostic of microbial driven sulfate reduction there is no measurable self potential (geobattery) effect associated with this microbial process.

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

    PubMed

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

    2016-11-01

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

  15. Euphorbia plant latex is inhabited by diverse microbial communities.

    PubMed

    Gunawardana, Manjula; Hyde, Embriette R; Lahmeyer, Sean; Dorsey, Brian L; La Val, Taylor P; Mullen, Madeline; Yoo, Jennifer; Knight, Rob; Baum, Marc M

    2015-12-01

    The antimicrobial properties and toxicity of Euphorbia plant latex should make it a hostile environment to microbes. However, when specimens from Euphorbia spp. were propagated in tissue culture, microbial growth was observed routinely, raising the question whether the latex of this diverse plant genus can be a niche for polymicrobial communities. Latex from a phylogenetically diverse set of Euphorbia species was collected and genomic microbial DNA extracted. Deep sequencing of bar-coded amplicons from taxonomically informative gene fragments was used to measure bacterial and fungal species richness, evenness, and composition. Euphorbia latex was found to contain unexpectedly complex bacterial (mean: 44.0 species per sample; 9 plants analyzed) and fungal (mean: 20.9 species per sample; 22 plants analyzed) communities using culture-independent methods. Many of the identified taxa are known plant endophytes, but have not been previously found in latex. Our results suggest that Euphorbia plant latex, a putatively hostile antimicrobial environment, unexpectedly supports diverse bacterial and fungal communities. The ecological roles of these microorganisms and potential interactions with their host plants are unknown and warrant further research. © 2015 Botanical Society of America.

  16. Adaptation of Aquatic Microbial Communities to Quaternary Ammonium Compounds

    PubMed Central

    Ventullo, Roy M.; Larson, Robert J.

    1986-01-01

    The effects of long-chain (C12 to C18) quaternary ammonium compounds (QACs) on the density, heterotrophic activity, and biodegradation capabilities of heterotrophic bacteria were examined in situ in a lake ecosystem. Monoalkyl and dialkyl substituted QACs were tested over a range of concentrations (0.001 to 10 mg/liter) in both acute (3 h) and chronic (21 day) exposures. In general, none of the QACs tested had significant adverse effects on bacterial densities in either acute or chronic studies. However, significant decreases in bacterial heterotrophic activity were noted in acute studies at QAC concentrations from 0.1 to 10 mg/liter. Chronic exposure of lake microbial communities to a specific monoalkyl QAC resulted in an adaptive response and recovery of heterotrophic activity. No-observable-effect level in the adapted populations was >10 mg/liter. Chronic exposure also resulted in significant increases in the number and activity of bacteria capable of biodegrading the material. The increase in biodegradation capability was observed at low (microgram per liter) concentrations which are approximately the same as realistic environmental levels. In general, our studies indicated that exposure of lake microbial communities to QACs results in the development of adapted communities which are less sensitive to potential toxic effects and more active in the biodegradation of these materials. PMID:16346991

  17. Shifts in Microbial Community and Its Correlation with Degradative Efficiency in a Wastewater Treatment Plant.

    PubMed

    Kapley, Atya; Liu, Ruyin; Jadeja, Niti B; Zhang, Yu; Yang, Min; Purohit, Hemant J

    2015-08-01

    A wastewater treatment plant controls the level of pollution reaching the environment. Yet, despite being the most common aerobic route for treatment of wastewater, the activated sludge process is not utilized to its full potential. This is mainly due to the lack of knowledge base correlating the microbial community in the activated sludge to its degradative performance. In this study, the activated biomass at the treatment site was monitored for five consecutive months. Even though operational parameters were kept constant, the microbial community was observed to change after 3 months. This shift was seen to correlate with 25 % loss of degradative efficiency. Target oxygenases were monitored at two time points, and results indicated that the dominating pathway operating in the common effluent treatment plant (CETP) is the degradation of chlorinated aromatics. This study demonstrates the change in degradative efficiency in a CETP with the change in microbial community and analyzes the parameters influencing the microbial community of activated sludge.

  18. Water management history affects GHG kinetics and microbial communities composition of an Italian rice paddy

    NASA Astrophysics Data System (ADS)

    Lagomarsino, Alessandra; Agnelli, Allessandroelio; Pastorelli, Roberta; Pallara, Grazia; Rasse, Daniel; Silvennoinen, Hanna

    2015-04-01

    The water management system of cultivated soils is one of the most important factors affecting the respective magnitudes of CH4 and N2O emissions. We hypothesized an effect of past management on soil microbial communities and greenhouse gas (GHG) production potential The objective of this study were to i) assess the influence of water management history on GHG production potential and microbial community structure, ii) relate GHGs fluxes to the microbial communities involved in CH4 and N2O production inhabiting the different soils. Moreover, the influence of different soil conditioning procedures on GHG potential fluxes was determined. To reach this aim, four soils with different history of water management were compared, using dried and sieved, pre-incubated and fresh soils. Soil conditioning procedures strongly affected GHG emissions potential: drying and sieving determined the highest emission rates and the largest differences among soil types, probably through the release of labile substrates. Conversely, soil pre-incubation tended to homogenize and level out the differences among soils. Microbial communities composition drove GHG emissions potential and was affected by past management. The water management history strongly affected microbial communities structure and the specific microbial pattern of each soil was strictly linked to the gas (CH4 or N2O) emitted. Aerobic soil stimulated N2O peaks, given a possible major contribution of coupled nitrification/denitrification process. As expected, CH4 was lower in aerobic soil, which showed a less abundant archeal community. This work added evidences to support the hypothesis of an adaptation of microbial communities to past land management that reflected in the potential GHG fluxes.

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

    PubMed Central

    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, 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. Also, the 17 down-dip wells

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

    PubMed

    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, 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. Also, the 17 down-dip wells

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

    USGS Publications Warehouse

    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, 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. Also, the 17 down-dip wells

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-06-06

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    Barkay, Tamar

    1987-01-01

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

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

    PubMed

    Ogilvie, Lesley A; Grant, Alistair

    2008-03-01

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

  9. Microbial community dynamics alleviate stoichiometric constraints during litter decay

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

    Vallino, Joseph J.

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  12. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2010-10-15

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

  14. Characterization of chlorinated and chloraminated drinking water microbial communities in a distribution system simulator using pyrosequencing data analysis

    EPA Science Inventory

    The molecular analysis of drinking water microbial communities has focused primarily on 16S rRNA gene sequence analysis. Since this approach provides limited information on function potential of microbial communities, analysis of whole-metagenome pyrosequencing data was used to...

  15. Characterization of chlorinated and chloraminated drinking water microbial communities in a distribution system simulator using pyrosequencing data analysis

    EPA Science Inventory

    The molecular analysis of drinking water microbial communities has focused primarily on 16S rRNA gene sequence analysis. Since this approach provides limited information on function potential of microbial communities, analysis of whole-metagenome pyrosequencing data was used to...

  16. Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

    PubMed

    Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

    2017-09-12

    Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

  17. Potential microbial contamination during sampling of permafrost soil assessed by tracers.

    PubMed

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S

    2017-02-23

    Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

  18. Potential microbial contamination during sampling of permafrost soil assessed by tracers

    PubMed Central

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

    2017-01-01

    Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores. PMID:28230151

  19. Potential microbial contamination during sampling of permafrost soil assessed by tracers

    NASA Astrophysics Data System (ADS)

    Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders; Elberling, Bo; Jacobsen, Carsten S.

    2017-02-01

    Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.

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

    PubMed

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

    2017-01-01

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

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

    PubMed Central

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

    2017-01-01

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

  2. Cultivation and quantitative proteomic analyses of acidophilic microbial communities

    SciTech Connect

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

    2010-01-01

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

  3. An affinity-effect relationship for microbial communities in plant-soil feedback loops.

    PubMed

    Lou, Yi; Clay, Sharon A; Davis, Adam S; Dille, Anita; Felix, Joel; Ramirez, Analiza H M; Sprague, Christy L; Yannarell, Anthony C

    2014-05-01

    Feedback loops involving soil microorganisms can regulate plant populations. Here, we hypothesize that microorganisms are most likely to play a role in plant-soil feedback loops when they possess an affinity for a particular plant and the capacity to consistently affect the growth of that plant for good or ill. We characterized microbial communities using whole-community DNA fingerprinting from multiple "home-and-away" experiments involving giant ragweed (Ambrosia trifida L.) and common sunflower (Helianthus annuus L.), and we looked for affinity-effect relationships in these microbial communities. Using canonical ordination and partial least squares regression, we developed indices expressing each microorganism's affinity for ragweed or sunflower and its putative effect on plant biomass, and we used linear regression to analyze the relationship between microbial affinity and effect. Significant linear affinity-effect relationships were found in 75 % of cases. Affinity-effect relationships were stronger for ragweed than for sunflower, and ragweed affinity-effect relationships showed consistent potential for negative feedback loops. The ragweed feedback relationships indicated the potential involvement of multiple microbial taxa, resulting in strong, consistent affinity-effect relationships in spite of large-scale microbial variability between trials. In contrast, sunflower plant-soil feedback may involve just a few key players, making it more sensitive to underlying microbial variation. We propose that affinity-effect relationship can be used to determine key microbial players in plant-soil feedback against a low "signal-to-noise" background of complex microbial datasets.

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

    PubMed

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

    2014-04-01

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

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

    SciTech Connect

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

    2014-04-01

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

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

    PubMed

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

    2004-03-01

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

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

    SciTech Connect

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

    2015-12-01

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

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

    DOE PAGES

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

    2015-12-01

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

  9. Characterization and Adaptation of Anaerobic Sludge Microbial Communities Exposed to Tetrabromobisphenol A

    PubMed Central

    Lefevre, Emilie; Cooper, Ellen; Stapleton, Heather M.

    2016-01-01

    The increasing occurrence of tetrabromobisphenol A (TBBPA) in the environment is raising questions about its potential ecological and human health impacts. TBBPA is microbially transformed under anaerobic conditions to bisphenol A (BPA). However, little is known about which taxa degrade TBBPA and the adaptation of microbial communities exposed to TBBPA. The objectives of this study were to characterize the effect of TBBPA on microbial community structure during the start-up phase of a bench-scale anaerobic sludge reactor, and identify taxa that may be associated with TBBPA degradation. TBBPA degradation was monitored using LC/MS-MS, and the microbial community was characterized using Ion Torrent sequencing and qPCR. TBBPA was nearly completely transformed to BPA via reductive debromination in 55 days. Anaerobic reactor performance was not negatively affected by the presence of TBBPA and the bulk of the microbial community did not experience significant shifts. Several taxa showed a positive response to TBBPA, suggesting they may be associated with TBBPA degradation. Some of these taxa had been previously identified as dehalogenating bacteria including Dehalococcoides, Desulfovibrio, Propionibacterium, and Methylosinus species, but most had not previously been identified as having dehalogenating capacities. This study is the first to provide in-depth information on the microbial dynamics of anaerobic microbial communities exposed to TBBPA. PMID:27463972

  10. Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

    PubMed Central

    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. PMID:26509157

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

    PubMed

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

    2014-01-01

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

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

    USGS Publications Warehouse

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

    2002-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-01-01

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

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

    PubMed

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

    2002-01-17

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

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

    PubMed

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

    2009-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2011-10-01

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

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

    DTIC Science & Technology

    1992-06-01

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

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

    PubMed

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

    2013-09-01

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

  1. Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast

    PubMed Central

    Balk, Melike; Keuskamp, Joost A.; Laanbroek, Hendrikus J.

    2015-01-01

    After oxygen, sulfate is the most important oxidant for the oxidation of organic matter in mangrove forest soils. As sulfate reducers are poor competitors for common electron donors, their relative success depends mostly on the surplus of carbon that is left by aerobic organisms due to oxygen depletion. We therefore hypothesized that sulfate-cycling in mangrove soils is influenced by the size of net primary production, and hence negatively affected by mangrove degradation and exploitation, as well as by carbon-exporting waves. To test this, we compared quantitative and qualitative traits of sulfate-reducing communities in two Saudi-Arabian mangrove stands near Jeddah, where co-occurring differences in camel-grazing pressure and tidal exposure led to a markedly different stand height and hence primary production. Potential sulfate reduction rates measured in anoxic flow-through reactors in the absence and presence of additional carbon sources were significantly higher in the samples from the non-grazed site. Near the surface (0–2 cm depth), numbers of dsrB gene copies and culturable cells also tended to be higher in the non-grazed sites, while these differences were not detected in the sub-surface (4–6 cm depth). It was concluded that sulfate-reducing microbes at the surface were indeed repressed at the low-productive site as could be expected from our hypothesis. At both sites, sulfate reduction rates as well as numbers of the dsrB gene copies and viable cells increased with depth suggesting repression of sulfate reduction near the surface in both irrespective of production level. Additionally, sequence analysis of DNA bands obtained from DGGE gels based on the dsrB gene, showed a clear difference in dominance of sulfate-reducing genera belonging to the Deltaproteobacteria and the Firmicutes between sampling sites and depths. PMID:26733999

  2. Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.

    PubMed

    Amaral-Zettler, Linda A; Rocca, Jennifer D; Lamontagne, Michael G; Dennett, Mark R; Gast, Rebecca J

    2008-12-15

    Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters thatthreaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit rRNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water, and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans, and raw sewage. Correspondence analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.

  3. Changes in microbial community structure in the wake of Hurricanes Katrina and Rita

    PubMed Central

    Amaral-Zettler, Linda A.; Rocca, Jennifer D.; LaMontagne, Michael G.; Dennett, Mark R.; Gast, Rebecca J.

    2009-01-01

    Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters that threaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit ribosomal RNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans and raw sewage. Correspondence Analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as “sentinels” of water quality in the environment. PMID:19174873

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

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

    2015-07-01

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

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

    PubMed Central

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

    2015-01-01

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

  11. Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe.

    PubMed

    Cline, Lauren C; Zak, Donald R; Upchurch, Rima A; Freedman, Zachary B; Peschel, Anna R

    2017-02-01

    Foraging intensity of large herbivores may exert an indirect top-down ecological force on soil microbial communities via changes in plant litter inputs. We investigated the responses of the soil microbial community to elk (Cervus elaphus) winter range occupancy across a long-term foraging exclusion experiment in the sagebrush steppe of the North American Rocky Mountains, combining phylogenetic analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays. Winter foraging intensity was associated with reduced bacterial richness and increasingly distinct bacterial communities. Although fungal communities did not respond linearly to foraging intensity, a greater β-diversity response to winter foraging exclusion was observed. Furthermore, winter foraging exclusion increased soil cellulolytic and hemicellulolytic enzyme potential and higher foraging intensity reduced chitinolytic gene abundance. Thus, future changes in winter range occupancy may shape biogeochemical processes via shifts in microbial communities and subsequent changes to their physiological capacities to cycle soil C and N.

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

    PubMed Central

    Yrjälä, Kim; Alakukku, Laura; Palojärvi, Ansa

    2012-01-01

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

  13. The Influence of Ecological Isolation on the Structural and Functional Stability of Complex Microbial Communities

    NASA Technical Reports Server (NTRS)

    Franklin, R. B.; Garland, J. L.; Mills, A. L.

    2005-01-01

    To help understand how the behavior of microorganisms and microbial communities in insular space habitats may differ from the behavior of these groups on Earth, long-term incubations (100+ days) were conducting using wastewater bioreactors (batch fed) designed to mimic "closed" and "open" ecological systems. The issue of immigration was considered, and the goal of the research was to determine whether the stability of microbial communities in space is reduced due to their prolonged isolation. Bioreactors were established by inoculating flasks of sterile synthetic wastewater with the microbial community obtained from a local treatment facility; each day, one-third of the medium in the flask was replaced with an equal volume of sterile artificial wastewater. Flasks were divided into two treatments: "closed" and "open" to recruitment of additional microorganisms. "Closed" flasks were maintained as described above, while the medium used to feed the "open" flasks was supplemented daily with a small amount of raw sewage (which provided a continuous source of new potential community members). Significant differences in microbial community structure and function developed in the two sets of communities, and the results suggest that the open community was more stable and better able to adjust to changing environmental conditions. Each community's resistance to environmental (temperature fluctuations) and biological stresses (starvation and invasion by an opportunistic pathogen Pseudomonas aeruginosa) was monitored. Experiments were also conducted to determine whether the effect of isolation changes depending on the microbial communities' initial diversity or composition; communities with a low(er) initial diversity were less stable. Overall, the results indicate that isolation will be an important factor influencing the activity of microbial communities on board spacecraft. A possible way of mitigating these effects would be to include communities with high initial

  14. Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

    PubMed

    Wepking, Carl; Avera, Bethany; Badgley, Brian; Barrett, John E; Franklin, Josh; Knowlton, Katharine F; Ray, Partha P; Smitherman, Crystal; Strickland, Michael S

    2017-03-29

    Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function.

  15. Similar Microbial Communities Found on Two Distant Seafloor Basalts

    PubMed Central

    Singer, Esther; Chong, Lauren S.; Heidelberg, John F.; Edwards, Katrina J.

    2015-01-01

    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. PMID:26733957

  16. Similar Microbial Communities Found on Two Distant Seafloor Basalts.

    PubMed

    Singer, Esther; Chong, Lauren S; Heidelberg, John F; Edwards, Katrina J

    2015-01-01

    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.

  17. Defining the normal core microbiome of conjunctival microbial communities.

    PubMed

    Huang, Y; Yang, B; Li, W

    2016-07-01

    Bacterial ocular infections are common. Traditional culture and molecular biological methods have obvious limitations to identify the conjunctival microbiota, while metagenomic studies can avoid the defects of these methods. We used the Illumina high-throughput sequencing technology (MiSeq Illumina Sequencing Platform) to sequence the 16S rDNA V3-V4 hypervariable region of all bacteria in conjunctival swab samples. The operational taxonomic units were obtained from the sequences. The bioinformatic analyses of taxonomy, abundance and alpha diversity were performed. A total of 840 373 high-quality sequencing reads were generated from 31 conjunctival samples. The number of the species operational taxonomic units ranged from 159 to 2042, indicating high microbial diversity. The combined bacterial community was classified into 25 phyla and 526 distinct genera. At the genus level, Corynebacterium (28.22%), Pseudomonas (26.75%), Staphylococcus (5.28%), Acinetobacter (4.74%), Streptococcus (2.85%), Millisia (2.16%), Anaerococcus (1.86%), Finegoldia (1.68%), Simonsiella (1.48%) and Veillonella (1.00%) accounted for over 76% of the microbial community, possibly representing the core genera in normal conjunctival microbiota. The composition and diversity of microbiota in the normal adult human conjunctiva were characterized using high-throughput sequencing. A framework for investigating potential roles played by the diverse microbiota in disease related with the ocular surface was provided. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  18. Similar microbial communities found on two distant seafloor basalts

    NASA Astrophysics Data System (ADS)

    Singer, E.; Chong, L. S.; Heidelberg, J. F.; Edwards, K. J.

    2016-12-01

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

    NASA Technical Reports Server (NTRS)

    Stolz, J. F.

    1984-01-01

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

  20. Microbial Community Succession During Lactate Amendment of Chromium Contaminated Groundwater Reveals a Predominance of Pelosinus spp.

    SciTech Connect

    Mosher, Jennifer J; Phelps, Tommy Joe; Drake, Meghan M; Campbell, James H; Moberly, James G; Schadt, Christopher Warren; Podar, Mircea; Brown, Steven D; Hazen, Terry; Arkin, Adam; Palumbo, Anthony Vito; Faybishenko, Boris A; Elias, Dwayne A

    2012-01-01

    Microbial community structure and metabolism in contaminated ecosystems are potentially controlled not only by the different populations within the community, but a myriad of dynamic physicochemical parameters as well. The goal of the current work was to determine the impact of organic acid enrichment, in this case lactate, on the succession of the native microbial community from a contaminated groundwater aquifer. Triplicate anaerobic, continuous-flow glass reactors were inoculated with Hanford 100-H groundwater and incubated for 95 days to obtain a stable, enriched community. The microbial community experienced a shift in the population dynamics over time to eventually form a community with far less diversity than the original. The final community was dominated by Pelosinus spp. and to a lesser degree, Acetobacterium spp. with small amounts of other bacteria and archaea including methanogens. The resultant diversity was far decreased from 63 genera within 12 phyla to 11 bacterial genera (from three phyla) and 2 archaeal genera (from one phylum). Isolation efforts were successful in attaining new species of Pelosinus and known members of Methanosarcina barkerii along with several sulfate- and Fe(III)- reducing consortia members. The continuous-flow reactors allowed for testing physiochemical factors with microbial community dynamics on a smaller, replicable, scale while also facilitating the isolation of several previously uncultured community members. These lab-scale simulations will presumably allow for a deeper understanding of the community metabolism with specific carbon amendments that can inform future in situ efforts.

  1. Microbial abundance and community in subsurface flow constructed wetland microcosms: role of plant presence.

    PubMed

    Wang, Qian; Xie, Huijun; Ngo, Huu Hao; Guo, Wenshan; Zhang, Jian; Liu, Cui; Liang, Shuang; Hu, Zhen; Yang, Zhongchen; Zhao, Congcong

    2016-03-01

    In this research, the role of plants in improving microorganism growth conditions in subsurface flow constructed wetland (CW) microcosms was determined. In particular, microbial abundance and community were investigated during summer and winter in Phragmites australis-planted CW microcosms (PA) and unplanted CW microcosms (control, CT). Results revealed that the removal efficiencies of pollutants and microbial community structure varied in winter with variable microbial abundance. During summer, PA comprised more dominant phyla (e.g., Proteobacteria, Actinobacteria, and Bacteroidetes), whereas CT contained more Cyanobacteria and photosynthetic bacteria. During winter, the abundance of Proteobacteria was >40 % in PA but dramatically decreased in CT. Moreover, Cyanobacteria and photosynthetic bacterial dominance in CT decreased. In both seasons, bacteria were more abundant in root surfaces than in sand. Plant presence positively affected microbial abundance and community. The potential removal ability of CT, in which Cyanobacteria and photosynthetic bacteria were abundant during summer, was more significantly affected by temperature reduction than that of PA with plant presence.

  2. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities

    SciTech Connect

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert {Bob} L

    2014-01-01

    Contemporary microbial ecology studies usually employ one or more omics approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other meta-omic approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.

  3. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

    PubMed

    Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

    2014-06-17

    Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.

  4. Phylogenetic approaches to microbial community classification.

    PubMed

    Ning, Jie; Beiko, Robert G

    2015-10-05

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

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

    SciTech Connect

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

    2016-07-29

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

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

    PubMed

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

    2012-08-01

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

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

    PubMed Central

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

    2016-01-01

    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. Comparative analysis of microbial community between different cathode systems of microbial fuel cells for denitrification.

    PubMed

    Li, Chao; Xu, Ming; Lu, Yi; Fang, Fang; Cao, Jiashun

    2016-01-01

    Two types of cathodic biofilm in microbial fuel cells (MFC) were established for comparison on their performance and microbial communities. Complete autotrophic simultaneous nitrification and denitrification (SND) without organics addition was achieved in nitrifying-MFC (N-MFC) with a total nitrogen (TN) removal rate of 0.35 mg/(L·h), which was even higher than that in denitrifying-MFC (D-MFC) at same TN level. Integrated denaturing gradient gel electrophoresis analysis based on both 16S rRNA and nirK genes showed that Alpha-, Gammaproteobacteria were the main denitrifier communities. Some potential autotrophic denitrifying bacteria which can use electrons and reducing power from cathodes, such as Shewanella oneidensis, Shewanella loihica, Pseudomonas aeruginosa, Starkeya novella and Rhodopseudomonas palustris were identified and selectively enriched on cathode biofilms. Further, relative abundance of denitrifying bacteria characterized by nirK/16S ratios was much higher in biofilm than suspended sludge according to real-time polymerase chain reaction. The highest enrichment efficiency for denitrifiers was obtained in N-MFC cathode biofilms, which confirmed autotrophic denitrifying bacteria enrichment is the key factor for a D-MFC system.

  9. Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales.

    PubMed

    Zeglin, L H; Bottomley, P J; Jumpponen, A; Rice, C W; Arango, M; Lindsley, A; McGowan, A; Mfombep, P; Myrold, D D

    2013-10-01

    Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting "Ambient" and "Altered" (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = -0.01 and -0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 +/- 0.03 > 0.46 +/- 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (beta-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal:bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet

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

    SciTech Connect

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

    2015-12-10

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

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

    PubMed

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

    2016-01-08

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

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

    USGS Publications Warehouse

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

    2016-01-01

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

  13. Relating Anaerobic Digestion Microbial Community and Process Function

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Gaikwad, Swapnil; Shouche, Yogesh S; Gade, Wasudev N

    2016-12-01

    Sponges are primitive metazoans that are known to harbour diverse and abundant microbes. All over the world attempts are being made to exploit these microbes for their biotechnological potential to produce, bioactive compounds and antimicrobial peptides. However, the majority of the studies are focussed on the marine sponges and studies on the freshwater sponges have been neglected so far. To increase our understanding of the microbial community structure of freshwater sponges, microbiota of two fresh water sponges namely, Eunapius carteri and Corvospongilla lapidosa is explored for the first time using Next Generation Sequencing (NGS) technology. Overall the microbial composition of these sponges comprises of 14 phyla and on an average, more than 2900 OTUs were obtained from C. lapidosa while E. carteri showed 980 OTUs which is higher than OTUs obtained in the marine sponges. Thus, our study showed that, fresh water sponges also posses highly diverse microbial community than previously thought and it is distinct from the marine sponge microbiota. The present study also revealed that microbial community structure of both the sponges is significantly different from each other and their respective water samples. In the present study, we have detected many bacterial lineages belonging to Firmicutes, Actinobacteria, Proteobacteria, Planctomycetes, etc. that are known to produce compounds of biotechnological importance. Overall, this study gives insight into the microbial composition of the freshwater sponges which is highly diverse and needs to be studied further to exploit their biotechnological capabilities.

  15. Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities.

    PubMed

    Lawson, Christopher E; Strachan, Cameron R; Williams, Dominique D; Koziel, Susan; Hallam, Steven J; Budwill, Karen

    2015-11-01

    Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity.

  16. Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

    PubMed Central

    Lawson, Christopher E.; Strachan, Cameron R.; Williams, Dominique D.; Koziel, Susan; Hallam, Steven J.

    2015-01-01

    Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity. PMID:26341214

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

    Matos, Anabelle; Garland, Jay L

    2005-01-01

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

  19. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

    DOE PAGES

    Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; ...

    2015-06-28

    Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

  20. Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

    SciTech Connect

    Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; Susilawati, Endang; Jackson, Randall D.; Balser, Teresa C.; Tiedje, James M.

    2015-06-28

    Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipid analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.

  1. Periphytic photosynthetic stimulation of extracellular enzyme activity in aquatic microbial communities associated with decaying typha litter.

    PubMed

    Francoeur, Steven N; Schaecher, Mark; Neely, Robert K; Kuehn, Kevin A

    2006-11-01

    We examined the effect of light on extracellular enzyme activities of periphytic/endogenous microbial assemblages associated with decomposing litter of an emergent macrophyte Typha angustifolia within a small inland wetland in southeastern Michigan. Standing-dead Typha leaf litter was collected, placed into floating wire mesh litter baskets, and submerged in a wetland pool. Enzyme saturation assays were conducted on three occasions following litter submergence (days 9, 28, and 44) to generate saturation curves for the individual enzymes tested and to examine potential differences in enzyme saturation kinetics during microbial colonization and development. Experimental light manipulations were conducted on two occasions during microbial development (days 10 and 29). Short-term (30 min) light exposure significantly increased extracellular beta-glucosidase activity of litter-associated microbial communities. Activities of beta-xylosidase and leucine-aminopeptidase were not stimulated, and stimulation of phosphatase activity was variable. The exact mechanism for increased enzyme activity remains unknown, but it may have been increased pH arising from periphytic algal photosynthesis. These results suggest that extracellular enzyme activity in microbial communities colonizing natural organic substrata may be influenced by light/photosynthesis, as has previously been demonstrated for periphyton communities grown on artificial, inert substrata. Thus, light/photosynthetic mediated stimulation of extracellular enzyme activities may be a common occurrence in microbial communities associated with natural decaying plant litter in wetlands and might engender diurnal patterns in other microbial decay processes (e.g., production, organic matter decomposition, and mineralization).

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

    PubMed

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

    2015-05-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

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

    PubMed

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

    2002-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

    Soils provide many basic ecosystem services for our society and most of these services are carried out by the soil communities, thus influencing soils quality. Soil organic matter (SOM) can be considered as one of the most important soil quality indices for it plays a determinant role in many physical, chemical and biological processes, such as soil structure and erosion resistance, cation exchange capacity, nutrient cycling and biological activity (Andrews et al., 2004). Since a long time, exogenous organic inputs are largely used for improving agricultural soils, affecting highly soil fertility and productivity. The use of organic amendments such as crop residues influences the soil microbial populations' diversity and abundance. In the meantime, soil microbial communities play a major role in the organic matter degradation, and the effect of different microbial communities on the decomposition of crop residues is not well documented. In this context, studying the impact of crop residues on soil microbial ecology and the processes controlling the fate of plant residues in different management practices is essential for understanding the long-term environmental and agronomic effects on soil and organic matters. Our purpose in the present work was to investigate the decomposition by two contrasting microbial communities of three crop residues, and compare the effect of different residues amendments on the abundance and function of each soil microbial communities. Among the main crops which produce large amounts of residues, we focused on three different plants: wheat (Triticum aestivum L.), rape (Brassica napus) and sunflower (Helianthus annuus). The residues degradation in two soils of different management practices and the microbial activity were evaluated by: microbial abundance (microbial carbon, culturable bacteria, total DNA, qPCR), in combination with functional indicators (enzymatic assays and Biolog substrate utilization), kinetics of C and N

  6. Soil and plant effects on microbial community structure.

    PubMed

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

    2002-11-01

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

  7. Characterization and identification of microbial communities in bovine necrotic vulvovaginitis.

    PubMed

    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.

  8. Ananke: temporal clustering reveals ecological dynamics of microbial communities

    PubMed Central

    Rohwer, Robin R.; Perrie, Jonathan; McMahon, Katherine D.

    2017-01-01

    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. PMID:28966891

  9. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities.

    PubMed

    Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

    2012-05-01

    Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu(2+), was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem.

  10. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

    PubMed Central

    Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

    2012-01-01

    Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu2+, was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem. PMID:22170424

  11. Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community.

    PubMed

    Wang, Yi; Li, Chunyue; Tu, Cong; Hoyt, Greg D; DeForest, Jared L; Hu, Shuijin

    2017-12-31

    Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination.

    PubMed

    Yin, Huaqun; Niu, Jiaojiao; Ren, Youhua; Cong, Jing; Zhang, Xiaoxia; Fan, Fenliang; Xiao, Yunhua; Zhang, Xian; Deng, Jie; Xie, Ming; He, Zhili; Zhou, Jizhong; Liang, Yili; Liu, Xueduan

    2015-09-22

    Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination.

  13. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination

    PubMed Central

    Yin, Huaqun; Niu, Jiaojiao; Ren, Youhua; Cong, Jing; Zhang, Xiaoxia; Fan, Fenliang; Xiao, Yunhua; Zhang, Xian; Deng, Jie; Xie, Ming; He, Zhili; Zhou, Jizhong; Liang, Yili; Liu, Xueduan

    2015-01-01

    Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination. PMID:26391875

  14. Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry

    SciTech Connect

    Y. Wang

    2004-11-18

    ''Evaluation of Potential Impacts of Microbial Activity on Drift Chemistry'' focuses on the potential for microbial communities that could be active in repository emplacement drifts to influence the in-drift bulk chemical environment. This report feeds analyses to support the inclusion or exclusion of features, events, and processes (FEPs) in the total system performance assessment (TSPA) for the license application (LA), but this work is not expected to generate direct feeds to the TSPA-LA. The purpose was specified by, and the evaluation was performed and is documented in accordance with, ''Technical Work Plan For: Near-Field Environment and Transport In-Drift Geochemistry Analyses'' (BSC 2004 [DIRS 172402], Section 2.1). This report addresses all of the FEPs assigned by the technical work plan (TWP), including the development of exclusion arguments for FEPs that are not carried forward to the TSPA-LA. Except for an editorial correction noted in Section 6.2, there were no other deviations from the TWP. This report documents the completion of all assigned tasks, as follows (BSC 2004 DIRS 172402, Section 1.2.1): (1) Perform analyses to evaluate the potential for microbial activity in the waste emplacement drift under the constraints of anticipated physical and chemical conditions. (2) Evaluate uncertainties associated with these analyses. (3) Determine whether the potential for microbes warrants a feed to TSPA-LA to account for predicted effects on repository performance. (4) Provide information to address the ''Yucca Mountain Review Plan, Final Report'' (NUREG-1804) (NRC 2003 [DIRS 163274]) and Key Technical Issues and agreements, as appropriate. (5) Develop information for inclusion or exclusion of FEPs.

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

    PubMed

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

    2012-04-01

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

  16. Changes in microbial community during removal of BDE-153 in four types of aquatic sediments.

    PubMed

    Pan, Ying; Chen, Juan; Zhou, Haichao; Tam, Nora F Y

    2017-09-18

    Indigenous microorganisms in sediments could degrade polybrominated diphenyl ethers (PBDEs), but how the microbial communities respond to PBDEs was seldom reported. The effect of BDE-153, a common congener in aquatic environments, on the microbial communities in four types of aquatic sediments was evaluated during the 150days' incubation under an anaerobic condition. The intrinsic potential to remove BDE-153 varied significantly among four sediment types, and the removal rates of mangrove, mudflat, marine and freshwater sediments were 0.013, 0.013, 0.011, and 0.009day(-1), respectively. The observed microbial species, Simpson, Shannon, and Chao1 indices in all sediments were rather stable and were not changed significantly by BDE-153 amendment. However, BDE-153 amendment altered the microbial community compositions in three saline sediments at the end of the incubation period. Distance-based multivariate multiple regression analysis revealed that salinity, total organic carbon (TOC) and BDE-52, the major debromination product of BDE-153, were the three main factors explaining the variations in microbial community compositions in BDE-treated sediments; whereas salinity, TOC and pH were the main contributing factors in control sediments without BDE-153. The daughter congeners generated during anaerobic debromination process need more attention, especially their effect on the microbial communities in aquatic sediments. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Microbial Community in High Arsenic Shallow Groundwater Aquifers in Hetao Basin of Inner Mongolia, China

    PubMed Central

    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, SO42-, SO42-/total sulfur ratio, and Fe2+ 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. PMID:25970606

  18. Systems-based approaches to unravel multi-species microbial community functioning

    PubMed Central

    Abram, Florence

    2014-01-01

    Some of the most transformative discoveries promising to enable the resolution of this century's grand societal challenges will most likely arise from environmental science and particularly environmental microbiology and biotechnology. Understanding how microbes interact in situ, and how microbial communities respond to environmental changes remains an enormous challenge for science. Systems biology offers a powerful experimental strategy to tackle the exciting task of deciphering microbial interactions. In this framework, entire microbial communities are considered as metaorganisms and each level of biological information (DNA, RNA, proteins and metabolites) is investigated along with in situ environmental characteristics. In this way, systems biology can help unravel the interactions between the different parts of an ecosystem ultimately responsible for its emergent properties. Indeed each level of biological information provides a different level of characterisation of the microbial communities. Metagenomics, metatranscriptomics, metaproteomics, metabolomics and SIP-omics can be employed to investigate collectively microbial community structure, potential, function, activity and interactions. Omics approaches are enabled by high-throughput 21st century technologies and this review will discuss how their implementation has revolutionised our understanding of microbial communities. PMID:25750697

  19. Microbial communities on flower surfaces act as signatures of pollinator visitation

    PubMed Central

    Ushio, Masayuki; Yamasaki, Eri; Takasu, Hiroyuki; Nagano, Atsushi J.; Fujinaga, Shohei; Honjo, Mie N.; Ikemoto, Mito; Sakai, Shoko; Kudoh, Hiroshi

    2015-01-01

    Microbes are easily dispersed from one place to another, and immigrant microbes might contain information about the environments from which they came. We hypothesized that part of the microbial community on a flower's surface is transferred there from insect body surfaces and that this community can provide information to identify potential pollinator insects of that plant. We collected insect samples from the field, and found that an insect individual harbored an average of 12.2 × 105 microbial cells on its surface. A laboratory experiment showed that the microbial community composition on a flower surface changed after contact with an insect, suggesting that microbes are transferred from the insect to the flower. Comparison of the microbial fingerprint approach and direct visual observation under field condition suggested that the microbial community on a flower surface could to some extent indicate the structure of plant–pollinator interactions. In conclusion, species-specific insect microbial communities specific to insect species can be transferred from an insect body to a flower surface, and these microbes can serve as a “fingerprint” of the insect species, especially for large-bodied insects. Dispersal of microbes is a ubiquitous phenomenon that has unexpected and novel applications in many fields and disciplines. PMID:25733079

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

    PubMed

    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.

  1. Recovery of microbial communities and carbon cycling processes following drought manipulation in southern California

    NASA Astrophysics Data System (ADS)

    Allison, S. D.; Martiny, J. B. H.; Martiny, A.; Berlemont, R.; Treseder, K. K.; Goulden, M.; Brodie, E.

    2016-12-01

    Predicting the functioning of microbial communities under changing environmental conditions remains a key challenge in Earth system science. Metagenomics and other high-throughput molecular approaches can help address this challenge by revealing the functional potential of microbial communities. We coupled metagenomics with models and experimental manipulations to address microbial responses to drought in a California grassland ecosystem along with the consequences for carbon cycling. We developed an approach for extracting trait information from metagenomic data and asked: 1) What is the phylogenetic structure of drought response traits? 2) What is the relationship between these traits and those involved in carbohydrate degradation? 3) How do both classes of traits vary seasonally and with precipitation manipulation? 4) How resilient are these traits in the face of perturbation? We found that drought response traits are phylogenetically conserved at an equivalent of 5-8% ribosomal RNA gene sequence dissimilarity. Experimental drought treatment selected for the genetic potential to degrade starch, xylan, and mixed polysaccharides, suggesting a link between drought response and carbon cycling traits. In addition, microbial communities exposed to experimental drought showed a reduced potential to degrade plant biomass. Particularly among bacteria, seasonal drought had a larger impact on microbial composition, abundance, and carbohydrate-degrading genes compared to experimental drought. Bacterial communities were also more resilient to drought perturbation than fungal communities, which showed legacies of drought perturbation for up to three years. Altogether, these findings imply that microbial communities exhibit trait diversity that facilitates resilience but