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Sample records for active microbial community

  1. 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.

  2. MICROBIAL COMMUNITY STRUCTURE AND ENZYME ACTIVITIES IN SEMIARID AGRICULTURAL SOILS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effect of management on the microbial community structure and enzyme activities of three semiarid soils from Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in cotton -peanut (Arachis h...

  3. Community Analysis of Dynamic Microbial Mat Communities from Actively Erupting Seamounts (Invited)

    NASA Astrophysics Data System (ADS)

    Davis, R.; Tebo, B.; Moyer, C. L.

    2009-12-01

    The actively erupting deep-sea volcanoes NW Rota-1 and W Mata have multiple diffuse low-temperature (Tmax= 20-30 degrees) vent sites which harbor dense populations of microbial mat communities driven by chemoautotrophy. These microbial mats were often composed of white filamentous bacteria growing in close proximity to focused hydrothermal flow. Eight microbial mats were sampled from discrete hydrothermal vents on NW Rota-1 and W Mata volcanoes in 2009. The microbial mat communities were analyzed with quantitative PCR (Q-PCR) and terminal-restriction fragment length polymorphism (T-RFLP) community fingerprinting. All of the sampled microbial mats were dominated by the class Epsilonproteobacteria. The microbial mat at Iceberg Vent contained 13.5% Archaea, while all other microbial mats contained less than 1% Archaea. Bacterial community fingerprints from NW Rota-1 and W Mata formed distinct clusters that were well separated from clusters formed by hydrothermal communities from Axial and Eifuku Seamounts that were also dominated by Epsilonproteobacteria. Iceberg vent communities from NW Rota-1 have transitioned from being dominated by Caminibacter phylotypes to Sulfuimonas group phylotypes since 2004. These data suggest that microbial communities found on actively erupting volcanoes are geographically distinct and provide a natural laboratory to study microbial colonization and community succession at hydrothermal systems.

  4. Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

    NASA Astrophysics Data System (ADS)

    Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

    2002-12-01

    The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

  5. An ecosystem analysis of the activated sludge microbial community.

    PubMed

    Yiannakopoulou, Trissevyene V

    2010-01-01

    This study was undertaken (i) to investigate the interactions of the activated sludge microbial community in a chemostat with the "environment", such as the substrate composition and variations, (ii) to investigate how these interactions affect the quality of the treated effluent and (iii) to determine the limits or applicability conditions to the indicators and to the prediction potential of the treated effluent quality. This work presents (a) the experimental results obtained from a reactor fed municipal wastewater (Data Set2-DS2) concerning the reactor's operating conditions and the microbial community of the sludge (b) comparisons between DS2 and an older Data Set (DS1) obtained when the reactor was fed synthetic substrate, all other experimental conditions being identical, and (c) simulation results and sensitivity analyses of two model runs (R1 and R2, corresponding to DS1 and DS2). The first trophic level (P(1)) of the DS2 microbial community consisted of bacteria, the second trophic level (P(2)) of bacteria-eating protozoa, rotifers and nematodes and the third trophic level (P(3)) of carnivorous protozoa and arthropods. Rotifers were an important constituent of the DS2 microbial community. The DS1 and DS1 communities differed in total size, trophic level sizes and species composition. Correlations between the major microbial groups of DS2 community and either loading rates or effluent quality attributes were generally low, but the correlation of bacteria with SVI and ammonia in the effluent was better. Also, the ratio of rotifers to protozoa in P(2) was correlated to BOD in the effluent. The results of this work indicate that predictions of the treated effluent quality based only on protozoa may not be safe. Sensitivity analysis of R2 run indicate that, when variation in Y and K(d) biokinetic coefficients of the sludge are combined with fluctuations in composition and quality of municipal wastewater entering the reactor, then sufficient significant

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

    NASA Astrophysics Data System (ADS)

    Morris, Brandon E. L.

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

  7. Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

    NASA Astrophysics Data System (ADS)

    Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

    2001-12-01

    Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

  8. Measurements of microbial community activities in individual soil macroaggregates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ß-glucosidase, N-acetyl-ß-D-glucosaminidase, lipase, and leucine...

  9. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated. PMID:26787774

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biochar has been shown to increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be...

  11. 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). PMID:17082997

  12. Effects of repeated applications of chlorimuron-ethyl on the soil microbial biomass, activity and microbial community in the greenhouse.

    PubMed

    Xu, Jun; Zhang, Ying; Dong, Fengshou; Liu, Xingang; Wu, Xiaohu; Zheng, Yongquan

    2014-02-01

    The impacts of repeated chlorimuron-ethyl applications on soil microbial community structure and function were studied under greenhouse conditions. Chlorimuron-ethyl was applied to soil samples at three different doses [1-,10-,100-fold of recommended field rate (T1, T10, T100)] for 3 years. The half-lives of chlorimuron-ethyl were 37.1-54.6 days. The soil microbial biomass (microbial biomass carbon and total phospholipid fatty acid), the microbial activity (basal respiration and average well color development), the ratio of Gram-negative/Gram-positive bacteria and Shannon index were stimulated by chlorimuron-ethyl during the initial period. Except for T100, the other treatments recovered to the untreated level. The ratio of fungi/bacteria decreased during the initial period and then recovered in the end. Principal component analysis of phospholipid fatty acid showed that chlorimuron-ethyl altered the microbial community structure. Except got T100, T1 and T10 were not different from the control at the end of experiment. These results suggested a dosage effect of chlorimuron-ethyl on the living microbial biomass and the microbial community. PMID:24264144

  13. 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

  14. 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. PMID:26284035

  15. 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.

  16. 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

    2014-01-01

    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. PMID:24939130

  17. Soil Enzyme Activities, Microbial Communities and Carbon and Nitrogen Availability in Organic Agroecosystems Across an Intensively-Managed Agricultural Landscape

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Variability in the activity and composition of soil microbial communities may have important implications for the suite of microbially-derived ecosystem functions upon which agricultural systems rely, particularly organic agriculture. An on-farm approach was used to investigate microbial communitie...

  18. Arctic Gypsum Endoliths: a biogeochemical characterization of a viable and active microbial community

    NASA Astrophysics Data System (ADS)

    Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

    2013-02-01

    evidence of microbial-mineral interaction, an alternative hypothesis is that the soluble and friable nature of the gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

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

    PubMed

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

    2010-07-15

    Electrokinetic remediation has been successfully used to remove organic contaminants and heavy metals within soil. The electrokinetic process changes basic soil properties, but little is known about the impact of this remediation technology on indigenous soil microbial activities. This study reports on the effects of electrokinetic remediation on indigenous microbial activity and community within diesel contaminated soil. The main removal mechanism of diesel was electroosmosis and most of the bacteria were transported by electroosmosis. After 25 days of electrokinetic remediation (0.63 mA cm(-2)), soil pH developed from pH 3.5 near the anode to pH 10.8 near the cathode. The soil pH change by electrokinetics reduced microbial cell number and microbial diversity. Especially the number of culturable bacteria decreased significantly and only Bacillus and strains in Bacillales were found as culturable bacteria. The use of EDTA as an electrolyte seemed to have detrimental effects on the soil microbial activity, particularly in the soil near the cathode. On the other hand, the soil dehydrogenase activity was enhanced close to the anode and the analysis of microbial community structure showed the increase of several microbial populations after electrokinetics. It is thought that the main causes of changes in microbial activities were soil pH and direct electric current. The results described here suggest that the application of electrokinetics can be a promising soil remediation technology if soil parameters, electric current, and electrolyte are suitably controlled based on the understanding of interaction between electrokinetics, contaminants, and indigenous microbial community. PMID:20452646

  20. The elevational pattern of microbial community and enzyme activity along the northern slop of Changbai Mountain

    NASA Astrophysics Data System (ADS)

    Xu, Zhiwei; Yu, Guirui; Zhang, Xinyu; Ge, Jianpin; He, Nianpeng; Wang, Qiufeng; Wang, Dan

    2014-05-01

    we present a comprehensive analysis of soil microbial community structure, enzyme activities and their role in soil organic matter mineralization along six elevations representing five typical vegetation types from forest to alpine tundra in Changbai Mountain, China. The results showed that the microbial PLFAs presented hump-shaped patterns along the elevation with the total microbial PLFAs highest in Ermans birch forest soil. The fungi to bacteria and gram positive to negative bacteria ratios increased along the elevation with the lowest values in Broad leaved forest and Dark-coniferous spruce-fir forest soil, respectively. The soil microbial community structures showed a biogeography distribution pattern in vertical direction with microbial community structures in Broad leaved forest and Mixed coniferous broad leaved forest different from other four sites. The soil enzyme activities in Broad leaved forest and Mixed coniferous broad leaved forest were significantly higher than in other four elevations. Principal component analysis (PCA) revealed substantial differences in soil microbial community composition among study sites, appeared to be driven primarily by MAT, MAP, soil temperature and content of silt & clay on the first principal component (PC1) which accounted for 87.1 % of the total sample variance. However, soil nutrients mainly responsible for the variation of soil enzyme activities. The soil organic matter mineralization rates tended to be highest in Ermans birch forest site and lowest in Dark-coniferous spruce-fir forest site and showed positive relationship with total microbial, bacterial and actinomycetes PLFAs. These findings could be used to facilitate interpretation of soil microbial community and ecological function in latitude forests ecosystem especially in volcanic forest ecosystem.

  1. Effects of Alkaline Phosphatase Activity on Nucleotide Measurements in Aquatic Microbial Communities

    PubMed Central

    Karl, D. M.; Craven, D. B.

    1980-01-01

    Alkaline phosphatase (APase) activity was detected in aquatic microbial assemblages from the subtropics to Antarctica. The occurrence of APase in environmental nucleotide extracts was shown to significantly affect the measured concentrations of cellular nucleotides (adenosine triphosphate, adenosine diphosphate, adenosine monophosphate, guanosine triphosphate, uridine triphosphate, and cytidine triphosphate), adenylate energy charge, and guanosine triphosphate/adenosine triphosphate ratios, when conventional methods of nucleotide extraction were employed. Under the reaction conditions specified in this report, the initial rate of hydrolysis of adenosine triphosphate was directly proportional to the activity of APase in the sample extracts and consequently can be used as a sensitive measure of APase activity. A method was devised for obtaining reliable nucleotide measurements in naturally occurring microbial populations containing elevated levels of APase activity. The metabolic significance of APase activity in microbial cells is discussed, and it is concluded that the occurrence and regulation of APase in nature is dependent upon microscale inorganic phosphate limitation of the autochthonous microbial communities. PMID:16345634

  2. Arctic gypsum endoliths: a biogeochemical characterization of a viable and active microbial community

    NASA Astrophysics Data System (ADS)

    Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

    2013-11-01

    , which contrasts with other endolithic habitats. While it is possible that these communities turn over carbon quickly and leave little evidence of microbe-mineral interaction, an alternative hypothesis is that the soluble and friable nature of gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

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

    PubMed

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

    2016-01-01

    Biochar can increase microbial activity, alter microbial community structure, and increase soil fertility in arid and semi-arid soils, but at relatively high rates that may be impractical for large-scale field studies. This contrasts with organic amendments such as manure, which can be abundant and inexpensive if locally available, and thus can be applied to fields at greater rates than biochar. In a field study comparing biochar and manure, a fast pyrolysis hardwood biochar (22.4 Mg ha(-1)), dairy manure (42 Mg ha(-1) dry wt), a combination of biochar and manure at the aforementioned rates, or no amendment (control) was applied to an Aridisol (n=3) in fall 2008. Plots were annually cropped to corn (Zea maize L.). Surface soils (0-30 cm) were sampled directly under corn plants in late June 2009 and early August 2012, and assayed for microbial community fatty acid methyl ester (FAME) profiles and six extracellular enzyme activities involved in soil C, N, and P cycling. Arbuscular mycorrhizal (AM) fungal colonization was assayed in corn roots in 2012. Biochar had no effect on microbial biomass, community structure, extracellular enzyme activities, or AM fungi root colonization of corn. In the short-term, manure amendment increased microbial biomass, altered microbial community structure, and significantly reduced the relative concentration of the AM fungal biomass in soil. Manure also reduced the percent root colonization of corn by AM fungi in the longer-term. Thus, biochar and manure had contrasting short-term effects on soil microbial communities, perhaps because of the relatively low application rate of biochar. PMID:26138708

  4. Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.

    PubMed

    Thureborn, Petter; Franzetti, Andrea; Lundin, Daniel; Sjöling, Sara

    2016-01-01

    Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning. PMID:26823996

  5. Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments

    PubMed Central

    Franzetti, Andrea; Lundin, Daniel; Sjöling, Sara

    2016-01-01

    Baltic Sea deep water and sediments hold one of the largest anthropogenically induced hypoxic areas in the world. High nutrient input and low water exchange result in eutrophication and oxygen depletion below the halocline. As a consequence at Landsort Deep, the deepest point of the Baltic Sea, anoxia in the sediments has been a persistent condition over the past decades. Given that microbial communities are drivers of essential ecosystem functions we investigated the microbial community metabolisms and functions of oxygen depleted Landsort Deep sediments by metatranscriptomics. Results show substantial expression of genes involved in protein metabolism demonstrating that the Landsort Deep sediment microbial community is active. Identified expressed gene suites of metabolic pathways with importance for carbon transformation including fermentation, dissimilatory sulphate reduction and methanogenesis were identified. The presence of transcripts for these metabolic processes suggests a potential for heterotrophic-autotrophic community synergism and indicates active mineralisation of the organic matter deposited at the sediment as a consequence of the eutrophication process. Furthermore, cyanobacteria, probably deposited from the water column, are transcriptionally active in the anoxic sediment at this depth. Results also reveal high abundance of transcripts encoding integron integrases. These results provide insight into the activity of the microbial community of the anoxic sediment at the deepest point of the Baltic Sea and its possible role in ecosystem functioning. PMID:26823996

  6. Why Microbial Communities?

    ScienceCinema

    Fredrickson, Jim (PNNL)

    2012-02-29

    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.

  7. Soil microbial communities and activities under different orchard floor management systems in Oregan Sweet Cherry Orchards

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the importance of microorganisms in nutrient cycling and productivity is well recognized in annual cropping systems, specific information regarding the size, composition and activity of soil microbes in orchard systems is lacking. This study assessed the soil microbial community structure (...

  8. Soil Microbial Communities and Activities Under Different Orchard Floor Management Systems in Oregon Sweet Cherry Orchards

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although the importance of microorganisms in nutrient cycling and productivity is well recognized in annual cropping systems, specific information regarding the size, composition and activity of soil microbes in orchard systems is lacking. This study assessed the soil microbial community structure (...

  9. 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. PMID:25912922

  10. Metaproteogenomics reveals the soil microbial communities active in nutrient cycling processes under different tree species

    NASA Astrophysics Data System (ADS)

    Keiblinger, Katharina Maria; Masse, Jacynthe; Zühlke, Daniela; Riedel, Katharina; Zechmeister-Boltenstern, Sophie; Prescott, Cindy E.; Grayston, Sue

    2016-04-01

    Tree species exert strong effects on microbial communities in litter and soil and may alter rates of soil processes fundamental to nutrient cycling and carbon fluxes (Prescott and Grayston 2013). However, the influence of tree species on decomposition processes are still contradictory and poorly understood. An understanding of the mechanisms underlying plant influences on soil processes is important for our ability to predict ecosystem response to altered global/environmental conditions. In order to link microbial community structure and function to forest-floor nutrient cycling processes, we sampled forest floors under western redcedar (Thuja plicata), Douglas-fir (Pseudotsuga menziesii) and Sitka spruce (Picea sitchensis) grown in nutrient-poor sites in common garden experiments on Vancouver island (Canada). We measured forest-floor total N, total C, initial NH4+ and NO3‑ concentrations, DOC, Cmic and Nmic. Gross rates of ammonification and NH4+ consumption were measured using the 15N pool-dilution method. Organic carbon quality was assessed through FTIR analyses. Microbial community structure was analysed by a metaproteogenomic approach using 16S and ITS amplification and sequencing with MiSeq platform. Proteins were extracted and peptides characterized via LC-MS/MS on a Velos Orbitrap to assess the active microbial community. Different microbial communities were active under the three tree species and variation in process rates were observed and will be discussed. This research provides new insights on microbial processes during organic matter decomposition. The metaproteogenomic approach enables us to investigate these changes with respect to possible effects on soil C-storage at even finer taxonomic resolution.

  11. Sediment Enzyme Activities and Microbial Community Diversity in an Oligotrophic Drinking Water Reservoir, Eastern China

    PubMed Central

    Zhang, Haihan; Huang, Tinglin; Liu, Tingting

    2013-01-01

    Drinking water reservoir plays a vital role in the security of urban water supply, yet little is known about microbial community diversity harbored in the sediment of this oligotrophic freshwater environmental ecosystem. In the present study, integrating community level physiological profiles (CLPPs), nested polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and clone sequence technologies, we examined the sediment urease and protease activities, bacterial community functional diversity, genetic diversity of bacterial and fungal communities in sediments from six sampling sites of Zhou cun drinking water reservoir, eastern China. The results showed that sediment urease activity was markedly distinct along the sites, ranged from 2.48 to 11.81 mg NH3-N/(g·24h). The highest average well color development (AWCD) was found in site C, indicating the highest metabolic activity of heterotrophic bacterial community. Principal component analysis (PCA) revealed tremendous differences in the functional (metabolic) diversity patterns of the sediment bacterial communities from different sites. Meanwhile, DGGE fingerprints also indicated spatial changes of genetic diversity of sediment bacterial and fungal communities. The sequence BLAST analysis of all the sediment samples found that Comamonas sp. was the dominant bacterial species harbored in site A. Alternaria alternate, Allomyces macrogynus and Rhizophydium sp. were most commonly detected fungal species in sediments of the Zhou cun drinking water reservoir. The results from this work provide new insights about the heterogeneity of sediment microbial community metabolic activity and genetic diversity in the oligotrophic drinking water reservoir. PMID:24205265

  12. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

    PubMed Central

    Deng, Jie; Deng, Ye; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Qin, Yujia; Zhou, Jiti; Zhou, Jizhong

    2015-01-01

    Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. coli nagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities

  13. Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors.

    PubMed

    Jo, Sung Jun; Kwon, Hyeokpil; Jeong, So-Yeon; Lee, Chung-Hak; Kim, Tae Gwan

    2016-09-15

    Operation of membrane bioreactors (MBRs) for wastewater treatment is hampered by the membrane biofouling resulting from microbial activities. However, the knowledge of the microbial ecology of both biofilm and activated sludge in MBRs has not been sufficient. In this study, we scrutinized microbial communities of biofilm and activated sludge from 10 full-scale MBR plants. Overall, Flavobacterium, Dechloromonas and Nitrospira were abundant in order of abundance in biofilm, whereas Dechloromonas, Flavobacterium and Haliscomenobacter in activated sludge. Community structure was analyzed in either biofilm or activated sludge. Among MBRs, as expected, not only diversity of microbial community but also its composition was different from one another (p < 0.05). Between the biofilm and activated sludge, community composition made significant difference, but its diversity measures (i.e., alpha diversity, e.g., richness, diversity and evenness) did not (p > 0.05). Effects of ten environmental factors on community change were investigated using Spearman correlation. MLSS, HRT, F/M ratio and SADm explained the variation of microbial composition in the biofilm, whereas only MLSS did in the activated sludge. Microbial networks were constructed with the 10 environmental factors. The network results revealed that there were different topological characteristics between the biofilm and activated sludge networks, in which each of the 4 factors had different associations with microbial nodes. These results indicated that the different microbial associations were responsible for the variation of community composition between the biofilm and activated sludge. PMID:27262549

  14. Active Microbial Communities Inhabit Sulphate-Methane Interphase in Deep Bedrock Fracture Fluids in Olkiluoto, Finland

    PubMed Central

    Bomberg, Malin; Nyyssönen, Mari; Pitkänen, Petteri; Lehtinen, Anne; Itävaara, Merja

    2015-01-01

    Active microbial communities of deep crystalline bedrock fracture water were investigated from seven different boreholes in Olkiluoto (Western Finland) using bacterial and archaeal 16S rRNA, dsrB, and mcrA gene transcript targeted 454 pyrosequencing. Over a depth range of 296–798 m below ground surface the microbial communities changed according to depth, salinity gradient, and sulphate and methane concentrations. The highest bacterial diversity was observed in the sulphate-methane mixing zone (SMMZ) at 250–350 m depth, whereas archaeal diversity was highest in the lowest boundaries of the SMMZ. Sulphide-oxidizing ε-proteobacteria (Sulfurimonas sp.) dominated in the SMMZ and γ-proteobacteria (Pseudomonas spp.) below the SMMZ. The active archaeal communities consisted mostly of ANME-2D and Thermoplasmatales groups, although Methermicoccaceae, Methanobacteriaceae, and Thermoplasmatales (SAGMEG, TMG) were more common at 415–559 m depth. Typical indicator microorganisms for sulphate-methane transition zones in marine sediments, such as ANME-1 archaea, α-, β- and δ-proteobacteria, JS1, Actinomycetes, Planctomycetes, Chloroflexi, and MBGB Crenarchaeota were detected at specific depths. DsrB genes were most numerous and most actively transcribed in the SMMZ while the mcrA gene concentration was highest in the deep methane rich groundwater. Our results demonstrate that active and highly diverse but sparse and stratified microbial communities inhabit the Fennoscandian deep bedrock ecosystems. PMID:26425566

  15. Effects of Soil Organic Matter Properties and Microbial Community Composition on Enzyme Activities in Cryoturbated Arctic Soils

    PubMed Central

    Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Hofer, Angelika; Kienzl, Sandra; Knoltsch, Anna; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Takriti, Mounir; Urich, Tim; Weltin, Georg; Richter, Andreas

    2014-01-01

    Enzyme-mediated decomposition of soil organic matter (SOM) is controlled, amongst other factors, by organic matter properties and by the microbial decomposer community present. Since microbial community composition and SOM properties are often interrelated and both change with soil depth, the drivers of enzymatic decomposition are hard to dissect. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this subduction to test if SOM properties shape microbial community composition, and to identify controls of both on enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acid analysis), was similar in cryoturbated material and in surrounding subsoil, although carbon and nitrogen contents were similar in cryoturbated material and topsoils. This suggests that the microbial community in cryoturbated material was not well adapted to SOM properties. We also measured three potential enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) and used structural equation models (SEMs) to identify direct and indirect drivers of the three enzyme activities. The models included microbial community composition, carbon and nitrogen contents, clay content, water content, and pH. Models for regular horizons, excluding cryoturbated material, showed that all enzyme activities were mainly controlled by carbon or nitrogen. Microbial community composition had no effect. In contrast, models for cryoturbated material showed that enzyme activities were also related to microbial community composition. The additional control of microbial community composition could have restrained enzyme activities and furthermore decomposition in general. The functional decoupling of SOM properties and microbial community composition might thus be one of the reasons for low decomposition rates and the persistence of 400 Gt

  16. Using dispersants after oil spills: impacts on the composition and activity of microbial communities.

    PubMed

    Kleindienst, Sara; Paul, John H; Joye, Samantha B

    2015-06-01

    Dispersants are globally and routinely applied as an emergency response to oil spills in marine ecosystems with the goal of chemically enhancing the dissolution of oil into water, which is assumed to stimulate microbially mediated oil biodegradation. However, little is known about how dispersants affect the composition of microbial communities or their biodegradation activities. The published findings are controversial, probably owing to variations in laboratory methods, the selected model organisms and the chemistry of different dispersant-oil mixtures. Here, we argue that an in-depth assessment of the impacts of dispersants on microorganisms is needed to evaluate the planning and use of dispersants during future responses to oil spills. PMID:25944491

  17. Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

    PubMed Central

    2012-01-01

    Background Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. Results In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. Conclusion The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels. PMID:22490508

  18. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales

    PubMed Central

    Maurice, Corinne Ferrier; Turnbaugh, Peter James

    2013-01-01

    Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small to moderately sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities. PMID:23550823

  19. Tracking Dynamics of Plant Biomass Composting by Changes in Substrate Structure, Microbial Community, and Enzyme Activity

    SciTech Connect

    Wei, H.; Tucker, M. P.; Baker, J. O.; Harris, M.; Luo, Y. H.; Xu, Q.; Himmel, M. E.; Ding, S. Y.

    2012-04-01

    Understanding the dynamics of the microbial communities that, along with their secreted enzymes, are involved in the natural process of biomass composting may hold the key to breaking the major bottleneck in biomass-to-biofuels conversion technology, which is the still-costly deconstruction of polymeric biomass carbohydrates to fermentable sugars. However, the complexity of both the structure of plant biomass and its counterpart microbial degradation communities makes it difficult to investigate the composting process. In this study, a composter was set up with a mix of yellow poplar (Liriodendron tulipifera) wood-chips and mown lawn grass clippings (85:15 in dry-weight) and used as a model system. The microbial rDNA abundance data obtained from analyzing weekly-withdrawn composted samples suggested population-shifts from bacteria-dominated to fungus-dominated communities. Further analyses by an array of optical microscopic, transcriptional and enzyme-activity techniques yielded correlated results, suggesting that such population shifts occurred along with early removal of hemicellulose followed by attack on the consequently uncovered cellulose as the composting progressed. The observed shifts in dominance by representative microbial groups, along with the observed different patterns in the gene expression and enzymatic activities between cellulases, hemicellulases, and ligninases during the composting process, provide new perspectives for biomass-derived biotechnology such as consolidated bioprocessing (CBP) and solid-state fermentation for the production of cellulolytic enzymes and biofuels.

  20. Earthworms facilitate the stabilization of pelletized dewatered sludge through shaping microbial biomass and activity and community.

    PubMed

    Fu, Xiaoyong; Cui, Guangyu; Huang, Kui; Chen, Xuemin; Li, Fusheng; Zhang, Xiaoyu; Li, Fei

    2016-03-01

    In this study, the effect of earthworms on microbial features during vermicomposting of pelletized dewatered sludge (PDS) was investigated through comparing two degradation systems with and without earthworm E isenia fetida involvement. After 60 days of experimentation, a relatively stable product with low organic matter and high nitrate and phosphorous was harvested when the earthworms were involved. During the process, earthworms could enhance microbial activity and biomass at the initial stage and thus accelerating the rapid decomposition of PDS. The end products of vermicomposting allowed the lower values of bacterial and eukaryotic densities comparison with those of no earthworm addition. In addition, the presence of earthworms modified the bacterial and fungal diversity, making the disappearances of some pathogens and specific decomposing bacteria of recalcitrant substrates in the vermicomposting process. This study evidences that earthworms can facilitate the stabilization of PDS through modifying microbial activity and number and community during vermicomposting. PMID:26514568

  1. No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

    PubMed

    Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

    2016-04-01

    Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable. PMID:26631020

  2. Effects of Environmental Toxicants on Metabolic Activity of Natural Microbial Communities

    PubMed Central

    Barnhart, Carole L. H.; Vestal, J. Robie

    1983-01-01

    Two methods of measuring microbial activity were used to study the effects of toxicants on natural microbial communities. The methods were compared for suitability for toxicity testing, sensitivity, and adaptability to field applications. This study included measurements of the incorporation of 14C-labeled acetate into microbial lipids and microbial glucosidase activity. Activities were measured per unit biomass, determined as lipid phosphate. The effects of various organic and inorganic toxicants on various natural microbial communities were studied. Both methods were useful in detecting toxicity, and their comparative sensitivities varied with the system studied. In one system, the methods showed approximately the same sensitivities in testing the effects of metals, but the acetate incorporation method was more sensitive in detecting the toxicity of organic compounds. The incorporation method was used to study the effects of a point source of pollution on the microbiota of a receiving stream. Toxic doses were found to be two orders of magnitude higher in sediments than in water taken from the same site, indicating chelation or adsorption of the toxicant by the sediment. The microbiota taken from below a point source outfall was 2 to 100 times more resistant to the toxicants tested than was that taken from above the outfall. Downstream filtrates in most cases had an inhibitory effect on the natural microbiota taken from above the pollution source. The microbial methods were compared with commonly used bioassay methods, using higher organisms, and were found to be similar in ability to detect comparative toxicities of compounds, but were less sensitive than methods which use standard media because of the influences of environmental factors. PMID:16346432

  3. Soil Rhizosphere Microbial Communities and Enzyme Activities under Organic Farming

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study investigated the activities of ß-glucosidase (C cycling, ß-glucosaminidase (C and N cycling), acid phosphatase (P cycling) and arylsulfatase (S cycling) under lettuce (Lactuca sativa), potato (Solanum Tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall f...

  4. Microbial Community Composition and Denitrifying Enzyme Activities in Salt Marsh Sediments▿

    PubMed Central

    Cao, Yiping; Green, Peter G.; Holden, Patricia A.

    2008-01-01

    Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh. PMID:18978080

  5. Active microbial community structure of deep subsurface sediments within Baltic Sea Basin

    NASA Astrophysics Data System (ADS)

    Reese, B. K.; Zinke, L.; Carvalho, G.; Lloyd, K. G.; Marshall, I.; Shumaker, A.; Amend, J.

    2014-12-01

    The Baltic Sea Basin (BSB) is a unique depositional setting that has experienced periods of glaciation and deglaciation as a result of climatic fluctuations over past tens of thousands of years. This has resulted in laminated sediments formed during periods with strong permanent salinity stratification. The high sedimentation rates make this an ideal setting to understand the microbial structure of a deep biosphere community in a relatively high carbon, and thus high-energy environment, compared to other deep subsurface sites. Samples were collected through scientific drilling during the International Ocean Discovery Program (IODP) Expedition 347 on board the Greatship Manisha, September-November 2013. We examined the active microbial community structure using the 16S rRNA gene transcript and active functional genes through metatranscriptome sequencing. Major biogeochemical shifts have been observed in response to the depositional history between the limnic, brackish, and marine phases. The active microbial community structure in the BSB is diverse and reflective of the unique changes in the geochemical profile. These data further refine our understanding of the existence life in the deep subsurface and the survival mechanisms required for this extreme environment.

  6. Dynamics of the diversity and structure of the overall and nitrifying microbial community in activated sludge along gradient copper exposures.

    PubMed

    Ouyang, Fan; Ji, Min; Zhai, Hongyan; Dong, Zhao; Ye, Lin

    2016-08-01

    Diversity and composition of the microbial community, especially the nitrifiers, are essential to the treatment efficiency of wastewater in activated sludge systems. Heavy metals commonly present in the wastewater influent such as Cu can alter the community structure of nitrifiers and lower their activity. However, the dynamics of microbial community along a gradient of metal exposure have largely been unexplored, partially due to the limitations in traditional molecular methods. This study explored the dynamics regarding the diversity and community structures of overall and nitrifying microbial communities in activated sludge under intermittent Cu gradient loadings using Illumina sequencing. We created a new local nitrifying bacterial database for sequence BLAST searches. High Cu loadings (>10.9 mg/L) impoverished microbial diversity and altered the microbial community. Overall, Proteobacteria was the predominant phylum in the activated sludge system, in which Zoogloea, Thauera, and Dechloromonas (genera within the Rhodocyclaceae family of the Beta-proteobacteria class) were the dominant genera in the presence of Cu. The abundance of unclassified bacteria at the phylum level increased substantially with increasing Cu loadings. Nitrosomonas and Nitrospira were the predominant nitrifiers. The nitrifying bacterial community changed through increasing abundance and shifting to Cu-tolerant species to reduce the toxic effects of Cu. Our local nitrifying bacterial database helped to improve the resolution of bacterial identification. Our results provide insights into the dynamics of microbial community in response to various metal concentrations in activated sludge systems and improve our understanding regarding the effect of metals on wastewater treatment efficiency. PMID:27098258

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  8. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

    PubMed Central

    Baldrian, Petr; Kolařík, Miroslav; Štursová, Martina; Kopecký, Jan; Valášková, Vendula; Větrovský, Tomáš; Žifčáková, Lucia; Šnajdr, Jaroslav; Rídl, Jakub; Vlček, Čestmír; Voříšková, Jana

    2012-01-01

    Soils of coniferous forest ecosystems are important for the global carbon cycle, and the identification of active microbial decomposers is essential for understanding organic matter transformation in these ecosystems. By the independent analysis of DNA and RNA, whole communities of bacteria and fungi and its active members were compared in topsoil of a Picea abies forest during a period of organic matter decomposition. Fungi quantitatively dominate the microbial community in the litter horizon, while the organic horizon shows comparable amount of fungal and bacterial biomasses. Active microbial populations obtained by RNA analysis exhibit similar diversity as DNA-derived populations, but significantly differ in the composition of microbial taxa. Several highly active taxa, especially fungal ones, show low abundance or even absence in the DNA pool. Bacteria and especially fungi are often distinctly associated with a particular soil horizon. Fungal communities are less even than bacterial ones and show higher relative abundances of dominant species. While dominant bacterial species are distributed across the studied ecosystem, distribution of dominant fungi is often spatially restricted as they are only recovered at some locations. The sequences of cbhI gene encoding for cellobiohydrolase (exocellulase), an essential enzyme for cellulose decomposition, were compared in soil metagenome and metatranscriptome and assigned to their producers. Litter horizon exhibits higher diversity and higher proportion of expressed sequences than organic horizon. Cellulose decomposition is mediated by highly diverse fungal populations largely distinct between soil horizons. The results indicate that low-abundance species make an important contribution to decomposition processes in soils. PMID:21776033

  9. Metabolic activity and genetic diversity of microbial communities inhabiting the rhizosphere of halophyton plants.

    PubMed

    Bárány, Agnes; Szili-Kovács, Tibor; Krett, Gergely; Füzy, Anna; Márialigeti, Károly; Borsodi, Andrea K

    2014-09-01

    A preliminary study was conducted to compare the community level physiological profile (CLPP) and genetic diversity of rhizosphere microbial communities of four plant species growing nearby Kiskunság soda ponds, namely Böddi-szék, Kelemen-szék and Zab-szék. CLPP was assessed by MicroResp method using 15 different substrates while Denaturing Gradient Gel Electrophoresis (DGGE) was used to analyse genetic diversity of bacterial communities. The soil physical and chemical properties were quite different at the three sampling sites. Multivariate statistics (PCA and UPGMA) revealed that Zab-szék samples could be separated according to their genetic profile from the two others which might be attributed to the geographical location and perhaps the differences in soil physical properties. Böddi-szék samples could be separated from the two others considering the metabolic activity which could be explained by their high salt and low humus contents. The number of bands in DGGE gels was related to the metabolic activity, and positively correlated with soil humus content, but negatively with soil salt content. The main finding was that geographical location, soil physical and chemical properties and the type of vegetation were all important factors influencing the metabolic activity and genetic diversity of rhizosphere microbial communities. PMID:25261946

  10. Effects of harvester ant (Messor spp.) activity on soil properties and microbial communities in a Negev Desert ecosystem

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Harvester ants (Messor spp.) function as an essential link between aboveground resources and belowground biota such as the microbial community. We examined changes in soil microbial biomass and functional diversity resulting from harvester ant (Messor spp.) activity in the Negev Desert, Israel. Abi...

  11. Primary succession of soil enzyme activity and heterotrophic microbial communities along the chronosequence of Tianshan Mountains No. 1 Glacier, China.

    PubMed

    Zeng, Jun; Wang, Xiao-Xia; Lou, Kai; Eusufzai, Moniruzzaman Khan; Zhang, Tao; Lin, Qing; Shi, Ying-Wu; Yang, Hong-Mei; Li, Zhong-Qing

    2015-02-01

    We investigated the primary successions of soil enzyme activity and heterotrophic microbial communities at the forefields of the Tianshan Mountains No. 1 Glacier by investigating soil microbial processes (microbial biomass and nitrogen mineralization), enzyme activity and community-level physiological profiling. Soils deglaciated between 1959 and 2008 (0, 5, 17, 31 and 44 years) were collected. Soils >1,500 years in age were used as a reference (alpine meadow soils). Soil enzyme activity and carbon-source utilization ability significantly increased with successional time. Amino-acid utilization rates were relatively higher in early, unvegetated soils (0 and 5 years), but carbohydrate utilization was higher in later stages (from 31 years to the reference soil). Discriminant analysis, including data on microbial processes and soil enzyme activities, revealed that newly exposed soils (0-5 years) and older soils (17-44 years) were well-separated from each other and obviously different from the reference soil. Correlation analysis revealed that soil organic carbon, was the primary factor influencing soil enzyme activity and heterotrophic microbial community succession. Redundancy analysis suggested that soil pH and available P were also affect microbial activity to a considerable degree. Our results indicated that glacier foreland soils have continued to develop over 44 years and soils were significantly affected by the geographic location of the glacier and the local topography. Soil enzyme activities and heterotrophic microbial communities were also significantly influenced by these variables. PMID:25472706

  12. Combined effects of cadmium and butachlor on soil enzyme activities and microbial community structure

    NASA Astrophysics Data System (ADS)

    Wang, Jinhua; Lu, Yitong; Shen, Guoqing

    2007-02-01

    The combined effects of cadmium (Cd, 10 mg/kg of soil) and butachlor (5, 10 and 50 mg/kg of soil) on enzyme activities and microbial community structure were assessed in phaeozem soil. The result showed that phosphatase activities were decreased in soils with Cd (10 mg/kg of soil) alone whereas urease acitivities were unaffected by Cd. Urease and phosphatase activities were significantly reduced by high butachlor concentration (50 mg/kg of soil). When Cd and butachlor concentrations in soils were added at milligram ratio of 2:1 or 1:2, urease and phosphatase activities were decreased, while enzyme activities were greatly improved at the ratio of 1:5. This study indicates that the combined effects of Cd and butachlor on soil urease and phosphatase activities depend largely on the addition concentration ratios to soils. The random amplified polymorphic DNA (RAPD) analysis showed that the changes occurring in RAPD profiles of different treated samples included variation in loss of normal bands and appearance of new bands compared with the control soil. The RAPD fingerprints showed substantial differences between the control and treated soil samples, with apparent changes in the number and size of amplified DNA fragments. The results showed that the addition of high concentration butachlor and the combined applied Cd and butachlor significantly affected the diversity of microbial community. The present results suggest that RAPD analysis in conjunction with other biomarkers such as soil enzyme parameter etc. would prove a powerful ecotoxicological tool.

  13. Microbial community characterization, activity analysis and purifying efficiency in a biofilter process.

    PubMed

    Xiang, Hong; Lu, Xiwu; Yin, Lihong; Yang, Fei; Zhu, Guangcan; Liu, Wuping

    2013-04-01

    The growth and metabolism of microbial communities on biologically activated carbon (BAC) play a crucial role in the purification of drinking water. To gain insight into the growth and metabolic characteristics of microbial communities and the efficiency of drinking water treatment in a BAC filter, we analyzed the heterotrophic plate count (HPC), phospholipid, dehydrogenase, metabolic function and water quality parameters during start-up and steady-state periods. In the start-up process of the filter with natural biofilm colonization, the variation in heterotrophic plate count levels was S-curved. The total phospholipid level was very low during the first 5 days and reached a maximum value after 40 days in the filter. The activity of dehydrogenase gradually increased during the first 30 days and then reached a plateau. The functional diversity of the microbial community in the filter increased, and then reached a relatively stable level by day 40. After an initial decrease, which was followed by an increase, the removal rate of NH4(+)-N and COD(Mn) became stable and was 80% and 28%, respectively, by day 40. The consumption rate of dissolved oxygen reached a steady level after 29 days, and remained at 18%. At the steady operation state, the levels of HPC, phospholipid, dehydrogenase activity and carbon source utilization had no significant differences after 6 months compared to levels measured on day 40. The filter was shown to be effective in removing NH4(+)-N, NO2(-)-N, COD(Mn), UV254, biodegradable dissolved organic carbon and trace organic pollutants from the influent. Our results suggest that understanding changes in the growth and metabolism of microorganisms in BAC filter could help to improve the efficiency of biological treatment of drinking water. PMID:23923776

  14. Extracellular polymeric substances, microbial activity and microbial community of biofilm and suspended sludge at different divalent cadmium concentrations.

    PubMed

    Wang, Zichao; Gao, Mengchun; Wei, Junfeng; Ma, Kedong; Zhang, Jing; Yang, Yusuo; Yu, Shuping

    2016-04-01

    The differences between biofilm and suspended sludge (S-sludge) in extracellular polymeric substances (EPS), microbial activity, and microbial community in an anoxic-aerobic sequencing batch biofilm reactor (SBBR) at different concentrations of divalent cadmium (Cd(II)) were investigated. As the increase of Cd(II) concentration from 0 to 50mgL(-1), the specific ammonium oxidation rate (SAOR), specific nitrite oxidation rate (SNOR), and specific nitrate reduction rate (SNRR) of biofilm decreased from 4.85, 5.22 and 45mgNg(-1) VSSh(-1) to 1.54, 2.38 and 26mgNg(-1)VSSh(-1), respectively, and the SAOR, SNOR and SNRR of S-sludge decreased from 4.80, 5.02 and 34mgNg(-1)VSSh(-1) to 1.46, 2.20 and 17mgNg(-1)VSSh(-1), respectively. Biofilm had higher protein (PN) content in EPS than S-sludge. Contrast to S-sludge, biofilm could provide Nitrobacter vulgaris, beta proteobacterium INBAF015, and Pseudoxanthomonas mexicana with the favorable conditions of growth and reproduction. PMID:26829529

  15. Comparative resistance and resilience of soil microbial communities and enzyme activities in adjacent native forest and agricultural soils.

    PubMed

    Chaer, Guilherme; Fernandes, Marcelo; Myrold, David; Bottomley, Peter

    2009-08-01

    Degradation of soil properties following deforestation and long-term soil cultivation may lead to decreases in soil microbial diversity and functional stability. In this study, we investigated the differences in the stability (resistance and resilience) of microbial community composition and enzyme activities in adjacent soils under either native tropical forest (FST) or in agricultural cropping use for 14 years (AGR). Mineral soil samples (0 to 5 cm) from both areas were incubated at 40 degrees C, 50 degrees C, 60 degrees C, or 70 degrees C for 15 min in order to successively reduce the microbial biomass. Three and 30 days after the heat shocks, fluorescein diacetate (FDA) hydrolysis, cellulase and laccase activities, and phospholipid-derived fatty acids-based microbial community composition were measured. Microbial biomass was reduced up to 25% in both soils 3 days after the heat shocks. The higher initial values of microbial biomass, enzyme activity, total and particulate soil organic carbon, and aggregate stability in the FST soil coincided with higher enzymatic stability after heat shocks. FDA hydrolysis activity was less affected (more resistance) and cellulase and laccase activities recovered more rapidly (more resilience) in the FST soil relative to the AGR counterpart. In the AGR soil, laccase activity did not show resilience to any heat shock level up to 30 days after the disturbance. Within each soil type, the microbial community composition did not differ between heat shock and control samples at day 3. However, at day 30, FST soil samples treated at 60 degrees C and 70 degrees C contained a microbial community significantly different from the control and with lower biomass regardless of high enzyme resilience. Results of this study show that deforestation followed by long-term cultivation changed microbial community composition and had differential effects on microbial functional stability. Both soils displayed similar resilience to FDA hydrolysis, a

  16. 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 ...

  17. Effect of pyrene and cadmium on microbial activity and community structure in soil.

    PubMed

    Lu, Mang; Xu, Kui; Chen, Jun

    2013-04-01

    In this study, a greenhouse experiment was conducted to investigate interactive effects of cadmium (Cd) × pyrene × plant treatments on soil microbial activity and community structure. The results demonstrated that the basal respiration, microbial biomass carbon and metabolic quotient in both unplanted and rhizosphere soil were significantly influenced by interaction of Cd and pyrene. The combined application of Cd and pyrene caused a significantly greater biocidal influence on the soil microorganisms than the single spiking of Cd or pyrene. The soil basal respiration increased with the spiking of 2.5 mg kg(-1) Cd in both unplanted and rhizosphere soil. The eco-physiological index of Cd-tolerant populations was significantly different among the unplanted soil, rhizoplane and rhizosphere soil of tall fescue, indicating a slightly uneven distribution of fast- and slow-growing tolerant bacteria. Obvious differences in microbial activity were observed among treatments due to different physicochemical characteristics of the rhizosphere soils depending on the plant species. PMID:23290945

  18. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota

    DOE PAGESBeta

    Xiong, Weili; Abraham, Paul E.; Li, Zhou; Pan, Chongle; Robert L. Hettich

    2015-01-01

    We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs.more » disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gut microbiota, yielding valuable insights into the broad functional profiles of even complex microbiota. Future developments are likely to expand into improved analysis throughput and coverage depth, as well as post-translational modification characterizations.« less

  19. Microbial community proteomics for characterizing the range of metabolic functions and activities of human gut microbiota

    SciTech Connect

    Xiong, Weili; Abraham, Paul E.; Li, Zhou; Pan, Chongle; Robert L. Hettich

    2015-01-01

    We found that the human gastrointestinal (GI) tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome component is not insignificant, but rather provides important functions that are absolutely critical to many aspects of human health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial community proteomics (sometimes referred to as metaproteomics) provides a powerful approach to measure the range and details of human gut microbiota functions and metabolic activities, revealing information about microbiome development and stability especially with regard to human health vs. disease states. In most cases, both microbial and human proteins are extracted from fecal samples and then measured by the high performance MS-based proteomics technology. We review the field of human gut microbiome community proteomics, with a focus on the experimental and informatics considerations involved in characterizing systems that range from low complexity defined model gut microbiota in gnotobiotic mice, to the simple gut microbiota in the GI tract of newborn infants, and finally to the complex gut microbiota in adults. Moreover, the current state-of-the-art in experimental and bioinformatics capabilities for community proteomics enable a detailed measurement of the gut microbiota, yielding valuable insights into the broad functional profiles of even complex microbiota. Future developments are likely to expand into improved analysis throughput and coverage depth, as well as post-translational modification characterizations.

  20. Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure▿

    PubMed Central

    Bassin, J. P.; Pronk, M.; Muyzer, G.; Kleerebezem, R.; Dezotti, M.; van Loosdrecht, M. C. M.

    2011-01-01

    The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescence in situ hybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance of Nitrospira sp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), “Candidatus Accumulibacter phosphatis” bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonas sp.) and phosphate removal (“Candidatus Accumulibacter”). PMID:21926194

  1. Active manipulation of native soil microbial community structure and function to suppress soilborne diseases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The reality of naturally occurring biologically-induced disease suppressive soils suggests opportunity for managing resident soil microbial communities as a disease control method. Disease suppressive soils have yielded a significant body of knowledge concerning operative mechanisms leading to t...

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

    PubMed Central

    Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

    2015-01-01

    The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system. PMID:26388851

  3. Highly Active Microbial Communities in the Ice and Snow Cover of High Mountain Lakes

    PubMed Central

    Felip, M.; Sattler, B.; Psenner, R.; Catalan, J.

    1995-01-01

    An exploratory study carried out in Pyrenean and Alpine lakes shows that a rich, active microbial community lives in the slush layers of the winter cover of such lakes in spite of the low temperature and the seasonal occurrence of the habitat. Bacteria were very diverse in morphology, with filaments reaching up to 100 (mu)m long; flagellates, both autotrophic (chrysophytes, cryptophytes, dinoflagellates, and volvocales) and heterotrophic, and ciliates were abundant, reaching biovolume values up to 2.7 x 10(sup6) (mu)m(sup3) ml(sup-1). Species composition was very variable, with dominance depending on date and depth. Although many species were typical of lake plankton communities, some were restricted to the slush, for instance the predatory ciliates Dileptus sp. and Lacrymaria sp., and others were restricted to the surface pools, such as the snow algae Chlamydomonas nivalis. Microbial biomasses and usually bacterial and algal activities were greater in the slush layers than in the lake water. Photosynthesis rate in the upper cover layers reached values up to 0.5 (mu)g of C liter(sup-1) h(sup-1), and high bacterial activities up to 226 pmol of leucine incorporated liter(sup-1) h(sup-1) and 25 pmol of thymidine incorporated liter(sup-1) h(sup-1) were measured. For most species, lake water flooding the ice and snow cover could provide an inoculum. Differential growth depending on the environmental conditions (nutrients, organic matter, light) of a particular slush layer could provide dominance of different groups or species. However, there was no obvious colonizing mechanism for those species not appearing either in plankton or in communities on top of the snowpack. PMID:16535056

  4. Highly active microbial communities in the ice and snow cover of high mountain lakes.

    PubMed

    Felip, M; Sattler, B; Psenner, R; Catalan, J

    1995-06-01

    An exploratory study carried out in Pyrenean and Alpine lakes shows that a rich, active microbial community lives in the slush layers of the winter cover of such lakes in spite of the low temperature and the seasonal occurrence of the habitat. Bacteria were very diverse in morphology, with filaments reaching up to 100 (mu)m long; flagellates, both autotrophic (chrysophytes, cryptophytes, dinoflagellates, and volvocales) and heterotrophic, and ciliates were abundant, reaching biovolume values up to 2.7 x 10(sup6) (mu)m(sup3) ml(sup-1). Species composition was very variable, with dominance depending on date and depth. Although many species were typical of lake plankton communities, some were restricted to the slush, for instance the predatory ciliates Dileptus sp. and Lacrymaria sp., and others were restricted to the surface pools, such as the snow algae Chlamydomonas nivalis. Microbial biomasses and usually bacterial and algal activities were greater in the slush layers than in the lake water. Photosynthesis rate in the upper cover layers reached values up to 0.5 (mu)g of C liter(sup-1) h(sup-1), and high bacterial activities up to 226 pmol of leucine incorporated liter(sup-1) h(sup-1) and 25 pmol of thymidine incorporated liter(sup-1) h(sup-1) were measured. For most species, lake water flooding the ice and snow cover could provide an inoculum. Differential growth depending on the environmental conditions (nutrients, organic matter, light) of a particular slush layer could provide dominance of different groups or species. However, there was no obvious colonizing mechanism for those species not appearing either in plankton or in communities on top of the snowpack. PMID:16535056

  5. Systematic investigation and microbial community profile of indole degradation processes in two aerobic activated sludge systems

    PubMed Central

    Ma, Qiao; Qu, Yuanyuan; Zhang, Xuwang; Liu, Ziyan; Li, Huijie; Zhang, Zhaojing; Wang, Jingwei; Shen, Wenli; Zhou, Jiti

    2015-01-01

    Indole is widely spread in various environmental matrices. Indole degradation by bacteria has been reported previously, whereas its degradation processes driven by aerobic microbial community were as-yet unexplored. Herein, eight sequencing batch bioreactors fed with municipal and coking activated sludges were constructed for aerobic treatment of indole. The whole operation processes contained three stages, i.e. stage I, glucose and indole as carbon sources; stage II, indole as carbon source; and stage III, indole as carbon and nitrogen source. Indole could be completely removed in both systems. Illumina sequencing revealed that alpha diversity was reduced after indole treatment and microbial communities were significantly distinct among the three stages. At genus level, Azorcus and Thauera were dominant species in stage I in both systems, while Alcaligenes, Comamonas and Pseudomonas were the core genera in stage II and III in municipal sludge system, Alcaligenes and Burkholderia in coking sludge system. In addition, four strains belonged to genera Comamonas, Burkholderia and Xenophilus were isolated using indole as sole carbon source. Burkholderia sp. IDO3 could remove 100 mg/L indole completely within 14 h, the highest degradation rate to date. These findings provide novel information and enrich our understanding of indole aerobic degradation processes. PMID:26657581

  6. Applying theories of microbial metabolism for induction of targeted enzyme activity in a methanogenic microbial community at a metabolic steady state.

    PubMed

    Speda, Jutta; Johansson, Mikaela A; Jonsson, Bengt-Harald; Karlsson, Martin

    2016-09-01

    Novel enzymes that are stable in diverse conditions are intensively sought because they offer major potential advantages in industrial biotechnology, and microorganisms in extreme environments are key sources of such enzymes. However, most potentially valuable enzymes are currently inaccessible due to the pure culturing problem of microorganisms. Novel metagenomic and metaproteomic techniques that circumvent the need for pure cultures have theoretically provided possibilities to identify all genes and all proteins in microbial communities, but these techniques have not been widely used to directly identify specific enzymes because they generate vast amounts of extraneous data.In a first step towards developing a metaproteomic approach to pinpoint targeted extracellular hydrolytic enzymes of choice in microbial communities, we have generated and analyzed the necessary conditions for such an approach by the use of a methanogenic microbial community maintained on a chemically defined medium. The results show that a metabolic steady state of the microbial community could be reached, at which the expression of the targeted hydrolytic enzymes were suppressed, and that upon enzyme induction a distinct increase in the targeted enzyme expression was obtained. Furthermore, no cross talk in expression was detected between the two focal types of enzyme activities under their respective inductive conditions. Thus, the described approach should be useful to generate ideal samples, collected before and after selective induction, in controlled microbial communities to clearly discriminate between constituently expressed proteins and extracellular hydrolytic enzymes that are specifically induced, thereby reducing the analysis to only those proteins that are distinctively up-regulated. PMID:27115757

  7. Effect of rice straw application on microbial community and activity in paddy soil under different water status.

    PubMed

    Pan, Fuxia; Li, Yaying; Chapman, Stephen James; Yao, Huaiying

    2016-03-01

    Rice straw application and flooding are common practices in rice production, both of which can induce changes in the microbial community. This study used soil microcosms to investigate the impact of water status (saturated and nonsaturated) and straw application (10 g kg(-1) soil) on soil microbial composition (phospholipid fatty acid analysis) and activity (MicroResp(™) method). Straw application significantly increased total PLFA amount and individual PLFA components independent of soil moisture level. The amount of soil fungal PLFA was less than Gram-negative, Gram-positive, and actinomycete PLFA, except the drained treatment with rice straw application, which had higher fungal PLFA than actinomycete PLFA at the initial incubation stage. Straw amendment and waterlogging had different effects on microbial community structure and substrate-induced pattern. PLFA profiles were primarily influenced by straw application, whereas soil water status had the greater influence on microbial respiration. Of the variation in PLFA and respiration data, straw accounted for 30.1 and 16.7 %, while soil water status explained 7.5 and 29.1 %, respectively. Our results suggest that (1) the size of microbial communities in paddy soil is more limited by carbon substrate availability rather than by the anaerobic conditions due to waterlogging and (2) that soil water status is more important as a control of fungal growth and microbial community activity. PMID:26596827

  8. Denitrification in a large river: consideration of geomorphic controls on microbial activity and community structure.

    PubMed

    Tatariw, Corianne; Chapman, Elise L; Sponseller, Ryan A; Mortazavi, Behzad; Edmonds, Jennifer W

    2013-10-01

    Ecological theory argues that the controls over ecosystem processes are structured hierarchically, with broader-scale drivers acting as constraints over the interactions and dynamics at nested levels of organization. In river ecosystems, these interactions may arise from broadscale variation in channel form that directly shapes benthic habitat structure and indirectly constrains resource supply and biological activity within individual reaches. To evaluate these interactions, we identified sediment characteristics, water chemistry, and denitrifier community structure as factors influencing benthic denitrification rates in a sixth-order river that flows through two physiographic provinces and the transitional zone between them, each with distinct geomorphological properties. We found that denitrification rates tracked spatial changes in sediment characteristics and varied seasonally with expected trends in stream primary production. Highest rates were observed during the spring and summer seasons in the physiographic province dominated by fine-grained sediments, illustrating how large-scale changes in river structure can constrain the location of denitrification hotspots. In addition, nirS and nirK community structure each responded differently to variation in channel form, possibly due to changes in dissolved oxygen and organic matter supply. This shift in denitrifier community structure coincident with higher rates of N removal via denitrification suggests that microbial community structure may influence biogeochemical processes. PMID:24358711

  9. Soil Microbial Community Structure and Metabolic Activity of Pinus elliottii Plantations across Different Stand Ages in a Subtropical Area

    PubMed Central

    Wu, Zeyan; Haack, Stacey Elizabeth; Lin, Wenxiong; Li, Bailian; Wu, Linkun; Fang, Changxun; Zhang, Zhixing

    2015-01-01

    Soil microbes play an essential role in the forest ecosystem as an active component. This study examined the hypothesis that soil microbial community structure and metabolic activity would vary with the increasing stand ages in long-term pure plantations of Pinus elliottii. The phospholipid fatty acids (PLFA) combined with community level physiological profiles (CLPP) method was used to assess these characteristics in the rhizospheric soils of P. elliottii. We found that the soil microbial communities were significantly different among different stand ages of P. elliottii plantations. The PLFA analysis indicated that the bacterial biomass was higher than the actinomycic and fungal biomass in all stand ages. However, the bacterial biomass decreased with the increasing stand ages, while the fungal biomass increased. The four maximum biomarker concentrations in rhizospheric soils of P. elliottii for all stand ages were 18:1ω9c, 16:1ω7c, 18:3ω6c (6,9,12) and cy19:0, representing measures of fungal and gram negative bacterial biomass. In addition, CLPP analysis revealed that the utilization rate of amino acids, polymers, phenolic acids, and carbohydrates of soil microbial community gradually decreased with increasing stand ages, though this pattern was not observed for carboxylic acids and amines. Microbial community diversity, as determined by the Simpson index, Shannon-Wiener index, Richness index and McIntosh index, significantly decreased as stand age increased. Overall, both the PLFA and CLPP illustrated that the long-term pure plantation pattern exacerbated the microecological imbalance previously described in the rhizospheric soils of P. elliottii, and markedly decreased the soil microbial community diversity and metabolic activity. Based on the correlation analysis, we concluded that the soil nutrient and C/N ratio most significantly contributed to the variation of soil microbial community structure and metabolic activity in different stand ages of P

  10. Effect of Monospecific and Mixed Sea-Buckthorn (Hippophae rhamnoides) Plantations on the Structure and Activity of Soil Microbial Communities

    PubMed Central

    Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

    2015-01-01

    This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4+) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4+ content, nitrate content (NH3−), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations. PMID:25658843

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

    PubMed

    Yu, Xuan; Liu, Xu; Zhao, Zhong; Liu, Jinliang; Zhang, Shunxiang

    2015-01-01

    This study aims to evaluate the effect of different afforestation models on soil microbial composition in the Loess Plateau in China. In particular, we determined soil physicochemical properties, enzyme activities, and microbial community structures in the top 0 cm to 10 cm soil underneath a pure Hippophae rhamnoides (SS) stand and three mixed stands, namely, H. rhamnoides and Robinia pseucdoacacia (SC), H. rhamnoides and Pinus tabulaeformis (SY), and H. rhamnoides and Platycladus orientalis (SB). Results showed that total organic carbon (TOC), total nitrogen, and ammonium (NH4(+)) contents were higher in SY and SB than in SS. The total microbial biomass, bacterial biomass, and Gram+ biomass of the three mixed stands were significantly higher than those of the pure stand. However, no significant difference was found in fungal biomass. Correlation analysis suggested that soil microbial communities are significantly and positively correlated with some chemical parameters of soil, such as TOC, total phosphorus, total potassium, available phosphorus, NH4(+) content, nitrate content (NH3(-)), and the enzyme activities of urease, peroxidase, and phosphatase. Principal component analysis showed that the microbial community structures of SB and SS could clearly be discriminated from each other and from the others, whereas SY and SC were similar. In conclusion, tree species indirectly but significantly affect soil microbial communities and enzyme activities through soil physicochemical properties. In addition, mixing P. tabulaeformis or P. orientalis in H. rhamnoides plantations is a suitable afforestation model in the Loess Plateau, because of significant positive effects on soil nutrient conditions, microbial community, and enzyme activities over pure plantations. PMID:25658843

  12. GeoChip 3.0: A High Throughput Tool for Analyzing Microbial Community, Composition, Structure, and Functional Activity

    SciTech Connect

    He, Zhili; Deng, Ye; Nostrand, Joy Van; Tu, Qichao; Xu, Meiying; Hemme, Chris; Wu, Liyou; Hazen, Terry; Zhou, Jizhong; Li, Xingyuan; Gentry, Terry; Yin, Yifeng; Liebich, Jost

    2010-05-17

    Microarray-based genomic technology has been widely used for microbial community analysis, and it is expected that microarray-based genomic technologies will revolutionize the analysis of microbial community structure, function and dynamics. A new generation of functional gene arrays (GeoChip 3.0) has been developed, with 27,812 probes covering 56,990 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance, and organic contaminant degradation. Those probes were derived from 2,744, 140, and 262 species for bacteria, archaea, and fungi, respectively. GeoChip 3.0 has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating, and the gyrB gene for phylogenetic analysis. Our computational evaluation of probe specificity indicated that all designed probes had a high specificity to their corresponding targets. Also, experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036percent-0.025percent false positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which demonstrated that the structure, composition, and potential activity of soil microbial communities significantly changed with the plant species diversity. All results indicate that GeoChip 3.0 is a high throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning. To our knowledge, GeoChip 3.0 is the most comprehensive microarrays currently available for studying microbial communities associated with geobiochemical cycling, global climate change, bioenergy

  13. Community Level Physiological Profiles (CLPP), Characterization and Microbial Activity of Soil Amended with Dairy Sewage Sludge

    PubMed Central

    Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy

    2012-01-01

    The aim of the present work was to assess the influence of organic amendment applications compared to mineral fertilization on soil microbial activity and functional diversity. The field experiment was set up on a soil classified as an Eutric Cambisol developed from loess (South-East Poland). Two doses of both dairy sewage sludge (20 Mg·ha−1 and 26 Mg·ha−1) and of mineral fertilizers containing the same amount of nutrients were applied. The same soil without any amendment was used as a control. The soil under undisturbed native vegetation was also included in the study as a representative background sample. The functional diversity (catabolic potential) was assessed using such indices as Average Well Color Development (AWCD), Richness (R) and Shannon–Weaver index (H). These indices were calculated, following the community level physiological profiling (CLPP) using Biolog Eco Plates. Soil dehydrogenase and respiratory activity were also evaluated. The indices were sensitive enough to reveal changes in community level physiological profiles due to treatment effects. It was shown that dairy sewage amended soil was characterized by greater AWCD, R, H and dehydrogenase and respiratory activity as compared to control or mineral fertilized soil. Analysis of variance (ANOVA) and principal component analysis (PCA) were used to depict the differences of the soil bacterial functional diversity between the treatments. PMID:22737006

  14. Radiocarbon Evidence of Active Endolithic Microbial Communities in the Hyperarid Core of the Atacama Desert

    PubMed Central

    Wierzchos, Jacek; Davila, Alfonso F.; Slater, Gregory F.

    2013-01-01

    Abstract The hyperarid core of the Atacama Desert is one of the driest and most inhospitable places on Earth, where life is most commonly found in the interior of rocks (i.e., endolithic habitats). Due to the extreme dryness, microbial activity in these habitats is expected to be low; however, the rate of carbon cycling within these microbial communities remains unknown. We address this issue by characterizing the isotopic composition (13C and 14C) of phospholipid fatty acids (PLFA) and glycolipid fatty acids (GLFA) in colonized rocks from four different sites inside the hyperarid core. δ13C results suggest that autotrophy and/or quantitative conversion of organic matter to CO2 are the dominant processes occurring with the rock. Most Δ14C signatures of PLFA and GLFA were consistent with modern atmospheric CO2, indicating that endoliths are using atmospheric carbon as a primary carbon source and are also cycling carbon quickly. However, at one site the PLFA contained 14C from atmospheric nuclear weapons testing that occurred during the 1950s and 1960s, indicating a decadal rate of carbon cycling. At the driest site (Yungay), based on the relative abundance and 14C content of GLFA and PLFA, there was evidence of possible preservation. Hence, in low-moisture conditions, glycolipids may persist while phospholipids are preferentially hydrolyzed. Key Words: Endoliths—Extremophile—Carbon isotopes—Radiocarbon—Lipids. Astrobiology 13, 607–616. PMID:23848470

  15. Archean Microbial Mat Communities

    NASA Astrophysics Data System (ADS)

    Tice, Michael M.; Thornton, Daniel C. O.; Pope, Michael C.; Olszewski, Thomas D.; Gong, Jian

    2011-05-01

    Much of the Archean record of microbial communities consists of fossil mats and stromatolites. Critical physical emergent properties governing the evolution of large-scale (centimeters to meters) topographic relief on the mat landscape are (a) mat surface roughness relative to the laminar sublayer and (b) cohesion. These properties can be estimated for fossil samples under many circumstances. A preliminary analysis of Archean mat cohesion suggests that mats growing in shallow marine environments from throughout this time had cohesions similar to those of modern shallow marine mats. There may have been a significant increase in mat strength at the end of the Archean.

  16. Primary effects of extracellular enzyme activity and microbial community on carbon and nitrogen mineralization in estuarine and tidal wetlands.

    PubMed

    Li, Xiaofei; Hou, Lijun; Liu, Min; Lin, Xianbiao; Li, Ye; Li, Shuwen

    2015-03-01

    Estuarine and tidal wetlands with high primary productivity and biological activity play a crucial role in coastal nutrient dynamics. Here, to better reveal the effects of extracellular enzymes and microbial community on carbon (C) and nitrogen (N) mineralization, the incubation experiments with different C and N addition patterns to the tidal sediments of the Yangtze Estuary (China) were conducted. The results suggested a significant increase in cumulative CO2 effluxes in the C and CN treatment experiments, while no significant difference in cumulative CO2 effluxes between the N treatment and control (CK) experiments was observed. In addition, the nutrient addition patterns had a great influence on dissolve organic C and N levels, but a small effect on microbial biomass C and N. Microbial community composition and microbial activity were found to be positively correlated with organic C (OC) and the molar ratio of C to N (C/N). Partial correlation analysis, controlling for C/N, supported direct effects of OC on the activity of carbon-cycling extracellular enzymes (cellulase and polyphenol oxidase), while C/N exhibited negatively correlations with urease and Gram-positive bacteria to Gram-negative bacteria (G+/G-). Strong relationships were found between CO2 efflux and mineral nitrogen with the activity of specific enzymes (sucrase, cellulase, and polyphenol oxidase) and abundances of Gram-negative bacteria, arbuscular mycorrhizal fungi, and fungi, suggesting the significant influences of microbial community and enzyme activity on C and N mineralization in the estuarine and tidal wetlands. Furthermore, this study could highlight the need to explore effects of nutrient supply on microbial communities and enzyme activity changes associated with the C and N mineralization in these wetlands induced by the climate change. PMID:25381491

  17. Vadose zone microbial community structure and activity in metal/radionuclide contaminated sediments. Final technical report

    SciTech Connect

    Balkwill, David L.

    2002-08-17

    This final technical report describes the research carried out during the final two months of the no-cost extension ending 11/14/01. The primary goals of the project were (1) to determine the potential for transformation of Cr(VI) (oxidized, mobile) to Cr(III) (reduced, immobile) under unsaturated conditions as a function of different levels and combinations of (a) chromium, (b) nitrate (co-disposed with Cr), and (c) molasses (inexpensive bioremediation substrate), and (2) to determine population structure and activity in experimental treatments by characterization of the microbial community by signature biomarker analysis and by RT-PCR and terminal restriction fragment length polymorphism (T-RFLP) and 16S ribosomal RNA genes. It was determined early in the one-year no-cost extension period that the T-RFLP approach was problematic in regard to providing information on the identities of microorganisms in the samples examined. As a result, it could not provide the detailed information on microbial community structure that was needed to assess the effects of treatments with chromium, nitrate, and/or molasses. Therefore, we decided to obtain the desired information by amplifying (using TR-PCR, with the same primers used for T-RFLP) and cloning 16S rRNA gene sequences from the same RNA extracts that were used for T-RFLP analysis. We also decided to use a restriction enzyme digest procedure (fingerprinting procedure) to place the clones into types. The primary focus of the research carried out during this report period was twofold: (a) to complete the sequencing of the clones, and (b) to analyze the clone sequences phylogenetically in order to determine the relatedness of the bacteria detected in the samples to each other and to previously described genera and species.

  18. Monitoring the Perturbation of Soil and Groundwater Microbial Communities Due to Pig Production Activities

    PubMed Central

    Hong, Pei-Ying; Yannarell, Anthony C.; Dai, Qinghua; Ekizoglu, Melike

    2013-01-01

    This study aimed to determine if biotic contaminants originating from pig production farms are disseminated into soil and groundwater microbial communities. A spatial and temporal sampling of soil and groundwater in proximity to pig production farms was conducted, and quantitative PCR (Q-PCR) was utilized to determine the abundances of tetracycline resistance genes (i.e., tetQ and tetZ) and integrase genes (i.e., intI1 and intI2). We observed that the abundances of tetZ, tetQ, intI1, and intI2 in the soils increased at least 6-fold after manure application, and their abundances remained elevated above the background for up to 16 months. Q-PCR further determined total abundances of up to 5.88 × 109 copies/ng DNA for tetZ, tetQ, intI1, and intI2 in some of the groundwater wells that were situated next to the manure lagoon and in the facility well used to supply water for one of the farms. We further utilized 16S rRNA-based pyrosequencing to assess the microbial communities, and our comparative analyses suggest that most of the soil samples collected before and after manure application did not change significantly, sharing a high Bray-Curtis similarity of 78.5%. In contrast, an increase in Bacteroidetes and sulfur-oxidizing bacterial populations was observed in the groundwaters collected from lagoon-associated groundwater wells. Genera associated with opportunistic human and animal pathogens, such as Acinetobacter, Arcobacter, Yersinia, and Coxiella, were detected in some of the manure-treated soils and affected groundwater wells. Feces-associated bacteria such as Streptococcus, Erysipelothrix, and Bacteroides were detected in the manure, soil, and groundwater ecosystems, suggesting a perturbation of the soil and groundwater environments by invader species from pig production activities. PMID:23396341

  19. Evidence and characteristics of a diverse and metabolically active microbial community in deep subsurface clay borehole water.

    PubMed

    Wouters, Katinka; Moors, Hugo; Boven, Patrick; Leys, Natalie

    2013-12-01

    The Boom Clay in Belgium is investigated in the context of geological nuclear waste disposal, making use of the High Activity Disposal Experimental Site (HADES) underground research facility. This facility, located in the Boom Clay at a depth of 225 m below the surface, offers a unique access to a microbial community in an environment, of which all geological and geochemical characteristics are being thoroughly studied. This study presents the first elaborate description of a microbial community in water samples retrieved from a Boom Clay piezometer (borehole water). Using an integrated approach of microscopy, metagenomics, activity screening and cultivation, the presence and activity of this community are disclosed. Despite the presumed low-energy environment, microscopy and molecular analyses show a large bacterial diversity and richness, tending to correlate positively with the organic matter content of the environment. Among 10 borehole water samples, a core bacterial community comprising seven bacterial phyla is defined, including both aerobic and anaerobic genera with a range of metabolic preferences. In addition, a corresponding large fraction of this community is found cultivable and active. In conclusion, this study shows the possibility of a microbial community of relative complexity to persist in subsurface Boom Clay borehole water. PMID:23802615

  20. Diversity and activity of benthic microbial communities at the North Alex mud volcano, Eastern Mediterranean

    NASA Astrophysics Data System (ADS)

    Makarow, Dorothee; Feseker, Tomas; Schmitz, Ruth; Treude, Tina

    2010-05-01

    North Alex mud volcano, located on the upper slope of the western Nile deep-sea fan, is characterized by an active seepage center transporting pore fluids, hydrocarbons and gases from deep subsurface sources to the sediment-water interface. Surface sediments feature steep temperature gradient of 8.5°C m-1. We sampled the top 40 cm of the sediments at different locations between the center and rim of the mud volcano to study the diversity, activity, and physiological characteristics of benthic microorganisms. The sediments revealed the activity of anaerobic oxidation of methane coupled to sulfate reduction with a mesophilic temperature optimum. Organisms involved in the process include consortia of methanotrophic archaea (ANME-2 group) and an unknown bacterial partner. Besides methanotrophic organisms the sediments harbored a variety of other bacterial and archaeal groups - including potentially thermophilic bacteria that could be involved in sulfur cycling. This poster presentation will provide an overview of microbial activities and community compositions of North Alex mud volcano sediments.

  1. Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

    NASA Astrophysics Data System (ADS)

    Dong, W. Y.; Zhang, X. Y.; Liu, X. Y.; Fu, X. L.; Chen, F. S.; Wang, H. M.; Sun, X. M.; Wen, X. F.

    2015-07-01

    Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-Glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the PLFA abundanceespecially in the N2P treatment, the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK. Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. There were also significant relationships between gram-positive (G+) bacteria and all three soil enzymes. These findings indicate that G+ bacteria is the most important microbial community in C, N, and P transformations in Chinese fir plantations, and that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil

  2. Long-term effects of ZnO nanoparticles on nitrogen and phosphorus removal, microbial activity and microbial community of a sequencing batch reactor.

    PubMed

    Wang, Sen; Gao, Mengchun; She, Zonglian; Zheng, Dong; Jin, Chunji; Guo, Liang; Zhao, Yangguo; Li, Zhiwei; Wang, Xuejiao

    2016-09-01

    The performance, microbial activity, and microbial community of a sequencing batch reactor (SBR) were investigated under the long-term exposure of ZnO nanoparticles (ZnO NPs). Low ZnO NPs concentration (less than 5mg/L) had no obvious effect on the SBR performance, whereas the removals of COD, NH4(+)-N, and phosphorus were affected at 10-60mg/L ZnO NPs. The variation trend of nitrogen and phosphorus removal rate was similar to that of microbial enzymatic activity with the increase of ZnO NPs concentrations. The richness and diversity of microbial community showed obvious variations at different ZnO NPs concentrations. ZnO NPs appeared on the surface and cell interior of activated sludge, and the Zn contents in the effluent and activated sludge increased with the increase of ZnO NPS concentration. The present results provide use information to understand the effect of ZnO NPS on the performance of wastewater biological treatment systems. PMID:27262098

  3. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland

    PubMed Central

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Čapek, Petr; Kaiser, Christina; Torsvik, Vigdis L.; Richter, Andreas; Schleper, Christa; Urich, Tim

    2014-01-01

    Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation (“buried topsoils”), resulting from a decrease in fungal abundance compared to recent (“unburied”) topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation. PMID

  4. Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland.

    PubMed

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Schnecker, Jörg; Wild, Birgit; Capek, Petr; Kaiser, Christina; Torsvik, Vigdis L; Richter, Andreas; Schleper, Christa; Urich, Tim

    2014-01-01

    Permafrost-affected soils in the Northern latitudes store huge amounts of organic carbon (OC) that is prone to microbial degradation and subsequent release of greenhouse gasses to the atmosphere. In Greenland, the consequences of permafrost thaw have only recently been addressed, and predictions on its impact on the carbon budget are thus still highly uncertain. However, the fate of OC is not only determined by abiotic factors, but closely tied to microbial activity. We investigated eight soil profiles in northeast Greenland comprising two sites with typical tundra vegetation and one wet fen site. We assessed microbial community structure and diversity (SSU rRNA gene tag sequencing, quantification of bacteria, archaea and fungi), and measured hydrolytic and oxidative enzyme activities. Sampling site and thus abiotic factors had a significant impact on microbial community structure, diversity and activity, the wet fen site exhibiting higher potential enzyme activities and presumably being a hot spot for anaerobic degradation processes such as fermentation and methanogenesis. Lowest fungal to bacterial ratios were found in topsoils that had been relocated by cryoturbation ("buried topsoils"), resulting from a decrease in fungal abundance compared to recent ("unburied") topsoils. Actinobacteria (in particular Intrasporangiaceae) accounted for a major fraction of the microbial community in buried topsoils, but were only of minor abundance in all other soil horizons. It was indicated that the distribution pattern of Actinobacteria and a variety of other bacterial classes was related to the activity of phenol oxidases and peroxidases supporting the hypothesis that bacteria might resume the role of fungi in oxidative enzyme production and degradation of phenolic and other complex substrates in these soils. Our study sheds light on the highly diverse, but poorly-studied communities in permafrost-affected soils in Greenland and their role in OC degradation. PMID:25360132

  5. Influence of benomyl and prometryn on the soil microbial activities and community structures in pasture grasslands of Slovakia.

    PubMed

    Javoreková, Sona; Svrceková, Ivana; Maková, Jana

    2010-10-01

    The effects of pesticides (a herbicide and a fungicide) on the microbial community structure and their activity were analyzed in soil from four alpine pasture grasslands in Slovakia. Specifically, the effects of the herbicide, Gesagard (prometryn active ingredient), and fungicide, Fundazol 50 WP (benomyl active ingredient), on the microbial respiration activity (CO2 production), the numbers of selective microbial physiological groups (CFU.g(-1)) and the structure (relative abundance) of soil microbial communities [(phospholipid fatty acid (PLFA)] were analyzed under controlled laboratory conditions. All treatments including the treatments with pesticides increased (statistically significantly) the production of CO2 in all fields during 21 days of incubation and posed a statistically insignificant negative influence on the numbers of the observed physiological groups of microorganisms. The significantly negative influence was evaluated only in the numbers of two physiological groups; spores of bacteria utilizing organic nitrogen and bacteria, and their spores utilizing inorganic nitrogen. A shift in the microbial composition was evident when the PLFA patterns of samples from different sites and treatments were compared by the Principal Component Analysis (PCA). According to the second component PCA 2 (15.95 %) the locations were grouped into two clusters. The first one involved the Donovaly and Dubakovo sites and the second one contained the Velka Fatra and Mala Fatra locations. The PLFA composition of the soils showed important changes after the treatment with pesticides according to PCA 1 (66.06 %). Other treatments had not had a significant effect on the soil microbial community with the exception of the population of fungi. The lower relative abundance (significant effect) of Gram-positive bacteria, actinomycetes and general group of bacteria were determined in samples treated by the herbicide Gesagard. The application of fungicide Fundazol decreased

  6. Effect of Cry3Bb transgenic corn and tefluthrin on the soil microbial community: biomass, activity, and diversity.

    PubMed

    Devare, M H; Jones, C M; Thies, J E

    2004-01-01

    Transgenic Bt corn expressing the Cry3Bb insecticidal protein active against corn rootworm (CRW) (Diabrotica spp.; Coleoptera: Chrysomelidae) was released for commercial use in 2003 and is expected to be widely adopted. Yet, the direct and indirect risks to soil microorganisms of growing this CRW-resistant Bt corn versus applying insecticides to control the rootworm have not been assessed under field conditions. The effects of CRW Bt corn and the insecticide tefluthrin [2,3,5,6-tetrafluoro-4-methylbenzyl (Z)-(1RS)-cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylate] on soil microbial biomass, activity (N mineralization potential, short-term nitrification rate, and soil respiration), and bacterial community structure as determined by terminal restriction fragment length polymorphism (T-RFLP) analysis were assessed over two seasons in a field experiment. Bt corn had no deleterious effects on microbial activity or bacterial community measures compared with the non-transgenic isoline. The T-RFLP analysis indicated that amplifiable bacterial species composition and relative abundance differed substantially between years, but did not differ between rhizosphere and bulk soils. The application of tefluthrin also had no effect on any microbial measure except decreased soil respiration observed in tefluthrin-treated plots compared with Bt and non-transgenic isoline (NoBt) plots in 2002. Our results indicate that the release of CRW Bt corn poses little threat to the ecology of the soil microbial community based on parameters measured in this study. PMID:15224918

  7. Main factors controlling microbial community structure, growth and activity after reclamation of a tailing pond with aided phytostabilization

    NASA Astrophysics Data System (ADS)

    Zornoza, Raúl; Acosta, José A.; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

    2015-04-01

    Reclamation on bare tailing ponds has the potential to represent soil genesis in Technosols favoring the understanding of the changes of microbial communities and function. In this study we used phytostabilization aided with calcium carbonate and pig slurry/manure to reclaim an acidic bare tailing pond with the aim of investigating the effect of amending and different species on microbial community structure and function. We sampled after two years of amending and planting: unamended tailing soil (UTS), non-rhizospheric amended tailing soil (ATS), rhizospheric soil from four species, and non-rhizospheric native forest soil (NS), which acted as reference. The application of amendments increased pH up to neutrality, organic carbon (Corg), C/N and aggregate stability, while decreased salinity and heavy metals availability. No effect of rhizosphere was observed on physicochemical properties, metals immobilization and microbial community structure and function. To account for confounding effects due to soil organic matter, microbial properties were expressed per Corg. The high increments in pH and Corg have been the main factors driving changes in microbial community structure and function. Bacterial biomass was higher in UTS, without significant differences among the rest of soils. Fungal biomass followed the trend UTS < ATS = rhizospheric soils < NS. Bacterial growth increased and fungal growth decreased with increasing pH, despite the high availability of metals at low pH. Enzyme activities were lower in UTS, being β-glucosidase and β-glucosaminidase activities highly correlated with bacterial growth. Microbial activities were not correlated with the exchangeable fraction of heavy metals, indicating that microbial function is not strongly affected by these metals, likely due to the efficiency of the reclamation procedure to reduce metals toxicity. Changes in microbial community composition were largely explained by changes in pH, heavy metals availability and Corg

  8. Profiling microbial community in a watershed heavily contaminated by an active antimony (Sb) mine in Southwest China.

    PubMed

    Sun, Weimin; Xiao, Enzong; Dong, Yiran; Tang, Song; Krumins, Valdis; Ning, Zengping; Sun, Min; Zhao, Yanlong; Wu, Shiliang; Xiao, Tangfu

    2016-04-15

    Located in Southwest China, the Chahe watershed has been severely contaminated by upstream active antimony (Sb) mines. The extremely high concentrations of Sb make the Chahe watershed an excellent model to elucidate the response of indigenous microbial activities within a severe Sb-contaminated environment. In this study, water and surface sediments from six locations in the Chahe watershed with different levels of Sb contamination were analyzed. Illumina sequencing of 16S rRNA amplicons revealed more than 40 phyla from the domain Bacteria and 2 phyla from the domain Archaea. Sequences assigned to the genera Flavobacterium, Sulfuricurvum, Halomonas, Shewanella, Lactobacillus, Acinetobacter, and Geobacter demonstrated high relative abundances in all sequencing libraries. Spearman's rank correlations indicated that a number of microbial phylotypes were positively correlated with different speciation of Sb, suggesting potential roles of these phylotypes in microbial Sb cycling. Canonical correspondence analysis further demonstrated that geochemical parameters, including water temperature, pH, total Fe, sulfate, aqueous Sb, and Eh, significantly structured the overall microbial community in Chahe watershed samples. Our findings offer a direct and reliable reference to the diversity of microbial communities in the presence of extremely high Sb concentrations, and may have potential implications for in situ bioremediation strategies of Sb contaminated sites. PMID:26820933

  9. Interactions Between Serpentinization, Hydrothermal Activity and Microbial Community at the Lost City Hydrothermal Field

    NASA Astrophysics Data System (ADS)

    Delacour, A.; Frueh-Green, G. L.; Bernasconi, S. M.; Schaeffer, P.; Frank, M.; Gutjahr, M.; Kelley, D. S.

    2008-12-01

    propose that the high seawater fluxes in the basement rocks favour the transport of marine organic carbon in the serpentinites and overprint any earlier abiotic signature. Serpentinites forming the basement of active hydrothermal chimneys have carbon and sulfur signatures, i.e. negative S-isotope compositions and high content of squalane biomarker, reflecting the influence of microbial activity in the subseafloor. Our geochemical study of the basement rocks, based on multiple isotopic systems, reveals the close relationships and reciprocal interactions between serpentinization, hydrothermal activity, and microbial community at Lost City. In addition, it sheds new light on the consequences of long-lived peridotite-hosted hydrothermal system on the chemical compositions of the oceanic lithosphere and global geochemical cycles.

  10. The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community.

    PubMed

    Guo, Xiaokan; Boedicker, James Q

    2016-09-01

    The activity of a biological community is the outcome of complex processes involving interactions between community members. It is often unclear how to accurately incorporate these interactions into predictive models. Previous work has shown a range of positive and negative metabolic pairwise interactions between species. Here we examine the ability of a modified general Lotka-Volterra model with cell-cell interaction coefficients to predict the overall metabolic rate of a well-mixed microbial community comprised of four heterotrophic natural isolates, experimentally quantifying the strengths of two, three, and four-species interactions. Within this community, interactions between any pair of microbial species were positive, while higher-order interactions, between 3 or more microbial species, slightly modulated community metabolism. For this simple community, the metabolic rate of can be well predicted only with taking into account pairwise interactions. Simulations using the experimentally determined interaction parameters revealed that spatial heterogeneity in the distribution of cells increased the importance of multispecies interactions in dictating function at both the local and global scales. PMID:27623159

  11. Microbial community composition and enzyme activities in cryoturbated arctic soils are controlled by environmental parameters rather than by soil organic matter properties

    NASA Astrophysics Data System (ADS)

    Schnecker, Jörg; Wild, Birgit; Hofhansl, Florian; Eloy Alves, Ricardo J.; Bárta, Jiří; Čapek, Petr; Fuchslueger, Lucia; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Lashchinskiy, Nikolay; Mikutta, Robert; Šantrůčková, Hana; Shibistova, Olga; Knoltsch, Anna; Takriti, Mounir; Urich, Tim; Richter, Andreas

    2014-05-01

    Enzyme-mediated decomposition of soil organic matter (SOM) is controlled by environmental parameters (i.e. temperature, moisture, pH) and organic matter properties. The role of these factors as well as the role of microbial community composition and therefore the main drivers of enzymatic decomposition of SOM are largely unknown, since all of these factors are often intercorrelated. We investigated soils from three regions in the Siberian Arctic, where carbon rich topsoil material has been incorporated into the subsoil (cryoturbation). We took advantage of this combination of topsoil organic matter and subsoil environmental conditions, to identify controls on microbial community composition and enzyme activities. We found that microbial community composition (estimated by phospholipid fatty acids analysis), was similar in cryoturbated OM and in surrounding subsoil, although C and N content were similar in cryoturbated material and topsoils. These results suggest that physical conditions rather than SOM properties shaped microbial community composition. To identify direct and indirect drivers of extracellular enzyme activities (cellobiohydrolase, leucine-amino-peptidase and phenoloxidase) we included microbial community composition, C, N and clay content, as well as pH in structural equation models. Models for regular horizons (excluding cryoturbated material), showed that enzyme activities were mainly controlled by C or N. Microbial community composition had no effect. In contrast models for cryoturbated OM, where the microbial community was adapted to subsoil environmental conditions, showed that enzyme activities were also related to microbial community composition. This indicates enzyme activities and more general decomposition to be limited by microbial community composition in cryoturbated organic matter, rather than by the availability of the substrates. The controlling cascade of physical parameters over microbial community composition to enzyme activities

  12. Effects of different bulking agents on the maturity, enzymatic activity, and microbial community functional diversity of kitchen waste compost.

    PubMed

    Wang, Xiaojuan; Zhang, Wenwei; Gu, Jie; Gao, Hua; Qin, Qingjun

    2016-10-01

    Aerobic composting is an effective method for the disposal and utilization of kitchen waste. However, the addition of a bulking agent is necessary during kitchen waste composting because of its high moisture content and low C/N ratio. In order to select a suitable bulking agent, we investigated the influence of leaf litter (LL), sawdust (SD), and wheat straw (WS) on the enzymatic activity, microbial community functional diversity, and maturity indices during the kitchen waste composting process. The results showed that the addition of WS yielded the highest maturity (the C/N ratio decreased from 25 to 13, T value = 0.5, and germination index (GI) = 114.7%), whereas the compost containing SD as a bulking agent had the lowest maturity (GI = 32.4%). The maximum cellulase and urease activities were observed with the WS treatment on day 8, whereas the SD treatment had the lowest cellulase activity and the LL treatment had the lowest urease activity. The compost temperature and microbial activity (as the average well color development) showed that bulking the composts with SD prolonged the composting process. The diversity index based on the community-level physiological profile showed that the composts bulked with LL and WS had greater microbial community functional diversity compared with those bulked with SD. Thus, the maturity indexes and enzymatic activities suggest that WS is a suitable bulking agent for use in kitchen waste composting systems. PMID:26895274

  13. Alternations of Structure and Functional Activity of Below Ground Microbial Communities at Elevated Atmospheric Carbon Dioxide

    SciTech Connect

    He, Zhili; Xu, Meiying; Deng, Ye; Kang, Sanghoon; Wu, Liyou; Van Nostrand, Joy D.; Hobbie, Sarah E.; Reich, Peter B.; Zhou, Jizhong

    2010-05-17

    The global atmospheric concentration of CO2 has increased by more than 30percent since the industrial revolution. Although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity have been well studied, its influences on belowground microbial communities are poorly understood and controversial. In this study, we showed a significant change in the structure and functional potential of soil microbial communities at eCO2 in a grassland ecosystem, the BioCON (Biodiversity, CO2 and Nitrogen) experimental site (http://www.biocon.umn.edu/) using a comprehensive functional gene array, GeoChip 3.0, which contains about 28,0000 probes and covers approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles as well as other functional processes. GeoChip data indicated that the functional structure of microbial communities was markedly different between ambient CO2 (aCO2) and eCO2 by detrended correspondence analysis (DCA) of all 5001 detected functional gene probes although no significant differences were detected in the overall microbial diversity. A further analysis of 1503 detected functional genes involved in C, N, P, and S cycles showed that a considerable portion (39percent) of them were only detected under either aCO2 (14percent) or eCO2 (25percent), indicating that the functional characteristics of the microbial community were significantly altered by eCO2. Also, for those shared genes (61percent) detected, some significantly (p<0.05) changed their abundance at eCO2. Especially, genes involved in labile C degradation, such as amyA, egl, and ara for starch, cellulose, and hemicelluloses, respectively, C fixation (e.g., rbcL, pcc/acc), N fixation (nifH), and phosphorus utilization (ppx) were significantly increased under eCO2, while those involved in decomposing recalcitrant C, such as glx, lip, and mnp for lignin degradation remained unchanged. This study provides insights

  14. Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

    PubMed

    Zheng, Lu; Gao, Naiyun; Deng, Yang

    2012-01-01

    It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples. PMID:22629615

  15. Microbial community analysis during continuous fermentation of thermally hydrolysed waste activated sludge.

    PubMed

    Cirne, D G; Bond, P; Pratt, S; Lant, P; Batstone, D J

    2012-01-01

    Acidogenic fermentation of thermally hydrolysed waste activated sludge was carried out at laboratory scale in two reactors operated under different hydraulic retention times (HRT). Process performance was assessed in terms of volatile fatty acid (VFA) composition and yield. The diversity of the microbial population was investigated by constructing a 16S rRNA gene library and subsequent phylogenetic analysis of clones. Fluorescence in situ hybridization (FISH) was used to assess the relative abundance of different bacterial groups. Bacteroidetes and Firmicutes were the dominant taxonomic groups representing 93% of the total sequences obtained in the reactor with 4 d HRT. A similar VFA yield (0.4-0.5 g VFA(COD) g SCOD(-1)) was obtained for the HRTs tested (1-4 d), indicating that extended retention times were not useful. Within Firmicutes, Clostridia was the major group detected in the clone sequences. These had close affiliation to Sporanaerobacter acetigenes, suggesting organisms of this group were important for hydrolysis of the protein fraction of the substrate. However, FISH analysis failed to detect the major portion of the bacteria, and this is most likely due to the lack of appropriate probes. This work emphasizes the diversity of fermentative communities, and indicates that more work is needed to identify and detect the important members. PMID:22173402

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

    PubMed Central

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS. PMID:25560234

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

    NASA Astrophysics Data System (ADS)

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS.

  18. (A)synchronous Availabilities of N and P Regulate the Activity and Structure of the Microbial Decomposer Community

    PubMed Central

    Fanin, Nicolas; Hättenschwiler, Stephan; Chavez Soria, Paola F.; Fromin, Nathalie

    2016-01-01

    Nitrogen (N) and phosphorus (P) availability both control microbial decomposers and litter decomposition. However, these two key nutrients show distinct release patterns from decomposing litter and are unlikely available at the same time in most ecosystems. Little is known about how temporal differences in N and P availability affect decomposers and litter decomposition, which may be particularly critical for tropical rainforests growing on old and nutrient-impoverished soils. Here we used three chemically contrasted leaf litter substrates and cellulose paper as a widely accessible substrate containing no nutrients to test the effects of temporal differences in N and P availability in a microcosm experiment under fully controlled conditions. We measured substrate mass loss, microbial activity (by substrate induced respiration, SIR) as well as microbial community structure (using phospholipid fatty acids, PLFAs) in the litter and the underlying soil throughout the initial stages of decomposition. We generally found a stronger stimulation of substrate mass loss and microbial respiration, especially for cellulose, with simultaneous NP addition compared to a temporally separated N and P addition. However, litter types with a relatively high N to P availability responded more to initial P than N addition and vice versa. A third litter species showed no response to fertilization regardless of the sequence of addition, likely due to strong C limitation. Microbial community structure in the litter was strongly influenced by the fertilization sequence. In particular, the fungi to bacteria ratio increased following N addition alone, a shift that was reversed with complementary P addition. Opposite to the litter layer microorganisms, the soil microbial community structure was more strongly influenced by the identity of the decomposing substrate than by fertilization treatments, reinforcing the idea that C availability can strongly constrain decomposer communities

  19. (A)synchronous Availabilities of N and P Regulate the Activity and Structure of the Microbial Decomposer Community.

    PubMed

    Fanin, Nicolas; Hättenschwiler, Stephan; Chavez Soria, Paola F; Fromin, Nathalie

    2015-01-01

    Nitrogen (N) and phosphorus (P) availability both control microbial decomposers and litter decomposition. However, these two key nutrients show distinct release patterns from decomposing litter and are unlikely available at the same time in most ecosystems. Little is known about how temporal differences in N and P availability affect decomposers and litter decomposition, which may be particularly critical for tropical rainforests growing on old and nutrient-impoverished soils. Here we used three chemically contrasted leaf litter substrates and cellulose paper as a widely accessible substrate containing no nutrients to test the effects of temporal differences in N and P availability in a microcosm experiment under fully controlled conditions. We measured substrate mass loss, microbial activity (by substrate induced respiration, SIR) as well as microbial community structure (using phospholipid fatty acids, PLFAs) in the litter and the underlying soil throughout the initial stages of decomposition. We generally found a stronger stimulation of substrate mass loss and microbial respiration, especially for cellulose, with simultaneous NP addition compared to a temporally separated N and P addition. However, litter types with a relatively high N to P availability responded more to initial P than N addition and vice versa. A third litter species showed no response to fertilization regardless of the sequence of addition, likely due to strong C limitation. Microbial community structure in the litter was strongly influenced by the fertilization sequence. In particular, the fungi to bacteria ratio increased following N addition alone, a shift that was reversed with complementary P addition. Opposite to the litter layer microorganisms, the soil microbial community structure was more strongly influenced by the identity of the decomposing substrate than by fertilization treatments, reinforcing the idea that C availability can strongly constrain decomposer communities

  20. Responses of soil microbial communities and enzyme activities to nitrogen and phosphorus additions in Chinese fir plantations of subtropical China

    NASA Astrophysics Data System (ADS)

    Dong, W. Y.; Zhang, X. Y.; Liu, X. Y.; Fu, X. L.; Chen, F. S.; Wang, H. M.; Sun, X. M.; Wen, X. F.

    2015-09-01

    Nitrogen (N) and phosphorus (P) additions to forest ecosystems are known to influence various above-ground properties, such as plant productivity and composition, and below-ground properties, such as soil nutrient cycling. However, our understanding of how soil microbial communities and their functions respond to nutrient additions in subtropical plantations is still not complete. In this study, we added N and P to Chinese fir plantations in subtropical China to examine how nutrient additions influenced soil microbial community composition and enzyme activities. The results showed that most soil microbial properties were responsive to N and/or P additions, but responses often varied depending on the nutrient added and the quantity added. For instance, there were more than 30 % greater increases in the activities of β-glucosidase (βG) and N-acetyl-β-D-glucosaminidase (NAG) in the treatments that received nutrient additions compared to the control plot, whereas acid phosphatase (aP) activity was always higher (57 and 71 %, respectively) in the P treatment. N and P additions greatly enhanced the phospholipid fatty acids (PLFAs) abundance especially in the N2P (100 kg ha-1 yr-1 of N +50 kg ha-1 yr-1 of P) treatment; the bacterial PLFAs (bacPLFAs), fungal PLFAs (funPLFAs) and actinomycic PLFAs (actPLFAs) were about 2.5, 3 and 4 times higher, respectively, than in the CK (control). Soil enzyme activities were noticeably higher in November than in July, mainly due to seasonal differences in soil moisture content (SMC). βG or NAG activities were significantly and positively correlated with microbial PLFAs. These findings indicate that βG and NAG would be useful tools for assessing the biogeochemical transformation and metabolic activity of soil microbes. We recommend combined additions of N and P fertilizer to promote soil fertility and microbial activity in this kind of plantation.

  1. Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau.

    PubMed

    Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Zhou, Huakun; Ganjurjav, Hasbagan; Wang, Xuexia

    2016-08-15

    Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems. PMID:27100015

  2. Microbial community distribution and extracellular enzyme activities in leach bed reactor treating food waste: effect of different leachate recirculation practices.

    PubMed

    Xu, Su Yun; Karthikeyan, Obuli P; Selvam, Ammaiyappan; Wong, Jonathan W C

    2014-09-01

    This study aimed at understanding the relationship between microbial community and extracellular enzyme activities of leach bed reactor (LBR) treating food waste under different leachate recirculation practices (once per day and continuous) and liquid to solid (L/S) ratios (1:1 and 0.5:1). Microbial community analysis using PCR-DGGE revealed that Lactobacillus sp., Bifidobacter sp., and Proteobacteria were the most abundant species. Number of phylotypes was higher in LBRs with intermittent recirculation; whereas, lower number of phylotypes dominated by the key players of degradation was observed with continuous recirculation. The L/S ratio of 1:1 significantly enhanced the volatile solids removal compared with 0.5:1; however, this effect was insignificant under once a day leachate recirculation. Continuous leachate recirculation with 1:1 L/S ratio significantly improved the organic leaching (240 g COD/kgvolatile solid) and showed distinct extracellular enzyme activities suitable for food waste acidogenesis. PMID:24972915

  3. Effect of cassava mill effluent on biological activity of soil microbial community.

    PubMed

    Igbinosa, Etinosa O

    2015-07-01

    This study assessed the effect of cassava effluent on soil microbiological characteristics and enzymatic activities were investigated in soil samples. Soil properties and heavy metal concentrations were evaluated using standard soil analytical and spectroscopic methods, respectively. The microbiological parameters measured include microbial biomass carbon, basal soil respiration, catalase, urease, dehydrogenase activities and number of culturable aerobic bacteria, fungi and actinomycetes. The pH and temperature regime vary significantly (p < 0.05) throughout the study period. All other physicochemical parameters studied were significantly different (p < 0.05) higher than the control site. Soil organic carbon content gave significant positive correlations with microbial biomass carbon, basal soil respiration, catalase activity and dehydrogenase activity (r = 0.450, 0.461, 0.574 and 0.591 at p < 0.01), respectively. The quantitative analysis of soil microbial density demonstrates a marked decrease in total culturable numbers of the different microbial groups of the polluted soil samples. Soil contamination decreased catalase, urease and dehydrogenase activities. The findings revealed that soil enzymes can be used as indices of soil contamination and bio-indicator of soil quality. PMID:26055654

  4. Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

    PubMed Central

    Yanagawa, Katsunori; Morono, Yuki; de Beer, Dirk; Haeckel, Matthias; Sunamura, Michinari; Futagami, Taiki; Hoshino, Tatsuhiko; Terada, Takeshi; Nakamura, Ko-ichi; Urabe, Tetsuro; Rehder, Gregor; Boetius, Antje; Inagaki, Fumio

    2013-01-01

    Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and p

  5. Metabolically active microbial communities in marine sediment under high-CO(2) and low-pH extremes.

    PubMed

    Yanagawa, Katsunori; Morono, Yuki; de Beer, Dirk; Haeckel, Matthias; Sunamura, Michinari; Futagami, Taiki; Hoshino, Tatsuhiko; Terada, Takeshi; Nakamura, Ko-Ichi; Urabe, Tetsuro; Rehder, Gregor; Boetius, Antje; Inagaki, Fumio

    2013-03-01

    Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO(2) in the seabed. The emission of CO(2) may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO(2) and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO(2)-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO(2) concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO(2) concentration, indicating that microbial activity and community structure are sensitive to CO(2) venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13-30 cm in depth) characterized by high CO(2). Measurement of the potential sulfate reduction rate at pH conditions of 3-9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO(2)-seep sedimentary environment; however

  6. Interchange of entire communities: microbial community coalescence.

    PubMed

    Rillig, Matthias C; Antonovics, Janis; Caruso, Tancredi; Lehmann, Anika; Powell, Jeff R; Veresoglou, Stavros D; Verbruggen, Erik

    2015-08-01

    Microbial communities are enigmatically diverse. We propose a novel view of processes likely affecting microbial assemblages, which could be viewed as the Great American Interchange en miniature: the wholesale exchange among microbial communities resulting from moving pieces of the environment containing entire assemblages. Incidental evidence for such 'community coalescence' is accumulating, but such processes are rarely studied, likely because of the absence of suitable terminology or a conceptual framework. We provide the nucleus for such a conceptual foundation for the study of community coalescence, examining factors shaping these events, links to bodies of ecological theory, and we suggest modeling approaches for understanding coalescent communities. We argue for the systematic study of community coalescence because of important functional and applied consequences. PMID:26111582

  7. Biodiversity and fermentative activity of caecal microbial communities in wild and farm rabbits from Spain.

    PubMed

    Abecia, L; Rodríguez-Romero, N; Yañez-Ruiz, D R; Fondevila, M

    2012-06-01

    In order to study the microbial caecal ecosystem of wild and domestic rabbits through the fermentation characteristics and concentration and diversity of bacterial and archaeal communities, caecal samples from sixteen wild rabbits (WR) were contrasted with two groups (n = 4) of farm rabbits receiving low (LSF) or high (HSF) soluble fibre diets from 28 (weaning) to 51 days of age. DNA was extracted for quantifying bacteria and Archaea by qPCR and for biodiversity analysis of microbial communities by DGGE. Samples from WR had lower caecal pH and ammonia and higher volatile fatty acids concentration than farm animals. Lower acetate and higher butyrate proportions were detected in WR. Bacterial and archaeal DGGE profiles were clearly different between wild and farm rabbits, and diet-affected population of farm rabbits. Similarity index of bacteria was lower than 0.40 among WR, and 0.52 among farm rabbits. In conclusion, caecal fermentation characteristics differ between wild and farm rabbits, which harbour clearly different bacterial and archaeal communities. In farm rabbits, diversity is influenced by the dietary level of soluble fibre. PMID:22561060

  8. 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

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

    PubMed

    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

  10. Coarse Woody Debris Increases Microbial Community Functional Diversity but not Enzyme Activities in Reclaimed Oil Sands Soils.

    PubMed

    Kwak, Jin-Hyeob; Chang, Scott X; Naeth, M Anne; Schaaf, Wolfgang

    2015-01-01

    Forest floor mineral soil mix (FMM) and peat mineral soil mix (PMM) are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD) can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP) and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM) × 2 (near CWD vs away from CWD) factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen) CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05) in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05) near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01) according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05) but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates) in both cover soils (p<0.05) in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05) regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining. PMID:26618605

  11. Coarse Woody Debris Increases Microbial Community Functional Diversity but not Enzyme Activities in Reclaimed Oil Sands Soils

    PubMed Central

    Kwak, Jin-Hyeob; Chang, Scott X.; Naeth, M. Anne; Schaaf, Wolfgang

    2015-01-01

    Forest floor mineral soil mix (FMM) and peat mineral soil mix (PMM) are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD) can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP) and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM) × 2 (near CWD vs away from CWD) factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen) CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05) in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05) near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01) according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05) but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates) in both cover soils (p<0.05) in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05) regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining. PMID:26618605

  12. 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.

  13. Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

    PubMed Central

    Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B.; Gaju, Nuria; Cazorla, Francisco M.

    2015-01-01

    One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. PMID:25769825

  14. Organic amendments to avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities.

    PubMed

    Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B; Gaju, Nuria; Cazorla, Francisco M; de Vicente, Antonio

    2015-05-15

    One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. PMID:25769825

  15. Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest

    PubMed Central

    Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W; Wickland, Kimberley P; Knight, Rob; Berhe, Asmeret Asefaw; Jorgenson, Torre; Waldrop, Mark P; Jansson, Janet K

    2014-01-01

    Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG—CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle. PMID:24722629

  16. Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest.

    PubMed

    Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W; Wickland, Kimberley P; Knight, Rob; Berhe, Asmeret Asefaw; Jorgenson, Torre; Waldrop, Mark P; Jansson, Janet K

    2014-09-01

    Permafrost soils are large reservoirs of potentially labile carbon (C). Understanding the dynamics of C release from these soils requires us to account for the impact of wildfires, which are increasing in frequency as the climate changes. Boreal wildfires contribute to global emission of greenhouse gases (GHG-CO2, CH4 and N2O) and indirectly result in the thawing of near-surface permafrost. In this study, we aimed to define the impact of fire on soil microbial communities and metabolic potential for GHG fluxes in samples collected up to 1 m depth from an upland black spruce forest near Nome Creek, Alaska. We measured geochemistry, GHG fluxes, potential soil enzyme activities and microbial community structure via 16SrRNA gene and metagenome sequencing. We found that soil moisture, C content and the potential for respiration were reduced by fire, as were microbial community diversity and metabolic potential. There were shifts in dominance of several microbial community members, including a higher abundance of candidate phylum AD3 after fire. The metagenome data showed that fire had a pervasive impact on genes involved in carbohydrate metabolism, methanogenesis and the nitrogen cycle. Although fire resulted in an immediate release of CO2 from surface soils, our results suggest that the potential for emission of GHG was ultimately reduced at all soil depths over the longer term. Because of the size of the permafrost C reservoir, these results are crucial for understanding whether fire produces a positive or negative feedback loop contributing to the global C cycle. PMID:24722629

  17. Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep

    PubMed Central

    Lloyd, Karen G.; Albert, Daniel B.; Biddle, Jennifer F.; Chanton, Jeffrey P.; Pizarro, Oscar; Teske, Andreas

    2010-01-01

    Background Subsurface fluids from deep-sea hydrocarbon seeps undergo methane- and sulfur-cycling microbial transformations near the sediment surface. Hydrocarbon seep habitats are naturally patchy, with a mosaic of active seep sediments and non-seep sediments. Microbial community shifts and changing activity patterns on small spatial scales from seep to non-seep sediment remain to be examined in a comprehensive habitat study. Methodology/Principal Findings We conducted a transect of biogeochemical measurements and gene expression related to methane- and sulfur-cycling at different sediment depths across a broad Beggiatoa spp. mat at Mississippi Canyon 118 (MC118) in the Gulf of Mexico. High process rates within the mat (∼400 cm and ∼10 cm from the mat's edge) contrasted with sharply diminished activity at ∼50 cm outside the mat, as shown by sulfate and methane concentration profiles, radiotracer rates of sulfate reduction and methane oxidation, and stable carbon isotopes. Likewise, 16S ribosomal rRNA, dsrAB (dissimilatory sulfite reductase) and mcrA (methyl coenzyme M reductase) mRNA transcripts of sulfate-reducing bacteria (Desulfobacteraceae and Desulfobulbaceae) and methane-cycling archaea (ANME-1 and ANME-2) were prevalent at the sediment surface under the mat and at its edge. Outside the mat at the surface, 16S rRNA sequences indicated mostly aerobes commonly found in seawater. The seep-related communities persisted at 12–20 cm depth inside and outside the mat. 16S rRNA transcripts and V6-tags reveal that bacterial and archaeal diversity underneath the mat are similar to each other, in contrast to oxic or microoxic habitats that have higher bacterial diversity. Conclusions/Significance The visual patchiness of microbial mats reflects sharp discontinuities in microbial community structure and activity over sub-meter spatial scales; these discontinuities have to be taken into account in geochemical and microbiological inventories of seep environments. In

  18. Systems biology of Microbial Communities

    SciTech Connect

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

    2008-04-11

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

  19. Effect of salinity tolerant PDH45 transgenic rice on physicochemical properties, enzymatic activities and microbial communities of rhizosphere soils

    PubMed Central

    Sahoo, Ranjan Kumar; Tuteja, Narendra

    2013-01-01

    The effect of genetically modified (GM) plants on environment is now major concern worldwide. The plant roots of rhizosphere soil interact with variety of bacteria which could be influenced by the transgene in GM plants. The antibiotic resistance genes in GM plants may be transferred to soil microbes. In this study we have examined the effect of overexpression of salinity tolerant pea DNA helicase 45 (PDH45) gene on microbes and enzymatic activities in the rhizosphere soil of transgenic rice IR64 in presence and absence of salt stress in two different rhizospheric soils (New Delhi and Odisha, India). The diversity of the microbial community and soil enzymes viz., dehydrogenase, alkaline phosphatase, urease and nitrate reductase was assessed. The results revealed that there was no significant effect of transgene expression on rhizosphere soil of the rice plants. The isolated bacteria were phenotyped both in absence and presence of salt and no significant changes were found in their phenotypic characters as well as in their population. Overall, the overexpression of PDH45 in rice did not cause detectable changes in the microbial population, soil enzymatic activities and functional diversity of the rhizosphere soil microbial community. PMID:23733066

  20. 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.

  1. Does iron inhibit cryptoendolithic microbial communities?

    PubMed

    Johnston, C G; Vestal, J R

    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. PMID:11538332

  2. Characterization of methane production and microbial community shifts during waste activated sludge degradation in microbial electrolysis cells.

    PubMed

    Sun, Rui; Zhou, Aijuan; Jia, Jianna; Liang, Qing; Liu, Qian; Xing, Defeng; Ren, Nanqi

    2015-01-01

    Microbial electrolysis cell (MECs) were investigated as a promising technology to manage waste activated sludge (WAS) reduction and bio-methane generation. The effect of WAS concentration on the MECs performance was discussed. At the optimal concentration of 15gCOD/L, maximum methane yield of MECs fed with alkaline pretreated WAS (A-WAS) were achieved with the value of 77.13±2.52LCH4/kg-COD on Day 3, which had been improved by 1.5-fold compared with MECs fed with raw WAS (R-WAS), while that was negligible in open circuit controls. Efficient sludge reduction was also obtained in terms of TCOD, total protein, TSS and VSS removal. Pyrosequencing revealed the dominance of exoelectrogen Geobacter and hydrogen-producing bacteria Petrimonas in MECs fed with WAS. Methanocorpusculum with the capacity of methane generation using CO2 and H2 also showed overwhelming dominance (96.01%). The large proportions of Petrimonas and Methanocorpusculum indicated the occurrence of hydrogenotrophic methanogenesis in our methane-producing MECs. PMID:25459805

  3. Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident.

    PubMed

    Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth; Greer, Charles W

    2015-09-01

    Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. PMID:26092461

  4. Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident

    PubMed Central

    Yergeau, Etienne; Maynard, Christine; Sanschagrin, Sylvie; Champagne, Julie; Juck, David; Lee, Kenneth

    2015-01-01

    Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments. PMID:26092461

  5. Impact of transgenic wheat with wheat yellow mosaic virus resistance on microbial community diversity and enzyme activity in rhizosphere soil.

    PubMed

    Wu, Jirong; Yu, Mingzheng; Xu, Jianhong; Du, Juan; Ji, Fang; Dong, Fei; Li, Xinhai; Shi, Jianrong

    2014-01-01

    The transgenic wheat line N12-1 containing the WYMV-Nib8 gene was obtained previously through particle bombardment, and it can effectively control the wheat yellow mosaic virus (WYMV) disease transmitted by Polymyxa graminis at turngreen stage. Due to insertion of an exogenous gene, the transcriptome of wheat may be altered and affect root exudates. Thus, it is important to investigate the potential environmental risk of transgenic wheat before commercial release because of potential undesirable ecological side effects. Our 2-year study at two different experimental locations was performed to analyze the impact of transgenic wheat N12-1 on bacterial and fungal community diversity in rhizosphere soil using polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE) at four growth stages (seeding stage, turngreen stage, grain-filling stage, and maturing stage). We also explored the activities of urease, sucrase and dehydrogenase in rhizosphere soil. The results showed that there was little difference in bacterial and fungal community diversity in rhizosphere soil between N12-1 and its recipient Y158 by comparing Shannon's, Simpson's diversity index and evenness (except at one or two growth stages). Regarding enzyme activity, only one significant difference was found during the maturing stage at Xinxiang in 2011 for dehydrogenase. Significant growth stage variation was observed during 2 years at two experimental locations for both soil microbial community diversity and enzyme activity. Analysis of bands from the gel for fungal community diversity showed that the majority of fungi were uncultured. The results of this study suggested that virus-resistant transgenic wheat had no adverse impact on microbial community diversity and enzyme activity in rhizosphere soil during 2 continuous years at two different experimental locations. This study provides a theoretical basis for environmental impact monitoring of transgenic wheat when the introduced gene is

  6. Impact of Transgenic Wheat with wheat yellow mosaic virus Resistance on Microbial Community Diversity and Enzyme Activity in Rhizosphere Soil

    PubMed Central

    Xu, Jianhong; Du, Juan; Ji, Fang; Dong, Fei; Li, Xinhai; Shi, Jianrong

    2014-01-01

    The transgenic wheat line N12-1 containing the WYMV-Nib8 gene was obtained previously through particle bombardment, and it can effectively control the wheat yellow mosaic virus (WYMV) disease transmitted by Polymyxa graminis at turngreen stage. Due to insertion of an exogenous gene, the transcriptome of wheat may be altered and affect root exudates. Thus, it is important to investigate the potential environmental risk of transgenic wheat before commercial release because of potential undesirable ecological side effects. Our 2-year study at two different experimental locations was performed to analyze the impact of transgenic wheat N12-1 on bacterial and fungal community diversity in rhizosphere soil using polymerase chain reaction-denaturing gel gradient electrophoresis (PCR-DGGE) at four growth stages (seeding stage, turngreen stage, grain-filling stage, and maturing stage). We also explored the activities of urease, sucrase and dehydrogenase in rhizosphere soil. The results showed that there was little difference in bacterial and fungal community diversity in rhizosphere soil between N12-1 and its recipient Y158 by comparing Shannon's, Simpson's diversity index and evenness (except at one or two growth stages). Regarding enzyme activity, only one significant difference was found during the maturing stage at Xinxiang in 2011 for dehydrogenase. Significant growth stage variation was observed during 2 years at two experimental locations for both soil microbial community diversity and enzyme activity. Analysis of bands from the gel for fungal community diversity showed that the majority of fungi were uncultured. The results of this study suggested that virus-resistant transgenic wheat had no adverse impact on microbial community diversity and enzyme activity in rhizosphere soil during 2 continuous years at two different experimental locations. This study provides a theoretical basis for environmental impact monitoring of transgenic wheat when the introduced gene is

  7. Electron donors and co-contaminants affect microbial community composition and activity in perchlorate degradation.

    PubMed

    Guan, Xiangyu; Xie, Yuxuan; Wang, Jinfeng; Wang, Jing; Liu, Fei

    2015-04-01

    Although microbial reduction of perchlorate (ClO4(-)) is a promising and effective method, our knowledge on the changes in microbial communities during ClO4(-) degradation is limited, especially when different electron donors are supplied and/or other contaminants are present. Here, we examined the effects of acetate and hydrogen as electron donors and nitrate and ammonium as co-contaminants on ClO4(-) degradation by anaerobic microcosms using six treatments. The process of degradation was divided into the lag stage (SI) and the accelerated stage (SII). Quantitative PCR was used to quantify four genes: pcrA (encoding perchlorate reductase), cld (encoding chlorite dismutase), nirS (encoding copper and cytochrome cd1 nitrite reductase), and 16S rRNA. While the degradation of ClO4(-) with acetate, nitrate, and ammonia system (PNA) was the fastest with the highest abundance of the four genes, it was the slowest in the autotrophic system (HYP). The pcrA gene accumulated in SI and played a key role in initiating the accelerated degradation of ClO4(-) when its abundance reached a peak. Degradation in SII was primarily maintained by the cld gene. Acetate inhibited the growth of perchlorate-reducing bacteria (PRB), but its effect was weakened by nitrate (NO3(-)), which promoted the growth of PRB in SI, and therefore, accelerated the ClO4(-) degradation rate. In addition, ammonia (NH4(+)), as nitrogen sources, accelerated the growth of PRB. The bacterial communities' structure and diversity were significantly affected by electron donors and co-contaminants. Under heterotrophic conditions, both ammonia and nitrate promoted Azospira as the most dominant genera, a fact that might significantly influence the rate of ClO4(-) natural attenuation by degradation. PMID:25382499

  8. Effect of a microbiota activator on accumulated ammonium and microbial community structure in a pilot-scale membrane bioreactor.

    PubMed

    Sato, Yuya; Hori, Tomoyuki; Navarro, Ronald R; Ronald, Navarro R; Habe, Hiroshi; Ogata, Atsushi

    2015-01-01

    Microbiota activators (MAs) have been used to improve the reactor performances of biological wastewater treatment processes. In this study, to remove ammonium (NH4(+)) accumulated during the pre-operation of a pilot-scale membrane bioreactor (MBR) under high-organic-loading conditions, an MA was added to the MBR system and the resulting changes in reactor performances and microbial communities were monitored for 12 days. The NH4(+) concentrations in the sludge and effluent decreased (from 427 to 246 mg/L in the sludge (days 1-9)), and mixed liquor suspended solid increased (from 6,793 to 11,283 mg/L (days 1-12)) after the addition of MA. High-throughput Illumina sequencing of 16S rRNA genes revealed that the microbial community structure changed along with the NH4(+) removal resulting from the MA addition. In particular, the relative abundance of an Acidovorax-related operational taxonomic unit (OTU) increased significantly, accounting for approximately 50% of the total microbial population at day 11. In contrast, the ammonia-oxidizing bacteria and archaea showed low abundances (<0.05%), and no anaerobic ammonia oxidizers were detected. These results suggested that the Acidovorax-related OTU was mainly involved in the NH4(+) removal in the MBR, probably due to its ammonia-assimilating metabolism. PMID:26377133

  9. Minor impact of ocean acidification to the composition of the active microbial community in an Arctic sediment.

    PubMed

    Tait, Karen; Laverock, Bonnie; Shaw, Jennifer; Somerfield, Paul J; Widdicombe, Steve

    2013-12-01

    Effects of ocean acidification on the composition of the active bacterial and archaeal community within Arctic surface sediment was analysed in detail using 16S rRNA 454 pyrosequencing. Intact sediment cores were collected and exposed to one of five different pCO(2) concentrations [380 (present day), 540, 750, 1120 and 3000 μatm] and RNA extracted after a period of 14 days exposure. Measurements of diversity and multivariate similarity indicated very little difference between pCO(2) treatments. Only when the highest and lowest pCO(2) treatments were compared were significant differences evident, namely increases in the abundance of operational taxonomic units most closely related to the Halobacteria and differences to the presence/absence structure of the Planctomycetes. The relative abundance of members of the classes Planctomycetacia and Nitrospira increased with increasing pCO(2) concentration, indicating that these groups may be able to take advantage of changing pH or pCO(2) conditions. The modest response of the active microbial communities associated with these sediments may be due to the low and fluctuating pore-water pH already experienced by sediment microbes, a result of the pH buffering capacity of marine sediments, or due to currently unknown factors. Further research is required to fully understand the impact of elevated CO(2) on sediment physicochemical parameters, biogeochemistry and microbial community dynamics. PMID:24249294

  10. 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.

  11. Response to shock load of engineered nanoparticles in an activated sludge treatment system: Insight into microbial community succession.

    PubMed

    Zhang, Jing; Dong, Qian; Liu, Yanchen; Zhou, Xiaohong; Shi, Hanchang

    2016-02-01

    The environmental impacts of the use of engineered nanoparticles (NPs) remain unclear and have attracted increasing concern worldwide. Considering that NPs eventually end up in wastewater treatment systems, the potential impact of ZnO and TiO2 NPs on the activated sludge was investigated using laboratory-scale sequencing batch reactors (SBRs). Short-term (24 h) exposure to 1, 10 and 100 mg/L shock loads of NPs reduced the oxygen uptake rate of the activated sludge by 3.55%-12.51% compared with the controls. In our experiment, the toxicities of TiO2 NPs were higher than those of ZnO NPs as reflected in the inhibition of oxygen utilization in the activated sludge. However, both the short-term (24 h) and long-term (21 days) exposure to ZnO and TiO2 NPs did not adversely affect the pollutant removal of the SBRs. Furthermore, the polymerase chain reaction-denaturing gel gradient electrophoresis revealed that the microbial community did not significantly vary after the short-term exposure (24 h) to 1, 10 and 100 mg/L shock loads of NPs; however, the cluster analysis in our experiment revealed that the slight difference caused by the NPs largely depended on exposure time rather than on NP type and NP concentration. The long-term exposure (13 days) to 10 mg/L shock load of ZnO or TiO2 NPs caused no substantial microbial community shifts in the activated sludge. The microbial diversity also showed no significant change when exposed to NPs as revealed by the Shannon-Wiener index. PMID:26539708

  12. Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge.

    PubMed

    Westerholm, Maria; Crauwels, Sam; Van Geel, Maarten; Dewil, Raf; Lievens, Bart; Appels, Lise

    2016-06-01

    Comparative analyses of bacterial and archaeal community structures and dynamics in three biogas digesters during start-up and subsequent operation using microwaved, ultrasonicated or untreated waste activated sludge were performed based on 454 pyrosequencing datasets of part of 16S ribosomal RNA sequences and quantitative PCR. The pre-treatment increased the solubility, and thus the availability of the substrate for microbial degradation and significantly affected the succession of the anaerobic community structure over the course of the digestion. Bacteroidetes, Proteobacteria and Firmicutes were the dominant phyla in all digesters throughout operation. Proteobacteria decreased in relative abundance from 23-26 % to 11-13 % in association with enhanced substrate availability. Negative correlations between relative abundance of Alpha-, Beta- and Gammaproteobacteria and the substrate availability and/or biogas production were disclosed in statistical analyses. Clostridiales was the dominant order in Firmicutes, and Clostridiales, Clostridia and Firmicutes relative abundance and richness were shown to positively correlate with substrate availability and biogas generation. Methanogenic communities had a fairly restricted structure, highly dominated by Methanosaeta and Methanobrevibacter phylotypes. A gradual decline in Methanobrevibacter and increased representation of Methanosaeta concilii over time were particularly apparent in the digester receiving untreated waste activated sludge, whereas more diversified archaeal communities were maintained in the pre-treatment digesters. The quantitative PCR analyses revealed a methanogenic community distribution that coincided with the 454 pyrosequencing data. PMID:26816092

  13. Correlating microbial community compositions with environmental factors in activated sludge from four full-scale municipal wastewater treatment plants in Shanghai, China.

    PubMed

    Gao, Pin; Xu, Wenli; Sontag, Philip; Li, Xiang; Xue, Gang; Liu, Tong; Sun, Weimin

    2016-05-01

    Activated sludge system is an important process of domestic and industrial wastewater treatment containing highly diverse microbial communities. In this study, high-throughput sequencing was applied to examine the microbial community composition and diversity of activated sludge samples from four full-scale municipal wastewater treatment plants (WWTPs) in Shanghai. A relationship between microbial communities and environmental variables was examined. Proteobacteria was the most dominant phylogenetic group, followed by Bacteroidetes and Firmicutes. A total of 166 genera were commonly shared by all seven sludge samples, including Zoogloea, Dechloromonas, Thauera, Nitrospira, Arcobacter, etc. Besides these shared populations, certain unique bacterial populations were found abundant in individual sludge sample. Canonical correspondence analysis (CCA) indicated that influent COD and pH had the greatest influence on microbial community compositions, whereas dissolved oxygen (DO) exhibited the least influence. The operating process was likely to foster diversity of the microbial communities inhabiting the wastewater treatment facilities. Alternative operation methods including a fluctuation of anoxic, oxic, and anaerobic conditions were favorable for promoting the growth of diverse microbial populations in activated sludge systems. PMID:26795962

  14. Influence of Heavy Metals and PCBs Pollution on the Enzyme Activity and Microbial Community of Paddy Soils around an E-Waste Recycling Workshop

    PubMed Central

    Tang, Xianjin; Hashmi, Muhammad Z.; Long, Dongyan; Chen, Litao; Khan, Muhammad I.; Shen, Chaofeng

    2014-01-01

    Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg−1) and Cu (69.2 mg·kg−1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg−1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination. PMID:24637907

  15. Influence of heavy metals and PCBs pollution on the enzyme activity and microbial community of paddy soils around an e-waste recycling workshop.

    PubMed

    Tang, Xianjin; Hashmi, Muhammad Z; Long, Dongyan; Chen, Litao; Khan, Muhammad I; Shen, Chaofeng

    2014-03-01

    Due to the emerging environmental issues related to e-waste there is concern about the quality of paddy soils near e-waste workshops. The levels of heavy metals and PCBs and their influence on the enzyme activity and microbial community of paddy soils obtained from the immediate vicinity of an e-waste workshop were investigated in the present study. The results indicated that the heavy metal and PCB pollution did not differ significantly with an increase of the sampling point distances (5 to 30 m). The concentration of Cd (2.16 mg·kg-1) and Cu (69.2 mg·kg-1) were higher, and the PCB pollution was also serious, ranging from 4.9 to 21.6 μg·kg-1. The highest enzyme activity was found for urease compared to phosphatase and catalase, and a fluctuating trend in soil enzyme activity was observed in soils from different sampling sites. The microbial analysis revealed that there was no apparent correlation between the microbial community and the pollutants. However, a slight influence for soil microbial communities could be found based on DGGE, the Shannon index and PCA analysis. The present study suggests that the contamination stress of heavy metals and PCBs might have a slight influence on microbial activity in paddy soils. This study provides the baseline data for enzyme activities and microbial communities in paddy soil under the influence of mixed contamination. PMID:24637907

  16. Colloid-based multiplexed method for screening plant biomass-degrading glycoside hydrolase activities in microbial communities

    SciTech Connect

    Reindl, W.; Deng, K.; Gladden, J.M.; Cheng, G.; Wong, A.; Singer, S.W.; Singh, S.; Lee, J.-C.; Yao, J.-S.; Hazen, T.C.; Singh, A.K; Simmons, B.A.; Adams, P.D.; Northen, T.R.

    2011-05-01

    The enzymatic hydrolysis of long-chain polysaccharides is a crucial step in the conversion of biomass to lignocellulosic biofuels. The identification and characterization of optimal glycoside hydrolases is dependent on enzyme activity assays, however existing methods are limited in terms of compatibility with a broad range of reaction conditions, sample complexity, and especially multiplexity. The method we present is a multiplexed approach based on Nanostructure-Initiator Mass Spectrometry (NIMS) that allowed studying several glycolytic activities in parallel under diverse assay conditions. Although the substrate analogs carried a highly hydrophobic perfluorinated tag, assays could be performed in aqueous solutions due colloid formation of the substrate molecules. We first validated our method by analyzing known {beta}-glucosidase and {beta}-xylosidase activities in single and parallel assay setups, followed by the identification and characterization of yet unknown glycoside hydrolase activities in microbial communities.

  17. Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core.

    PubMed

    Kaci, Assia; Petit, Fabienne; Fournier, Matthieu; Cécillon, Sébastien; Boust, Dominique; Lesueur, Patrick; Berthe, Thierry

    2016-03-01

    In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha-Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community. PMID:25934230

  18. Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery.

    PubMed

    Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie; Lantz, Anna Eliasson

    2015-06-01

    Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil-brine system after addition of a complex carbon source, molasses, with or without nitrate to boost microbial growth. Growth of the indigenous microbes was stimulated by addition of molasses. Pyrosequencing showed that specifically Anaerobaculum, Petrotoga, and Methanothermococcus were enriched. Addition of nitrate favored the growth of Petrotoga over Anaerobaculum. The microbial growth caused changes in the crude oil-brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil-brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs. PMID:25894951

  19. Response of soil microbial activity and community structure to land use changes in a mountain rainforest region of Southern Ecuador

    NASA Astrophysics Data System (ADS)

    Potthast, Karin; Hamer, Ute; Makeschin, Franz

    2010-05-01

    Over the past several decades the mountain rainforest region of Southern Ecuador, a hotspot of biodiversity, is undergoing a rapid conversion to pastureland through slash and burn practice. Frequently this pastureland is invaded by the tropical bracken fern. When the bracken becomes dominant on the pasture sites the productivity decreases and the sites are abandoned. To assess the effect of these land use changes on nutrient turnover and on ecosystem functioning, a study was conducted in the area of the German research station Estación Científica San Francisco (ECSF) in Southern Ecuador. At 2000 m above sea level three adjacent sites were selected: a mountain rainforest site, an active pasture site dominated by the grass species Setaria sphacelata and an abandoned pasture site overgrown by bracken. Mineral soil samples of all three sites (0-5, 5-10 and 10-20 cm) as well as samples from the organic layer (Oi and Oa) of the natural forest site were taken to analyze biogeochemical properties. Besides pH-value, total organic C and N contents, the amounts of microbial biomass (CFE-method), microbial activity (basal respiration, net N mineralization (KCl-extraction); gross N mineralization (15N dilution technique) rates) and microbial community structure (PLFA-analysis) were determined. 17 years after pasture establishment, twofold higher stocks of soil microbial biomass carbon (Cmic) and nitrogen (Nmic) as well as significant lower C:N ratios were determined compared to the natural forest including the 11 cm thick organic layer. 10 years after bracken invasion and pasture abandonment the microbial biomass (Cmic) decreased and the C:N ratio increased again to forest levels. Generally, land use change from forest to pasture and from pasture to abandoned pasture induced shifts in the soil microbial community structure. The relative abundance of the fast growing copiotrophic Gram(-) bacteria was positively correlated with the amounts of readily available organic carbon

  20. Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community

    SciTech Connect

    Verberkmoes, Nathan C; Singer, Steven; Shah, Manesh B; Thelen, Michael P.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2008-01-01

    We have discovered and characterized a novel membrane cytochrome of an iron oxidizing microbial biofilm obtained from the surface of extremely acidic mine water. This protein was initially identified through proteogenomic analysis as one of many novel gene products of Leptospirillum group II, the dominant bacterium of this community (Ram et al, 2005, Science 308, 1915-20). Extraction of proteins directly from environmental biofilm samples followed by membrane fractionation, detergent solubilization and gel filtration chromatography resulted in the purification of an abundant yellow-red protein. Covalently bound to heme, the purified cytochrome has a unique spectral signature at 572 nm and is thus called Cyt572. It readily oxidizes Fe2+ even in the presence of Fe3+ over a pH range from 0.95 to 3.4. Independent experiments involving 2D blue-native polyacrylamide gel electrophoresis and chemical crosslinking establish a homotetrameric structure for Cyt572. Also, circular dichroism spectroscopy indicates that the protein is largely beta-stranded, consistent with an outer membrane location. Although no significant sequence homology to the full-length cytochrome is detected in protein databases, environmental DNA sequences from both Leptospirillum groups II and III reveal at least 17 strain variants of Cyt572. Due to its abundance, cellular location and Fe2+ oxidation activity, we propose Cyt572 is the iron oxidase of the Leptospirillum bacteria, providing a critical function for fitness within the ecological niche of this acidophilic microbial community.

  1. Unraveling characteristics of nutrient removal and microbial community in a novel aerated landscape - Activated sludge ecological system.

    PubMed

    Hong, Jun-Ming; Hu, Miao-Miao; Sun, Rong; Chen, Bor-Yann

    2016-07-01

    In this study, a novel landscape-activated sludge ecological system (LASeM) was constructed with the advantages of promising treatment, less land need and significant landscape services. Compared to literature, this study provided promising integrated wastewater treatment and landscape for wastewater treatment. This first-attempt study clearly deciphered interactive effect of aeration rate (AR) on nutrient removal and microbial community structure in LASeM. When AR was 0.016m(3)h(-1), the most appropriate removal of COD, NH4(+)-N and TP were 96%, 97% and 74% with the effluent of 14.3, 1.7 and 0.7mgL(-1), respectively, which showed satisfactory capabilities for rural domestic wastewater treatment. According to clone library analysis, Proteobacteria (71%), Bacteroidetes (17%) were found to be the dominant bacterial phylums present in LASeM for biodegradation. In particular, the incorporation of plants altered the microbial community and strengthened capability for the nutrients removal likely due to synergistic interactions among species in the ecosystem. PMID:27111873

  2. 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.

  3. Belowground carbon allocation by trees drives seasonal patterns of extracellular enzyme activities by altering microbial community composition in a beech forest soil

    PubMed Central

    Kaiser, Christina; Koranda, Marianne; Kitzler, Barbara; Fuchslueger, Lucia; Schnecker, Jörg; Schweiger, Peter; Rasche, Frank; Zechmeister-Boltenstern, Sophie; Sessitsch, Angela; Richter, Andreas

    2010-01-01

    Plant seasonal cycles alter carbon (C) and nitrogen (N) availability for soil microbes, which may affect microbial community composition and thus feed back on microbial decomposition of soil organic material and plant N availability. The temporal dynamics of these plant–soil interactions are, however, unclear. Here, we experimentally manipulated the C and N availability in a beech forest through N fertilization or tree girdling and conducted a detailed analysis of the seasonal pattern of microbial community composition and decomposition processes over 2 yr. We found a strong relationship between microbial community composition and enzyme activities over the seasonal course. Phenoloxidase and peroxidase activities were highest during late summer, whereas cellulase and protease peaked in late autumn. Girdling, and thus loss of mycorrhiza, resulted in an increase in soil organic matter-degrading enzymes and a decrease in cellulase and protease activity. Temporal changes in enzyme activities suggest a switch of the main substrate for decomposition between summer (soil organic matter) and autumn (plant litter). Our results indicate that ectomycorrhizal fungi are possibly involved in autumn cellulase and protease activity. Our study shows that, through belowground C allocation, trees significantly alter soil microbial communities, which may affect seasonal patterns of decomposition processes. PMID:20553392

  4. Effects of slow-release urea fertilizers on urease activity, microbial biomass, and nematode communities in an aquic brown soil.

    PubMed

    Jiao, Xiaoguang; Liang, Wenju; Chen, Lijun; Zhang, Haijun; Li, Qi; Wang, Peng; Wen, Dazhong

    2005-05-01

    A field experiment was carried out at the Shenyang Experimental Station of Ecology (CAS) in order to study the effects of slow-release urea fertilizers high polymer-coated urea (SRU1), SRU1 mixed with dicyandiamide DCD (SRU2), and SRU1 mixed with calcium carbide CaC2 (SRU3) on urease activity, microbial biomass C and N, and nematode communities in an aquic brown soil during the maize growth period. The results demonstrated that the application of slow-release urea fertilizers inhibits soil urease activity and increases the soil NH4+-N content. Soil available N increment could promote its immobilization by microorganisms. Determination of soil microbial biomass N indicated that a combined application of coated urea and nitrification inhibitors increased the soil active N pool. The population of predators/omnivores indicated that treatment with SRU2 could provide enough soil NH4+-N to promote maize growth and increased the food resource for the soil fauna compared with the other treatments. PMID:16089326

  5. Microbial community structure and biodegradation activity of particle-associated bacteria in a coal tar contaminated creek

    SciTech Connect

    Jennifer M. DeBruyn; Gary S. Sayler

    2009-05-01

    The Chattanooga Creek Superfund site (Chattanooga, TN) is one of the most polluted waterways in the southeastern U.S. with high polycyclic aromatic hydrocarbon (PAH) concentrations in the sediments. PAHs associate with suspended solids in the water column, and may be redeposited onto the floodplain. These suspended particles represent an interesting but understudied environment for PAH-degrading microbial communities. This study tested the hypotheses that particle-associated bacterial (PAB) communities have genotypic potential (PAH-dioxygenase genes) and activity (naphthalene and pyrene mineralization), and can contribute to natural attenuation of PAHs in Chattanooga Creek. Upstream of the Superfund site, mineralization ranged from 0.2 to 2.0% of added {sup 14}C-naphthalene and 0 to 0.1% {sup 14}C-pyrene (after 40 h), with first order biodegradation rate constants (k{sub 1}) ranging from 1.09 to 9.18 x 10{sup -5} h{sup -1} and 0 to 1.13 x 10{sup -6} h{sup -1}, respectively. Mineralization was significantly greater in PAB communities within the contaminated zone, with 11.8 to 31.2% {sup 14}C-naphthalene (k{sup 1} 5.34 to 14.2 x 10-4 h{sup -1}) and 1.3 to 6.6% {sup 14}C-pyrene mineralized (k{sub 1} 2.89 to 15.0 x 10{sup -5} h{sup -1}). Abundances of nagAc (naphthalene dioxygenase) and nidA (pyrene dioxygenase) genes indicated that PAB communities harbored populations with genetic potential for both low- and high-molecular weight PAH degradation, and quantification of Mycobacterium 16S rDNA genes indicated that PAH-degrading mycobacteria are also prevalent in this environment. Phylogenetic comparisons (T-RFLPs) between PAB and sediments indicated these microbial communities were taxonomically distinct, but shared some functional similarities, namely PAH catabolic genotypes, mineralization capabilities, and community structuring along a contamination gradient. 38 refs., 4 figs., 2 tabs.

  6. 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

  7. Microbial community and metabolism activity in a bioelectrochemical denitrification system under long-term presence of p-nitrophenol.

    PubMed

    Chen, Dan; Yang, Kai; Wei, Li; Wang, Hongyu

    2016-10-01

    Bioelectrochemical denitrification system (BEDS) is a promising technology for nitrate removal from wastewaters. The hazards and effects concerning p-nitrophenol (PNP) towards BEDS lack enough investigations and possess great research prospects. This study investigated how PNP affected the nitrate removal efficiency, microbial communities, functional denitrifying genes abundances, nitrate and nitrite reductase activities, diffusible signal factors (DSF) release, and extracellular polymeric substances (EPS) production in the BEDS. Results indicated that nitrate removal efficiency decreased with initial PNP concentration increased from 0 to 100mg/L. Phylum Firmicutes and class Clostridia were the main contributors for denitrification process in this BEDS. The abundances of the denitrifying genes nirS, nirK, napA, and narG all presented decreased trends with increasing PNP. In addition, the concentrations of nitrate reductase (NR), nitrite reductase (NIR), and EPS obviously decreased, while the concentration of DSF increased with increasing PNP, which demonstrated that higher PNP would inhibit the biofilm formation. PMID:27367815

  8. Microbial biomass, activity, and community structure of water and particulates retrieved by backflow from a waterflood injection well.

    PubMed

    McKinley, V L; Costerton, J W; White, D C

    1988-06-01

    Oil field injection water was allowed to back flow from two wells at the Packard drill site in Los Angeles, Calif., and was sampled at various times to obtain information about the biomass, potential activity, and community structure of the microbiota in the reservoir formation and in the injection water. Biomass was greatest in water samples that came from the zone near the injection site and dropped off sharply in subsequent samples, which were assumed to come from zones farther away from the well. Samples obtained from near the well also had visible exopolysaccharide blankets, as seen in scanning electron microscopic preparations. In one of the wells that was sampled, rates of glucose or acetate incorporation into microbial lipids correlated with biomass; but in the other well, activities correlated with the sampling time (volume of water that back flowed). Transmission electron micrographs showed a diverse, gram-negative bacterial population in a variety of physiological states. The analysis of the phospholipid ester-linked fatty acid profiles of the samples revealed consistently large proportions of 18:1omega7c fatty acids, indicating the presence of many anaerobes, facultative organisms, or both. Proportions of cyclopropyl fatty acids and ratios of trans/cis monoenoic compounds increased with the volume of water that back flowed (analogous with the distance into the formation), while the ratio of unsaturated/saturated compounds decreased, possibly indicating higher levels of stress or starvation in the microbial communities farthest from the injection well. Greater than 90% of the total biomass was trapped on glass fiber filters, indicating that the microbiota were largely attached to particles or were clumped. These sampling techniques and analytical methods may prove useful in monitoring for problems with microbes (e.g., plugging) in waterflood operations and in the preparation of water injection wells for enhanced oil recovery by the use of microbes. PMID

  9. Microbial Biomass, Activity, and Community Structure of Water and Particulates Retrieved by Backflow from a Waterflood Injection Well

    PubMed Central

    McKinley, Vicky L.; Costerton, J. William; White, David C.

    1988-01-01

    Oil field injection water was allowed to back flow from two wells at the Packard drill site in Los Angeles, Calif., and was sampled at various times to obtain information about the biomass, potential activity, and community structure of the microbiota in the reservoir formation and in the injection water. Biomass was greatest in water samples that came from the zone near the injection site and dropped off sharply in subsequent samples, which were assumed to come from zones farther away from the well. Samples obtained from near the well also had visible exopolysaccharide blankets, as seen in scanning electron microscopic preparations. In one of the wells that was sampled, rates of glucose or acetate incorporation into microbial lipids correlated with biomass; but in the other well, activities correlated with the sampling time (volume of water that back flowed). Transmission electron micrographs showed a diverse, gram-negative bacterial population in a variety of physiological states. The analysis of the phospholipid ester-linked fatty acid profiles of the samples revealed consistently large proportions of 18:1ω7c fatty acids, indicating the presence of many anaerobes, facultative organisms, or both. Proportions of cyclopropyl fatty acids and ratios of trans/cis monoenoic compounds increased with the volume of water that back flowed (analogous with the distance into the formation), while the ratio of unsaturated/saturated compounds decreased, possibly indicating higher levels of stress or starvation in the microbial communities farthest from the injection well. Greater than 90% of the total biomass was trapped on glass fiber filters, indicating that the microbiota were largely attached to particles or were clumped. These sampling techniques and analytical methods may prove useful in monitoring for problems with microbes (e.g., plugging) in waterflood operations and in the preparation of water injection wells for enhanced oil recovery by the use of microbes. Images

  10. Oil removal and effects of spilled oil on active microbial communities in close to salt-saturation brines.

    PubMed

    Corsellis, Yannick Y; Krasovec, Marc M; Sylvi, Léa L; Cuny, Philippe P; Militon, Cécile C

    2016-05-01

    Abiotic and biotic processes associated with the degradation of a light petroleum in brines close to the salt-saturation (~31 %) and the effect of labile organic matter (LOM) supply (casaminoacids/citrate; 0.2 and 0.1 % w/v, respectively) were followed during an incubation of 30 days. After 4-week incubation at 40 °C under light/dark cycles, a 24 % of abiotic degradation was observed in untreated brines. The stimulation of native brines community with LOM addition allowed an additional 12.8 % oil attenuation due to biodegradation processes. Successional changes in the active microbial community structure due to the oil contamination (16S rRNA DGGE approach) showed the selection of one phylotype affiliated to Salinibacter and the disappearance of Haloquadratum walsbyi in untreated brines. In LOM-amended microcosms, phylotypes related to Salinibacter, Haloarcula, Haloterrigena and Halorhabdus were selected. An effect of hydrocarbon contamination was only observed in the bacterial community with the inhibition of two dominant proteobacterial phylotypes. This study further confirms that short-term and moderate oil biodegradation is possible in LOM-stimulated brines. Biodegradation should be much more reduced under in situ conditions. Self-cleaning capacities of close to saturation hypersaline lakes appears, therefore very limited compared to non-extreme haline environments. PMID:26955981

  11. Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions.

    PubMed

    Shchegolkova, Nataliya M; Krasnov, George S; Belova, Anastasia A; Dmitriev, Alexey A; Kharitonov, Sergey L; Klimina, Kseniya M; Melnikova, Nataliya V; Kudryavtseva, Anna V

    2016-01-01

    Activated sludge (AS) plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants, and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewage in three wastewater treatment plants (WWTPs) responsible for processing sewage with different origins: municipal wastewater, slaughterhouse wastewater, and refinery sewage. In contrast to incoming wastewater, the taxonomic structure of AS biocenosis was found to become stable in time, and each WWTP demonstrated a unique taxonomic pattern. Most pathogenic microorganisms (Streptococcus, Trichococcus, etc.), which are abundantly represented in incoming sewage, were significantly decreased in AS of all WWTPs, except for the slaughterhouse wastewater. Additional load of bioreactors with influent rich in petroleum products and organic matter was associated with the increase of bacteria responsible for AS bulking and foaming. Here, we present a novel approach enabling the prediction of the metabolic potential of bacterial communities based on their taxonomic structures and MetaCyc database data. We developed a software application, XeDetect, to implement this approach. Using XeDetect, we found that the metabolic potential of the three bacterial communities clearly reflected the substrate composition. We revealed that the microorganisms responsible for AS bulking and foaming (most abundant in AS of slaughterhouse wastewater) played a leading role in the degradation of substrates such as fatty acids, amino acids, and other bioorganic compounds. Moreover, we discovered that the chemical, rather than the bacterial composition of the incoming wastewater was the main factor in AS structure formation. XeDetect (freely available: https://sourceforge.net/projects/xedetect) represents a novel powerful tool for the analysis of the metabolic capacity of bacterial communities. The tool will

  12. Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions

    PubMed Central

    Shchegolkova, Nataliya M.; Krasnov, George S.; Belova, Anastasia A.; Dmitriev, Alexey A.; Kharitonov, Sergey L.; Klimina, Kseniya M.; Melnikova, Nataliya V.; Kudryavtseva, Anna V.

    2016-01-01

    Activated sludge (AS) plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants, and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewage in three wastewater treatment plants (WWTPs) responsible for processing sewage with different origins: municipal wastewater, slaughterhouse wastewater, and refinery sewage. In contrast to incoming wastewater, the taxonomic structure of AS biocenosis was found to become stable in time, and each WWTP demonstrated a unique taxonomic pattern. Most pathogenic microorganisms (Streptococcus, Trichococcus, etc.), which are abundantly represented in incoming sewage, were significantly decreased in AS of all WWTPs, except for the slaughterhouse wastewater. Additional load of bioreactors with influent rich in petroleum products and organic matter was associated with the increase of bacteria responsible for AS bulking and foaming. Here, we present a novel approach enabling the prediction of the metabolic potential of bacterial communities based on their taxonomic structures and MetaCyc database data. We developed a software application, XeDetect, to implement this approach. Using XeDetect, we found that the metabolic potential of the three bacterial communities clearly reflected the substrate composition. We revealed that the microorganisms responsible for AS bulking and foaming (most abundant in AS of slaughterhouse wastewater) played a leading role in the degradation of substrates such as fatty acids, amino acids, and other bioorganic compounds. Moreover, we discovered that the chemical, rather than the bacterial composition of the incoming wastewater was the main factor in AS structure formation. XeDetect (freely available: https://sourceforge.net/projects/xedetect) represents a novel powerful tool for the analysis of the metabolic capacity of bacterial communities. The tool will

  13. Examining the impact of acetylene on N-fixation and the active sediment microbial community

    PubMed Central

    Fulweiler, Robinson W.; Heiss, Elise M.; Rogener, Mary Kate; Newell, Silvia E.; LeCleir, Gary R.; Kortebein, Sarah M.; Wilhelm, Steven W.

    2015-01-01

    Here we examined the impact of a commonly employed method used to measure nitrogen fixation, the acetylene reduction assay (ARA), on a marine sediment community. Historically, the ARA technique has been broadly employed for its ease of use, in spite of numerous known artifacts. To gauge the severity of these effects in a natural environment, we employed high-throughput 16S rRNA gene sequencing to detect differences in acetylene-treated sediments vs. non-treated control sediments after a 7 h incubation. Within this short time period, significant differences were seen across all activity of microbes identified in the sediment, implying that the changes induced by acetylene occur quickly. The results have important implications for our understanding of marine nitrogen budgets. Moreover, because the ARA technique has been widely used in terrestrial and freshwater habitats, these results may be applicable to other ecosystems. PMID:26029177

  14. 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

  15. [Effects of different cropping patterns on soil enzyme activities and soil microbial community diversity in oasis farmland].

    PubMed

    Li, Rui; Liu, Yu; Chu, Gui-xin

    2015-02-01

    Effects of long-term cropping patterns on the activities of peroxidase, invertase, arylsulfatase, dehydrogenase and protease were investigated in this paper. Four long-term cropping patterns included (1) 10 years continuous cropping of corn, (2) 8 years continuous cropping of wheat followed by 10 years continuous cropping of cotton, (3) 15 years continuous cropping of cotton, and (4) 6 years continuous cropping of cotton followed by 6 years of wheat/sunflower rotation. The responses of soil bacteria, fungi, ammonia oxidizing bacteria (AOB) , and the ammonia oxidizing archaea (AOA) to different copping patterns were analyzed. The results showed that cropping patterns significantly affected the activities of soil peroxidase, arylsulfatase, dehydrogenase and protease, while had no significant effect on soil invertase activity. The cropping patterns significantly influenced the diversity index of AOA, but had no significant influence on that of soil bacteria, fungi and AOB. The community structures of soil fungi and AOB were more sensitive to cropping patterns than soil bacteria and AOA. In conclusion, long-term continuous cropping of cotton decreased the activities of soil enzymes activities and soil microbial diversity in oasis farmland, while crop rotation could alleviate the negative influence. PMID:26094465

  16. Long-term soil microbial community and enzyme activity responses to an integrated cropping-livestock system in a semi-arid region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study is part of a larger long-term project to develop and evaluate integrated crop and livestock systems in order to reduce dependence on underground water sources by optimizing cotton (Gossypium hirsutum) production in the Texas High Plains of U.S. Microbial communities and activities were e...

  17. Can transgenic maize affect soil microbial communities?

    PubMed

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

    2006-09-29

    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

  18. 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

  19. 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.

  20. Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils.

    PubMed

    Boteva, Silvena; Radeva, Galina; Traykov, Ivan; Kenarova, Anelia

    2016-03-01

    Ore mining and processing have greatly altered ecosystems, often limiting their capacity to provide ecosystem services critical to our survival. The soil environments of two abandoned uranium mines were chosen to analyze the effects of long-term uranium and heavy metal contamination on soil microbial communities using dehydrogenase and phosphatase activities as indicators of metal stress. The levels of soil contamination were low, ranging from 'precaution' to 'moderate', calculated as Nemerow index. Multivariate analyses of enzyme activities revealed the following: (i) spatial pattern of microbial endpoints where the more contaminated soils had higher dehydrogenase and phosphatase activities, (ii) biological grouping of soils depended on both the level of soil contamination and management practice, (iii) significant correlations between both dehydrogenase and alkaline phosphatase activities and soil organic matter and metals (Cd, Co, Cr, and Zn, but not U), and (iv) multiple relationships between the alkaline than the acid phosphatase and the environmental factors. The results showed an evidence of microbial tolerance and adaptation to the soil contamination established during the long-term metal exposure and the key role of soil organic matter in maintaining high microbial enzyme activities and mitigating the metal toxicity. Additionally, the results suggested that the soil microbial communities are able to reduce the metal stress by intensive phosphatase synthesis, benefiting a passive environmental remediation and provision of vital ecosystem services. PMID:26578378

  1. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments.

    PubMed

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the "secondary compound hypothesis" and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  2. Sensitive and substrate-specific detection of metabolically active microorganisms in natural microbial consortia using community isotope arrays.

    PubMed

    Tourlousse, Dieter M; Kurisu, Futoshi; Tobino, Tomohiro; Furumai, Hiroaki

    2013-05-01

    The goal of this study was to develop and validate a novel fosmid-clone-based metagenome isotope array approach - termed the community isotope array (CIArray) - for sensitive detection and identification of microorganisms assimilating a radiolabeled substrate within complex microbial communities. More specifically, a sample-specific CIArray was used to identify anoxic phenol-degrading microorganisms in activated sludge treating synthetic coke-oven wastewater in a single-sludge predenitrification-nitrification process. Hybridization of the CIArray with DNA from the (14) C-phenol-amended sample indicated that bacteria assimilating (14) C-atoms, presumably directly from phenol, under nitrate-reducing conditions were abundant in the reactor, and taxonomic assignment of the fosmid clone end sequences suggested that they belonged to the Gammaproteobacteria. The specificity of the CIArray was validated by quantification of fosmid-clone-specific DNA in density-resolved DNA fractions from samples incubated with (13) C-phenol, which verified that all CIArray-positive probes stemmed from microorganisms that assimilated isotopically labeled carbon. This also demonstrated that the CIArray was more sensitive than DNA-SIP, as the former enabled positive detection at a phenol concentration that failed to yield a 'heavy' DNA fraction. Finally, two operational taxonomic units distantly related to marine Gammaproteobacteria were identified to account for more than half of 16S rRNA gene clones in the 'heavy' DNA library, corroborating the CIArray-based identification. PMID:23441921

  3. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    PubMed Central

    Musilova, Lucie; Ridl, Jakub; Polivkova, Marketa; Macek, Tomas; Uhlik, Ondrej

    2016-01-01

    Secondary plant metabolites (SPMEs) play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs) and polyaromatic hydrocarbons (PAHs). Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes. PMID:27483244

  4. Biochar, activated carbon, and carbon nanotubes have different effects on fate of 14C-catechol and microbial community in soil

    NASA Astrophysics Data System (ADS)

    Shan, Jun; Ji, Rong; Yu, Yongjie; Xie, Zubin; Yan, Xiaoyuan

    2015-10-01

    This study investigated the effects of biochar, activated carbon (AC)-, and single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) in various concentrations (0, 0.2, 20, and 2,000 mg/kg dry soil) on the fate of 14C-catechol and microbial community in soil. The results showed that biochar had no effect on the mineralization of 14C-catechol, whereas AC at all amendment rates and SWCNTs at 2,000 mg/kg significantly reduced mineralization. Particularly, MWCNTs at 0.2 mg/kg significantly stimulated mineralization compared with the control soil. The inhibitory effects of AC and SWCNTs on the mineralization were attributed to the inhibited soil microbial activities and the shifts in microbial communities, as suggested by the reduced microbial biomass C and the separated phylogenetic distance. In contrast, the stimulatory effects of MWCNTs on the mineralization were attributed to the selective stimulation of specific catechol-degraders by MWCNTs at 0.2 mg/kg. Only MWCNTs amendments and AC at 2,000 mg/kg significantly changed the distribution of 14C residues within the fractions of humic substances. Our findings suggest biochar, AC, SWCNTs and MWCNTs have different effects on the fate of 14C-catechol and microbial community in soil.

  5. Biochar, activated carbon, and carbon nanotubes have different effects on fate of 14C-catechol and microbial community in soil

    PubMed Central

    Shan, Jun; Ji, Rong; Yu, Yongjie; Xie, Zubin; Yan, Xiaoyuan

    2015-01-01

    This study investigated the effects of biochar, activated carbon (AC)-, and single-walled and multi-walled carbon nanotubes (SWCNTs and MWCNTs) in various concentrations (0, 0.2, 20, and 2,000 mg/kg dry soil) on the fate of 14C-catechol and microbial community in soil. The results showed that biochar had no effect on the mineralization of 14C-catechol, whereas AC at all amendment rates and SWCNTs at 2,000 mg/kg significantly reduced mineralization. Particularly, MWCNTs at 0.2 mg/kg significantly stimulated mineralization compared with the control soil. The inhibitory effects of AC and SWCNTs on the mineralization were attributed to the inhibited soil microbial activities and the shifts in microbial communities, as suggested by the reduced microbial biomass C and the separated phylogenetic distance. In contrast, the stimulatory effects of MWCNTs on the mineralization were attributed to the selective stimulation of specific catechol-degraders by MWCNTs at 0.2 mg/kg. Only MWCNTs amendments and AC at 2,000 mg/kg significantly changed the distribution of 14C residues within the fractions of humic substances. Our findings suggest biochar, AC, SWCNTs and MWCNTs have different effects on the fate of 14C-catechol and microbial community in soil. PMID:26515132

  6. Microbial communities and SOM dynamics along a precipitation gradient

    NASA Astrophysics Data System (ADS)

    Tiemann, Lisa; Billings, Sharon

    2014-05-01

    Many microbial communities are not resistant to changes in their environment, and the subsequently new and structurally distinct communities are not always functionally redundant with their predecessors. As a result, environmental change can lead to long-term changes in microbially-mediated ecosystem processes. More specifically, changes in soil moisture regimes can alter microbial physiology and resource demands, and therefore alter how microbes process soil organic matter (SOM). To better understand how current and future precipitation regimes can influence microbial communities and SOM transformations, we assessed microbial community structure and activity in soils reciprocally transplanted across four sites within a grassland precipitation gradient of 485 to 1003 mm y-1. We show that the soil microbial communities residing at these sites are compositionally distinct from each other, and C mineralization rates and microbial biomass C are highly correlated with contemporary site soil moisture. After sols had been subjected to altered precipitation regimes for1.5 and 2.5 years, microbial community structure shifted. Copiotrophs were more abundant relative to oligotrophs in soils experiencing the largest shifts from their native precipitation regimes, and oligotrophs were more dominant in the soils under the most severe soil moisture stress. In general, microbial community structure, in soils from the driest site, was more resistant to change when subjected to novel precipitation regimes. SOM processing rates were distinct in all transplanted soils from their native controls. These changes were dependent on a significant interaction between the initial microbial community structure and the degree of change in precipitation regime, suggesting the importance of initial microbial community structure as a determinant of future structural trajectories, which can drive SOM transformations. Soils transplanted to drier sites with more variable precipitation exhibited lower

  7. Active microbial community in gas reservoirs in the North German Plain and the effects of high CO2 concentrations

    NASA Astrophysics Data System (ADS)

    Frerichs, Janin; Gniese, Claudia; Mühling, Martin; Krüger, Martin

    2010-05-01

    From the IPCC report on global warming, it is clear that large-scale solutions are needed immediately to reduce emissions of greenhouse gases. The CO2 capture and storage offers one option for reducing the greenhouse gas emissions. Favourable CO2 storage sites are depleted gas and oil fields and thus, are currently investigated by the BMBF-Geotechnologien RECOBIO-2 project. Our study is focussing on the direct influence of high CO2 concentrations on the autochthonous microbial population and environmental parameters (e.g. availability of nutrients). The gas fields Schneeren in the 'North German Plain' is operated by Gaz de France SUEZ E&V Deutschland GmbH. The conditions in the reservoir formation waters of two bore wells differ in various geochemical parameters (pH, salinity and temperature). In previous studies the community of this gas field was described by Ehinger et al. 2009. Based on these results our study included cultivation and molecular biological approaches. Our results showed significant differences of the community structure in regional distinctions of the gas reservoir. The activity profiles of two wells differed clearly in the inducible activity after substrate addition. The fluids of well A showed a high methane production rate after the addition of methanol or acetate. Well B showed a high sulphide production after the addition of sulphate and hydrogen. The molecular biological analysis of the original fluids supports the activity profile for both sites. The community analysis via real-time PCR showed for the production well head A a higher abundances for Archaea than for B. The community at site B in contrast was dominated by Bacteria. Fluids of both wells were also incubated with high CO2 concentrations in the headspace. These enrichments showed a significant decrease of methane and sulphide production with increasing CO2 levels. Currently, the community composition is analysed to identify changes connected to increased CO2 concentrations. This

  8. Microbial communities in acid mine drainage.

    PubMed

    Baker, Brett J; Banfield, Jillian F

    2003-05-01

    The dissolution of sulfide minerals such as pyrite (FeS2), arsenopyrite (FeAsS), chalcopyrite (CuFeS2), sphalerite (ZnS), and marcasite (FeS2) yields hot, sulfuric acid-rich solutions that contain high concentrations of toxic metals. In locations where access of oxidants to sulfide mineral surfaces is increased by mining, the resulting acid mine drainage (AMD) may contaminate surrounding ecosystems. Communities of autotrophic and heterotrophic archaea and bacteria catalyze iron and sulfur oxidation, thus may ultimately determine the rate of release of metals and sulfur to the environment. AMD communities contain fewer prokaryotic lineages than many other environments. However, it is notable that at least two archaeal and eight bacterial divisions have representatives able to thrive under the extreme conditions typical of AMD. AMD communities are characterized by a very limited number of distinct species, probably due to the small number of metabolically beneficial reactions available. The metabolisms that underpin these communities include organoheterotrophy and autotrophic iron and sulfur oxidation. Other metabolic activity is based on anaerobic sulfur oxidation and ferric iron reduction. Evidence for physiological synergy in iron, sulfur, and carbon flow in these communities is reviewed. The microbial and geochemical simplicity of these systems makes them ideal targets for quantitative, genomic-based analyses of microbial ecology and evolution and community function. PMID:19719632

  9. 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

  10. Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

    NASA Astrophysics Data System (ADS)

    Wilton, E.; Flanagan, L. B.

    2014-12-01

    Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex

  11. Beyond microbial community composition: functional activities of the oral microbiome in health and disease

    PubMed Central

    Duran-Pinedo, Ana E.; Frias-Lopez, Jorge

    2015-01-01

    The oral microbiome plays a relevant role in the health status of the host and is a key element in a variety of oral and non-oral diseases. Despite advances in our knowledge of changes in microbial composition associated with different health conditions the functional aspects of the oral microbiome that lead to dysbiosis remain for the most part unknown. In this review, we discuss the progress made towards understanding the functional role of the oral microbiome in health and disease and how novel technologies are expanding our knowledge on this subject. PMID:25862077

  12. Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge.

    PubMed

    Westerholm, Maria; Crauwels, Sam; Houtmeyers, Sofie; Meerbergen, Ken; Van Geel, Maarten; Lievens, Bart; Appels, Lise

    2016-10-01

    The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the

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

    EPA Science Inventory

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

  14. 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.

  15. Long term effect of alkali types on waste activated sludge hydrolytic acidification and microbial community at low temperature.

    PubMed

    Jin, Baodan; Wang, Shuying; Xing, Liqun; Li, Baikun; Peng, Yongzhen

    2016-01-01

    The effect of four alkali reagents (NaOH, KOH, Ca(OH)2, mixed alkali) on waste activated sludge (WAS) hydrolytic acidification and microbial community was studied in semi-continuous fermentation systems at low temperature (15°C) over long term operational time (65day). The results showed that protein and polysaccharide of NaOH (124.26, 11.92) was similar to that of KOH (109.53, 11.30), both were higher than Ca(OH)2 (70.66, 3.74) and mixed alkali (90.66, 8.71). The short chain fatty acids (SCFAs) of NaOH (231.62) was higher than KOH (220.62mg chemical oxygen demand (COD)/g VSS). Although Ca(OH)2 system had strong acidification capacity, the shortage of SCFAs occurred due to the low activity of hydrolase. Illumina MiSeq sequencing revealed that Tissierella and Erysipelothrix were enriched in the NaOH and Ca(OH)2 systems, where Peptostreptococcaceae incertae_sedis was enriched in the NaOH and KOH systems, less Anaerolinea was involved in Ca(OH)2 condition. PMID:26546788

  16. Effects of DO levels on surface force, cell membrane properties and microbial community dynamics of activated sludge.

    PubMed

    Ma, Si-Jia; Ding, Li-Li; Huang, Hui; Geng, Jin-Ju; Xu, Ke; Zhang, Yan; Ren, Hong-Qiang

    2016-08-01

    In this paper, we employ atomic force microscopy (AFM), fluorescence recovery after photobleaching (FRAP) technique, phospholipid fatty acids (PLFA) and MiSeq analysis to study the effects of traditional dissolved oxygen (DO) levels (0.71-1.32mg/L, 2.13-3.02mg/L and 4.31-5.16mg/L) on surface force, cell membrane properties and microbial community dynamics of activated sludge. Results showed that low DO level enhanced the surface force and roughness of activated sludge; the medium DO level decreased cell membrane fluidity by reducing the synthesis of branched fatty acids in the cell membrane; high DO level resulted in the highest protein content in the effluent by EEM scanning. Abundance of Micropruina, Zoogloea and Nakamurella increased and Paracoccus and Rudaea decreased with the increase of DO levels. RDA analysis suggested that saturated fatty acids (SFA), anteiso-fatty acids (AFA) and iso-fatty acids (IFA) were closely related to effluent quality as well as some genera. PMID:27187569

  17. [Effects of rotation and fallowing on the microbial communities and enzyme activities in a solar greenhouse soil under continuous cucumber cropping].

    PubMed

    Yang, Feng-juan; Wu, Huan-tao; Wei, Min; Wang, Xiu-feng; Shi, Qing-hua

    2009-12-01

    A pot experiment was conducted to study the effects of rotation and fallowing on the microbial communities and enzyme activities in a greenhouse soil continuously cropped with cucumber and on the growth and yield of followed cucumber. Comparing with continuous cropping, rotation improved the components of soil microbial communities, which was manifested in the increase of bacteria and actinomycetes and the decrease of fungi. Rotation and fallowing enhanced the activities of soil invertase, urease, catalase, and polyphenol oxidase significantly. The quantities of soil bacteria and actinomycetes and the activity of soil invertase increased at the fruiting stage of cucumber plants, being the maximum at harvest stage, but decreased thereafter. In contrast, the quantity of soil fungi had a linear increase, and the activities of soil urease, catalase, and polyphenol oxidase decreased gradually during fruit development. Welsh onion and waxy maize promoted the growth and fruiting of the followed cucumber plants significantly, being the optimal rotation crops for cucumber. PMID:20353066

  18. 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...

  19. Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

    PubMed Central

    Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

    2012-01-01

    The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

  20. GeoChip 3.0 as a high-thoughput tool for analyzing microbial community composition, structure, and functional activity

    SciTech Connect

    He, Z.; Deng, Y.; Van Nostrand, J.D.; Tu, Q.; Xu, M.; Hemme, C.L.; Li, X.; Wu, L.; Gentry, T.J.; Yin, Y.; Liebich, J.; Hazen, T.C.; Zhou, J.

    2010-04-01

    A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with {approx}28,000 probes covering approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.

  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. Which Microbial Communities Are Present? Sequence-Based Metagenomics

    NASA Astrophysics Data System (ADS)

    Caffrey, Sean M.

    The use of metagenomic methods that directly sequence environmental samples has revealed the extraordinary microbial diversity missed by traditional culture-based methodologies. Therefore, to develop a complete and representative model of an environment's microbial community and activities, metagenomic analysis is an essential tool.

  3. Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

    PubMed

    Larsen, Peter; Hamada, Yuki; Gilbert, Jack

    2012-07-31

    Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science. PMID:22465599

  4. Response of microbial community structure to microbial plugging in a mesothermic petroleum reservoir in China.

    PubMed

    Zhang, Fan; She, Yue Hui; Ma, Sha Sha; Hu, Ji Ming; Banat, Ibrahim M; Hou, Du Jie

    2010-12-01

    Microbial plugging, a microbial enhancement of oil recovery (MEOR) technique, has been applied in a candidate oil reservoir of Daqing Oil Field (China). The goal of this study is to monitor the survival of injected bacteria and reveal the response of microbial communities in field trial of microbial plugging through injection of selected microbial culture broth and nutrients. Culture-dependent enrichment and culture-independent 16S rDNA clone library methods were used. The results show that it was easy to activate targeted biopolymer-producing bacteria in a laboratory environment, and it was difficult for injected exogenous bacteria to survive. In addition, microbial communities in the oil reservoir also changed before and after the field trial. However, microbial communities, activated by fermentative medium for biopolymer-producing bacteria, appeared to show greater differences in the laboratory than in the natural reservoir. It was concluded that microbial populations monitoring was important to MEOR; results of response of microbial communities could provide a guide for the future field trials. PMID:20803140

  5. Effects of sludge inoculum and organic feedstock on active microbial communities and methane yield during anaerobic digestion

    PubMed Central

    Wilkins, David; Rao, Subramanya; Lu, Xiaoying; Lee, Patrick K. H.

    2015-01-01

    Anaerobic digestion (AD) is a widespread microbial technology used to treat organic waste and recover energy in the form of methane (“biogas”). While most AD systems have been designed to treat a single input, mixtures of digester sludge and solid organic waste are emerging as a means to improve efficiency and methane yield. We examined laboratory anaerobic cultures of AD sludge from two sources amended with food waste, xylose, and xylan at mesophilic temperatures, and with cellulose at meso- and thermophilic temperatures, to determine whether and how the inoculum and substrate affect biogas yield and community composition. All substrate and inoculum combinations yielded methane, with food waste most productive by mass. Pyrosequencing of transcribed bacterial and archaeal 16S rRNA showed that community composition varied across substrates and inocula, with differing ratios of hydrogenotrophic/acetoclastic methanogenic archaea associated with syntrophic partners. While communities did not cluster by either inoculum or substrate, additional sequencing of the bacterial 16S rRNA gene in the source sludge revealed that the bacterial communities were influenced by their inoculum. These results suggest that complete and efficient AD systems could potentially be assembled from different microbial inocula and consist of taxonomically diverse communities that nevertheless perform similar functions. PMID:26528262

  6. Illumina MiSeq Sequencing Reveals Diverse Microbial Communities of Activated Sludge Systems Stimulated by Different Aromatics for Indigo Biosynthesis from Indole

    PubMed Central

    Zhang, Xuwang; Qu, Yuanyuan; Ma, Qiao; Zhang, Zhaojing; Li, Duanxing; Wang, Jingwei; Shen, Wenli; Shen, E; Zhou, Jiti

    2015-01-01

    Indole, as a typical N-heteroaromatic compound existed in coking wastewater, can be used for bio-indigo production. The microbial production of indigo from indole has been widely reported during the last decades using culture-dependent methods, but few studies have been carried out by microbial communities. Herein, three activated sludge systems stimulated by different aromatics, i.e. naphthalene plus indole (G1), phenol plus indole (G2) and indole only (G3), were constructed for indigo production from indole. During the operation, G1 produced the highest indigo yield in the early stage, but it switched to G3 in the late stage. Based on LC-MS analysis, indigo was the major product in G1 and G3, while the purple product 2-(7-oxo-1H-indol-6(7H)-ylidene) indolin-3-one was dominant in G2. Illumina MiSeq sequencing of 16S rRNA gene amplicons was applied to analyze the microbial community structure and composition. Detrended correspondence analysis (DCA) and dissimilarity tests showed that the overall community structures of three groups changed significantly during the operation (P<0.05). Nevertheless, the bacteria assigned to phylum Proteobacteria, family Comamonadaceae, and genera Diaphorobacter, Comamonas and Aquamicrobium were commonly shared dominant populations. Pearson correlations were calculated to discern the relationship between microbial communities and indigo yields. The typical indigo-producing populations Comamonas and Pseudomonas showed no positive correlations with indigo yields, while there emerged many other genera that exhibited positive relationships, such as Aquamicrobium, Truepera and Pusillimonas, which had not been reported for indigo production previously. The present study should provide new insights into indigo bio-production by microbial communities from indole. PMID:25928424

  7. 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

  8. 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.

  9. Patterns and Processes of Microbial Community Assembly

    PubMed Central

    Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

    2013-01-01

    SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity. PMID:24006468

  10. Differential methane oxidation activity and microbial community composition at cold seeps in the Arctic off western Svalbard

    NASA Astrophysics Data System (ADS)

    Gründger, Friederike; Svenning, Mette M.; Niemann, Helge; Silyakova, Anna; Serov, Pavel; Li Hong, Wei; Wegener, Gunter; Panieri, Giuliana; Carroll, JoLynn

    2016-04-01

    Most models considering climate change related bottom water warming suggest that gas hydrates may become destabilized, leading to the mobilization of methane into seabed and water column ecosystems, and, eventually, into the atmosphere. However, the capacity of methanotrophic microbes retaining methane in sediments and the hydrosphere is not well constrained. Here, we investigate the microbial utilization of methane in sediments and the water column, focusing on cold seeps discovered at the arctic continental margin of western Svalbard. We measured ex situ rates of methane oxidation and sulfate reduction in two active gas flare sites with different geological settings at the Vestnesa Ridge (1204 m water depth) and within a pingolike feature area southwest off Svalbard (PLF; 380 m water depth). Our results show contrarily situations at our two sampling sites: At Vestnesa Ridge we find high methane oxidation rates with values up to 2055 nmol cm‑3 d‑1 at the sediment surface where the sediments are oversaturated with methane. Whereas, methane concentration and oxidation rates are low in the overlying water column (2 pmol cm‑3 d‑1). In contrast, at the sediment surface at PLF methane concentration and oxidation rates are considerably lower (up to 1.8 nmol cm‑3 d‑1). While the overlying bottom water contains high concentration of methane and shows oxidation rates with values of up to 3.8 nmol cm‑3 d‑1. The data on methane oxidation and sulfate reduction activity are compared to the sediment geochemistry and to data from metagenomic analysis identifying the methanotrophic community composition. These results provide unique insight into the dynamic responses of the seabed biological filter at cold seeps in the Arctic off western Svalbard. This study is part of the Centre for Arctic Gas Hydrate, Environment and Climate and was supported by the Research Council of Norway through its Centres of Excellence funding scheme grant No. 223259.

  11. Soil microbial abundance, activity and diversity response in two different altitude-adapted plant communities affected by wildfire in Sierra Nevada National Park (Granada, Spain)

    NASA Astrophysics Data System (ADS)

    Bárcenas-Moreno, Gema; Zavala, Lorena; Jordan, Antonio; Bååth, Erland; Mataix-Beneyto, Jorge

    2013-04-01

    Plant communities can play an important role in fire severity and post-fire ecosystem recovery due to their role as combustible and different plant-soil microorganisms interactions. Possible differences induced by plant and microorganisms response after fire could affect the general ecosystem short and long-term response and its sustainability. The main objective of this work was the evaluation of the effect of wildfire on soil microbial abundance, activity and diversity in two different plant communities associated to different altitudes in Sierra Nevada National Park (Granada, Spain). Samples were collected in two areas located on the Sierra Nevada Mountain between 1700 and 2000 m above sea level which were affected by a large wildfire in 2005. Two samplings were carried out 8 and 20 months after fire and samples were collected in both burned and unburned (control) zones in each plant community area. Area A is located at 1700m and it is formed by Quercus rotundifolia forest while area B is located at 2000 m altitude and is composed of alpine vegetation formed by creeping bearing shrubs. Microbial biomass measured by Fumigation-Extraction method followed the same trend in both areas showing slight and no significant differences between burned and unburned area during the study period while viable and cultivable bacteria abundance were markedly higher in fire affected samples than in the control ones in both samplings. Viable and cultivable filamentous fungi had different behavior depending of plant vegetation community studied showing no differences between burned and unburned area in area A while was significantly higher in burned samples than in the control ones in area B. Microbial activity monitoring with soil microbial respiration appears to had been affected immediately after fire since microbial respiration was lower in burned samples from area A than in unburned one only 8 months after fire and no significant differences were observed between burned and

  12. Enhanced Lipid and Biodiesel Production from Glucose-Fed Activated Sludge: Kinetics an Microbial Community Analysis

    EPA Science Inventory

    An innovative approach to increase biofuel feedstock lipid yields from municipal sewage sludge via manipulation of carbon:nitrogen (C:N) ratio and glucose loading in activated sludge bioreactors was investigated. Sludge lipid and fatty acid methyl ester (biodiesel) yields (% cel...

  13. Microbial interactions in building of communities

    PubMed Central

    Wright, Christopher J.; Burns, Logan H.; Jack, Alison A.; Back, Catherine R.; Dutton, Lindsay C.; Nobbs, Angela H.; Lamont, Richard J.; Jenkinson, Howard F.

    2012-01-01

    SUMMARY Establishment of a community is considered to be essential for microbial growth and survival in the human oral cavity. Biofilm communities have increased resilience to physical forces, antimicrobial agents, and nutritional variations. Specific cell-to-cell adherence processes, mediated by adhesin-receptor pairings on respective microbial surfaces, are able to direct community development. These interactions co-localize species in mutually beneficial relationships, such as streptococci, veillonellae, Porphyromonas gingivalis and Candida albicans. In transition from the planktonic mode of growth to a biofilm community, microorganisms undergo major transcriptional and proteomic changes. These occur in response to sensing of diffusible signals, such as autoinducer molecules, and to contact with host tissues or other microbial cells. Underpinning many of these processes are intracellular phosphorylation events that regulate a large number of microbial interactions relevant to community formation and development. PMID:23253299

  14. Long term tillage, cover crop and fertilization effects on microbial community structure and activity: Implications on soil quality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Reduced tillage, cover crops and fertilization are associated with greater microbial biomass and activity that are linked to improvements in soil quality, but their impacts vary widely with climate, soils and cropping systems. This study aimed to characterize the impact of long term (31 years) tilla...

  15. Rapid mass spectrometric DNA diagnostics for assessing microbial community activity during bioremediation. 1997 annual progress report

    SciTech Connect

    Benner, W.H.; Hunter-Cevera, J.

    1997-01-01

    'The effort of the past year''s activities, which covers the first year of the project, was directed at developing DNA-based diagnostic procedures for implementation in high through-put analytical instrumentation. The diagnostic procedures under evaluation are designed to identify specific genes in soil microorganisms that code for pollutant-degrading enzymes. Current DNA-based diagnostic procedures, such as the ligase chain reaction (LCR) and the polymerase chain reaction (PCR), rely on gel electrophoresis as a way to score a diagnostic test. The authors are attempting to implement time-of-flight (TOF) mass spectrometry as a replacement for gel separations because of its speed advantage and potential for sample automation. The authors anticipate that if TOF techniques can be implemented in the procedures, then a very large number of microorganisms and soil samples can be screened for the presence of specific pollutant-degrading genes. The use of DNA-based procedures for the detection of biodegrading organisms or genes that code for pollutant-degrading enzymes constitutes a critical technology for following biochemical transformation and substantiating the impact of bioremediation. DNA-based technology has been demonstrated to be a sensitive technique for tracking micro-organism activity at the molecular level. These procedures can be tuned to identify groups of organisms, specific organisms, and activity at the molecular level. They are developing a P-monitoring strategy that relies on the combined use of DNA diagnostics with mass spectrometry as the detection scheme. The intent of this work is a two-fold evaluation of (1) the feasibility of replacing the use of gel separations for identifying polymerase chain reaction (PCR) products with a rapid and automatable form of electrospray mass spectrometry and (2) the use of matrix-assisted-laser-desorption-ionization mass spectrometry (MALDI-MS) as a tool to score oligonucleotide ligation assays (OLA).'

  16. Resistance, resilience, and redundancy in microbial communities

    PubMed Central

    Allison, Steven D.; Martiny, Jennifer B. H.

    2008-01-01

    Although it is generally accepted that plant community composition is key for predicting rates of ecosystem processes in the face of global change, microbial community composition is often ignored in ecosystem modeling. To address this issue, we review recent experiments and assess whether microbial community composition is resistant, resilient, or functionally redundant in response to four different disturbances. We find that the composition of most microbial groups is sensitive and not immediately resilient to disturbance, regardless of taxonomic breadth of the group or the type of disturbance. Other studies demonstrate that changes in composition are often associated with changes in ecosystem process rates. Thus, changes in microbial communities due to disturbance may directly affect ecosystem processes. Based on these relationships, we propose a simple framework to incorporate microbial community composition into ecosystem process models. We conclude that this effort would benefit from more empirical data on the links among microbial phylogeny, physiological traits, and disturbance responses. These relationships will determine how readily microbial community composition can be used to predict the responses of ecosystem processes to global change. PMID:18695234

  17. Seasonal variation of postmortem microbial communities.

    PubMed

    Carter, David O; Metcalf, Jessica L; Bibat, Alexander; Knight, Rob

    2015-06-01

    Body-associated microbes were recently shown to change significantly during decomposition, undergoing an ecological succession in experimental conditions using rodent and swine models. We investigated microbial succession in soils associated with swine carcasses under experimental field conditions in summer and winter. We demonstrate that these postmortem microbial communities change in a specific, reproducible fashion, and that soil microbes represent a significant component of the postmortem microbial community, contrary to widespread belief in forensic science. However, the effects of decomposition on soil microbial communities were different in summer and winter. We suggest that the microbial ecological succession will be useful in medicolegal death investigation; however, observations in winter might not be applicable to summer, which indicates a need for a greater understanding of the seasonality of decomposition. PMID:25737335

  18. Microbial community distribution and activity dynamics of granular biomass in a CANON reactor.

    PubMed

    Vázquez-Padín, Jose; Mosquera-Corral, Anuska; Campos, Jose Luis; Méndez, Ramón; Revsbech, Niels Peter

    2010-08-01

    The application of microelectrodes to measure oxygen and nitrite concentrations inside granules operated at 20 degrees C in a CANON (Complete Autotrophic Nitrogen-removal Over Nitrite) reactor and the application of the FISH (Fluorescent In Situ Hybridization) technique to cryosectioned slices of these granules showed the presence of two differentiated zones inside of them: an external nitrification zone and an internal anammox zone. The FISH analysis of these layers allowed the identification of Nitrosomonas spp. and Candidatus Kuenenia Stutgartiensis as the main populations carrying out aerobic and anaerobic ammonia oxidation, respectively. Concentration microprofiles measured at different oxygen concentrations in the bulk liquid (from 1.5 to 35.2 mg O(2) L(-1)) revealed that oxygen was consumed in a surface layer of 100-350 microm width. The obtained consumption rate of the most active layers was of 80 g O(2) (L(granule))(-1) d(-1). Anammox activity was registered between 400 and 1000 microm depth inside the granules. The nitrogen removal capacity of the studied sequencing batch reactor containing the granular biomass was of 0.5 g N L(-1) d(-1). This value is similar to the mean nitrogen removal rate obtained from calculations based on in- and outflow concentrations. Information obtained in the present work allowed the establishment of a simple control strategy based on the measurements of NH(4)(+) and NO(2)(-) in the bulk liquid and acting over the dissolved oxygen concentration in the bulk liquid and the hydraulic retention time of the reactor. PMID:20646732

  19. [Microbial activity and community structure analysis under the different land use patterns in farmland soils: based on the methods PLFA and MicroResp].

    PubMed

    Chen, Xiao-Juan; Wu, Xiao-Hong; Liu, Shou-Long; Yuan, Hong-Zhao; Li, Miao-Miao; Zhu, Han-Hua; Ge, Ti-D; Tong, Cheng-Li; Wu, Jin-Shui

    2013-06-01

    Soil microbe plays an essential role in terrestrial ecosystem through its role in cycling mineral compounds and decomposing organic matter. The objective of this paper is to determine the influences of different land use patterns on soil microbial activity and community structure, which were analyzed by phospholipids fatty acid (PLFA) and MicroResp method, based on a long-term fertilization experiment in Taoyuan County, Hunan Province. There were three land use patterns included, i. e. paddy fields (PS), paddy-upland rotation (PU) and upland land (US) soils. The results showed that the amounts of bacteria PLFA, fungi PLFA and the total PLFA were generally following the order PS > PU > US. The ratio of bacteria PLFA/fungi PLFA followed the order PU > US > PS, however, the ratio of Gram-positive bacteria PLFA (G+ PLFA) to Gram-negative bacteria PLFA (G(-) PLFA) in PU was the highest, and there's no significant difference in PU and US. In addition, principal components analysis (PCA) and the average concentration (mol x mol(-1)) of biomarker-PLFAs also revealed that the relative content of fungi and G(-) in PS was much higher than those of in PU and US (P < 0.05). However, the relative content of G(+) in PU was higher than those of other two land use patters. Therefore, Microbial community structure was influenced significantly by land use patterns in our study. Soil microbial biomass had significant relationships (P < 0.05) with SOC, TN and MBC, but had no significant correlation with CEC. Meanwhile, MicroResp analysis indicated that most of the carbon substrate addition enhanced the microbial respiration rates, although different substrate had different use efficiency. The average of carbon substrate use efficiency could be also ranked in the order: PS > PU > US. We conclude that microbial activity and community structure were influenced significantly by land use patterns in farmlands. PMID:23947059

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

    PubMed

    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

  1. 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

  2. Metabolic Network Modeling of Microbial Communities

    PubMed Central

    Biggs, Matthew B.; Medlock, Gregory L.; Kolling, Glynis L.

    2015-01-01

    Genome-scale metabolic network reconstructions and constraint-based analysis are powerful methods that have the potential to make functional predictions about microbial communities. Current use of genome-scale metabolic networks to characterize the metabolic functions of microbial communities includes species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the “enzyme-soup” approach, multi-scale modeling, and others. There are many challenges inherent to the field, including a need for tools that accurately assign high-level omics signals to individual community members, new automated reconstruction methods that rival manual curation, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be proportional advances in the fields of ecology, health science, and microbial community engineering. PMID:26109480

  3. Two-stage microbial community experimental design.

    PubMed

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

    2013-12-01

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

  4. 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

  5. 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. PMID:23226147

  6. 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. PMID:21451582

  7. 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.

  8. Succession in a microbial mat community: a gaian perspective.

    PubMed

    Stolz, J F

    1984-01-01

    The Gaia hypothesis originally proposed by James E. Lovelock states that the composition, oxidation-reduction state and temperature of the troposphere are actively regulated by the activities of the biota. The gaian concept has been extrapolated to include the composition of surface sediments through the process of biomineralization. The stratified microbial community dominated by the cyanobacterium Microcoleus chthonoplastes is actively involved in the deposition of laminated sediments at Laguna Figueroa, Baja California, Mexico. Unusually heavy rains in the winters of 1979 and 1980 flooded the evaporite flat with up to 3 meters of meteoric water and deposited 5-10 cm of allocthonous sediment. The composition of the microbial community changed as a succession of dominating microbial species ensued, ultimately leading to the recolonization of the surface sediment by the original Microcoleus-dominated community. The resiliency of bacterial communities is suggested to be an important mechanism of gaian control systems. PMID:11537776

  9. 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.

  10. Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities.

    PubMed

    Arnosti, Carol; Steen, Andrew D

    2013-01-01

    The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburg Fjord), and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in "downstream" aspects of microbial metabolism (metabolism of monomers and biomass production). Only four of six polysaccharide substrates were hydrolyzed in Smeerenburg Fjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO2. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments. PMID:24198812

  11. Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities

    PubMed Central

    Arnosti, Carol; Steen, Andrew D.

    2013-01-01

    The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburg Fjord), and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in “downstream” aspects of microbial metabolism (metabolism of monomers and biomass production). Only four of six polysaccharide substrates were hydrolyzed in Smeerenburg Fjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO2. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments. PMID:24198812

  12. Posttranslational modification and sequence variation of redox-active proteins correlate with biofilm life cycle in natural microbial communities

    SciTech Connect

    Singer, Steven; Erickson, Brian K; Verberkmoes, Nathan C; Hwang, Mona; Shah, Manesh B; Hettich, Robert {Bob} L; Banfield, Jillian F.; Thelen, Michael P.

    2010-01-01

    Characterizing proteins recovered from natural microbial communities affords the opportunity to correlate protein expression and modification with environmental factors, including species composition and successional stage. Proteogenomic and biochemical studies of pellicle biofilms from subsurface acid mine drainage streams have shown abundant cytochromes from the dominant organism, Leptospirillum Group II. These cytochromes are proposed to be key proteins in aerobic Fe(II) oxidation, the dominant mode of cellular energy generation by the biofilms. In this study, we determined that posttranslational modification and expression of amino-acid sequence variants change as a function of biofilm maturation. For Cytochrome579 (Cyt579), the most abundant cytochrome in the biofilms, late developmental-stage biofilms differed from early-stage biofilms in N-terminal truncations and decreased redox potentials. Expression of sequence variants of two monoheme c-type cytochromes also depended on biofilm development. For Cyt572, an abundant membrane-bound cytochrome, the expression of multiple sequence variants was observed in both early and late developmental-stage biofilms; however, redox potentials of Cyt572 from these different sources did not vary significantly. These cytochrome analyses show a complex response of the Leptospirillum Group II electron transport chain to growth within a microbial community and illustrate the power of multiple proteomics techniques to define biochemistry in natural systems.

  13. Microbial community modeling using reliability theory.

    PubMed

    Zilles, Julie L; Rodríguez, Luis F; Bartolerio, Nicholas A; Kent, Angela D

    2016-08-01

    Linking microbial community composition with the corresponding ecosystem functions remains challenging. Because microbial communities can differ in their functional responses, this knowledge gap limits ecosystem assessment, design and management. To develop models that explicitly incorporate microbial populations and guide efforts to characterize their functional differences, we propose a novel approach derived from reliability engineering. This reliability modeling approach is illustrated here using a microbial ecology dataset from denitrifying bioreactors. Reliability modeling is well-suited for analyzing the stability of complex networks composed of many microbial populations. It could also be applied to evaluate the redundancy within a particular biochemical pathway in a microbial community. Reliability modeling allows characterization of the system's resilience and identification of failure-prone functional groups or biochemical steps, which can then be targeted for monitoring or enhancement. The reliability engineering approach provides a new perspective for unraveling the interactions between microbial community diversity, functional redundancy and ecosystem services, as well as practical tools for the design and management of engineered ecosystems. PMID:26882268

  14. Human and environmental impacts on river sediment microbial communities.

    PubMed

    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

  15. 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

  16. The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils.

    PubMed

    Lin, Zhong; Zhen, Zhen; Wu, Zhihao; Yang, Jiewen; Zhong, Laiyuan; Hu, Hanqiao; Luo, Chunling; Bai, Jing; Li, Yongtao; Zhang, Dayi

    2016-01-15

    The ecological effect of earthworms on the fate of soil pentachlorophenol (PCP) differs with species. This study addressed the roles and mechanisms by which two earthworm species (epigeic Eisenia fetida and endogeic Amynthas robustus E. Perrier) affect the soil microbial community and enzyme activity during the bioremediation of PCP-contaminated soils. A. robustus removed more soil PCP than did E. foetida. A. robustus improved nitrogen utilisation efficiency and soil oxidation more than did E. foetida, whereas the latter promoted the organic matter cycle in the soil. Both earthworm species significantly increased the amount of cultivable bacteria and actinomyces in soils, enhancing the utilisation rate of the carbon source (i.e. carbohydrates, carboxyl acids, and amino acids) and improving the richness and evenness of the soil microbial community. Additionally, earthworm treatment optimized the soil microbial community and increased the amount of the PCP-4-monooxygenase gene. Phylogenic classification revealed stimulation of indigenous PCP bacterial degraders, as assigned to the families Flavobacteriaceae, Pseudomonadaceae and Sphingobacteriacea, by both earthworms. A. robustus and E. foetida specifically promoted Comamonadaceae and Moraxellaceae PCP degraders, respectively. PMID:26342149

  17. 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

  18. Soil organic carbon (SOC) accumulation in rice paddies under long-term agro-ecosystem experiments in southern China - VI. Changes in microbial community structure and respiratory activity

    NASA Astrophysics Data System (ADS)

    Liu, D.; Liu, X.; Liu, Y.; Li, L.; Pan, G.; Crowley, D.; Tippkötter, R.

    2011-02-01

    Biological stabilization within accumulated soil organic carbon (SOC) has not been well understood, while its role in physical and chemical protection as well as of chemical recalcitrance had been addressed in Chinese rice paddies. In this study, topsoil samples were collected and respiratory activity measured in situ following rice harvest under different fertilization treatments of three long-term experimental sites across southern China in 2009. The SOC contents, microbial biomass carbon (SMBC) and nitrogen (SMBN) were analysed using chemical digestion and microbial community structure assessment via clony dilute plate counting methods. While SOC contents were consistently higher under compound chemical fertilization (Comp-Fert) or combined organic and inorganic fertilization (Comb-Fert) compared to N fertilization only (N-Fert), there was significantly higher fungal-bacterial ratio under Comb-Fert than under N-Fert and Comp-Fert. When subtracting the background effect under no fertilization treatment (Non-Fert), the increase both in SMBC and SMBN under fertilization treatment was found very significantly correlated to the increase in SOC over controls across the sites. Also, the ratio of culturable fungal to bacterial population numbers (F/B ratio) was well correlated with soil organic carbon contents in all samples across the sites studied. SOC accumulation favoured a build-up the microbial community with increasing fungal dominance in the rice paddies under fertilization treatments. While soil respiration rates were high under Comb-Fert as a result of enhanced microbial community build-up, the specific soil respiratory activity based on microbial biomass carbon was found in a significantly negatively correlation with the SOC contents for overall samples. Thus, a fungal-dominated microbial community seemed to slow SOC turnover, thereby favouring SOC accumulation under Comp-Fert or under Comb-Fert in the rice paddies. Therefore, the biological stabilization

  19. High-resolution phylogenetic microbial community profiling.

    PubMed

    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

    2016-08-01

    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

  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. Surface reflectance degradation by microbial communities

    DOE PAGESBeta

    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 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

  2. Microbial communities play important roles in modulating paddy soil fertility

    NASA Astrophysics Data System (ADS)

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-02-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production.

  3. Microbial communities play important roles in modulating paddy soil fertility

    PubMed Central

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-01-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production. PMID:26841839

  4. 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

  5. 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. PMID:27242723

  6. 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

  7. 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

  8. The Microbial Database for Danish wastewater treatment plants with nutrient removal (MiDas-DK) - a tool for understanding activated sludge population dynamics and community stability.

    PubMed

    Mielczarek, A T; Saunders, A M; Larsen, P; Albertsen, M; Stevenson, M; Nielsen, J L; Nielsen, P H

    2013-01-01

    Since 2006 more than 50 Danish full-scale wastewater treatment plants with nutrient removal have been investigated in a project called 'The Microbial Database for Danish Activated Sludge Wastewater Treatment Plants with Nutrient Removal (MiDas-DK)'. Comprehensive sets of samples have been collected, analyzed and associated with extensive operational data from the plants. The community composition was analyzed by quantitative fluorescence in situ hybridization (FISH) supported by 16S rRNA amplicon sequencing and deep metagenomics. MiDas-DK has been a powerful tool to study the complex activated sludge ecosystems, and, besides many scientific articles on fundamental issues on mixed communities encompassing nitrifiers, denitrifiers, bacteria involved in P-removal, hydrolysis, fermentation, and foaming, the project has provided results that can be used to optimize the operation of full-scale plants and carry out trouble-shooting. A core microbial community has been defined comprising the majority of microorganisms present in the plants. Time series have been established, providing an overview of temporal variations in the different plants. Interestingly, although most microorganisms were present in all plants, there seemed to be plant-specific factors that controlled the population composition thereby keeping it unique in each plant over time. Statistical analyses of FISH and operational data revealed some correlations, but less than expected. MiDas-DK (www.midasdk.dk) will continue over the next years and we hope the approach can inspire others to make similar projects in other parts of the world to get a more comprehensive understanding of microbial communities in wastewater engineering. PMID:23752384

  9. Metabolic interactions and dynamics in microbial communities

    NASA Astrophysics Data System (ADS)

    Segre', Daniel

    Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

  10. Cry1Ac Transgenic Sugarcane Does Not Affect the Diversity of Microbial Communities and Has No Significant Effect on Enzyme Activities in Rhizosphere Soil within One Crop Season

    PubMed Central

    Zhou, Dinggang; Xu, Liping; Gao, Shiwu; Guo, Jinlong; Luo, Jun; You, Qian; Que, Youxiong

    2016-01-01

    Cry1Ac transgenic sugarcane provides a promising way to control stem-borer pests. Biosafety assessment of soil ecosystem for cry1Ac transgenic sugarcane is urgently needed because of the important role of soil microorganisms in nutrient transformations and element cycling, however little is known. This study aimed to explore the potential impact of cry1Ac transgenic sugarcane on rhizosphere soil enzyme activities and microbial community diversity, and also to investigate whether the gene flow occurs through horizontal gene transfer. We found no horizontal gene flow from cry1Ac sugarcane to soil. No significant difference in the population of culturable microorganisms between the non-GM and cry1Ac transgenic sugarcane was observed, and there were no significant interactions between the sugarcane lines and the growth stages. A relatively consistent trend at community-level, represented by the functional diversity index, was found between the cry1Ac sugarcane and the non-transgenic lines. Most soil samples showed no significant difference in the activities of four soil enzymes: urease, protease, sucrose, and acid phosphate monoester between the non-transgenic and cry1Ac sugarcane lines. We conclude, based on one crop season, that the cry1Ac sugarcane lines may not affect the microbial community structure and functional diversity of the rhizosphere soil and have few negative effects on soil enzymes. PMID:27014291

  11. Community proteomics of a natural microbial biofilm.

    PubMed

    Ram, Rachna J; Verberkmoes, Nathan C; Thelen, Michael P; Tyson, Gene W; Baker, Brett J; Blake, Robert C; Shah, Manesh; Hettich, Robert L; Banfield, Jillian F

    2005-06-24

    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. PMID:15879173

  12. 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.

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

    PubMed Central

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

    2016-01-01

    Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology. PMID:27092245

  14. 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.

  15. Toxicity of TiO₂ nanoparticle to denitrifying strain CFY1 and the impact on microbial community structures in activated sludge.

    PubMed

    Li, Dapeng; Li, Bin; Wang, Qiaoruo; Hou, Ning; Li, Chunyan; Cheng, Xiaosong

    2016-02-01

    The antibacterial activity of titanium dioxide nanoparticles (TiO2 NPs) is well described, but little is known of their impact on specific microbial functions such as denitrification, nor on microbial community structure. In this study, a denitrifier (named as Pseudomonas stutzeri CFY1), which was isolated from the activated sludge and could remove up to 111.68 mg/L of NO3(-)-N under aerobic conditions, was utilized to evaluate the influences of TiO2 NPs on its nitrogen removal ability and associated gene expression under aerobic conditions. The variations of the bacterial diversity of activated sludge were also observed. The results showed that antibacterial activity increased with increasing concentrations of TiO2 NPs. Increased production of reactive oxygen species was responsible for TiO2 NPs toxicity. An up-regulation of denitrification genes was observed with increasing concentrations of TiO2 NPs under aerobic conditions. Accordingly, denitrification by P. stutzeri was accelerated when the concentration of TiO2 NPs was increased to 50 mg/L. However, the denitrification of CFY1 was inhibited at low concentrations of TiO2 NPs (5-25 mg/L), indicating that assimilatory and dissimilatory denitrification were synchronized in P. stutzeri CFY1; the latter process plays a major role in denitrification. Further study of the community using 454 pyrosequencing showed that after 7 days of exposure to 50 mg/L TiO2 NPs, the microbial composition of the activated sludge was significantly different and had a lower diversity compared to the controls. PMID:26479452

  16. 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. PMID:27140688

  17. Principles for designing synthetic microbial communities.

    PubMed

    Johns, Nathan I; Blazejewski, Tomasz; Gomes, Antonio Lc; Wang, Harris H

    2016-06-01

    Advances in synthetic biology to build microbes with defined and controllable properties are enabling new approaches to design and program multispecies communities. This emerging field of synthetic ecology will be important for many areas of biotechnology, bioenergy and bioremediation. This endeavor draws upon knowledge from synthetic biology, systems biology, microbial ecology and evolution. Fully realizing the potential of this discipline requires the development of new strategies to control the intercellular interactions, spatiotemporal coordination, robustness, stability and biocontainment of synthetic microbial communities. Here, we review recent experimental, analytical and computational advances to study and build multi-species microbial communities with defined functions and behavior for various applications. We also highlight outstanding challenges and future directions to advance this field. PMID:27084981

  18. 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

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

    PubMed

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

    2004-02-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  1. Metagenomic analysis of an anaerobic alkane-degrading microbial culture: potential hydrocarbon-activating pathways and inferred roles of community members.

    PubMed

    Tan, Boonfei; Dong, Xiaoli; Sensen, Christoph W; Foght, Julia

    2013-10-01

    A microbial community (short-chain alkane-degrading culture, SCADC) enriched from an oil sands tailings pond was shown to degrade C6-C10 alkanes under methanogenic conditions. Total genomic DNA from SCADC was subjected to 454 pyrosequencing, Illumina paired-end sequencing, and 16S rRNA amplicon pyrotag sequencing; the latter revealed 320 operational taxonomic units at 5% distance. Metagenomic sequences were subjected to in-house quality control and co-assembly, yielding 984 086 contigs, and annotation using MG-Rast and IMG. Substantial nucleotide and protein recruitment to Methanosaeta concilii, Syntrophus aciditrophicus, and Desulfobulbus propionicus reference genomes suggested the presence of closely related strains in SCADC; other genomes were not well mapped, reflecting the paucity of suitable reference sequences for such communities. Nonetheless, we detected numerous homologues of putative hydrocarbon succinate synthase genes (e.g., assA, bssA, and nmsA) implicated in anaerobic hydrocarbon degradation, suggesting the ability of the SCADC microbial community to initiate methanogenic alkane degradation by addition to fumarate. Annotation of a large contig revealed analogues of the ass operon 1 in the alkane-degrading sulphate-reducing bacterium Desulfatibacillum alkenivorans AK-01. Despite being enriched under methanogenic-fermentative conditions, additional metabolic functions inferred by COG profiling indicated multiple CO(2) fixation pathways, organic acid utilization, hydrogenase activity, and sulphate reduction. PMID:24237341

  2. 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.

  3. Temporal and spatial variations of contaminant removal, enzyme activities, and microbial community structure in a pilot horizontal subsurface flow constructed wetland purifying industrial runoff.

    PubMed

    Yi, Xiao-Hui; Jing, Dan-Dan; Wan, Jinquan; Ma, Yongwen; Wang, Yan

    2016-05-01

    A pilot-scale horizontal subsurface flow constructed wetland (HSSFCW) was operated to purify industrial runoff containing polycyclic aromatic hydrocarbons (PAHs) in Guangzhou, China. Synthetic industrial runoff was fed into the HSSFCW with continuous flow at an average loading rate of 0.128 m(3)/(m(2)/day) for about 2 years. Pollutants such as chemical oxygen demand (COD), total phosphorus (TP), and phenanthrene were mainly removed in the front quarter of the HSSFCW, and in the vertical direction, the average removal rates of COD, TP, total nitrogen (TN), ammonia, and phenanthrene of the upper layer were 64.23, 71.16, 50.81, 65.38, and 92.47 %, which were 1.23, 2.08, 1.48, 1.72, and 1.17 times higher than those of the bottom, respectively. Correlations among pollutant removal, soil environmental indexes, enzyme activities, and soil microbial community structure were evaluated. Enzyme assays (dehydrogenase, catalase, nitrate reductase, and polyphenol oxidase) showed significant associations between enzyme activities and pollutant removal (p < 0.01 and p < 0.05). Soil microbial community structure was assessed with denaturing gradient gel electrophoresis (DGGE) fingerprinting method, and results demonstrated that bacterial communities remained relatively stable in different seasons. Proteobacteria and Bacteroidetes were found to be the dominant phyla of the bacteria communities, and three clones which might be related to the biodegradation of phenanthrene were also detected. Results of the present work would broaden the knowledge of the purification mechanism of contaminants in the constructed wetlands (CWs), and identification of the treatment performances and temporal and spatial variations of biological activities of subsurface flow constructed wetlands (SSFCWs) would help to improve the operations of CWs for surface water protection. PMID:26797946

  4. Effects of Winter Cover Crops Residue Returning on Soil Enzyme Activities and Soil Microbial Community in Double-Cropping Rice Fields

    PubMed Central

    Hai-Ming, Tang; Xiao-Ping, Xiao; Wen-Guang, Tang; Ye-Chun, Lin; Ke, Wang; Guang-Li, Yang

    2014-01-01

    Residue management in cropping systems is useful to improve soil quality. However, the studies on the effects of residue management on the enzyme activities and microbial community of soils in South China are few. Therefore, the effects of incorporating winter cover crop residue with a double-cropping rice (Oryza sativa L.) system on soil enzyme activities and microbial community in Southern China fields were studied. The experiment has conducted at the experimental station of the Institute of Soil and Fertilizer Research, Hunan Academy of Agricultural Science, China since winter 2004. Four winter cropping systems were used: rice–rice–ryegrass (Lolium multiflorum L.) (R-R-Ry), rice–rice–Chinese milk vetch (Astragalus sinicus L.) (R-R-Mv), rice–rice–rape (Brassica napus L.) (R-R-Ra) and rice–rice with winter fallow (R-R-Fa). The result indicated that the enzyme activities in the R-R-Ry, R-R-Mv and R-R-Ra systems were significantly higher (P<0.05) than in the R-R-Fa system during the early and late rice season. The β-glucosidase activities reached peak values at the tillering stage after residue application, and alkaline phosphatase activities reached peak values at the booting stage after residue application, respectively, the activities of β-glucosidase and alkaline phosphatase gradually decreased after this. Arylsulfatase activities reached peak values at the maturity stage. Arylamidase activities reached peak values at the maturity stage. The numbers of aerobic bacteria, actinomycete and fungus of residue treatments were significantly higher (P<0.05) than that the R-R-Ra system. However, the number of anaerobic bacteria under the R-R-Ry and R-R-Mv systems was significantly lower (P<0.05) than that under the R-R-Fa system during early rice and late rice growth stage. Thus, incorporation of winter cover crops into rotations may increase enzyme activities and microbial community in soil and therefore improve soil quality. PMID:24956152

  5. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

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

    PubMed Central

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

    2011-01-01

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

  7. Microbial communities evolve faster in extreme environments

    PubMed Central

    Li, Sheng-Jin; Hua, Zheng-Shuang; Huang, Li-Nan; Li, Jie; Shi, Su-Hua; Chen, Lin-Xing; Kuang, Jia-Liang; Liu, Jun; Hu, Min; Shu, Wen-Sheng

    2014-01-01

    Evolutionary analysis of microbes at the community level represents a new research avenue linking ecological patterns to evolutionary processes, but remains insufficiently studied. Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. We show that the rERs of microbial communities are mainly shaped by environmental conditions, and the microbes inhabiting extreme habitats (acid mine drainage, saline lake and hot spring) evolve faster than those populating benign environments (surface ocean, fresh water and soil). These findings were supported by the observation of more relaxed purifying selection and potentially frequent horizontal gene transfers in communities from extreme habitats. The mechanism of high rERs was proposed as high mutation rates imposed by stressful conditions during the evolutionary processes. This study brings us one stage closer to an understanding of the evolutionary mechanisms underlying the adaptation of microbes to extreme environments. PMID:25158668

  8. Sequencing and beyond: integrating molecular ‘omics for microbial community profiling

    PubMed Central

    Franzosa, Eric A.; Hsu, Tiffany; Sirota-Madi, Alexandra; Shafquat, Afrah; Abu-Ali, Galeb; Morgan, Xochitl C.

    2016-01-01

    High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring additional multi'omic data types that better capture community functional activity, such as transcriptomics, proteomics, and metabolomics; and combining multiple forms of multi'omic data in an integrated framework. We highlight studies in which the multi'omics approach has led to improved mechanistic models of microbial community structure and function. PMID:25915636

  9. Start-Up of an Anaerobic Dynamic Membrane Digester for Waste Activated Sludge Digestion: Temporal Variations in Microbial Communities

    PubMed Central

    Yu, Hongguang; Wang, Qiaoying; Wang, Zhiwei; Sahinkaya, Erkan; Li, Yongli; Ma, Jinxing; Wu, Zhichao

    2014-01-01

    An anaerobic dynamic membrane digester (ADMD) was developed to digest waste sludge, and pyrosequencing was used to analyze the variations of the bacterial and archaeal communities during the start-up. Results showed that bacterial community richness decreased and then increased over time, while bacterial diversity remained almost the same during the start-up. Proteobacteria and Bacteroidetes were the major phyla. At the class level, Betaproteobacteria was the most abundant at the end of start-up, followed by Sphingobacteria. In the archaeal community, richness and diversity peaked at the end of the start-up stage. Principle component and cluster analyses demonstrated that archaeal consortia experienced a distinct shift and became stable after day 38. Methanomicrobiales and Methanosarcinales were the two predominant orders. Further investigations indicated that Methanolinea and Methanosaeta were responsible for methane production in the ADMD system. Hydrogenotrophic pathways might prevail over acetoclastic means for methanogenesis during the start-up, supported by specific methanogenic activity tests. PMID:24695488

  10. 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. PMID:25852658

  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. Microbial Communities of Pavilion Lake Microbialites

    NASA Astrophysics Data System (ADS)

    Russell, J. A.; Biddle, J.; Pointing, S.; Cardman, Z.; Brady, A. L.; Slater, G. F.; Lim, D. S.

    2011-12-01

    Fossilized remnants of microbial mat growth, called stromatolites, are found in the rock record and are thought to be some of the earliest evidence for life on Earth. On the modern Earth, living versions of these stromatolites, called microbialites, are found in few environments across the globe. Pavilion Lake in British Columbia was found to host these microbialites, even though conditions are not extreme in the lake and grazers exist amongst the microbial growths. The Pavilion Lake Research Project, funded by NASA, the CSA and others, has developed the lake into an analog research site for the exploration of extraplanetary bodies since 2004. Pavilion Lake began to be explored for microbial ecology in 2007 to attempt to determine how the microbial communities change over time, location and depth to build these microbialite structures. DNA extracted from microbialites at two different locations and 3 depths at each location were analyzed by T-RFLP patterns. Significant differences were seen in the total communities from each location. Additional samples were taken in the summer and budding seasons, and significant differences were seen by season. A survey performed on just the cyanobacterial populations show less differences between taxa between sites, but significant differences with depth above and below the chemocline and between mineralized and non-mineralized mats. Differences were also examined between purple and green nodules, which are thought to be the growth forms of the microbialites. Detailed sequence analysis shows that Pavilion Lake microorganisms are similar, yet different, from microbial communities seen in other microbialite systems. In 2011, the research project moved to Kelly Lake, a lake nearby Pavilion Lake, that also contain microbialite structures. Similar morphologies were seen in Kelly Lake with an approximate 20 ft. offset in the typical depths where morphologies were seen. Continued analysis of Kelly Lake microbialites will be performed

  13. Microbial community functional change during vertebrate carrion decomposition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  14. Post fumigation recovery of soil microbial community structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil fumigants have been extensively used to control target soil-borne pathogens and weeds for the past few decades. It is known that the fumigants with broad biocidal activity can affect both target and non-target soil organisms, but the recovery of soil microbial communities are unknown until rece...

  15. Multilevel Samplers to Assess Microbial Community Response to Biostimulation

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  16. The shift of the microbial community in activated sludge with calcium treatment and its implication to sludge settleability.

    PubMed

    Ye, Chengchen; Yang, Xinping; Zhao, Fang-Jie; Ren, Lifei

    2016-05-01

    The sludge settleability is of prime importance for the activated sludge process. The effect of calcium ion on the biological performance of sludge was investigated in a lab-scale activated sludge system with varying Ca(2+) concentration. Results indicated that addition of 150mg/L Ca(2+) to the influent significantly improved the settling characteristics and metabolic reactivity of activated sludge in the bioreactors. Analyses using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA sequencing showed that a significant difference in the presence of certain bacterial groups between the sludge systems with 150mg/L Ca(2+) and those with 0-100mg/L Ca(2+) addition. Ca(2+) also increased the production of the extracellular polymeric substance (EPS) and facilitated the development of microbial cluster in the bioreactor. Study showed that an addition of 150mg/L Ca(2+) to the influent provides a simple approach to improve the settling properties of activated sludge and maintain high pollutant removal efficiency. PMID:26868150

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

    PubMed

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

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture. PMID:21865033

  18. Phylogenetic survey of metabolically active microbial communities associated with the deep-sea coral Lophelia pertusa from the Apulian plateau, Central Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Yakimov, Michail M.; Cappello, Simone; Crisafi, Ermanno; Tursi, Angelo; Savini, Alessandra; Corselli, Cesare; Scarfi, Simona; Giuliano, Laura

    2006-01-01

    Living deep-water coral assemblages were discovered recently inhabiting the Mediterranean Sea between the depths of 300 and 1000 m off the Cape of Santa Maria di Leuca (Apulian platform, Ionian Sea). This living assemblage was dominated by two colonial scleractinian corals, Lophelia pertusa and Madrepora oculata. Two other corals, Desmophyllum crystagalli and Stenocyathus vermiformis were also recovered from this site, but were much less common. The composition of the metabolically active fraction of the microbial community associated with living specimens of L. pertusa was determined. Dead corals, proximal sediments and overlying seawater were also sampled and analyzed. Complementary 16S ribosomal DNA (crDNA) was obtained from total RNA extracted from all samples that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct four different 16S crDNA libraries containing 45 Archaea and 201 Bacteria clones. Using Archaea-specific primers, no amplification products were obtained from any coral samples (live and dead). Living specimens of L. pertusa seem to possess a specific microbial community different from that of dead coral and sediment samples. The majority of all coral-associated riboclones was related to the Holophaga-Acidobacterium and Nitrospira divisions (80%). Moreover, more than 12% of all coral-associated riboclones formed a separate deep-branching cluster within the α- Proteobacteria with no known close relatives. The metabolically active fraction of the bacterial community colonizing the dead corals was dominated by Proteobacteria related to the gamma and epsilon subdivisions (74% and 26% of all clones, respectively). Phylogenetic analysis of the Archaea clone library retrieved from proximal sediments indicated an exclusive dominance by the members of Crenarchaea Marine Group I (MGI), a lineage of unculturable microorganisms, widely distributed in marine habitats. In contrast, bacterial

  19. Impact of land-use and long-term (>150 years) charcoal accumulation on microbial activity, biomass and community structure in temperate soils (Belgium).

    NASA Astrophysics Data System (ADS)

    Hardy, Brieuc; Cornelis, Jean-Thomas; Dufey, Joseph E.

    2015-04-01

    In the last decade, biochar has been increasingly investigated as a soil amendment for long-term soil carbon sequestration while improving soil fertility. On the short term, biochar application to soil generally increases soil respiration as well as microbial biomass and activity and affects significantly the microbial community structure. However, such effects are relatively short-term and tend to vanish over time. In our study, we investigated the long-term impact of charcoal accumulation and land-use on soil biota in temperate haplic Luvisols developed in the loess belt of Wallonia (Belgium). Charcoal-enriched soils were collected in the topsoil of pre-industrial (>150 years old) charcoal kilns in forest (4 sites) and cropland (5 sites). The topsoil of the adjacent charcoal-unaffected soils was sampled in a comparable way. Soils were characterized (pH, total, organic and inorganic C, total N, exchangeable Ca, Mg, K, Na, cation exchange capacity and available P) and natural soil organic matter (SOM) and black carbon (BC) contents were determined by differential scanning calorimetry. After rewetting at pF 2.5, soils were incubated during 140 days at 20 °C. At 70 days of incubation, 10 g of each soil were freeze dried in order to measure total microbial biomass and community structure by PLFA analysis. The PLFA dataset was analyzed by principal component analysis (PCA) while soil parameters were used as supplementary variables. For both agricultural and forest soils, the respiration rate is highly related to the total microbial biomass (R²=0.90). Both soil respiration and microbial biomass greatly depend on the SOM content, which indicates that the BC pool is relatively inert microbiologically. Land-use explains most of the variance in the PLFA dataset, largely governing the first principal component of the ACP. In forest soils, we observe a larger proportion of gram + bacteria, actinomycetes and an increased bacteria:fungi ratio compared to cropland, where gram

  20. Community structure and activity of a highly dynamic and nutrient-limited hypersaline microbial mat in Um Alhool Sabkha, Qatar.

    PubMed

    Al-Thani, Roda; Al-Najjar, Mohammad A A; Al-Raei, Abdul Munem; Ferdelman, Tim; Thang, Nguyen M; Al Shaikh, Ismail; Al-Ansi, Mehsin; de Beer, Dirk

    2014-01-01

    The Um Alhool area in Qatar is a dynamic evaporative ecosystem that receives seawater from below as it is surrounded by sand dunes. We investigated the chemical composition, the microbial activity and biodiversity of the four main layers (L1-L4) in the photosynthetic mats. Chlorophyll a (Chl a) concentration and distribution (measured by HPLC and hyperspectral imaging, respectively), the phycocyanin distribution (scanned with hyperspectral imaging), oxygenic photosynthesis (determined by microsensor), and the abundance of photosynthetic microorganisms (from 16S and 18S rRNA sequencing) decreased with depth in the euphotic layer (L1). Incident irradiance exponentially attenuated in the same zone reaching 1% at 1.7-mm depth. Proteobacteria dominated all layers of the mat (24%-42% of the identified bacteria). Anoxygenic photosynthetic bacteria (dominated by Chloroflexus) were most abundant in the third red layer of the mat (L3), evidenced by the spectral signature of Bacteriochlorophyll as well as by sequencing. The deep, black layer (L4) was dominated by sulfate reducing bacteria belonging to the Deltaproteobacteria, which were responsible for high sulfate reduction rates (measured using 35S tracer). Members of Halobacteria were the dominant Archaea in all layers of the mat (92%-97%), whereas Nematodes were the main Eukaryotes (up to 87%). Primary productivity rates of Um Alhool mat were similar to those of other hypersaline microbial mats. However, sulfate reduction rates were relatively low, indicating that oxygenic respiration contributes more to organic material degradation than sulfate reduction, because of bioturbation. Although Um Alhool hypersaline mat is a nutrient-limited ecosystem, it is interestingly dynamic and phylogenetically highly diverse. All its components work in a highly efficient and synchronized way to compensate for the lack of nutrient supply provided during regular inundation periods. PMID:24658360

  1. Community Structure and Activity of a Highly Dynamic and Nutrient-Limited Hypersaline Microbial Mat in Um Alhool Sabkha, Qatar

    PubMed Central

    Al-Thani, Roda; Al-Najjar, Mohammad A. A.; Al-Raei, Abdul Munem; Ferdelman, Tim; Thang, Nguyen M.; Shaikh, Ismail Al; Al-Ansi, Mehsin; de Beer, Dirk

    2014-01-01

    The Um Alhool area in Qatar is a dynamic evaporative ecosystem that receives seawater from below as it is surrounded by sand dunes. We investigated the chemical composition, the microbial activity and biodiversity of the four main layers (L1–L4) in the photosynthetic mats. Chlorophyll a (Chl a) concentration and distribution (measured by HPLC and hyperspectral imaging, respectively), the phycocyanin distribution (scanned with hyperspectral imaging), oxygenic photosynthesis (determined by microsensor), and the abundance of photosynthetic microorganisms (from 16S and 18S rRNA sequencing) decreased with depth in the euphotic layer (L1). Incident irradiance exponentially attenuated in the same zone reaching 1% at 1.7-mm depth. Proteobacteria dominated all layers of the mat (24%–42% of the identified bacteria). Anoxygenic photosynthetic bacteria (dominated by Chloroflexus) were most abundant in the third red layer of the mat (L3), evidenced by the spectral signature of Bacteriochlorophyll as well as by sequencing. The deep, black layer (L4) was dominated by sulfate reducing bacteria belonging to the Deltaproteobacteria, which were responsible for high sulfate reduction rates (measured using 35S tracer). Members of Halobacteria were the dominant Archaea in all layers of the mat (92%–97%), whereas Nematodes were the main Eukaryotes (up to 87%). Primary productivity rates of Um Alhool mat were similar to those of other hypersaline microbial mats. However, sulfate reduction rates were relatively low, indicating that oxygenic respiration contributes more to organic material degradation than sulfate reduction, because of bioturbation. Although Um Alhool hypersaline mat is a nutrient-limited ecosystem, it is interestingly dynamic and phylogenetically highly diverse. All its components work in a highly efficient and synchronized way to compensate for the lack of nutrient supply provided during regular inundation periods. PMID:24658360

  2. Microbial interactions and community assembly at microscales.

    PubMed

    Cordero, Otto X; Datta, Manoshi S

    2016-06-01

    In most environments, microbial interactions take place within microscale cell aggregates. At the scale of these aggregates (∼100μm), interactions are likely to be the dominant driver of population structure and dynamics. In particular, organisms that exploit interspecific interactions to increase ecological performance often co-aggregate. Conversely, organisms that antagonize each other will tend to spatially segregate, creating distinct micro-communities and increased diversity at larger length scales. We argue that, in order to understand the role that biological interactions play in microbial community function, it is necessary to study microscale spatial organization with enough throughput to measure statistical associations between taxa and possible alternative community states. We conclude by proposing strategies to tackle this challenge. PMID:27232202

  3. 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

  4. 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.

  5. Bioaugmentation as a Tool To Protect the Structure and Function of an Activated-Sludge Microbial Community against a 3-Chloroaniline Shock Load

    PubMed Central

    Boon, Nico; Top, Eva M.; Verstraete, Willy; Siciliano, Steven D.

    2003-01-01

    Bioaugmentation of bioreactors focuses on the removal of xenobiotics, with little attention typically paid to the recovery of disrupted reactor functions such as ammonium-nitrogen removal. Chloroanilines are widely used in industry as a precursor to a variety of products and are occasionally released into wastewater streams. This work evaluated the effects on activated-sludge reactor functions of a 3-chloroaniline (3-CA) pulse and bioaugmentation by inoculation with the 3-CA-degrading strain Comamonas testosteroni I2 gfp. Changes in functions such as nitrification, carbon removal, and sludge compaction were studied in relation to the sludge community structure, in particular the nitrifying populations. Denaturing gradient gel electrophoresis (DGGE), real-time PCR, and fluorescent in situ hybridization (FISH) were used to characterize and enumerate the ammonia-oxidizing microbial community immediately after a 3-CA shock load. Two days after the 3-CA shock, ammonium accumulated, and the nitrification activity did not recover over a 12-day period in the nonbioaugmented reactors. In contrast, nitrification in the bioaugmented reactor started to recover on day 4. The DGGE patterns and the FISH and real-time PCR data showed that the ammonia-oxidizing microbial community of the bioaugmented reactor recovered in structure, activity, and abundance, while the number of ribosomes of the ammonia oxidizers in the nonbioaugmented reactor decreased drastically and the community composition changed and did not recover. The settleability of the activated sludge was negatively influenced by the 3-CA addition, with the sludge volume index increasing by a factor of 2.3. Two days after the 3-CA shock in the nonbioaugmented reactor, chemical oxygen demand (COD) removal efficiency decreased by 36% but recovered fully by day 4. In contrast, in the bioaugmented reactor, no decrease of the COD removal efficiency was observed. This study demonstrates that bioaugmentation of wastewater

  6. Ecological restoration alters microbial communities in mine tailings profiles

    NASA Astrophysics Data System (ADS)

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

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

    PubMed

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-01-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings. PMID:27126064

  8. Ecological restoration alters microbial communities in mine tailings profiles

    PubMed Central

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-01-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings. PMID:27126064

  9. 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.

  10. Characterizing microbial communities through space and time

    PubMed Central

    Gonzalez, Antonio; King, Andrew; Robeson, Michael S.; Song, Sejin; Shade, Ashley; Metcalf, Jessica; Knight, Rob

    2011-01-01

    Until recently, the study of microbial diversity has mainly been limited to descriptive approaches, rather than predictive model-based analyses. The development of advanced analytical tools and decreasing cost of high-throughput multi-omics technologies has made the later approach more feasible. However, consensus is lacking as to which spatial and temporal scales best facilitate understanding of the role of microbial diversity in determining both public and environmental health. Here, we review the potential for combining these new technologies with both traditional and nascent spatio-temporal analysis methods. The fusion of proper spatio-temporal sampling, combined with modern multi-omics and computational tools, will provide insight into the tracking, development and manipulation of microbial communities. PMID:22154467

  11. 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. PMID:22531018

  12. Microbial communities in streambed sediments recovering from desiccation.

    PubMed

    Marxsen, Jürgen; Zoppini, Annamaria; Wilczek, Sabine

    2010-03-01

    Climate change affects running waters not only by increasing temperatures but also by increasing discharge variability as more frequent and severe floods and more frequent and longer droughts occur, especially in upper reaches. Mediterranean streams are known to experience droughts, but Central European headwaters are also beginning to be affected. The development of bacterial communities (abundance, composition) and the recovery of microbial functions (bacterial production, extracellular enzyme activity) were explored after rewetting desiccated streambed sediments via a sediment core perfusion technique. The bacterial community composition changed only slightly in the sediments from the Central European stream Breitenbach (Germany), but distinctly in the Mediterranean Mulargia River (Sardinia, Italy) during 4 days of experimental rewetting. Breitenbach sediments probably enabled survival of bacterial communities more similar to indigenous streambed communities, because they were less dry. High activity of enzymes involved in polymer degradation at the beginning of rewetting in both sediments indicated the persistence of extracellular enzymes during drought. After 4 days, nearly all microbial activities reached a level similar to unaffected sediments for the Breitenbach, but not for Mulargia. Here, much more intense drying resulted in a more distinct change and reduction of the microbial community, responsible for slower recovery of structure and functions. PMID:20041952

  13. Legacy effects overwhelm the short-term effects of exotic plant invasion and restoration on soil microbial community structure, enzyme activities, and nitrogen cycling.

    PubMed

    Elgersma, Kenneth J; Ehrenfeld, Joan G; Yu, Shen; Vor, Torsten

    2011-11-01

    Plant invasions can have substantial consequences for the soil ecosystem, altering microbial community structure and nutrient cycling. However, relatively little is known about what drives these changes, making it difficult to predict the effects of future invasions. In addition, because most studies compare soils from uninvaded areas to long-established dense invasions, little is known about the temporal dependence of invasion impacts. We experimentally manipulated forest understory vegetation in replicated sites dominated either by exotic Japanese barberry (Berberis thunbergii), native Viburnums, or native Vacciniums, so that each vegetation type was present in each site-type. We compared the short-term effect of vegetation changes to the lingering legacy effects of the previous vegetation type by measuring soil microbial community structure (phospholipid fatty acids) and function (extracellular enzymes and nitrogen mineralization). We also replaced the aboveground litter in half of each plot with an inert substitute to determine if changes in the soil microbial community were driven by aboveground or belowground plant inputs. We found that after 2 years, the microbial community structure and function was largely determined by the legacy effect of the previous vegetation type, and was not affected by the current vegetation. Aboveground litter removal had only weak effects, suggesting that changes in the soil microbial community and nutrient cycling were driven largely by belowground processes. These results suggest that changes in the soil following either invasion or restoration do not occur quickly, but rather exhibit long-lasting legacy effects from previous belowground plant inputs. PMID:21618010

  14. Linking Nitrogen-Cycling Microbial Communities to Environmental Fluctuations and Biogeochemical Activity in a Large, Urban Estuary: the San Francisco Bay-Delta

    NASA Astrophysics Data System (ADS)

    Francis, C.

    2015-12-01

    Nitrogen (N) availability is an important factor controlling productivity and thus carbon cycling in estuaries. The fate of N in estuaries depends on the activities of the microbes that carry out the N-cycle, which in turn depend on factors such as organic matter availability, dissolved inorganic N, salinity, oxygen, and temperature. Key microbial N transformations include nitrification (the aerobic oxidation of ammonia to nitrite and nitrate) and denitrification (the anaerobic reduction of nitrate to dinitrogen gas). While denitrification leads to N loss, nitrification is the only link between reduced N (produced by decomposition) and oxidized N (substrates for N loss processes), and both processes are known to produce nitrous oxide (N2O), a potent greenhouse gas. Understanding controls of N-cycling in the San Francisco Bay-Delta (SFBD)—the largest estuary on the west coast of North America—is particularly important, as this urban estuary is massively polluted with N, even compared to classic "eutrophic" systems. Interestingly, the SFBD has been spared the detrimental consequences of nutrient enrichment, largely due to high suspended sediment concentrations (and thus low light penetration) throughout the water column, combined with high grazing pressure. However, the recent "clearing" of SFBD waters due to a sharp decrease in suspended sediments may significantly alter the ecology of the estuary, by increasing phytoplankton growth. Thus, the SFBD may be losing its historical resilience to eutrophication, and may soon be "high-nutrient, low-chlorophyll" no more. Elucidating the environmental factors affecting the community structure, activity, and functioning of N-cycling microbes in SFBD is crucial for determining how changes in turbidity and productivity will be propagated throughout the ecosystem. While substantial ecological research in the SFBD has focused on phytoplankton and food webs, bacterial and archaeal communities have received far less attention

  15. 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

  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. Geological Sources of Hydrogen for Subsurface Microbial Communities

    NASA Astrophysics Data System (ADS)

    McCollom, T. M.

    2008-12-01

    Subsurface microbial communities can be conveniently divided into two general types: heterotrophic communities that rely primarily on input of photosynthetically derived organic matter, and autotrophic communities that rely on inorganic chemical sources of energy. In situ production of H2 has been proposed to support subsurface autotrophic microbial communities within basalts and ultramafic rocks in both subaerial and submarine settings. The extent and activity of such communities, and even their very ability to inhabit subsurface environments, depends largely on the balance between the supply of H2 for metabolic energy and the energetic costs of existence (T. Hoehler, Geobiology, 2004). As a consequence, the capacity for H2 generation in basaltic and ultramafic environments places significant constraints on the distribution and productivity of microbial populations. At present, however, geochemical reactions that might generate H2 in basaltic and ultramafic systems at temperatures sufficiently low to allow life to exist (<~150 ° C) remain very poorly known. I will summarize the currently available experimental data on H2 production during low-temperature alteration of basaltic and ultramfic rocks, including ongoing laboratory studies to refine the chemical reactions responsible for H2 generation. In addition, potential thermodynamic constraints on H2 production will be considered. Overall, the presently available data indicate that H2-based communities are likely to be considerably more productive in basaltic than ultramafic systems.

  18. Microbial Population and Community Dynamics on Plant Roots and Their Feedbacks on Plant Communities

    PubMed Central

    Bever, James D.; Platt, Thomas G.; Morton, Elise R.

    2012-01-01

    The composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology. PMID:22726216

  19. Effects of organic matter in livestock manure digester liquid on microbial community structure and in situ activity of anammox granules.

    PubMed

    Kindaichi, Tomonori; Awata, Takanori; Mugimoto, Yuichiro; Rathnayake, Rathnayake M L D; Kasahara, Shinsuke; Satoh, Hisashi

    2016-09-01

    Anaerobic ammonium oxidation (anammox) is a promising process for NH4(+)-rich wastewaters such as anaerobic digester liquids. In the present study, we investigated various properties of an up-flow column reactor containing anammox granules and fed with a real digester liquid at four different concentrations (Phases 1 to 4). The efficiencies of NH4(+) and NO2(-) removal decreased by up to 32% and 42%, respectively, in the digester-liquid-fed reactor (reactor-DL). When the performance of reactor-DL deteriorated, the community structure, spatial distribution, and in situ anammox activity in the two reactors were further investigated using 16S rRNA gene-based phylogenetic analysis, fluorescence in situ hybridization (FISH), and microelectrode measurements. The phylogenetic analysis and FISH results showed that non-anammox bacteria were predominant in the granule outer layers in reactor-DL, whereas anammox bacteria still dominated the granule interiors. Microelectrode measurements showed clear evidence of NH4(+) oxidation activity in the interiors of granules from reactor-DL. Batch experiments using anammox granules at different acetate concentrations indicated that concentrations up to 50 mM had no effects on the anammox activity, whereas inorganic carbon uptake decreased in the presence of acetate. The present study clearly shows that the anammox activity and anammox bacterial density in the granules were maintained after feeding the digester liquid to the reactor for 140 days. PMID:27314631

  20. Co-digestion of molasses or kitchen waste with high-rate activated sludge results in a diverse microbial community with stable methane production.

    PubMed

    De Vrieze, Jo; Plovie, Kristof; Verstraete, Willy; Boon, Nico

    2015-04-01

    Kitchen waste and molasses are organic waste streams with high organic content, and therefore are interesting substrates for renewable energy production by means of anaerobic digestion. Both substrates, however, often cause inhibition of the anaerobic digestion process, when treated separately, hence, co-digestion with other substrates is required to ensure stable methane production. In this research, A-sludge (sludge harvested from a high rate activated sludge system) was used to stabilize co-digestion with kitchen waste or molasses. Lab-scale digesters were fed with A-sludge and kitchen waste or molasses for a total period of 105 days. Increased methane production values revealed a stabilizing effect of concentrated A-sludge on kitchen waste digestion. Co-digestion of molasses with A-sludge also resulted in a higher methane production. Volumetric methane production rates up to 1.53 L L(-1) d(-1) for kitchen waste and 1.01 L L(-1) d(-1) for molasses were obtained by co-digestion with A-sludge. The stabilizing effect of A-sludge was attributed to its capacity to supplement various nutrients. Microbial community results demonstrated that both reactor conditions and substrate composition determined the nature of the bacterial community, although there was no direct influence of micro-organisms in the substrate itself, while the methanogenic community profile remained constant as long as optimal conditions were maintained. PMID:25617871

  1. Effects of biochar blends on microbial community composition in two Coastal Plain soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated both positive and negative effects on soil microbial communities. These effect...

  2. Impact of no-tillage and conventional tillage systems on soil microbial communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil management practices influence soil physical and chemical characteristics and bring about changes in the soil microbial community structure and function. In this study, the effects of long-term conventional and no-tillage practices on microbial community structure, enzyme activities, and select...

  3. Enhanced waste activated sludge digestion using a submerged anaerobic dynamic membrane bioreactor: performance, sludge characteristics and microbial community

    PubMed Central

    Yu, Hongguang; Wang, Zhiwei; Wu, Zhichao; Zhu, Chaowei

    2016-01-01

    Anaerobic digestion (AD) plays an important role in waste activated sludge (WAS) treatment; however, conventional AD (CAD) process needs substantial improvements, especially for the treatment of WAS with low solids content and poor anaerobic biodegradability. Herein, we propose a submerged anaerobic dynamic membrane bioreactor (AnDMBR) for simultaneous WAS thickening and digestion without any pretreatment. During the long-term operation, the AnDMBR exhibited an enhanced sludge reduction and improved methane production over CAD process. Moreover, the biogas generated in the AnDMBR contained higher methane content than CAD process. Stable carbon isotopic signatures elucidated the occurrence of combined methanogenic pathways in the AnDMBR process, in which hydrogenotrophic methanogenic pathway made a larger contribution to the total methane production. It was also found that organic matter degradation was enhanced in the AnDMBR, thus providing more favorable substrates for microorganisms. Pyrosequencing revealed that Proteobacteria and Bacteroidetes were abundant in bacterial communities and Methanosarcina and Methanosaeta in archaeal communities, which played an important role in the AnDMBR system. This study shed light on the enhanced digestion of WAS using AnDMBR technology. PMID:26830464

  4. Enhanced waste activated sludge digestion using a submerged anaerobic dynamic membrane bioreactor: performance, sludge characteristics and microbial community

    NASA Astrophysics Data System (ADS)

    Yu, Hongguang; Wang, Zhiwei; Wu, Zhichao; Zhu, Chaowei

    2016-02-01

    Anaerobic digestion (AD) plays an important role in waste activated sludge (WAS) treatment; however, conventional AD (CAD) process needs substantial improvements, especially for the treatment of WAS with low solids content and poor anaerobic biodegradability. Herein, we propose a submerged anaerobic dynamic membrane bioreactor (AnDMBR) for simultaneous WAS thickening and digestion without any pretreatment. During the long-term operation, the AnDMBR exhibited an enhanced sludge reduction and improved methane production over CAD process. Moreover, the biogas generated in the AnDMBR contained higher methane content than CAD process. Stable carbon isotopic signatures elucidated the occurrence of combined methanogenic pathways in the AnDMBR process, in which hydrogenotrophic methanogenic pathway made a larger contribution to the total methane production. It was also found that organic matter degradation was enhanced in the AnDMBR, thus providing more favorable substrates for microorganisms. Pyrosequencing revealed that Proteobacteria and Bacteroidetes were abundant in bacterial communities and Methanosarcina and Methanosaeta in archaeal communities, which played an important role in the AnDMBR system. This study shed light on the enhanced digestion of WAS using AnDMBR technology.

  5. Enhanced waste activated sludge digestion using a submerged anaerobic dynamic membrane bioreactor: performance, sludge characteristics and microbial community.

    PubMed

    Yu, Hongguang; Wang, Zhiwei; Wu, Zhichao; Zhu, Chaowei

    2016-01-01

    Anaerobic digestion (AD) plays an important role in waste activated sludge (WAS) treatment; however, conventional AD (CAD) process needs substantial improvements, especially for the treatment of WAS with low solids content and poor anaerobic biodegradability. Herein, we propose a submerged anaerobic dynamic membrane bioreactor (AnDMBR) for simultaneous WAS thickening and digestion without any pretreatment. During the long-term operation, the AnDMBR exhibited an enhanced sludge reduction and improved methane production over CAD process. Moreover, the biogas generated in the AnDMBR contained higher methane content than CAD process. Stable carbon isotopic signatures elucidated the occurrence of combined methanogenic pathways in the AnDMBR process, in which hydrogenotrophic methanogenic pathway made a larger contribution to the total methane production. It was also found that organic matter degradation was enhanced in the AnDMBR, thus providing more favorable substrates for microorganisms. Pyrosequencing revealed that Proteobacteria and Bacteroidetes were abundant in bacterial communities and Methanosarcina and Methanosaeta in archaeal communities, which played an important role in the AnDMBR system. This study shed light on the enhanced digestion of WAS using AnDMBR technology. PMID:26830464

  6. Next-Generation Pyrosequencing Analysis of Microbial Biofilm Communities on Granular Activated Carbon in Treatment of Oil Sands Process-Affected Water

    PubMed Central

    Islam, M. Shahinoor; Zhang, Yanyan; McPhedran, Kerry N.

    2015-01-01

    The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>109 gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds. PMID:25841014

  7. Next-generation pyrosequencing analysis of microbial biofilm communities on granular activated carbon in treatment of oil sands process-affected water.

    PubMed

    Islam, M Shahinoor; Zhang, Yanyan; McPhedran, Kerry N; Liu, Yang; Gamal El-Din, Mohamed

    2015-06-15

    The development of biodegradation treatment processes for oil sands process-affected water (OSPW) has been progressing in recent years with the promising potential of biofilm reactors. Previously, the granular activated carbon (GAC) biofilm process was successfully employed for treatment of a large variety of recalcitrant organic compounds in domestic and industrial wastewaters. In this study, GAC biofilm microbial development and degradation efficiency were investigated for OSPW treatment by monitoring the biofilm growth on the GAC surface in raw and ozonated OSPW in batch bioreactors. The GAC biofilm community was characterized using a next-generation 16S rRNA gene pyrosequencing technique that revealed that the phylum Proteobacteria was dominant in both OSPW and biofilms, with further in-depth analysis showing higher abundances of Alpha- and Gammaproteobacteria sequences. Interestingly, many known polyaromatic hydrocarbon degraders, namely, Burkholderiales, Pseudomonadales, Bdellovibrionales, and Sphingomonadales, were observed in the GAC biofilm. Ozonation decreased the microbial diversity in planktonic OSPW but increased the microbial diversity in the GAC biofilms. Quantitative real-time PCR revealed similar bacterial gene copy numbers (>10(9) gene copies/g of GAC) for both raw and ozonated OSPW GAC biofilms. The observed rates of removal of naphthenic acids (NAs) over the 2-day experiments for the GAC biofilm treatments of raw and ozonated OSPW were 31% and 66%, respectively. Overall, a relatively low ozone dose (30 mg of O3/liter utilized) combined with GAC biofilm treatment significantly increased NA removal rates. The treatment of OSPW in bioreactors using GAC biofilms is a promising technology for the reduction of recalcitrant OSPW organic compounds. PMID:25841014

  8. Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China.

    PubMed

    Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

    2016-01-01

    The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community. PMID:27241173

  9. Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China

    NASA Astrophysics Data System (ADS)

    Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

    2016-05-01

    The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community.

  10. Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China

    PubMed Central

    Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

    2016-01-01

    The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community. PMID:27241173

  11. Succession in a microbial mat community: A gaian perspective

    NASA Astrophysics Data System (ADS)

    Stolz, J. F.

    The Gaia hypothesis originally proposed by James E. Lovelock states that the composition, oxidation-reduction state and temperature of the troposphere are actively regulated by the activities of the biota. The gaian concept has been extrapolated to include the composition of surface sediments through the process of biomineralization. The stratified microbial community dominated by the cyanobacterium Microcoleus chthonoplastes is actively involved in the deposition of laminated sediments at Laguna Figueroa, Baja California, Mexico. Unusually heavy rains in the winters of 1979 and 1980 flooded the evaporite flat with up to 3 meters of meteoric water and deposited 5 - 10 cm of allocthonous sediment. The composition of the microbial community changed as a succession of dominating microbial species ensued, ultimately leading to the recolonization of the surface sediment by the original Microcoleus-dominated community. The resiliency of bacterial communities is suggested to be an important mechanism of gaian control systems. Present address: Control and Energy Conversion Division, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, U.S.A.

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

    PubMed

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

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. PMID:26974565

  13. 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...

  14. 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. PMID:19020556

  15. Prevention of microbial communities: novel approaches based natural products.

    PubMed

    Mogosanu, George D; Grumezescu, Alexandru M; Huang, Keng-Shiang; Bejenaru, Ludovic E; Bejenaru, Cornelia

    2015-01-01

    Firmly attached to different living or non-living, solid or fluid surfaces rich in nutrients and moisture, microbial biofilm is a matter of great interest due to its major importance for the healthcare community. Depending on common strategies such as mutual protection and hibernation (quiescent bacteria), the resistance, survival and virulence of microbial communities have large implications for human pathology, clinical environment and biomedical devices. The microbial biofilm is continuously changing, stimulating inflammation, increasing vascular permeability and preventing the action of macrophages. About 80% of human infections affecting the gastrointestinal, genitourinary and respiratory systems, oral mucosa and teeth, eyes, middle ear and skin are caused by biofilm-associated microorganisms. Therefore, the search for modern strategies is even more important as microbial biofilms resistant to conventional antibiotics, antiseptics and disinfectants are involved in the frequent treatment failures of some chronic inflammatory diseases and wounds. Natural products containing secondary metabolites, such as aromatic compounds, sulphurated derivatives, terpenoids (essential oils) and alkaloids as quorum-sensing inhibitors and biofilm disruptors, are promising alternatives for the prophylaxis and treatment of chronic infections. Surface modification of medical devices with non-polar functionalized nanoparticles stabilizes the natural compounds antibiofilm activity and inhibits microbial adhesion and biofilm formation and growth for a longer period of time. In this regard, an interdisciplinary approach is needed due to the large number of natural derivatives alone or in combination with biocompatible and biodegradable micro-/ nano-engineered materials. PMID:25594287

  16. 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

    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 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.

  17. 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

  18. Microbial communities in pre-columbian coprolites.

    PubMed

    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

  19. Functional analysis of natural microbial consortia using community proteomics

    SciTech Connect

    Verberkmoes, Nathan C; Denef, Vincent; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2009-01-01

    It is widely accepted that microbial communities, not individual microorganisms, are the relevant ecological units, yet what we know about metabolic functioning of microbial communities could be written on a postage stamp. The recent developments in comprehensive molecular methods promise to gain a better understanding of how organisms within communities interact and how communities and their populations evolve. Here we highlight recent advances and insights gathered by the application of proteogenomics to microbial communities. We explore the history of how unrelated fields of microbial ecology, genomics, biological mass spectrometry and informatics converge to the development of a new field of metaproteomics.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-11-28

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

  2. 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

  3. Long-Term Field Study of Microbial Community and Dechlorinating Activity Following Carboxymethyl Cellulose-Stabilized Nanoscale Zero-Valent Iron Injection.

    PubMed

    Kocur, Chris M D; Lomheim, Line; Molenda, Olivia; Weber, Kela P; Austrins, Leanne M; Sleep, Brent E; Boparai, Hardiljeet K; Edwards, Elizabeth A; O'Carroll, Denis M

    2016-07-19

    Nanoscale zerovalent iron (nZVI) is an emerging technology for the remediation of contaminated sites. However, there are concerns related to the impact of nZVI on in situ microbial communities. In this study, the microbial community composition at a contaminated site was monitored over two years following the injection of nZVI stabilized with carboxymethyl cellulose (nZVI-CMC). Enhanced dechlorination of chlorinated ethenes to nontoxic ethene was observed long after the expected nZVI oxidation. The abundance of Dehalococcoides (Dhc) and vinyl chloride reductase (vcrA) genes, monitored using qPCR, increased by over an order of magnitude in nZVI-CMC-impacted wells. The entire microbial community was tracked using 16S rRNA gene amplicon pyrosequencing. Following nZVI-CMC injection, a clear shift in microbial community was observed, with most notable increases in the dechlorinating genera Dehalococcoides and Dehalogenimonas. This study suggests that coupled abiotic degradation (i.e., from reaction with nZVI) and biotic degradation fueled by CMC led to the long-term degradation of chlorinated ethenes at this field site. Furthermore, nZVI-CMC addition stimulated dehalogenator growth (e.g., Dehalococcoides) and biotic degradation of chlorinated ethenes. PMID:27305345

  4. Next-Generation Sequencing of Microbial Communities in the Athabasca River and Its Tributaries in Relation to Oil Sands Mining Activities

    PubMed Central

    Yergeau, Etienne; Lawrence, John R.; Sanschagrin, Sylvie; Waiser, Marley J.; Korber, Darren R.

    2012-01-01

    The Athabasca oil sands deposit is the largest reservoir of crude bitumen in the world. Recently, the soaring demand for oil and the availability of modern bitumen extraction technology have heightened exploitation of this reservoir and the potential unintended consequences of pollution in the Athabasca River. The main objective of the present study was to evaluate the potential impacts of oil sands mining on neighboring aquatic microbial community structure. Microbial communities were sampled from sediments in the Athabasca River and its tributaries as well as in oil sands tailings ponds. Bacterial and archaeal 16S rRNA genes were amplified and sequenced using next-generation sequencing technology (454 and Ion Torrent). Sediments were also analyzed for a variety of chemical and physical characteristics. Microbial communities in the fine tailings of the tailings ponds were strikingly distinct from those in the Athabasca River and tributary sediments. Microbial communities in sediments taken close to tailings ponds were more similar to those in the fine tailings of the tailings ponds than to the ones from sediments further away. Additionally, bacterial diversity was significantly lower in tailings pond sediments. Several taxonomic groups of Bacteria and Archaea showed significant correlations with the concentrations of different contaminants, highlighting their potential as bioindicators. We also extensively validated Ion Torrent sequencing in the context of environmental studies by comparing Ion Torrent and 454 data sets and by analyzing control samples. PMID:22923391

  5. Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity.

    PubMed

    Sun, Weimin; Dong, Yiran; Gao, Pin; Fu, Meiyan; Ta, Kaiwen; Li, Jiwei

    2015-06-01

    Although oilfields harbor a wide diversity of microorganisms with various metabolic potentials, our current knowledge about oil-degrading bacteria is limited because the vast majority of oil-degrading bacteria remain uncultured. In the present study, microbial communities in nine oil-contaminated soils collected from Daqing and Changqing, two of the largest oil fields in China, were characterized through highthroughput sequencing of 16S rRNA genes. Bacteria related to the phyla Proteobacteria and Actinobacteria were dominant in four and three samples, respectively. At the genus level, Alkanindiges, Arthrobacter, Pseudomonas, Mycobacterium, and Rhodococcus were frequently detected in nine soil samples. Many of the dominant genera were phylogenetically related to the known oil-degrading species. The correlation between physiochemical parameters within the microbial communities was also investigated. Canonical correspondence analysis revealed that soil moisture, nitrate, TOC, and pH had an important impact in shaping the microbial communities of the hydrocarbon-contaminated soil. This study provided an in-depth analysis of microbial communities in oilcontaminated soil and useful information for future bioremediation of oil contamination. PMID:26025169

  6. 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

  7. 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. PMID

  8. 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

  9. Microbial communities in the deep subsurface

    NASA Astrophysics Data System (ADS)

    Krumholz, Lee R.

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

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

    ScienceCinema

    Konopka, Allan

    2012-02-29

    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.

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

    SciTech Connect

    Konopka, Allan

    2009-10-09

    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.

  12. Survival of a microbial soil community under Martian conditions

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

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

  13. Microbial Community Dynamics Associated with Rhizosphere Carbon Flow

    PubMed Central

    Butler, Jessica L.; Williams, Mark A.; Bottomley, Peter J.; Myrold, David D.

    2003-01-01

    Root-deposited photosynthate (rhizodeposition) is an important source of readily available carbon (C) for microbes in the vicinity of growing roots. Plant nutrient availability is controlled, to a large extent, by the cycling of this and other organic materials through the soil microbial community. Currently, our understanding of microbial community dynamics associated with rhizodeposition is limited. We used a 13C pulse-chase labeling procedure to examine the incorporation of rhizodeposition into individual phospholipid fatty acids (PLFAs) in the bulk and rhizosphere soils of greenhouse-grown annual ryegrass (Lolium multiflorum Lam. var. Gulf). Labeling took place during a growth stage in transition between active root growth and rapid shoot growth on one set of plants (labeling period 1) and 9 days later during the rapid shoot growth stage on another set of plants (labeling period 2). Temporal differences in microbial community composition were more apparent than spatial differences, with a greater relative abundance of PLFAs from gram-positive organisms (i15:0 and a15:0) in the second labeling period. Although more abundant, gram-positive organisms appeared to be less actively utilizing rhizodeposited C in labeling period 2 than in labeling period 1. Gram-negative bacteria associated with the 16:1ω5 PLFA were more active in utilizing 13C-labeled rhizodeposits in the second labeling period than in the first labeling period. In both labeling periods, however, the fungal PLFA 18:2ω6,9 was the most highly labeled. These results demonstrate the effectiveness of using 13C labeling and PLFA analysis to examine the microbial dynamics associated with rhizosphere C cycling by focusing on the members actively involved. PMID:14602642

  14. Environmental controls on microbial community cycling in modern marine stromatolites

    NASA Astrophysics Data System (ADS)

    Bowlin, Emily M.; Klaus, James S.; Foster, Jamie S.; Andres, Miriam S.; Custals, Lillian; Reid, R. Pamela

    2012-07-01

    Living stromatolites on the margins of Exuma Sound, Bahamas, are the only examples of modern stromatolites forming in open marine conditions similar to those that may have existed on Precambrian platforms. Six microbial mat types have previously been documented on the surfaces of stromatolites along the eastern side of Highborne Cay (Schizothrix, Solentia, heterotrophic biofilm, stalked diatom, tube diatom and Phormidium mats). Cycling of these communities create laminae with distinct microstructures. Subsurface laminae thus represent a chronology of former surface mats. The present study documents the effects of environmental factors on surface microbial communities of modern marine stromatolites and identifies potential causes of microbial mat cycling. Mat type and burial state at 43 markers along a stromatolitic reef on the margin of Highborne Cay were monitored over a two-year period (2005-2006). Key environmental parameters (i.e., temperature, light, wind, water chemistry) were also monitored. Results indicated that the composition of stromatolite surface mats and transitions from one mat type to another are controlled by both seasonal and stochastic events. All six stromatolite mat communities at Highborne Cay showed significant correlations with water temperature. Heterotrophic biofilms, Solentia, stalked diatom and Phormidium mats showed positive correlations with temperature, whereas Schizothrix and tube diatom communities showed negative correlations. A significant correlation with light (photosynthetically active radiation, PAR) was detected only for the heterotrophic biofilm community. No significant correlations were found between mat type and the monitored wind intensity data, but field observations indicated that wind-related events such as storms and sand abrasion play important roles in the transitions from one mat type to another. An integrated model of stromatolite mat community cycling is developed that includes both predictable seasonal

  15. 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. PMID:26150308

  16. Computational meta'omics for microbial community studies

    PubMed Central

    Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis

    2013-01-01

    Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges. PMID:23670539

  17. Sampling microbial communities in the National Ecological Observatory Network

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  18. Principal methods for isolation and identification of soil microbial communities.

    PubMed

    Stefanis, Christos; Alexopoulos, Athanasios; Voidarou, Chrissa; Vavias, Stavros; Bezirtzoglou, Eugenia

    2013-01-01

    Soil microbial populations play crucial role in soil properties and influence below-ground ecosystem processes. Microbial composition and functioning changes the soil quality through decomposition of organic matter, recycling of nutrients, and biological control of parasites of plants. Moreover, the discovery that soil microbes may translate into benefits for biotechnology, management of agricultural, forest, and natural ecosystems, biodegradation of pollutants, and waste treatment systems maximized the need of scientists for the isolation and their characterization. Operations such as the production of antibiotics and enzymic activities from microorganisms of soil constitute objectives of industry in her effort to cope with the increase of population of earth and disturbance of environment and may ameliorate the effects of global climate change. In the past decades, new biochemical and molecular techniques have been developed in our effort to identify and classify soil bacteria. The goal of measuring the soil microbial diversity is difficult because of the limited knowledge about bacteria species and classification through families and orders. Molecular techniques extend our knowledge about microbial diversity and help the taxonomy of species. Measuring and monitoring soil microbial communities can lead us to better understanding of their composition and function in many ecosystem processes. PMID:22791233

  19. 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

  20. 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

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (<20 yrs old) from six different sites along the ridge axis at 9°N, East Pacific Rise were examined for microbial life. Total DNA was extracted from the basalt glass and screened for the presence of both bacteria and archaea using the PCR. Repeated attempts with different primer sets yielded no bacterial genes, whereas archaeal genes were quite abundant. A genetic fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP), was used to compare the archaeal community compositions among the six different basalts. Filtered deep-sea water samples (~15 L) were examined in parallel to identify any overlap between rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal

  1. 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

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

    PubMed Central

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

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm3 for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas. PMID:25674080

  3. Microbial Community Analysis of Fresh and Old Microbial Biofilms on Bayon Temple Sandstone of Angkor Thom, Cambodia

    PubMed Central

    Lan, Wensheng; Li, Hui; Wang, Wei-Dong; Katayama, Yoko

    2010-01-01

    The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences. The results showed that the retrieved sequences were clustered in 11 bacterial, 11 eukaryotic and two archaeal divisions with disparate communities (Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria; Alveolata, Fungi, Metazoa, Viridiplantae; Crenarchaeote, and Euyarchaeota). A comparison of the microbial communities between the fresh and old biofilms revealed that the bacterial community of old biofilm was very similar to the newly formed fresh biofilm in terms of bacterial composition, but the eukaryotic communities were distinctly different between these two. This information has important implications for understanding the formation process and development of the microbial diversity on the sandstone surfaces, and furthermore to the relationship between the extent of biodeterioration and succession of microbial communities on sandstone in tropic region. Electronic supplementary material The online version of this article (doi:10.1007/s00248-010-9707-5) contains supplementary material, which is available to authorized users. PMID:20593173

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  5. Subglacial Microbial Communities and Their Relationship to Bedrock Lithology

    NASA Astrophysics Data System (ADS)

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

    2002-12-01

    Recent studies have demonstrated the presence of abundant and metabolically active microbial communities in subglacial systems. However, the composition of these communities and the effect that they have on the geochemical dynamics of these systems is unclear. We compared the microbial community composition of samples from two glaciers: the Bench Glacier, Alaska, USA (BG), which overlies Cretaceous metasediments, and the John Evans Glacier, Ellesmere Island, Nunavut, Canada, (JEG) which overlies a carbonate/evaporite sequence of Cambrian/Ordovician/Silurian age. Bulk meltwater chemistry indicates that sulfide oxidation and carbonate dissolution account for 90% of the solute flux from BG, whereas gypsum/anhydrite and carbonate dissolution alone accounts for most of the flux from JEG. Microbes are abundant in the subglacial environment (ca. 1-5 x 105 cells ml-1) at both sites based on DAPI direct counts. Furthermore, early season subglacial waters (2002) at BG, have higher counts than both supraglacial and ice marginal environments. These data are consistent with previous findings in other subglacial systems. Two hundred and thirty three 16S rDNA clones were recovered from subglacial samples from the two glaciers in 1999 and grouped by RFLP analysis, followed by phylogenetic analysis of gene sequences. Interestingly, many (46%) 16S rDNAs from BG were most closely related to organisms that are capable of oxidation of sulfide and/or iron, whereas only a few (7%) of rDNAs from JEG were related to similar groups. The abundance of putative sulfide oxidizers in BG and their scarcity in JEG correlates with the meltwater chemistry of the two systems. These results are consistent with the hypothesis that microbial activity has an important role in contributing to the solute flux from glaciers. Group-specific phylogenetic probes have been developed for rDNAs that are abundant in these clone libraries. These probes are currently being used for quantitative dot

  6. Redox-driven regulation of microbial community morphogenesis

    PubMed Central

    Okegbe, Chinweike; Price-Whelan, Alexa; Dietrich, Lars E.P.

    2014-01-01

    During growth on surfaces, diverse microbial communities display topographies with captivating patterns. The quality and quantity of matrix excreted by resident cells play major roles in determining community architecture. Two current publications indicate that the cellular redox state and respiratory activity are important parameters affecting matrix output in the divergent bacteria Pseudomonas aeruginosa and Bacillus subtilis. These and related studies have identified regulatory proteins with the potential to respond to changes in redox state and respiratory electron transport and modulate the activity of the signal transduction pathways that control matrix production. These developments hint at the critical mechanistic links between environmental sensing and community behavior, and provide an exciting new context within which to interpret the molecular details of biofilm structure determination. PMID:24607644

  7. Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Ali; Or, Dani

    2016-04-01

    Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Mechanistic models of microbial processes in unsaturated aggregate pore networks revealed dynamic interplay between oxic and anoxic microsites that are jointly shaped by hydration and by aerobic and anaerobic microbial communities. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support significant anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3-D angular pore networks with profiles of water, carbon, and oxygen that vary with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain biogeochemical fluxes over the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of interest for hydrological and climate models.

  8. Effects of ultrasonic-assisted thermophilic bacteria pretreatment on hydrolysis, acidification, and microbial communities in waste-activated sludge fermentation process.

    PubMed

    Yang, Chunxue; Zhou, Aijuan; He, Zhangwei; Jiang, Lei; Guo, Zechong; Wang, Aijie; Liu, Wenzong

    2015-06-01

    A novel pretreatment method combining ultrasonic with thermophilic bacteria (Geobacillus sp. G1) was employed to pretreat waste-activated sludge (WAS) for enhancing the WAS hydrolysis and subsequent volatile fatty acids (VFAs) production. The soluble protein and carbohydrate were mostly released from intracellular ultrasonic-assisted Geobacillus sp. G1 pretreatment, and accumulated to 917 ± 70 and 772 ± 89 mg COD/L, respectively, which were 2.53- and 2.62-fold higher than that obtained in control test. Excitation emission matrix (EEM) fluorescence spectroscopy revealed the highest fluorescence intensity (FI) of protein-like substances, indicating the synergistic effect of ultrasonic and Geobacillus sp. G1 pretreatments on WAS hydrolysis. The maximum VFAs accumulation was 4437 ± 15 mg COD/L obtained in ultrasonic-assisted Geobacillus sp. G1 pretreatment test. High-throughput pyrosequencing analysis investigated that the microbial communities were substantial determined by the pretreatment used. The hydrolysis enhancement was caused by an increase in extracellular enzymes, which was produced by one of dominant species Caloramator sp. The positive effect was well explained to the enhancement of WAS hydrolysis and final VFAs accumulation. PMID:25874413

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

    NASA Astrophysics Data System (ADS)

    Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

    2016-09-01

    Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

  10. Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities

    PubMed Central

    Knierim, Bernhard; Luef, Birgit; Wilmes, Paul; Webb, Richard I.; Auer, Manfred; Comolli, Luis R.; Banfield, Jillian F.

    2014-01-01

    Transmission electron microscopy (TEM) can provide ultrastructural information for cells in microbial community samples and phylogenetic information can be recovered via molecular surveys. Here we report an approach to link these datasets by coupling fluorescence in situ hybridization (FISH) with either conventional biological or cryogenic TEM. The method could revolutionize understanding of the organization and functioning of microbial communities in natural systems. PMID:23757227

  11. Factors Affecting Soil Microbial Community Structure in Tomato Cropping Systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. We identified some of the most important factors controlling microbial biomass and community structure in an agroecosystem utilizing tomato plants with the following nine tre...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  13. Soil amendments yield persisting changes in the microbial communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  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. Community history affects the predictability of microbial ecosystem development

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

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

    2011-03-01

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

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

    PubMed

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

    2011-03-01

    Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types. PMID:21608471

  18. Carbon availability structures microbial community composition and function in soil aggregate fractions

    NASA Astrophysics Data System (ADS)

    Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

    2014-12-01

    Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of

  19. Water regime history drives responses of soil Namib Desert microbial communities to wetting events

    PubMed Central

    Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

    2015-01-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities. PMID:26195343

  20. Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

    PubMed

    Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A

    2015-01-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities. PMID:26195343

  1. Water regime history drives responses of soil Namib Desert microbial communities to wetting events

    NASA Astrophysics Data System (ADS)

    Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

    2015-07-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

  2. Microbial activity at gigapascal pressures.

    PubMed

    Sharma, Anurag; Scott, James H; Cody, George D; Fogel, Marilyn L; Hazen, Robert M; Hemley, Russell J; Huntress, Wesley T

    2002-02-22

    We observed physiological and metabolic activity of Shewanella oneidensis strain MR1 and Escherichia coli strain MG1655 at pressures of 68 to 1680 megapascals (MPa) in diamond anvil cells. We measured biological formate oxidation at high pressures (68 to 1060 MPa). At pressures of 1200 to 1600 MPa, living bacteria resided in fluid inclusions in ice-VI crystals and continued to be viable upon subsequent release to ambient pressures (0.1 MPa). Evidence of microbial viability and activity at these extreme pressures expands by an order of magnitude the range of conditions representing the habitable zone in the solar system. PMID:11859192

  3. 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

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

    PubMed

    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

  5. Characterization Of Sponge-Associated Microbial Communities

    NASA Astrophysics Data System (ADS)

    Bailey, K. L.; Weisz, J.; Lindquist, N.

    2004-12-01

    To more fully understand the endosymbiotic relationship between sponges and microorganisms, it is necessary to characterize the microbial communities of the sponges. In this study, DNA was extracted from each of three individual sponges from four sponge species collected in a shallow mangrove cut in Florida Bay near Key Largo, Florida. A fragment of the 16S rRNA gene from sponge-associated bacteria was amplified using the polymerase chain reaction (PCR). The resulting PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), which separates DNA fragments based on their sequence differences. Some 16S sequences appeared to be shared by each of the four sponge species, while other fragments found in only particular species likely represent unique bacterial strains that play a role in sponge nutrition.

  6. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community

    PubMed Central

    Zoccarato, Luca; Celussi, Mauro; Pallavicini, Alberto; Fonda Umani, Serena

    2016-01-01

    Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of

  7. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community.

    PubMed

    Zoccarato, Luca; Celussi, Mauro; Pallavicini, Alberto; Fonda Umani, Serena

    2016-01-01

    Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of

  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. Field Evidence for Magnetite Formation by a Methanogenic Microbial Community

    NASA Astrophysics Data System (ADS)

    Rossbach, S.; Beaver, C. L.; Williams, A.; Atekwana, E. A.; Slater, L. D.; Ntarlagiannis, D.; Lund, A.

    2015-12-01

    The aged, subsurface petroleum spill in Bemidji, Minnesota, has been surveyed with magnetic susceptibility (MS) measurements. High MS values were found in the free-product phase around the fluctuating water table. Although we had hypothesized that high MS values are related to the occurrence of the mineral magnetite resulting from the activity of iron-reducing bacteria, our microbial analysis pointed to the presence of a methanogenic microbial community at the locations and depths of the highest MS values. Here, we report on a more detailed microbial analysis based on high-throughput sequencing of the 16S rRNA gene of sediment samples from four consecutive years. In addition, we provide geochemical data (FeII/FeIII concentrations) to refine our conceptual model of methanogenic hydrocarbon degradation at aged petroleum spills and demonstrate that the microbial induced changes of sediment properties can be monitored with MS. The methanogenic microbial community at the Bemidji site consisted mainly of the syntrophic, hydrocarbon-degrading Smithella and the hydrogenotrophic, methane-generating Methanoregula. There is growing evidence in the literature that not only Bacteria, but also some methanogenic Archaea are able to reduce iron. In fact, a recent study reported that the methanogen Methanosarcina thermophila produced magnetite during the reduction of ferrihydrite in a laboratory experiment when hydrogen was present. Therefore, our finding of high MS values and the presence of magnetite in the methanogenic zone of an aged, subsurface petroleum spill could very well be the first field evidence for magnetite formation during methanogenic hydrocarbon degradation.

  10. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal.

    SciTech Connect

    Wilmes, P; Andersson, Anders F.; Lefsrud, Mark G; Wexler, Margaret; Shah, Manesh B; Zhang, B; Hettich, Robert {Bob} L; Bond, P. L.; Verberkmoes, Nathan C; Banfield, Jillian F.

    2008-01-01

    Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating organisms to achieve phosphate removal from wastewater. We used highresolution community proteomics to identify key metabolic pathways in "Candidatus Accumulibacter phosphatis"-mediated EBPR and to evaluate the contributions of co- 5 existing strains within the dominant population. Results highlight the importance of denitrification, fatty acid cycling and the glyoxylate bypass in EBPR. Despite overall strong similarity in protein profiles under anaerobic and aerobic conditions, fatty acid degradation proteins were more abundant during the anaerobic phase. By comprehensive genome-wide alignment of orthologous proteins, we uncovered strong 10 functional partitioning for enzyme variants involved in both core-metabolism and EBPR-specific pathways among the dominant strains. These findings emphasize the importance of genetic diversity in maintaining the stable performance of EBPR systems and demonstrate the power of integrated cultivation-independent genomics and proteomics for analysis of complex biotechnological systems.

  11. Microbial Community Functional Structures in Wastewater Treatment Plants as Characterized by GeoChip

    PubMed Central

    Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

    2014-01-01

    Background Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. Aims To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. Methods 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. Results High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. Conclusions This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs. PMID:24671164

  12. 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

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

    PubMed Central

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

    2014-01-01

    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. PMID:25388562

  14. Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.

    PubMed

    Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu

    2013-01-01

    Shotgun metagenomics has been applied to the studies of the functionality of various microbial communities. As a critical analysis step in these studies, biological pathways are reconstructed based on the genes predicted from metagenomic shotgun sequences. Pathway reconstruction provides insights into the functionality of a microbial community and can be used for comparing multiple microbial communities. The utilization of pathway reconstruction, however, can be jeopardized because of imperfect functional annotation of genes, and ambiguity in the assignment of predicted enzymes to biochemical reactions (e.g., some enzymes are involved in multiple biochemical reactions). Considering that metabolic functions in a microbial community are carried out by many enzymes in a collaborative manner, we present a probabilistic sampling approach to profiling functional content in a metagenomic dataset, by sampling functions of catalytically promiscuous enzymes within the context of the entire metabolic network defined by the annotated metagenome. We test our approach on metagenomic datasets from environmental and human-associated microbial communities. The results show that our approach provides a more accurate representation of the metabolic activities encoded in a metagenome, and thus improves the comparative analysis of multiple microbial communities. In addition, our approach reports likelihood scores of putative reactions, which can be used to identify important reactions and metabolic pathways that reflect the environmental adaptation of the microbial communities. Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/. PMID:23555216

  15. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure.

    PubMed

    Hanemaaijer, Mark; Röling, Wilfred F M; Olivier, Brett G; Khandelwal, Ruchir A; Teusink, Bas; Bruggeman, Frank J

    2015-01-01

    Microbial communities play important roles in health, industrial applications and earth's ecosystems. With current molecular techniques we can characterize these systems in unprecedented detail. However, such methods provide little mechanistic insight into how the genetic properties and the dynamic couplings between individual microorganisms give rise to their dynamic activities. Neither do they give insight into what we call "the community state", that is the fluxes and concentrations of nutrients within the community. This knowledge is a prerequisite for rational control and intervention in microbial communities. Therefore, the inference of the community structure from experimental data is a major current challenge. We will argue that this inference problem requires mathematical models that can integrate heterogeneous experimental data with existing knowledge. We propose that two types of models are needed. Firstly, mathematical models that integrate existing genomic, physiological, and physicochemical information with metagenomics data so as to maximize information content and predictive power. This can be achieved with the use of constraint-based genome-scale stoichiometric modeling of community metabolism which is ideally suited for this purpose. Next, we propose a simpler coarse-grained model, which is tailored to solve the inference problem from the experimental data. This model unambiguously relate to the more detailed genome-scale stoichiometric models which act as heterogeneous data integrators. The simpler inference models are, in our opinion, key to understanding microbial ecosystems, yet until now, have received remarkably little attention. This has led to the situation where the modeling of microbial communities, using only genome-scale models is currently more a computational, theoretical exercise than a method useful to the experimentalist. PMID:25852671

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

    PubMed Central

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

    2015-01-01

    Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

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

    PubMed

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

    2015-06-01

    Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

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

    PubMed

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

    2015-12-01

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

  19. Spatial variation in microbial community structure, richness, and diversity in an alluvial aquifer.

    PubMed

    Medihala, P G; Lawrence, J R; Swerhone, G D W; Korber, D R

    2012-09-01

    Relatively little is known regarding the spatial variability of microbial communities in aquifers where well fouling is an issue. In this study 2 water wells were installed in an alluvial aquifer located adjacent to the North Saskatchewan River and an associated piezometer network developed to facilitate the study of microbial community structure, richness, and diversity. Carbon utilization data analysis revealed reduced microbial activity in waters collected close to the wells. Functional PCR and quantitative PCR analysis indicated spatial variability in the potential for iron-, sulphate-, and nitrate-reducing activity at all locations in the aquifer. Denaturing gradient gel electrophoresis analysis of aquifer water samples using principal components analyses indicated that the microbial community composition was spatially variable, and denaturing gradient gel electrophoresis sequence analysis revealed that bacteria belonging to the genera Acidovorax , Rhodobacter , and Sulfuricurvum were common throughout the aquifer. Shannon's richness (H') and Pielou's evenness (J') indices revealed a varied microbial diversity (H' = 1.488-2.274) and an even distribution of microbial communities within the aquifer (J' = 0.811-0.917). Overall, these analyses revealed that the aquifer's microbial community varied spatially in terms of composition, richness, and metabolic activity. Such information may facilitate the diagnosis, prevention, and management of fouling. PMID:22913282

  20. Environmental Controls on the Activity of Aquifer Microbial Communities in the 300 Area of the Hanford Site

    SciTech Connect

    Konopka, Allan; Plymale, Andrew E.; Carvajal, Denny A.; Lin, Xueju; McKinley, James P.

    2013-11-06

    Aquifer microbes in the 300 Area of the Hanford Site in southeastern Washington State, USA are periodically exposed to U(VI) concentrations that can range up to 10 μM in small sediment fractures. Assays of 35 H-leucine incorporation indicated that both sediment-associated and planktonic microbes were metabolically active, and that organic C was growth-limiting in the sediments. Although bacteria suspended in native groundwater retained high activity when exposed to 100 μM U(VI), they were inhibited by U(VI) < 1 μM in synthetic groundwater that lacked added bicarbonate. Chemical speciation modeling suggested that positively-charged species and particularly (UO2)3(OH)5+ rose in concentration as more U(VI) was added to synthetic groundwater, but that carbonate complexes dominated U(VI) speciation in natural groundwater. U toxicity was relieved when increasing amounts of bicarbonate were added to synthetic groundwater containing 4.5 μM U(VI). Pertechnetate, an oxyanion that is another contaminant of concern at the Hanford Site, was not toxic to groundwater microbes at concentrations up to 125 μM.

  1. Microbial community structure accompanied with electricity production in a constructed wetland plant microbial fuel cell.

    PubMed

    Lu, Lu; Xing, Defeng; Ren, Zhiyong Jason

    2015-11-01

    This study reveals the complex structure of bacterial and archaeal communities associated with a Canna indica plant microbial fuel cell (PMFC) and its electricity production. The PMFC produced a maximum current of 105 mA/m(2) by utilizing rhizodeposits as the sole electron donor without any external nutrient or buffer supplements, which demonstrates the feasibility of PMFCs in practical oligotrophic conditions with low solution conductivity. The microbial diversity was significantly higher in the PMFC than non-plant controls or sediment-only controls, and pyrosequencing and clone library reveal that rhizodeposits conversion to current were carried out by syntrophic interactions between fermentative bacteria (e.g., Anaerolineaceae) and electrochemically active bacteria (e.g., Geobacter). Denitrifying bacteria and acetotrophic methanogens play a minor role in organics degradation, but abundant hydrogenotrophic methanogens and thermophilic archaea are likely main electron donor competitors. PMID:26066972

  2. Denitrification of industrial wastewater: Influence of glycerol addition on metabolic activity and community shifts in a microbial consortium.

    PubMed

    Cyplik, Paweł; Juzwa, Wojciech; Marecik, Roman; Powierska-Czarny, Jolanta; Piotrowska-Cyplik, Agnieszka; Czarny, Jakub; Drożdżyńska, Agnieszka; Chrzanowski, Lukasz

    2013-11-01

    The wastewater originating from explosives manufacturing plants are characterized by a high concentration of nitrates (3200mgNL(-1)), sulfates (1470mgL(-1)) and low pH (1.5) as well as the presence of organic compounds, such as nitroglycerin (1.9mgL(-1)) and nitroglycol (4.8mgL(-1)). The application of glycerol (C/N=3) at such a high concentration enabled complete removal of nitrates and did not cause the anaerobic glycerol metabolic pathway of the DNC4 consortium to activate, as confirmed by the low concentrations of 1,3-propanediol (0.16gL(-1)) and acetic acid (0.11gL(-1)) in the wastewater. Increasing the glycerol content (C/N=5) contributed to a notable increase in the concentration of both compounds: 1.12gL(-1) for acetic acid and 1.82 for 1,3-PD (1,3-propanediol). The nitrate reduction rate was at 44mgNg(-1) biomass d(-1). In order to assess the metabolic activity of the microorganisms, a method to determine the redox potential was employed. It was established, that the microorganisms can be divided into four groups, based on the determined denitrification efficiency and zero-order nitrate removal constants. The first group, involving Pseudomonas putida and Pseudomonas stutzeri, accounts for microorganisms capable of the most rapid denitrification, the second involves rapid denitrifying microbes (Citrobacter freundi and Pseudomonas alcaligenes), the third group are microorganisms exhibiting moderate denitrification ability: Achrobactrum xylosoxidans, Ochrobactrum intermedium and Stenotrophomonas maltophila, while the last group consists of slow denitrifying bacteria: Rodococcus rubber and Sphignobacterium multivorum. PMID:24161581

  3. 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

  4. Microbial Species Richness and Metabolic Activities in Hypersaline Microbial Mats: Insight into Biosignature Formation Through Lithification

    NASA Astrophysics Data System (ADS)

    Baumgartner, Laura K.; Dupraz, Christophe; Buckley, Daniel H.; Spear, John R.; Pace, Norman R.; Visscher, Pieter T.

    2009-11-01

    Microbial mats in the hypersaline lake of Salt Pan, Eleuthera, Bahamas, display a gradient of lithification along a transect from the center to the shore of the lake. These mats exist under similar geochemical conditions, with light quantity and quality as the sole major environmental difference. Therefore, we hypothesized that the microbial community may be driving the differences in lithification and, by extension, mineral biosignature formation. The lithifying and non-lithifying mat communities were compared (via 16S rRNA gene sequencing, 485 and 464 sequences, respectively) over both temporal and spatial scales. Seven bacterial groups dominated in all the microbial mat libraries: bacteriodetes, alphaproteobacteria, deltaproetobacteria, chloroflexi, spirochaetes, cyanobacteria, and planctomycetes. The mat communities were all significantly different over space, time, and lithification state. Species richness is significantly higher in the non-lithifying mats, potentially due to differences in mat structure and activity. This increased richness may impact lithification and, hence, biosignature production.

  5. Quantitative determination of microbial activity and community nutritional status in estuarine sediments: evidence for a disturbance artifact

    NASA Technical Reports Server (NTRS)

    Findlay, R. H.; Pollard, P. C.; Moriarty, D. J.; White, D. C.

    1985-01-01

    In estuarine sediments with a high degree of vertical heterogeneity in reduced substrate and terminal electron acceptor concentrations, the method of exposure of the microbiota to labeled substrates can introduce a "disturbance artifact" into measures of metabolic activity. The detection of this artifact is based on quantitative measurement of the relative rates of incorporation of [14C]acetate into phospholipid fatty acids (PLFA) and endogenous storage lipid, poly-beta-hydroxyalkanoate (PHA). Previous studies have shown that PLFA synthesis measures cellular growth and that PHA synthesis measures carbon accumulation (unbalanced growth). The "disturbance artifact" of exposure to [14C]acetate was demonstrated by comparing injection of a core with the usual or pore-water replacement or slurry techniques. Only injection of labeled substrate allowed detection of preassay disturbance of the sediment with a garden rake. The raking increased PLFA synthesis with little effect to differences in concentration or distribution of [14C]acetate in the 10-min incubation. Bioturbation induced by sand dollar feeding in estuarine sediment could be detected in an increased PLFA/PHA ratio which was due to decreased PHA synthesis if the addition of labeled substrate was by the injection technique. Addition of labeled precursors to sediment by slurry or pore-water replacement induces greater disturbance artifacts than injection techniques.

  6. 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

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

    PubMed

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

    2016-01-01

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

  8. 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

  9. The viability of native microbial communities in martian environment (model)

    NASA Astrophysics Data System (ADS)

    Vorobyova, Elena; Cheptcov, Vladimir; Pavlov, Anatolyi; Vdovina, Mariya; Lomasov, Vladimir

    For today the important direction in astrobiology is the experimental simulation of extraterrestrial habitats with the assessment of survivability of microorganisms in such conditions. A new task is to investigate the resistance of native microbial ecosystems which are well adapted to the environment and develop unique protection mechanisms that enable to ensure biosphere formation. The purpose of this research was to study the viability of microorganisms as well as viability of native microbial communities of arid soils and permafrost under stress conditions simulating space environment and martian regolith environment, estimation of duration of Earth like life in the Martian soil. The experimental data obtained give the proof of the preservation of high population density, biodiversity, and reproduction activity under favorable conditions in the Earth analogues of Martian soil - arid soils (Deserts of Israel and Morocco) and permafrost (East Siberia, Antarctica), after the treatment of samples by ionizing radiation dose up to 100 kGy at the pressure of 1 torr, temperature (- 50oC) and in the presence of perchlorate (5%). It was shown that in simulated conditions close to the parameters of the Martian regolith, the diversity of natural bacterial communities was not decreased, and in some cases the activation of some bacterial populations occurred in situ. Our results allow suggesting that microbial communities like those that inhabit arid and permafrost ecosystems on the Earth, can survive at least 500 thousand years under conditions of near surface layer of the Martian regolith. Extrapolation of the data according to the intensity of ionizing radiation to the open space conditions allows evaluating the potential lifespan of cells inside meteorites as 20-50 thousand years at least. In this work new experimental data have been obtained confirming the occurrence of liquid water and the formation of wet soil layer due to sublimation of ice when the temperature of the

  10. 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.

  11. Marine microbial community dynamics and their ecological interpretation.

    PubMed

    Fuhrman, Jed A; Cram, Jacob A; Needham, David M

    2015-03-01

    Recent advances in studying the dynamics of marine microbial communities have shown that the composition of these communities follows predictable patterns and involves complex network interactions, which shed light on the underlying processes regulating these globally important organisms. Such 'holistic' (or organism- and system-based) studies of these communities complement popular reductionist, often culture-based, approaches for understanding organism function one gene or protein at a time. In this Review, we summarize our current understanding of marine microbial community dynamics at various scales, from hours to decades. We also explain how the data illustrate community resilience and seasonality, and reveal interactions among microorganisms. PMID:25659323

  12. Interspecies interactions are an integral determinant of microbial community dynamics

    PubMed Central

    Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

    2015-01-01

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

  13. Interspecies interactions are an integral determinant of microbial community dynamics.

    PubMed

    Aziz, Fatma A A; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

    2015-01-01

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and "interspecies interaction," were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, "interspecies interaction," a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

  14. Microbial community dynamics alleviate stoichiometric constraints during litter decay

    PubMed Central

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

    2014-01-01

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

  15. Microbial community dynamics alleviate stoichiometric constraints during litter decay.

    PubMed

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

    2014-06-01

    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

  16. Denitrification and the denitrifier community in coastal microbial mats.

    PubMed

    Fan, Haoxin; Bolhuis, Henk; Stal, Lucas J

    2015-03-01

    Denitrification was measured in three structurally different coastal microbial mats by using the stable isotope technique. The composition of the denitrifying community was determined by analyzing the nitrite reductase (nirS and nirK) genes using clone libraries and the GeoChip. The highest potential rate of denitrification (7.0 ± 1.0 mmol N m(-2) d(-1)) was observed during summer at station 1 (supra-littoral). The rates of denitrification were much lower in the stations 2 (marine) and 3 (intermediate) (respectively 0.1 ± 0.05 and 0.7 ± 0.2 mmol N m(-2) d(-1)) and showed less seasonality when compared to station 1. The denitrifying community at station 1 was also more diverse than that at station 2 and 3, which were more similar to each other than either of these stations to station 1. In all three stations, the diversity of both nirS and nirK denitrifiers was higher in summer when compared to winter. The location along the tidal gradient seems to determine the composition, diversity and activity of the denitrifier community, which may be driven by salinity, nitrate/nitrite and organic carbon. Both nirS and nirK denitrifiers are equally present and therefore they are likely to play a role in the denitrification of the microbial mats studied. PMID:25764561

  17. Temporal variation in the nitrogen uptake competition between plant community and soil microbial community

    NASA Astrophysics Data System (ADS)

    Legay, N.; Lavorel, S.; Personeni, E.; Bataillé, M. P.; Robson, T. M.; Clément, J. C.

    2012-04-01

    1. Subalpine grasslands are characterized by important seasonal variations and like in others cold environments, the existence of seasonal variations of nitrogen (N) dynamics is strongly plausible. It has been shown that plants and microbes were in competition for nitrogen acquisition mainly during the growing season and particularly at plant biomass peak. During snowmelt, plants could benefit from a decrease in competition potential by microbes given a greater N uptake and freeze-thaw cycles restricting microbial growth. In managed grasslands, these probable interactions are furthermore influenced by recent changes in management, and associated modifications in plant and microbial communities. A previous isotope tracing experiment during the biomass peak suggested that in more intensely managed grasslands, plants exerted a greater control over N cycling than microorganisms, and that soil N availability was stimulated by a greater nitrogen uptake by plants and microbes allowing nutrients to be more readily returned to the soil. 2. A pulse of 15N was added to estimate if the dynamics of N uptake between plants and microbes observed at the biomass peak was applicable at snowmelt. We also asked if the modifications of N dynamics observed depend on management activities across four different grassland types representing decreasing management intensities, from formerly cultivated terraces, either mown or only lightly grazed to unterraced permanent grasslands, either mown or only very lightly grazed. 3. In all grasslands, N pools of aboveground plants were smaller in May than in July while root N pools were greater, and the intrinsic plant uptake was 2 at 5 times weaker in May. N microbial pools were higher in May that in July, while microbial N uptake was 10 to 100 times smaller during snowmelt than at the biomass peak. In spite of the fact that microbial N pools were still larger than the plant N pool, in terms of plants vs microbes competition for N, a microbe N

  18. [Methanogenic destruction of (amino)aromatic compounds by anaerobic microbial communities].

    PubMed

    Lin'kova, Iu V; D'iakonova, A T; Gladchenko, M A; Kaliuzhnyĭ, S A; Kotova, I B; Stams, A; Netrusov, A I

    2011-01-01

    Destruction of a number of aromatic substrates by anaerobic microbial communities was studied. Active methanogenic microbial communities decomposing aminoaromatic acids and azo dyes into CH4 and CO2 were isolated. Products of primary conversion were found to be 2-hydroxybenzyl and benzyl alcohols gradually transforming into benzoate. It was shown that isolated microbial communities are capable of converting the initial substrates--benzyl alcohol, benzoate, salicylic acid, and golden yellow azo dye--into biogas without a lag-phase but with different velocities. Aromatic and linear intermediates of biodestruction of aromatic amines by obtained enrichment cultures were determined for the first time. Selective effect of aromatic substrates on a microbial community that was expressed in decrease in diversity and gradual change of dominant morphotypes was revealed. PMID:22232897

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

    DOE PAGESBeta

    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 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

  20. 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.

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

    PubMed

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

    2011-09-01

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

  2. 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.

  3. Distributions of microbial activities in deep subseafloor sediments

    NASA Technical Reports Server (NTRS)

    D'Hondt, Steven; Jorgensen, Bo Barker; Miller, D. Jay; Batzke, Anja; Blake, Ruth; Cragg, Barry A.; Cypionka, Heribert; Dickens, Gerald R.; Ferdelman, Timothy; Hinrichs, Kai-Uwe; Holm, Nils G.; Mitterer, Richard; Spivack, Arthur; Wang, Guizhi; Bekins, Barbara; Engelen, Bert; Ford, Kathryn; Gettemy, Glen; Rutherford, Scott D.; Sass, Henrik; Skilbeck, C. Gregory; Aiello, Ivano W.; Guerin, Gilles; House, Christopher H.; Inagaki, Fumio

    2004-01-01

    Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.

  4. In-Drift Microbial Communities Model Validation Calculations

    SciTech Connect

    D. M. Jolley

    2001-09-24

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

  5. In-Drift Microbial Communities Model Validation Calculation

    SciTech Connect

    D. M. Jolley

    2001-10-31

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

  6. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    SciTech Connect

    D.M. Jolley

    2001-12-18

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

  7. The subzero microbiome: microbial activity in frozen and thawing soils.

    PubMed

    Nikrad, Mrinalini P; Kerkhof, Lee J; Häggblom, Max M

    2016-06-01

    Most of the Earth's biosphere is characterized by low temperatures (<5°C) and cold-adapted microorganisms are widespread. These psychrophiles have evolved a complex range of adaptations of all cellular constituents to counteract the potentially deleterious effects of low kinetic energy environments and the freezing of water. Microbial life continues into the subzero temperature range, and this activity contributes to carbon and nitrogen flux in and out of ecosystems, ultimately affecting global processes. Microbial responses to climate warming and, in particular, thawing of frozen soils are not yet well understood, although the threat of microbial contribution to positive feedback of carbon flux is substantial. To date, several studies have examined microbial community dynamics in frozen soils and permafrost due to changing environmental conditions, and some have undertaken the complicated task of characterizing microbial functional groups and how their activity changes with changing conditions, either in situ or by isolating and characterizing macromolecules. With increasing temperature and wetter conditions microbial activity of key microbes and subsequent efflux of greenhouse gases also increase. In this review, we aim to provide an overview of microbial activity in seasonally frozen soils and permafrost. With a more detailed understanding of the microbiological activities in these vulnerable soil ecosystems, we can begin to predict and model future expectations for carbon release and climate change. PMID:27106051

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

    PubMed

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

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  9. Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure

    PubMed Central

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

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

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

    USGS Publications Warehouse

    Chapelle, F.H.; O'Neill, K.; 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.

  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. PMID:26509157

  12. Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities

    PubMed Central

    Deng, Ye; He, Zhili; Xu, Meiying; Qin, Yujia; Van Nostrand, Joy D.; Wu, Liyou; Roe, Bruce A.; Wiley, Graham; Hobbie, Sarah E.; Reich, Peter B.

    2012-01-01

    Pyrosequencing analysis of 16S rRNA genes was used to examine impacts of elevated CO2 (eCO2) on soil microbial communities from 12 replicates each from ambient CO2 (aCO2) and eCO2 settings. The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO2, which was closely associated with soil and plant properties. PMID:22307288

  13. Importance of Mobile Genetic Elements and Conjugal Gene Transfer for Subsurface Microbial Community Adaptation to Biotransformation of Metals

    SciTech Connect

    Sorensen, Soren J.

    2005-06-01

    The overall goal of this project is to investigate the effect of mobile genetic elements and conjugal gene transfer on subsurface microbial community adaptation to mercury and chromium stress and biotransformation. Our studies focus on the interaction between the fate of these metals in the subsurface and the microbial community structure and activity.

  14. 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.

  15. 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.

  16. The Ecology of Microbial Communities Associated with Macrocystis pyrifera

    PubMed Central

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

    2013-01-01

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

  17. 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

  18. 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.

  19. 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

  20. 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

    2016-01-01

    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. PMID:26657285

  1. 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.

  2. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

    DOE PAGESBeta

    Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.; Simmons, Blake A.; Singer, Steven W.; VanderGheynst, Jean S.

    2015-12-02

    Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methodsmore » included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival

  3. Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

    SciTech Connect

    Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.; Simmons, Blake A.; Singer, Steven W.; VanderGheynst, Jean S.

    2015-12-02

    Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under

  4. Soil disturbance increases soil microbial enzymatic activity in arid ecoregion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Functional diversity of the soil microbial community is commonly used in the assessment of soil health as it relates to the activity of soil microflora involved in carbon cycling. Soil microbes in different microenvironments will have varying responses to different substrates, thus catabolic fingerp...

  5. Analysis of the microbial community and geochemistry of a sediment core from Great Slave Lake, Canada.

    PubMed

    Lim, Jesmine; Woodward, John; Tulaczyk, Slawek; Christoffersen, Poul; Cummings, Stephen P

    2011-02-01

    Sediment cores taken from Great Slave Lake, Canada, were analysed to investigate their metabolically active microbial populations and geochemistry. The amplification of cDNA detected metabolically active bacterial (50 separate bands) and archaeal (49 separate band) communities. The bacterial communities were further resolved indicating active actinobacterial and γ-proteobacterial communities (36 and 43 individual bands respectively). Redundancy discriminate analysis and Monte Carlo permutation testing demonstrated the significant impact of geochemical parameters on microbial community structures. Geochemical analyses suggest that the upper 0.4 m represents soil weathering and erosion in the lake catchment. An increase in organic carbon in the lower core suggests either more primary productivity, indicating warmer climate conditions, associated with Holocene Climatic Optimum conditions pre 5,000 years BP or change from a reducing environment in the lower core to an oxidizing environment during more recent deposition. Drivers for bacterial, archaeal and actinobacterial community structures were sediment particle size, and its mineral composition. Depth also significantly affected γ- proteobacterial community structure. In contrast the organic carbon content did not significantly shape the microbial community structures within the sediment. This study indicates that geochemical parameters significantly contribute to microbial community structure in these sediments. PMID:20803250

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

    NASA Technical Reports Server (NTRS)

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

    2010-01-01

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

  7. Culturability as an indicator of succession in microbial communities

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

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

    PubMed

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

    2001-08-01

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

  9. 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

  10. 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

  11. Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

    SciTech Connect

    White, G.J.

    1996-08-01

    Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.

  12. Isolation and analysis of mRNA from environmental microbial communities.

    PubMed

    McGrath, Ken C; Thomas-Hall, Skye R; Cheng, Chu Ting; Leo, Lesina; Alexa, Andrei; Schmidt, Susanne; Schenk, Peer M

    2008-10-01

    The advent of metagenomics has revealed that our planet harbors millions of previously undiscovered microbial species. However, functional insights into the activities of microbial communities cannot easily be obtained using metagenomics. Using transcriptional analyses to study microbial gene functions is currently problematic due to difficulties working with unstable microbial mRNA as a small fraction of total cellular RNA. Current techniques can be expensive and time consuming, and still result in significant levels of rRNA contamination. We have adapted techniques to rapidly isolate high high-quality RNA from environmental samples and developed a simple method for specific isolation of mRNA by size separation. This new technique was evaluated by constructing cDNA libraries directly from uncultured environmental microbial communities, including agricultural soil samples, aquatic flocculants, organic composts, mammalian oral and faecal samples, and wastewater sludge. The sequencing of a fraction of these cDNA clones revealed a high degree of novelty, demonstrating the potential of this approach to capture a large number of unique transcripts directly from the environment. To our knowledge, this is the first study that uses gel electrophoresis to isolate mRNA from microbial communities. We conclude that this method could be used to provide insights into the microbial 'metatranscriptome' of entire microbial communities. Coupled with high-throughput sequencing or the construction of cDNA microarrays, this approach will provide a useful tool to study the transcriptional activities of microorganisms, including those of entire microbial communities and of non-culturable microorganisms. PMID:18582973

  13. Profiling In Situ Microbial Community Structure with an Amplification Microarray

    PubMed Central

    Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

    2013-01-01

    The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

  14. The Microbial Community Structure in Petroleum-Contaminated Sediments Corresponds to Geophysical Signatures▿ †

    PubMed Central

    Allen, Jonathan P.; Atekwana, Estella A.; Atekwana, Eliot A.; Duris, Joseph W.; Werkema, D. Dale; Rossbach, Silvia

    2007-01-01

    The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueous-phase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. PMID:17351087

  15. Alteration of soil microbial communities and water quality in restored wetlands

    USGS Publications Warehouse

    Bossio, D.A.; Fleck, J.A.; Scow, K.M.; Fujii, R.

    2006-01-01

    Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage. ?? 2005 Elsevier Ltd. All

  16. Microbial communities, processes and functions in acid mine drainage ecosystems.

    PubMed

    Chen, Lin-Xing; Huang, Li-Nan; Méndez-García, Celia; Kuang, Jia-Liang; Hua, Zheng-Shuang; Liu, Jun; Shu, Wen-Sheng

    2016-04-01

    Acid mine drainage (AMD) is generated from the oxidative dissolution of metal sulfides when water and oxygen are available largely due to human mining activities. This process can be accelerated by indigenous microorganisms. In the last several decades, culture-dependent researches have uncovered and validated the roles of AMD microorganisms in metal sulfides oxidation and acid generation processes, and culture-independent studies have largely revealed the diversity and metabolic potentials and activities of AMD communities, leading towards a full understanding of the microbial diversity, functions and interactions in AMD ecosystems. This review describes the diversity of microorganisms and their functions in AMD ecosystems, and discusses their biotechnological applications in biomining and AMD bioremediation according to their capabilities. PMID:26921733

  17. Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

    NASA Astrophysics Data System (ADS)

    Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

    2014-05-01

    Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community

  18. Epigeic Earthworms Exert a Bottleneck Effect on Microbial Communities through Gut Associated Processes

    PubMed Central

    Gómez-Brandón, María; Aira, Manuel; Lores, Marta; Domínguez, Jorge

    2011-01-01

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

  19. Soil microbial communities of postpyrogenic pine forests (case study in Russia)

    NASA Astrophysics Data System (ADS)

    Maksimova, Ekaterina

    2015-04-01

    Soil microbial communities of postpyrogenic pine forests (case study in Russia) Ekaterina Maksimova Saint-Petersburg State University, Department of Applied Ecology, Saint-Petersburg, Russian Federation Institute of Ecology of Volga basin, Togljatty city, Russian Federation Soils, affected by catastrophic wildfires in 2010, were investigated in pine woods of Togljatty city, Samara region with the special reference to soil biological parameters. The analysis of microbial community of pine wood soils was carried out. It was revealed that wildfires have a negative impact on structure and functional activity of the microbial community postpyrogenic soils. In particular, they influence on values of eukaryotes-prokaryotes ratios, on CO2 emission intensity and on microorganisms functional state (as it was determined by microbial metabolic quotient) after wildfires. It has been revealed that microbial biomass values and basal respiration rate shows the trend to decrease in case of postfire sites compared with control (in 6.5 and 3.4 times respectively). The microbial biomass and basal respiration values have annual natural variability that testifies to a correlation of this process with soil hydrothermal conditions. However, it was also noted that wildfires don't affect on measured microbiological parameters in layers situated deeper than top 10 cm of soil. An increasing of the values, mentioned above, was observed 2-3 years after wildfires. Zone of microorganisms' activity has been moved to the lowermost soil layers. A disturbance of soil microbial communities' ecophysiological status after the fire is diagnosed by an increase of microbial metabolic quotient value. The metabolic activity of the microbial community decreases in a row: control→crown fire→ground fire. That testifies to certain intensive changes in the microbial community. High-temperature influence on microbial community has a significant effect on a total amount of bacteria, on a length of actinomycetes

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

    PubMed Central

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

    2016-01-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions. PMID:27469056

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

    PubMed

    Stegen, James C; Konopka, Allan; McKinley, James P; Murray, Chris; Lin, Xueju; Miller, Micah D; Kennedy, David W; Miller, Erin A; Resch, Charles T; Fredrickson, Jim K

    2016-01-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies-oxidized, reduced, and transition-within one lithofacies and elucidate relationships among facies features and