Epiphytic Macrolichen Community Composition Database—epiphytic lichen synusiae in forested areas of the US

Treesearch

Sarah. Jovan

2012-01-01

The Forest Inventory and Analysis (FIA) Program's Lichen Communities Indicator is used for tracking epiphytic macrolichen diversity and is applied for monitoring air quality and climate change effects on forest health in the United States. Started in 1994, the Epiphytic Macrolichen Community Composition Database (GIVD ID NA-US-012) now has over 8,000 surveys of...

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 carbon stored in cryoturbated material. PMID:24705618

Microbial Community Composition of Polyhydroxyalkanoate-Accumulating Organisms in Full-Scale Wastewater Treatment Plants Operated in Fully Aerobic Mode

PubMed Central

Oshiki, Mamoru; Onuki, Motoharu; Satoh, Hiroyasu; Mino, Takashi

2013-01-01

The removal of biodegradable organic matter is one of the most important objectives in biological wastewater treatments. Polyhydroxyalkanoate (PHA)-accumulating organisms (PHAAOs) significantly contribute to the removal of biodegradable organic matter; however, their microbial community composition is mostly unknown. In the present study, the microbial community composition of PHAAOs was investigated at 8 full-scale wastewater treatment plants (WWTPs), operated in fully aerobic mode, by fluorescence in situ hybridization (FISH) analysis and post-FISH Nile blue A (NBA) staining techniques. Our results demonstrated that 1) PHAAOs were in the range of 11–18% in the total number of cells, and 2) the microbial community composition of PHAAOs was similar at the bacterial domain/phylum/class/order level among the 8 full-scale WWTPs, and dominant PHAAOs were members of the class Alphaproteobacteria and Betaproteobacteria. The microbial community composition of α- and β-proteobacterial PHAAOs was examined by 16S rRNA gene clone library analysis and further by applying a set of newly designed oligonucleotide probes targeting 16S rRNA gene sequences of α- or β-proteobacterial PHAAOs. The results demonstrated that the microbial community composition of PHAAOs differed in the class Alphaproteobacteria and Betaproteobacteria, which possibly resulted in a different PHA accumulation capacity among the WWTPs (8.5–38.2 mg-C g-VSS−1 h−1). The present study extended the knowledge of the microbial diversity of PHAAOs in full-scale WWTPs operated in fully aerobic mode. PMID:23257912

Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin.

PubMed

Fry, John C; Webster, Gordon; Cragg, Barry A; Weightman, Andrew J; Parkes, R John

2006-10-01

The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophoresis banding patterns of deep-sediment Bacteria, Archaea, Euryarchaeota and the novel candidate division JS1, followed by multiple regression, showed strong relationships with prokaryotic activity and geochemistry (R(2)=55-100%). Further correlation analysis, at one site, between the principal components from the community composition profiles for Bacteria and 12 other variables quantitatively confirmed their relationship with activity and geochemistry, which had previously only been implied. Comparison with previously published cell counts enumerated by fluorescent in situ hybridization with rRNA-targeted probes confirmed that these denaturing gradient gel electrophoresis profiles described an active prokaryotic community.

Seasonal Patterns in Microbial Community Composition in Denitrifying Bioreactors Treating Subsurface Agricultural Drainage.

PubMed

Porter, Matthew D; Andrus, J Malia; Bartolerio, Nicholas A; Rodriguez, Luis F; Zhang, Yuanhui; Zilles, Julie L; Kent, Angela D

2015-10-01

Denitrifying bioreactors, consisting of water flow control structures and a woodchip-filled trench, are a promising approach for removing nitrate from agricultural subsurface or tile drainage systems. To better understand the seasonal dynamics and the ecological drivers of the microbial communities responsible for denitrification in these bioreactors, we employed microbial community "fingerprinting" techniques in a time-series examination of three denitrifying bioreactors over 2 years, looking at bacteria, fungi, and the denitrifier functional group responsible for the final step of complete denitrification. Our analysis revealed that microbial community composition responds to depth and seasonal variation in moisture content and inundation of the bioreactor media, as well as temperature. Using a geostatistical analysis approach, we observed recurring temporal patterns in bacterial and denitrifying bacterial community composition in these bioreactors, consistent with annual cycling. The fungal communities were more stable, having longer temporal autocorrelations, and did not show significant annual cycling. These results suggest a recurring seasonal cycle in the denitrifying bioreactor microbial community, likely due to seasonal variation in moisture content.

Effects of transgenic cry1Ie maize on non-lepidopteran pest abundance, diversity and community composition.

PubMed

Guo, Jingfei; He, Kanglai; Bai, Shuxiong; Zhang, Tiantao; Liu, Yunjun; Wang, Fuxin; Wang, Zhenying

2016-12-01

Non-lepidopteran pests are exposed to, and may be influenced by, Bt toxins when feeding on Bt maize that express insecticidal Cry proteins derived from Bacillus thuringiensis (Bt). In order to assess the potential effects of transgenic cry1Ie maize on non-lepidopteran pest species and ecological communities, a 2-year field study was conducted to compare the non-lepidopteran pest abundance, diversity and community composition between transgenic cry1Ie maize (Event IE09S034, Bt maize) and its near isoline (Zong 31, non-Bt maize) by whole plant inspections. Results showed that Bt maize had no effects on non-lepidopteran pest abundance and diversity (Shannon-Wiener diversity index, Simpson's diversity index, species richness, and Pielou's index). There was a significant effect of year and sampling time on those indices analyzed. Redundancy analysis indicated maize type, sampling time and year totally explained 20.43 % of the variance in the non-lepidopteran pest community composition, but no association was presented between maize type (Bt maize and non-Bt maize) and the variance. Nonmetric multidimensional scaling analysis showed that sampling time and year, rather than maize type had close relationship with the non-lepidopteran pest community composition. These results corroborated the hypothesis that, at least in the short-term, the transgenic cry1Ie maize had negligible effects on the non-lepidopteran pest abundance, diversity and community composition.

Root controls on soil microbial community structure in forest soils.

PubMed

Brant, Justin B; Myrold, David D; Sulzman, Elizabeth W

2006-07-01

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

Accuracy, reproducibility, and interpretation of fatty acid methyl ester profiles of model bacterial communities

USGS Publications Warehouse

Kidd, Haack S.; Garchow, H.; Odelson, D.A.; Forney, L.J.; Klug, M.J.

1994-01-01

We determined the accuracy and reproducibility of whole-community fatty acid methyl ester (FAME) analysis with two model bacterial communities differing in composition by using the Microbial ID, Inc. (MIDI), system. The biomass, taxonomic structure, and expected MIDI-FAME profiles under a variety of environmental conditions were known for these model communities a priori. Not all members of each community could be detected in the composite profile because of lack of fatty acid 'signatures' in some isolates or because of variations (approximately fivefold) in fatty acid yield across taxa. MIDI- FAME profiles of replicate subsamples of a given community were similar in terms of fatty acid yield per unit of community dry weight and relative proportions of specific fatty acids. Principal-components analysis (PCA) of MIDI-FAME profiles resulted in a clear separation of the two different communities and a clustering of replicates of each community from two separate experiments on the first PCA axis. The first PCA axis accounted for 57.1% of the variance in the data and was correlated with fatty acids that varied significantly between communities and reflected the underlying community taxonomic structure. On the basis of our data, community fatty acid profiles can be used to assess the relative similarities and differences of microbial communities that differ in taxonomic composition. However, detailed interpretation of community fatty acid profiles in terms of biomass or community taxonomic composition must be viewed with caution until our knowledge of the quantitative and qualitative distribution of fatty acids over a wide variety of taxa and the effects of growth conditions on fatty acid profiles is more extensive.

Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water.

PubMed

Frank, Alexander H; Garcia, Juan A L; Herndl, Gerhard J; Reinthaler, Thomas

2016-06-01

To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep-water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Spatial Variability of PAHs and Microbial Community Structure in Surrounding Surficial Soil of Coal-Fired Power Plants in Xuzhou, China

PubMed Central

Ma, Jing; Zhang, Wangyuan; Chen, Yi; Zhang, Shaoliang; Feng, Qiyan; Hou, Huping; Chen, Fu

2016-01-01

This work investigated the spatial profile and source analysis of polycyclic aromatic hydrocarbons (PAHs) in soil that surrounds coal-fired power plants in Xuzhou, China. High-throughput sequencing was employed to investigate the composition and structure of soil bacterial communities. The total concentration of 15 PAHs in the surface soils ranged from 164.87 to 3494.81 μg/kg dry weight. The spatial profile of PAHs was site-specific with a concentration of 1400.09–3494.81 μg/kg in Yaozhuang. Based on the qualitative and principal component analysis results, coal burning and vehicle emission were found to be the main sources of PAHs in the surface soils. The phylogenetic analysis revealed differences in bacterial community compositions among different sampling sites. Proteobacteria was the most abundant phylum, while Acidobacteria was the second most abundant. The orders of Campylobacterales, Desulfobacterales and Hydrogenophilales had the most significant differences in relative abundance among the sampling sites. The redundancy analysis revealed that the differences in bacterial communities could be explained by the organic matter content. They could also be explicated by the acenaphthene concentration with longer arrows. Furthermore, OTUs of Proteobacteria phylum plotted around particular samples were confirmed to have a different composition of Proteobacteria phylum among the sample sites. Evaluating the relationship between soil PAHs concentration and bacterial community composition may provide useful information for the remediation of PAH contaminated sites. PMID:27598188

Spatial Variability of PAHs and Microbial Community Structure in Surrounding Surficial Soil of Coal-Fired Power Plants in Xuzhou, China.

PubMed

Ma, Jing; Zhang, Wangyuan; Chen, Yi; Zhang, Shaoliang; Feng, Qiyan; Hou, Huping; Chen, Fu

2016-09-02

This work investigated the spatial profile and source analysis of polycyclic aromatic hydrocarbons (PAHs) in soil that surrounds coal-fired power plants in Xuzhou, China. High-throughput sequencing was employed to investigate the composition and structure of soil bacterial communities. The total concentration of 15 PAHs in the surface soils ranged from 164.87 to 3494.81 μg/kg dry weight. The spatial profile of PAHs was site-specific with a concentration of 1400.09-3494.81 μg/kg in Yaozhuang. Based on the qualitative and principal component analysis results, coal burning and vehicle emission were found to be the main sources of PAHs in the surface soils. The phylogenetic analysis revealed differences in bacterial community compositions among different sampling sites. Proteobacteria was the most abundant phylum, while Acidobacteria was the second most abundant. The orders of Campylobacterales, Desulfobacterales and Hydrogenophilales had the most significant differences in relative abundance among the sampling sites. The redundancy analysis revealed that the differences in bacterial communities could be explained by the organic matter content. They could also be explicated by the acenaphthene concentration with longer arrows. Furthermore, OTUs of Proteobacteria phylum plotted around particular samples were confirmed to have a different composition of Proteobacteria phylum among the sample sites. Evaluating the relationship between soil PAHs concentration and bacterial community composition may provide useful information for the remediation of PAH contaminated sites.

Temporal dynamics of bird community composition: an analysis of baseline conditions from long-term data.

PubMed

Kampichler, Christian; Angeler, David G; Holmes, Richard T; Leito, Aivar; Svensson, Sören; van der Jeugd, Henk P; Wesołowski, Tomasz

2014-08-01

Numerous anthropogenic activities threaten the biodiversity found on earth. Because all ecological communities constantly experience temporal turnover due to natural processes, it is important to distinguish between change due to anthropogenic impact and the underlying natural rate of change. In this study, we used data sets on breeding bird communities that covered at least 20 consecutive years, from a variety of terrestrial ecosystems, to address two main questions. (1) How fast does the composition of bird communities change over time, and can we identify a baseline of natural change that distinguishes primeval systems from systems experiencing varying degrees of human impact? (2) How do patterns of temporal variation in composition vary among bird communities in ecosystems with different anthropogenic impacts? Time lag analysis (TLA) showed a pattern of increasing rate of temporal compositional change from large-scale primeval systems to disturbed and protected systems to distinctly successional systems. TLA slopes of <0.04 were typical for breeding bird communities with natural turnover, while communities subjected to anthropogenic impact were characterised by TLA slopes of >0.04. Most of the temporal variability of breeding bird communities was explained by slow changes occurring over decades, regardless of the intensity of human impact. In most of the time series, medium- and short-wave periodicity was not detected, with the exception of breeding bird communities subjected to periodic pulses (e.g. caterpillar outbreaks causing food resource peaks).

Temporal Dynamics of the Human Vaginal Microbiota

PubMed Central

Gajer, Pawel; Brotman, Rebecca M.; Bai, Guoyun; Sakamoto, Joyce; Schütte, Ursel M.E.; Zhong, Xue; Koenig, Sara S.K.; Fu, Li; Ma, Zhanshan; Zhou, Xia; Abdo, Zaid; Forney, Larry J.; Ravel, Jacques

2012-01-01

Elucidating the factors that impinge on the stability of bacterial communities in the vagina may help in predicting the risk of diseases that affect women’s health. Here, we describe the temporal dynamics of the composition of vaginal bacterial communities in 32 reproductive age women over a 16-week period. The analysis revealed the dynamics of five major classes of bacterial communities and showed that some communities change markedly over short time periods, whereas others are relatively stable. Modeling community stability using new quantitative measures indicates that deviation from stability correlates with time in the menstrual cycle, bacterial community composition and sexual activity. The women studied are healthy, thus it appears that neither variation in community composition per se, nor higher levels of observed diversity (co-dominance) are necessarily indicative of dysbiosis, in which there is microbial imbalance accompanied by symptoms. PMID:22553250

Human gut bacterial communities are altered by addition of cruciferous vegetables to a controlled fruit- and vegetable-free diet.

PubMed

Li, Fei; Hullar, Meredith A J; Schwarz, Yvonne; Lampe, Johanna W

2009-09-01

In the human gut, commensal bacteria metabolize food components that typically serve as energy sources. These components have the potential to influence gut bacterial community composition. Cruciferous vegetables, such as broccoli and cabbage, contain distinctive compounds that can be utilized by gut bacteria. For example, glucosinolates can be hydrolyzed by certain bacteria, and dietary fibers can be fermented by a range of species. We hypothesized that cruciferous vegetable consumption would alter growth of certain bacteria, thereby altering bacterial community composition. We tested this hypothesis in a randomized, crossover, controlled feeding study. Fecal samples were collected from 17 participants at the end of 2 14-d intake periods: a low-phytochemical, low-fiber basal diet (i.e. refined grains without fruits or vegetables) and a high ("double") cruciferous vegetable diet [basal diet + 14 g cruciferous vegetables/(kg body weightd)]. Fecal bacterial composition was analyzed by the terminal restriction fragment length polymorphism (tRFLP) method using the bacterial 16S ribosomal RNA gene and nucleotide sequencing. Using blocked multi-response permutation procedures analysis, we found that overall bacterial community composition differed between the 2 consumption periods (delta = 0.603; P = 0.011). The bacterial community response to cruciferous vegetables was individual-specific, as revealed by nonmetric multidimensional scaling ordination analysis. Specific tRFLP fragments that characterized each of the diets were identified using indicator species analysis. Putative species corresponding to these fragments were identified through gene sequencing as Eubacterium hallii, Phascolarctobacterium faecium, Burkholderiales spp., Alistipes putredinis, and Eggerthella spp. In conclusion, human gut bacterial community composition was altered by cruciferous vegetable consumption, which could ultimately influence gut metabolism of bioactive food components and host exposure to these compounds.

Elevated carbon dioxide is predicted to promote coexistence among competing species in a trait-based model

DOE PAGES

Ali, Ashehad A.; Medlyn, Belinda E.; Aubier, Thomas G.; ...

2015-10-06

Differential species responses to atmospheric CO 2 concentration (C a) could lead to quantitative changes in competition among species and community composition, with flow-on effects for ecosystem function. However, there has been little theoretical analysis of how elevated C a (eC a) will affect plant competition, or how composition of plant communities might change. Such theoretical analysis is needed for developing testable hypotheses to frame experimental research. Here, we investigated theoretically how plant competition might change under eC a by implementing two alternative competition theories, resource use theory and resource capture theory, in a plant carbon and nitrogen cycling model.more » The model makes several novel predictions for the impact of eC a on plant community composition. Using resource use theory, the model predicts that eC a is unlikely to change species dominance in competition, but is likely to increase coexistence among species. Using resource capture theory, the model predicts that eC a may increase community evenness. Collectively, both theories suggest that eC a will favor coexistence and hence that species diversity should increase with eC a. Our theoretical analysis leads to a novel hypothesis for the impact of eC a on plant community composition. In this study, the hypothesis has potential to help guide the design and interpretation of eC a experiments.« less

Spatial variation in the bacterial and denitrifying bacterial community in a biofilter treating subsurface agricultural drainage.

PubMed

Andrus, J Malia; Porter, Matthew D; Rodríguez, Luis F; Kuehlhorn, Timothy; Cooke, Richard A C; Zhang, Yuanhui; Kent, Angela D; Zilles, Julie L

2014-02-01

Denitrifying biofilters can remove agricultural nitrates from subsurface drainage, reducing nitrate pollution that contributes to coastal hypoxic zones. The performance and reliability of natural and engineered systems dependent upon microbially mediated processes, such as the denitrifying biofilters, can be affected by the spatial structure of their microbial communities. Furthermore, our understanding of the relationship between microbial community composition and function is influenced by the spatial distribution of samples.In this study we characterized the spatial structure of bacterial communities in a denitrifying biofilter in central Illinois. Bacterial communities were assessed using automated ribosomal intergenic spacer analysis for bacteria and terminal restriction fragment length polymorphism of nosZ for denitrifying bacteria.Non-metric multidimensional scaling and analysis of similarity (ANOSIM) analyses indicated that bacteria showed statistically significant spatial structure by depth and transect,while denitrifying bacteria did not exhibit significant spatial structure. For determination of spatial patterns, we developed a package of automated functions for the R statistical environment that allows directional analysis of microbial community composition data using either ANOSIM or Mantel statistics.Applying this package to the biofilter data, the flow path correlation range for the bacterial community was 6.4 m at the shallower, periodically in undated depth and 10.7 m at the deeper, continually submerged depth. These spatial structures suggest a strong influence of hydrology on the microbial community composition in these denitrifying biofilters. Understanding such spatial structure can also guide optimal sample collection strategies for microbial community analyses.

Species diversity and drivers of arbuscular mycorrhizal fungal communities in a semi-arid mountain in China

PubMed Central

Zhang, Zhiming; Yang, Jiantao; Zhu, Yiwei

2017-01-01

Arbuscular mycorrhizal fungi (AMF) play an essential role in complex ecosystems. However, the species diversity and composition of AMF communities remain unclear in semi-arid mountains. Further, it is not well understood if the characteristics of AMF community assemblies differ for different habitat types, e.g., agricultural arable land, artificial forest land, natural grassland, and bush/wood land. Here, using the high-throughput technology by Illumina sequencing on the MiSeq platform, we explored the species diversity and composition of soil AMF communities among different habitat types in a semi-arid mountain (Taihang Mountain, Mid-western region of China). Then, we analyzed the effect of nutrient composition and soil texture on AMF community assembly. Our results showed that members of the Glomus genera were predominated in all soil types. The distance-based redundancy analysis indicated that the content of water, available phosphorus, and available potassium were the most crucial geochemical factors that significantly affected AMF communities (p < 0.05). The analysis of the soil texture confirmed that AMF diversity was negatively correlated with soil clay content. The comparison of AMF diversity among the various habitat types revealed that the artificial forest land had the lowest AMF diversity in comparison with other land types. Our findings suggest that there were differences in species diversity and composition of soil AMF communities among different habitat types. These findings shed new light on the characteristics of community structure and drivers of community assembly in AMF in semi-arid mountains, and point to the potential importance of different habitat types on AMF communities. PMID:29230378

Analysis of Structure and Composition of Bacterial Core Communities in Mature Drinking Water Biofilms and Bulk Water of a Citywide Network in Germany

PubMed Central

Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid

2012-01-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity. PMID:22389373

Analysis of structure and composition of bacterial core communities in mature drinking water biofilms and bulk water of a citywide network in Germany.

PubMed

Henne, Karsten; Kahlisch, Leila; Brettar, Ingrid; Höfle, Manfred G

2012-05-01

The bacterial core communities of bulk water and corresponding biofilms of a more than 20-year-old drinking water network were compared using 16S rRNA single-strand confirmation polymorphism (SSCP) fingerprints based on extracted DNA and RNA. The structure and composition of the bacterial core community in the bulk water was highly similar (>70%) across the city of Braunschweig, Germany, whereas all biofilm samples contained a unique community with no overlapping phylotypes from bulk water. Biofilm samples consisted mainly of Alphaproteobacteria (26% of all phylotypes), Gammaproteobacteria (11%), candidate division TM6 (11%), Chlamydiales (9%), and Betaproteobacteria (9%). The bulk water community consisted primarily of Bacteroidetes (25%), Betaproteobacteria (20%), Actinobacteria (16%), and Alphaproteobacteria (11%). All biofilm communities showed higher relative abundances of single phylotypes and a reduced richness compared to bulk water. Only biofilm communities sampled at nearby sampling points showed similar communities irrespective of support materials. In all of our bulk water studies, the community composition determined from 16S rRNA was completely different from the 16S rRNA gene-based community composition, whereas in biofilms both molecular fractions resulted in community compositions that were similar to each other. We hypothesize that a higher fraction of active bacterial phylotypes and a better protection from oxidative stress in drinking water biofilms are responsible for this higher similarity.

Macrofaunal production and biological traits: Spatial relationships along the UK continental shelf

NASA Astrophysics Data System (ADS)

Bolam, S. G.; Eggleton, J. D.

2014-04-01

Biological trait analysis (BTA) is increasingly being employed to improve our understanding of the ecological functioning of marine benthic invertebrate communities. However, changes in trait composition are seldomly compared with concomitant changes in metrics of ecological function. Consequently, inferences regarding the functional implications of any changes are often anecdotal; we currently have a limited understanding of the functional significance of the traits commonly used. In this study, we quantify the relationship between benthic invertebrate trait composition and secondary production estimates using data spanning almost the breadth of the UK continental shelf. Communities described by their composition of 10 traits representing life history, morphology and behaviour showed strong relationships with variations in total secondary production. A much weaker relationship was observed for community productivity (or P:B), a measure of rate of energy turnover. Furthermore, the relationship between total production and multivariate taxonomic community composition was far weaker than that for trait composition. Indeed, the similarities between communities as defined by taxonomy were very different from those depicted by their trait composition. That is, as many studies have demonstrated, taxonomically different communities may display similar trait compositions, and vice versa. Finally, we found that descriptions of community trait composition vary greatly depending on whether abundance or biomass is used as the enumeration weighting method during BTA, and trait assessments based on biomass produced better relations with secondary production than those based on abundance. We discuss the significance of these findings with respect to BTA using marine benthic invertebrates.

Associations between retail food store exterior advertisements and community demographic and socioeconomic composition.

PubMed

Isgor, Zeynep; Powell, Lisa; Rimkus, Leah; Chaloupka, Frank

2016-05-01

This paper examines the association between the prevalence of various types of outdoor food and beverage advertising found on the building exteriors and properties of retail food outlets and community racial/ethnic and socioeconomic composition in a nationwide sample of food outlets in the U.S. Our major finding from multivariable analysis is that food stores in low-income communities have higher prevalence of all food and beverage ads, including those for unhealthy products such as regular soda, controlling for community racial/ethnic composition and other covariates. This adds to growing research pointing to socioeconomic disparities in food and beverage marketing exposure. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biofilm composition in the Olt River (Romania) reservoirs impacted by a chlor-alkali production plant.

PubMed

Dranguet, P; Cosio, C; Le Faucheur, S; Hug Peter, D; Loizeau, J-L; Ungureanu, V-Gh; Slaveykova, V I

2017-05-24

Freshwater biofilms can be useful indicators of water quality and offer the possibility to assess contaminant effects at the community level. The present field study examines the effects of chlor-alkali plant effluents on the community composition of biofilms grown in the Olt River (Romania) reservoirs. The relationship between ambient water quality variables and community composition alterations was explored. Amplicon sequencing revealed a significant modification of the composition of microalgal, bacterial and fungal communities in the biofilms collected in the impacted reservoirs in comparison with those living in the uncontaminated control reservoir. The abundance corrected Simpson index showed lower richness and diversity in biofilms collected in the impacted reservoirs than in the control reservoir. The biofilm bacterial communities of the impacted reservoirs were characterized by the contaminant-tolerant Cyanobacteria and Bacteroidetes, whereas microalgal communities were predominantly composed of Bacillariophyta and fungal communities of Lecanoromycetes and Paraglomycetes. A principal component analysis revealed that major contaminants present in the waste water of the chlor-alkali production plant, i.e. Na + , Ca 2+ , Cl - and Hg, were correlated with the alteration of biofilm community composition in the impacted reservoirs. However, the biofilm composition was also influenced by water quality variables such as NO 3 - , SO 4 2- , DOC and Zn from unknown sources. The results of the present study imply that, even when below the environmental quality standards, typical contaminants of chlor-alkali plant releases may affect biofilm composition and that their impacts on the microbial biodiversity might be currently overlooked.

Composition Influences the Pathway but not the Outcome of the Metabolic Response of Bacterioplankton to Resource Shifts

PubMed Central

Comte, Jérôme; del Giorgio, Paul A.

2011-01-01

Bacterioplankton community metabolism is central to the functioning of aquatic ecosystems, and strongly reactive to changes in the environment, yet the processes underlying this response remain unclear. Here we explore the role that community composition plays in shaping the bacterial metabolic response to resource gradients that occur along aquatic ecotones in a complex watershed in Québec. Our results show that the response is mediated by complex shifts in community structure, and structural equation analysis confirmed two main pathways, one involving adjustments in the level of activity of existing phylotypes, and the other the replacement of the dominant phylotypes. These contrasting response pathways were not determined by the type or the intensity of the gradients involved, as we had hypothesized, but rather it would appear that some compositional configurations may be intrinsically more plastic than others. Our results suggest that community composition determines this overall level of community plasticity, but that composition itself may be driven by factors independent of the environmental gradients themselves, such that the response of bacterial communities to a given type of gradient may alternate between the adjustment and replacement pathways. We conclude that community composition influences the pathways of response in these bacterial communities, but not the metabolic outcome itself, which is driven by the environment, and which can be attained through multiple alternative configurations. PMID:21980410

Receding Water Line and Interspecific Competition Determines Plant Community Composition and Diversity in Wetlands in Beijing

PubMed Central

Wang, Zhengjun; Gong, Huili; Zhang, Jing

2015-01-01

Climate and human-induced wetland degradation has accelerated in recent years, not only resulting in reduced ecosystem services but also greatly affecting the composition and diversity of wetland plant communities. To date, the knowledge of the differences in community parameters and their successional trends in degraded wetlands remains scarce. Here based on remote sensing images, geographic information system technology, and statistical methods, we produced a successional gradient map of the Yeyahu Wetland Nature Reserve in Beijing, which has experienced a steady decline in water level in recent decades. In addition, we analyzed community composition and diversity along with each identified gradient. The results showed that community diversity decreases while dominance increases with the progress of succession, with the highest diversity occurring during the early stage of succession. Moreover, the community demonstrates greater similarity among subareas during later successional stages, and the similarity coefficients calculated from the important value (IV) of each species are more accurate. Correlation analysis showed that the impact of soil factors on diversity was not significant at a subarea scale, although these nutrients showed an increasing trend with the community succession. Furthermore, the IVs of the dominant species had a particularly significant impact on diversity, showing a significantly negative correlation with diversity indices and a significantly positive correlation with dominance indices. Further analysis showed that the retreat of water level resulted from sustained drought and local human activities was a major extrinsic driving force resulting in observed differences in the community successional stages, which resulted in differences in community composition and diversity. On the other hand, interspecific competition was the main intrinsic mechanism, which significantly influenced the IVs of the dominant species and community diversity. The results of this study could aid in improving the understanding of community composition, diversity, and its successional trends in degraded wetlands. PMID:25848799

Functional composition of epifauna in the south-eastern North Sea in relation to habitat characteristics and fishing effort

NASA Astrophysics Data System (ADS)

Neumann, Hermann; Diekmann, Rabea; Kröncke, Ingrid

2016-02-01

Analysis of ecosystem functioning is essential to describe the ecological status of ecosystems and is therefore directly requested in international directives. There is a lack of knowledge regarding functional aspects of benthic communities and their environmental and anthropogenic driving forces in the southern North Sea. This study linked functional composition of epibenthic communities to environmental conditions and fishing effort and investigated spatial correlations between habitat characteristics to gain insight into potential synergistic and/or cumulative effects. Functional composition of epifauna was assessed by using biological trait analysis (BTA), which considered 15 ecological traits of 54 species. Functional composition was related to ten predictor variables derived from sediment composition, bottom temperature and salinity, hydrodynamics, annual primary production and fishing effort. Our results revealed significantly different functional composition between the Dogger Bank, the Oyster Ground, the West and North Frisian coast. Mobility, feeding type, size and adult longevity were the most important traits differentiating the communities. A high proportion of trait modalities related to an opportunistic life mode were obvious in coastal areas especially at the West Frisian coast and in the area of the Frisian Front indicating disturbed communities. In contrast, functional composition in the Dogger Bank area indicated undisturbed communities with prevalence of large, long-lived and permanently attached species being sensitive towards disturbance such as fishing. Tidal stress, mud content of sediments, salinity, stratification and fishing effort were found to be the most important habitat characteristics shaping functional composition. Strong correlations were found between variables, especially between those which changed gradually from the coast to offshore areas including fishing effort. Unfavourable extremes of these factors in coastal areas resulted in disturbed epibenthic communities, while the relative influence of a single factor on functional composition cannot be quantified. Coastal communities seemed to be well adapted to disturbance and the prevalence of opportunistic trait modalities not necessarily revealed a poor ecological status according to the Marine Strategy Framework Directive (MSFD). The integration of functional aspects into the assessment of ecosystem health is recommended, since widely used structural measures failed in naturally disturbed habitats.

A comparative study of AMF diversity in annual and perennial plant species from semiarid gypsum soils.

NASA Astrophysics Data System (ADS)

Alguacil, M. M.; Torrecillas, E.; Roldán, A.; Díaz, G.; Torres, P.

2012-04-01

The arbuscular mycorrhizal fungi (AMF) communities composition regulate plant interactions and determine the structure of plant communities. In this study we analysed the diversity of AMF in the roots of two perennial gypsophyte plant species, Herniaria fruticosa and Senecio auricula, and an annual herbaceous species, Bromus rubens, growing in a gypsum soil from a semiarid area. The objective was to determine whether perennial and annual host plants support different AMF communities in their roots and whether there are AMF species that might be indicators of specific functional plant roles in these ecosystems. The roots were analysed by nested PCR, cloning, sequencing of the ribosomal DNA small subunit region and phylogenetic analysis. Twenty AMF sequence types, belonging to the Glomus group A, Glomus group B, Diversisporaceae, Acaulosporaceae, Archaeosporaceae and Paraglomeraceae, were identified. Both gypsophyte perennial species had differing compositions of the AMF community and higher diversity when compared with the annual species, showing preferential selection by specific AMF sequences types. B. rubens did not show host specificity, sharing the full composition of its AMF community with both perennial plant species. Seasonal variations in the competitiveness of AM fungi could explain the observed differences in AMF community composition, but this is still a working hypothesis that requires the analysis of further data obtained from a higher number of both annual and perennial plant species in order to be fully tested.

Evaluation of phytoplankton community composition in the eutrophic Masan Bay by HPLC pigment analysis.

PubMed

Kim, Jeong Bae; Hong, Sokjin; Lee, Won-Chan; Lee, Yong-Woo; Kim, Hyung Chul; Cho, Yoonsik

2015-03-01

To assess the spatiotemporal changes in phytoplankton community composition in relation to the environment of Masan Bay, a semi-enclosed bay on the southern coast of Korea, photosynthetic pigments and environmental variables were analyzed in seawater, every month between March and November 2010. The level of dissolved inorganic nutrients was highest between July and September when the freshwater influx was at its peak, whereas chlorophyll a level was highest in April and August. Phosphate concentration was low in April (average: 0.22 +/- 0.17 microM), indicating the role of phosphate as a growth-limiting factor for phytoplankton. The results of pigment analysis indicate that dinoflagellate blooms occurred under favorable conditions, where competition with diatoms occurred. Fucoxanthin- and chlorophyll b-containing phytoplankton dominated the surface layer of Masan Bay from July to September. The composition of phytoplankton community in Masan Bay changed dramatically each month according to variations in the amount and composition of nutrients introduced through surface runoff.

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India.

PubMed

Sha, Shankar Prasad; Jani, Kunal; Sharma, Avinash; Anupma, Anu; Pradhan, Pooja; Shouche, Yogesh; Tamang, Jyoti Prakash

2017-09-08

Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing.

Microbial community composition and dynamics of moving bed biofilm reactor systems treating municipal sewage.

PubMed

Biswas, Kristi; Turner, Susan J

2012-02-01

Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of the Gammaproteobacteria and Betaproteobacteria. This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.

Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones.

PubMed

Peng, Xuefeng; Jayakumar, Amal; Ward, Bess B

2013-01-01

Ammonia-oxidizing archaea (AOA) have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs), where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA). The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP) AOA assemblages was investigated using principal component analysis (PCA) and redundancy analysis (RDA). In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature (higher in the Arabian Sea than in the ETSP) was the main factor that correlated with the differences between the AOA communities. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition.

Learning How to Feel: Conversion Narratives and Community Membership in First-Year Composition

ERIC Educational Resources Information Center

Kurtyka, Faith M.

2017-01-01

This article examines the rhetoric of the conversion narratives told by a group of women joining a new social sorority on campus. I argue that these sorority conversion narratives are of interest to composition scholars because they document the emotional work involved in entering a community in one's first year of college. My close analysis of…

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

PubMed

de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

2015-08-01

Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing.

PubMed

Zuo, Yu; Xie, Wenfang; Pang, Yue; Li, Tiesong; Li, Qingwei; Li, Yingying

2017-01-01

The composition of the bacterial communities in the hindgut contents of Lampetrs japonica was surveyed by Illumina MiSeq of the 16S rRNA gene. An average of 32385 optimized reads was obtained from three samples. The rarefaction curve based on the operational taxonomic units tended to approach the asymptote. The rank abundance curve representing the species richness and evenness was calculated. The composition of microbe in six classification levels was also analyzed. Top 20 members in genera level were displayed as the classification tree. The abundance of microorganisms in different individuals was displayed as the pie charts at the branch nodes in the classification tree. The differences of top 50 genera in abundance between individuals of lamprey are displayed as a heatmap. The pairwise comparison of bacterial taxa abundance revealed that there are no significant differences of gut microbiota between three individuals of lamprey at a given rarefied depth. Also, the gut microbiota derived from L. japonica displays little similarity with other aquatic organism of Vertebrata after UPGMA analysis. The metabolic function of the bacterial communities was predicted through KEGG analysis. This study represents the first analysis of the bacterial community composition in the gut content of L. japonica. The investigation of the gut microbiota associated with L. japonica will broaden our understanding of this unique organism.

Community composition and diversity of ground beetles (Coleoptera: Carabidae) in Yaoluoping National Nature Reserve

PubMed Central

Li, Wen-Bo; Liu, Nai-Yi; Wu, Yun-He; Zhang, Yu-Cai; Xu, Qin; Chu, Jun; Wang, Shu-Yan

2017-01-01

Abstract This study used pitfall trapping to examine community composition and diversity of ground beetles in five different habitats (coniferous, deciduous, mixed coniferous, farmland, and settlements) within Anhui Yaoluoping National Nature Reserve from May to September 2014. In total, 1,352 ground beetles were collected, belonging to 16 genera and 44 species. Of these, four dominant species Dolichus halensis, Harpalus pastor, Carabus casaleianus, and Pheropsophus jessoensis were identified, respectively, comprising 370, 177, 131, and 123 individuals. The deciduous forest showed greater diversity (3.78 according to Shannon–Weiner index), equitability (0.80 according to Pielou’s index), and dominance (9.52 according to Simpson’s index) when compared with farmland, but species richness in the deciduous forest (27) was lower than that in farmland (35). One-way analysis of variance showed that ground beetle species composition and abundance among different habitats varied significantly. Cluster analysis and principal coordinate analysis showed that farmland shared low community similarity with other habitat types, and coniferous and mixed coniferous forests shared similar community types. Our results indicate that species composition, abundance, and diversity of ground beetles are affected by different habitat types, with deciduous forest types being critical in maintaining the diversity of rare species. We recommend reducing cultivated farmland area and increasing the area of carefully planned deciduous forest in order to better protect ground beetle diversity in the region.

First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea

NASA Astrophysics Data System (ADS)

Lee, Jiyoung; Lim, Jae-Hyun; Park, Junhyung; Youn, Seok-Hyun; Oh, Hyun-Ju; Kim, Ju-Hyoung; Kim, Myung Kyum; Cho, Hyeyoun; Yoon, Joo-Eun; Kim, Soyeon; Markkandan, Kesavan; Park, Ki-Tae; Kim, Il-Nam

2018-02-01

Microbial community composition varies based on seasonal dynamics (summer: strongly stratified water column; autumn: weakly stratified water column; winter: vertically homogeneous water column) and vertical distributions (surface, middle, and bottom depths) in the Gadeok Channel, which is the primary passage to exchange waters and materials between the Jinhae-Masan Bay and the South Sea waters. The microbial community composition was analyzed from June to December 2016 using 16S rRNA gene sequencing. The community was dominated by the phyla Proteobacteria (45%), Bacteroidetes (18%), Cyanobacteria (15%), Verrucomicrobia (6%), and Actinobacteria (6%). Alphaproteobacteria (29%) was the most abundant microbial class, followed by Flavobacteria (15%) and Gammaproteobacteria (15%) in all samples. The composition of the microbial communities was found to vary vertically and seasonally. The orders Flavobacteriales and Stramenopiles showed opposing seasonal patterns; Flavobacteriales was more abundant in August and December while Stramenopiles showed high abundance in June and October at all depths. The genus Synechococcus reached extremely high abundance (14%) in the June surface water column, but was much less abundant in December water columns. Clustering analysis showed that there was a difference in the microbial community composition pattern between the strongly stratified season and well-mixed season. These results indicate that the seasonal dynamics of physicochemical and hydrologic conditions throughout the water column are important parameters in shaping the microbial community composition in the Gadeok Channel.

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

PubMed Central

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

PubMed

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

Community analysis of pitcher plant bogs of the Little River Canyon National Preserve, Alabama

Treesearch

Robert Carter; Terry Boyer; Heather McCoy; Andrew J. Londo

2006-01-01

Pitcher plant bogs of the Little River Canyon National Preserve in northern Alabama contain the federally endangered green pitcher plant [Sarracenia oreophila (Kearney) Wherry]. Multivariate analysis of the bog vegetation and environmental variables revealed three communities with unique species compositions and soil characteristics. The significant...

[Epiphytic communities of arboreal formations in Southern Vietnam: an analysis of species composition and synusias structure in dependence on the extent of anthropogenic impact].

PubMed

Es'kov, A K

2013-01-01

Species composition of epiphytic communities within different formations of Phú Quôc Island (Southern Vietnam) is studied. The dependence of species composition and structural complexity of epiphytic communities on formation quality is demonstrated. Representatives of different families differ notably in their sensitivity to disturbances. Most vulnerable are Orchidaceae which represent the dominant group in epiphytic community of rain forest and which drop out almost completely under anthropogenic impacts. In less disturbed forests, epiphyte species diversity increases mainly at the expense of "lower" synusias and directly depends on the formation layering. Diminishing of layering numbers leads to dropping out of species belonging to "lower" synusias. Among epiphytes, the indicators of disturbed communities can be detected, namely species of ruderal strategy (explerents). In primal rain forest, they are absent or barely noticeable. An index is proposed for estimation of epiphytic communitiy complexity.

Salinity affects compositional traits of epibacterial communities on the brown macroalga Fucus vesiculosus.

PubMed

Stratil, Stephanie B; Neulinger, Sven C; Knecht, Henrik; Friedrichs, Anette K; Wahl, Martin

2014-05-01

Epibiotic biofilms have the potential to control major aspects of the biology and ecology of their hosts. Their composition and function may thus be essential for the health of the host. We tested the influence of salinity on the composition of epibacterial communities associated with the brown macroalga Fucus vesiculosus. Algal individuals were incubated at three salinities (5, 19, and 25) for 14 days and nonliving reference substrata (stones) were included in the experiment. Subsequently, the composition of their surface-associated bacterial communities was analyzed by 454 pyrosequencing of 16S rRNA gene sequences. Redundancy analysis revealed that the composition of epiphytic and epilithic communities significantly differed and were both affected by salinity. We found that 5% of 2494 epiphytic operational taxonomic units at 97% sequence similarity were responsible for the observed shifts. Epibacterial α-diversity was significantly lower at salinity 5 but did not differ between substrata. Our results indicate that salinity is an important factor in structuring alga-associated epibacterial communities with respect to composition and/or diversity. Whether direct or indirect mechanisms (via altered biotic interactions) may have been responsible for the observed shifts is discussed. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing.

PubMed

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-09

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing's built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

NASA Astrophysics Data System (ADS)

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-01

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Global Biogeographic Analysis of Methanogenic Archaea Identifies Community-Shaping Environmental Factors of Natural Environments

PubMed Central

Wen, Xi; Yang, Sizhong; Horn, Fabian; Winkel, Matthias; Wagner, Dirk; Liebner, Susanne

2017-01-01

Methanogenic archaea are important for the global greenhouse gas budget since they produce methane under anoxic conditions in numerous natural environments such as oceans, estuaries, soils, and lakes. Whether and how environmental change will propagate into methanogenic assemblages of natural environments remains largely unknown owing to a poor understanding of global distribution patterns and environmental drivers of this specific group of microorganisms. In this study, we performed a meta-analysis targeting the biogeographic patterns and environmental controls of methanogenic communities using 94 public mcrA gene datasets. We show a global pattern of methanogenic archaea that is more associated with habitat filtering than with geographical dispersal. We identify salinity as the control on methanogenic community composition at global scale whereas pH and temperature are the major controls in non-saline soils and lakes. The importance of salinity for structuring methanogenic community composition is also reflected in the biogeography of methanogenic lineages and the physiological properties of methanogenic isolates. Linking methanogenic alpha-diversity with reported values of methane emission identifies estuaries as the most diverse methanogenic habitats with, however, minor contribution to the global methane budget. With salinity, temperature and pH our study identifies environmental drivers of methanogenic community composition facing drastic changes in many natural environments at the moment. However, consequences of this for the production of methane remain elusive owing to a lack of studies that combine methane production rate with community analysis. PMID:28769904

Household waste compositional analysis variation from insular communities in the framework of waste prevention strategy plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zorpas, Antonis A., E-mail: antonis.zorpas@ouc.ac.cy; Lasaridi, Katia, E-mail: klasaridi@hua.gr; Voukkali, Irene

Highlights: • Waste framework directive has set clear waste prevention procedures. • Household Compositional analysis. • Waste management plans. • Zero waste approach. • Waste generation. - Abstract: Waste management planning requires reliable data regarding waste generation, affecting factors on waste generation and forecasts of waste quantities based on facts. In order to decrease the environmental impacts of waste management the choice of prevention plan as well as the treatment method must be based on the features of the waste that are produced in a specific area. Factors such as culture, economic development, climate, and energy sources have an impactmore » on waste composition; composition influences the need of collecting waste more or less frequently of waste collection and disposition. The research question was to discover the main barriers concerning the compositional analysis in Insular Communities under warm climate conditions and the findings from this study enabled the main contents of a waste management plan to be established. These included advice to residents on waste minimisation, liaison with stakeholders and the expansion of kerbside recycling schemes.« less

Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

PubMed

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P A; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes

Legacy effects of no-analogue disturbances alter plant community diversity and composition in semi-arid sagebrush steppe

USGS Publications Warehouse

Ripplinger, Julie; Franklin, Janet; Edwards, Thomas C.

2015-01-01

Questions(i) What role does the type of managed disturbance play in structuring sagebrush steppe plant communities? (ii) How does the composition of post-disturbance plant communities change with time since disturbance? (iii) Does plant community diversity change over time following managed disturbance?LocationField study within the sagebrush steppe ecosystem. Rich County, Utah, USA.MethodsWe developed a chronosequence spanning up to 50 yrs post-treatment to study sagebrush steppe vegetation dynamics. Direct ordination was used to examine plant community composition by managed disturbance type and time since disturbance, and factorial analysis of covariance was used to examine diversity dynamics following disturbance. Indicator species values were calculated in order to identify characteristic species for each disturbance type.ResultsPlant communities experienced a shift toward distinct community composition for each of the three managed disturbance types, and gave no indication of returning to untreated community composition or diversity. Small post-disturbance increases in the number of non-native grass species were observed in the treatments relative to reference, with native forb species making the largest contribution to altered composition. On fire- and chemically-treated sites the proportional native forb species richness increased over time since disturbance, while the proportional contribution of non-native forbs to total species richness decreased. For all three treatment types, native grasses contributed less on average to total richness than on reference sites, while non-native grasses made up a higher proportion of total richness.ConclusionsCommon shrubland management techniques have legacy effects on the composition and diversity of sagebrush steppe plant communities, and no-analogue disturbances, such as chemical or mechanical treatments, have more pronounced legacy effects than treatments similar to natural disturbance regimes (fire). This study informs a broader understanding of how management actions affect natural systems by highlighting the importance of long-term management legacies as drivers of plant community structure and function.

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

PubMed Central

Emerson, Brent C.; Cicconardi, Francesco; Fanciulli, Pietro P.; Shaw, Peter J. A.

2011-01-01

There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages. PMID:21768154

Response of soil bacterial community to repeated applications of carbendazim.

PubMed

Wang, Xiuguo; Song, Min; Wang, Yiqi; Gao, Chunming; Zhang, Qun; Chu, Xiaoqiang; Fang, Hua; Yu, Yunlong

2012-01-01

The effect of repeated carbendazim applications on functional diversity of culturable microorganisms and bacterial community composition was studied under field conditions. The functional diversity of soil culturable microbial community (Shannon index, H') reduced significantly (P<0.05) after the first introduction of carbendazim at levels of 0.94, 1.88 and 4.70 kg active ingredient (a.i.)ha(-1) and then recovered to that in the control with subsequent applications. An evident (P<0.01) difference in the bacterial community composition was observed after the second carbendazim application by Temperature Gradient Gel Electrophoresis (TGGE) analysis of 16S rRNA genes amplified from treated and control soils, which remained after the third and fourth treatments. Our results indicated that repeated carbendazim applications have a transient harmful effect on functional diversity of soil culturable microbial community and result in an alteration in bacterial community composition largely due to one species within the γ-proteobacterium. Copyright © 2011 Elsevier Inc. All rights reserved.

Illumina sequencing-based analysis of a microbial community enriched under anaerobic methane oxidation condition coupled to denitrification revealed coexistence of aerobic and anaerobic methanotrophs.

PubMed

Siniscalchi, Luciene Alves Batista; Leite, Laura Rabelo; Oliveira, Guilherme; Chernicharo, Carlos Augusto Lemos; de Araújo, Juliana Calabria

2017-07-01

Methane is produced in anaerobic environments, such as reactors used to treat wastewaters, and can be consumed by methanotrophs. The composition and structure of a microbial community enriched from anaerobic sewage sludge under methane-oxidation condition coupled to denitrification were investigated. Denaturing gradient gel electrophoresis (DGGE) analysis retrieved sequences of Methylocaldum and Chloroflexi. Deep sequencing analysis revealed a complex community that changed over time and was affected by methane concentration. Methylocaldum (8.2%), Methylosinus (2.3%), Methylomonas (0.02%), Methylacidiphilales (0.45%), Nitrospirales (0.18%), and Methanosarcinales (0.3%) were detected. Despite denitrifying conditions provided, Nitrospirales and Methanosarcinales, known to perform anaerobic methane oxidation coupled to denitrification (DAMO) process, were in very low abundance. Results demonstrated that aerobic and anaerobic methanotrophs coexisted in the reactor together with heterotrophic microorganisms, suggesting that a diverse microbial community was important to sustain methanotrophic activity. The methanogenic sludge was a good inoculum to enrich methanotrophs, and cultivation conditions play a selective role in determining community composition.

Seasonal variation of plankton communities influenced by environmental factors in an artificial lake

NASA Astrophysics Data System (ADS)

Li, Xuemei; Yu, Yuhe; Zhang, Tanglin; Feng, Weisong; Ao, Hongyi; Yan, Qingyun

2012-05-01

We evaluated the seasonal variation in plankton community composition in an artificial lake. We conducted microscopic analysis and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA and 18S rRNA genes to characterize the plankton community. The clustering of unweighted pair group method with arithmetic mean (UPGMA) was then used to investigate the similarity of these plankton communities. DGGE fingerprinting revealed that samples collected at the different sites within a season shared high similarity and were generally grouped together. In contrast, we did not observe any seasonal variation based on microscopic analysis. Redundancy analysis (RDA) of the plankton operational taxonomic units (OTUs) in relation to environmental factors revealed that transparency was negatively correlated with the first axis ( R=-0.931), and temperature and total phosphorus (TP) were positively correlated with the first axis ( R=0.736 and R=0.660, respectively). In conclusion, plankton communities in the artificial lake exhibited significant seasonal variation. Transparency, phosphorus and temperature appear to be the major factors driving the differences in plankton composition.

Community composition of soil bacteria nearly a decade after a fire in a tropical rainforest in East Kalimantan, Indonesia.

PubMed

Isobe, Kazuo; Otsuka, Shigeto; Sudiana, Imade; Nurkanto, Arif; Senoo, Keishi

2009-10-01

Soil bacterial community compositions in burnt and unburnt areas in a tropical rainforest in East Kalimantan, Indonesia, were investigated 8 and 9 years after a fire by denaturing gradient gel electrophoresis analysis targeting the 16S rRNA gene. Three study sites were set in the forest area devoid of fire damage (control), and in the lightly damaged and heavily damaged forest areas. Succession of aboveground vegetation in the two damaged areas had clearly proceeded after the fire, but the vegetation types still differed from the unburnt area at the time of this study. Community composition of total soil bacteria was similar among the three areas, and so was that of actinobacteria. However, the composition of ammonia oxidizing bacteria clearly differed depending on the presence or absence of past fire damage. These results indicate that even nearly a decade after the forest fire, impacts of the fire remained on the community composition of ammonia oxidizing bacteria, but not apparently on those of dominant bacteria and actinobacteria.

Arbuscular mycorrhizal fungi inoculation mediated changes in rhizosphere bacterial community structure while promoting revegetation in a semiarid ecosystem.

PubMed

Rodríguez-Caballero, G; Caravaca, F; Fernández-González, A J; Alguacil, M M; Fernández-López, M; Roldán, A

2017-04-15

The main goal of this study was to assess the effect of the inoculation of four autochthonous shrub species with the arbuscular mycorrhizal (AM) fungus Rhizophagus intraradices on the rhizosphere bacterial community and to ascertain whether such an effect is dependent on the host plant species. Additionally, analysis of rhizosphere soil chemical and biochemical properties was performed to find relationships between them and the rhizosphere bacterial communities. Non-metric multidimensional scaling analysis and subsequent permutational multivariate analysis of variance revealed differences in bacterial community composition and structure between non-inoculated and inoculated rhizospheres. Moreover, an influence of the plant species was observed. Different bacterial groups were found to be indicator taxonomic groups of non-inoculated and inoculated rhizospheres, Gemmatimonadetes and Anaerolineaceae, respectively, being the most notable indicators. As shown by distance based redundancy analysis, the shifts in bacterial community composition and structure mediated by the inoculation with the AM fungus were mainly related to changes in plant nutrients and growth parameters, such as the shoot phosphorus content. Our findings suggest that the AM fungal inoculum was able to modify the rhizosphere bacterial community assemblage while improving the host plant performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Comparison of Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Aquatic Bacterial Communities: an Ecological Perspective▿

PubMed Central

Jones, Stuart E.; Shade, Ashley L.; McMahon, Katherine D.; Kent, Angela D.

2007-01-01

Two primer sets for automated ribosomal intergenic spacer analysis (ARISA) were used to assess the bacterial community composition (BCC) in Lake Mendota, Wisconsin, over 3 years. Correspondence analysis revealed differences in community profiles generated by different primer sets, but overall ecological patterns were conserved in each case. ARISA is a powerful tool for evaluating BCC change through space and time, regardless of the specific primer set used. PMID:17122397

Relationship between the Decomposition Process of Coarse Woody Debris and Fungal Community Structure as Detected by High-Throughput Sequencing in a Deciduous Broad-Leaved Forest in Japan

PubMed Central

Yamashita, Satoshi; Masuya, Hayato; Abe, Shin; Masaki, Takashi; Okabe, Kimiko

2015-01-01

We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process. PMID:26110605

Biofilm bacterial communities in urban drinking water distribution systems transporting waters with different purification strategies.

PubMed

Wu, Huiting; Zhang, Jingxu; Mi, Zilong; Xie, Shuguang; Chen, Chao; Zhang, Xiaojian

2015-02-01

Biofilm formation in drinking water distribution systems (DWDS) has many adverse consequences. Knowledge of microbial community structure of DWDS biofilm can aid in the design of an effective control strategy. However, biofilm bacterial community in real DWDS and the impact of drinking water purification strategy remain unclear. The present study investigated the composition and diversity of biofilm bacterial community in real DWDSs transporting waters with different purification strategies (conventional treatment and integrated treatment). High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the diversity and structure of biofilm bacterial community in real DWDS. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Nitrospirae, and Cyanobacteria were the major components of biofilm bacterial community. Proteobacteria (mainly Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria) predominated in each DWDS biofilm, but the compositions of the dominant proteobacterial classes and genera and their proportions varied among biofilm samples. Drinking water purification strategy could shape DWDS biofilm bacterial community. Moreover, Pearson's correlation analysis indicated that Actinobacteria was positively correlated with the levels of total alkalinity and dissolved organic carbon in tap water, while Firmicutes had a significant positive correlation with nitrite nitrogen.

Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

PubMed

Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

2011-08-01

During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality. Copyright © 2011 Elsevier Ltd. All rights reserved.

Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities

PubMed Central

Kent, Angela D.; Smith, Dan J.; Benson, Barbara J.; Triplett, Eric W.

2003-01-01

Culture-independent DNA fingerprints are commonly used to assess the diversity of a microbial community. However, relating species composition to community profiles produced by community fingerprint methods is not straightforward. Terminal restriction fragment length polymorphism (T-RFLP) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (T-RF) sizes through the use of web-based resources that predict T-RF sizes for known bacteria. The process quickly becomes computationally intensive due to the need to analyze profiles produced by multiple restriction digests and the complexity of profiles generated by natural microbial communities. A web-based tool is described here that rapidly generates phylogenetic assignments from submitted community T-RFLP profiles based on a database of fragments produced by known 16S rRNA gene sequences. Users have the option of submitting a customized database generated from unpublished sequences or from a gene other than the 16S rRNA gene. This phylogenetic assignment tool allows users to employ T-RFLP to simultaneously analyze microbial community diversity and species composition. An analysis of the variability of bacterial species composition throughout the water column in a humic lake was carried out to demonstrate the functionality of the phylogenetic assignment tool. This method was validated by comparing the results generated by this program with results from a 16S rRNA gene clone library. PMID:14602639

Combined Analyses of Bacterial, Fungal and Nematode Communities in Andosolic Agricultural Soils in Japan

PubMed Central

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols. PMID:22223474

Combined analyses of bacterial, fungal and nematode communities in andosolic agricultural soils in Japan.

PubMed

Bao, Zhihua; Ikunaga, Yoko; Matsushita, Yuko; Morimoto, Sho; Takada-Hoshino, Yuko; Okada, Hiroaki; Oba, Hirosuke; Takemoto, Shuhei; Niwa, Shigeru; Ohigashi, Kentaro; Suzuki, Chika; Nagaoka, Kazunari; Takenaka, Makoto; Urashima, Yasufumi; Sekiguchi, Hiroyuki; Kushida, Atsuhiko; Toyota, Koki; Saito, Masanori; Tsushima, Seiya

2012-01-01

We simultaneously examined the bacteria, fungi and nematode communities in Andosols from four agro-geographical sites in Japan using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and statistical analyses to test the effects of environmental factors including soil properties on these communities depending on geographical sites. Statistical analyses such as Principal component analysis (PCA) and Redundancy analysis (RDA) revealed that the compositions of the three soil biota communities were strongly affected by geographical sites, which were in turn strongly associated with soil characteristics such as total C (TC), total N (TN), C/N ratio and annual mean soil temperature (ST). In particular, the TC, TN and C/N ratio had stronger effects on bacterial and fungal communities than on the nematode community. Additionally, two-way cluster analysis using the combined DGGE profile also indicated that all soil samples were classified into four clusters corresponding to the four sites, showing high site specificity of soil samples, and all DNA bands were classified into four clusters, showing the coexistence of specific DGGE bands of bacteria, fungi and nematodes in Andosol fields. The results of this study suggest that geography relative to soil properties has a simultaneous impact on soil microbial and nematode community compositions. This is the first combined profile analysis of bacteria, fungi and nematodes at different sites with agricultural Andosols.

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities.

PubMed

Strickland, Michael S; McCulley, Rebecca L; Nelson, Jim A; Bradford, Mark A

2015-01-01

Inputs of low molecular weight carbon (LMW-C) to soil - primarily via root exudates- are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands) were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ∼3% of the variation observed in function. In comparison, land cover and site explained ∼46 and ∼41% of the variation, respectively. This suggests that exudate composition has little influence on function compared to site/land cover specific factors. Supporting the finding that exudate effects were minor, we found that an absence of LMW-C elicited the greatest difference in function compared to those treatments receiving any LMW-C. Additionally, exudate treatments did not alter microbial community composition and observable differences were instead due to land cover. These results confirm the strong effects of land cover/site legacies on soil microbial communities. In contrast, short-term changes in exudate composition, at meaningful concentrations, may have little impact on microbial function and composition.

Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

PubMed Central

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P. A.; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes

Habitat connectivity shapes urban arthropod communities: the key role of green roofs.

PubMed

Braaker, S; Ghazoul, J; Obrist, M K; Moretti, M

2014-04-01

The installation of green roofs, defined here as rooftops with a shallow soil cover and extensive vegetation, has been proposed as a possible measure to mitigate the loss of green space caused by the steady growth of cities. However, the effectiveness of green roofs in supporting arthropod communities, and the extent to which they facilitate connectivity of these communities within the urban environment is currently largely unknown. We investigated the variation of species community composition (beta diversity) of four arthropod groups with contrasting mobility (Carabidae, Araneae, Curculionidae, and Apidae) on 40 green roofs and 40 extensively managed green sites on the ground in the city of Zurich, Switzerland. With redundancy analysis and variation partitioning, we (1) disentangled the relative importance of local environmental conditions, the surrounding land cover composition, and habitat connectivity on species community composition, (2) searched for specific spatial scales of habitat connectivity for the different arthropod groups, and (3) discussed the ecological and functional value of green roofs in cities. Our study revealed that on green roofs community composition of high-mobility arthropod groups (bees and weevils) were mainly shaped by habitat connectivity, while low-mobility arthropod groups (carabids and spiders) were more influenced by local environmental conditions. A similar but less pronounced pattern was found for ground communities. The high importance of habitat connectivity in shaping high-mobility species community composition indicates that these green roof communities are substantially connected by the frequent exchange of individuals among surrounding green roofs. On the other hand, low-mobility species communities on green roofs are more likely connected to ground sites than to other green roofs. The integration of green roofs in urban spatial planning strategies has great potential to enable higher connectivity among green spaces, so that eventually even communities of low-mobility species become connected. Furthermore, improving the design of green roofs (composition and configuration of vegetation and soil types) could enhance the ecological value, particularly for low-mobility species.

Bacterial responses to environmental change on the Tibetan Plateau over the past half century.

PubMed

Liu, Yongqin; Priscu, John C; Yao, Tandong; Vick-Majors, Trista J; Xu, Baiqing; Jiao, Nianzhi; Santibáñez, Pamela; Huang, Sijun; Wang, Ninglian; Greenwood, Mark; Michaud, Alexander B; Kang, Shichang; Wang, Jianjun; Gao, Qun; Yang, Yunfeng

2016-06-01

Climate change and anthropogenic factors can alter biodiversity and can lead to changes in community structure and function. Despite the potential impacts, no long-term records of climatic influences on microbial communities exist. The Tibetan Plateau is a highly sensitive region that is currently undergoing significant alteration resulting from both climate change and increased human activity. Ice cores from glaciers in this region serve as unique natural archives of bacterial abundance and community composition, and contain concomitant records of climate and environmental change. We report high-resolution profiles of bacterial density and community composition over the past half century in ice cores from three glaciers on the Tibetan Plateau. Statistical analysis showed that the bacterial community composition in the three ice cores converged starting in the 1990s. Changes in bacterial community composition were related to changing precipitation, increasing air temperature and anthropogenic activities in the vicinity of the plateau. Collectively, our ice core data on bacteria in concert with environmental and anthropogenic proxies indicate that the convergence of bacterial communities deposited on glaciers across a wide geographical area and situated in diverse habitat types was likely induced by climatic and anthropogenic drivers. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Abundance and community structure of ammonia-oxidizing Archaea and Bacteria in response to fertilization and mowing in a temperate steppe in Inner Mongolia.

PubMed

Chen, Yong-Liang; Hu, Hang-Wei; Han, Hong-Yan; Du, Yue; Wan, Shi-Qiang; Xu, Zhu-Wen; Chen, Bao-Dong

2014-07-01

Based on a 6-year field trial in a temperate steppe in Inner Mongolia, we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. The results showed that N fertilization changed AOB community composition and increased AOB abundance in both May and August, but significantly decreased AOA abundance in May. By contrast, P fertilization significantly influenced AOB abundance only in August. Mowing significantly decreased AOA abundance and had little effect on AOA community compositions in May, while significantly influencing AOB abundance in both May and August, Moreover, AOA and AOB community structures showed obvious seasonal variations between May and August. Phylogenetic analysis showed that all AOA sequences fell into the Nitrososphaera cluster, and the AOB community was dominated by Nitrosospira Cluster 3. The results suggest that fertilization and mowing play important roles in affecting the abundance and community compositions of AOA and AOB. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

PubMed

Shang, Shuanghua; Yi, Yanli

2015-12-01

The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.

2016-10-01

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz

PubMed Central

Coelho, Francisco J. R. C.; Louvado, António; Domingues, Patrícia M.; Cleary, Daniel F. R.; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R.; Cunha, Ângela; Gomes, Newton C. M.

2016-01-01

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults. PMID:27762306

Integrated analysis of bacterial and microeukaryotic communities from differentially active mud volcanoes in the Gulf of Cadiz.

PubMed

Coelho, Francisco J R C; Louvado, António; Domingues, Patrícia M; Cleary, Daniel F R; Ferreira, Marina; Almeida, Adelaide; Cunha, Marina R; Cunha, Ângela; Gomes, Newton C M

2016-10-20

The present study assesses the diversity and composition of sediment bacterial and microeukaryotic communities from deep-sea mud volcanoes (MVs) associated with strike-slip faults in the South-West Iberian Margin (SWIM). We used a 16S/18S rRNA gene based pyrosequencing approach to characterize and correlate the sediment bacterial and microeukaryotic communities from MVs with differing gas seep regimes and from an additional site with no apparent seeping activity. In general, our results showed significant compositional changes of bacterial and microeukaryotic communities in sampling sites with different seepage regimes. Sediment bacterial communities were enriched with Methylococcales (putative methanotrophs) but had lower abundances of Rhodospirillales, Nitrospirales and SAR202 in the more active MVs. Within microeukaryotic communities, members of the Lobosa (lobose amoebae) were enriched in more active MVs. We also showed a strong correlation between Methylococcales populations and lobose amoeba in active MVs. This study provides baseline information on the diversity and composition of bacterial and microeukaryotic communities in deep-sea MVs associated with strike-slip faults.

Water or sediment? Partitioning the role of water column and sediment chemistry as drivers of macroinvertebrate communities in an austral South African stream.

PubMed

Dalu, Tatenda; Wasserman, Ryan J; Tonkin, Jonathan D; Mwedzi, Tongayi; Magoro, Mandla L; Weyl, Olaf L F

2017-12-31

Water pollution is a critical management issue, with many rivers and streams draining urban areas being polluted by the disposal of untreated solid waste and wastewater discharge, storm water and agricultural runoff. This has implications for biodiversity, and many rivers in the developing world are now considered compromised. We investigated benthic macroinvertebrate community structure and composition in relation to physico-chemical conditions of the water column and sediments. The study was conducted in an Austral catchment subject to both urban and agricultural pollutants in two different seasons. We assessed whether sediment characteristics were more important drivers of macroinvertebrate community composition than water column characteristics. We expected clear differences in macroinvertebrate community composition and in the associated community metrics due to distinct flow conditions between the two seasons. A combination of multivariate analyses (canonical correspondence analysis (CCA)) and biological indicator analysis were used to examine these patterns. Chironomidae was the most abundant family (>60%) in the upper mainstem river and stream sites. Stream sites were positively associated with CCA axis 2, being characterised by high turbidity and lower pH, salinity, phosphate concentration, channel width and canopy cover. Canopy cover, channel width, substrate embeddedness, phosphate concentration, pH, salinity and turbidity all had a significant effect on macroinvertebrate community composition. Using CCA variation partitioning, water quality was, however, a better predictor of benthic macroinvertebrate composition than sediment chemical conditions. Furthermore, our results suggest that seasonality had little effect on structuring benthic macroinvertebrate communities in this south-eastern zone of South Africa, despite clear changes in sediment chemistry. This likely reflects the relative lack of major variability in water chemistry compared to sediment chemistry between seasons and the relatively muted variability in precipitation between seasons than the more classic Austral temperate climates. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular analysis of microbiota along the digestive tract of juvenile Atlantic salmon (Salmo salar L.).

PubMed

Navarrete, P; Espejo, R T; Romero, J

2009-04-01

Dominant bacterial microbiota of the gut of juvenile farmed Atlantic salmon was investigated using a combination of molecular approaches. Bacterial community composition from the stomach, the pyloric caeca, and the intestine was assessed by extracting DNA directly from each gut compartment. Temporal temperature gradient gel electrophoresis (TTGE) analysis of 16S ribosomal DNA (rDNA) amplicons showed very similar bacterial compositions throughout the digestive tract. Band sequencing revealed a narrow diversity of species with a dominance of Pseudomonas in the three compartments. However, cloning revealed more diversity among the Pseudomonas sequences. To confirm these results, we analyzed the bacterial community by amplifying the variable 16S-23S rDNA intergenic spacer region (ITS). Similar ITS profiles were observed among gastrointestinal compartments of salmon, confirming the TTGE results. Moreover, the dominant ITS band at 650 bp, identified as Pseudomonas, was observed in the ITS profile from fish collected in two seasons (July 2003 and 2004). In contrast, aerobic culture analysis revealed Shewanella spp. as the most prevalent isolate. This discrepancy was resolved by evaluating 16S rDNA and ITS polymerase chain reaction amplification efficiency from both Shewanella and Pseudomonas isolates. Very similar efficiencies were observed in the two bacteria. Hence, this discrepancy may be explained by preferential cultivation of Shewanella spp. under the experimental conditions. Also, we included analyses of pelleted feed and the water influent to explore environmental influences on the bacterial composition of the gut microbiota. Overall, these results indicate a homogeneous composition of the bacterial community composition along the gastrointestinal tract of reared juvenile salmon. This community is mainly composed of Pseudomonas spp., which could be derived from water influent and may be selectively associated with salmon in this hatchery.

A phylogenetic transform enhances analysis of compositional microbiota data.

PubMed

Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A

2017-02-15

Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.

Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean

PubMed Central

Chappell, P. Dreux; Whitney, LeAnn P.; Haddock, Traci L.; Menden-Deuer, Susanne; Roy, Eric G.; Wells, Mark L.; Jenkins, Bethany D.

2013-01-01

Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response. PMID:24065961

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

PubMed Central

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

PubMed

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

Variability of community interaction networks in marine reserves and adjacent exploited areas

USGS Publications Warehouse

Montano-Moctezuma, G.; Li, H.W.; Rossignol, P.A.

2008-01-01

Regional and small-scale local oceanographic conditions can lead to high variability in community structure even among similar habitats. Communities with identical species composition can depict distinct networks due to different levels of disturbance as well as physical and biological processes. In this study we reconstruct community networks in four different areas off the Oregon Coast by matching simulated communities with observed dynamics. We compared reserves with harvested areas. Simulations suggested that different community networks, but with the same species composition, can represent each study site. Differences were found in predator-prey interactions as well as non-predatory interactions between community members. In addition, each site can be represented as a set of models, creating alternative stages among sites. The set of alternative models that characterize each study area depicts a sequence of functional responses where each specific model or interaction structure creates different species composition patterns. Different management practices, either in the past or of the present, may lead to alternative communities. Our findings suggest that management strategies should be analyzed at a community level that considers the possible consequences of shifting from one community scenario to another. This analysis provides a novel conceptual framework to assess the consequences of different management options for ecological communities. ?? 2008 Elsevier B.V. All rights reserved.

A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

PubMed Central

Oates, Lawrence G.; Read, Harry W.; Gutknecht, Jessica L. M.; Duncan, David S.; Balser, Teri B.; Jackson, Randall D.

2017-01-01

Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition. An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step. PMID:28745639

nirS-Encoding denitrifier community composition, distribution, and abundance along the coastal wetlands of China.

PubMed

Gao, Juan; Hou, Lijun; Zheng, Yanling; Liu, Min; Yin, Guoyu; Li, Xiaofei; Lin, Xianbiao; Yu, Chendi; Wang, Rong; Jiang, Xiaofen; Sun, Xiuru

2016-10-01

For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10(5) to 3.7 × 10(7) copies g(-1) dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China.

Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic alaska

DOE PAGES

Kao-Kniffin, J.; Woodcroft, B. J.; Carver, S. M.; ...

2015-12-18

We examined patterns in soil microbial community composition across a successional gradient of drained lake basins in the Arctic Coastal Plain. Analysis of 16S rRNA gene sequences revealed that methanogens closely related to Candidatus ‘Methanoflorens stordalenmirensis’ were the dominant archaea, comprising >50% of the total archaea at most sites, with particularly high levels in the oldest basins and in the top 57 cm of soil (active and transition layers). Bacterial community composition was more diverse, with lineages from OP11, Actinobacteria, Bacteroidetes, and Proteobacteria found in high relative abundance across all sites. Notably, microbial composition appeared to converge in the activemore » layer, but transition and permafrost layer communities across the sites were significantly different to one another. Microbial biomass using fatty acid-based analysis indicated that the youngest basins had increased abundances of gram-positive bacteria and saprotrophic fungi at higher soil organic carbon levels, while the oldest basins displayed an increase in only the gram-positive bacteria. While this study showed differences in microbial populations across the sites relevant to basin age, the dominance of Candidatus ‘M. stordalenmirensis’ across the chronosequence indicates the potential for changes in local carbon cycling, depending on how these methanogens and associated microbial communities respond to warming temperatures.« less

Bacterial community compositions of coking wastewater treatment plants in steel industry revealed by Illumina high-throughput sequencing.

PubMed

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

2015-03-01

In this study, Illumina high-throughput sequencing was used to reveal the community structures of nine coking wastewater treatment plants (CWWTPs) in China for the first time. The sludge systems exhibited a similar community composition at each taxonomic level. Compared to previous studies, some of the core genera in municipal wastewater treatment plants such as Zoogloea, Prosthecobacter and Gp6 were detected as minor species. Thiobacillus (20.83%), Comamonas (6.58%), Thauera (4.02%), Azoarcus (7.78%) and Rhodoplanes (1.42%) were the dominant genera shared by at least six CWWTPs. The percentages of autotrophic ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were unexpectedly low, which were verified by both real-time PCR and fluorescence in situ hybridization analyses. Hierarchical clustering and canonical correspondence analysis indicated that operation mode, flow rate and temperature might be the key factors in community formation. This study provides new insights into our understanding of microbial community compositions and structures of CWWTPs. Copyright © 2014 Elsevier Ltd. All rights reserved.

Top-down and bottom-up control on bacterial diversity in a western Norwegian deep-silled fjord.

PubMed

Storesund, Julia E; Erga, Svein Rune; Ray, Jessica L; Thingstad, T Frede; Sandaa, Ruth-Anne

2015-07-01

We investigated the relationship between viruses and co-occurring bacterial communities in the Sognefjord, a deep-silled fjord in Western Norway. A combination of flow cytometry and automated ribosomal intergenic spacer analysis (ARISA) was used to assess prokaryote and viral abundances, and bacterial diversity and community composition, respectively, in depth profiles and at two different sampling seasons (November and May). With one exception, bacterial diversity did not vary between samples regardless of depth or season. The virus and prokaryote abundances as well as bacterial community composition, however, varied significantly with season and depth, suggesting a link between the Sognefjord viral community and potential bacterial host community diversity. To our knowledge, these findings provide the first description of microbial communities in the unique Sognefjord ecosystem, and in addition are in agreement with the simple model version of the 'Killing the Winner' theory (KtW), which postulates that microbial community diversity is a feature that is essentially top-down controlled by viruses, while community composition is bottom-up controlled by competition for limiting growth substrates. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles

PubMed Central

van Agtmaal, Maaike; van Os, Gera J.; Hol, W.H. Gera; Hundscheid, Maria P.J.; Runia, Willemien T.; Hordijk, Cornelis A.; de Boer, Wietse

2015-01-01

There is increasing evidence that microbial volatiles (VOCs) play an important role in natural suppression of soil-borne diseases, but little is known on the factors that influence production of suppressing VOCs. In the current study we examined whether a stress-induced change in soil microbial community composition would affect the production by soils of VOCs suppressing the plant-pathogenic oomycete Pythium. Using pyrosequencing of 16S ribosomal gene fragments we compared the composition of bacterial communities in sandy soils that had been exposed to anaerobic disinfestation (AD), a treatment used to kill harmful soil organisms, with the composition in untreated soils. Three months after the AD treatment had been finished, there was still a clear legacy effect of the former anaerobic stress on bacterial community composition with a strong increase in relative abundance of the phylum Bacteroidetes and a significant decrease of the phyla Acidobacteria, Planctomycetes, Nitrospirae, Chloroflexi, and Chlorobi. This change in bacterial community composition coincided with loss of production of Pythium suppressing soil volatiles (VOCs) and of suppression of Pythium impacts on Hyacinth root development. One year later, the composition of the bacterial community in the AD soils was reflecting that of the untreated soils. In addition, both production of Pythium-suppressing VOCs and suppression of Pythium in Hyacinth bioassays had returned to the levels of the untreated soil. GC/MS analysis identified several VOCs, among which compounds known to be antifungal, that were produced in the untreated soils but not in the AD soils. These compounds were again produced 15 months after the AD treatment. Our data indicate that soils exposed to a drastic stress can temporarily lose pathogen suppressive characteristics and that both loss and return of these suppressive characteristics coincides with shifts in the soil bacterial community composition. Our data are supporting the suggested importance of microbial VOCs in the natural buffer of soils against diseases caused by soil-borne pathogens. PMID:26217330

Spatial variations of bacterial community and its relationship with water chemistry in Sanya Bay, South China Sea as determined by DGGE fingerprinting and multivariate analysis.

PubMed

Ling, Juan; Zhang, Yan-Ying; Dong, Jun-De; Wang, You-Shao; Feng, Jing-Bing; Zhou, Wei-Hua

2015-10-01

Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted environments in the world.

Metabarcoding of the kombucha microbial community grown in different microenvironments.

PubMed

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

2015-12-01

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

Effect of polybrominated diphenyl ether (PBDE) treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis

PubMed Central

Tian, Ren-Mao; Lee, On On; Wang, Yong; Cai, Lin; Bougouffa, Salim; Chiu, Jill Man Ying; Wu, Rudolf Shiu Sun; Qian, Pei-Yuan

2014-01-01

Marine sponges play important roles in benthic environments and are sensitive to environmental stresses. Polybrominated diphenyl ethers (PBDEs) have been widely used as flame retardants since the 1970s and are cytotoxic and genotoxic to organisms. In the present study, we studied the short-period effect of PBDE-47 (2,2′,4,4′-tetrabromodiphenyl ether) treatment on the community structure and functional gene composition of the bacterial community inhabiting the marine sponge Haliclona cymaeformis. Our results showed that the bacterial community shifted from an autotrophic bacteria-dominated community to a heterotrophic bacteria-dominated community in response to PBDE-47 in a time- and concentration-dependent manner. A potentially symbiotic sulfur-oxidizing bacterium (SOB) was dominant (>80% in abundance) in the untreated sponge. However, exposure to a high concentration (1 μg/L) of PBDE-47 caused a substantial decrease in the potential symbiont and an enrichment of heterotrophic bacteria like Clostridium. A metagenomic analysis showed a selective effect of the high concentration treatment on the functional gene composition of the enriched heterotrophic bacteria, revealing an enrichment for the functions responsible for DNA repair, multidrug efflux pumping, and bacterial chemotaxis and motility. This study demonstrated that PBDE-47 induced a shift in the composition of the community and functional genes in the sponge-associated bacterial community, revealing the selective effect of PBDE-47 treatment on the functions of the bacterial community in the microenvironment of the sponge. PMID:25642227

Competing factors of compost concentration and proximity to root affect the distribution of streptomycetes.

PubMed

Inbar, Ehud; Green, Stefan J; Hadar, Yitzhak; Minz, Dror

2005-07-01

Streptomycetes are important members of soil microbial communities and are particularly active in the degradation of recalcitrant macromolecules and have been implicated in biological control of plant disease. Using a streptomycetes-specific polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) methodology coupled with band excision and sequence analysis, we examined the effect of grape marc compost amendment to soil on cucumber plant-associated streptomycetes community composition. We observed that both compost amendment and proximity to the root surface influenced the streptomycetes community composition. A strong root selection for a soil-derived Streptomycete, most closely related to Streptomyces thermotolerans, S. iakyrus, and S. thermocarboxydus, was independent of compost amendment rate. However, while the impact of compost amendment was mitigated with increasing proximity to the root, high levels of compost amendment resulted in the detection of compost-derived species on the root surface. Conversely, in rhizosphere and non-rhizosphere soils, the community composition of streptomycetes was affected strongly even by modest compost amendment. The application of a streptomycetes-specific PCR primer set combined with DGGE analysis provided a rapid means of examining the distribution and ecology of streptomycetes in soils and plant-associated environments.

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome

PubMed Central

Schloter-Hai, Brigitte; Kublik, Susanne; Granitsiotis, Michael S.; Boschetto, Piera; Stendardo, Mariarita; Barta, Imre; Dome, Balazs; Deleuze, Jean-François; Boland, Anne; Müller-Quernheim, Joachim; Prasse, Antje; Welte, Tobias; Hohlfeld, Jens; Subramanian, Deepak; Parr, David; Gut, Ivo Glynne; Greulich, Timm; Koczulla, Andreas Rembert; Nowinski, Adam; Gorecka, Dorota; Singh, Dave; Gupta, Sumit; Brightling, Christopher E.; Hoffmann, Harald; Frankenberger, Marion; Hofer, Thomas P.; Burggraf, Dorothe; Heiss-Neumann, Marion; Ziegler-Heitbrock, Loems; Schloter, Michael; zu Castell, Wolfgang

2017-01-01

Background Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited. Methods Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons. Results We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype. Conclusion Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system. PMID:28704452

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

USGS Publications Warehouse

Cleveland, Cory C.; Reed, Sasha C.; Keller, Adrienne B.; Nemergut, Diana R.; O'Neill, Sean P.; Ostertag, Rebecca; Vitousek, Peter M.

2014-01-01

The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in response to increasing atmospheric CO2 concentrations or atmospheric nutrient deposition.

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome.

PubMed

Engel, Marion; Endesfelder, David; Schloter-Hai, Brigitte; Kublik, Susanne; Granitsiotis, Michael S; Boschetto, Piera; Stendardo, Mariarita; Barta, Imre; Dome, Balazs; Deleuze, Jean-François; Boland, Anne; Müller-Quernheim, Joachim; Prasse, Antje; Welte, Tobias; Hohlfeld, Jens; Subramanian, Deepak; Parr, David; Gut, Ivo Glynne; Greulich, Timm; Koczulla, Andreas Rembert; Nowinski, Adam; Gorecka, Dorota; Singh, Dave; Gupta, Sumit; Brightling, Christopher E; Hoffmann, Harald; Frankenberger, Marion; Hofer, Thomas P; Burggraf, Dorothe; Heiss-Neumann, Marion; Ziegler-Heitbrock, Loems; Schloter, Michael; Zu Castell, Wolfgang

2017-01-01

Changes in microbial community composition in the lung of patients suffering from moderate to severe COPD have been well documented. However, knowledge about specific microbiome structures in the human lung associated with CT defined abnormalities is limited. Bacterial community composition derived from brush samples from lungs of 16 patients suffering from different CT defined subtypes of COPD and 9 healthy subjects was analyzed using a cultivation independent barcoding approach applying 454-pyrosequencing of 16S rRNA gene fragment amplicons. We could show that bacterial community composition in patients with changes in CT (either airway or emphysema type changes, designated as severe subtypes) was different from community composition in lungs of patients without visible changes in CT as well as from healthy subjects (designated as mild COPD subtype and control group) (PC1, Padj = 0.002). Higher abundance of Prevotella in samples from patients with mild COPD subtype and from controls and of Streptococcus in the severe subtype cases mainly contributed to the separation of bacterial communities of subjects. No significant effects of treatment with inhaled glucocorticoids on bacterial community composition were detected within COPD cases with and without abnormalities in CT in PCoA. Co-occurrence analysis suggests the presence of networks of co-occurring bacteria. Four communities of positively correlated bacteria were revealed. The microbial communities can clearly be distinguished by their associations with the CT defined disease phenotype. Our findings indicate that CT detectable structural changes in the lung of COPD patients, which we termed severe subtypes, are associated with alterations in bacterial communities, which may induce further changes in the interaction between microbes and host cells. This might result in a changed interplay with the host immune system.

Shifts in phylogenetic diversity of archaeal communities in mangrove sediments at different sites and depths in southeastern Brazil.

PubMed

Mendes, Lucas William; Taketani, Rodrigo Gouvêa; Navarrete, Acácio Aparecido; Tsai, Siu Mui

2012-06-01

This study focused on the structure and composition of archaeal communities in sediments of tropical mangroves in order to obtain sufficient insight into two Brazilian sites from different locations (one pristine and another located in an urban area) and at different depth levels from the surface. Terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16S rRNA gene fragments was used to scan the archaeal community structure, and 16S rRNA gene clone libraries were used to determine the community composition. Redundancy analysis of T-RFLP patterns revealed differences in archaeal community structure according to location, depth and soil attributes. Parameters such as pH, organic matter, potassium and magnesium presented significant correlation with general community structure. Furthermore, phylogenetic analysis revealed a community composition distributed differently according to depth where, in shallow samples, 74.3% of sequences were affiliated with Euryarchaeota and 25.7% were shared between Crenarchaeota and Thaumarchaeota, while for the deeper samples, 24.3% of the sequences were affiliated with Euryarchaeota and 75.7% with Crenarchaeota and Thaumarchaeota. Archaeal diversity measurements based on 16S rRNA gene clone libraries decreased with increasing depth and there was a greater difference between depths (<18% of sequences shared) than sites (>25% of sequences shared). Taken together, our findings indicate that mangrove ecosystems support a diverse archaeal community; it might possibly be involved in nutrient cycles and are affected by sediment properties, depth and distinct locations. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Microbial Community Analysis in Water Storage Tank Sediment Exposed to Monochloramine - Portland

EPA Science Inventory

Sediment accumulation in water storage facilities causes water quality degradation, including enhanced biological growth and more rapid disinfectant decay. The current research evaluated the microbial community composition after a drinking water storage facility’s sediment was e...

Molecular Survey of Concrete Sewer Biofilm Microbial Communities

EPA Science Inventory

Although bacteria are implicated in deteriorating concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different concrete biofilms by performing sequence analysis of 16S rDNA concrete clone libraries. ...

Microbial Community Analysis in Water Storage Tank Sediment Exposed to Monochloramine

EPA Science Inventory

Sediment accumulation in water storage facilities causes water quality degradation, including enhanced biological growth and more rapid disinfectant decay. The current research evaluated the microbial community composition after a drinking water storage facility’s sediment was e...

Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake.

PubMed

Qin, H; Han, C; Jin, Z; Wu, L; Deng, H; Zhu, G; Zhong, W

2018-07-01

The aim of this study was to explore the vertical distribution traits of anaerobic ammonium-oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake. The Illumina Miseq-based sequencing and quantitative polymerase chain reactions were utilized to analyse relative abundance of anammox hydrazine synthase (hzsB) gene in comparison with bacterial 16S rRNA genes, anammox bacterial relative abundance (the number of anammox sequences divided by total number of sequences), community composition and diversity in sediments. The relative abundance of hzsB gene at the low-nitrogen (LN) site in the lake sediments showed that the vertical distribution of anammox bacteria increased to a peak, then decreased with increasing depth. Moreover, the relative abundance of hzsB gene at the high-nitrogen site was significantly lower than that at the LN site. Additionally, the community composition results showed that Candidatus Brocadia sp. was the dominant genus. In addition, the anammox bacterial diversity was also site specific. Redundancy analysis showed that the total N and the NH 4 + -N content might be the most important factors affecting anammox bacterial community composition in the studied sites. The results revealed the specific vertical variance of anammox bacterial distribution and community composition in oxic/anoxic sediments of a eutrophic shallow lake. This is the first study to demonstrate that anammox bacteria displayed the particular distribution in freshwater sediments, which implied a strong response to the anthropogenic eutrophication. © 2018 The Society for Applied Microbiology.

[Effects of intercropping Chinese milk vetch on functional characteristics of soil microbial community in rape rhizosphere].

PubMed

Zhou, Quan; Wang, Long Chang; Xing, Yi; Ma, Shu Min; Zhang, Xiao Duan; Chen, Jiao; Shi, Chao

2018-03-01

The application of green manure is facing serious problems in purple soil region of southwest China. With the aim to explore the potential application of green manure, we examined the functional characteristics of soil microbial community in a system of Chinese milk vetch intercropped with rape. The innovations are the application of Chinese milk vetch in dry land of the southwest China and the establishment of new planting pattern of rape by providing empirical data. Results showed that the intercropping with Chinese milk vetch decreased the carbon resource use efficiency of microbial community in rape rhizosphere, especially for the utilization of carbohydrates. At the same time, Shannon index, Simpson index, and richness were reduced, but evenness index was increased by intercropping. Those results from cluster analysis and principal component analysis suggest that the soil microbial community composition was significantly different between monocropping and intercropping. The carbohydrates, amino acids and carboxylic acids were the sensitive carbon sources for differentiating the changes of the microbial community induced by monocropping and intercropping. Intercropping Chinese milk vetch could decrease functional activity, change community composition, and reduce diversity of soil microbial community in rape rhizosphere.

Soil disturbance as a grassland restoration measure-effects on plant species composition and plant functional traits.

PubMed

Schnoor, Tim; Bruun, Hans Henrik; Olsson, Pål Axel

2015-01-01

Soil disturbance is recognized as an important driver of biodiversity in dry grasslands, and can therefore be implemented as a restoration measure. However, because community re-assembly following disturbance includes stochastic processes, a focus only on species richness or establishment success of particular species will not inform on how plant communities respond ecologically to disturbance. We therefore evaluated vegetation development following disturbance by quantifying species richness, species composition and functional trait composition. Degraded calcareous sandy grassland was subjected to experimental disturbance treatments (ploughing or rotavation), and the vegetation was surveyed during four subsequent years of succession. Treated plots were compared with control plots representing untreated grassland, as well as nearby plots characterized by plant communities representing the restoration target. Species richness and functional diversity both increased in response to soil disturbance, and rotavation, but not ploughing, had a persistent positive effect on the occurrence of specialist species of calcareous sandy grassland. However, no type of soil disturbance caused the plant species composition to develop towards the target vegetation. The disturbance had an immediate and large impact on the vegetation, but the vegetation developed rapidly back towards the control sites. Plant functional composition analysis indicated that the treatments created habitats different both from control sites and target sites. Community-weighted mean Ellenberg indicator values suggested that the observed plant community response was at least partially due to an increase in nitrogen and water availability following disturbance. This study shows that a mild type of disturbance, such as rotavation, may be most successful in promoting specialist species in calcareous sandy grassland, but that further treatments are needed to reduce nutrient availability. We conclude that a functional trait based analysis provides additional information of the vegetation response and the abiotic conditions created, complementing the information from the species composition.

Soil Disturbance as a Grassland Restoration Measure—Effects on Plant Species Composition and Plant Functional Traits

PubMed Central

Schnoor, Tim; Bruun, Hans Henrik; Olsson, Pål Axel

2015-01-01

Soil disturbance is recognized as an important driver of biodiversity in dry grasslands, and can therefore be implemented as a restoration measure. However, because community re-assembly following disturbance includes stochastic processes, a focus only on species richness or establishment success of particular species will not inform on how plant communities respond ecologically to disturbance. We therefore evaluated vegetation development following disturbance by quantifying species richness, species composition and functional trait composition. Degraded calcareous sandy grassland was subjected to experimental disturbance treatments (ploughing or rotavation), and the vegetation was surveyed during four subsequent years of succession. Treated plots were compared with control plots representing untreated grassland, as well as nearby plots characterized by plant communities representing the restoration target. Species richness and functional diversity both increased in response to soil disturbance, and rotavation, but not ploughing, had a persistent positive effect on the occurrence of specialist species of calcareous sandy grassland. However, no type of soil disturbance caused the plant species composition to develop towards the target vegetation. The disturbance had an immediate and large impact on the vegetation, but the vegetation developed rapidly back towards the control sites. Plant functional composition analysis indicated that the treatments created habitats different both from control sites and target sites. Community-weighted mean Ellenberg indicator values suggested that the observed plant community response was at least partially due to an increase in nitrogen and water availability following disturbance. This study shows that a mild type of disturbance, such as rotavation, may be most successful in promoting specialist species in calcareous sandy grassland, but that further treatments are needed to reduce nutrient availability. We conclude that a functional trait based analysis provides additional information of the vegetation response and the abiotic conditions created, complementing the information from the species composition. PMID:25875745

The Relationship between Phytoplankton Distribution and Water Column Characteristics in North West European Shelf Sea Waters

PubMed Central

Davidson, Keith; Bolch, Christopher J. S.; Brand, Tim D.; Narayanaswamy, Bhavani E.

2012-01-01

Phytoplankton underpin the marine food web in shelf seas, with some species having properties that are harmful to human health and coastal aquaculture. Pressures such as climate change and anthropogenic nutrient input are hypothesized to influence phytoplankton community composition and distribution. Yet the primary environmental drivers in shelf seas are poorly understood. To begin to address this in North Western European waters, the phytoplankton community composition was assessed in light of measured physical and chemical drivers during the “Ellett Line” cruise of autumn 2001 across the Scottish Continental shelf and into adjacent open Atlantic waters. Spatial variability existed in both phytoplankton and environmental conditions, with clear differences not only between on and off shelf stations but also between different on shelf locations. Temperature/salinity plots demonstrated different water masses existed in the region. In turn, principal component analysis (PCA), of the measured environmental conditions (temperature, salinity, water density and inorganic nutrient concentrations) clearly discriminated between shelf and oceanic stations on the basis of DIN∶DSi ratio that was correlated with both salinity and temperature. Discrimination between shelf stations was also related to this ratio, but also the concentration of DIN and DSi. The phytoplankton community was diatom dominated, with multidimensional scaling (MDS) demonstrating spatial variability in its composition. Redundancy analysis (RDA) was used to investigate the link between environment and the phytoplankton community. This demonstrated a significant relationship between community composition and water mass as indexed by salinity (whole community), and both salinity and DIN∶DSi (diatoms alone). Diatoms of the Pseudo-nitzschia seriata group occurred at densities potentially harmful to shellfish aquaculture, with the potential for toxicity being elevated by the likelihood of DSi limitation of growth at most stations and depths. PMID:22479533

Drivers of metacommunity structure diverge for common and rare Amazonian tree species.

PubMed

Bispo, Polyanna da Conceição; Balzter, Heiko; Malhi, Yadvinder; Slik, J W Ferry; Dos Santos, João Roberto; Rennó, Camilo Daleles; Espírito-Santo, Fernando D; Aragão, Luiz E O C; Ximenes, Arimatéa C; Bispo, Pitágoras da Conceição

2017-01-01

We analysed the flora of 46 forest inventory plots (25 m x 100 m) in old growth forests from the Amazonian region to identify the role of environmental (topographic) and spatial variables (obtained using PCNM, Principal Coordinates of Neighbourhood Matrix analysis) for common and rare species. For the analyses, we used multiple partial regression to partition the specific effects of the topographic and spatial variables on the univariate data (standardised richness, total abundance and total biomass) and partial RDA (Redundancy Analysis) to partition these effects on composition (multivariate data) based on incidence, abundance and biomass. The different attributes (richness, abundance, biomass and composition based on incidence, abundance and biomass) used to study this metacommunity responded differently to environmental and spatial processes. Considering standardised richness, total abundance (univariate) and composition based on biomass, the results for common species differed from those obtained for all species. On the other hand, for total biomass (univariate) and for compositions based on incidence and abundance, there was a correspondence between the data obtained for the total community and for common species. Our data also show that in general, environmental and/or spatial components are important to explain the variability in tree communities for total and common species. However, with the exception of the total abundance, the environmental and spatial variables measured were insufficient to explain the attributes of the communities of rare species. These results indicate that predicting the attributes of rare tree species communities based on environmental and spatial variables is a substantial challenge. As the spatial component was relevant for several community attributes, our results demonstrate the importance of using a metacommunities approach when attempting to understand the main ecological processes underlying the diversity of tropical forest communities.

Composition and development of oral bacterial communities.

PubMed

Palmer, Robert J

2014-02-01

The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries. Published 2013. This article is a US Government work and is in the public domain in the USA.

Microbial community and performance of slaughterhouse wastewater treatment filters.

PubMed

Stets, M I; Etto, R M; Galvão, C W; Ayub, R A; Cruz, L M; Steffens, M B R; Barana, A C

2014-06-16

The performance of anaerobic filter bioreactors (AFs) is influenced by the composition of the substrate, support medium, and the microbial species present in the sludge. In this study, the efficiency of a slaughterhouse effluent treatment using three AFs containing different support media was tested, and the microbial diversity was investigated by amplified ribosomal DNA restriction analysis and 16S rRNA gene sequencing. The physicochemical analysis of the AF systems tested suggested their feasibility, with rates of chemical oxygen demand removal of 72±8% in hydraulic retention times of 1 day. Analysis of pH, alkalinity, volatile acidity, total solids, total volatile solids, total Kjeldahl nitrogen, and the microbial community structures indicated high similarity among the three AFs. The composition of prokaryotic communities showed a prevalence of Proteobacteria (27.3%) and Bacteroidetes (18.4%) of the Bacteria domain and Methanomicrobiales (36.4%) and Methanosarcinales (35.3%) of the Archaea domain. Despite the high similarity of the microbial communities among the AFs, the reactor containing pieces of clay brick as a support medium presented the highest richness and diversity of bacterial and archaeal operational taxonomic units.

Floral and nesting resources, habitat structure, and fire influence bee distribution across an open-forest gradient

USGS Publications Warehouse

Grundel, R.; Jean, R.P.; Frohnapple, K.J.; Glowacki, G.A.; Scott, P.E.; Pavlovic, N.B.

2010-01-01

Given bees' central effect on vegetation communities, it is important to understand how and why bee distributions vary across ecological gradients. We examined how plant community composition, plant diversity, nesting suitability, canopy cover, land use, and fire history affected bee distribution across an open-forest gradient in northwest Indiana, USA, a gradient similar to the historic Midwest United States landscape mosaic. When considered with the other predictors, plant community composition was not a significant predictor of bee community composition. Bee abundance was negatively related to canopy cover and positively to recent fire frequency, bee richness was positively related to plant richness and abundance of potential nesting resources, and bee community composition was significantly related to plant richness, soil characteristics potentially related to nesting suitability, and canopy cover. Thus, bee abundance was predicted by a different set of environmental characteristics than was bee species richness, and bee community composition was predicted, in large part, by a combination of the significant predictors of bee abundance and richness. Differences in bee community composition along the woody vegetation gradient were correlated with relative abundance of oligolectic, or diet specialist, bees. Because oligoleges were rarer than diet generalists and were associated with open habitats, their populations may be especially affected by degradation of open habitats. More habitat-specialist bees were documented for open and forest/scrub habitats than for savanna/woodland habitats, consistent with bees responding to habitats of intermediate woody vegetation density, such as savannas, as ecotones rather than as distinct habitat types. Similarity of bee community composition, similarity of bee abundance, and similarity of bee richness between sites were not significantly related to proximity of sites to each other. Nestedness analysis indicated that species composition in species-poor sites was not merely a subset of species composition at richer sites. The lack of significant proximity or nestedness effects suggests that factors at a small spatial scale strongly influence bees' use of sites. The findings indicate that patterns of plant diversity, nesting resource availability, recent fire, and habitat shading, present at the scale of a few hundred meters, are key determinants of bee community patterns in the mosaic open-savanna-forest landscape. ?? 2010 by the Ecological Society of America.

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

PubMed Central

Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. PMID:29538438

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields.

PubMed

Song, Xuhong; Pan, Yuan; Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

Microbial community composition affects soil fungistasis.

PubMed

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

2003-02-01

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

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

PubMed Central

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X.; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-01-01

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems. PMID:27824160

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta.

PubMed

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-11-08

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

Mapping gradients of community composition with nearest-neighbour imputation: extending plot data for landscape analysis

Treesearch

Janet L. Ohmann; Matthew J. Gregory; Emilie B. Henderson; Heather M. Roberts

2011-01-01

Question: How can nearest-neighbour (NN) imputation be used to develop maps of multiple species and plant communities? Location: Western and central Oregon, USA, but methods are applicable anywhere. Methods: We demonstrate NN imputation by mapping woody plant communities for >100 000 km2 of diverse forests and woodlands. Species abundances on...

Regional gradient analysis and spatial pattern of woody plant communities in Oregon forests.

Treesearch

J.L. Ohmann; T.A. Spies

1998-01-01

Knowledge of regional-scale patterns of ecological community structure, and of factors that control them, is largely conceptual. Regional- and local-scale factors associated with regional variation in community composition have not been quantified. We analyzed data on woody plant species abundance from 2443 field plots across natural and seminatural forests and...

Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status

PubMed Central

Yang, Ching-Hong; Crowley, David E.

2000-01-01

Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status. PMID:10618246

Competitive and demographic leverage points of community shifts under climate warming

PubMed Central

Sorte, Cascade J. B.; White, J. Wilson

2013-01-01

Accelerating rates of climate change and a paucity of whole-community studies of climate impacts limit our ability to forecast shifts in ecosystem structure and dynamics, particularly because climate change can lead to idiosyncratic responses via both demographic effects and altered species interactions. We used a multispecies model to predict which processes and species' responses are likely to drive shifts in the composition of a space-limited benthic marine community. Our model was parametrized from experimental manipulations of the community. Model simulations indicated shifts in species dominance patterns as temperatures increase, with projected shifts in composition primarily owing to the temperature dependence of growth, mortality and competition for three critical species. By contrast, warming impacts on two other species (rendering them weaker competitors for space) and recruitment rates of all species were of lesser importance in determining projected community changes. Our analysis reveals the importance of temperature-dependent competitive interactions for predicting effects of changing climate on such communities. Furthermore, by identifying processes and species that could disproportionately leverage shifts in community composition, our results contribute to a mechanistic understanding of climate change impacts, thereby allowing more insightful predictions of future biodiversity patterns. PMID:23658199

Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils.

PubMed

Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

2018-01-01

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline-alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity ( P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi ( P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

Analysis of factors affecting the accuracy, reproducibility, and interpretation of microbial community carbon source utilization patterns

USGS Publications Warehouse

Haack, S.K.; Garchow, H.; Klug, M.J.; Forney, L.J.

1995-01-01

We determined factors that affect responses of bacterial isolates and model bacterial communities to the 95 carbon substrates in Biolog microliter plates. For isolates and communities of three to six bacterial strains, substrate oxidation rates were typically nonlinear and were delayed by dilution of the inoculum. When inoculum density was controlled, patterns of positive and negative responses exhibited by microbial communities to each of the carbon sources were reproducible. Rates and extents of substrate oxidation by the communities were also reproducible but were not simply the sum of those exhibited by community members when tested separately. Replicates of the same model community clustered when analyzed by principal- components analysis (PCA), and model communities with different compositions were clearly separated un the first PCA axis, which accounted for >60% of the dataset variation. PCA discrimination among different model communities depended on the extent to which specific substrates were oxidized. However, the substrates interpreted by PCA to be most significant in distinguishing the communities changed with reading time, reflecting the nonlinearity of substrate oxidation rates. Although whole-community substrate utilization profiles were reproducible signatures for a given community, the extent of oxidation of specific substrates and the numbers or activities of microorganisms using those substrates in a given community were not correlated. Replicate soil samples varied significantly in the rate and extent of oxidation of seven tested substrates, suggesting microscale heterogeneity in composition of the soil microbial community.

Do temperate tree species diversity and identity influence soil microbial community function and composition?

PubMed

Khlifa, Rim; Paquette, Alain; Messier, Christian; Reich, Peter B; Munson, Alison D

2017-10-01

Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. This study investigates intertrophic links between tree diversity and soil microbial community function and composition. We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM), and tree identity. The site was a 4-year-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles, and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroResp ™ system, respectively. The relationship between tree species richness and glucose-induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO 2 ) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration [BR]), with higher biomass (glucose-induced respiration [GIR]), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity-leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified functional traits related to life-history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.

Characterisation of the physical composition and microbial community structure of biofilms within a model full-scale drinking water distribution system.

PubMed

Fish, Katherine E; Collins, Richard; Green, Nicola H; Sharpe, Rebecca L; Douterelo, Isabel; Osborn, A Mark; Boxall, Joby B

2015-01-01

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS.

Characterisation of the Physical Composition and Microbial Community Structure of Biofilms within a Model Full-Scale Drinking Water Distribution System

PubMed Central

Fish, Katherine E.; Collins, Richard; Green, Nicola H.; Sharpe, Rebecca L.; Douterelo, Isabel; Osborn, A. Mark; Boxall, Joby B.

2015-01-01

Within drinking water distribution systems (DWDS), microorganisms form multi-species biofilms on internal pipe surfaces. A matrix of extracellular polymeric substances (EPS) is produced by the attached community and provides structure and stability for the biofilm. If the EPS adhesive strength deteriorates or is overcome by external shear forces, biofilm is mobilised into the water potentially leading to degradation of water quality. However, little is known about the EPS within DWDS biofilms or how this is influenced by community composition or environmental parameters, because of the complications in obtaining biofilm samples and the difficulties in analysing EPS. Additionally, although biofilms may contain various microbial groups, research commonly focuses solely upon bacteria. This research applies an EPS analysis method based upon fluorescent confocal laser scanning microscopy (CLSM) in combination with digital image analysis (DIA), to concurrently characterize cells and EPS (carbohydrates and proteins) within drinking water biofilms from a full-scale DWDS experimental pipe loop facility with representative hydraulic conditions. Application of the EPS analysis method, alongside DNA fingerprinting of bacterial, archaeal and fungal communities, was demonstrated for biofilms sampled from different positions around the pipeline, after 28 days growth within the DWDS experimental facility. The volume of EPS was 4.9 times greater than that of the cells within biofilms, with carbohydrates present as the dominant component. Additionally, the greatest proportion of EPS was located above that of the cells. Fungi and archaea were established as important components of the biofilm community, although bacteria were more diverse. Moreover, biofilms from different positions were similar with respect to community structure and the quantity, composition and three-dimensional distribution of cells and EPS, indicating that active colonisation of the pipe wall is an important driver in material accumulation within the DWDS. PMID:25706303

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing.

PubMed

O'Connell, Lauren; Gao, Song; McCorquodale, Donald; Fleisher, Jay; Lopez, Jose V

2018-01-01

Similar to natural rivers, manmade inlets connect inland runoff to the ocean. Port Everglades Inlet (PEI) is a busy cargo and cruise ship port in South Florida, which can act as a source of pollution to surrounding beaches and offshore coral reefs. Understanding the composition and fluctuations of bacterioplankton communities ("microbiomes") in major port inlets is important due to potential impacts on surrounding environments. We hypothesize seasonal microbial fluctuations, which were profiled by high throughput 16S rRNA amplicon sequencing and analysis. Surface water samples were collected every week for one year. A total of four samples per month, two from each sampling location, were used for statistical analysis creating a high sampling frequency and finer sampling scale than previous inlet microbiome studies. We observed significant differences in community alpha diversity between months and seasons. Analysis of composition of microbiomes (ANCOM) tests were run in QIIME 2 at genus level taxonomic classification to determine which genera were differentially abundant between seasons and months. Beta diversity results yielded significant differences in PEI community composition in regard to month, season, water temperature, and salinity. Analysis of potentially pathogenic genera showed presence of Staphylococcus and Streptococcus . However, statistical analysis indicated that these organisms were not present in significantly high abundances throughout the year or between seasons. Significant differences in alpha diversity were observed when comparing microbial communities with respect to time. This observation stems from the high community evenness and low community richness in August. This indicates that only a few organisms dominated the community during this month. August had lower than average rainfall levels for a wet season, which may have contributed to less runoff, and fewer bacterial groups introduced into the port surface waters. Bacterioplankton beta diversity differed significantly by month, season, water temperature, and salinity. The 2013-2014 dry season (October-April), was warmer and wetter than historical averages. This may have driven significant differences in beta diversity. Increased nitrogen and phosphorous concentrations were observed in these dry season months, possibly creating favorable bacterial growth conditions. Potentially pathogenic genera were present in the PEI. However their relatively low, non-significant abundance levels highlight their relatively low risk for public health concerns. This study represents the first to sample a large port at this sampling scale and sequencing depth. These data can help establish the inlet microbial community baseline and supplement the vital monitoring of local marine and recreational environments, all the more poignant in context of local reef disease outbreaks and worldwide coral reef collapse in wake of a harsh 2014-16 El Niño event.

Are cattle surrogate wildlife? Savanna plant community composition explained by total herbivory more than herbivore type.

PubMed

Veblen, Kari E; Porensky, Lauren M; Riginos, Corinna; Young, Truman P

2016-09-01

The widespread replacement of wild ungulate herbivores by domestic livestock in African savannas is composed of two interrelated phenomena: (1) loss or reduction in numbers of individual wildlife species or guilds and (2) addition of livestock to the system. Each can have important implications for plant community dynamics. Yet very few studies have experimentally addressed the individual, combined, and potentially interactive effects of wild vs. domestic herbivore species on herbaceous plant communities within a single system. Additionally, there is little information about whether, and in which contexts, livestock might functionally replace native herbivore wildlife or, alternatively, have fundamentally different effects on plant species composition. The Kenya Long-term Exclosure Experiment, which has been running since 1995, is composed of six treatment combinations of mega-herbivores, meso-herbivore ungulate wildlife, and cattle. We sampled herbaceous vegetation 25 times between 1999 and 2013. We used partial redundancy analysis and linear mixed models to assess effects of herbivore treatments on overall plant community composition and key plant species. Plant communities in the six different herbivore treatments shifted directionally over time and diverged from each other substantially by 2013. Plant community composition was strongly related (R 2  = 0.92) to residual plant biomass, a measure of herbivore utilization. Addition of any single herbivore type (cattle, wildlife, or mega-herbivores) caused a shift in plant community composition that was proportional to its removal of plant biomass. These results suggest that overall herbivory pressure, rather than herbivore type or complex interactions among different herbivore types, was the main driver of changes in plant community composition. Individual plant species, however, did respond most strongly to either wild ungulates or cattle. Although these results suggest considerable functional similarity between a suite of native wild herbivores (which included grazers, browsers, and mixed feeders) and cattle (mostly grazers) with respect to understory plant community composition, responses of individual plant species demonstrate that at the plant-population-level impacts of a single livestock species are not functionally identical to those of a diverse group of native herbivores. © 2016 by the Ecological Society of America.

Composition and Dynamics of Bacterial Communities of a Drinking Water Supply System as Assessed by RNA- and DNA-Based 16S rRNA Gene Fingerprinting

PubMed Central

Eichler, Stefan; Christen, Richard; Höltje, Claudia; Westphal, Petra; Bötel, Julia; Brettar, Ingrid; Mehling, Arndt; Höfle, Manfred G.

2006-01-01

Bacterial community dynamics of a whole drinking water supply system (DWSS) were studied from source to tap. Raw water for this DWSS is provided by two reservoirs with different water characteristics in the Harz mountains of Northern Germany. Samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. RNA and DNA were extracted from the sampled water. The 16S rRNA or its genes were partially amplified by reverse transcription-PCR or PCR and analyzed by single-strand conformation polymorphism community fingerprints. The bacterial community structures of the raw water samples from the two reservoirs were very different, but no major changes of these structures occurred after flocculation and sand filtration. Chlorination of the processed raw water strongly affected bacterial community structure, as reflected by the RNA-based fingerprints. This effect was less pronounced for the DNA-based fingerprints. After chlorination, the bacterial community remained rather constant from the storage containers to the tap. Furthermore, the community structure of the tap water did not change substantially for several months. Community composition was assessed by sequencing of abundant bands and phylogenetic analysis of the sequences obtained. The taxonomic compositions of the bacterial communities from both reservoirs were very different at the species level due to their different limnologies. On the other hand, major taxonomic groups, well known to occur in freshwater, such as Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes, were found in both reservoirs. Significant differences in the detection of the major groups were observed between DNA-based and RNA-based fingerprints irrespective of the reservoir. Chlorination of the drinking water seemed to promote growth of nitrifying bacteria. Detailed analysis of the community dynamics of the whole DWSS revealed a significant influence of both source waters on the overall composition of the drinking water microflora and demonstrated the relevance of the raw water microflora for the drinking water microflora provided to the end user. PMID:16517632

Fish communities of fixed sites in the Western Lake Michigan Drainages, Wisconsin and Michigan, 1993-95

USGS Publications Warehouse

Sullivan, D.J.

1997-01-01

Canonical correspondence analysis (CCA) revealed that soil credibility was a significant predictor of species composition. Though not statistically significant, land use, soil permeability, and bedrock permeability also were indicated as predictors of fish-species composition by CCA.

Exploring the patterns of alpine vegetation of Eastern Bhutan: a case study from the Merak Himalaya.

PubMed

Jamtsho, Karma; Sridith, Kitichate

2015-01-01

A survey was conducted from March to September 2012 along the altitudinal gradient of the Jomokungkhar trail in the Merak Himalaya of Sakteng Wildlife Sanctuary to study the floristic compositions and the patterns of alpine vegetation of Eastern Bhutan. The vegetation of the sampled plots is classified into five types of communities based on the hierarchical cluster analysis at similarity index 63% viz., (1) Riverine Community; (2) Abies-Rhododendron Woodland Community; (3) Juniperus Scrub Community; (4) Rhododendron Krummholz and (5) Alpine Meadow, based on the floristic compositions. In addition, it was noticed that the fragile alpine environment of the Merak Himalaya has high plant diversity and important plants that are susceptible to the anthropogenic pressures.

Household waste compositional analysis variation from insular communities in the framework of waste prevention strategy plans.

PubMed

Zorpas, Antonis A; Lasaridi, Katia; Voukkali, Irene; Loizia, Pantelitsa; Chroni, Christina

2015-04-01

Waste management planning requires reliable data regarding waste generation, affecting factors on waste generation and forecasts of waste quantities based on facts. In order to decrease the environmental impacts of waste management the choice of prevention plan as well as the treatment method must be based on the features of the waste that are produced in a specific area. Factors such as culture, economic development, climate, and energy sources have an impact on waste composition; composition influences the need of collecting waste more or less frequently of waste collection and disposition. The research question was to discover the main barriers concerning the compositional analysis in Insular Communities under warm climate conditions and the findings from this study enabled the main contents of a waste management plan to be established. These included advice to residents on waste minimisation, liaison with stakeholders and the expansion of kerbside recycling schemes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Baseline results from the Lichen Community Indicator Program in the Pacific Northwest: Air quality patterns and evidence of a nitrogen pollution problem

Treesearch

Sarah Jovan

2009-01-01

Why Are Epiphytic Lichen Communities Important? Lichens are one of the bioindicators used by the Forest Inventory and Analysis (FIA) Program to monitor forest health. To obtain data for use in its Lichen Community Indicator Program, FIA samples a regular network of permanent field plots to determine the composition of epiphytic, i.e., tree dwelling, lichen communities...

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

PubMed Central

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-01-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration. PMID:28349918

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

NASA Astrophysics Data System (ADS)

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-03-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration.

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

PubMed Central

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m. PMID:24205246

Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

PubMed

Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

2013-01-01

Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

Microplastic-associated bacterial assemblages in the intertidal zone of the Yangtze Estuary.

PubMed

Jiang, Peilin; Zhao, Shiye; Zhu, Lixin; Li, Daoji

2018-05-15

Plastic trash is common in oceans. Terrestrial and marine ecosystem interactions occur in the intertidal zone where accumulation of plastic frequently occurs. However, knowledge of the plastic-associated microbial community (the plastisphere) in the intertidal zone is scanty. We used high-throughput sequencing to profile the bacterial communities attached to microplastic samples from intertidal locations around the Yangtze estuary in China. The structure and composition of plastisphere communities varied significantly among the locations. We found the taxonomic composition on microplastic samples was related to their sedimentary and aquatic origins. Correlation network analysis was used to identify keystone bacterial genera (e.g. Rhodobacterales, Sphingomonadales and Rhizobiales), which represented important microbial associations within the plastisphere community. Other species (i.e. potential pathogens) were considered as hitchhikers in the plastic attached microbial communities. Metabolic pathway analysis suggested adaptations of these bacterial assemblages to the plastic surface-colonization lifestyle. These adaptations included reduced "cell motility" and greater "xenobiotics biodegradation and metabolism." The findings illustrate the diverse microbial assemblages that occur on microplastic and increase our understanding of plastisphere ecology. Copyright © 2017 Elsevier B.V. All rights reserved.

The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods

PubMed Central

Kahlert, Maria; Fink, Patrick

2017-01-01

An increasing number of studies use next generation sequencing (NGS) to analyze complex communities, but is the method sensitive enough when it comes to identification and quantification of species? We compared NGS with morphology-based identification methods in an analysis of microalgal (periphyton) communities. We conducted a mesocosm experiment in which we allowed two benthic grazer species to feed upon benthic biofilms, which resulted in altered periphyton communities. Morphology-based identification and 454 (Roche) pyrosequencing of the V4 region in the small ribosomal unit (18S) rDNA gene were used to investigate the community change caused by grazing. Both the NGS-based data and the morphology-based method detected a marked shift in the biofilm composition, though the two methods varied strongly in their abilities to detect and quantify specific taxa, and neither method was able to detect all species in the biofilms. For quantitative analysis, we therefore recommend using both metabarcoding and microscopic identification when assessing the community composition of eukaryotic microorganisms. PMID:28234997

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.

PubMed

Kuramae, Eiko; Gamper, Hannes; van Veen, Johannes; Kowalchuk, George

2011-08-01

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

A phylogenetic transform enhances analysis of compositional microbiota data

PubMed Central

Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A

2017-01-01

Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities. DOI: http://dx.doi.org/10.7554/eLife.21887.001 PMID:28198697

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

PubMed

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

2015-09-01

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

Pycnoscelus surinamensis cockroach gut microbiota respond consistently to a fungal diet without mirroring those of fungus-farming termites.

PubMed

Richards, Callum; Otani, Saria; Mikaelyan, Aram; Poulsen, Michael

2017-01-01

The gut microbiotas of cockroaches and termites play important roles in the symbiotic digestion of dietary components, such as lignocellulose. Diet has been proposed as a primary determinant of community structure within the gut, acting as a selection force to shape the diversity observed within this "bioreactor", and as a key factor for the divergence of the termite gut microbiota from the omnivorous cockroach ancestor. The gut microbiota in most termites supports primarily the breakdown of lignocellulose, but the fungus-farming sub-family of higher termites has become similar in gut microbiota to the ancestral omnivorous cockroaches. To assess the importance of a fungus diet as a driver of community structure, we compare community compositions in the guts of experimentally manipulated Pycnoscelus surinamensis cockroaches fed on fungus cultivated by fungus-farming termites. MiSeq amplicon analysis of gut microbiotas from 49 gut samples showed a step-wise gradient pattern in community similarity that correlated with an increase in the proportion of fungal material provided to the cockroaches. Comparison of the taxonomic composition of manipulated communities to that of gut communities of a fungus-feeding termite species showed that although some bacteria OTUs shared by P. surinamensis and the farming termites increased in the guts of cockroaches on a fungal diet, cockroach communities remained distinct from those of termites. These results demonstrate that a fungal diet can play a role in structuring gut community composition, but at the same time exemplifies how original community compositions constrain the magnitude of such change.

Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization.

PubMed

Enwall, Karin; Philippot, Laurent; Hallin, Sara

2005-12-01

The objective of this study was to explore the long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil. Soil from the following six treatments was analyzed in an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, and unfertilized and unfertilized bare fallow. All plots but the fallow were planted with corn. The activity was measured in terms of potential denitrification rate and basal soil respiration. The nosZ and narG genes were used as functional markers of the denitrifying community, and the composition was analyzed using denaturing gradient gel electrophoresis of nosZ and restriction fragment length polymorphism of narG, together with cloning and sequencing. A fingerprint of the total bacterial community was assessed by ribosomal intergenic spacer region analysis (RISA). The potential denitrification rates were higher in plots treated with organic fertilizer than in those with only mineral fertilizer. The basal soil respiration rates were positively correlated to soil carbon content, and the highest rates were found in the plots with the addition of sewage sludge. Fingerprints of the nosZ and narG genes, as well as the RISA, showed significant differences in the corresponding communities in the plots treated with (NH4)2SO4 and sewage sludge, which exhibited the lowest pH. In contrast, similar patterns were observed among the other four treatments, unfertilized plots with and without crops and the plots treated with Ca(NO3)2 or with manure. This study shows that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a long-term basis. However, the treatments in which the denitrifying and bacterial community composition differed the most did not correspond to treatments with the most different activities, showing that potential activity was uncoupled to community composition.

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium.

PubMed

Pereira, Arthur Prudêncio de Araujo; Andrade, Pedro Avelino Maia de; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

2017-01-01

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil.

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium

PubMed Central

de Andrade, Pedro Avelino Maia; Bini, Daniel; Durrer, Ademir; Robin, Agnès; Bouillet, Jean Pierre; Andreote, Fernando Dini; Cardoso, Elke Jurandy Bran Nogueira

2017-01-01

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil. PMID:28686690

Microbial community composition of a multi-stage moving bed biofilm reactor and its interaction with kinetic model parameters estimation.

PubMed

Wang, Xiaodong; Bi, Xuejun; Hem, Lars John; Ratnaweera, Harsha

2018-07-15

Microbial community diversity determines the function of each chamber of multi-stage moving bed biofilm reactor (MBBR) systems. How the microbial community data can be further used to serve wastewater treatment process modelling and optimization has been rarely studied. In this study, a MBBR system was set up to investigate the microbial community diversity of biofilm in each functional chamber. The compositions of microbial community of biofilm from different chambers of MBBR were quantified by high-throughput sequencing. Significantly higher proportion of autotrophs were found in the second aerobic chamber (15.4%), while 4.3% autotrophs were found in the first aerobic chamber. Autotrophs in anoxic chamber were negligible. Moreover, ratios of active heterotrophic biomass and autotrophic biomass (X H /X A ) were obtained by performing respiration tests. By setting heterotroph/autotroph ratios obtained from sequencing analysis equal to X H /X A , a novel approach for kinetic model parameters estimation was developed. This work not only investigated microbial community of MBBR system, but also it provided an approach to make further use of molecular microbiology analysis results. Copyright © 2018 Elsevier Ltd. All rights reserved.

Inference methods for spatial variation in species richness and community composition when not all species are detected

USGS Publications Warehouse

Nichols, J.D.; Boulinier, T.; Hines, J.E.; Pollock, K.H.; Sauer, J.R.

1998-01-01

Inferences about spatial variation in species richness and community composition are important both to ecological hypotheses about the structure and function of communities and to community-level conservation and management. Few sampling programs for animal communities provide censuses, and usually some species present. We present estimators useful for drawing inferences about comparative species richness and composition between different sampling locations when not all species are detected in sampling efforts. Based on capture-recapture models using the robust design, our methods estimate relative species richness, proportion of species in one location that are also found in another, and number of species found in one location but not in another. The methods use data on the presence or absence of each species at different sampling occasions (or locations) to estimate the number of species not detected at any occasions (or locations). This approach permits estimation of the number of species in the sampled community and in subsets of the community useful for estimating the fraction of species shared by two communities. We provide an illustration of our estimation methods by comparing bird species richness and composition in two locations sampled by routes of the North American Breeding Bird Survey. In this example analysis, the two locations (an associated bird communities) represented different levels of urbanization. Estimates of relative richness, proportion of shared species, and number of species present on one route but not the other indicated that the route with the smaller fraction of urban area had greater richness and a larer number of species that were not found on the more urban route than vice versa. We developed a software package, COMDYN, for computing estimates based on the methods. Because these estimation methods explicitly deal with sampling in which not all species are detected, we recommend their use for addressing questions about species richness and community composition.

Reduced flexibility associated with metabolic syndrome in community-dwelling elders.

PubMed

Chang, Ke-Vin; Hung, Chen-Yu; Li, Chia-Ming; Lin, Yu-Hung; Wang, Tyng-Guey; Tsai, Keh-Sung; Han, Der-Sheng

2015-01-01

The ageing process may lead to reductions in physical fitness, a known risk factor in the development of metabolic syndrome. The purpose of the current study was to evaluate cross-sectional and combined associations of metabolic syndrome with body composition and physical fitness in a community based geriatric population. A total of 628 community-dwelling elders attending a geriatric health examination were enrolled in the study. The diagnosis of metabolic syndrome was based on the modified National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) criterion with Asian cutoff of waist girth was adopted in this study. Body composition was obtained using bioimpedance analysis, and physical fitness was evaluated through the measurement of muscle strength (handgrip force), lower extremity muscle endurance (sit-to-stand test), flexibility (sit-and-reach test), and cardiorespiratory endurance (2-minute step test). Multivariable logistic regression and correlation analysis were performed to determine the association of metabolic syndrome with body composition and functionality variables. Metabolic syndrome was associated with increased skeletal muscle index (SMI) (odds ratio (OR), 1.61, 95% confidence interval (CI), 1.25-2.07) and decreased flexibility (OR, 0.97, 95% CI, 0.95-0.99) compared with those without metabolic syndrome. When body mass index was accounted for in the analysis, the association of SMI with metabolic syndrome was reduced. Waist circumference was positively correlated with SMI but negatively correlated with flexibility, whereas high density lipoprotein was positively correlated with flexibility but negatively correlated with SMI. Reduced flexibility was positively associated with metabolic syndrome independent of age, gender, body composition, and functionality measurements in a community based geriatric population. Significant associations between metabolic syndrome with muscle strength and cardiorespiratory fitness in the elderly were not observed. Furthermore, flexibility should be included in the complete evaluation for metabolic syndrome.

Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

PubMed

Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

2014-04-01

With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation.

PubMed

Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M; Young, Vincent B; Jansson, Janet K; Fredricks, David N; Borenstein, Elhanan

2016-01-01

Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites' abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease. Studies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on metabolite concentrations and evaluating whether these predictions agree with measured metabolomic profiles. We find that a surprisingly large proportion of metabolite variation in the vaginal microbiome can be predicted based on species composition (including dramatic shifts associated with disease), identify putative mechanisms underlying these predictions, and evaluate the roles of individual bacterial species and genes. Analysis of gut microbiome data using this framework recovers similar community metabolic trends. This framework lays the foundation for model-based multi-omic integrative studies, ultimately improving our understanding of microbial community metabolism.

Path analyses of cross-sectional and longitudinal data suggest that variability in natural communities of blood-associated parasites is derived from host characteristics and not interspecific interactions.

PubMed

Cohen, Carmit; Einav, Monica; Hawlena, Hadas

2015-08-19

The parasite composition of wild host individuals often impacts their behavior and physiology, and the transmission dynamics of pathogenic species thereby determines disease risk in natural communities. Yet, the determinants of parasite composition in natural communities are still obscure. In particular, three fundamental questions remain open: (1) what are the relative roles of host and environmental characteristics compared with direct interactions between parasites in determining the community composition of parasites? (2) do these determinants affect parasites belonging to the same guild and those belonging to different guilds in similar manners? and (3) can cross-sectional and longitudinal analyses work interchangeably in detecting community determinants? Our study was designed to answer these three questions in a natural community of rodents and their fleas, ticks, and two vector-borne bacteria. We sampled a natural population of Gerbillus andersoni rodents and their blood-associated parasites on two occasions. By combining path analysis and model selection approaches, we then explored multiple direct and indirect paths that connect (i) the environmental and host-related characteristics to the infection probability of a host by each of the four parasite species, and (ii) the infection probabilities of the four species by each other. Our results suggest that the majority of paths shaping the blood-associated communities are indirect, mostly determined by host characteristics and not by interspecific interactions or environmental conditions. The exact effects of host characteristics on infection probability by a given parasite depend on its life history and on the method of sampling, in which the cross-sectional and longitudinal methods are complementary. Despite the awareness of the need of ecological investigations into natural host-vector-parasite communities in light of the emergence and re-emergence of vector-borne diseases, we lack sampling methods that are both practical and reliable. Here we illustrated how comprehensive patterns can be revealed from observational data by applying path analysis and model selection approaches and combining cross-sectional and longitudinal analyses. By employing this combined approach on blood-associated parasites, we were able to distinguish between direct and indirect effects and to predict the causal relationships between host-related characteristics and the parasite composition over time and space. We concluded that direct interactions within the community play only a minor role in determining community composition relative to host characteristics and the life history of the community members.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha

ABSTRACT Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community.more » Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease. IMPORTANCEStudies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on metabolite concentrations and evaluating whether these predictions agree with measured metabolomic profiles. We find that a surprisingly large proportion of metabolite variation in the vaginal microbiome can be predicted based on species composition (including dramatic shifts associated with disease), identify putative mechanisms underlying these predictions, and evaluate the roles of individual bacterial species and genes. Analysis of gut microbiome data using this framework recovers similar community metabolic trends. This framework lays the foundation for model-based multi-omic integrative studies, ultimately improving our understanding of microbial community metabolism.« less

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

PubMed Central

Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M.; Young, Vincent B.; Jansson, Janet K.; Fredricks, David N.

2016-01-01

ABSTRACT Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease. IMPORTANCE Studies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on metabolite concentrations and evaluating whether these predictions agree with measured metabolomic profiles. We find that a surprisingly large proportion of metabolite variation in the vaginal microbiome can be predicted based on species composition (including dramatic shifts associated with disease), identify putative mechanisms underlying these predictions, and evaluate the roles of individual bacterial species and genes. Analysis of gut microbiome data using this framework recovers similar community metabolic trends. This framework lays the foundation for model-based multi-omic integrative studies, ultimately improving our understanding of microbial community metabolism. PMID:27239563

Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.

PubMed

Levy, Roie; Borenstein, Elhanan

2014-01-01

The human microbiome is a key contributor to health and development. Yet little is known about the ecological forces that are at play in defining the composition of such host-associated communities. Metagenomics-based studies have uncovered clear patterns of community structure but are often incapable of distinguishing alternative structuring paradigms. In a recent study, we integrated metagenomic analysis with a systems biology approach, using a reverse ecology framework to model numerous human microbiota species and to infer metabolic interactions between species. Comparing predicted interactions with species composition data revealed that the assembly of the human microbiome is dominated at the community level by habitat filtering. Furthermore, we demonstrated that this habitat filtering cannot be accounted for by known host phenotypes or by the metabolic versatility of the various species. Here we provide a summary of our findings and offer a brief perspective on related studies and on future approaches utilizing this metagenomic systems biology framework.

Metagenetic analysis of the bacterial communities of edible insects from diverse production cycles at industrial rearing companies.

PubMed

Vandeweyer, D; Crauwels, S; Lievens, B; Van Campenhout, L

2017-11-16

Despite the continuing development of new insect-derived food products, microbial research on edible insects and insect-based foods is still very limited. The goal of this study was to increase the knowledge on the microbial quality of edible insects by comparing the bacterial community composition of mealworms (Tenebrio molitor) and crickets (Acheta domesticus and Gryllodes sigillatus) from several production cycles and rearing companies. Remarkable differences in the bacterial community composition were found between different mealworm rearing companies and mealworm production cycles from the same company. In comparison with mealworms, the bacterial community composition of the investigated crickets was more similar among different companies, and was highly similar between both cricket species investigated. Mealworm communities were dominated by Spiroplasma and Erwinia species, while crickets were abundantly colonised by (Para)bacteroides species. With respect to food safety, only a few operational taxonomic units could be associated with potential human pathogens such as Cronobacter or spoilage bacteria such as Pseudomonas. In summary, our results implicate that at least for cricket rearing, production cycles of constant and good quality in terms of bacterial composition can be obtained by different rearing companies. For mealworms however, more variation in terms of microbial quality occurs between companies. Copyright © 2017 Elsevier B.V. All rights reserved.

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities.

PubMed

Liu, Jun; He, Xiao-Xin; Lin, Xue-Rui; Chen, Wen-Ce; Zhou, Qi-Xing; Shu, Wen-Sheng; Huang, Li-Nan

2015-06-02

The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

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

2017-01-01

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

Effects of copper on the composition and diversity of microbial communities in laboratory-scale swine manure composting.

PubMed

Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Tuo, Xiaxia; Zhang, Kaiyu; Zhang, Li; Guo, Aiyun; Zhang, Xin

2018-06-01

This study investigated the effects of adding copper at 3 treatment levels (0 (control: CK), 200 (low: L), and 2000 (high: H) mg·kg -1 treatments) on the bacterial communities during swine manure composting. The abundances of the bacteria were determined by quantitative PCR and their compositions were evaluated by high-throughput sequencing. The results showed that the abundance of bacteria was inhibited by the H treatment during days 7-35, and principal component analysis clearly separated the H treatment from the CK and L treatments. Actinobacteria, Firmicutes, and Proteobacteria were the dominant bacterial taxa, and a high copper concentration decreased the abundances of bacteria that degrade cellulose and lignin (e.g., class Bacilli and genus Truepera), especially in the mesophilic and thermophilic phases. Moreover, network analysis showed that copper might alter the co-occurrence patterns of bacterial communities by changing the properties of the networks and the keystone taxa, and increase the competition by increasing negative associations between bacteria during composting. Temperature, water-soluble carbohydrates, and copper significantly affected the variations in the bacterial community according to redundancy analysis. The copper content mainly contributed to the bacterial community in the thermophilic and cooling phases, where it had positive relationships with potentially pathogenic bacteria (e.g., Corynebacterium_1 and Acinetobacter).

Characterizing bacterial communities in tilapia pond surface sediment and their responses to pond differences and temporal variations.

PubMed

Fan, Limin; Barry, Kamira; Hu, Gengdong; Meng, Shunlong; Song, Chao; Qiu, Liping; Zheng, Yao; Wu, Wei; Qu, Jianhong; Chen, Jiazhang; Xu, Pao

2017-01-01

Bacterial community compositions in the surface sediment of tilapia ponds and their responses to pond characteristics or seasonal variations were investigated. For that, three ponds with different stocking densities were selected to collect the samples. And the method of Illumina high-throughput sequencing was used to amplify the bacterial 16S rRNA genes. A total of 662, 876 valid reads and 5649 operational taxonomic units were obtained. Further analysis showed that the dominant phyla in all three ponds were Proteobacteria, Bacteroidetes, Chloroflexi, and Acidobacteria. The phyla Planctomycetes, Firmicutes, Chlorobi, and Spirochaetae were also relatively abundant. Among the eight phyla, the abundances of only Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetae were affected by seasonal variations, while seven of these (with the exception of Acidobacteria) were affected by pond differences. A comprehensive analysis of the richness and diversity of the bacterial 16S rRNA gene, and of the similarity in bacterial community composition in sediment also showed that the communities in tilapia pond sediment were shaped more by pond differences than by seasonal variations. Linear discriminant analysis further indicated that the influences of pond characteristics on sediment bacterial communities might be related to feed coefficients and stocking densities of genetically improved farmed tilapia (GIFT).

Intertidal nematode communities in the Mekong estuaries of Vietnam and their potential for biomonitoring.

PubMed

Quang, Ngo Xuan; Chau, Nguyen Ngoc; Smol, Nic; Prozorova, Larisa; Vanreusel, Ann

2016-02-01

Nematode communities in eight Mekong estuaries were investigated during the dry season. The aim of the study was to identify the structure and the diversity of the communities in relation to the main environmental characteristics. In each estuary, three to four intertidal sampling stations were identified at regular distances from the mouth to up to 45 km land inward. The nematode communities showed a strong correlation with sediment composition and to a lesser degree with chlorophyll a concentrations. Multivariate analysis resulted in the identification of four types of communities. We identified two types of Desmodora communities in the sandy mouth stations and two types of Parodontophora communities in the silty sand stations. One of the silt associated communities showed a preference for higher chlorophyll a concentrations, resulting in higher densities and higher diversity, mainly of monhysterid species. Because of the strong association between community structure and sediment composition, nematodes are a meaningful tool for monitoring changes in their environment. In case their community deviates from what is expected based on sediment, it may serve as an early warning for disturbance.

Degradation of organophosphate esters in sewage sludge: Effects of aerobic/anaerobic treatments and bacterial community compositions.

PubMed

Pang, Long; Ge, Liming; Yang, Peijie; He, Han; Zhang, Hongzhong

2018-05-01

In this study, the degradation of organophosphate esters (OPEs) in sewage sludge with aerobic composting and anaerobic digestion was investigated. The total concentrations of six OPEs (ΣOPEs) in the whole treatment process reduced in the order of anaerobic digestion combined with pig manure (T3) > aerobic composting combined with pig manure (T1) > aerobic composting (T2) > anaerobic digestion (T4). The addition of pig manure significantly enhanced the removal rate of OPEs in both aerobic and anaerobic treatments. The abundance and diversity of bacterial community reduced after the treatment process. Shannon index, principal component analysis, network analysis, and heat map further confirmed the variation of bacterial community compositions among different treatments. Five genera (i.e., Flavobacterium, Bacillus, Alcaligene, Pseudomonas, and Bacillus megaterium) might be responsible for the degradation of OPE compounds in sewage sludge. Copyright © 2018 Elsevier Ltd. All rights reserved.

Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)

PubMed Central

Besemer, Katharina; Moeseneder, Markus M.; Arrieta, Jesus M.; Herndl, Gerhard J.; Peduzzi, Peter

2005-01-01

Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition. PMID:15691909

Phytoplankton Pigment Communities Can be Modeled Using Unique Relationships With Spectral Absorption Signatures in a Dynamic Coastal Environment

NASA Astrophysics Data System (ADS)

Catlett, D.; Siegel, D. A.

2018-01-01

Understanding the roles of phytoplankton community composition in the functioning of marine ecosystems and ocean biogeochemical cycles is important for many ocean science problems of societal relevance. Remote sensing currently offers the only feasible method for continuously assessing phytoplankton community structure on regional to global scales. However, methods are presently hindered by the limited spectral resolution of most satellite sensors and by uncertainties associated with deriving quantitative indices of phytoplankton community structure from phytoplankton pigment concentrations. Here we analyze a data set of concurrent phytoplankton pigment concentrations and phytoplankton absorption coefficient spectra from the Santa Barbara Channel, California, to develop novel optical oceanographic models for retrieving metrics of phytoplankton community composition. Cluster and Empirical Orthogonal Function analyses of phytoplankton pigment concentrations are used to define up to five phytoplankton pigment communities as a representation of phytoplankton functional types. Unique statistical relationships are found between phytoplankton pigment communities and absorption features isolated using spectral derivative analysis and are the basis of predictive models. Model performance is substantially better for phytoplankton pigment community indices compared with determinations of the contributions of individual pigments or taxa to chlorophyll a. These results highlight the application of data-driven chemotaxonomic approaches for developing and validating bio-optical algorithms and illustrate the potential and limitations for retrieving phytoplankton community composition from hyperspectral satellite ocean color observations.

Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline–Alkaline Soils

PubMed Central

Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

2018-01-01

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi. PMID:29535703

Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom

PubMed Central

Bunse, Carina; Bertos-Fortis, Mireia; Sassenhagen, Ingrid; Sildever, Sirje; Sjöqvist, Conny; Godhe, Anna; Gross, Susanna; Kremp, Anke; Lips, Inga; Lundholm, Nina; Rengefors, Karin; Sefbom, Josefin; Pinhassi, Jarone; Legrand, Catherine

2016-01-01

In temperate systems, phytoplankton spring blooms deplete inorganic nutrients and are major sources of organic matter for the microbial loop. In response to phytoplankton exudates and environmental factors, heterotrophic microbial communities are highly dynamic and change their abundance and composition both on spatial and temporal scales. Yet, most of our understanding about these processes comes from laboratory model organism studies, mesocosm experiments or single temporal transects. Spatial-temporal studies examining interactions of phytoplankton blooms and bacterioplankton community composition and function, though being highly informative, are scarce. In this study, pelagic microbial community dynamics (bacteria and phytoplankton) and environmental variables were monitored during a spring bloom across the Baltic Proper (two cruises between North Germany to Gulf of Finland). To test to what extent bacterioplankton community composition relates to the spring bloom, we used next generation amplicon sequencing of the 16S rRNA gene, phytoplankton diversity analysis based on microscopy counts and population genotyping of the dominating diatom Skeletonema marinoi. Several phytoplankton bloom related and environmental variables were identified to influence bacterial community composition. Members of Bacteroidetes and Alphaproteobacteria dominated the bacterial community composition but the bacterial groups showed no apparent correlation with direct bloom related variables. The less abundant bacterial phyla Actinobacteria, Planctomycetes, and Verrucomicrobia, on the other hand, were strongly associated with phytoplankton biomass, diatom:dinoflagellate ratio, and colored dissolved organic matter (cDOM). Many bacterial operational taxonomic units (OTUs) showed high niche specificities. For example, particular Bacteroidetes OTUs were associated with two distinct genetic clusters of S. marinoi. Our study revealed the complexity of interactions of bacterial taxa with inter- and intraspecific genetic variation in phytoplankton. Overall, our findings imply that biotic and abiotic factors during spring bloom influence bacterial community dynamics in a hierarchical manner. PMID:27148206

Microbial Communities as Experimental Units

PubMed Central

DAY, MITCH D.; BECK, DANIEL; FOSTER, JAMES A.

2011-01-01

Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis. PMID:21731083

Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere.

PubMed

Knief, Claudia; Ramette, Alban; Frances, Lisa; Alonso-Blanco, Carlos; Vorholt, Julia A

2010-06-01

The plant phyllosphere constitutes a habitat for numerous microorganisms; among them are members of the genus Methylobacterium. Owing to the ubiquitous occurrence of methylobacteria on plant leaves, they represent a suitable target for studying plant colonization patterns. The influence of the factor site, host plant species, time and the presence of other phyllosphere bacteria on Methylobacterium community composition and population size were evaluated in this study. Leaf samples were collected from Arabidopsis thaliana or Medicago truncatula plants and from the surrounding plant species at several sites. The abundance of cultivable Methylobacterium clearly correlated with the abundance of other phyllosphere bacteria, suggesting that methylobacteria constitute a considerable and rather stable fraction of the phyllosphere microbiota under varying environmental conditions. Automated ribosomal intergenic spacer analysis (ARISA) was applied to characterize the Methylobacterium community composition and showed the presence of similar communities on A. thaliana plants at most sites in 2 consecutive years of sampling. A substantial part of the observed variation in the community composition was explained by site and plant species, especially in the case of the plants collected at the Arabidopsis sites (50%). The dominating ARISA peaks that were detected on A. thaliana plants were found on other plant species grown at the same site, whereas some different peaks were detected on A. thaliana plants from other sites. This indicates that site-specific factors had a stronger impact on the Methylobacterium community composition than did plant-specific factors and that the Methylobacterium-plant association is not highly host plant species specific.

Shifts in coastal Antarctic marine microbial communities during and after melt water-related surface stratification.

PubMed

Piquet, Anouk M-T; Bolhuis, Henk; Meredith, Michael P; Buma, Anita G J

2011-06-01

Antarctic coastal waters undergo major physical alterations during summer. Increased temperatures induce sea-ice melting and glacial melt water input, leading to strong stratification of the upper water column. We investigated the composition of micro-eukaryotic and bacterial communities in Ryder Bay, Antarctic Peninsula, during and after summertime melt water stratification, applying community fingerprinting (denaturing gradient gel electrophoresis) and sequencing analysis of partial 18S and 16S rRNA genes. Community fingerprinting of the eukaryotic community revealed two major patterns, coinciding with a period of melt water stratification, followed by a period characterized by regular wind-induced breakdown of surface stratification. During the first stratified period, we observed depth-related differences in eukaryotic fingerprints while differences in bacterial fingerprints were weak. Wind-induced breakdown of the melt water layer caused a shift in the eukaryotic community from an Actinocyclus sp.- to a Thalassiosira sp.-dominated community. In addition, a distinct transition in the bacterial community was found, but with a few days' delay, suggesting a response to the changes in the eukaryotic community rather than to the mixing event itself. Sequence analysis revealed a shift from an Alpha- and Gammaproteobacteria to a Cytophaga-Flavobacterium-Bacteroides-dominated community under mixed conditions. Our results show that melt water stratification and the transition to nonstabilized Antarctic surface waters may have an impact not only on micro-eukaryotic but also bacterial community composition. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Does Tropical Forest Fragmentation Increase Long-Term Variability of Butterfly Communities?

PubMed Central

Leidner, Allison K.; Haddad, Nick M.; Lovejoy, Thomas E.

2010-01-01

Habitat fragmentation is a major driver of biodiversity loss. Yet, the overall effects of fragmentation on biodiversity may be obscured by differences in responses among species. These opposing responses to fragmentation may be manifest in higher variability in species richness and abundance (termed hyperdynamism), and in predictable changes in community composition. We tested whether forest fragmentation causes long-term hyperdynamism in butterfly communities, a taxon that naturally displays large variations in species richness and community composition. Using a dataset from an experimentally fragmented landscape in the central Amazon that spanned 11 years, we evaluated the effect of fragmentation on changes in species richness and community composition through time. Overall, adjusted species richness (adjusted for survey duration) did not differ between fragmented forest and intact forest. However, spatial and temporal variation of adjusted species richness was significantly higher in fragmented forests relative to intact forest. This variation was associated with changes in butterfly community composition, specifically lower proportions of understory shade species and higher proportions of edge species in fragmented forest. Analysis of rarefied species richness, estimated using indices of butterfly abundance, showed no differences between fragmented and intact forest plots in spatial or temporal variation. These results do not contradict the results from adjusted species richness, but rather suggest that higher variability in butterfly adjusted species richness may be explained by changes in butterfly abundance. Combined, these results indicate that butterfly communities in fragmented tropical forests are more variable than in intact forest, and that the natural variability of butterflies was not a buffer against the effects of fragmentation on community dynamics. PMID:20224772

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

PubMed

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

2018-06-15

Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P < 0.05). The bacterial diversity in sediments was significantly higher than their corresponding water samples. Additionally, archaeal communities showed obvious spatial variability in the surface water. The construction of the hydropower station resulted in increased Cyanobacteria abundance in the upstream (32.2%) compared to its downstream (10.3%). Several taxonomic groups of potential fecal indicator bacteria, like Flavobacteria and Bacteroidia, showed an increasing trend in the urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P < 0.01) and NO 3 - (P < 0.05), and metals (Zn, Fe) (P < 0.05) were the most significant drivers determining the microbial community composition in the urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations. Copyright © 2018 Elsevier B.V. All rights reserved.

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries.

PubMed

Rudney, Joel D; Jagtap, Pratik D; Reilly, Cavan S; Chen, Ruoqiong; Markowski, Todd W; Higgins, LeeAnn; Johnson, James E; Griffin, Timothy J

2015-12-19

The etiology of dental caries is multifactorial, but frequent consumption of free sugars, notably sucrose, appears to be a major factor driving the supragingival microbiota in the direction of dysbiosis. Recent 16S rRNA-based studies indicated that caries-associated communities were less diverse than healthy supragingival plaque but still displayed considerable taxonomic diversity between individuals. Metagenomic studies likewise have found that healthy oral sites from different people were broadly similar with respect to gene function, even though there was an extensive individual variation in their taxonomic profiles. That pattern may also extend to dysbiotic communities. In that case, shifts in community-wide protein relative abundance might provide better biomarkers of dysbiosis that can be achieved through taxonomy alone. In this study, we used a paired oral microcosm biofilm model of dental caries to investigate differences in community composition and protein relative abundance in the presence and absence of sucrose. This approach provided large quantities of protein, which facilitated deep metaproteomic analysis. Community composition was evaluated using 16S rRNA sequencing and metaproteomic approaches. Although taxonomic diversity was reduced by sucrose pulsing, considerable inter-subject variation in community composition remained. By contrast, functional analysis using the SEED ontology found that sucrose induced changes in protein relative abundance patterns for pathways involving glycolysis, lactate production, aciduricity, and ammonia/glutamate metabolism that were conserved across taxonomically diverse dysbiotic oral microcosm biofilm communities. Our findings support the concept of using function-based changes in protein relative abundance as indicators of dysbiosis. Our microcosm model cannot replicate all aspects of the oral environment, but the deep level of metaproteomic analysis it allows makes it suitable for discovering which proteins are most consistently abundant during dysbiosis. It then may be possible to define biomarkers that could be used to detect at-risk tooth surfaces before the development of overt carious lesions.

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils.

PubMed

Wu, Meng; Liu, Jia; Li, Weitao; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2017-10-01

Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There has been few studies evaluating the toxicological effects of CAP on soil-associated microbes. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP in three types of paddy soils in subtropical China. The effects of CAP on microbial activities (microbial biomass carbon-MBC, basal soil respiration-BSR, microbial metabolic quotient-qCO 2 , acid phosphatase and sucrose invertase activities) in the soils were periodically evaluated. Microbial phospholipid fatty acid (PLFA) analysis was used to evaluate the change of soil microbial community composition on day 14 and 50 of the experiment. CAP residues were extracted using the quick, easy, cheap, effective, rugged, and safe (QuChERS) method and quantification was measured by high performance liquid chromatography (HPLC). The half-lives (DT 50 ) of CAP were in the range of 41.0-53.0 days in the three soils. The results showed that CAP did not impart negative effects on MBC during the incubation. CAP inhibited BSR, qCO 2 , acid phosphatase and sucrose invertase activities in the first 14 days of incubation in all the soils. After day 14, the soil microbial parameters of CAP-treated soils became statistically at par with their controls. Principal component analysis (PCA) determining abundance of biomarker PLFAs indicated that the application of CAP significantly changed the compositions of microbial communities in all three paddy soils on day 14 but the compositions of soil microbial communities recovered by day 50. This study indicates that CAP does not ultimately impair microbial activities and microbial compositions of these three paddy soil types. Copyright © 2017 Elsevier Inc. All rights reserved.

Effects of low dose silver nanoparticle treatment on the structure and community composition of bacterial freshwater biofilms.

PubMed

Grün, Alexandra Y; App, Constantin B; Breidenbach, Andreas; Meier, Jutta; Metreveli, George; Schaumann, Gabriele E; Manz, Werner

2018-01-01

The application of engineered silver nanoparticles (AgNPs) in a considerable amount of registered commercial products inevitably will result in the continuous release of AgNPs into the natural aquatic environment. Therefore, native biofilms, as the prominent life form of microorganisms in almost all known ecosystems, will be subjected to AgNP exposure. Despite the exponentially growing research activities worldwide, it is still difficult to assess nanoparticle-mediated toxicity in natural environments. In order to obtain an ecotoxicologically relevant exposure scenario, we performed experiments with artificial stream mesocosm systems approaching low dose AgNP concentrations close to predicted environmental concentrations. Pregrown freshwater biofilms were exposed for 14 days to citrate-stabilized AgNPs at a concentration of 600 μg l-1 in two commonly used sizes (30 and 70 nm). Sublethal effects of AgNP treatment were assessed with regard to biofilm structure by gravimetric measurements (biofilm thickness and density) and by two biomass parameters, chlorophyll a and protein content. The composition of bacterial biofilm communities was characterized by t-RFLP fingerprinting combined with phylogenetic studies based on the 16S gene. After 14 days of treatment, the structural parameters of the biofilm such as thickness, density, and chlorophyll a and protein content were not statistically significantly changed by AgNP exposure. Furthermore, t-RFLP fingerprint analysis showed that the bacterial diversity was not diminished by AgNPs, as calculated by Shannon Wiener and evenness indices. Nevertheless, t-RFLP analysis also indicated that AgNPs led to an altered biofilm community composition as was shown by cluster analysis and multidimensional scaling (MDS) based on the Bray Curtis index. Sequence analysis of cloned 16S rRNA genes further revealed that changes in community composition were related with the displacement of putatively AgNP-sensitive bacterial taxa Actinobacteria, Chloroflexi, and Cyanobacteria by taxa known for their enhanced adaptability towards metal stress, such as Acidobacteria, Sphingomonadales, and Comamonadaceae. This measurable community shift, even after low dose AgNP treatment, causes serious concerns with respect to the broad application of AgNPs and their potentially adverse impact on the ecological function of lotic biofilms, such as biodegradation or biostabilization.

Seasonal Variations and Resilience of Bacterial Communities in a Sewage Polluted Urban River

PubMed Central

Ouattara, Nouho Koffi; Anzil, Adriana; Verbanck, Michel A.; Brion, Natacha; Servais, Pierre

2014-01-01

The Zenne River in Brussels (Belgium) and effluents of the two wastewater treatment plants (WWTPs) of Brussels were chosen to assess the impact of disturbance on bacterial community composition (BCC) of an urban river. Organic matters, nutrients load and oxygen concentration fluctuated highly along the river and over time because of WWTPs discharge. Tag pyrosequencing of bacterial 16S rRNA genes revealed the significant effect of seasonality on the richness, the bacterial diversity (Shannon index) and BCC. The major grouping: -winter/fall samples versus spring/summer samples- could be associated with fluctuations of in situ bacterial activities (dissolved and particulate organic carbon biodegradation associated with oxygen consumption and N transformation). BCC of the samples collected upstream from the WWTPs discharge were significantly different from BCC of downstream samples and WWTPs effluents, while no significant difference was found between BCC of WWTPs effluents and the downstream samples as revealed by ANOSIM. Analysis per season showed that allochthonous bacteria brought by WWTPs effluents triggered the changes in community composition, eventually followed by rapid post-disturbance return to the original composition as observed in April (resilience), whereas community composition remained altered after the perturbation by WWTPs effluents in the other seasons. PMID:24667680

Influence of Effluent Irrigation on Community Composition and Function of Ammonia-Oxidizing Bacteria in Soil

PubMed Central

Oved, Tamar; Shaviv, Avi; Goldrath, Tal; Mandelbaum, Raphi T.; Minz, Dror

2001-01-01

The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the α-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospira-like populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein. PMID:11472914

Microbial Community Composition Affects Soil Fungistasis†

PubMed Central

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

2003-01-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis. PMID:12571002

Saugus River and Tributaries, Lynn Malden, Revere and Saugus, Massachusetts. Flood Damage Reduction. Volume 8. Appendix K. Environmental

DTIC Science & Technology

1989-06-01

K10 Summary of Soil Analyses for the Salt Marsh Transects K32 KI1 Plant Community Composition Data Along Compartment K33 B Transect K12 Plant...Community Composition Data Along Compartment K33 I Transect K13 Plant Community Composition Data Along Compartment K33 K1 Transect K14 Plant Community... Composition Data Along Compartment K34 K3 Transect K15 Plant Community Composition Data Along Compartment K34 L2 Transect K16 Plant Community Composition

Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil

PubMed Central

Zhu, Chen; Ling, Ning; Guo, Junjie; Wang, Min; Guo, Shiwei; Shen, Qirong

2016-01-01

The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical black soil (Chernozem) was conducted and high-throughput sequencing approach was used to investigate the effects of different fertilizations on the variation of AMF community in the rhizosphere soil of maize crop. The results showed that AMF diversity in the maize rhizosphere was significantly altered by different fertilization regimes. As revealed by redundancy analysis, the application of organic manure was the most important factor impacting AMF community composition between samples with and without organic manure, followed by N fertilizer and P fertilizer inputs. Moreover, the organic matter composition in the rhizosphere, determined by GC–MS, was significantly altered by the organic manure amendment. Many of the chemical components displayed significant relationships with the AMF community composition according to the Mantel test, among those, 2-ethylnaphthalene explained the highest percentage (54.2%) of the variation. The relative contents of 2-ethylnaphthalene and 2, 6, 10-trimethyltetradecane had a negative correlation with Glomus relative abundance, while the relative content of 3-methylbiphenyl displayed a positive correlation with Rhizophagus. The co-occurrence patterns in treatments with and without organic manure amendment were analyzed, and more hubs were detected in the network of soils with organic manure amendment. Additionally, three operational taxonomic units (OTUs) belonging to Glomerales were identified as hubs in all treatments, indicating these OTUs likely occupied broad ecological niches and were always active for mediating AMF species interaction in the maize rhizosphere. Taken together, impacts of fertilization regimes on AMF community composition were correlated with organic matter composition in maize rhizosphere soil and the application of manure could activate more AMF species to interact with other species in the maize rhizosphere. This knowledge can be valuable in regulating the symbiotic system of plants and AMF, maintaining the health and high yields of crops and providing a primary basis for rational fertilization. PMID:27899920

Characterization, Microbial Community Structure, and Pathogen Occurrence in Urban Faucet Biofilms in South China

PubMed Central

Lin, Huirong; Zhang, Shuting; Gong, Song; Zhang, Shenghua; Yu, Xin

2015-01-01

The composition and microbial community structure of the drinking water system biofilms were investigated using microstructure analysis and 454 pyrosequencing technique in Xiamen city, southeast of China. SEM (scanning electron microscope) results showed different features of biofilm morphology in different fields of PVC pipe. Extracellular matrix material and sparse populations of bacteria (mainly rod-shaped and coccoid) were observed. CLSM (confocal laser scanning microscope) revealed different distributions of attached cells, extracellular proteins, α-polysaccharides, and β-polysaccharides. The biofilms had complex bacterial compositions. Differences in bacteria diversity and composition from different tap materials and ages were observed. Proteobacteria was the common and predominant group in all biofilms samples. Some potential pathogens (Legionellales, Enterobacteriales, Chromatiales, and Pseudomonadales) and corrosive microorganisms were also found in the biofilms. This study provides the information of characterization and visualization of the drinking water biofilms matrix, as well as the microbial community structure and opportunistic pathogens occurrence. PMID:26273617

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate.

PubMed

Niu, Jiaojiao; Chao, Jin; Xiao, Yunhua; Chen, Wu; Zhang, Chao; Liu, Xueduan; Rang, Zhongwen; Yin, Huaqun; Dai, Linjian

2017-01-01

Rotation is an effective strategy to control crop disease and improve plant health. However, the effects of crop rotation on soil bacterial community composition and structure, and crop health remain unclear. In this study, using 16S rRNA gene sequencing, we explored the soil bacterial communities under four different cropping systems, continuous tobacco cropping (control group), tobacco-maize rotation, tobacco-lily rotation, and tobacco-turnip rotation. Results of detrended correspondence analysis and dissimilarity tests showed that soil bacterial community composition and structure changed significantly among the four groups, such that Acidobacteria and Actinobacteria were more abundant in the maize rotation group (16.6 and 11.5%, respectively) than in the control (8.5 and 7.1%, respectively). Compared with the control group (57.78%), maize and lily were effective rotation crops in controlling tobacco bacterial wilt (about 23.54 and 48.67%). On the other hand, tobacco bacterial wilt rate was increased in the turnip rotation (59.62%) relative to the control. Further study revealed that the abundances of several bacterial populations were directly correlated with tobacco bacterial wilt. For example, Acidobacteria and Actinobacteria were significantly negatively correlated to the tobacco bacterial wilt rate, so they may be probiotic bacteria. Canonical correspondence analysis showed that soil pH and calcium content were key factors in determining soil bacterial communities. In conclusion, our study revealed the composition and structure of bacterial communities under four different cropping systems and may unveil molecular mechanisms for the interactions between soil microorganisms and crop health. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

PubMed Central

Weiland-Bräuer, Nancy; Neulinger, Sven C.; Pinnow, Nicole; Künzel, Sven; Baines, John F.

2015-01-01

The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle. PMID:26116680

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE PAGES

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.; ...

2016-01-22

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwon, Man Jae; O’Loughlin, Edward J.; Boyanov, Maxim I.

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over timemore » revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. As a result, these data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.« less

Impact of Organic Carbon Electron Donors on Microbial Community Development under Iron- and Sulfate-Reducing Conditions.

PubMed

Kwon, Man Jae; O'Loughlin, Edward J; Boyanov, Maxim I; Brulc, Jennifer M; Johnston, Eric R; Kemner, Kenneth M; Antonopoulos, Dionysios A

2016-01-01

Although iron- and sulfate-reducing bacteria in subsurface environments have crucial roles in biogeochemical cycling of C, Fe, and S, how specific electron donors impact the compositional structure and activity of native iron- and/or sulfate-reducing communities is largely unknown. To understand this better, we created bicarbonate-buffered batch systems in duplicate with three different electron donors (acetate, lactate, or glucose) paired with ferrihydrite and sulfate as the electron acceptors and inoculated them with subsurface sediment as the microbial inoculum. Sulfate and ferrihydrite reduction occurred simultaneously and were faster with lactate than with acetate. 16S rRNA-based sequence analysis of the communities over time revealed that Desulfotomaculum was the major driver for sulfate reduction coupled with propionate oxidation in lactate-amended incubations. The reduction of sulfate resulted in sulfide production and subsequent abiotic reduction of ferrihydrite. In contrast, glucose promoted faster reduction of ferrihydrite, but without reduction of sulfate. Interestingly, the glucose-amended incubations led to two different biogeochemical trajectories among replicate bottles that resulted in distinct coloration (white and brown). The two outcomes in geochemical evolution might be due to the stochastic evolution of the microbial communities or subtle differences in the initial composition of the fermenting microbial community and its development via the use of different glucose fermentation pathways available within the community. Synchrotron-based x-ray analysis indicated that siderite and amorphous Fe(II) were formed in the replicate bottles with glucose, while ferrous sulfide and vivianite were formed with lactate or acetate. These data sets reveal that use of different C utilization pathways projects significant changes in microbial community composition over time that uniquely impact both the geochemistry and mineralogy of subsurface environments.

Reduced densities of the invasive wasp, Vespula vulgaris (Hymenoptera: Vespidae), did not alter the invertebrate community composition of Nothofagus forests in New Zealand.

PubMed

Duthie, Catherine; Lester, Philip J

2013-04-01

Invasive common wasps (Vespula vulgaris L.) are predators of invertebrates in Nothofagus forests of New Zealand. We reduced wasp densities by poisoning in three sites over three y. We predicted an increase in the number of invertebrates and a change in the community composition in sites where wasps were poisoned (wasps removed) relative to nearby sites where wasps were not poisoned (wasps maintained). Wasp densities were significantly reduced by an average of 58.9% by poisoning. Despite this reduction in wasp densities, native bush ants (Prolasius advenus Forel) were the only taxa that was significantly influenced by wasp removal. However, contrary to our predictions there were more ants caught in pitfall traps where wasps were maintained. We believe that the higher abundance of these ants is probably because of the scarcity of honeydew in wasp-maintained sites and compensatory foraging by ants in these areas. Otherwise, our results indicated no significant effects of reduced wasp densities on the total number of invertebrates, or the number of invertebrate families, observed in pitfall or Malaise traps. An analysis of community composition (permutational multivariate analysis of variance) also indicated no significant difference between wasp-removed or wasp-maintained communities. The most parsimonious explanation for our results is that although we significantly reduced wasp numbers, we may not have reduced numbers sufficiently or for a sufficiently long period, to see a change or recovery in the community.

Analysis of Microbial Community Composition and Methane Production From Northern Peatlands Across a Climate Gradient

NASA Astrophysics Data System (ADS)

Sarno, A. F.; Humphreys, E.; Olefeldt, D.; Heffernan, L.; Roman, T. D.; Sebestyen, S.; Kolka, R.; Yavitt, J. B.; Finn, D.; Cadillo-Quiroz, H.

2017-12-01

Northern peatland ecosystems allow for the accumulation of a carbon (C) pool as the rate of photosynthesis exceeds the rate of organic carbon decomposition. Under current climate conditions, many northern peatlands act as a C sink; however, changes in climate and other environmental conditions, such as soil permafrost melting, are capable of changing the decomposition cascade. Here we take advantage of four peatlands situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess how the relative abundance of microbial functional groups and substrate availability within the microbial community might impact the decomposition of soil organic matter to methane. The four peatlands had similar hydrology and geochemistry and were poor fen types. Soil, water and gas samples were collected at the water table level. Microbial community composition, derived from Illumina amplicon sequencing of the 16S rRNA gene, and geochemical and climate variables were analyzed with principal component regression analysis to determine major drivers of community variation. Mean annual temperature (r2=0.53), mean annual precipitation (r2=0.36), water table level (r2=0.43) and soil temperature (r2=0.49), were all statistically significant drivers of both general microbial and methanogen community composition (p value < 0.001). The relative abundance of Methanocella, Methanosarcina and Methanobacterium varied significantly across the climate gradient (p value < 0.05), however the majority of methanogen genera did not. Interestingly, dissolved methane (r2=0.24) was statistically significant at the general community level (p value < 0.001), but not significant when tested against only the methanogen community. The results demonstrate that environmental factors predicted to change over time due to climate change will have a significant impact on microbial community composition and C sinks within Northern peatlands. Further analyses of microbial processes that produce methanogenic substrates such as fermentation and syntrophic reactions, in tandem with the further identification and quantification of methanogens, will elucidate other drivers of methane production in Northern peatlands.

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil

PubMed Central

Yang, Wei; Gu, Siyu; Xin, Ying; Bello, Ayodeji; Sun, Wenpeng; Xu, Xiuhong

2018-01-01

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species in agricultural ecosystems, and are conspicuously influenced by various agricultural practices. To understand the impact of compost addition on AM fungi, we examined effect of four compost rates (0, 11.25, 22.5, and 45 Mg/ha) on the abundance and community composition of AM fungi in seedling, flowering, and mature stage of soybean in a 1-year compost addition experiment system in Northeast China. Soybean [Glycine max (L.) Merrill] was used as test plant. Moderate (22.5 Mg/ha) and high (45 Mg/ha) levels of compost addition significantly increased AM root colonization and extraradical hyphal (ERH) density compared with control, whereas low (11.5 Mg/ha) level of compost addition did not cause significant increase in AM root colonization and ERH density. AM fungal spore density was significantly enhanced by all the compost rates compared with control. The temporal variations analysis revealed that, AM root colonization in seedling stage was significantly lower than in flowering and mature stage. Although AM fungal operational taxonomic unit richness and community composition was unaffected by compost addition, some abundant AM fungal species showed significantly different response to compost addition. In mature stage, Rhizophagus fasciculatum showed increasing trend along with compost addition gradient, whereas the opposite was observed with Paraglomus sp. In addition, AM fungal community composition exhibited significant temporal variation during growing season. Further analysis indicated that the temporal variation in AM fungal community only occurred in control treatment, but not in low, moderate, and high level of compost addition treatments. Our findings highlighted the significant effects of compost addition on AM growth and sporulation, and emphasized that growth stage is a stronger determinant than 1-year compost addition in shaping AM fungal community in black soil of Northeast China. PMID:29467752

Soil Bacterial Community Response to Differences in Agricultural Management along with Seasonal Changes in a Mediterranean Region

PubMed Central

Bevivino, Annamaria; Paganin, Patrizia; Bacci, Giovanni; Florio, Alessandro; Pellicer, Maite Sampedro; Papaleo, Maria Cristiana; Mengoni, Alessio; Ledda, Luigi; Fani, Renato; Benedetti, Anna; Dalmastri, Claudia

2014-01-01

Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity. PMID:25144665

Compost Addition Enhanced Hyphal Growth and Sporulation of Arbuscular Mycorrhizal Fungi without Affecting Their Community Composition in the Soil.

PubMed

Yang, Wei; Gu, Siyu; Xin, Ying; Bello, Ayodeji; Sun, Wenpeng; Xu, Xiuhong

2018-01-01

Arbuscular mycorrhizal (AM) fungi form symbiotic associations with most crop plant species in agricultural ecosystems, and are conspicuously influenced by various agricultural practices. To understand the impact of compost addition on AM fungi, we examined effect of four compost rates (0, 11.25, 22.5, and 45 Mg/ha) on the abundance and community composition of AM fungi in seedling, flowering, and mature stage of soybean in a 1-year compost addition experiment system in Northeast China. Soybean [ Glycine max (L.) Merrill] was used as test plant. Moderate (22.5 Mg/ha) and high (45 Mg/ha) levels of compost addition significantly increased AM root colonization and extraradical hyphal (ERH) density compared with control, whereas low (11.5 Mg/ha) level of compost addition did not cause significant increase in AM root colonization and ERH density. AM fungal spore density was significantly enhanced by all the compost rates compared with control. The temporal variations analysis revealed that, AM root colonization in seedling stage was significantly lower than in flowering and mature stage. Although AM fungal operational taxonomic unit richness and community composition was unaffected by compost addition, some abundant AM fungal species showed significantly different response to compost addition. In mature stage, Rhizophagus fasciculatum showed increasing trend along with compost addition gradient, whereas the opposite was observed with Paraglomus sp. In addition, AM fungal community composition exhibited significant temporal variation during growing season. Further analysis indicated that the temporal variation in AM fungal community only occurred in control treatment, but not in low, moderate, and high level of compost addition treatments. Our findings highlighted the significant effects of compost addition on AM growth and sporulation, and emphasized that growth stage is a stronger determinant than 1-year compost addition in shaping AM fungal community in black soil of Northeast China.

Climate and soil texture influence patterns of forb species richness and composition in big sagebrush plant communities across their spatial extent in the western US

USGS Publications Warehouse

Pennington, Victoria E.; Palmquist, Kyle A.; Bradford, John B.; Lauenroth, William K.

2017-01-01

Article for outlet: Plant Ecology. Abstract: Big sagebrush (Artemisia tridentata Nutt.) plant communities are widespread non-forested drylands in western North American and similar to all shrub steppe ecosystems world-wide are composed of a shrub overstory layer and a forb and graminoid understory layer. Forbs account for the majority of plant species diversity in big sagebrush plant communities and are important for ecosystem function. Few studies have explored the geographic patterns of forb species richness and composition and their relationships with environmental variables in these communities. Our objectives were to examine the small and large-scale spatial patterns in forb species richness and composition and the influence of environmental variables. We sampled forb species richness and composition along transects at 15 field sites in Colorado, Idaho, Montana, Nevada, Oregon, Utah, and Wyoming, built species-area relationships to quantify differences in forb species richness at sites, and used Principal Components Analysis and nonmetric multidimensional scaling to identify relationships among environmental variables and forb species richness and composition. We found that species richness was most strongly correlated with soil texture, while species composition was most related to climate. The combination of climate and soil texture influences water availability, with important consequences for forb species richness and composition, which suggests climate-change induced modification of soil water availability may have important implications for plant species diversity in the future. Our paper is the first to our knowledge to examine forb biodiversity patterns in big sagebrush ecosystems in relation to environmental factors across the big sagebrush region.

Long-term (1998 vs. 2010) large-scale comparison of soft-bottom benthic macrofauna composition in the Gulf of Lions, NW Mediterranean Sea

NASA Astrophysics Data System (ADS)

Bonifácio, Paulo; Grémare, Antoine; Gauthier, Olivier; Romero-Ramirez, Alicia; Bichon, Sabrina; Amouroux, Jean-Michel; Labrune, Céline

2018-01-01

We achieved a long term (i.e., 1998 vs. 2010) large scale (i.e., whole Gulf of Lions) study of benthic macrofauna composition in the Gulf of Lions based on the resampling of 91 stations located along 21 inshore-offshore transects. Results show that the 3 main benthic communities identified in 1998 were still present in 2010 although their composition changed. Using only year and station of sampling we found a significant space-time interaction explaining changes in macrofaunal community composition, and, in this study, stations differ primarily in terms of depth and distance to the Rhône river mouth. Temporal changes in benthic macrofauna composition were clearly most important at shallow stations (i.e., in the Littoral Fine Sand community) than at deep ones (i.e., Terrigenous Coastal Mud community). These results are in good agreement with the current paradigm according to which climatic oscillations such as NAO (North Atlantic Oscillation) and WeMO (Western Mediterranean Oscillation) are indirectly (i.e., through changes in the frequency of occurrence and the intensity of storms) controlling benthic macrofauna composition in the Gulf of Lions. This hypothesis is further supported by a meta-analysis of changes in the average and maximal yearly abundances of the polychaete Ditrupa arietina. At last, the spatial modelling of 1998 and 2010 benthic macrofauna compositions both suggested a significant effect of Rhône River inputs on the spatial distribution of benthic macrofauna in the Gulf of Lions.

Temporal variations in the abundance and composition of biofilm communities colonizing drinking water distribution pipes.

PubMed

Kelly, John J; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

2014-01-01

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter.

Afforestation alters community structure of soil fungi.

PubMed

Carson, Jennifer K; Gleeson, Deirdre B; Clipson, Nicholas; Murphy, Daniel V

2010-07-01

Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Local environment rather than past climate determines community composition of mountain stream macroinvertebrates across Europe.

PubMed

Múrria, Cesc; Bonada, Núria; Vellend, Mark; Zamora-Muñoz, Carmen; Alba-Tercedor, Javier; Sainz-Cantero, Carmen Elisa; Garrido, Josefina; Acosta, Raul; El Alami, Majida; Barquín, Jose; Derka, Tomáš; Álvarez-Cabria, Mario; Sáinz-Bariain, Marta; Filipe, Ana F; Vogler, Alfried P

2017-11-01

Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes. Using DNA barcoding of four insect families (>3100 individuals, 118 species) across 62 streams, we found that measures of local and regional diversity and intraregional turnover generally declined slightly towards northern latitudes. However, at all hierarchical levels we found complete (haplotype) or high (species, genus) turnover among regions (and even among sites within regions), which counters the expectations of Pleistocene postglacial northward expansion from southern refugia. Species distributions were mostly correlated with environmental conditions, suggesting a strong role of lineage- or species-specific traits in determining local and latitudinal community composition, lineage diversification and phylogenetic community structure (e.g., loss of Coleoptera, but not Ephemeroptera, at northern sites). High intraspecific genetic structure within regions, even in northernmost sites, reflects species-specific dispersal and demographic histories and indicates postglacial migration from geographically scattered refugia, rather than from only southern areas. Overall, patterns were not strongly concordant across hierarchical levels, but consistent with the overriding influence of environmental factors determining community composition at the species and genus levels. © 2017 John Wiley & Sons Ltd.

Bird communities of gambel oak: a descriptive analysis

Treesearch

Andreas Leidolf; Michael L. Wolfe; Rosemary L. Pendleton

2000-01-01

Gambel oak (Quercus gambelii Nutt.) covers 3.75 million hectares (9.3 million acres) of the western United States. This report synthesizes current knowledge on the composition, structure, and habitat relationships of gambel oak avian communities. It lists life history attributes of 183 bird species documented from gambel oak habitats of the western...

Riparian Communities of the Sierra Nevada and their Environmental Relationships

Treesearch

Richard R. Harris

1989-01-01

Data on riparian community composition and environmental conditions were collected on over 20 streams in the Sierra Nevada as part of hydropower licensing studies. Over 1,000 samples were analyzed using two-way indicator species analysis (TWINSPAN), to determine riparian dominance types. Ordination techniques were applied to evaluate associations between environmental...

Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone.

PubMed

Richa, Kumari; Balestra, Cecilia; Piredda, Roberta; Benes, Vladimir; Borra, Marco; Passarelli, Augusto; Margiotta, Francesca; Saggiomo, Maria; Biffali, Elio; Sanges, Remo; Scanlan, David J; Casotti, Raffaella

2017-09-01

Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria , Gammaproteobacteria , and Bacteroidetes Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for <0.1% of the total sequence abundance), the majority of which were unique to each site. The relationship between 16S rRNA and the 16S rRNA gene, i.e., between potential metabolic activity and abundance, was positive for the whole community. However, analysis of individual OTUs revealed high rRNA-to-rRNA gene ratios for most (71.6% ± 16.7%) of the rare taxa, suggesting that these low-abundance organisms were potentially active and hence might be playing an important role in ecosystem diversity and functioning in the GON. IMPORTANCE The study of bacterioplankton in coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically impacted. Their richness and evenness, as well as their potential activity, are very important to assess ecosystem health and functioning. Here, we investigated bacterial distribution, community composition, and potential metabolic activity in the GON, which is an ideal test site due to its heterogeneous environment characterized by a complex hydrodynamics and terrestrial inputs of varied quantities and quality. Our study demonstrates that bacterioplankton communities in this region are highly diverse and strongly regulated by a combination of different environmental factors leading to their heterogeneous distribution, with the rare taxa contributing to a major proportion of diversity and shifts in community composition and potentially holding a key role in ecosystem functioning. Copyright © 2017 American Society for Microbiology.

Distribution, Community Composition, and Potential Metabolic Activity of Bacterioplankton in an Urbanized Mediterranean Sea Coastal Zone

PubMed Central

Richa, Kumari; Balestra, Cecilia; Piredda, Roberta; Benes, Vladimir; Borra, Marco; Passarelli, Augusto; Margiotta, Francesca; Saggiomo, Maria; Biffali, Elio; Sanges, Remo; Scanlan, David J.

2017-01-01

ABSTRACT Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to the global biogeochemical cycles of key elements. Yet, there is a significant gap in knowledge about their diversity and specific activities, as well as environmental factors that shape their community composition and function. Here, the distribution and diversity of surface bacterioplankton along the coastline of the Gulf of Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing of the 16S rRNA gene. Heterotrophic bacteria numerically dominated the bacterioplankton and comprised mainly Alphaproteobacteria, Gammaproteobacteria, and Bacteroidetes. Distinct communities occupied river-influenced, coastal, and offshore sites, as indicated by Bray-Curtis dissimilarity, distance metric (UniFrac), linear discriminant analysis effect size (LEfSe), and multivariate analyses. The heterogeneity in diversity and community composition was mainly due to salinity and changes in environmental conditions across sites, as defined by nutrient and chlorophyll a concentrations. Bacterioplankton communities were composed of a few dominant taxa and a large proportion (92%) of rare taxa (here defined as operational taxonomic units [OTUs] accounting for <0.1% of the total sequence abundance), the majority of which were unique to each site. The relationship between 16S rRNA and the 16S rRNA gene, i.e., between potential metabolic activity and abundance, was positive for the whole community. However, analysis of individual OTUs revealed high rRNA-to-rRNA gene ratios for most (71.6% ± 16.7%) of the rare taxa, suggesting that these low-abundance organisms were potentially active and hence might be playing an important role in ecosystem diversity and functioning in the GON. IMPORTANCE The study of bacterioplankton in coastal zones is of critical importance, considering that these areas are highly productive and anthropogenically impacted. Their richness and evenness, as well as their potential activity, are very important to assess ecosystem health and functioning. Here, we investigated bacterial distribution, community composition, and potential metabolic activity in the GON, which is an ideal test site due to its heterogeneous environment characterized by a complex hydrodynamics and terrestrial inputs of varied quantities and quality. Our study demonstrates that bacterioplankton communities in this region are highly diverse and strongly regulated by a combination of different environmental factors leading to their heterogeneous distribution, with the rare taxa contributing to a major proportion of diversity and shifts in community composition and potentially holding a key role in ecosystem functioning. PMID:28667110

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China.

PubMed

Yao, Xiaodong; Zhang, Naili; Zeng, Hui; Wang, Wei

2018-07-15

Although the patterns and drivers of soil microbial community composition are well studied, little is known about the effects of plant-soil interactions and soil depth on soil microbial distribution at a regional scale. We examined 195 soil samples from 13 sites along a climatic transect in the temperate grasslands of northern China to measure the composition of and factors influencing soil microbial communities within a 1-m soil profile. Soil microbial community composition was measured using phospholipid fatty acids (PLFA) analysis. Fungi predominated in topsoil (0-10 cm) and bacteria and actinomycetes in deep soils (40-100 cm), independent of steppe types. This variation was explained by contemporary environmental factors (including above- and below-ground plant biomass, soil physicochemical and climatic factors) >58% in the 0-40 cm of soil depth, but <45% in deep soils. Interestingly, when we considered the interactive effects between plant traits (above ground biomass and root biomass) and soil factors (pH, clay content, and soil total carbon, nitrogen, phosphorous), we observed a significant interaction effect occurring at depths of 10-20 cm soil layer, due to different internal and external factors of the plant-soil system along the soil profile. These results improve understanding of the drivers of soil microbial community composition at regional scales. Copyright © 2018 Elsevier B.V. All rights reserved.

Soil moisture and chemistry influence diversity of ectomycorrhizal fungal communities associating with willow along an hydrologic gradient.

PubMed

Erlandson, Sonya R; Savage, Jessica A; Cavender-Bares, Jeannine M; Peay, Kabir G

2016-01-01

Influences of soil environment and willow host species on ectomycorrhizal fungi communities was studied across an hydrologic gradient in temperate North America. Soil moisture, organic matter and pH strongly predicted changes in fungal community composition. In contrast, increased fungal richness strongly correlated with higher plant-available phosphorus. The 93 willow trees sampled for ectomycorrhizal fungi included seven willow species. Host identity did not influence fungal richness or community composition, nor was there strong evidence of willow host preference for fungal species. Network analysis suggests that these mutualist interaction networks are not significantly nested or modular. Across a strong environmental gradient, fungal abiotic niche determined the fungal species available to associate with host plants within a habitat. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Metals other than uranium affected microbial community composition in a historical uranium-mining site.

PubMed

Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

2015-12-01

To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

Profiling Hyporheic Microbial Community Nitrogen Cycle and Carbohydrate Active Enzyme Gene Abundances across Seasons

NASA Astrophysics Data System (ADS)

Nelson, W. C.; Graham, E.; Stegen, J.

2016-12-01

The hyporheic zone (HZ) is the permanently inundated sediment layer between a surface channel and adjacent groundwater-saturated sediments. It has been hypothesized to play a major role in macronutrient (C, N, P) cycling in rivers. The correlation between community taxonomic composition dynamics and functional gene representation is poorly understood for hyporheic communities. To explore how microbial communities respond to temporal changes in environmental conditions, metagenomes were derived from communities captured in sterile sandpacks deployed within the HZ of the Columbia River. HMM databases were used to enumerate protein families present. Functional classification of reads allowed a general assessment of community function over time, while targeted assembly of specific genes enabled investigation of the diversity of organisms encoding these functions. Preliminary analysis of nitrogen cycle pathways shows most gene families examined to have quite steady representation across seasons, with most observed changes being less than an order of magnitude. Analysis of ammonia oxidation genes showed bacterial ammonia oxidizers (AOB) to be stably present across the year, while the archaeal amoA gene increased in late summer, peaking sharply in November, mirroring results from 16S rRNA amplicon analysis which showed an increase in Thaumarcheal OTUs during that same period. Most glycosyl hydrolase GH families had low representation. Highly abundant classes of GH included the GH94 (beta-glucosidase), GH95 (1-2-alpha-L-fucosidase) and GH103 (lytic transglycosylase) families, suggesting activity on plant, fungus and insect polysaccharides and peptidoglycans. Further work is investigating the taxonomy of the sequences identified, to determine how changes in the community composition contribute to the stable gene family profiles observed. These results are intended to work towards a greater understanding of the role of species diversity and functional redundancy in the dynamics of community composition in response to changes in environmental conditions and stochastic processes. In addition, it will serve as a foundation enabling modeling of generalized microbial function in the hyporheic zone, improving our ability to predict fluxes of carbon and nitrogen through riverine systems.

Diversity, composition, and geographical distribution of microbial communities in California salt marsh sediments

USGS Publications Warehouse

Cordova-Kreylos, A. L.; Cao, Y.; Green, P.G.; Hwang, H.-M.; Kuivila, K.M.; LaMontagne, M.G.; Van De Werfhorst, L. C.; Holden, P.A.; Scow, K.M.

2006-01-01

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. Copyright ?? 2006, American Society for Microbiology. All Rights Reserved.

Diversity, Composition, and Geographical Distribution of Microbial Communities in California Salt Marsh Sediments

PubMed Central

Córdova-Kreylos, Ana Lucía; Cao, Yiping; Green, Peter G.; Hwang, Hyun-Min; Kuivila, Kathryn M.; LaMontagne, Michael G.; Van De Werfhorst, Laurie C.; Holden, Patricia A.; Scow, Kate M.

2006-01-01

The Pacific Estuarine Ecosystem Indicators Research Consortium seeks to develop bioindicators of toxicant-induced stress and bioavailability for wetland biota. Within this framework, the effects of environmental and pollutant variables on microbial communities were studied at different spatial scales over a 2-year period. Six salt marshes along the California coastline were characterized using phospholipid fatty acid (PLFA) analysis and terminal restriction fragment length polymorphism (TRFLP) analysis. Additionally, 27 metals, six currently used pesticides, total polychlorinated biphenyls and polycyclic aromatic hydrocarbons, chlordanes, nonachlors, dichlorodiphenyldichloroethane, and dichlorodiphenyldichloroethylene were analyzed. Sampling was performed over large (between salt marshes), medium (stations within a marsh), and small (different channel depths) spatial scales. Regression and ordination analysis suggested that the spatial variation in microbial communities exceeded the variation attributable to pollutants. PLFA analysis and TRFLP canonical correspondence analysis (CCA) explained 74 and 43% of the variation, respectively, and both methods attributed 34% of the variation to tidal cycles, marsh, year, and latitude. After accounting for spatial variation using partial CCA, we found that metals had a greater effect on microbial community composition than organic pollutants had. Organic carbon and nitrogen contents were positively correlated with PLFA biomass, whereas total metal concentrations were positively correlated with biomass and diversity. Higher concentrations of heavy metals were negatively correlated with branched PLFAs and positively correlated with methyl- and cyclo-substituted PLFAs. The strong relationships observed between pollutant concentrations and some of the microbial indicators indicated the potential for using microbial community analyses in assessments of the ecosystem health of salt marshes. PMID:16672478

Microbial diversity and community structure across environmental gradients in an seawater intruded shallow confined aquifer

NASA Astrophysics Data System (ADS)

Zhang, X.; Hu, B.

2017-12-01

Seawater intrusion has been an important topic in coastal hydrogeology and making previously freshwater ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have been well studied in the coastal zone. However, little is known about the biogeography or stability of microbial community response to seawater intrusion. The objective of this study is to characterize and compare bacterial and archaea community diversity and composition in 15 groundwater samples with varied salinity using high-throughput-sequencing of 16S ribosomal RNA genes. The dominant taxonomic group identified in all samples are proteobacteria for bacteria and crenarchaeota for archaea. The other main bacterial groups are varied in samples with different salinities including bacteroidetes, firmicutes and several unidentified taxonomys. A combination of environmental factors seems to influence the microbial community composition where organic carbon is a primary factor shaping microbial communities. Correlation analysis between the relative abundance of bacterial taxa and geochemical parameters uggested that rare taxa may contribute to biogeochemical processes taking place at the mixing zone of freshewater and saltwater. Our results help to understand how the physical and chemical factors shape the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes and the efficacy of new remediation efforts.

Comparison of bacterial community structures of terrestrial cyanobacterium Nostoc flagelliforme in three different regions of China using PCR-DGGE analysis.

PubMed

Han, Pei-pei; Shen, Shi-gang; Jia, Shi-ru; Wang, Hui-yan; Zhong, Cheng; Tan, Zhi-lei; Lv, He-xin

2015-07-01

Filamentous Nostoc flagelliforme form colloidal complex, with beaded cells interacting with other bacteria embedded in the complex multilayer sheath. However, the species of bacteria in the sheath and the interaction between N. flagelliforme and associated bacteria remain unclear. In this study, PCR-denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities of N. flagelliforme from three regions of China. DGGE patterns showed variations in all samples, exhibiting 25 discrete bands with various intensities. The diversity index analysis of bands profiles suggested the high similarity of bacterial communities to each other but also the dependence of microbial composition on each location. Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria, Cyanobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, of which Cyanobacteria was dominant, followed the Proteobacteria. Members of the genus Nostoc were the most abundant in all samples. Rhizobiales and Actinobacteria were identified, whereas, Craurococcus, Caulobacter, Pseudomonas, Terriglobus and Mucilaginibacter were also identified at low levels. Through comparing the bacterial composition of N. flagelliforme from different regions, it was revealed that N. flagelliforme could facilitate the growth of other microorganisms including both autotrophic bacteria and heterotrophic ones and positively contributed to their harsh ecosystems. The results indicated N. flagelliforme played an important role in diversifying the microbial community composition and had potential application in soil desertification.

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study.

PubMed

Nuy, Julia K; Lange, Anja; Beermann, Arne J; Jensen, Manfred; Elbrecht, Vasco; Röhl, Oliver; Peršoh, Derek; Begerow, Dominik; Leese, Florian; Boenigk, Jens

2018-08-15

Stream ecosystems are affected by multiple anthropogenic stressors worldwide. Even though effects of many single stressors are comparatively well studied, the effects of multiple stressors are difficult to predict. In particular bacteria and protists, which are responsible for the majority of ecosystem respiration and element flows, are infrequently studied with respect to multiple stressors responses. We conducted a stream mesocosm experiment to characterize the responses of single and multiple stressors on microbiota. Two functionally important stream habitats, leaf litter and benthic phototrophic rock biofilms, were exposed to three stressors in a full factorial design: fine sediment deposition, increased chloride concentration (salinization) and reduced flow velocity. We analyzed the microbial composition in the two habitat types of the mesocosms using an amplicon sequencing approach. Community analysis on different taxonomic levels as well as principle component analyses (PCoAs) based on realtive abundances of operational taxonomic units (OTUs) showed treatment specific shifts in the eukaryotic biofilm community. Analysis of variance (ANOVA) revealed that Bacillariophyta responded positively salinity and sediment increase, while the relative read abundance of chlorophyte taxa decreased. The combined effects of multiple stressors were mainly antagonistic. Therefore, the community composition in multiply stressed environments resembled the composition of the unstressed control community in terms of OTU occurrence and relative abundances. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

On designing of a low leakage patient-centric provider network.

PubMed

Zheng, Yuchen; Lin, Kun; White, Thomas; Pickreign, Jeremy; Yuen-Reed, Gigi

2018-03-27

When a patient in a provider network seeks services outside of their community, the community experiences a leakage. Leakage is undesirable as it typically leads to higher out-of-network cost for patient and increases barrier for care coordination, which is particularly problematic for Accountable Care Organization (ACO) as the in-network providers are financially responsible for quality of care and outcome. We aim to design a data-driven method to identify naturally occurring provider networks driven by diabetic patient choices, and understand the relationship among provider composition, patient composition, and service leakage pattern. By doing so, we learn the features of low service leakage provider networks that can be generalized to different patient population. Data used for this study include de-identified healthcare insurance administrative data acquired from Capital District Physicians' Health Plan (CDPHP) for diabetic patients who resided in four New York state counties (Albany, Rensselaer, Saratoga, and Schenectady) in 2014. We construct a healthcare provider network based on patients' historical medical insurance claims. A community detection algorithm is used to identify naturally occurring communities of collaborating providers. For each detected community, a profile is built using several new key measures to elucidate stakeholders of our findings. Finally, import-export analysis is conducted to benchmark their leakage pattern and identify further leakage reduction opportunity. The design yields six major provider communities with diverse profiles. Some communities are geographically concentrated, while others tend to draw patients with certain diabetic co-morbidities. Providers from the same healthcare institution are likely to be assigned to the same community. While most communities have high within-community utilization and spending, at 85% and 86% respectively, leakage still persists. Hence, we utilize a metric from import-export analysis to detect leakage, gaining insight on how to minimize leakage. We identify patient-driven provider organization by surfacing providers who share a large number of patients. By analyzing the import-export behavior of each identified community using a novel approach and profiling community patient and provider composition we understand the key features of having a balanced number of PCP and specialists and provider heterogeneity.

Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison

PubMed Central

Febria, Catherine M.; Hosen, Jacob D.; Crump, Byron C.; Palmer, Margaret A.; Williams, D. Dudley

2015-01-01

Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied. We compared environmental and microbial community datasets for permanent and temporary tributaries of two different North American headwater stream systems: Speed River (Ontario, Canada) and Parkers Creek (Maryland, USA). We explored whether taxonomic diversity and community composition were altered as a result of flow permanence and compared community composition amongst streams using different 16S microbial community methods (i.e., T-RFLP and Illumina MiSeq). Contrary to our hypotheses, and irrespective of method, community composition did not respond strongly to drying. In both systems, community composition was related to site rather than drying condition. Additional network analysis on the Parkers Creek dataset indicated a shift in the central microbial relationships between temporary and permanent streams. In the permanent stream at Parkers Creek, associations of methanotrophic taxa were most dominant, whereas associations with taxa from the order Nitrospirales were more dominant in the temporary stream, particularly during dry conditions. We compared these results with existing published studies from around the world and found a wide range in community responses to drying. We conclude by proposing three hypotheses that may address contradictory results and, when tested across systems, may expand understanding of the responses of microbial communities in temporary streams to natural and human-induced fluctuations in flow-status and permanence. PMID:26089816

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.

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties.

PubMed

Chai, Bei-Bei; Huang, Ting-Lin; Zhao, Xiao-Guang; Li, Ya-Jiao

2015-07-01

Microbial communities in three drinking water reservoirs, with different depth in Xi'an city, were quantified by phospholipids fatty acids analysis and multivariate statistical analysis was employed to interpret their response to different hydrostatic pressure and other physico-chemical properties of sediment and overlying water. Principle component analyses of sediment characteristics parameters showed that hydrostatic pressure was the most important effect factor to differentiate the overlying water quality from three drinking water reservoirs from each other. NH4+ content in overlying water was positive by related to hydrostatic pressure, while DO in water-sediment interface and sediment OC in sediment were negative by related with it. Three drinking water reservoir sediments were characterized by microbial communities dominated by common and facultative anaerobic Gram-positive bacteria, as well as, by sulfur oxidizing bacteria. Hydrostatic pressure and physico-chemical properties of sediments (such as sediment OC, sediment TN and sediment TP) were important effect factors to microbial community structure, especially hydrostatic pressure. It is also suggested that high hydrostatic pressure and low dissolved oxygen concentration stimulated Gram-positive and sulfate-reducing bacteria (SRB) bacterial population in drinking water reservoir sediment. This research supplied a successful application of phospholipids fatty acids and multivariate analysis to investigate microbial community composition response to different environmental factors. Thus, few physico-chemical factors can be used to estimate composition microbial of community as reflected by phospholipids fatty acids, which is difficult to detect.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments.

PubMed

Rocha, Lidianne L; Colares, Geórgia B; Nogueira, Vanessa L R; Paes, Fernanda A; Melo, Vânia M M

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

PubMed Central

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

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.

Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut.

PubMed

Zhao, Yi; Su, Jian-Qiang; An, Xin-Li; Huang, Fu-Yi; Rensing, Christopher; Brandt, Kristian Koefoed; Zhu, Yong-Guan

2018-04-15

Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Antibiotics and metals are widely used as feed additives and could consequently affect ARGs in swine gut. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) based ARG chip and next-generation 16S rRNA gene amplicon sequencing data were analyzed using multiple statistical approaches to profile the antibiotic resistome and investigate its linkages to antibiotics and metals used as feed additives and to the microbial community composition in freshly collected swine manure samples from three large-scale Chinese pig farms. A total of 146 ARGs and up to 1.3×10 10 total ARG copies per gram of swine feces were detected. ARGs conferring resistance to aminoglycoside, macrolide-lincosamide-streptogramin B (MLSB) and tetracycline were dominant in pig gut. Total abundance of ARGs was positively correlated with in-feed antibiotics, microbial biomass and abundance of mobile genetic elements (MGEs) (P<0.05). A significant correlation between microbial communities and ARG profiles was observed by Procrustes analysis. Network analysis revealed that Bacteroidetes and Firmicutes were the most dominant phyla co-occurring with specific ARGs. Partial redundancy analysis indicated that the variance in ARG profiles could be primarily attributed to antibiotics and metals in feed (31.8%), gut microbial community composition (23.3%) and interaction between feed additives and community composition (16.5%). These results suggest that increased levels of in-feed additives could aggravate the enrichment of ARGs and MGEs in swine gut. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial community composition in different sediments from the Eastern Mediterranean Sea: a comparison of four 16S ribosomal DNA clone libraries.

PubMed

Polymenakou, Paraskevi N; Bertilsson, Stefan; Tselepides, Anastasios; Stephanou, Euripides G

2005-10-01

The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.

Effect of the chemical composition of filter media on the microbial community in wastewater biofilms at different temperatures† †Electronic supplementary information (ESI) available: Tables S1–S6 are available. See DOI: 10.1039/c6ra21040f Click here for additional data file.

PubMed Central

Naz, Iffat; Hodgson, Douglas; Smith, Ann; Marchesi, Julian; Ahmed, Safia; Avignone-Rossa, Claudio

2016-01-01

This study investigates the microbial community composition in the biofilms grown on two different support media in fixed biofilm reactors for aerobic wastewater treatment, using next generation sequencing (NGS) technology. The chemical composition of the new type of support medium (TDR) was found to be quite different from the conventionally used support medium (stone). The analysis of 16S rRNA gene fragments recovered from the laboratory scale biofilm system show that biofilm support media and temperature conditions influence bacterial community structure and composition. Greater bacterial diversity was observed under each condition, primarily due to the large number of sequences available and sustenance of rare species. There were 6 phyla found, with the highest relative abundance shown by the phylum Proteobacteria (52.71%) followed by Bacteroidetes (33.33%), Actinobacteria (4.65%), Firmicutes, Verrucomicrobia (3.1%) and Chloroflex (>1%). The dataset showed 17 genera of bacterial populations to be commonly shared under all conditions, suggesting the presence of a core microbial community in the biofilms for wastewater treatment. However, some genera in the biofilms on TDR were observed in high proportions, which may be attributed to its chemical composition, explaining the improved level of wastewater treatment. The findings show that the structure of microbial communities in biofilm systems for wastewater treatment is affected by the properties of support matrix. PMID:28018581

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

PubMed

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

2016-01-01

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

Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Taïb, Najwa; Mangot, Jean-François; Bronner, Gisèle; Boucher, Delphine; Debroas, Didier

2013-07-01

Understanding the spatial distribution of aquatic microbial diversity and the underlying mechanisms causing differences in community composition is a challenging and central goal for ecologists. Recent insights into protistan diversity and ecology are increasing the debate over their spatial distribution. In this study, we investigate the importance of spatial and environmental factors in shaping the small protists community structure in lakes. We analyzed small protists community composition (beta-diversity) and richness (alpha-diversity) at regional scale by different molecular methods targeting the gene coding for 18S rRNA gene (T-RFLP and 454 pyrosequencing). Our results show a distance-decay pattern for rare and dominant taxa and the spatial distribution of the latter followed the prediction of the island biogeography theory. Furthermore, geographic distances between lakes seem to be the main force shaping the protists community composition in the lakes studied here. Finally, the spatial distribution of protists was discussed at the global scale (11 worldwide distributed lakes) by comparing these results with those present in the public database. UniFrac analysis showed 18S rRNA gene OTUs compositions significantly different among most of lakes, and this difference does not seem to be related to the trophic status. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Impact of storage conditions on fungal community composition of green coffee beans Coffea arabica L. stored in jute sacks during 1 year.

PubMed

Broissin-Vargas, L M; Snell-Castro, R; Godon, J J; González-Ríos, O; Suárez-Quiroz, M L

2018-02-01

The purpose of this study was to evaluate the effect of warehouse storage conditions on the composition of the fungal community of green coffee beans (GCB) that were stored in jute sacks for 1 year. Molecular characterization of the fungal community composition and population dynamics obtained by Q-PCR, CE-SSCP (Simpson's diversity index D) and Illumina MiSeq sequencing indicated that Saccharomycetales dominated during the first 6 months of storage period with species as Meyerozyma guilliermondii and Pichia kluyveri. However, after 6 months of storage, the filamentous genus Wallemia became dominant. Principal components analysis correlated this fungal dynamic with storage conditions and other variables as chromaticity (colour), water activity, moisture content, reducing sugars concentration, fungal infection and ochratoxin A production. This study demonstrated that GCB stored in jute sacks after 6 months of storage lead to fungal population dynamics, decreased chromaticity in GCB by bleaching and, then, affected overall quality. Storage plays an important role in the quality evolution during the handling of the GCB. In this context, the composition of the microbial community could be considered a marker to assess the trade value of the coffee beans. © 2017 The Society for Applied Microbiology.

The bacterial community composition of the surface microlayer in a high mountain lake.

PubMed

Hörtnagl, Paul; Pérez, Maria Teresa; Zeder, Michael; Sommaruga, Ruben

2010-09-01

The existence of bacterioneuston in aquatic ecosystems is well established, but little is known about its composition and dynamics, particularly in lakes. The bacterioneuston underlies extreme conditions at the air-water boundary, which may influence its dynamics in a different way compared with the bacterioplankton. In this study, we assessed quantitative changes in major bacterial groups of the surface microlayer (SML) (upper 900 microm) and the underlying water (ULW) (0.2-0.5 m depth) of an alpine lake during two consecutive ice-free seasons. Analysis of the bacterial community composition was done using catalyzed reporter deposition FISH with oligonucleotide probes. In addition, several physicochemical parameters were measured to characterize these two water layers. Dissolved organic carbon was consistently enriched in the SML and the dissolved organic matter pool presented clear signals of photodegradation and photobleaching. The water temperature was generally colder in the SML than in the subsurface. The bacterial community of the SML and the ULW was dominated by Betaproteobacteria and Actinobacteria. The bacterial community composition was associated with different combinations of physicochemical factors in these two layers, but temporal changes showed similar trends in both layers over the two seasons. Our results identify the SML of alpine lakes as a microhabitat where specific bacterial members such as of Betaproteobacteria seem to be efficient colonizers.

Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic)

PubMed Central

Zhang, Tao; Wang, Neng-Fei; Liu, Hong-Yu; Zhang, Yu-Qin; Yu, Li-Yan

2016-01-01

This study assessed the fungal community composition and its relationships with properties of surface soils in the Ny-Ålesund Region (Svalbard, High Arctic). A total of thirteen soil samples were collected and soil fungal community was analyzed by 454 pyrosequencing with fungi-specific primers targeting the rDNA internal transcribed spacer (ITS) region. The following eight soil properties were analyzed: pH, organic carbon (C), organic nitrogen (N), ammonium nitrogen (NH4+-N), silicate silicon (SiO42--Si), nitrite nitrogen (NO2--N), phosphate phosphorus (PO43--P), and nitrate nitrogen (NO3--N). A total of 57,952 reads belonging to 541 operational taxonomic units (OTUs) were found. of these OTUs, 343 belonged to Ascomycota, 100 to Basidiomycota, 31 to Chytridiomycota, 22 to Glomeromycota, 11 to Zygomycota, 10 to Rozellomycota, whereas 24 belonged to unknown fungi. The dominant orders were Helotiales, Verrucariales, Agaricales, Lecanorales, Chaetothyriales, Lecideales, and Capnodiales. The common genera (>eight soil samples) were Tetracladium, Mortierella, Fusarium, Cortinarius, and Atla. Distance-based redundancy analysis (db-rda) and analysis of similarities (ANOSIM) revealed that soil pH (p = 0.001) was the most significant factor in determining the soil fungal community composition. Members of Verrucariales were found to predominate in soils of pH 8–9, whereas Sordariales predominated in soils of pH 7–8 and Coniochaetales predominated in soils of pH 6–7. The results suggest the presence and distribution of diverse soil fungal communities in the High Arctic, which can provide reliable data for studying the ecological responses of soil fungal communities to climate changes in the Arctic. PMID:26955371

Regional variation in Caribbean dry forest tree species composition

Treesearch

Janet Franklin; Julie Ripplinger; Ethan H. Freid; Humfredo Marcano-Vega; David W. Steadman

2015-01-01

How does tree species composition vary in relation to geographical and environmental gradients in a globally rare tropical/subtropical broadleaf dry forest community in the Caribbean? We analyzed data from 153 Forest Inventory and Analysis (FIA) plots from Puerto Rico and the U.S. Virgin Islands (USVI), along with 42 plots that we sampled in the Bahamian Archipelago (...

DAILY VARIATION IN ORGANIC COMPOSITION OF FINE PARTICULATE MATTER IN THE DETROIT EXPOSURE AND AEROSOL RESEARCH STUDY

EPA Science Inventory

Organic composition of fine particulate matter (PM2.5) was investigated as a part of the Detroit Exposure and Aerosol Research Study (DEARS). A high volume (113 liters/minute) sampler was used at the Allen Park community air monitoring station to collect PM2.5 for analysis by ga...

Biogeochemical drivers of microbial community convergence across actively retreating glaciers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castle, Sarah C.; Nemergut, Diana R.; Grandy, A. Stuart

The ecological processes that influence biogeographical patterns of microorganisms are actively debated. To investigate how such patterns emerge during ecosystem succession, we examined the biogeochemical drivers of bacterial community assembly in soils over two environmentally distinct, recently deglaciated chronosequences separated by a distance of more than 1,300 kilometers. Our results show that despite different geographic, climatic, and soil chemical and physical characteristics at the two sites, soil bacterial community structure and decomposer function converged during plant succession. In a comparative analysis, we found that microbial communities in early succession soils were compositionally distinct from a group of diverse, mature forestmore » soils, but that the differences between successional soils and mature soils decreased from early to late stages of succession. Differences in bacterial community composition across glacial sites were largely explained by pH. However, successional patterns and community convergence across sites were more consistently related to soil organic carbon and organic matter chemistry, which appeared to be tightly coupled with bacterial community structure across both young and mature soils.« less

Microbial Response to High Temperature Hydrothermal Forcing: AISICS Vent (Lucky Strike, 37°N, MAR) and Prokaryote Community as Example.

NASA Astrophysics Data System (ADS)

Henri, P. A.; Rommevaux, C.; Chavagnac, V.; Degboe, J.; Destrigneville, C.; Boulart, C.; Lesongeur, F.; Castillo, A.; Goodfroy, A.

2015-12-01

To study the hydrothermal forcing on microbial colonization, and impacts on the oceanic crust alteration, an integrated study was led at the Tour Eiffel hydrothermal site (Lucky Strike hydrothermal field, 37°N, MAR). We benefited from an annual survey between 2009 and 2011 of temperatures, along with sampling of focused and diffused fluids for chemical analysis, and chimney sampling and samples from microbial colonization experiments analyzed for prokaryotic composition and rock alteration study. The chemical composition of the fluids show an important increase in the CO2 concentration at the Eiffel Tower site between 2009 and 2010 followed by a decrease between 2010 and 2011. In 2011, several fluid samples show an important depletion in Si, suggesting that some Si was removed by interaction with the stockwork before emission. Our observations, regarding the previous studies of chemical fluid affected by a magmatic event lead us to suppose that a magmatic/tectonic event occurred under the Lucky Strike hydrothermal field between 2009 and 2010. The results of the prokaryotic communities' analysis show that a shift occurred in the dominant microbial metabolisms present in the colonizer retrieved in 2010 and the one retrieved in 2011. Archaeal communities shifted from chemolithoautotropic sulfite/thiosulfate reducers-dominated in 2010 to ammonia oxidizers-dominated in 2011. The bacterial communities also undergo a shift, from a community with diversified metabolisms in 2010 to a community strongly dominated by chemolithoautotrophic sulfide or hydrogen oxidation in 2011. Moreover, in terms of ecological preferendum, the Archaeal communities shifted from thermophilic-dominated to mesophilic-dominated. The present study underline the influence of modifications in gases compositions of hydrothermal fluids subsequently to a degassing of the magma chamber and their impact on the microbial communities living in the vicinity of hydrothermal vents at the Eiffel Tower site.

Influence of Salinity on Bacterioplankton Communities from the Brazilian Rain Forest to the Coastal Atlantic Ocean

PubMed Central

Silveira, Cynthia B.; Vieira, Ricardo P.; Cardoso, Alexander M.; Paranhos, Rodolfo; Albano, Rodolpho M.; Martins, Orlando B.

2011-01-01

Background Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. Methodology/Principal Findings We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. Conclusions/Significance Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean. PMID:21408023

Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean.

PubMed

Silveira, Cynthia B; Vieira, Ricardo P; Cardoso, Alexander M; Paranhos, Rodolfo; Albano, Rodolpho M; Martins, Orlando B

2011-03-09

Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.

Fire severity mediates climate-driven shifts in understorey community composition of black spruce stands of interior Alaska

Treesearch

Emily L. Bernhardt; Teresa N. Hollingsworth; F. Stuart Chapin

2011-01-01

Question: How do pre-fire conditions (community composition and environmental characteristics) and climate-driven disturbance characteristics (fire severity) affect post-fire community composition in black spruce stands? Location: Northern boreal forest, interior Alaska. Methods: We compared plant community composition and environmental stand characteristics in 14...

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing.

PubMed

Kelly, L C; Colin, Y; Turpault, M-P; Uroz, S

2016-08-01

Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site.

The interacting roles of climate, soils, and plant production on soil microbial communities at a continental scale

USGS Publications Warehouse

Waldrop, Mark P.; Holloway, JoAnn M.; Smith, David; Goldhaber, Martin B.; Drenovsky, R.E.; Scow, K.M.; Dick, R.; Howard, Daniel M.; Wylie, Bruce K.; Grace, James B.

2017-01-01

Soil microbial communities control critical ecosystem processes such as decomposition, nutrient cycling, and soil organic matter formation. Continental scale patterns in the composition and functioning of microbial communities are related to climatic, biotic, and edaphic factors such as temperature and precipitation, plant community composition, and soil carbon, nitrogen, and pH. Although these relationships have been well explored individually, the examination of the factors that may act directly on microbial communities vs. those that may act indirectly through other ecosystem properties has not been well developed. To further such understanding, we utilized structural equation modeling (SEM) to evaluate a set of hypotheses about the direct and indirect effects of climatic, biotic, and edaphic variables on microbial communities across the continental United States. The primary goals of this work were to test our current understanding of the interactions among climate, soils, and plants in affecting microbial community composition, and to examine whether variation in the composition of the microbial community affects potential rates of soil enzymatic activities. A model of interacting factors created through SEM shows several expected patterns. Distal factors such as climate had indirect effects on microbial communities by influencing plant productivity, soil mineralogy, and soil pH, but factors related to soil organic matter chemistry had the most direct influence on community composition. We observed that both plant productivity and soil mineral composition were important indirect influences on community composition at the continental scale, both interacting to affect organic matter content and microbial biomass and ultimately community composition. Although soil hydrolytic enzymes were related to the moisture regime and soil carbon, oxidative enzymes were also affected by community composition, reflected in the abundance of soil fungi. These results highlight that soil microbial communities can be modeled within the context of multiple interacting ecosystem properties acting both directly and indirectly on their composition and function, and this provides a rich and informative context with which to examine communities. This work also highlights that variation in climate, microbial biomass, and microbial community composition can affect maximum rates of soil enzyme activities, potentially influencing rates of decomposition and nutrient mineralization in soils.

The Skin-Mucus Microbial Community of Farmed Atlantic Salmon (Salmo salar)

PubMed Central

Minniti, Giusi; Hagen, Live Heldal; Porcellato, Davide; Jørgensen, Sven Martin; Pope, Phillip B.; Vaaje-Kolstad, Gustav

2017-01-01

The skin of the teleost is a flexible and scaled structure that protects the fish toward the external environment. The outermost surface of the skin is coated with mucus, which is believed to be colonized by a diverse bacterial community (commensal and/or opportunistic). Little is known about such communities and their role in fish welfare. In aquaculture, fish seem to be more susceptible to pathogens compared to wild fish. Indeed common fish farming practices may play important roles in promoting their vulnerability, possibly by causing changes to their microbiomes. In the present study, 16S rRNA gene amplicon sequencing was employed to analyze the composition of the farmed Salmo salar skin-mucus microbiome before and after netting and transfer. The composition of the bacterial community present in the rearing water was also investigated in order to evaluate its correlation with the community present on the fish skin. Our results reveal variability of the skin-mucus microbiome among the biological replicates before fish handling. On the contrary, after fish handling, the skin-mucus community exhibited structural similarity among the biological replicates and significant changes were observed in the bacterial composition compared to the fish analyzed prior to netting and transfer. Limited correlation was revealed between the skin-mucus microbiome and the bacterial community present in the rearing water. Finally, analysis of skin-mucus bacterial biomasses indicated low abundance for some samples, highlighting the need of caution when interpreting community data due to the possible contamination of water-residing bacteria. PMID:29104567

Reduced Flexibility Associated with Metabolic Syndrome in Community-Dwelling Elders

PubMed Central

Chang, Ke-Vin; Hung, Chen-Yu; Li, Chia-Ming; Lin, Yu-Hung; Wang, Tyng-Guey; Tsai, Keh-Sung; Han, Der-Sheng

2015-01-01

Background The ageing process may lead to reductions in physical fitness, a known risk factor in the development of metabolic syndrome. The purpose of the current study was to evaluate cross-sectional and combined associations of metabolic syndrome with body composition and physical fitness in a community based geriatric population. Methods A total of 628 community-dwelling elders attending a geriatric health examination were enrolled in the study. The diagnosis of metabolic syndrome was based on the modified National Cholesterol Education Program Adult Treatment Panel III (NCEP ATP III) criterion with Asian cutoff of waist girth was adopted in this study. Body composition was obtained using bioimpedance analysis, and physical fitness was evaluated through the measurement of muscle strength (handgrip force), lower extremity muscle endurance (sit-to-stand test), flexibility (sit-and-reach test), and cardiorespiratory endurance (2-minute step test). Multivariable logistic regression and correlation analysis were performed to determine the association of metabolic syndrome with body composition and functionality variables. Results Metabolic syndrome was associated with increased skeletal muscle index (SMI) (odds ratio (OR), 1.61, 95% confidence interval (CI), 1.25–2.07) and decreased flexibility (OR, 0.97, 95% CI, 0.95–0.99) compared with those without metabolic syndrome. When body mass index was accounted for in the analysis, the association of SMI with metabolic syndrome was reduced. Waist circumference was positively correlated with SMI but negatively correlated with flexibility, whereas high density lipoprotein was positively correlated with flexibility but negatively correlated with SMI. Conclusion Reduced flexibility was positively associated with metabolic syndrome independent of age, gender, body composition, and functionality measurements in a community based geriatric population. Significant associations between metabolic syndrome with muscle strength and cardiorespiratory fitness in the elderly were not observed. Furthermore, flexibility should be included in the complete evaluation for metabolic syndrome. PMID:25614984

Spatial and Temporal Comparison of DNRA Communities in New River Estuary, USA

NASA Astrophysics Data System (ADS)

Song, B.; Lisa, J.; Tobias, C. R.

2016-02-01

Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate respiring pathway, competing with denitrification, in various ecosystems. Studies examining the diversity and composition of DNRA communities are limited and their link to DNRA activity is unknown. We conducted a multidisciplinary investigation of sediment communities in the upper reaches of a eutrophic estuary to examine spatial and temporal variation of DNRA community structures and determine their linkage to activities. Sediment samples were collected seasonally from two study sites (AA2 and JAX) in the New River Estuary, North Carolina, USA. 15N-nitrate tracer experiments were conducted to measure potential DNRA rates while abundance of DNRA communities was measured using quantitative PCR of cytochrome C nitrite reductase genes (nrfA). Composition and diversity of DNRA communities were also examined based on next generation sequencing (NGS) of nrfA genes using an Ion Torrent PGM. Bioinformatic analysis was conducted using the FunGene pipeline and Mothur program. Higher DNRA activities were measured at JAX and associated with higher abundance of nrfA genes. Seasonal variation in DNRA rates and nrfA gene abundance was more evident at JAX than AA2. Nitrate concentration and dissolved oxygen in bottom water were significantly and positively correlated with activities and abundance of DNRA communities. The nrfA NGS analysis revealed that spatial variation of DNRA communities was much greater than temporal variation with salinity, dissolved organic carbon, and nitrate as the most important environmental variables affecting these communities. Diversity of DNRA communities was negative correlated with the DNRA rates and nrfA gene abundance, which suggests that dominant members of the DNRA community are responsible for higher rates. Thus, our multidisciplinary study clearly demonstrates the linkage between structure and activities of DNRA communities in the upper reaches of New River Estuary.

Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

PubMed

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.

Soil Mineral Composition Matters: Response of Microbial Communities to Phenanthrene and Plant Litter Addition in Long-Term Matured Artificial Soils

PubMed Central

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications. PMID:25222697

A High Burden of Asymptomatic Gastrointestinal Infections in Traditional Communities in Papua New Guinea.

PubMed

Horwood, Paul F; Soli, Kevin W; Maure, Tobias; Naito, Yuichi I; Morita, Ayako; Natsuhara, Kazumi; Tadokoro, Kiyoshi; Baba, Jun; Odani, Shingo; Tomitsuka, Eriko; Igai, Katsura; Larkins, Jo-Ann; Siba, Peter M; Pomat, William; McBryde, Emma S; Umezaki, Masahiro; Greenhill, Andrew R

2017-12-01

Stool samples were collected from 148 healthy adults living a traditional subsistence lifestyle in Papua New Guinea and screened for enteric pathogens using real-time RT-PCR/PCR assays. Enteric pathogens were detected in a high proportion (41%) of individuals. Clear differences were observed in the detection of pathogens between highland and lowland communities. In particular, there was a marked difference in detection rates of norovirus GII (20% and 0%, respectively) and Shigella sp. (15% and 0%, respectively). Analysis of the relationship between enteric pathogen carriage and microbial community composition of participants, using box plots to compare specific normal flora population numbers, did not suggest that gut microbial composition was directly associated with pathogen carriage. This study suggests that enteric pathogens are common in healthy individuals in Papua New Guinean highland communities, presumably acting as a reservoir of infection and thus contributing to a high burden of gastrointestinal illnesses.

Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols.

PubMed

Ma, Mingchao; Jiang, Xin; Wang, Qingfeng; Ongena, Marc; Wei, Dan; Ding, Jianli; Guan, Dawei; Cao, Fengming; Zhao, Baisuo; Li, Jun

2018-03-23

How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Zhili; Deng, Ye; Nostrand, Joy Van

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 oligomore » 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, agricuture, land use, ecosystem management, environmental cleanup and restoration, bioreactor systems, and human health.« less

Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva ▿

PubMed Central

Takeshita, Toru; Suzuki, Nao; Nakano, Yoshio; Shimazaki, Yoshihiro; Yoneda, Masahiro; Hirofuji, Takao; Yamashita, Yoshihisa

2010-01-01

Oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. In this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (T-RFLP) profiles using hierarchical cluster analysis, and the patterns of the microbial community composition of those exhibiting higher and lower malodor were explored. Four types of bacterial community compositions were detected (clusters I, II, III, and IV). Two parameters for measuring oral malodor intensity (the concentration of volatile sulfur compounds in mouth air and the organoleptic score) were noticeably lower in cluster I than in the other clusters. Using multivariate analysis, the differences in the levels of oral malodor were significant after adjustment for potential confounding factors such as total bacterial count, mean periodontal pocket depth, and tongue coating score (P < 0.001). Among the four clusters with different proportions of indigenous members, the T-RFLP profiles of cluster I were implicated as the bacterial populations with higher proportions of Streptococcus, Granulicatella, Rothia, and Treponema species than those of the other clusters. These results clearly correlate the global composition of indigenous bacterial populations with the severity of oral malodor. PMID:20228112

Compositional stability of a salivary bacterial population against supragingival microbiota shift following periodontal therapy.

PubMed

Yamanaka, Wataru; Takeshita, Toru; Shibata, Yukie; Matsuo, Kazuki; Eshima, Nobuoki; Yokoyama, Takeshi; Yamashita, Yoshihisa

2012-01-01

Supragingival plaque is permanently in contact with saliva. However, the extent to which the microbiota contributes to the salivary bacterial population remains unclear. We compared the compositional shift in the salivary bacterial population with that in supragingival plaque following periodontal therapy. Samples were collected from 19 patients with periodontitis before and after periodontal therapy (mean sample collection interval, 25.8 ± 2.6 months), and their bacterial composition was investigated using barcoded pyrosequencing analysis of the 16S rRNA gene. Phylogenetic community analysis using the UniFrac distance metric revealed that the overall bacterial community composition of saliva is distinct from that of supragingival plaque, both pre- and post-therapy. Temporal variation following therapy in the salivary bacterial population was significantly smaller than in the plaque microbiota, and the post-therapy saliva sample was significantly more similar to that pre-therapy from the same individual than to those from other subjects. Following periodontal therapy, microbial richness and biodiversity were significantly decreased in the plaque microbiota, but not in the salivary bacterial population. The operational taxonomic units whose relative abundances changed significantly after therapy were not common to the two microbiotae. These results reveal the compositional stability of salivary bacterial populations against shifts in the supragingival microbiota, suggesting that the effect of the supragingival plaque microbiota on salivary bacterial population composition is limited.

Shifts of community composition and population density substantially affect ecosystem function despite invariant richness.

PubMed

Spaak, Jurg W; Baert, Jan M; Baird, Donald J; Eisenhauer, Nico; Maltby, Lorraine; Pomati, Francesco; Radchuk, Viktoriia; Rohr, Jason R; Van den Brink, Paul J; De Laender, Frederik

2017-10-01

There has been considerable focus on the impacts of environmental change on ecosystem function arising from changes in species richness. However, environmental change may affect ecosystem function without affecting richness, most notably by affecting population densities and community composition. Using a theoretical model, we find that, despite invariant richness, (1) small environmental effects may already lead to a collapse of function; (2) competitive strength may be a less important determinant of ecosystem function change than the selectivity of the environmental change driver and (3) effects on ecosystem function increase when effects on composition are larger. We also present a complementary statistical analysis of 13 data sets of phytoplankton and periphyton communities exposed to chemical stressors and show that effects on primary production under invariant richness ranged from -75% to +10%. We conclude that environmental protection goals relying on measures of richness could underestimate ecological impacts of environmental change. © 2017 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Temporal Variations in the Abundance and Composition of Biofilm Communities Colonizing Drinking Water Distribution Pipes

PubMed Central

Kelly, John J.; Minalt, Nicole; Culotti, Alessandro; Pryor, Marsha; Packman, Aaron

2014-01-01

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities within the pipes were analyzed by heterotrophic plate counts and tag pyrosequencing of 16S rRNA genes, respectively. Bacterial numbers varied significantly based on sampling date and were positively correlated with water temperature and the concentration of nitrate. However, there was no significant relationship between the concentration of disinfectant in the drinking water (monochloramine) and the abundance of bacteria within the biofilms. Pyrosequencing analysis identified a total of 677 operational taxonomic units (OTUs) (3% distance) within the biofilms but indicated that community diversity was low and varied between sampling dates. Biofilms were dominated by a few taxa, specifically Methylomonas, Acinetobacter, Mycobacterium, and Xanthomonadaceae, and the dominant taxa within the biofilms varied dramatically between sampling times. The drinking water characteristics most strongly correlated with bacterial community composition were concentrations of nitrate, ammonium, total chlorine and monochloramine, as well as alkalinity and hardness. Biofilms from the sampling date with the highest nitrate concentration were the most abundant and diverse and were dominated by Acinetobacter. PMID:24858562

Impact of copper on the diazotroph abundance and community composition during swine manure composting.

PubMed

Yin, Yanan; Gu, Jie; Wang, Xiaojuan; Zhang, Kaiyu; Hu, Ting; Ma, Jiyue; Wang, Qianzhi

2018-05-01

Biological nitrogen fixation is a major pathway in ecosystems. This study investigated the effects of adding Cu at different levels (0, 200, and 2000 mg kg -1 ) on the diazotroph community during swine manure composting. Quantitative PCR and high-throughput sequencing were used to analyze the abundances of diazotrophs and the community composition based on the nifH gene. The nifH gene copy number was relatively high in the early stage of composting and Cu had a significant inhibitory effect on the nifH copy number. Furthermore, Cu decreased the diversity of nifH and changed the microbial community structure in the early stage. The nifH genes from members of Firmicutes and Clostridium were most abundant. Co-occurrence ecological network analysis showed that the Cu treatments affected the co-occurrence patterns of diazotroph communities and reduced the associations between different diazotrophs. Interestingly, Cu may weaken symbiotic diazotrophic interactions and enhance the roles of free-living diazotrophs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Influence of biochar on heavy metals and microbial community during composting of river sediment with agricultural wastes.

PubMed

Chen, Yaoning; Liu, Yao; Li, Yuanping; Wu, Yanxin; Chen, Yanrong; Zeng, Guangming; Zhang, Jiachao; Li, Hui

2017-11-01

Studies were performed to evaluate influence of biochar addition on physico-chemical process, heavy metals transformation and bacterial community diversity during composting of sediment with agricultural wastes. Simultaneously, the relationships between those parameters including heavy metals and bacterial community compositions were evaluated by redundancy analysis (RDA). The results show that the extraction efficiency of DTPA extractable heavy metals decreased in both piles, and reduced more in pile with biochar addition about 0.1-2.96%. Biochar addition dramatically influenced the bacterial community structure during the composting process. Moreover, the bacterial community composition was significantly correlated with C/N ratio, water soluble carbon (WSC), and organic matter (OM) (P<0.05) in pile with biochar addition; while significantly correlated with temperature, WSC, and C/N ratio in pile which was free of biochar. This study would provide some valuable information for improving the composting for disposal of river sediment with heavy metals contamination. Copyright © 2017 Elsevier Ltd. All rights reserved.

Long-term effects of timber harvesting on forest soil communities and their catabolic capacity

NASA Astrophysics Data System (ADS)

Mohn, W. W.

2016-12-01

We examined the effect of forest harvesting on metagenomes of soil communities in ecozones across North America. The overall effect of harvesting on community composition was very small relative to major differences between soil horizons and among geographically distinct ecozones. However, in some ecozones, harvesting substantially altered bacterial and fungal community composition and diminished the genetic potential for biomass decomposition while increasing the potential for nitrogen cycling. Stable isotope probing identified populations involved in hemicellulose and cellulose decomposition. Known cellulolytic organisms were found in the organic soil layer, while novel cellulolytic organisms were identified in the mineral soil layer. Lignolytic populations identified were mainly bacterial, and metagenomics analysis identified lignin degradation enzymes in the genomes of some of these populations. In some ecozones, cellulolytic and hemicellulolytic populations were substantially impacted by harvesting. Soil carbon, nitrogen and pH were related to the relative susceptibility of forest soil communities in the different ecozones to harvesting impacts.

Community change and evidence for variable warm-water temperature adaptation of corals in Northern Male Atoll, Maldives.

PubMed

McClanahan, T R; Muthiga, N A

2014-03-15

This study provides a descriptive analysis of the North Male, Maldives seven years after the 1998 bleaching disturbance to determine the state of the coral community composition, the recruitment community, evidence for recovery, and adaptation to thermal stress. Overall, hard coral cover recovered at a rate commonly reported in the literature but with high spatial variability and shifts in taxonomic composition. Massive Porites, Pavona, Synarea, and Goniopora were unusually common in both the recruit and adult communities. Coral recruitment was low and some coral taxa, namely Tubipora, Seriatopora, and Stylophora, were rarer than expected. A study of the bleaching response to a thermal anomaly in 2005 indicated that some taxa, including Leptoria, Platygyra, Favites, Fungia, Hydnophora, and Galaxea astreata, bleached as predicted while others, including Acropora, Pocillopora, branching Porites, Montipora, Stylophora, and Alveopora, bleached less than predicted. This indicates variable-adaptation potentials among the taxa and considerable potential for ecological reorganization of the coral community. Copyright © 2014 Elsevier Ltd. All rights reserved.

Native Perennial Forb Variation Between Mountain Big Sagebrush and Wyoming Big Sagebrush Plant Communities

NASA Astrophysics Data System (ADS)

Davies, Kirk W.; Bates, Jon D.

2010-09-01

Big sagebrush ( Artemisia tridentata Nutt.) occupies large portions of the western United States and provides valuable wildlife habitat. However, information is lacking quantifying differences in native perennial forb characteristics between mountain big sagebrush [ A. tridentata spp. vaseyana (Rydb.) Beetle] and Wyoming big sagebrush [ A. tridentata spp. wyomingensis (Beetle & A. Young) S.L. Welsh] plant communities. This information is critical to accurately evaluate the quality of habitat and forage that these communities can produce because many wildlife species consume large quantities of native perennial forbs and depend on them for hiding cover. To compare native perennial forb characteristics on sites dominated by these two subspecies of big sagebrush, we sampled 106 intact big sagebrush plant communities. Mountain big sagebrush plant communities produced almost 4.5-fold more native perennial forb biomass and had greater native perennial forb species richness and diversity compared to Wyoming big sagebrush plant communities ( P < 0.001). Nonmetric multidimensional scaling (NMS) and the multiple-response permutation procedure (MRPP) demonstrated that native perennial forb composition varied between these plant communities ( P < 0.001). Native perennial forb composition was more similar within plant communities grouped by big sagebrush subspecies than expected by chance ( A = 0.112) and composition varied between community groups ( P < 0.001). Indicator analysis did not identify any perennial forbs that were completely exclusive and faithful, but did identify several perennial forbs that were relatively good indicators of either mountain big sagebrush or Wyoming big sagebrush plant communities. Our results suggest that management plans and habitat guidelines should recognize differences in native perennial forb characteristics between mountain and Wyoming big sagebrush plant communities.

Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances.

PubMed

Zhou, Xingang; Wang, Zhilin; Jia, Huiting; Li, Li; Wu, Fengzhi

2018-01-01

Soil microbial communities have profound effects on the growth, nutrition and health of plants in agroecosystems. Understanding soil microbial dynamics in cropping systems can assist in determining how agricultural practices influence soil processes mediated by microorganisms. In this study, soil bacterial communities were monitored in a continuously monocropped Jerusalem artichoke (JA) system, in which JA was successively monocropped for 3 years in a wheat field. Soil bacterial community compositions were estimated by amplicon sequencing of the 16S rRNA gene. Abundances of ammonia-oxidizing and denitrifying bacteria were estimated by quantitative PCR analysis of the amoA , nirS , and nirK genes. Results showed that 1-2 years of monocropping of JA did not significantly impact the microbial alpha diversity, and the third cropping of JA decreased the microbial alpha diversity ( P < 0.05). Principal coordinates analysis and permutational multivariate analysis of variance analyses revealed that continuous monocropping of JA changed soil bacterial community structure and function profile ( P < 0.001). At the phylum level, the wheat field was characterized with higher relative abundances of Latescibacteria , Planctomycetes , and Cyanobacteria , the first cropping of JA with Actinobacteria , the second cropping of JA with Acidobacteria , Armatimonadetes , Gemmatimonadetes , and Proteobacteria . At the genus level, the first cropping of JA was enriched with bacterial species with pathogen-antagonistic and/or plant growth promoting potentials, while members of genera that included potential denitrifiers increased in the second and third cropping of JA. The first cropping of JA had higher relative abundances of KO terms related to lignocellulose degradation and phosphorus cycling, the second cropping of JA had higher relative abundances of KO terms nitrous-oxide reductase and nitric-oxide reductase, and the third cropping of JA had higher relative abundances of KO terms nitrate reductase and nitrite reductase. The abundances of amoA genes decreased while nirK increased in the third cropping of JA, nirS continuously increased in the second and third cropping of JA ( P < 0.05). Redundancy analysis and Mantel test found that soil organic carbon and Olsen phosphorus contents played important roles in shaping soil bacterial communities. Overall, our results revealed that continuous monocropping of JA changed soil bacterial community composition and its functional potentials.

Metabolic and structural response of hyporheic microbial communities to variations in supply of dissolved organic matter

USGS Publications Warehouse

Findlay, S.E.G.; Sinsabaugh, R. L.; Sobczak, W.V.; Hoostal, M.

2003-01-01

Hyporheic sediment bacterial communities were exposed to dissolved organic matter (DOM) from a variety of sources to assess the interdependence of bacterial metabolism and community composition. Experiments ranged from small-scale core perfusions with defined compounds (glucose, bovine serum albumin) to mesocosms receiving natural leaf leachate or water from different streams. Response variables included bacterial production, oxygen consumption, extracellular enzyme activity, and community similarity as manifest by changes in banding patterns of randomly amplified polymorphic DNA (RAPD). All DOM manipulations generated responses in at least one metabolic variable. Additions of both labile and recalcitrant materials increased either oxygen consumption, production, or both depending on background DOM. Enzyme activities were affected by both types of carbon addition with largest effects from the labile mixture. Cluster analysis of RAPD data showed strong divergence of communities exposed to labile versus recalcitrant DOM. Additions of leaf leachate to mesocosms representing hyporheic flow-paths caused increases in oxygen consumption and some enzyme activities with weaker effects on production. Community structure yeas strongly affected; samples from the leachate-amended mesocosms clustered separately from the control samples. In mesocosms receiving water from streams ranging in DOC (0.5-4.5 mg L-1), there were significant differences in bacterial growth, oxygen consumption, and enzyme activities. RAPD analysis showed strongest clustering of samples by stream type with more subtle effects of position along the flowpaths. Responses in community metabolism were always accompanied by shifts in community composition, suggesting carbon supply affects both functional and structural attributes of hyporheic bacterial communities.

Patterns in bacterial and archaeal community structure and diversity in western Beaufort Sea sediments and waters

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Sikaroodi, M.; Coffin, R. B.; Gillevet, P. M.

2010-12-01

A culture-independent phylogenetic study of microbial communities in water samples and sediment cores recovered from the Beaufort Sea slope east of Point Barrow, Alaska was conducted. The goal of the work was to describe community composition in sediment and water samples and determine the influence of local environmental conditions on microbial populations. Archaeal and bacterial community composition was studied using length heterogeneity-polymerase chain reaction (LH-PCR) and multitag pyrosequencing (MTPS). Sediment samples were obtained from three piston cores on the slope (~1000m depth) arrayed along an east-west transect and one core from a depth of approximately 2000m. Discrete water samples were obtained using a CTD-rosette from three locations adjacent to piston core sites. Water sample were selected at three discrete depths within a vertically stratified (density) water column. The microbial community in near surface waters was distinct from the community observed in deeper stratified layers of the water column. Multidimensional scaling analysis (MDS) revealed that water samples from mid and deep stratified layers bore high similarity to communities in cores collected in close proximity. Overall, the highest diversity (bacteria and archaea) was observed in a core which had elevated methane concentration relative to other locations. Geochemical (e.g., bulk organic and inorganic carbon pools, nutrients, metabolites) and physical data (e.g. depth, water content) were used to reveal the abiotic factors structuring microbial communities. The analysis indicates that sediment water content (porosity) and inorganic carbon concentration are the most significant structuring elements on Beaufort shelf sedimentary microbial communities.

Composition and diversity of weed communities in Al-Jouf province, northern Saudi Arabia

PubMed Central

Gomaa, Nasr H.

2012-01-01

The aim of this study was to identify the main weed communities in Al-Jouf province in northern Saudi Arabia. Moreover, the composition and diversity of these communities were studied in relation to soil variables and crop type. Some 54 stands representing olive orchards, date palm orchards, wheat crop and watermelon crop were studied, using ten quadrats (1 × 1 m) per stand. A total of 71 species belonging to 22 families and 61 genera were observed. The classification of vegetation using the Two Way Indicator Species Analysis (TWINSPAN) resulted in the recognition of four vegetation groups representing wheat crop, orchards in winter season, orchards in summer season and watermelon crop. These results suggested the importance of both crop and season for the formation of weed community. Detrended Correspondence Analysis (DCA) showed that these groups are clearly distinguished by the first two DCA axes. The species richness was higher in both olive and date palm orchards than in wheat and watermelon crops. This pattern of species richness could be related to farm management practices and habitat micro-heterogeneity. Soil electrical conductivity, organic carbon and soil texture showed significant correlations with species richness and the cover values of some dominant species, suggesting the significant role of soil characteristics in weed community structure and diversity. PMID:23961198

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

PubMed Central

Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

2017-01-01

The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries.

PubMed

Jangid, Kamlesh; Kao, Ming-Hung; Lahamge, Aishwarya; Williams, Mark A; Rathbun, Stephen L; Whitman, William B

2016-01-01

K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley's K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing.

CCLasso: correlation inference for compositional data through Lasso.

PubMed

Fang, Huaying; Huang, Chengcheng; Zhao, Hongyu; Deng, Minghua

2015-10-01

Direct analysis of microbial communities in the environment and human body has become more convenient and reliable owing to the advancements of high-throughput sequencing techniques for 16S rRNA gene profiling. Inferring the correlation relationship among members of microbial communities is of fundamental importance for genomic survey study. Traditional Pearson correlation analysis treating the observed data as absolute abundances of the microbes may lead to spurious results because the data only represent relative abundances. Special care and appropriate methods are required prior to correlation analysis for these compositional data. In this article, we first discuss the correlation definition of latent variables for compositional data. We then propose a novel method called CCLasso based on least squares with [Formula: see text] penalty to infer the correlation network for latent variables of compositional data from metagenomic data. An effective alternating direction algorithm from augmented Lagrangian method is used to solve the optimization problem. The simulation results show that CCLasso outperforms existing methods, e.g. SparCC, in edge recovery for compositional data. It also compares well with SparCC in estimating correlation network of microbe species from the Human Microbiome Project. CCLasso is open source and freely available from https://github.com/huayingfang/CCLasso under GNU LGPL v3. dengmh@pku.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

PCR-DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau.

PubMed

Han, Rui; Yuan, Yongze; Cao, Qianwen; Li, Quanhui; Chen, Laisheng; Zhu, Derui; Liu, Deli

2018-05-01

To investigate contribution of environmental factor(s) to microbial community structure(s) involved in rural household biogas fermentation at Qinghai Plateau, we collected slurry samples from 15 digesters, with low-temperature working conditions (11.1-15.7 °C) and evenly distributed at three counties (Datong, Huangyuan, and Ledu) with cold plateau climate, to perform polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and further sequencing. The bacterial communities in the total 15 digesters were classified into 38 genera with Mangroviflexus (12.1%) as the first dominant, and the archaeal communities into ten genera with Methanogenium (38.5%) as the most dominant. For each county, the digesters with higher biogas production, designated as HP digesters, exclusively had 1.6-3.1 °C higher fermentation temperature and the unique bacterial structure composition related, i.e., unclassified Clostridiales for all the HP digesters and unclassified Marinilabiliaceae and Proteiniclasticum for Ledu HP digesters. Regarding archaeal structure composition, Methanogenium exhibited significantly higher abundances at all the HP digesters and Thermogymnomonas was the unique species only identified at Ledu HP digesters with higher-temperature conditions. Redundancy analysis also confirmed the most important contribution of temperature to the microbial community structures investigated. This report emphasized the correlation between temperature and specific microbial community structure(s) that would benefit biogas production of rural household digesters at Qinghai Plateau.

Microbial community composition during anaerobic mineralization of tert-butyl alcohol (TBA) in fuel-contaminated aquifer material.

PubMed

Wei, Na; Finneran, Kevin T

2011-04-01

Anaerobic mineralization of tert-butyl alcohol (TBA) and methyl tert-butyl ether (MTBE) were studied in sediment incubations prepared with fuel-contaminated aquifer material. Microbial community compositions in all incubations were characterized by amplified ribosomal DNA restriction analysis (ARDRA). The aquifer material mineralized 42.3±9.9% of [U-(14)C]-TBA to 14CO2 without electron acceptor amendment. Fe(III), sulfate, and Fe(III) plus anthraquinone-2,6-disulfonate addition also promoted U-[14C]-TBA mineralization at levels similar to those of the unamended controls. Nitrate actually inhibited TBA mineralization relative to unamended controls. In contrast to TBA, [U-(14)C]-MTBE was not significantly mineralized in 400 days regardless of electron acceptor amendment. Microbial community analysis indicated that the abundance of one dominant clone group correlated closely with anaerobic TBA mineralization. The clone was phylogenetically distinct from known aerobic TBA-degrading microorganisms, Fe(III)- or sulfate-reducing bacteria. It was most closely associated with organisms belonging to the alphaproteobacteria. Microbial communities were different in MTBE and TBA amended incubations. Shannon indices and Simpson indices (statistical community comparison tools) both demonstrated that microbial community diversity decreased in incubations actively mineralizing TBA, with distinct "dominant" clones developing. These data contribute to our understanding of anaerobic microbial transformation of fuel oxygenates in contaminated aquifer material and the organisms that may catalyze the reactions.

Signals of Climate Change in Butterfly Communities in a Mediterranean Protected Area

PubMed Central

Zografou, Konstantina; Kati, Vassiliki; Grill, Andrea; Wilson, Robert J.; Tzirkalli, Elli; Pamperis, Lazaros N.; Halley, John M.

2014-01-01

The European protected-area network will cease to be efficient for biodiversity conservation, particularly in the Mediterranean region, if species are driven out of protected areas by climate warming. Yet, no empirical evidence of how climate change influences ecological communities in Mediterranean nature reserves really exists. Here, we examine long-term (1998–2011/2012) and short-term (2011–2012) changes in the butterfly fauna of Dadia National Park (Greece) by revisiting 21 and 18 transects in 2011 and 2012 respectively, that were initially surveyed in 1998. We evaluate the temperature trend for the study area for a 22-year-period (1990–2012) in which all three butterfly surveys are included. We also assess changes in community composition and species richness in butterfly communities using information on (a) species’ elevational distributions in Greece and (b) Community Temperature Index (calculated from the average temperature of species' geographical ranges in Europe, weighted by species' abundance per transect and year). Despite the protected status of Dadia NP and the subsequent stability of land use regimes, we found a marked change in butterfly community composition over a 13 year period, concomitant with an increase of annual average temperature of 0.95°C. Our analysis gave no evidence of significant year-to-year (2011–2012) variability in butterfly community composition, suggesting that the community composition change we recorded is likely the consequence of long-term environmental change, such as climate warming. We observe an increased abundance of low-elevation species whereas species mainly occurring at higher elevations in the region declined. The Community Temperature Index was found to increase in all habitats except agricultural areas. If equivalent changes occur in other protected areas and taxonomic groups across Mediterranean Europe, new conservation options and approaches for increasing species’ resilience may have to be devised. PMID:24489880

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

PubMed

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing.

Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days

PubMed Central

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2016-01-01

To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

Characterizing fish community diversity across Virginia landscapes: Prerequisite for conservation

USGS Publications Warehouse

Angermeier, P.L.; Winston, M.R.

1999-01-01

The number of community types occurring within landscapes is an important, but often unprotected, component of biological diversity. Generally applicable protocols for characterizing community diversity need to be developed to facilitate conservation. We used several multivariate techniques to analyze geographic variation in the composition of fish communities in Virginia streams. We examined relationships between community composition and six landscape variables: drainage basin, physiography, stream order, elevation, channel slope, and map coordinates. We compared patterns at two scales (statewide and subdrainage-specific) to assess sensitivity of community classification to spatial scale. We also compared patterns based on characterizing communities by species composition vs. ecological composition. All landscape variables explained significant proportions of the variance in community composition. Statewide, they explained 32% of the variance in species composition and 48% of the variance in ecological composition. Typical communities in each drainage or physiography were statistically distinctive. Communities in different combinations of drainage, physiography, and stream size were even more distinctive, but composition was strongly spatially autocorrelated. Ecological similarity and species similarity of community pairs were strongly related, but replacement by ecologically similar species was common among drainage-physiography combinations. Landscape variables explained significant proportions of variance in community composition within selected subdrainages, but proportions were less than at the statewide scale, and the explanatory power of individual variables varied considerably among subdrainages. Community variation within subdrainages appeared to be much more closely related to environmental variation than to replacement among ecologically similar species. Our results suggest that taxonomic and ecological characterizations of community composition are complementary; both are useful in a conservation context. Landscape features such as drainage, physiography, and water body size generally may provide a basis for assessing aquatic community diversity, especially in regions where the biota is poorly known. Systematic conservation of community types would be a major advance relative to most current conservation programs, which typically focus narrowly on populations of imperiled species. More effective conservation of aquatic biodiversity will require new approaches that recognize the value of both species and assemblages, and that emphasize protection of key landscape-scale processes.

Changes in the Composition of Drinking Water Bacterial Clone Libraries Introduced by Using Two Different 16S rRna Gene PCR Primers

EPA Science Inventory

Sequence analysis of 16S rRNA gene clone libraries is a popular tool used to describe the composition of natural microbial communities. Commonly, clone libraries are developed by direct cloning of 16S rRNA gene PCR products. Different primers are often employed in the initial amp...

Changes in the Composition of Drinking Water Bacterial Clone Libraries Introduced by Using Two Different 16S rRNA Gene PCR Primers

EPA Science Inventory

Sequence analysis of 16S rRNA gene clone libraries is a popular tool used to describe the composition of natural microbial communities. Commonly, clone libraries are developed by direct cloning of 16S rRNA gene PCR products. Different primers are often employed in the initial amp...

Bacterial community profile of contaminated soils in a typical antimony mining site.

PubMed

Wang, Ningning; Zhang, Suhuan; He, Mengchang

2018-01-01

The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb DGT , As DGT , potential ecological risk index (RI), TC, TN), among which pH, Sb DGT , and As DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

Aspect has a greater impact on alpine soil bacterial community structure than elevation.

PubMed

Wu, Jieyun; Anderson, Barbara J; Buckley, Hannah L; Lewis, Gillian; Lear, Gavin

2017-03-01

Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The Response of Heterotrophic Prokaryote and Viral Communities to Labile Organic Carbon Inputs Is Controlled by the Predator Food Chain Structure.

PubMed

Sandaa, Ruth-Anne; Pree, Bernadette; Larsen, Aud; Våge, Selina; Töpper, Birte; Töpper, Joachim P; Thyrhaug, Runar; Thingstad, Tron Frede

2017-08-23

Factors controlling the community composition of marine heterotrophic prokaryotes include organic-C, mineral nutrients, predation, and viral lysis. Two mesocosm experiments, performed at an Arctic location and bottom-up manipulated with organic-C, had very different results in community composition for both prokaryotes and viruses. Previously, we showed how a simple mathematical model could reproduce food web level dynamics observed in these mesocosms, demonstrating strong top-down control through the predator chain from copepods via ciliates and heterotrophic nanoflagellates. Here, we use a steady-state analysis to connect ciliate biomass to bacterial carbon demand. This gives a coupling of top-down and bottom-up factors whereby low initial densities of ciliates are associated with mineral nutrient-limited heterotrophic prokaryotes that do not respond to external supply of labile organic-C. In contrast, high initial densities of ciliates give carbon-limited growth and high responsiveness to organic-C. The differences observed in ciliate abundance, and in prokaryote abundance and community composition in the two experiments were in accordance with these predictions. Responsiveness in the viral community followed a pattern similar to that of prokaryotes. Our study provides a unique link between the structure of the predator chain in the microbial food web and viral abundance and diversity.

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau.

PubMed

Hu, Weigang; Zhang, Qi; Tian, Tian; Li, Dingyao; Cheng, Gang; Mu, Jing; Wu, Qingbai; Niu, Fujun; An, Lizhe; Feng, Huyuan

2016-05-01

Permafrost on the Qinghai-Tibet Plateau is one of the most sensitive regions to climate warming, thus characterizing its microbial diversity and community composition may be important for understanding their potential responses to climate changes. Here, we investigated the prokaryotic diversity in a 10-m-long permafrost core from the Qinghai-Tibet Plateau by restriction fragment length polymorphism analysis targeting the 16S rRNA gene. We detected 191 and 17 bacterial and archaeal phylotypes representing 14 and 2 distinct phyla, respectively. Proteobacteria was the dominant bacterial phylum, while archaeal communities were characterized by a preponderance of Thaumarchaeota. Some of prokaryotic phylotypes were closely related to characterized species involved in carbon and nitrogen cycles, including nitrogen fixation, methane oxidation and nitrification. However, the majority of the phylotypes were only distantly related to known taxa at order or species level, suggesting the potential of novel diversity. Additionally, both bacterial α diversity and community composition changed significantly with sampling depth, where these communities mainly distributed according to core horizons. Arthrobacter-related phylotypes presented at high relative abundance in two active layer soils, while the deeper permafrost soils were dominated by Psychrobacter-related clones. Changes in bacterial community composition were correlated with most measured soil variables, such as carbon and nitrogen contents, pH, and conductivity.

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

DOE PAGES

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley; ...

2017-06-28

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.« less

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Linz, Alexandra M.; Crary, Benjamin C.; Shade, Ashley

Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likelymore » reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “CandidatusOmnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.« less

Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

PubMed

Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

2014-03-01

Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

Metagenomic analysis of fungal diversity on strawberry plants and the effect of management practices on the fungal community structure of aerial organs

USDA-ARS?s Scientific Manuscript database

Metabarcoding, defined as Next Generation Sequencing (NGS) of amplicons of the ITS2 region (DNA barcode), was used to identify the composition of the fungal community on different strawberry organs i.e. leaves, flowers, and immature and mature fruits grown on a farm using disease and insect control ...

Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog.

PubMed

Reumer, Max; Harnisz, Monika; Lee, Hyo Jung; Reim, Andreas; Grunert, Oliver; Putkinen, Anuliina; Fritze, Hannu; Bodelier, Paul L E; Ho, Adrian

2018-02-01

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA -based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities. IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects. Copyright © 2018 American Society for Microbiology.

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

PubMed

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

2016-06-01

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

Development of a molecular approach to describe the composition of Trichoderma communities.

PubMed

Meincke, Remo; Weinert, Nicole; Radl, Viviane; Schloter, Michael; Smalla, Kornelia; Berg, Gabriele

2010-01-01

Trichoderma and its teleomorphic stage Hypocrea play a key role for ecosystem functioning in terrestrial habitats. However, little is known about the ecology of the fungus. In this study we developed a novel Trichoderma-specific primer pair for diversity analysis. Based on a broad range master alignment, specific Trichoderma primers (ITSTrF/ITSTrR) were designed that comprise an approximate 650bp fragment of the internal transcribed spacer region from all taxonomic clades of the genus Trichoderma. This amplicon is suitable for identification with TrichoKey and TrichoBLAST. Moreover, this primer system was successfully applied to study the Trichoderma communities in the rhizosphere of different potato genotypes grown at two field sites in Germany. Cloning and sequencing confirmed the specificity of the primer and revealed a site-dependent Trichoderma composition. Based on the new primer system a semi-nested approach was used to generate amplicons suitable for denaturing gradient gel electrophoresis (DGGE) analysis and applied to analyse Trichoderma communities in the rhizosphere of potatoes. High field heterogeneity of Trichoderma communities was revealed by both DGGE. Furthermore, qPCR showed significantly different Trichoderma copy numbers between the sites. Copyright 2009 Elsevier B.V. All rights reserved.

Relation of physical and chemical characteristics of streams to fish communities in the Red River of the North basin, Minnesota and North Dakota, 1993-95

USGS Publications Warehouse

Goldstein, R.M.; Stauffer, J.C.; Larson, P.R.; Lorenz, D.L.

1996-01-01

Within the instream habitat data set, measures of habitat volume (channel width and depth) and habitat diversity were most significant in explaining the variability of the fish communities. The amount of nonagricultural land and riparian zone integrity from the terrestrial habitat data set were also useful in explaining fish community composition. Variability of mean monthly discharge and the frequency of high and low discharge events during the three years prior to fish sampling were the most influential of the hydrologic variables.The first two axes of the canonical correspondence analysis accounted for 43.3 percent of the variation in the fish community and 52.5 percent of the variation in the environmental-species relation. Water-quality indicators such as the percent of fine material in suspended sediment, minimum dissolved oxygen concentrations, minimum concentrations of dissolved organic carbon, and the range of concentrations of major ions and nutrients were the variables that were most important in the canonical correspondence analysis of water-quality data with fish. No single environmental variable or data set appeared to be more important than another in explaining variation in the fish community. The environmental factors affecting the fish communities of the Red River of the North are interrelated. For the most part, instream environmental conditions (instream habitat, hydrology, and water chemistry) appear to be more important in explaining variability in fish community composition than factors related to the agricultural nature of the basin.

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar

PubMed Central

Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T.; Halpern, Malka

2015-01-01

Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness. PMID:26122961

Pyridine-type alkaloid composition affects bacterial community composition of floral nectar.

PubMed

Aizenberg-Gershtein, Yana; Izhaki, Ido; Santhanam, Rakesh; Kumar, Pavan; Baldwin, Ian T; Halpern, Malka

2015-06-30

Pyridine-type alkaloids are most common in Nicotiana species. To study the effect of alkaloid composition on bacterial community composition in floral nectar, we compared the nicotine-rich wild type (WT) N. attenuata, the nicotine biosynthesis-silenced N. attenuata that was rich in anatabine and the anabasine-rich WT N. glauca plants. We found that the composition of these secondary metabolites in the floral nectar drastically affected the bacterial community richness, diversity and composition. Significant differences were found between the bacterial community compositions in the nectar of the three plants with a much greater species richness and diversity in the nectar from the transgenic plant. The highest community composition similarity index was detected between the two wild type plants. The different microbiome composition and diversity, caused by the different pyridine-type alkaloid composition, could modify the nutritional content of the nectar and consequently, may contribute to the change in the nectar consumption and visitation. These may indirectly have an effect on plant fitness.

Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

PubMed Central

Hu, Ziye; Meng, Han; Shi, Jin-Huan; Bu, Nai-Shun; Fang, Chang-Ming; Quan, Zhe-Xue

2014-01-01

Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA) are much higher than that of ammonia oxidizing bacteria (AOB). The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition. PMID:25101072

Archaeal and bacterial community analysis of several Yellowstone National Park hot springs

NASA Astrophysics Data System (ADS)

Colman, D. R.; Takacs-Vesbach, C. D.

2012-12-01

The hot springs of Yellowstone National Park (YNP) are home to a diverse assemblage of microorganisms. Culture-independent studies have significantly expanded our understanding of the diversity of both Bacteria and Archaea present in YNP springs as well as the geochemical and ecological controls on communities. While the ecological analysis of Bacteria among the physicochemically heterogenous springs of YNP has been previously conducted, less is known about the extent of diversity of Archaeal communities and the chemical and ecological controls on their populations. Here we report a culture-independent analysis of 31 hot spring archaeal and bacterial communities of YNP springs using next generation sequencing. We found the phylogenetic diversity of Archaea to be generally comparable to that of co-occurring bacterial communities although overall, in the springs we investigated, diversity was higher for Bacteria than Archaea. Chemical and physical controls were similar for both domains with pH correlating most strongly with community composition. Community differences reflected the partitioning of taxonomic groups in low or high pH springs for both domains. Results will be discussed in a geochemical and ecological context.

Alteration of chromophoric dissolved organic matter by solar UV radiation causes rapid changes in bacterial community composition.

PubMed

Piccini, Claudia; Conde, Daniel; Pernthaler, Jakob; Sommaruga, Ruben

2009-09-01

We evaluated the effect of photochemical alterations of chromophoric dissolved organic matter (CDOM) on bacterial abundance, activity and community composition in a coastal lagoon of the Atlantic Ocean with high dissolved organic carbon concentration. On two occasions during the austral summer, bacteria-free water of the lagoon was exposed to different regions of the solar spectrum (full solar radiation, UV-A+PAR, PAR) or kept in the dark. Subsequently, dilution cultures were established with bacterioplankton from the lagoon that were incubated in the pre-exposed water for 5 h in the dark. Cell abundance, activity, and community composition of bacterioplankton were assessed before and after incubation in the different treatments. Changes in absorption, fluorescence, and DOC concentration were used as proxies for CDOM photoalteration. We found a significant CDOM photobleaching signal, DOC loss, as well as a stimulation of bacterial activity in the treatments pre-exposed to UV radiation, suggesting increased bioavailability of DOM. Bacterial community analysis by fluorescence in situ hybridization revealed that this stimulation was mainly accompanied by the specific enrichment of Alpha- and Betaproteobacteria. Thus, our results suggest that CDOM photoalteration not only stimulates bacterioplankton growth, but also induces rapid changes in bacterioplankton composition, which can be of relevance for ecosystem functioning, particularly considering present and future changes in the input of terrestrial CDOM to aquatic systems.

Composition of breeding bird communities in Gulf Coast Chenier Plain marshes: Effects of winter burning

USGS Publications Warehouse

Gabrey, S.W.; Afton, A.D.

2004-01-01

Marsh managers along the Gulf Coast Chenier Plain frequently use winter burns to alter marsh vegetation and improve habitat quality for wintering waterfowl. However, effects of these burns on marsh avifauna are not well documented. We recorded abundances of breeding bird species and vegetation structure in burned and unburned control marshes during one breeding season before (1996) and two breeding seasons after (1997, 1998) experimental winter burns. We used non-metric multidimensional scaling analysis to assess the extent and direction of changes in bird community compositions of burned and unburned control marshes and to investigate the influence of vegetation structure on bird community composition. Overall, we found that Seaside Sparrows (Emberizidae: Ammodramus maritimus [Wilson]) and Red-winged Blackbirds and Boat-tailed Grackles (Icteridae: Agelaius phoeniceus [L.] and Quiscalus major Vieillot, respectively) comprised > 85% of observed birds. In burned marshes during the first breeding season following experimental burns (1997), icterid abundance increased while Seaside Sparrow abundance decreased relative to pre-burn (1996) conditions. This pattern was reversed during the second breeding season post-burn. No obvious patterns of change in avian abundance were detected in unburned control marshes over the 3-year period. Qualitative changes in breeding bird community composition were related to effects of winter burning on percent cover of dead vegetation and Spartina patens (Aiton) Muhl.

Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.

PubMed

Alsop, Eric B; Boyd, Eric S; Raymond, Jason

2014-05-28

The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.

Microbial community changes as a possible factor controlling carbon sequestration in subsoil

NASA Astrophysics Data System (ADS)

Strücker, Juliane; Jörgensen, Rainer Georg

2015-04-01

In order to gain more knowledge regarding the microbial community and their influence on carbon sequestration in subsoil two depth profiles with different soil organic carbon (SOC) concentrations were sampled. The SOC concentrations developed naturally due to deposition and erosion. This experiment offers the opportunity to investigate to which extend natural SOC availability or other subsoil specific conditions influence the composition and the functional diversity of the microbial community and in return if there is any evidence how the microbial community composition affects carbon sequestration under these conditions. Soil samples were taken at four different depths on two neighbouring arable sites; one Kolluvisol with high SOC concentrations (8-12 g/kg) throughout the profile and one Luvisol with low SOC concentrations (3-4 g/kg) below 30 cm depth. The multi substrate induced respiration (MSIR) method was used to identify shifts in the functional diversity of the microbial community along the depth profiles. Amino sugars Muramic Acid and Glucosamine were measured as indicators for bacterial and fungal residues and ergosterol was determined as marker for saprotrophic fungi. The results of the discriminant analysis of the respiration values obtained from the 17 substrates used in the MSIR show that the substrate use in subsoil is different from the substrate use in topsoil. The amino sugar analysis and the ratio of ergosterol to microbial biomass C indicate that the fungal dominance of the microbial community decreases with depth. The results from this study support previous findings, which also observed decreasing fungal dominance with depth. Furthermore the MSIR approach shows clearly that not only the composition of the microbial community but also their substrate use changes with depth. Thus, a different microbial community with altered substrate requirements could be an important reason for enhanced carbon sequestration in subsoil. The fact that the MSIR was also able to differentiate between the two sites proves the assumption that resources are an important factor controlling the functional diversity of the microbial community, as abiotic factors are very similar for the two profiles, but the sites show a different depth gradient for SOC.

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

Diversity and Composition of Sulfate-Reducing Microbial Communities Based on Genomic DNA and RNA Transcription in Production Water of High Temperature and Corrosive Oil Reservoir

PubMed Central

Li, Xiao-Xiao; Liu, Jin-Feng; Zhou, Lei; Mbadinga, Serge M.; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

2017-01-01

Deep subsurface petroleum reservoir ecosystems harbor a high diversity of microorganisms, and microbial influenced corrosion is a major problem for the petroleum industry. Here, we used high-throughput sequencing to explore the microbial communities based on genomic 16S rDNA and metabolically active 16S rRNA analyses of production water samples with different extents of corrosion from a high-temperature oil reservoir. Results showed that Desulfotignum and Roseovarius were the most abundant genera in both genomic and active bacterial communities of all the samples. Both genomic and active archaeal communities were mainly composed of Archaeoglobus and Methanolobus. Within both bacteria and archaea, the active and genomic communities were compositionally distinct from one another across the different oil wells (bacteria p = 0.002; archaea p = 0.01). In addition, the sulfate-reducing microorganisms (SRMs) were specifically assessed by Sanger sequencing of functional genes aprA and dsrA encoding the enzymes adenosine-5′-phosphosulfate reductase and dissimilatory sulfite reductase, respectively. Functional gene analysis indicated that potentially active Archaeoglobus, Desulfotignum, Desulfovibrio, and Thermodesulforhabdus were frequently detected, with Archaeoglobus as the most abundant and active sulfate-reducing group. Canonical correspondence analysis revealed that the SRM communities in petroleum reservoir system were closely related to pH of the production water and sulfate concentration. This study highlights the importance of distinguishing the metabolically active microorganisms from the genomic community and extends our knowledge on the active SRM communities in corrosive petroleum reservoirs. PMID:28638372

Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest.

PubMed

Sun, Hui; Terhonen, Eeva; Kovalchuk, Andriy; Tuovila, Hanna; Chen, Hongxin; Oghenekaro, Abbot O; Heinonsalo, Jussi; Kohler, Annegret; Kasanen, Risto; Vasander, Harri; Asiegbu, Fred O

2016-05-01

Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P< 0.001) and tree species (P< 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (P< 0.04). The availability of soil nutrients (Ca [P= 0.002], Fe [P= 0.003], and P [P= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera of Agaricomycotina identified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest

PubMed Central

Terhonen, Eeva; Kovalchuk, Andriy; Tuovila, Hanna; Chen, Hongxin; Oghenekaro, Abbot O.; Heinonsalo, Jussi; Kohler, Annegret; Kasanen, Risto; Vasander, Harri; Asiegbu, Fred O.

2016-01-01

Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P < 0.001) and tree species (P < 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (P < 0.04). The availability of soil nutrients (Ca [P = 0.002], Fe [P = 0.003], and P [P = 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P < 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera of Agaricomycotina identified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands. PMID:26896139

Component Composition for Embedded Systems Using Semantic Aspect-Oriented Programming

DTIC Science & Technology

2004-10-01

real - time systems for the defense community. Our research focused on Real-Time Java implementation and analysis techniques. Real-Time Java is important for the defense community because it holds out the promise of enabling developers to apply COTS Java technology to specialized military embedded systems. It also promises to allow the defense community to utilize a large Java-literate workforce for building defense systems. Our research has delivered several techniques that may make Real-Time Java a better platform for developing embedded

Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken

PubMed Central

Lu, Jiangrang; Idris, Umelaalim; Harmon, Barry; Hofacre, Charles; Maurer, John J.; Lee, Margie D.

2003-01-01

The diversity of bacterial floras in the ilea and ceca of chickens that were fed a vegetarian corn-soy broiler diet devoid of feed additives was examined by analysis of 1,230 partial 16S rRNA gene sequences. Nearly 70% of sequences from the ileum were related to those of Lactobacillus, with the majority of the rest being related to Clostridiaceae (11%), Streptococcus (6.5%), and Enterococcus (6.5%). In contrast, Clostridiaceae-related sequences (65%) were the most abundant group detected in the cecum, with the other most abundant sequences being related to Fusobacterium (14%), Lactobacillus (8%), and Bacteroides (5%). Statistical analysis comparing the compositions of the different 16S rRNA libraries revealed that population succession occurred during some sampling periods. The significant differences among cecal libraries at 3 and 7 days of age, at 14 to 28 days of age, and at 49 days of age indicated that successions occurred from a transient community to one of increasing complexity as the birds aged. Similarly, the ileum had a stable bacterial community structure for birds at 7 to 21 days of age and between 21 to 28 days of age, but there was a very unique community structure at 3 and 49 days of age. It was also revealed that the composition of the ileal and cecal libraries did not significantly differ when the birds were 3 days old, and in fact during the first 14 days of age, the cecal microflora was a subset of the ileal microflora. After this time, the ileum and cecum had significantly different library compositions, suggesting that each region developed its own unique bacterial community as the bird matured. PMID:14602645

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

PubMed Central

Sullam, Karen E.; Essinger, Steven D.; Lozupone, Catherine A.; O’Connor, Michael P.; Rosen, Gail L.; Knight, Rob; Kilham, Susan S.; Russell, Jacob A.

2013-01-01

Symbiotic bacteria often help their hosts acquire nutrients from their diet, showing trends of co-evolution and independent acquisition by hosts from the same trophic levels. While these trends hint at important roles for biotic factors, the effects of the abiotic environment on symbiotic community composition remain comparably understudied. In this investigation, we examined the influence of abiotic and biotic factors on the gut bacterial communities of fish from different taxa, trophic levels and habitats. Phylogenetic and statistical analyses of 25 16S rRNA libraries revealed that salinity, trophic level and possibly host phylogeny shape the composition of fish gut bacteria. When analysed alongside bacterial communities from other environments, fish gut communities typically clustered with gut communities from mammals and insects. Similar consideration of individual phylotypes (vs. communities) revealed evolutionary ties between fish gut microbes and symbionts of animals, as many of the bacteria from the guts of herbivorous fish were closely related to those from mammals. Our results indicate that fish harbour more specialized gut communities than previously recognized. They also highlight a trend of convergent acquisition of similar bacterial communities by fish and mammals, raising the possibility that fish were the first to evolve symbioses resembling those found among extant gut fermenting mammals. PMID:22486918

Patterns of fish community composition along a river affected by agricultural and urban disturbance in south-central Chile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orrego, Rodrigo; Barra, Ricardo; Chiang, Gustavo

2008-03-01

Patterns of fish community composition in a south-central Chile river were investigated along the altitudinal-spatial and environmental gradient and as a function of anthropogenic factors. The spatial pattern of fish communities in different biocoenotic zones of the Chillan River is influenced by both natural factors such a hydrologic features, habitat, and feeding types, and also by water quality variables which can reduce the diversity and abundance of sensitive species. A principal component analysis incorporating both water quality parameters and biomarker responses of representative fish species was used to evaluate the status of fish communities along the spatial gradient of themore » stream. The abundance and diversity of the fish community changed from a low in the upper reaches where the low pollution-tolerant species such as salmonid dominated, to a reduced diversity in the lower reaches of the river where tolerant browser species such as cypriniformes dominated. Even though the spatial pattern of fish community structure is similar to that found for the Chilean Rivers, the structure of these communities is highly influenced by human disturbance, particularly along the lower reaches of the river.« less

From source to filter: changes in bacterial community composition during potable water treatment.

PubMed

Zanacic, Enisa; McMartin, Dena W; Stavrinides, John

2017-06-01

Rural communities rely on surface water reservoirs for potable water. Effective removal of chemical contaminants and bacterial pathogens from these reservoirs requires an understanding of the bacterial community diversity that is present. In this study, we carried out a 16S rRNA-based profiling approach to describe the bacterial consortia in the raw surface water entering the water treatment plants of 2 rural communities. Our results show that source water is dominated by the Proteobacteria, Bacteroidetes, and Cyanobacteria, with some evidence of seasonal effects altering the predominant groups at each location. A subsequent community analysis of transects of a biological carbon filter in the water treatment plant revealed a significant increase in the proportion of Proteobacteria, Acidobacteria, Planctomycetes, and Nitrospirae relative to raw water. Also, very few enteric coliforms were identified in either the source water or within the filter, although Mycobacterium was of high abundance and was found throughout the filter along with Aeromonas, Legionella, and Pseudomonas. This study provides valuable insight into bacterial community composition within drinking water treatment facilities, and the importance of implementing appropriate disinfection practices to ensure safe potable water for rural communities.

Changes in fungal communities along a boreal forest soil fertility gradient.

PubMed

Sterkenburg, Erica; Bahr, Adam; Brandström Durling, Mikael; Clemmensen, Karina E; Lindahl, Björn D

2015-09-01

Boreal forests harbour diverse fungal communities with decisive roles in decomposition and plant nutrition. Although changes in boreal plant communities along gradients in soil acidity and nitrogen (N) availability are well described, less is known about how fungal taxonomic and functional groups respond to soil fertility factors. We analysed fungal communities in humus and litter from 25 Swedish old-growth forests, ranging from N-rich Picea abies stands to acidic and N-poor Pinus sylvestris stands. 454-pyrosequencing of ITS2 amplicons was used to analyse community composition, and biomass was estimated by ergosterol analysis. Fungal community composition was significantly related to soil fertility at the levels of species, genera/orders and functional groups. Ascomycetes dominated in less fertile forests, whereas basidiomycetes increased in abundance in more fertile forests, both in litter and humus. The relative abundance of mycorrhizal fungi in the humus layer remained high even in the most fertile soils. Tolerance to acidity and nitrogen deficiency seems to be of greater importance than plant carbon (C) allocation patterns in determining responses of fungal communities to soil fertility, in old-growth boreal forests. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

PubMed Central

Hu, Yinhong; Dou, Xiaolin; Li, Juanyong; Li, Feng

2018-01-01

The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across areas with different types of land cover, and soil properties play a more important role than heavy metals. PMID:29545776

Structural Variation in the Bacterial Community Associated with Airborne Particulate Matter in Beijing, China, during Hazy and Nonhazy Days.

PubMed

Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

2018-05-01

The structural variation of the bacterial community associated with particulate matter (PM) was assessed in an urban area of Beijing during hazy and nonhazy days. Sampling for different PM fractions (PM 2.5 [<2.5 μm], PM 10 [<10 μm], and total suspended particulate) was conducted using three portable air samplers from September 2014 to February 2015. The airborne bacterial community in these samples was analyzed using the Illumina MiSeq platform with bacterium-specific primers targeting the 16S rRNA gene. A total of 1,707,072 reads belonging to 6,009 operational taxonomic units were observed. The airborne bacterial community composition was significantly affected by PM fractions ( R = 0.157, P < 0.01). In addition, the relative abundances of several genera significantly differed between samples with various haze levels; for example, Methylobacillus , Tumebacillus , and Desulfurispora spp. increased in heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature, SO 2 concentration, relative humidity, PM 10 concentration, and CO concentration were significant factors that associated with airborne bacterial community composition. Only six genera increased across PM 10 samples ( Dokdonella , Caenimonas , Geminicoccus , and Sphingopyxis ) and PM 2.5 samples ( Cellulomonas and Rhizobacter ), while a large number of taxa significantly increased in total suspended particulate samples, such as Paracoccus , Kocuria , and Sphingomonas Network analysis indicated that Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Overall, the findings presented here suggest that diverse airborne bacterial communities are associated with PM and provide further understanding of bacterial community structure in the atmosphere during hazy and nonhazy days. IMPORTANCE The results presented here represent an analysis of the airborne bacterial community associated with particulate matter (PM) and advance our understanding of the structural variation of these communities. We observed a shift in bacterial community composition with PM fractions but no significant difference with haze levels. This may be because the bacterial differences are obscured by high bacterial diversity in the atmosphere. However, we also observed that a few genera (such as Methylobacillus , Tumebacillus , and Desulfurispora ) increased significantly on heavy-haze days. In addition, Paracoccus , Rubellimicrobium , Kocuria , and Arthrobacter were the key genera in the airborne PM samples. Accurate and real-time techniques, such as metagenomics and metatranscriptomics, should be developed for a future survey of the relationship of airborne bacteria and haze. Copyright © 2018 American Society for Microbiology.

Alteration of Microbial Communities Colonizing Leaf Litter in a Temperate Woodland Stream by Growth of Trees under Conditions of Elevated Atmospheric CO2 ▿

PubMed Central

Kelly, John J.; Bansal, Amit; Winkelman, Jonathan; Janus, Lori R.; Hell, Shannon; Wencel, Marie; Belt, Patricia; Kuehn, Kevin A.; Rier, Steven T.; Tuchman, Nancy C.

2010-01-01

Elevated atmospheric CO2 can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO2 would result in changes in the size and composition of microbial communities colonizing leaves in a woodland stream. Three tree species, Populus tremuloides, Salix alba, and Acer saccharum, were grown under ambient (360 ppm) or elevated (720 ppm) CO2, and their leaves were incubated in a woodland stream. Elevated-CO2 treatment resulted in significant increases in the phenolic and tannin contents and C/N ratios of leaves. Microbial effects, which occurred only for P. tremuloides leaves, included decreased fungal biomass and decreased bacterial counts. Analysis of fungal and bacterial communities on P. tremuloides leaves via terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing revealed that fungal community composition was mostly unchanged by the elevated-CO2 treatment, whereas bacterial communities showed a significant shift in composition and a significant increase in diversity. Specific changes in bacterial communities included increased numbers of alphaproteobacterial and cytophaga-flavobacter-bacteroides (CFB) group sequences and decreased numbers of betaproteobacterial and firmicutes sequences, as well as a pronounced decrease in overall Gram-positive bacterial sequences. PMID:20543045

Alteration of microbial communities colonizing leaf litter in a temperate woodland stream by growth of trees under conditions of elevated atmospheric CO2.

PubMed

Kelly, John J; Bansal, Amit; Winkelman, Jonathan; Janus, Lori R; Hell, Shannon; Wencel, Marie; Belt, Patricia; Kuehn, Kevin A; Rier, Steven T; Tuchman, Nancy C

2010-08-01

Elevated atmospheric CO(2) can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO(2) would result in changes in the size and composition of microbial communities colonizing leaves in a woodland stream. Three tree species, Populus tremuloides, Salix alba, and Acer saccharum, were grown under ambient (360 ppm) or elevated (720 ppm) CO(2), and their leaves were incubated in a woodland stream. Elevated-CO(2) treatment resulted in significant increases in the phenolic and tannin contents and C/N ratios of leaves. Microbial effects, which occurred only for P. tremuloides leaves, included decreased fungal biomass and decreased bacterial counts. Analysis of fungal and bacterial communities on P. tremuloides leaves via terminal restriction fragment length polymorphism (T-RFLP) and clone library sequencing revealed that fungal community composition was mostly unchanged by the elevated-CO(2) treatment, whereas bacterial communities showed a significant shift in composition and a significant increase in diversity. Specific changes in bacterial communities included increased numbers of alphaproteobacterial and cytophaga-flavobacter-bacteroides (CFB) group sequences and decreased numbers of betaproteobacterial and firmicutes sequences, as well as a pronounced decrease in overall gram-positive bacterial sequences.

Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system.

PubMed

Douterelo, I; Sharpe, R L; Boxall, J B

2013-02-01

Microbial biofilms formed on the inner-pipe surfaces of drinking water distribution systems (DWDS) can alter drinking water quality, particularly if they are mechanically detached from the pipe wall to the bulk water, such as due to changes in hydraulic conditions. Results are presented here from applying 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene to investigate the influence of different hydrological regimes on bacterial community structure and to study the potential mobilisation of material from the pipe walls to the network using a full scale, temperature-controlled experimental pipeline facility accurately representative of live DWDS. Analysis of pyrosequencing and water physico-chemical data showed that habitat type (water vs. biofilm) and hydraulic conditions influenced bacterial community structure and composition in our experimental DWDS. Bacterial community composition clearly differed between biofilms and bulk water samples. Gammaproteobacteria and Betaproteobacteria were the most abundant phyla in biofilms while Alphaproteobacteria was predominant in bulk water samples. This suggests that bacteria inhabiting biofilms, predominantly species belonging to genera Pseudomonas, Zooglea and Janthinobacterium, have an enhanced ability to express extracellular polymeric substances to adhere to surfaces and to favour co-aggregation between cells than those found in the bulk water. Highest species richness and diversity were detected in 28 days old biofilms with this being accentuated at highly varied flow conditions. Flushing altered the pipe-wall bacterial community structure but did not completely remove bacteria from the pipe walls, particularly under highly varied flow conditions, suggesting that under these conditions more compact biofilms were generated. This research brings new knowledge regarding the influence of different hydraulic regimes on the composition and structure of bacterial communities within DWDS and the implication that this might have on drinking water quality. Copyright © 2012 Elsevier Ltd. All rights reserved.

Soil Microbe Active Community Composition and Capability of Responding to Litter Addition after 12 Years of No Inputs

PubMed Central

Brewer, Elizabeth; Yarwood, Rockie; Lajtha, Kate; Myrold, David

2013-01-01

One explanation given for the high microbial diversity found in soils is that they contain a large inactive biomass that is able to persist in soils for long periods of time. This persistent microbial fraction may help to buffer the functionality of the soil community during times of low nutrients by providing a reservoir of specialized functions that can be reactivated when conditions improve. A study was designed to test the hypothesis: in soils lacking fresh root or detrital inputs, microbial community composition may persist relatively unchanged. Upon addition of new inputs, this community will be stimulated to grow and break down litter similarly to control soils. Soils from two of the Detrital Input and Removal Treatments (DIRT) at the H. J. Andrews Experimental Forest, the no-input and control treatment plots, were used in a microcosm experiment where Douglas-fir needles were added to soils. After 3 and 151 days of incubation, soil microbial DNA and RNA was extracted and characterized using quantitative PCR (qPCR) and 454 pyrosequencing. The abundance of 16S and 28S gene copies and RNA copies did not vary with soil type or amendment; however, treatment differences were observed in the abundance of archaeal ammonia-oxidizing amoA gene abundance. Analysis of ∼110,000 bacterial sequences showed a significant change in the active (RNA-based) community between day 3 and day 151, but microbial composition was similar between soil types. These results show that even after 12 years of plant litter exclusion, the legacy of community composition was well buffered against a dramatic disturbance. PMID:23263952

Community Capacity for Watershed Conservation: A Quantitative Assessment of Indicators and Core Dimensions

NASA Astrophysics Data System (ADS)

Brinkman, Elliot; Seekamp, Erin; Davenport, Mae A.; Brehm, Joan M.

2012-10-01

Community capacity for watershed management has emerged as an important topic for the conservation of water resources. While much of the literature on community capacity has focused primarily on theory construction, there have been few efforts to quantitatively assess community capacity variables and constructs, particularly for watershed management and conservation. This study seeks to identify predictors of community capacity for watershed conservation in southwestern Illinois. A subwatershed-scale survey of residents from four communities located within the Lower Kaskaskia River watershed of southwestern Illinois was administered to measure three specific capacity variables: community empowerment, shared vision and collective action. Principal component analysis revealed key dimensions of each variable. Specifically, collective action was characterized by items relating to collaborative governance and social networks, community empowerment was characterized by items relating to community competency and a sense of responsibility and shared vision was characterized by items relating to perceptions of environmental threats, issues with development, environmental sense of place and quality of life. From the emerging factors, composite measures were calculated to determine the extent to which each variable contributed to community capacity. A stepwise regression revealed that community empowerment explained most of the variability in the composite measure of community capacity for watershed conservation. This study contributes to the theoretical understanding of community capacity by quantifying the role of collective action, community empowerment and shared vision in community capacity, highlighting the need for multilevel interaction to address watershed issues.

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

PubMed

Dassen, Sigrid; Cortois, Roeland; Martens, Henk; de Hollander, Mattias; Kowalchuk, George A; van der Putten, Wim H; De Deyn, Gerlinde B

2017-08-01

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Metagenomic analysis of microbial communities yields insight into impacts of nanoparticle design

NASA Astrophysics Data System (ADS)

Metch, Jacob W.; Burrows, Nathan D.; Murphy, Catherine J.; Pruden, Amy; Vikesland, Peter J.

2018-01-01

Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings. We observed that the gold-nanoparticle morphology imposes a stronger force in shaping the microbial community structure than does the surface coating. Trends were consistent in terms of the compositions of both taxonomic and functional genes, which include antibiotic resistance genes, metal resistance genes and gene-transfer elements associated with cell stress that are relevant to public health. Given that nanoparticle morphology remained constant, the potential influence of gold dissolution was minimal. Surface coating governed the nanoparticle partitioning between the bioparticulate and aqueous phases.

Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods.

PubMed

Tymensen, Lisa; Barkley, Cindy; McAllister, Tim A

2012-01-01

Protozoa are common inhabitants of the rumen where they play roles in host nutrition and methanogenesis. Knowledge of how changes in the composition of protozoa communities affect these processes is limited in part due to a lack of efficient methods for protozoa community analysis. In this study, a terminal-restriction fragment length polymorphism (T-RFLP) assay targeting the 18S rRNA gene was developed for comparative analysis of rumen protozoa communities. Comparison of diversity and structure of protozoa communities from hay-fed versus silage/grain-fed cattle via T-RFLP analysis yielded similar overall results to microscopy analysis. According to both methods, Entodinium spp. were more abundant in the silage/grain-fed cattle and protozoa diversity (as calculated using the Shannon index) was higher for the hay-fed cattle due to greater species evenness. Type B protozoa were more prevalent in the hay-fed cattle, whereas Type A protozoa were more prevalent in the silage/grain-fed cattle. Analysis of similarity (ANOSIM) indicated that the protozoa communities from hay-fed and silage/grain-fed cattle were different, and multivariate analysis indicated that pen mates (i.e., cattle fed the same diet and housed together) tended to have similar protozoa communities types. In summary, we present a T-RFLP method for analyzing rumen protozoa communities which complements traditional microscopy approaches but has the advantage of being amenable to high-throughput. Copyright © 2011. Published by Elsevier B.V.

Bacterial Community Shift and Coexisting/Coexcluding Patterns Revealed by Network Analysis in a Uranium-Contaminated Site after Bioreduction Followed by Reoxidation.

PubMed

Li, Bing; Wu, Wei-Min; Watson, David B; Cardenas, Erick; Chao, Yuanqing; Phillips, D H; Mehlhorn, Tonia; Lowe, Kenneth; Kelly, Shelly D; Li, Pengsong; Tao, Huchun; Tiedje, James M; Criddle, Craig S; Zhang, Tong

2018-05-01

A site in Oak Ridge, TN, USA, has sediments that contain >3% iron oxides and is contaminated with uranium (U). The U(VI) was bioreduced to U(IV) and immobilized in situ through intermittent injections of ethanol. It then was allowed to reoxidize via the invasion of low-pH (3.6 to 4.0), high-nitrate (up to 200 mM) groundwater back into the reduced zone for 1,383 days. To examine the biogeochemical response, high-throughput sequencing and network analysis were applied to characterize bacterial population shifts, as well as cooccurrence and coexclusion patterns among microbial communities. A paired t test indicated no significant changes of α-diversity for the bioactive wells. However, both nonmetric multidimensional scaling and analysis of similarity confirmed a significant distinction in the overall composition of the bacterial communities between the bioreduced and the reoxidized sediments. The top 20 major genera accounted for >70% of the cumulative contribution to the dissimilarity in the bacterial communities before and after the groundwater invasion. Castellaniella had the largest dissimilarity contribution (17.7%). For the bioactive wells, the abundance of the U(VI)-reducing genera Geothrix , Desulfovibrio , Ferribacterium , and Geobacter decreased significantly, whereas the denitrifying Acidovorax abundance increased significantly after groundwater invasion. Additionally, seven genera, i.e., Castellaniella , Ignavibacterium , Simplicispira , Rhizomicrobium , Acidobacteria Gp1, Acidobacteria Gp14, and Acidobacteria Gp23, were significant indicators of bioactive wells in the reoxidation stage. Canonical correspondence analysis indicated that nitrate, manganese, and pH affected mostly the U(VI)-reducing genera and indicator genera. Cooccurrence patterns among microbial taxa suggested the presence of taxa sharing similar ecological niches or mutualism/commensalism/synergism interactions. IMPORTANCE High-throughput sequencing technology in combination with a network analysis approach were used to investigate the stabilization of uranium and the corresponding dynamics of bacterial communities under field conditions with regard to the heterogeneity and complexity of the subsurface over the long term. The study also examined diversity and microbial community composition shift, the common genera, and indicator genera before and after long-term contaminated-groundwater invasion and the relationship between the target functional community structure and environmental factors. Additionally, deciphering cooccurrence and coexclusion patterns among microbial taxa and environmental parameters could help predict potential biotic interactions (cooperation/competition), shared physiologies, or habitat affinities, thus, improving our understanding of ecological niches occupied by certain specific species. These findings offer new insights into compositions of and associations among bacterial communities and serve as a foundation for future bioreduction implementation and monitoring efforts applied to uranium-contaminated sites. Copyright © 2018 American Society for Microbiology.

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession.

PubMed

Ortiz-Álvarez, Rüdiger; Fierer, Noah; de Los Ríos, Asunción; Casamayor, Emilio O; Barberán, Albert

2018-02-20

Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.

Analysis of Composition and Structure of Coastal to Mesopelagic Bacterioplankton Communities in the Northern Gulf of Mexico

PubMed Central

King, Gary M.; Smith, Conor B.; Tolar, Bradley; Hollibaugh, James T.

2013-01-01

16S rRNA gene amplicons were pyrosequenced to assess bacterioplankton community composition, diversity, and phylogenetic community structure for 17 stations in the northern Gulf of Mexico (nGoM) sampled in March 2010. Statistical analyses showed that samples from depths ≤100 m differed distinctly from deeper samples. SAR 11 α-Proteobacteria and Bacteroidetes dominated communities at depths ≤100 m, which were characterized by high α-Proteobacteria/γ-Proteobacteria ratios (α/γ > 1.7). Thaumarchaeota, Firmicutes, and δ-Proteobacteria were relatively abundant in deeper waters, and α/γ ratios were low (<1). Canonical correlation analysis indicated that δ- and γ-Proteobacteria, Thaumarchaeota, and Firmicutes correlated positively with depth; α-Proteobacteria and Bacteroidetes correlated positively with temperature and dissolved oxygen; Actinobacteria, β-Proteobacteria, and Verrucomicrobia correlated positively with a measure of suspended particles. Diversity indices did not vary with depth or other factors, which indicated that richness and evenness elements of bacterioplankton communities might develop independently of nGoM physical-chemical variables. Phylogenetic community structure as measured by the net relatedness (NRI) and nearest taxon (NTI) indices also did not vary with depth. NRI values indicated that most of the communities were comprised of OTUs more distantly related to each other in whole community comparisons than expected by chance. NTI values derived from phylogenetic distances of the closest neighbor for each OTU in a given community indicated that OTUs tended to occur in clusters to a greater extent than expected by chance. This indicates that “habitat filtering” might play an important role in nGoM bacterioplankton species assembly, and that such filtering occurs throughout the water column. PMID:23346078

Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi.

PubMed

Gacura, Matthew D; Sprockett, Daniel D; Heidenreich, Bess; Blackwood, Christopher B

2016-04-01

Fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this study we developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from 40 fungal genomes. The primers were used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senesced tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communities were up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystem type were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes. Copyright © 2016 Elsevier B.V. All rights reserved.

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops.

PubMed

Chen, Zhaojin; Zheng, Yuan; Ding, Chuanyu; Ren, Xuemin; Yuan, Jian; Sun, Feng; Li, Yuying

2017-11-01

Two energy crops (maize and soybean) were used in the remediation of cadmium-contaminated soils. These crops were used because they are fast growing, have a large biomass and are good sources for bioenergy production. The total accumulation of cadmium in maize and soybean plants was 393.01 and 263.24μg pot -1 , respectively. The rhizosphere bacterial community composition was studied by MiSeq sequencing. Phylogenetic analysis was performed using 16S rRNA gene sequences. The rhizosphere bacteria were divided into 33 major phylogenetic groups according to phyla. The dominant phylogenetic groups included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Bacteroidetes. Based on principal component analysis (PCA) and unweighted pair group with arithmetic mean (UPGMA) analysis, we found that the bacterial community was influenced by cadmium addition and bioenergy cropping. Three molecular ecological networks were constructed for the unplanted, soybean- and maize-planted bacterial communities grown in 50mgkg -1 cadmium-contaminated soils. The results indicated that bioenergy cropping increased the complexity of the bacterial community network as evidenced by a higher total number of nodes, the average geodesic distance (GD), the modularity and a shorter geodesic distance. Proteobacteria and Acidobacteria were the keystone bacteria connecting different co-expressed operational taxonomic units (OTUs). The results showed that bioenergy cropping altered the topological roles of individual OTUs and keystone populations. This is the first study to reveal the effects of bioenergy cropping on microbial interactions in the phytoremediation of cadmium-contaminated soils by network reconstruction. This method can greatly enhance our understanding of the mechanisms of plant-microbe-metal interactions in metal-polluted ecosystems. Copyright © 2017 Elsevier Inc. All rights reserved.

Tailoring community-based wellness initiatives with latent class analysis--Massachusetts Community Transformation Grant projects.

PubMed

Arcaya, Mariana; Reardon, Timothy; Vogel, Joshua; Andrews, Bonnie K; Li, Wenjun; Land, Thomas

2014-02-13

Community-based approaches to preventing chronic diseases are attractive because of their broad reach and low costs, and as such, are integral components of health care reform efforts. Implementing community-based initiatives across Massachusetts' municipalities presents both programmatic and evaluation challenges. For effective delivery and evaluation of the interventions, establishing a community typology that groups similar municipalities provides a balanced and cost-effective approach. Through a series of key informant interviews and exploratory data analysis, we identified 55 municipal-level indicators of 6 domains for the typology analysis. The domains were health behaviors and health outcomes, housing and land use, transportation, retail environment, socioeconomics, and demographic composition. A latent class analysis was used to identify 10 groups of municipalities based on similar patterns of municipal-level indicators across the domains. Our model with 10 latent classes yielded excellent classification certainty (relative entropy = .995, minimum class probability for any class = .871), and differentiated distinct groups of municipalities based on health-relevant needs and resources. The classes differentiated healthy and racially and ethnically diverse urban areas from cities with similar population densities and diversity but worse health outcomes, affluent communities from lower-income rural communities, and mature suburban areas from rapidly suburbanizing communities with different healthy-living challenges. Latent class analysis is a tool that may aid in the planning, communication, and evaluation of community-based wellness initiatives such as Community Transformation Grants projects administrated by the Centers for Disease Control and Prevention.

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre

PubMed Central

Bryant, Jessica A; Aylward, Frank O; Eppley, John M; Karl, David M; Church, Matthew J; DeLong, Edward F

2016-01-01

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces. PMID:26645474

Modeled hydrologic metrics show links between hydrology and the functional composition of stream assemblages.

PubMed

Patrick, Christopher J; Yuan, Lester L

2017-07-01

Flow alteration is widespread in streams, but current understanding of the effects of differences in flow characteristics on stream biological communities is incomplete. We tested hypotheses about the effect of variation in hydrology on stream communities by using generalized additive models to relate watershed information to the values of different flow metrics at gauged sites. Flow models accounted for 54-80% of the spatial variation in flow metric values among gauged sites. We then used these models to predict flow metrics in 842 ungauged stream sites in the mid-Atlantic United States that were sampled for fish, macroinvertebrates, and environmental covariates. Fish and macroinvertebrate assemblages were characterized in terms of a suite of metrics that quantified aspects of community composition, diversity, and functional traits that were expected to be associated with differences in flow characteristics. We related modeled flow metrics to biological metrics in a series of stressor-response models. Our analyses identified both drying and base flow instability as explaining 30-50% of the observed variability in fish and invertebrate community composition. Variations in community composition were related to variations in the prevalence of dispersal traits in invertebrates and trophic guilds in fish. The results demonstrate that we can use statistical models to predict hydrologic conditions at bioassessment sites, which, in turn, we can use to estimate relationships between flow conditions and biological characteristics. This analysis provides an approach to quantify the effects of spatial variation in flow metrics using readily available biomonitoring data. © 2017 by the Ecological Society of America.

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre.

PubMed

Bryant, Jessica A; Aylward, Frank O; Eppley, John M; Karl, David M; Church, Matthew J; DeLong, Edward F

2016-06-01

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria.

PubMed

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J; Thomas, David J

2017-09-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12-14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa.

Impact of enzymatic digestion on bacterial community composition in CF airway samples.

PubMed

Williamson, Kayla M; Wagner, Brandie D; Robertson, Charles E; Johnson, Emily J; Zemanick, Edith T; Harris, J Kirk

2017-01-01

Previous studies have demonstrated the importance of DNA extraction methods for molecular detection of Staphylococcus, an important bacterial group in cystic fibrosis (CF). We sought to evaluate the effect of enzymatic digestion (EnzD) prior to DNA extraction on bacterial communities identified in sputum and oropharyngeal swab (OP) samples from patients with CF. DNA from 81 samples (39 sputum and 42 OP) collected from 63 patients with CF was extracted in duplicate with and without EnzD. Bacterial communities were determined by rRNA gene sequencing, and measures of alpha and beta diversity were calculated. Principal Coordinate Analysis (PCoA) was used to assess differences at the community level and Wilcoxon Signed Rank tests were used to compare relative abundance (RA) of individual genera for paired samples with and without EnzD. Shannon Diversity Index (alpha-diversity) decreased in sputum and OP samples with the use of EnzD. Larger shifts in community composition were observed for OP samples (beta-diversity, measured by Morisita-Horn), whereas less change in communities was observed for sputum samples. The use of EnzD with OP swabs resulted in significant increase in RA for the genera Gemella ( p  < 0.01), Streptococcus ( p  < 0.01), and Rothia ( p  < 0.01). Staphylococcus ( p  < 0.01) was the only genus with a significant increase in RA from sputum, whereas the following genera decreased in RA with EnzD: Veillonella ( p  < 0.01), Granulicatella ( p  < 0.01), Prevotella ( p  < 0.01), and Gemella ( p  = 0.02). In OP samples, higher RA of Gram-positive taxa was associated with larger changes in microbial community composition. We show that the application of EnzD to CF airway samples, particularly OP swabs, results in differences in microbial communities detected by sequencing. Use of EnzD can result in large changes in bacterial community composition, and is particularly useful for detection of Staphylococcus in CF OP samples. The enhanced identification of Staphylococcus aureus is a strong indication to utilize EnzD in studies that use OP swabs to monitor CF airway communities.

Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

PubMed

Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

2017-12-01

Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ( 3 H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the existence of three particle types characterized by different bacterial communities in ETM, ETM-impacted, and non-ETM-impacted brackish waters. Taxonomic analysis suggests that ETM key biological function is to remineralize organic matter. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries

PubMed Central

Jangid, Kamlesh; Kao, Ming-Hung; Lahamge, Aishwarya; Williams, Mark A.; Rathbun, Stephen L.; Whitman, William B.

2016-01-01

K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley’s K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing. PMID:27911946

Rocky-shore communities as indicators of water quality: a case study in the Northwestern Mediterranean.

PubMed

Pinedo, Susana; García, María; Satta, Maria Paola; de Torres, Mariona; Ballesteros, Enric

2007-01-01

The collection of 152 samples from the upper sublittoral zone along the rocky coasts of Catalonia (Northwestern Mediterranean) was carried out in 1999 in order to test the suitability of littoral communities to be used as indicators of water quality in the frame of the European Water Framework Directive. Detrended correspondence analysis were performed to distinguish between different communities and to relate communities composition to water quality. Samples collected in reference sites were included in the analysis. Mediterranean rocky shore communities situated in the upper sublittoral zone can be used as indicators of the water quality: there is a gradient from high to bad status that comprises from dense Cystoseira mediterranea forests to green algae dominated communities. The geographical patterns in the distribution of these communities show that the best areas are situated in the Northern coast, where tourism is the main economic resource of the area, and the worst area is situated close to the metropolitan zone of Barcelona with high population and industrial development. Thus, Mediterranean sublittoral rocky shore communities are useful indicators of water quality and multivariate analysis are a suitable statistical tool for the assessment of the ecological status.

Integration of community structure data reveals observable effects below sediment guideline thresholds in a large estuary.

PubMed

Tremblay, Louis A; Clark, Dana; Sinner, Jim; Ellis, Joanne I

2017-09-20

The sustainable management of estuarine and coastal ecosystems requires robust frameworks due to the presence of multiple physical and chemical stressors. In this study, we assessed whether ecological health decline, based on community structure composition changes along a pollution gradient, occurred at levels below guideline threshold values for copper, zinc and lead. Canonical analysis of principal coordinates (CAP) was used to characterise benthic communities along a metal contamination gradient. The analysis revealed changes in benthic community distribution at levels below the individual guideline values for the three metals. These results suggest that field-based measures of ecological health analysed with multivariate tools can provide additional information to single metal guideline threshold values to monitor large systems exposed to multiple stressors.

The arthropod, but not the vertebrate host or its environment, dictates bacterial community composition of fleas and ticks

PubMed Central

Hawlena, Hadas; Rynkiewicz, Evelyn; Toh, Evelyn; Alfred, Andrew; Durden, Lance A; Hastriter, Michael W; Nelson, David E; Rong, Ruichen; Munro, Daniel; Dong, Qunfeng; Fuqua, Clay; Clay, Keith

2013-01-01

Bacterial community composition in blood-sucking arthropods can shift dramatically across time and space. We used 16S rRNA gene amplification and pyrosequencing to investigate the relative impact of vertebrate host-related, arthropod-related and environmental factors on bacterial community composition in fleas and ticks collected from rodents in southern Indiana (USA). Bacterial community composition was largely affected by arthropod identity, but not by the rodent host or environmental conditions. Specifically, the arthropod group (fleas vs ticks) determined the community composition of bacteria, where bacterial communities of ticks were less diverse and more dependent on arthropod traits—especially tick species and life stage—than bacterial communities of fleas. Our data suggest that both arthropod life histories and the presence of arthropod-specific endosymbionts may mask the effects of the vertebrate host and its environment. PMID:22739493

The impact of industrial anthropization on mosquito (Diptera, Culicidae) communities in mangrove areas of Guanabara Bay (Rio de Janeiro, Brazil).

PubMed

de Souza, A S; Couri, M S; Florindo, L

2012-02-01

The effects of industrial anthropization on species composition and community diversity of Culicidae (Diptera) were studied in a mangrove area impacted by industrial activities as compared to a preserved area, both around Guanabara Bay in the state of Rio de Janeiro, Brazil. Diversity, equitability, and species richness in Culicidae community differed between the studied areas. Indicator species analysis and correspondence analysis were carried out and indicated that the Sabethini, especially Wyeomyia (Phoniomyia) theobaldi Lane, Wyeomyia (Phoniomyia) fuscipes (Edwards), and a non-identified species of Wyeomyia sp. were associated to the preserved area, whereas Aedes taeniorhynchus Wiedemann and Aedes scapularis (Rondani) to the impacted area.

Resource availability controls fungal diversity across a plant diversity gradient

USGS Publications Warehouse

Waldrop, M.P.; Zak, D.R.; Blackwood, C.B.; Curtis, C.D.; Tilman, D.

2006-01-01

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales. ?? 2006 Blackwell Publishing Ltd/CNRS.

Intraspecies variation in a widely distributed tree species regulates the responses of soil microbiome to different temperature regimes.

PubMed

Zhang, Cui-Jing; Delgado-Baquerizo, Manuel; Drake, John E; Reich, Peter B; Tjoelker, Mark G; Tissue, David T; Wang, Jun-Tao; He, Ji-Zheng; Singh, Brajesh K

2018-04-01

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Z.; Deng, Y.; Van Nostrand, J.D.

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.more » 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.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

DOE PAGES

Rinke, Christian; Low, Serene; Woodcroft, Ben J.; ...

2016-09-22

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rinke, Christian; Low, Serene; Woodcroft, Ben J.

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

PubMed Central

Low, Serene; Raina, Jean-Baptiste; Skarshewski, Adam; Le, Xuyen H.; Butler, Margaret K.; Stocker, Roman; Seymour, Justin; Tyson, Gene W.

2016-01-01

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics. PMID:27688978

A decade of predatory control of zooplankton species composition of Lake Michigan

USGS Publications Warehouse

Makarewicz, Joseph C.; Bertram, Paul; Lewis, Theodore; Brown, Edward H.

1995-01-01

From 1983 to 1992, 71 species representing 38 genera from the Calanoida, Cladocera, Cyclopoida, Mysidacea, Rotifera, Mollusca and Harpacticoida comprised the offshore zooplankton community of Lake Michigan. Our data demonstrate that the composition and abundance of the calanoid community after 1983 is not unlike that of 1960s and that species diversity of the calanoid community is more diverse than the cladoceran community in the 1990s as compared to the early 1980s. Even though the relative biomass of the cladocerans has remained similar over the 1983-1993 period, the species diversity and evenness of the Cladocera community in the early 1990s is unlike anything that has been previously reported for Lake Michigan. Cladocera dominance is centered in one species, Daphnia galeata mendotae, and only three species of Cladocera were observed in the pelagic region of the lake in 1991 and 1992. Nutrient levels, phytoplankton biomass, and the abundance of planktivorous alewife and bloater chub and Bythotrephes are examined as possible causes of these changes in zooplankton species composition. The increase in Rotifera biomass, but not Crustacea, was correlated with an increase in relative biomass of unicellular algae. Food web models suggest Bythotrephes will cause Lake Michigan's plankton to return to a community similar to that of the 1970s; that is Diaptomus dominated. Such a change has occurred. However, correlational analysis suggest that alewife and bloater chubs (especially juveniles) are affecting size and biomass of larger species of zooplankton as well as Bythotrephes.

Microbial community structure and density under different tree species in an acid forest soil (Morvan, France).

PubMed

Lejon, David P H; Chaussod, Rémi; Ranger, Jacques; Ranjard, Lionel

2005-11-01

Overexploitation of forests to increase wood production has led to the replacement of native forest by large areas of monospecific tree plantations. In the present study, the effects of different monospecific tree cover plantations on density and composition of the indigenous soil microbial community are described. The experimental site of "Breuil-Chenue" in the Morvan (France) was the site of a comparison of a similar mineral soil under Norway spruce (Picea abies), Douglas fir (Pseudotuga menziesii), oak (Quercus sessiflora), and native forest [mixed stand dominated by oak and beech (Fagus sylvatica)]. Sampling was performed during winter (February) at three depths (0-5, 5-10, and 10-15 cm). Abundance of microorganisms was estimated via microbial biomass measurements, using the fumigation-extraction method. The genetic structure of microbial communities was investigated using the bacterial- and fungal-automated ribosomal intergenic spacer analysis (B-ARISA and F-ARISA, respectively) DNA fingerprint. Only small differences in microbial biomass were observed between tree species, the highest values being recorded under oak forest and the lowest under Douglas fir. B- and F-ARISA community profiles of the different tree covers clustered separately, but noticeable similarities were observed for soils under Douglas fir and oak. A significant stratification was revealed under each tree species by a decrease in microbial biomass with increasing depths and by distinct microbial communities for each soil layer. Differences in density and community composition according to tree species and depth were related to soil physicochemical characteristics and organic matter composition.

Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials.

PubMed

Ziganshin, Ayrat M; Liebetrau, Jan; Pröter, Jürgen; Kleinsteuber, Sabine

2013-06-01

The influence of the feedstock type on the microbial communities involved in anaerobic digestion was investigated in laboratory-scale biogas reactors fed with different agricultural waste materials. Community composition and dynamics over 2 months of reactors' operation were investigated by amplicon sequencing and profiling terminal restriction fragment length polymorphisms of 16S rRNA genes. Major bacterial taxa belonged to the Clostridia and Bacteroidetes, whereas the archaeal community was dominated by methanogenic archaea of the orders Methanomicrobiales and Methanosarcinales. Correlation analysis revealed that the community composition was mainly influenced by the feedstock type with the exception of a temperature shift from 38 to 55 °C which caused the most pronounced community shifts. Bacterial communities involved in the anaerobic digestion of conventional substrates such as maize silage combined with cattle manure were relatively stable and similar to each other. In contrast, special waste materials such as chicken manure or Jatropha press cake were digested by very distinct and less diverse communities, indicating partial ammonia inhibition or the influence of other inhibiting factors. Anaerobic digestion of chicken manure relied on syntrophic acetate oxidation as the dominant acetate-consuming process due to the inhibition of aceticlastic methanogenesis. Jatropha as substrate led to the enrichment of fiber-degrading specialists belonging to the genera Actinomyces and Fibrobacter.

Ants impact the composition of the aquatic macroinvertebrate communities of a myrmecophytic tank bromeliad.

PubMed

Dejean, Alain; Compin, Arthur; Leponce, Maurice; Azémar, Frédéric; Bonhomme, Camille; Talaga, Stanislas; Pelozuelo, Laurent; Hénaut, Yann; Corbara, Bruno

2018-03-01

In an inundated Mexican forest, 89 out of 92 myrmecophytic tank bromeliads (Aechmea bracteata) housed an associated ant colony: 13 sheltered Azteca serica, 43 Dolichoderus bispinosus, and 33 Neoponera villosa. Ant presence has a positive impact on the diversity of the aquatic macroinvertebrate communities (n=30 bromeliads studied). A Principal Component Analysis (PCA) showed that the presence and the species of ant are not correlated to bromeliad size, quantity of water, number of wells, filtered organic matter or incident radiation. The PCA and a generalized linear model showed that the presence of Azteca serica differed from the presence of the other two ant species or no ants in its effects on the aquatic invertebrate community (more predators). Therefore, both ant presence and species of ant affect the composition of the aquatic macroinvertebrate communities in the tanks of A. bracteata, likely due to ant deposition of feces and other waste in these tanks. Copyright © 2018. Published by Elsevier Masson SAS.

Patterns of vegetation and grasshopper community composition.

PubMed

Kemp, W P; Harvey, S J; O'Neill, K M

1990-06-01

A study was conducted to evaluate differences in rangeland grasshopper communities over environmental gradients in Gallatin Valley, Montana, USA. The concept of habitat type (Daubenmire 1966) was used as a basis for discriminating between groupings of patches based on vegetation. A total of 39 patches were selected that represented five recognized grassland habitat types (Mueggler and Stewart 1980), as well as two disturbed types (replanting within a known habitat type). Repeated sampling in 1988 of both the insect and plant communities yielded a total of 40 grasshopper (19 664 individuals) and 97 plant species. Detrended Correspondence Analysis (DCA) indicated that patch classifications based on presence and percent cover of plants were appropriate and showed good between-group (habitat type) separation for patches along gradients of precipitation/elevation and plant community complexity. Results from undisturbed habitats showed that plant and grasshopper species composition changed over observed environmental gradients and suggested that habitat type influenced not only species presence, but also relative abundance. Discussion is presented that relates results with patch-use and core and satellite species paradigms.

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

PubMed Central

Franzenburg, Sören; Walter, Jonas; Künzel, Sven; Wang, Jun; Baines, John F.; Bosch, Thomas C. G.; Fraune, Sebastian

2013-01-01

Animals are colonized by coevolved bacterial communities, which contribute to the host’s health. This commensal microbiota is often highly specific to its host-species, inferring strong selective pressures on the associated microbes. Several factors, including diet, mucus composition, and the immune system have been proposed as putative determinants of host-associated bacterial communities. Here we report that species-specific antimicrobial peptides account for different bacterial communities associated with closely related species of the cnidarian Hydra. Gene family extensions for potent antimicrobial peptides, the arminins, were detected in four Hydra species, with each species possessing a unique composition and expression profile of arminins. For functional analysis, we inoculated arminin-deficient and control polyps with bacterial consortia characteristic for different Hydra species and compared their selective preferences by 454 pyrosequencing of the bacterial microbiota. In contrast to control polyps, arminin-deficient polyps displayed decreased potential to select for bacterial communities resembling their native microbiota. This finding indicates that species-specific antimicrobial peptides shape species-specific bacterial associations. PMID:24003149

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions.

PubMed

Szabó, Attila; Korponai, Kristóf; Kerepesi, Csaba; Somogyi, Boglárka; Vörös, Lajos; Bartha, Dániel; Márialigeti, Károly; Felföldi, Tamás

2017-05-01

Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties. Results showed a taxonomically complex bacterial community which was distinct from other soda lakes regarding its composition, e.g. the dominance of class Alphaproteobacteria was observed within phylum Proteobacteria. The shotgun metagenomic analysis revealed several functional gene components related to the harsh and at the same time hypertrophic environmental conditions, e.g. proteins involved in stress response, transport and hydrolase systems targeting phytoplankton-derived organic matter. This is the first detailed report on the indigenous planktonic bacterial communities coping with the multiple extreme conditions present in the unique soda pans of the Pannonian steppe.

Impact of protists on a hydrocarbon-degrading bacterial community from deep-sea Gulf of Mexico sediments: A microcosm study

NASA Astrophysics Data System (ADS)

Beaudoin, David J.; Carmichael, Catherine A.; Nelson, Robert K.; Reddy, Christopher M.; Teske, Andreas P.; Edgcomb, Virginia P.

2016-07-01

In spite of significant advancements towards understanding the dynamics of petroleum hydrocarbon degrading microbial consortia, the impacts (direct or indirect via grazing activities) of bacterivorous protists remain largely unknown. Microcosm experiments were used to examine whether protistan grazing affects the petroleum hydrocarbon degradation capacity of a deep-sea sediment microbial community from an active Gulf of Mexico cold seep. Differences in n-alkane content between native sediment microcosms and those treated with inhibitors of eukaryotes were assessed by comprehensive two-dimensional gas chromatography following 30-90 day incubations and analysis of shifts in microbial community composition using small subunit ribosomal RNA gene clone libraries. More biodegradation was observed in microcosms supplemented with eukaryotic inhibitors. SSU rRNA gene clone libraries from oil-amended treatments revealed an increase in the number of proteobacterial clones (particularly γ-proteobacteria) after spiking sediments with diesel oil. Bacterial community composition shifted, and degradation rates increased, in treatments where protists were inhibited, suggesting protists affect the hydrocarbon degrading capacity of microbial communities in sediments collected at this Gulf of Mexico site.

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water.

PubMed

Tang, Junying; Bu, Yuanqing; Zhang, Xu-Xiang; Huang, Kailong; He, Xiwei; Ye, Lin; Shan, Zhengjun; Ren, Hongqiang

2016-10-01

The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river. Copyright © 2016 Elsevier Inc. All rights reserved.

Microbial ecological associations in the surface sediments of Bohai strait

NASA Astrophysics Data System (ADS)

Wang, Bin; Liu, Hongmei; Tang, Haitian; Hu, Xiaoke

2017-09-01

Microbial communities play key roles in the marine ecosystem. Despite a few studies on marine microbial communities in deep straits, ecological associations among microbial communities in the sediments of shallow straits have not been fully investigated. The Bohai Strait in northern China (average depth less than 20 m) separates the Bohai Sea from the Yellow Sea and has organic-rich sediments. In this study, in the summer of 2014, six stations across the strait were selected to explore the taxonomic composition of microbial communities and their ecological associations. The four most abundant classes were Gammaproteobacteria, Deltaproteobacteria, Bacilli and Flavobacteriia. Temperature, total carbon, depth, nitrate, fishery breeding and cold water masses influenced the microbial communities, as suggested by representational difference and composition analyses. Network analysis of microbial associations revealed that key families included Flavobacteriaceae, Pirellulaceae and Piscirickettsiaceae. Our findings suggest that the families with high phylogenetic diversity are key populations in the microbial association network that ensure the stability of microbial ecosystems. Our study contributes to a better understanding of microbial ecology in complex hydrological environments.

Pyrosequencing reveals bacterial community differences in composting and vermicomposting on the stabilization of mixed sewage sludge and cattle dung.

PubMed

Lv, Baoyi; Xing, Meiyan; Yang, Jian; Zhang, Liangbo

2015-12-01

This study aimed to compare the microbial community structures and compositions in composting and vermicomposting processes. We applied 454 high-throughput pyrosequencing to analyze the 16S rRNA gene of bacteria obtained from bio-stabilization of sewage sludge and cattle dung. Results demonstrated that vermicomposting process presented higher operational taxonomic units and bacterial diversity than the composting. Analysis using weighted UniFrac indicated that composting exhibited higher effects on shaping microbial community structure than the vermicomposting. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting and shifted to Actinomycetes in the maturing stage. By contrast, Proteobacteria accounted for the highest proportions in the whole process of the vermicomposting. Furthermore, vermicomposting contained more uncultured and unidentified bacteria at the taxonomy level of genus than the composting. In summary, the bacterial community during composting significantly differed from that during vermicomposting. These two techniques played different roles in changing the diversity and composition of microbial communities.

Community composition of known and uncultured archaeal lineages in anaerobic or anoxic wastewater treatment sludge.

PubMed

Kuroda, Kyohei; Hatamoto, Masashi; Nakahara, Nozomi; Abe, Kenichi; Takahashi, Masanobu; Araki, Nobuo; Yamaguchi, Takashi

2015-04-01

Microbial systems are widely used to treat different types of wastewater from domestic, agricultural, and industrial sources. Community composition is an important factor in determining the successful performance of microbial treatment systems; however, a variety of uncultured and unknown lineages exist in sludge that requires identification and characterization. The present study examined the archaeal community composition in methanogenic, denitrifying, and nitrogen-/phosphate-removing wastewater treatment sludge by Archaea-specific 16S rRNA gene sequencing analysis using Illumina sequencing technology. Phylotypes belonging to Euryarchaeota, including methanogens, were most abundant in all samples except for nitrogen-/phosphate-removing wastewater treatment sludge. High levels of Deep Sea Hydrothermal Vent Group 6 (DHVEG-6), WSA2, Terrestrial Miscellaneous Euryarchaeotal Group, and Miscellaneous Crenarchaeotic Group were also detected. Interestingly, DHVEG-6 was dominant in nitrogen-/phosphate-removing wastewater treatment sludge, indicating that unclear lineages of Archaea still exist in the anaerobic wastewater treatment sludges. These results reveal a previously unknown diversity of Archaea in sludge that can potentially be exploited for the development of more efficient wastewater treatment strategies.

Stable and Variable Parts of Microbial Community in Siberian Deep Subsurface Thermal Aquifer System Revealed in a Long-Term Monitoring Study

PubMed Central

Frank, Yulia A.; Kadnikov, Vitaly V.; Gavrilov, Sergey N.; Banks, David; Gerasimchuk, Anna L.; Podosokorskaya, Olga A.; Merkel, Alexander Y.; Chernyh, Nikolai A.; Mardanov, Andrey V.; Ravin, Nikolai V.; Karnachuk, Olga V.; Bonch-Osmolovskaya, Elizaveta A.

2016-01-01

The goal of this work was to study the diversity of microorganisms inhabiting a deep subsurface aquifer system in order to understand their functional roles and interspecies relations formed in the course of buried organic matter degradation. A microbial community of a deep subsurface thermal aquifer in the Tomsk Region, Western Siberia was monitored over the course of 5 years via a 2.7 km deep borehole 3P, drilled down to a Palaeozoic basement. The borehole water discharges with a temperature of ca. 50°C. Its chemical composition varies, but it steadily contains acetate, propionate, and traces of hydrocarbons and gives rise to microbial mats along the surface flow. Community analysis by PCR-DGGE 16S rRNA genes profiling, repeatedly performed within 5 years, revealed several dominating phylotypes consistently found in the borehole water, and highly variable diversity of prokaryotes, brought to the surface with the borehole outflow. The major planktonic components of the microbial community were Desulfovirgula thermocuniculi and Methanothermobacter spp. The composition of the minor part of the community was unstable, and molecular analysis did not reveal any regularity in its variations, except some predominance of uncultured Firmicutes. Batch cultures with complex organic substrates inoculated with water samples were set in order to enrich prokaryotes from the variable part of the community. PCR-DGGE analysis of these enrichments yielded uncultured Firmicutes, Chloroflexi, and Ignavibacteriae. A continuous-flow microaerophilic enrichment culture with a water sample amended with acetate contained Hydrogenophilus thermoluteolus, which was previously detected in the microbial mat developing at the outflow of the borehole. Cultivation results allowed us to assume that variable components of the 3P well community are hydrolytic organotrophs, degrading buried biopolymers, while the constant planktonic components of the community degrade dissolved fermentation products to methane and CO2, possibly via interspecies hydrogen transfer. Occasional washout of minor community components capable of oxygen respiration leads to the development of microbial mats at the outflow of the borehole where residual dissolved fermentation products are aerobically oxidized. Long-term community analysis with the combination of molecular and cultivation techniques allowed us to characterize stable and variable parts of the community and propose their environmental roles. PMID:28082967

Does stability in local community composition depend on temporal variation in rates of dispersal and connectivity?

NASA Astrophysics Data System (ADS)

Valanko, Sebastian; Norkko, Joanna; Norkko, Alf

2015-04-01

In ecology understanding variation in connectivity is central for how biodiversity is maintained. Field studies on dispersal and temporal dynamics in community regulating processes are, however, rare. We test the short-term temporal stability in community composition in a soft-sediment benthic community by determining among-sampling interval similarity in community composition. We relate stability to in situ measures of connectivity (wind, wave, current energy) and rates of dispersal (quantified in different trap types). Waves were an important predictor of when local community taxa are most likely to disperse in different trap-types, suggesting that wave energy is important for connectivity in a region. Community composition at the site was variable and changed stochastically over time. We found changes in community composition (occurrence, abundance, dominance) to be greater at times when connectivity and rates of dispersal were low. In response to periods of lower connectedness dominant taxa in the local community only exhibited change in their relative abundance. In contrast, locally less abundant taxa varied in both their presence, as well as in relative abundance. Constancy in connectivity and rates of dispersal promotes community stability and persistence, suggesting that local community composition will be impacted by changes in the spatial extent over which immigration and emigration operates in the region. Few empirical studies have actually measured dispersal directly in a multi-species context to demonstrate the role it plays in maintaining local community structure. Even though our study does not evaluate coexistence over demographic time scales, it importantly demonstrates that dispersal is not only important in initial recruitment or following a disturbance, but also key in maintaining local community composition.

Comparison of Microbial Community Compositions of Injection and Production Well Samples in a Long-Term Water-Flooded Petroleum Reservoir

PubMed Central

Ren, Hong-Yan; Zhang, Xiao-Jun; Song, Zhi-yong; Rupert, Wieger; Gao, Guang-Jun; Guo, Sheng-xue; Zhao, Li-Ping

2011-01-01

Water flooding plays an important role in recovering oil from depleted petroleum reservoirs. Exactly how the microbial communities of production wells are affected by microorganisms introduced with injected water has previously not been adequately studied. Using denaturing gradient gel electrophoresis (DGGE) approach and 16S rRNA gene clone library analysis, the comparison of microbial communities is carried out between one injection water and two production waters collected from a working block of the water-flooded Gudao petroleum reservoir located in the Yellow River Delta. DGGE fingerprints showed that the similarities of the bacterial communities between the injection water and production waters were lower than between the two production waters. It was also observed that the archaeal composition among these three samples showed no significant difference. Analysis of the 16S rRNA gene clone libraries showed that the dominant groups within the injection water were Betaproteobacteria, Gammaproteobacteria and Methanomicrobia, while the dominant groups in the production waters were Gammaproteobacteria and Methanobacteria. Only 2 out of 54 bacterial operational taxonomic units (OTUs) and 5 out of 17 archaeal OTUs in the injection water were detected in the production waters, indicating that most of the microorganisms introduced by the injection water may not survive to be detected in the production waters. Additionally, there were 55.6% and 82.6% unique OTUs in the two production waters respectively, suggesting that each production well has its specific microbial composition, despite both wells being flooded with the same injection water. PMID:21858049

Effects of habitat management treatments on plant community composition and biomass in a Montane wetland

USGS Publications Warehouse

Austin, J.E.; Keough, J.R.; Pyle, W.H.

2007-01-01

Grazing and burning are commonly applied practices that can impact the diversity and biomass of wetland plant communities. We evaluated the vegetative response of wetlands and adjacent upland grasslands to four treatment regimes (continuous idle, fall prescribed burning followed by idle, annual fall cattle grazing, and rotation of summer grazing and idle) commonly used by the U.S. Fish and Wildlife Service. Our study area was Grays Lake, a large, montane wetland in southeastern Idaho that is bordered by extensive wet meadows. We identified seven plant cover types, representing the transition from dry meadow to deep wetland habitats: mixed deep marsh, spikerush slough, Baltic rush (Juncus balticus), moist meadow, alkali, mesic meadow, and dry meadow. We compared changes in community composition and total aboveground biomass of each plant cover type between 1998, when all units had been idled for three years, and 1999 (1 yr post-treatment) and 2000 (2 yr post-treatment). Analysis using non-metric multidimensional scaling indicated that compositional changes varied among cover types, treatments, and years following treatment. Treatment-related changes in community composition were greatest in mixed deep marsh, Baltic rush, and mesic meadow. In mixed deep marsh and Baltic rush, grazing and associated trampling contributed to changes in the plant community toward more open water and aquatic species and lower dominance of Baltic rush; grazing and trampling also seemed to contribute to increased cover in mesic meadow. Changing hydrological conditions, from multiple years of high water to increasing drought, was an important factor influencing community composition and may have interacted with management treatments. Biomass differed among treatments and between years within cover types. In the wettest cover types, fall burning and grazing rotation treatments had greater negative impact on biomass than the idle treatment, but in drier cover types, summer grazing stimulated biomass production. Our results illustrate the spatial and temporal complexity of the transition between dry meadow and wetland habitats, and variable interactions among plant communities, treatments, and annual wetland conditions. ?? 2007, The Society of Wetland Scientists.

Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea)

PubMed Central

Delport, Tiffany C.; Power, Michelle L.; Harcourt, Robert G.; Webster, Koa N.

2016-01-01

ABSTRACT Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria. The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability. PMID:27037116

Molecular analysis of long-term biofilm formation on PVC and cast iron surfaces in drinking water distribution system.

PubMed

Liu, Ruyin; Zhu, Junge; Yu, Zhisheng; Joshi, DevRaj; Zhang, Hongxun; Lin, Wenfang; Yang, Min

2014-04-01

To understand the impacts of different plumbing materials on long-term biofilm formation in water supply system, we analyzed microbial community compositions in the bulk water and biofilms on faucets with two different materials-polyvinyl chloride (PVC) and cast iron, which have been frequently used for more than10 years. Pyrosequencing was employed to describe both bacterial and eukaryotic microbial compositions. Bacterial communities in the bulk water and biofilm samples were significantly different from each other. Specific bacterial populations colonized on the surface of different materials. Hyphomicrobia and corrosion associated bacteria, such as Acidithiobacillus spp., Aquabacterium spp., Limnobacter thiooxidans, and Thiocapsa spp., were the most dominant bacteria identified in the PVC and cast iron biofilms, respectively, suggesting that bacterial colonization on the material surfaces was selective. Mycobacteria and Legionella spp. were common potential pathogenic bacteria occurred in the biofilm samples, but their abundance was different in the two biofilm bacterial communities. In contrast, the biofilm samples showed more similar eukaryotic communities than the bulk water. Notably, potential pathogenic fungi, i.e., Aspergillus spp. and Candida parapsilosis, occurred in similar abundance in both biofilms. These results indicated that microbial community, especially bacterial composition was remarkably affected by the different pipe materials (PVC and cast iron). Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Bacterial diversity and composition in the fluid of pitcher plants of the genus Nepenthes.

PubMed

Takeuchi, Yayoi; Chaffron, Samuel; Salcher, Michaela M; Shimizu-Inatsugi, Rie; Kobayashi, Masaki J; Diway, Bibian; von Mering, Christian; Pernthaler, Jakob; Shimizu, Kentaro K

2015-07-01

Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by ≥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria. Copyright © 2015 The Authors. Published by Elsevier GmbH.. All rights reserved.

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yan, Qingyun; Stegen, James C.; Yu, Yuhe

Uncovering which environmental factors have the greatest influence on community diversity patterns and how ecological processes govern community turnover are key questions related to understanding community assembly mechanisms. Although we have good understanding of plant and animal community assembly, the mechanisms regulating diversity patterns of aquatic bacterial communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long time-series study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing. We found strong repeatable seasonal patterns for the overall community, common (detected in more than 50% samples) and dominant bacterial taxa (relativemore » abundance > 1%). Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is an important environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern across the main lake areas was overwhelmed by temporal variability in this eutrophic lake system. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection, suggesting that the bacterioplankton communities are mainly controlled by niche-based processes. However, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout this lake system. This study gives us important insights into community assembly and seasonal turnover of lake bacterioplankton, it may be also useful to predict temporal patterns of other planktonic communities.« less

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

PubMed Central

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

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

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

PubMed

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

2016-01-01

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

Seasonality in the dung beetle community in a Brazilian tropical dry forest: Do small changes make a difference?

PubMed

Medina, Anderson Matos; Lopes, Priscila Paixão

2014-01-01

Dung beetle (Coleoptera: Scarabaeoidea: Scarabaeinae) activity is influenced by rainfall seasonality. We hypothesized that rainfall might also play a major role in regulating the community structure of this group. In this study, we describe seasonal changes in the richness, composition, and structure of the Scarabaeinae community in a Brazilian tropical dry forest. A fragment of arboreal Caatinga was sampled using baited pitfall traps during the early dry season (EDS), late dry season (LDS), early wet season (EWS), and middle wet season (MWS). We compared the dung beetle community in each season in relationship to species richness, rank-dominance, curves, and composition. We collected 1352 Scarabaeinae individuals , belonging to 15 species. Dichotomius aff. laevicollis Felsche (Coleoptera: Scarabaeidae) was the dominant species, representing 73.89% of the individuals. There were no seasonal changes in the rank dominance curves; all had a single dominant species and a few species with low abundance, typical for arid areas. Estimated richness was highest in MWS, followed by EWS. Dry-season samples (EDS and LDS) had lower richness, with no significant difference between the dry seasons. Although species richness increased as the habitat became wetter, the difference between the wet and dry seasons was small, which differs completely from the findings of other studies in Neotropical dry forests, where almost all species cease activities in the dry season. Species composition changes were found in non-metric multidimensional scaling and sustained by analysis of similarity. All the seasons had pairwise differences in composition, with the exception of EDS and MWS, which indicates that the dung beetle community in this fragment requires more than three months of drought to trigger changes in species composition; this is probably due to small changes in the forest canopy. There was no difference in composition between EDS and MWS. As in other tropical dry forests, although to a lesser extent, the dung beetle community of this fragment responded to rainfall seasonality with changes in species composition and reduced species richness. Such responses, even to this lesser extent, may occur because of small changes in tree cover and minor microclimate changes. This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed.

Microbial community dynamics of an urban drinking water distribution system subjected to phases of chloramination and chlorination treatments.

PubMed

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L; LeChevallier, Mark W; Liu, Wen-Tso

2012-11-01

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations, Cyanobacteria, Methylobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae were more abundant in chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine.

Microbial Community Dynamics of an Urban Drinking Water Distribution System Subjected to Phases of Chloramination and Chlorination Treatments

PubMed Central

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L.; LeChevallier, Mark W.

2012-01-01

Water utilities in parts of the U.S. control microbial regrowth in drinking water distribution systems (DWDS) by alternating postdisinfection methods between chlorination and chloramination. To examine how this strategy influences drinking water microbial communities, an urban DWDS (population ≅ 40,000) with groundwater as the source water was studied for approximately 2 years. Water samples were collected at five locations in the network at different seasons and analyzed for their chemical and physical characteristics and for their microbial community composition and structure by examining the 16S rRNA gene via terminal restriction fragment length polymorphism and DNA pyrosequencing technology. Nonmetric multidimension scaling and canonical correspondence analysis of microbial community profiles could explain >57% of the variation. Clustering of samples based on disinfection types (free chlorine versus combined chlorine) and sampling time was observed to correlate to the shifts in microbial communities. Sampling location and water age (<21.2 h) had no apparent effects on the microbial compositions of samples from most time points. Microbial community analysis revealed that among major core populations, Cyanobacteria, Methylobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae were more abundant in chlorinated water, and Methylophilaceae, Methylococcaceae, and Pseudomonadaceae were more abundant in chloraminated water. No correlation was observed with minor populations that were detected frequently (<0.1% of total pyrosequences), which were likely present in source water and survived through the treatment process. Transient microbial populations including Flavobacteriaceae and Clostridiaceae were also observed. Overall, reversible shifts in microbial communities were especially pronounced with chloramination, suggesting stronger selection of microbial populations from chloramines than chlorine. PMID:22941076

Ectomycorrhizal communities of ponderosa pine and lodgepole pine in the south-central Oregon pumice zone.

PubMed

Garcia, Maria O; Smith, Jane E; Luoma, Daniel L; Jones, Melanie D

2016-05-01

Forest ecosystems of the Pacific Northwest of the USA are changing as a result of climate change. Specifically, rise of global temperatures, decline of winter precipitation, earlier loss of snowpack, and increased summer drought are altering the range of Pinus contorta. Simultaneously, flux in environmental conditions within the historic P. contorta range may facilitate the encroachment of P. ponderosa into P. contorta territory. Furthermore, successful pine species migration may be constrained by the distribution or co-migration of ectomycorrhizal fungi (EMF). Knowledge of the linkages among soil fungal diversity, community structure, and environmental factors is critical to understanding the organization and stability of pine ecosystems. The objectives of this study were to establish a foundational knowledge of the EMF communities of P. ponderosa and P. contorta in the Deschutes National Forest, OR, USA, and to examine soil characteristics associated with community composition. We examined EMF root tips of P. ponderosa and P. contorta in soil cores and conducted soil chemistry analysis for P. ponderosa cores. Results indicate that Cenococcum geophilum, Rhizopogon salebrosus, and Inocybe flocculosa were dominant in both P. contorta and P. ponderosa soil cores. Rhizopogon spp. were ubiquitous in P. ponderosa cores. There was no significant difference in the species composition of EMF communities of P. ponderosa and P. contorta. Ordination analysis of P. ponderosa soils suggested that soil pH, plant-available phosphorus (Bray), total phosphorus (P), carbon (C), mineralizable nitrogen (N), ammonium (NH4), and nitrate (NO3) are driving EMF community composition in P. ponderosa stands. We found a significant linear relationship between EMF species richness and mineralizable N. In conclusion, P. ponderosa and P. contorta, within the Deschutes National Forest, share the same dominant EMF species, which implies that P. ponderosa may be able to successfully establish within the historic P. contorta range and dominant EMF assemblages may be conserved.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Analysis of Bacterial Community Composition of Corroded Steel Immersed in Sanya and Xiamen Seawaters in China via Method of Illumina MiSeq Sequencing

PubMed Central

Li, Xiaohong; Duan, Jizhou; Xiao, Hui; Li, Yongqian; Liu, Haixia; Guan, Fang; Zhai, Xiaofan

2017-01-01

Metal corrosion is of worldwide concern because it is the cause of major economic losses, and because it creates significant safety issues. The mechanism of the corrosion process, as influenced by bacteria, has been studied extensively. However, the bacterial communities that create the biofilms that form on metals are complicated, and have not been well studied. This is why we sought to analyze the composition of bacterial communities living on steel structures, together with the influence of ecological factors on these communities. The corrosion samples were collected from rust layers on steel plates that were immersed in seawater for two different periods at Sanya and Xiamen, China. We analyzed the bacterial communities on the samples by targeted 16S rRNA gene (V3–V4 region) sequencing using the Illumina MiSeq. Phylogenetic analysis revealed that the bacteria fell into 13 phylotypes (similarity level = 97%). Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla, accounting for 88.84% of the total. Deltaproteobacteria, Clostridia and Gammaproteobacteria were the dominant classes, and accounted for 70.90% of the total. Desulfovibrio spp., Desulfobacter spp. and Desulfotomaculum spp. were the dominant genera and accounted for 45.87% of the total. These genera are sulfate-reducing bacteria that are known to corrode steel. Bacterial diversity on the 6 months immersion samples was much higher than that of the samples that had been immersed for 8 years (P < 0.001, Student’s t-test). The average complexity of the biofilms from the 8-years immersion samples from Sanya was greater than those from Xiamen, but not significantly so (P > 0.05, Student’s t-test). Overall, the data showed that the rust layers on the steel plates carried many bacterial species. The bacterial community composition was influenced by the immersion time. The results of our study will be of benefit to the further studies of bacterial corrosion mechanisms and corrosion resistance. PMID:28955315

Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

PubMed Central

Pereira-Marques, Joana; Pinto-Ribeiro, Ines; Costa, Jose L; Carneiro, Fatima; Machado, Jose C

2018-01-01

Objective Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastric carcinoma. Design The gastric microbiota was retrospectively investigated in 54 patients with gastric carcinoma and 81 patients with chronic gastritis by 16S rRNA gene profiling, using next-generation sequencing. Differences in microbial composition of the two patient groups were assessed using linear discriminant analysis effect size. Associations between the most relevant taxa and clinical diagnosis were validated by real-time quantitative PCR. Predictive functional profiling of microbial communities was obtained with PICRUSt. Results The gastric carcinoma microbiota was characterised by reduced microbial diversity, by decreased abundance of Helicobacter and by the enrichment of other bacterial genera, mostly represented by intestinal commensals. The combination of these taxa into a microbial dysbiosis index revealed that dysbiosis has excellent capacity to discriminate between gastritis and gastric carcinoma. Analysis of the functional features of the microbiota was compatible with the presence of a nitrosating microbial community in carcinoma. The major observations were confirmed in validation cohorts from different geographic origins. Conclusions Detailed analysis of the gastric microbiota revealed for the first time that patients with gastric carcinoma exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of patients with chronic gastritis. PMID:29102920

Diet compositions and trophic guild structure of the eastern Chukchi Sea demersal fish community

NASA Astrophysics Data System (ADS)

Whitehouse, George A.; Buckley, Troy W.; Danielson, Seth L.

2017-01-01

Fishes are an important link in Arctic marine food webs, connecting production of lower trophic levels to apex predators. We analyzed 1773 stomach samples from 39 fish species collected during a bottom trawl survey of the eastern Chukchi Sea in the summer of 2012. We used hierarchical cluster analysis of diet dissimilarities on 21 of the most well sampled species to identify four distinct trophic guilds: gammarid amphipod consumers, benthic invertebrate generalists, fish and shrimp consumers, and zooplankton consumers. The trophic guilds reflect dominant prey types in predator diets. We used constrained analysis of principal coordinates (CAP) to determine if variation within the composite guild diets could be explained by a suite of non-diet variables. All CAP models explained a significant proportion of the variance in the diet matrices, ranging from 7% to 25% of the total variation. Explanatory variables tested included latitude, longitude, predator length, depth, and water mass. These results indicate a trophic guild structure is present amongst the demersal fish community during summer in the eastern Chukchi Sea. Regular monitoring of the food habits of the demersal fish community will be required to improve our understanding of the spatial, temporal, and interannual variation in diet composition, and to improve our ability to identify and predict the impacts of climate change and commercial development on the structure and functioning of the Chukchi Sea ecosystem.

Microbial community biofabrics in a geothermal mine adit.

PubMed

Spear, John R; Barton, Hazel A; Robertson, Charles E; Francis, Christopher A; Pace, Norman R

2007-10-01

Speleothems such as stalactites and stalagmites are usually considered to be mineralogical in composition and origin; however, microorganisms have been implicated in the development of some speleothems. We have identified and characterized the biological and mineralogical composition of mat-like biofabrics in two novel kinds of speleothems from a 50 degrees C geothermal mine adit near Glenwood Springs, CO. One type of structure consists of 2- to 3-cm-long, 3- to 4-mm-wide, leather-like, hollow, soda straw stalactites. Light and electron microscopy indicated that the stalactites are composed of a mineralized biofabric with several cell morphotypes in a laminated form, with gypsum and sulfur as the dominant mineral components. A small-subunit rRNA gene phylogenetic community analysis along the stalactite length yielded a diverse gradient of organisms, with a relatively simple suite of main constituents: Thermus spp., crenarchaeotes, Chloroflexi, and Gammaproteobacteria. PCR analysis also detected putative crenarchaeal ammonia monooxygenase subunit A (amoA) genes in this community, the majority related to sequences from other geothermal systems. The second type of speleothem, dumpling-like rafts floating on a 50 degrees C pool on the floor of the adit, showed a mat-like fabric of evidently living organisms on the outside of the dumpling, with a multimineral, amorphous, gypsum-based internal composition. These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments.

Qualitative Analysis of Microbial Dynamics during Anaerobic Digestion of Microalgal Biomass in a UASB Reactor

PubMed Central

Doloman, Anna; Soboh, Yousef; Walters, Andrew J.; Sims, Ronald C.

2017-01-01

Anaerobic digestion (AD) is a microbiologically coordinated process with dynamic relationships between bacterial players. Current understanding of dynamic changes in the bacterial composition during the AD process is incomplete. The objective of this research was to assess changes in bacterial community composition that coordinates with anaerobic codigestion of microalgal biomass cultivated on municipal wastewater. An upflow anaerobic sludge blanket reactor was used to achieve high rates of microalgae decomposition and biogas production. Samples of the sludge were collected throughout AD and extracted DNA was subjected to next-generation sequencing using methanogen mcrA gene specific and universal bacterial primers. Analysis of the data revealed that samples taken at different stages of AD had varying bacterial composition. A group consisting of Bacteroidales, Pseudomonadales, and Enterobacteriales was identified to be putatively responsible for the hydrolysis of microalgal biomass. The methanogenesis phase was dominated by Methanosarcina mazei. Results of observed changes in the composition of microbial communities during AD can be used as a road map to stimulate key bacterial species identified at each phase of AD to increase yield of biogas and rate of substrate decomposition. This research demonstrates a successful exploitation of methane production from microalgae without any biomass pretreatment. PMID:29259629

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

PubMed Central

Williams, Ryan J.; Howe, Adina; Hofmockel, Kirsten S.

2014-01-01

Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied across multiple ecosystems or multiple scales of biological organization within the same study. Here we outline an approach to produce co-occurrence analyses that are focused at three different scales: co-occurrence patterns between ecosystems at the community scale, modules of co-occurring microorganisms within communities, and co-occurring pairs within modules that are nested within microbial communities. To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. We found differences in community composition and co-occurrence that reflect environmental filtering at the community scale and consistent pairwise occurrences that may be used to infer ecological traits about poorly understood microbial taxa. However, we also found that conclusions derived from applying network statistics to microbial relationships can vary depending on the taxonomic level chosen and criteria used to build co-occurrence networks. We present our statistical analysis and code for public use in analysis of co-occurrence patterns across microbial communities. PMID:25101065

Urban stormwater runoff drives denitrifying community composition through changes in sediment texture and carbon content.

PubMed

Perryman, Shane E; Rees, Gavin N; Walsh, Christopher J; Grace, Michael R

2011-05-01

The export of nitrogen from urban catchments is a global problem, and denitrifying bacteria in stream ecosystems are critical for reducing in-stream N. However, the environmental factors that control the composition of denitrifying communities in streams are not well understood. We determined whether denitrifying community composition in sediments of nine streams on the eastern fringe of Melbourne, Australia was correlated with two measures of catchment urban impact: effective imperviousness (EI, the proportion of a catchment covered by impervious surfaces with direct connection to streams) or septic tank density (which affects stream water chemistry, particularly stream N concentrations). Denitrifying community structure was examined by comparing terminal restriction fragment length polymorphisms of nosZ genes in the sediments, as the nosZ gene codes for nitrous oxide reductase, the last step in the denitrification pathway. We also determined the chemical and physical characteristics of the streams that were best correlated with denitrifying community composition. EI was strongly correlated with community composition and sediment physical and chemical properties, while septic tank density was not. Sites with high EI were sandier, with less fine sediment and lower organic carbon content, higher sediment cations (calcium, sodium and magnesium) and water filterable reactive phosphorus concentrations. These were also the best small-scale environmental variables that explained denitrifying community composition. Among our study streams, which differed in the degree of urban stormwater impact, sediment grain size and carbon content are the most likely drivers of change in community composition. Denitrifying community composition is another in a long list of ecological indicators that suggest the profound degradation of streams is caused by urban stormwater runoff. While the relationships between denitrifying community composition and denitrification rates are yet to be unequivocally established, landscape-scale indices of environmental impact such as EI may prove to be useful indicators of change in microbial communities.

Effect of reclamation of abandoned salinized farmland on soil bacterial communities in arid northwest China.

PubMed

Cheng, Zhibo; Chen, Yun; Zhang, Fenghua

2018-07-15

Understanding the impact of reclamation of abandoned salinized farmland on soil bacterial community is of great importance for maintaining soil health and sustainability in arid regions. In this study, we used field sampling and 454 pyrosequencing methods to investigate the effects of 5-year reclamation treatments on soil properties, bacterial community composition and diversity. The four reclamation treatments are: abandoned salinized farmland (CK), cropland (CL), grassland (GL) and woodland (WL). We have found soil properties are significantly altered by abandoned salinized farmland reclamation. In particular, the lowest soil pH and electrical conductivity (EC) values are observed in CL (P<0.05). The dominant phyla are Firmicutes, Proteobacteria, Chloroflexi, Actinobacteria and Acidobacteria in all treatments. At the genus levels, the relative abundance of Bacillus, Lactococcus, Streptococcus and Enterococcus in CK, GL and WL is significantly higher than in CL. Bacterial diversity indices (i.e. ACE, Chao and Shannon) dramatically increase after the reclamation, with the highest in CL. Similar patterns of bacterial communities have been observed in CK, GL and WL soils, but significantly different from CL. Regression analyses indicate that the relative abundance of these phyla are significantly correlated with soil Fe, pH and EC. Results from non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) indicate that soil Fe content, EC and pH are the most important factors in shaping soil bacterial communities. Overall, results indicate that abandoned salinized farmland reclaimed for CL significantly decrease soil pH and EC, and increase soil bacterial community diversity. Soil Fe concentration, EC and pH are the dominant environmental factors affecting soil bacterial community composition. The important role of Fe concentration in shaping bacterial community composition is a new discovery among the similar studies. Copyright © 2018. Published by Elsevier B.V.

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

PubMed

Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

2013-07-01

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation.

PubMed

McGuire, Krista L; Fierer, Noah; Bateman, Carling; Treseder, Kathleen K; Turner, Benjamin L

2012-05-01

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6 months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.

Microbial composition and diversity are associated with plant performance: a case study on long-term fertilization effect on wheat growth in an Ultisol.

PubMed

Li, Lihua; Fan, Fenliang; Song, Alin; Yin, Chang; Cui, Peiyuan; Li, Zhaojun; Liang, Yongchao

2017-06-01

The association between microbial communities and plant growth in long-term fertilization system has not been fully studied. In the present study, impacts of long-term fertilization have been determined on the size and activity of soil microbial communities and wheat performance in a red soil (Ultisol) collected from Qiyang Experimental Station, China. For this, different microbial communities originating from long-term fertilized pig manure (M), mineral fertilizer (NPK), pig manure plus mineral fertilizer (MNPK), and no fertilizer (CK) were used as inocula for the Ultisol tested. Changes in total bacterial and fungal community composition and structures using Ion Torrent sequencing were determined. The results show that the biomass of wheat was significantly higher in both sterilized soil inoculated with NPK (SNPK) and sterilized soil inoculated with MNPK (SMNPK) treatments than in other treatments (P < 0.05). The activities of β-1,4-N-acetylglucosaminidase (NAG) and cellobiohydrolase (CBH) were significantly correlated with wheat biomass. Among the microbial communities, the largest Ascomycota phylum in soils was negatively correlated with β-1,4-glucosidase (βG) (P < 0.05). The phylum Basidiomycota was negatively correlated with plant biomass (PB) and tillers per plant (TI) (P < 0.05). Nonmetric multidimensional scaling analysis shows that fungal community was strongly correlated with long-term fertilization strategy, while the bacterial community was strongly correlated with β-1,4-N-acetylglucosaminidase activity. According to the Mantel test, the growth of wheat was affected by fungal community. Taken together, microbial composition and diversity in soils could be a good player in predicting soil fertility and consequently plant growth.

Do honeybees shape the bacterial community composition in floral nectar?

PubMed

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers' nectar, but not from those in the uncovered flowers' nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves.

Soil bacterial diversity in degraded and restored lands of Northeast Brazil.

PubMed

Araújo, Ademir Sérgio Ferreira; Borges, Clovis Daniel; Tsai, Siu Mui; Cesarz, Simone; Eisenhauer, Nico

2014-11-01

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.

Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

PubMed Central

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

Deposition and postdeposition mechanisms as possible drivers of microbial population variability in glacier ice.

PubMed

Xiang, Shu-Rong; Shang, Tian-Cui; Chen, Yong; Yao, Tan-Dong

2009-11-01

Glaciers accumulate airborne microorganisms year by year and thus are good archives of microbial communities and their relationship to climatic and environmental changes. Hypotheses have focused on two possible drivers of microbial community composition in glacier systems. One is aeolian deposition, in which the microbial load by aerosol, dust, and precipitation events directly determines the amount and composition of microbial species in glacier ice. The other is postdepositional selection, in which the metabolic activity in surface snow causes microbial community shifts in glacier ice. An additional possibility is that both processes occur simultaneously. Aeolian deposition initially establishes a microbial community in the ice, whereas postdeposition selection strengthens the deposition patterns of microorganisms with the development of tolerant species in surface snow, resulting in varying structures of microbial communities with depth. In this minireview, we examine these postulations through an analysis of physical-chemical and biological parameters from the Malan and Vostok ice cores, and the Kuytun 51 Glacial surface and deep snow. We discuss these and other recent results in the context of the hypothesized mechanisms driving microbial community succession in glaciers. We explore our current gaps in knowledge and point out future directions for research on microorganisms in glacial ecosystems.

Microbial community succession in alkaline, saline bauxite residue: a cross-refinery study

NASA Astrophysics Data System (ADS)

Santini, T.; Malcolm, L. I.; Tyson, G. W.; Warren, L. A.

2015-12-01

Bauxite residue, a byproduct of the Bayer process for alumina refining, is an alkaline, saline tailings material that is generally considered to be inhospitable to microbial life. In situ remediation strategies promote soil formation in bauxite residue by enhancing leaching of saline, alkaline pore water, and through incorporation of amendments to boost organic matter content, decrease pH, and improve physical structure. The amelioration of chemical and physical conditions in bauxite residue is assumed to support diversification of microbial communities from narrow, poorly functioning microbial communities towards diverse, well-functioning communities. This study aimed to characterise microbial communities in fresh and remediated bauxite residues from refineries worldwide, to identify (a) whether initial microbial communities differed between refineries; (b) major environmental controls on microbial community composition; and (c) whether remediation successfully shifts the composition of microbial communities in bauxite residue towards those found in reference (desired endpoint) soils. Samples were collected from 16 refineries and characterised using 16S amplicon sequencing to examine microbial community composition and structure, in conjunction with physicochemical analyses. Initial microbial community composition was similar across refineries but partitioned into two major groups. Microbial community composition changes slowly over time and indicates that alkalinity and salinity inhibit diversification. Microbially-based strategies for in situ remediation should consider the initial microbial community composition and whether the pre-treatment of chemical properties would optimise subsequent bioremediation outcomes. During in situ remediation, microbial communities become more diverse and develop wider functional capacity, indicating progression towards communities more commonly observed in natural grassland and forest soils.

Biogas Production from Protein-Rich Biomass: Fed-Batch Anaerobic Fermentation of Casein and of Pig Blood and Associated Changes in Microbial Community Composition

PubMed Central

Kovács, Etelka; Wirth, Roland; Maróti, Gergely; Bagi, Zoltán; Rákhely, Gábor; Kovács, Kornél L.

2013-01-01

It is generally accepted as a fact in the biogas technology that protein-rich biomass substrates should be avoided due to inevitable process inhibition. Substrate compositions with a low C/N ratio are considered difficult to handle and may lead to process failure, though protein-rich industrial waste products have outstanding biogas generation potential. This common belief has been challenged by using protein-rich substrates, i.e. casein and precipitated pig blood protein in laboratory scale continuously stirred mesophilic fed-batch biogas fermenters. Both substrates proved suitable for sustained biogas production (0.447 L CH4/g protein oDM, i.e. organic total solids) in high yield without any additives, following a period of adaptation of the microbial community. The apparent key limiting factors in the anaerobic degradation of these proteinaceous materials were the accumulation of ammonia and hydrogen sulfide. Changes in time in the composition of the microbiological community were determined by next-generation sequencing-based metagenomic analyses. Characteristic rearrangements of the biogas-producing community upon protein feeding and specific differences due to the individual protein substrates were recognized. The results clearly demonstrate that sustained biogas production is readily achievable, provided the system is well-characterized, understood and controlled. Biogas yields (0.45 L CH4/g oDM) significantly exceeding those of the commonly used agricultural substrates (0.25-0.28 L CH4/g oDM) were routinely obtained. The results amply reveal that these high-energy-content waste products can be converted to biogas, a renewable energy carrier with flexible uses that can replace fossil natural gas in its applications. Process control, with appropriate acclimation of the microbial community to the unusual substrate, is necessary. Metagenomic analysis of the microbial community by next-generation sequencing allows a precise determination of the alterations in the community composition in the course of the process. PMID:24146974

Composition of the bacterial community in the gut of the pine engraver, Ips pini (Say) (Coloptera) colonizing red pine

Treesearch

Italo Jr. Delalibera; Archana Vasanthakumar; Benjamin J. Burwitz; Patrick D. Schloss; Kier D. Klepzig; Jo Handelsman; Kenneth F. Raffa

2007-01-01

The gut bacterial community of a bark beetle, the pine engraver Ips pini (Say), was characterized using culture-dependent and culture-independent methods. Bacteria from individual guts of larvae, pupae and adults were cultured and DNA was extracted from samples of pooled larval guts. Analysis of 16S rRNA gene sequences amplified directly from the gut...

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.

Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositionalmore » difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.« less

Bacterial composition in a metropolitan drinking water distribution system utilizing different source waters.

PubMed

Gomez-Alvarez, Vicente; Humrighouse, Ben W; Revetta, Randy P; Santo Domingo, Jorge W

2015-03-01

We investigated the bacterial composition of water samples from two service areas within a drinking water distribution system (DWDS), each associated with a different primary source of water (groundwater, GW; surface water, SW) and different treatment process. Community analysis based on 16S rRNA gene clone libraries indicated that Actinobacteria (Mycobacterium spp.) and α-Proteobacteria represented nearly 43 and 38% of the total sequences, respectively. Sequences closely related to Legionella, Pseudomonas, and Vibrio spp. were also identified. In spite of the high number of sequences (71%) shared in both areas, multivariable analysis revealed significant differences between the GW and SW areas. While the dominant phylotypes where not significantly contributing in the ordination of samples, the populations associated with the core of phylotypes (1-10% in each sample) significantly contributed to the differences between both service areas. Diversity indices indicate that the microbial community inhabiting the SW area is more diverse and contains more distantly related species coexisting with local assemblages as compared with the GW area. The bacterial community structure of SW and GW service areas were dissimilar, suggesting that their respective source water and/or water quality parameters shaped by the treatment processes may contribute to the differences in community structure observed.

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 rights reserved.

Influence of matrix type on tree community assemblages along tropical dry forest edges.

PubMed

Benítez-Malvido, Julieta; Gallardo-Vásquez, Julio César; Alvarez-Añorve, Mariana Y; Avila-Cabadilla, Luis Daniel

2014-05-01

• Anthropogenic habitat edges have strong negative consequences for the functioning of tropical ecosystems. However, edge effects on tropical dry forest tree communities have been barely documented.• In Chamela, Mexico, we investigated the phylogenetic composition and structure of tree assemblages (≥5 cm dbh) along edges abutting different matrices: (1) disturbed vegetation with cattle, (2) pastures with cattle and, (3) pastures without cattle. Additionally, we sampled preserved forest interiors.• All edge types exhibited similar tree density, basal area and diversity to interior forests, but differed in species composition. A nonmetric multidimensional scaling ordination showed that the presence of cattle influenced species composition more strongly than the vegetation structure of the matrix; tree assemblages abutting matrices with cattle had lower scores in the ordination. The phylogenetic composition of tree assemblages followed the same pattern. The principal plant families and genera were associated according to disturbance regimes as follows: pastures and disturbed vegetation (1) with cattle and (2) without cattle, and (3) pastures without cattle and interior forests. All habitats showed random phylogenetic structures, suggesting that tree communities are assembled mainly by stochastic processes. Long-lived species persisting after edge creation could have important implications in the phylogenetic structure of tree assemblages.• Edge creation exerts a stronger influence on TDF vegetation pathways than previously documented, leading to new ecological communities. Phylogenetic analysis may, however, be needed to detect such changes. © 2014 Botanical Society of America, Inc.

Fire regime, not time-since-fire, affects soil fungal community diversity and composition in temperate grasslands.

PubMed

Egidi, Eleonora; McMullan-Fisher, Sapphire; Morgan, John W; May, Tom; Zeeman, Ben; Franks, Ashley E

2016-09-01

Frequent burning is commonly undertaken to maintain diversity in temperate grasslands of southern Australia. How burning affects below-ground fungal community diversity remains unknown. We show, using a fungal rDNA metabarcoding approach (Illumina MiSeq), that the fungal community composition was influenced by fire regime (frequency) but not time-since-fire. Fungal community composition was resilient to direct fire effects, most likely because grassland fires transfer little heat to the soil. Differences in the fungal community composition due to fire regime was likely due to associated changes that occur in vegetation with recurrent fire, via the break up of obligate symbiotic relationships. However, fire history only partially explains the observed dissimilarity in composition among the soil samples, suggesting a distinctiveness in composition in each grassland site. The importance of considering changes in soil microbe communities when managing vegetation with fire is highlighted. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Community structure and elevational diversity patterns of soil Acidobacteria.

PubMed

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Qu, Yuanyuan; Su, Xiujiang; Zhou, Jizhong; Li, Diqiang

2014-08-01

Acidobacteria is one of the most dominant and abundant phyla in soil, and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest, deciduous broadleaved forest, coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition, elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites, and Subdivision 6 has the highest number of detectable operational taxonomic units (OTUs). A significant single peak distribution pattern (P<0.05) between the OTU number and the elevation was observed. The Jaccard and Bray-Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased (P<0.01) with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship (P<0.01) with different soil enzymes. Therefore, soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH, soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure. Copyright © 2014. Published by Elsevier B.V.

Community composition, diversity, and metabolism of intestinal microbiota in cultivated European eel (Anguilla anguilla).

PubMed

Huang, Wei; Cheng, Zhiqiang; Lei, Shaonan; Liu, Lanying; Lv, Xin; Chen, Lihua; Wu, Miaohong; Wang, Chao; Tian, Baoyu; Song, Yongkang

2018-05-01

The intestinal tract, which harbours tremendous numbers of bacteria, plays a pivotal role in the digestion and absorption of nutrients. Here, high-throughput sequencing technology was used to determine the community composition and complexity of the intestinal microbiota in cultivated European eels during three stages of their lifecycle, after which the metabolic potentials of their intestinal microbial communities were assessed. The results demonstrated that European eel intestinal microbiota were dominated by bacteria in the phyla Proteobacteria and Fusobacteria. Statistical analyses revealed that the three cultured European eel life stages (elver, yellow eel, and silver eel) shared core microbiota dominated by Aeromonas. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictions of metagenome function revealed that the European eel intestinal microbiota might play significant roles in host nutrient metabolism. Biolog AN MicroPlate™ analysis and extracellular enzyme assays of culturable intestinal bacteria showed that the intestinal microbiota have a marked advantage in the metabolism of starch, which is the main carbohydrate component in European eel formulated feed. Understanding the ecology and functions of the intestinal microbiota during different developmental stages will help us improve the effects of fish-based bacteria on the composition and metabolic capacity of nutrients in European eels.

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets.

PubMed

Lucas, Rico; Groeneveld, Jürgen; Harms, Hauke; Johst, Karin; Frank, Karin; Kleinsteuber, Sabine

2017-01-01

In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers.

PubMed

Nilsson, Louise K J; Sharma, Anil; Bhatnagar, Raj K; Bertilsson, Stefan; Terenius, Olle

2018-06-01

Water-storage containers are common in households where access to water is scarce and often act as breeding sites for vector mosquitoes. Bacteria in these containers may be important for attracting or repelling ovipositing mosquitoes. We hypothesized that bacterial community composition in water-storage containers would represent either inhibitory or suitable environmental conditions for mosquito larvae. To investigate this, we characterized the bacterial community composition in water-storage containers and correlated these communities to Aedes and Anopheles larval densities. Water samples were collected over two years from 13 containers in an Indian village and analyzed by high throughput 16S rRNA gene amplicon sequencing. Comparisons of bacterial community composition between water with and without mosquito larvae showed that Xanthomonadaceae, Comamonadaceae and Burkholderiaceae were more common (P < 0.05) in absence of larvae, while Lachnospiraceae, Synechococcaceae, Alcaligenaceae and Cryomorphaceae were more common (P < 0.05) in presence of larvae. Indicator analysis identified operational taxonomic units designated as CL500-29 marine group (Acidimicrobiaceae) and FukuN101 (Microbacteriaceae) for absence and presence of larvae, respectively. These results contribute to the understanding of which bacteria, directly or indirectly, can be linked to absence or presence of mosquitoes around households and set the basis for potential measures to be taken against these vector mosquitoes.

Forecasting climate change impacts to plant community composition in the Sonoran Desert region

USGS Publications Warehouse

Munson, Seth M.; Webb, Robert H.; Belnap, Jayne; Hubbard, J. Andrew; Swann, Don E.; Rutman, Sue

2012-01-01

Hotter and drier conditions projected for the southwestern United States can have a large impact on the abundance and composition of long-lived desert plant species. We used long-term vegetation monitoring results from 39 large plots across four protected sites in the Sonoran Desert region to determine how plant species have responded to past climate variability. This cross-site analysis identified the plant species and functional types susceptible to climate change, the magnitude of their responses, and potential climate thresholds. In the relatively mesic mesquite savanna communities, perennial grasses declined with a decrease in annual precipitation, cacti increased, and there was a reversal of the Prosopis velutina expansion experienced in the 20th century in response to increasing mean annual temperature (MAT). In the more xeric Arizona Upland communities, the dominant leguminous tree, Cercidium microphyllum, declined on hillslopes, and the shrub Fouquieria splendens decreased, especially on south- and west-facing slopes in response to increasing MAT. In the most xeric shrublands, the codominant species Larrea tridentata and its hemiparasite Krameria grayi decreased with a decrease in cool season precipitation and increased aridity, respectively. This regional-scale assessment of plant species response to recent climate variability is critical for forecasting future shifts in plant community composition, structure, and productivity.

Uranium reduction and microbial community development in response to stimulation with different electron donors.

PubMed

Barlett, Melissa; Moon, Hee Sun; Peacock, Aaron A; Hedrick, David B; Williams, Kenneth H; Long, Philip E; Lovley, Derek; Jaffe, Peter R

2012-07-01

Stimulating microbial reduction of soluble U(VI) to less soluble U(IV) shows promise as an in situ bioremediation strategy for uranium contaminated groundwater, but the optimal electron donors for promoting this process have yet to be identified. The purpose of this study was to better understand how the addition of various electron donors to uranium-contaminated subsurface sediments affected U(VI) reduction and the composition of the microbial community. The simple electron donors, acetate or lactate, or the more complex donors, hydrogen-release compound (HRC) or vegetable oil, were added to the sediments incubated in flow-through columns. The composition of the microbial communities was evaluated with quantitative PCR probing specific 16S rRNA genes and functional genes, phospholipid fatty acid analysis, and clone libraries. All the electron donors promoted U(VI) removal, even though the composition of the microbial communities was different with each donor. In general, the overall biomass, rather than the specific bacterial species, was the factor most related to U(VI) removal. Vegetable oil and HRC were more effective in stimulating U(VI) removal than acetate. These results suggest that the addition of more complex organic electron donors could be an excellent option for in situ bioremediation of uranium-contaminated groundwater.

Lead Toxicity to the Performance, Viability, And Community Composition of Activated Sludge Microorganisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, L; Zhi, W; Liu, YS

Lead (Pb) is a prominent toxic metal in natural and engineered systems. Current knowledge on Pb toxicity to the activated sludge has been limited to short-term (<= 24 h) toxicity. The effect of extended Pb exposure on process performance, bacterial viability, and community compositions remains unknown. We quantified the 24-h and 7-day Pb toxicity to chemical oxygen demand (COD) and NH3-N removal, bacterial viability, and community compositions using lab-scale experiments. Our results showed that 7-day toxicity was significantly higher than the short-term 24-h toxicity. Ammonia-oxidizing bacteria were more susceptible than the heterotrophs to Pb toxicity. The specific oxygen uptake ratemore » responded quickly to Pb addition and could serve as a rapid indicator for detecting Pb pollutions. Microbial viability decreased linearly with the amount of added Pb at extended exposure. The bacterial community diversity was markedly reduced with elevated Pb concentrations. Surface analysis suggested that the adsorbed form of Pb could have contributed to its toxicity along with the dissolved form. Our study provides for the first time a systematic investigation of the effect of extended exposure of Pb on the performance and microbiology of aerobic treatment processes, and it indicates that long-term Pb toxicity has been underappreciated by previous studies.« less

[Effects of tree species transition on soil microbial community composition and functions in subtropical China].

PubMed

Ding, Guo Chang; Wang, Xiao Hua; Yang, Qi Fan; Lin, Qun Xing; Huang, Zhi Qun

2017-11-01

We employed a comparative study to examine the effects of tree species transition on soil microbial biomass, community composition and enzymes activities under Cunninghamia lanceolata (Lamb.) Hook, Eucalyptus grandis and a N-fixing species, Acacia melanoxylon in subtropical China. Results showed that the effect of tree species on soil microbial community and enzymes activities was significant only in the 0-10 cm soil layer. Reforestation with N-fixing species A. melanoxylon on the C. lanceolata harvest site significantly increased the total phospholipid fatty acid (PLFA), fungal PLFAs, Gram-positive bacterial PLFAs, Gram-negative bacterial PLFAs and actinomycetes biomasses in the 0-10 cm soil layer. The principal component analysis (PCA) showed that the soil microbial community composition in A. melanoxylon soil differed significantly from that in C. lanceolata and E. grandis soils. N-fixing species (A. melanoxylon) significantly enhanced the percent abundance of Gram-positive bacteria, Gram-negative bacteria and actinomycetes. Activities of cellobiohydrolase, N-acetyl-β-d-glucosaminidase and acid phosphatase were significantly higher under A. melanoxylon than under C. lanceolata and E. grandis plantations. Our results suggested that reforestation with N-fixing species, A. melanoxylon on C. lanceolata harvest site could increase soil microbial biomass, enzyme activities and soil organic matter content.

Subseafloor microbial communities in hydrogen‐rich vent fluids from hydrothermal systems along the Mid‐Cayman Rise

PubMed Central

Reveillaud, Julie; Reddington, Emily; McDermott, Jill; Algar, Christopher; Meyer, Julie L.; Sylva, Sean; Seewald, Jeffrey; German, Christopher R.

2016-01-01

Summary Warm fluids emanating from hydrothermal vents can be used as windows into the rocky subseafloor habitat and its resident microbial community. Two new vent systems on the Mid‐Cayman Rise each exhibits novel geologic settings and distinctively hydrogen‐rich vent fluid compositions. We have determined and compared the chemistry, potential energy yielding reactions, abundance, community composition, diversity, and function of microbes in venting fluids from both sites: Piccard, the world's deepest vent site, hosted in mafic rocks; and Von Damm, an adjacent, ultramafic‐influenced system. Von Damm hosted a wider diversity of lineages and metabolisms in comparison to Piccard, consistent with thermodynamic models that predict more numerous energy sources at ultramafic systems. There was little overlap in the phylotypes found at each site, although similar and dominant hydrogen‐utilizing genera were present at both. Despite the differences in community structure, depth, geology, and fluid chemistry, energetic modelling and metagenomic analysis indicate near functional equivalence between Von Damm and Piccard, likely driven by the high hydrogen concentrations and elevated temperatures at both sites. Results are compared with hydrothermal sites worldwide to provide a global perspective on the distinctiveness of these newly discovered sites and the interplay among rocks, fluid composition and life in the subseafloor. PMID:26663423

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils

PubMed Central

Torres, Maria Pilar; Montesinos-Navarro, Alicia; Roldán, Antonio

2016-01-01

ABSTRACT We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. IMPORTANCE Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions. PMID:27016567

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils.

PubMed

Alguacil, Maria Del Mar; Torres, Maria Pilar; Montesinos-Navarro, Alicia; Roldán, Antonio

2016-06-01

We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Implications of dredging induced changes in sediment particle size composition for the structure and function of marine benthic macrofaunal communities.

PubMed

Cooper, K M; Curtis, M; Wan Hussin, W M R; Barrio Froján, C R S; Defew, E C; Nye, V; Paterson, D M

2011-10-01

A meta-analysis approach was used to assess the effect of dredging induced changes in sediment composition, under different conditions of natural physical disturbance, for the structure and function of marine benthic macrofaunal communities. Results showed the sensitivity of macrofaunal communities increased as both the proportion of gravel increased and the level of natural physical disturbance decreased. These findings may be explained by the close association of certain taxa with the gravel fraction, and the influence of natural physical disturbance which, as it increases, tends to restrict the colonisation by these species. We conclude that maintaining the gravel content of surface sediments after dredging and, where practicable, locating extraction sites in areas of higher natural disturbance will minimise the potential for long-term negative impacts on the macrofauna. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Arbuscular mycorrhizal fungal community composition associated with Juniperus brevifolia in native Azorean forest

NASA Astrophysics Data System (ADS)

Melo, Catarina Drumonde; Luna, Sara; Krüger, Claudia; Walker, Christopher; Mendonça, Duarte; Fonseca, Henrique M. A. C.; Jaizme-Vega, Maria; da Câmara Machado, Artur

2017-02-01

The communities of glomeromycotan fungi (arbuscular mycorrhizal fungi, AMF) under native Juniperus brevifolia forest from two Azorean islands, Terceira and São Miguel, were compared, mainly by spore morphology, and when possible, by molecular analysis. Thirty-nine morphotypes were detected from 12 genera. Glomeromycotan fungal richness was similar in Terceira and São Miguel, but significantly different among the four fragments of native forest. Spore diversity and community composition differed significantly between the two islands. The less degraded island, Terceira, showed 10 exclusive morphotypes including more rare types, whereas the more disturbed forest on São Miguel showed 13 morphs, mostly of common types. Forests from Terceira were dominated by Acaulosporaceae and Glomeraceae. Whereas members of Acaulosporaceae, Glomeraceae and Ambisporaceae were most frequent and abundant in those from São Miguel. Spore abundance was greatest on Terceira, and correlated with soil chemical properties (pH), average monthly temperature and relative humidity.

Who perceives what? A demographic analysis of subjective perception in rural Thailand

PubMed Central

Meijer-Irons, Jacqueline

2016-01-01

Rural households that rely on natural resources for their livelihoods are expected to face increased vulnerability due to climate variability. A number of empirical papers have assessed the impact of environmental shocks on these households, including demographic research that has investigated the impact of shocks on migration. To date, few studies have explicitly modeled how individual and household characteristics influence a household respondent’s subjective perceptions of environmental or other shocks. My paper uses a unique panel dataset from rural Thailand to predict a respondent’s probability of attributing a reduction in income to an environmental shock based on household composition and income, as well as on community-level effects. Preliminary results suggest that household composition influences respondents’ perceptions of environmental risk, and that policies aimed at vulnerable communities should consider the life courses of the households within a given community. PMID:28058054

Soil Bacterial Community Shift Correlated with Change from Forest to Pasture Vegetation in a Tropical Soil

PubMed Central

Nüsslein, Klaus; Tiedje, James M.

1999-01-01

The change in vegetative cover of a Hawaiian soil from forest to pasture led to significant changes in the composition of the soil bacterial community. DNAs were extracted from both soil habitats and compared for the abundance of guanine-plus-cytosine (G+C) content, by analysis of abundance of phylotypes of small-subunit ribosomal DNA (SSU rDNA) amplified from fractions with 63 and 35% G+C contents, and by phylogenetic analysis of the dominant rDNA clones in the 63% G+C content fraction. All three methods showed differences between the forest and pasture habitats, providing evidence that vegetation had a strong influence on microbial community composition at three levels of taxon resolution. The forest soil DNA had a peak in G+C content of 61%, while the DNA of the pasture soil had a peak in G+C content of 67%. None of the dominant phylotypes found in the forest soil were detected in the pasture soil. For the 63% G+C fraction SSU rDNA sequence analysis of the three most dominant members revealed that their phyla changed from Fibrobacter and Syntrophomonas assemblages in the forest soil to Burkholderia and Rhizobium–Agrobacterium assemblages in the pasture soil. PMID:10427058

The role of plant mycorrhizal type and status in modulating the relationship between plant and arbuscular mycorrhizal fungal communities.

PubMed

Neuenkamp, Lena; Moora, Mari; Öpik, Maarja; Davison, John; Gerz, Maret; Männistö, Minna; Jairus, Teele; Vasar, Martti; Zobel, Martin

2018-01-25

Interactions between communities of plants and arbuscular mycorrhizal (AM) fungi shape fundamental ecosystem properties. Experimental evidence suggests that compositional changes in plant and AM fungal communities should be correlated, but empirical data from natural ecosystems are scarce. We investigated the dynamics of covariation between plant and AM fungal communities during three stages of grassland succession, and the biotic and abiotic factors shaping these dynamics. Plant communities were characterised using vegetation surveys. AM fungal communities were characterised by 454-sequencing of the small subunit rRNA gene and identification against the AM fungal reference database MaarjAM. AM fungal abundance was estimated using neutral-lipid fatty acids (NLFAs). Multivariate correlation analysis (Procrustes) revealed a significant relationship between plant and AM fungal community composition. The strength of plant-AM fungal correlation weakened during succession following cessation of grassland management, reflecting changes in the proportion of plants exhibiting different AM status. Plant-AM fungal correlation was strong when the abundance of obligate AM plants was high, and declined as the proportion of facultative AM plants increased. We conclude that the extent to which plants rely on AM symbiosis can determine how tightly communities of plants and AM fungi are interlinked, regulating community assembly of both symbiotic partners. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

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

PubMed

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

2015-01-01

This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p < 0.05). We also found a high ratio of fungal-to-bacterial PLFAs in black soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p < 0.05). These results indicated that the application of corn straw positively influences soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Final Technical Report to DOE for the Award DE-SC0004601

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, Jizhong

Understanding the responses, adaptations and feedback mechanisms of biological communities to climate change is critical to project future state of earth and climate systems. Although significant amount of knowledge is available on the feedback responses of aboveground communities to climate change, little is known about the responses of belowground microbial communities due to the challenges in analyzing soil microbial community structure. Thus the goal overall goal of this study is to provide system-level, predictive mechanistic understanding of the temperature sensitivity of soil carbon (C) decomposition to climate warming by using cutting-edge integrated metagenomic technologies. Towards this goal, the following fourmore » objectives will be pursued: (i) To determine phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems; (ii) To delineate the responses of microbial community structure, functions and activities to climate change in the temperate grassland and tundra ecosystems; (iii) To determine the temperature sensitivity of microbial respiration in soils with different mixtures of labile versus recalcitrant C, and the underlying microbiological basis for temperature sensitivity of these pools; and (iv) To synthesize all experimental data for revealing microbial control of ecosystem carbon processes in responses to climate change. We have achieved our goals for all four proposed objectives. First, we determined the phylogenetic composition and metabolic diversity of microbial communities in the temperate grassland and tundra ecosystems. For this objective, we have developed a novel phasing amplicon sequencing (PAS) approach for MiSeq sequencing of amplicons. This approach has been used for sequencing various phylogenetic and functional genes related to ecosystem functioning. A comprehensive functional gene array (e.g., GeoChip 5.0) has also been developed and used for soil microbial community analysis in this study. In addition, shot-gun metagenome sequencing along with the above approaches have been used to understand the phylogenetic and functional diversity, composition, and structure of soil microbial communities in both temperature grassland and tundra ecosystems. Second, we determined the response of soil microbial communities to climate warming in both temperate grassland and tundra ecosystems using various methods. Our major findings are: (i) Microorganisms are very rapid to respond to climate warming in the tundra ecosystem, AK, which is vulnerable, too. (ii) Climate warming also significantly shifted the metabolic diversity, composition and structure of microbial communities, and key metabolic pathways related to carbon turnover, such as cellulose degradation (~13%) and CO2 production (~10%), and to nitrogen cycling, including denitrification (~12%) were enriched by warming. (iii) Warming also altered the expression patterns of microbial functional genes important to ecosystem functioning and stability through GeoChip and metatranscriptomic analysis of soil microbial communities at the OK site. Third, we analyzed temperature sensitivity of C decomposition to climate warming for both AK and OK soils through laboratory incubations. Key results include: (i) Alaska tundra soils showed that after one year of incubation, CT in the top 15 cm could be as high as 25% and 15% of the initial soil C content at 25°C and 15°C incubations, respectively. (ii) analysis of 456 incubated soil samples with 16S rRNA gene, ITS and GeoChip hybridization showed that warming shifted the phylogenretic and functional diversity, composition, structure and metabolic potential of soil microbial communities, and at different stages of incubation, key populations and functional genes significantly changed along with soil substrate changes. Functional gene diversity and functional genes for degrading labile C components decrease along incubation when labile C components are exhausting, but the genes related to degrading recalcitrant C increase. These molecular data will be directly used for modeling. Fourth, we have developed novel approaches to integrate and model experimental data to understand microbial control of ecosystem C processes in response to climate change. We compared different methods to calculate Q10 for estimating temperature sensitivity, and new approaches for Q10 calculation and molecular ecological network analysis were also developed. Using those newly developed approaches, our result indicated that Q10s increased with the recalcitrance of C pools, suggesting that longer incubation studies are needed in order to assess the temperature sensitivity of slower C pools, especially at low temperature regimes. This project has been very productive, resulting in 42 papers published or in press, 4 submitted, and 13 in preparation.« less

Ectomycorrhizal fungal diversity and community structure associated with cork oak in different landscapes.

PubMed

Reis, Francisca; Valdiviesso, Teresa; Varela, Carolina; Tavares, Rui M; Baptista, Paula; Lino-Neto, Teresa

2018-05-01

Cork oak (Quercus suber L.) forests play an important ecological and economic role. Ectomycorrhizal fungi (ECMF) are key components for the sustainability and functioning of these ecosystems. The community structure and composition of ECMF associated with Q. suber in different landscapes of distinct Mediterranean bioclimate regions have not previously been compared. In this work, soil samples from cork oak forests residing in different bioclimates (arid, semi-arid, sub-humid, and humid) were collected and surveyed for ectomycorrhizal (ECM) root tips. A global analysis performed on 3565 ECM root tips revealed that the ECMF community is highly enriched in Russula, Tomentella, and Cenoccocum, which correspond to the ECMF genera that mainly contribute to community differences. The ECMF communities from the rainiest and the driest cork oak forests were distinct, with soils from the rainiest climates being more heterogeneous than those from the driest climates. The analyses of several abiotic factors on the ECMF communities revealed that bioclimate, precipitation, soil texture, and forest management strongly influenced ECMF structure. Shifts in ECMF with different hyphal exploration types were also detected among forests, with precipitation, forest system, and soil texture being the main drivers controlling their composition. Understanding the effects of environmental factors on the structuring of ECM communities could be the first step for promoting the sustainability of this threatened ecosystem.

Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak.

PubMed

Langer, Julia A F; Sharma, Rahul; Schmidt, Susanne I; Bahrdt, Sebastian; Horn, Henriette G; Algueró-Muñiz, María; Nam, Bora; Achterberg, Eric P; Riebesell, Ulf; Boersma, Maarten; Thines, Marco; Schwenk, Klaus

2017-01-01

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2.

Community barcoding reveals little effect of ocean acidification on the composition of coastal plankton communities: Evidence from a long-term mesocosm study in the Gullmar Fjord, Skagerrak

PubMed Central

Sharma, Rahul; Schmidt, Susanne I.; Bahrdt, Sebastian; Horn, Henriette G.; Algueró-Muñiz, María; Nam, Bora; Achterberg, Eric P.; Riebesell, Ulf; Boersma, Maarten; Thines, Marco; Schwenk, Klaus

2017-01-01

The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta). Analyses based on predicted operational taxonomical units as well as taxonomical compositions revealed no differences between communities in high CO2 mesocosms (~ 760 μatm) and those exposed to present-day CO2 conditions. Observed shifts in the planktonic community composition were mainly related to seasonal changes in temperature and nutrients. Furthermore, based on our investigations, the elevated CO2 did not affect the intraspecific diversity of the most common mesozooplankter, the calanoid copepod Pseudocalanus acuspes. Nevertheless, accompanying studies found temporary effects attributed to a raise in CO2. Differences in taxa composition between the CO2 treatments could, however, only be observed in a specific period of the experiment. Based on our genetic investigations, no compositional long-term shifts of the plankton communities exposed to elevated CO2 conditions were observed. Thus, we conclude that the compositions of planktonic communities, especially those in coastal areas, remain rather unaffected by increased CO2. PMID:28445483

Activity and Diversity of Methanotrophic Bacteria at Methane Seeps in Eastern Lake Constance Sediments ▿

PubMed Central

Deutzmann, Jörg S.; Wörner, Susanne; Schink, Bernhard

2011-01-01

The activity and community structure of aerobic methanotrophic communities were investigated at methane seeps (pockmarks) in the littoral and profundal zones of an oligotrophic freshwater lake (Lake Constance, Germany). Measurements of potential methane oxidation rates showed that sediments inside littoral pockmarks are hot spots of methane oxidation. Potential methane oxidation rates at littoral pockmark sites exceeded the rates of the surrounding sediment by 2 orders of magnitude. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the pmoA gene revealed major differences in the methanotrophic community composition between littoral pockmarks and the surrounding sediments. Clone library analysis confirmed that one distinct Methylobacter-related group dominates the community at littoral pockmarks. In profundal sediments, the differences between pockmarks and surrounding sediments were found to be less pronounced. PMID:21335392

Forest Inventory and Analysis Database of the United States of America (FIA)

Treesearch

Andrew N. Gray; Thomas J. Brandeis; John D. Shaw; William H. McWilliams; Patrick Miles

2012-01-01

Extensive vegetation inventories established with a probabilistic design are an indispensable tool in describing distributions of species and community types and detecting changes in composition in response to climate or other drivers. The Forest Inventory and Analysis Program measures vegetation in permanent plots on forested lands across the United States of America...

Preliminary evaluation of an in vivo fluorometer to quantify algal periphyton biomass and community composition

USGS Publications Warehouse

Harris, Theodore D.; Graham, Jennifer L.

2015-01-01

The bbe-Moldaenke BenthoTorch (BT) is an in vivo fluorometer designed to quantify algal biomass and community composition in benthic environments. The BT quantifies total algal biomass via chlorophyll a (Chl-a) concentration and may differentiate among cyanobacteria, green algae, and diatoms based on pigment fluorescence. To evaluate how BT measurements of periphytic algal biomass (as Chl-a) compared with an ethanol extraction laboratory analysis, we collected BT- and laboratory-measured Chl-a data from 6 stream sites in the Indian Creek basin, Johnson County, Kansas, during August and September 2012. BT-measured Chl-a concentrations were positively related to laboratory-measured concentrations (R2 = 0.47); sites with abundant filamentous algae had weaker relations (R2 = 0.27). Additionally, on a single sample date, we used the BT to determine periphyton biomass and community composition upstream and downstream from 2 wastewater treatment facilities (WWTF) that discharge into Indian Creek. We found that algal biomass increased immediately downstream from the WWTF discharge then slowly decreased as distance from the WWTF increased. Changes in periphyton community structure also occurred; however, there were discrepancies between BT- and laboratory-measured community composition data. Most notably, cyanobacteria were present at all sites based on BT measurements but were present at only one site based on laboratory-analyzed samples. Overall, we found that the BT compared reasonably well with laboratory methods for relative patterns in Chl-a but not as well with absolute Chl-aconcentrations. Future studies need to test the BT over a wider range of Chl-aconcentrations, in colored waters, and across various periphyton assemblages.

The potential influence of short-term environmental variability on the composition of testate amoeba communities in Sphagnum peatlands.

PubMed

Sullivan, Maura E; Booth, Robert K

2011-07-01

Testate amoebae are a group of moisture-sensitive, shell-producing protozoa that have been widely used as indicators of changes in mean water-table depth within oligotrophic peatlands. However, short-term environmental variability (i.e., sub-annual) also probably influences community composition. The objective of this study was to assess the potential influence of short-term environmental variability on the composition of testate amoeba communities in Sphagnum-dominated peatlands. Testate amoebae and environmental conditions, including hourly measurements of relative humidity within the upper centimeter of the peatland surface, were examined throughout the 2008 growing season at 72 microsites within 11 peatlands of Pennsylvania and Wisconsin, USA. Relationships among testate amoeba communities, vegetation, depth to water table, pH, and an index of short-term environmental variability (EVI), were examined using nonmetric multidimensional scaling and correlation analysis. Results suggest that EVI influences testate amoeba communities, with some taxa more abundant under highly variable conditions (e.g., Arcella discoides, Difflugia pulex, and Hyalosphenia subflava) and others more abundant when environmental conditions at the peatland surface were relatively stable (e.g., Archerella flavum and Bullinularia indica). The magnitude of environmental variability experienced at the peatland surface appears to be primarily controlled by vegetation composition and density. In particular, sites with dense Sphagnum cover had lower EVI values than sites with loose-growing Sphagnum or vegetation dominated by vascular plants and/or non-Sphagnum bryophytes. Our results suggest that more environmental information may be inferred from testate amoebae than previously recognized. Knowledge of relationships between testate amoebae and short-term environmental variability should lead to more detailed and refined environmental inferences.

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

Environmental and ecological controls of coral community metabolism on Palmyra Atoll

NASA Astrophysics Data System (ADS)

Koweek, David; Dunbar, Robert B.; Rogers, Justin S.; Williams, Gareth J.; Price, Nichole; Mucciarone, David; Teneva, Lida

2015-03-01

Accurate predictions of how coral reefs may respond to global climate change hinge on understanding the natural variability to which these ecosystems are exposed and to which they contribute. We present high-resolution estimates of net community calcification (NCC) and net community production (NCP) from Palmyra Atoll, an uninhabited, near-pristine coral reef ecosystem in the central Pacific. In August-October 2012, we employed a combination of Lagrangian and Eulerian frameworks to establish high spatial (~2.5 km2) and temporal (hourly) resolution coral community metabolic estimates. Lagrangian drifts, all conducted during daylight hours, resulted in NCC estimates of -51 to 116 mmol C m-2 h-1, although most NCC estimates were in the range of 0-40 mmol C m-2 h-1. Lagrangian drift NCP estimates ranged from -7 to 67 mmol C m-2 h-1. In the Eulerian setup, we present carbonate system parameters (dissolved inorganic carbon, total alkalinity, pH, and pCO2) at sub-hourly resolution through several day-night cycles and provide hourly NCC and NCP rate estimates. We compared diel cycles of all four carbonate system parameters to the offshore surface water (0-50 m depth) and show large departures from offshore surface water chemistry. Hourly Eulerian estimates of NCC aggregated over the entire study ranged from 14 to 53 mmol C m-2 h-1, showed substantial variability during daylight hours, and exhibited a diel cycle with elevated NCC in the afternoons and depressed, but positive, NCC at night. The Eulerian NCP range was very high (-55 to 177 mmol C m-2 h-1) and exhibited strong variability during daylight hours. Principal components analysis revealed that NCC and NCP were most closely aligned with diel cycle forcing, whereas the NCC/NCP ratio was most closely aligned with reef community composition. Our analysis demonstrates that ecological community composition is the primary determinant of coral reef biogeochemistry on a near-pristine reef and that reef biogeochemistry is likely to be responsive to human behaviors that alter community composition.

Intestinal microbiota composition in fishes is influenced by host ecology and environment.

PubMed

Wong, Sandi; Rawls, John F

2012-07-01

The digestive tracts of vertebrates are colonized by complex assemblages of micro-organisms, collectively called the gut microbiota. Recent studies have revealed important contributions of gut microbiota to vertebrate health and disease, stimulating intense interest in understanding how gut microbial communities are assembled and how they impact host fitness (Sekirov et al. 2010). Although all vertebrates harbour a gut microbiota, current information on microbiota composition and function has been derived primarily from mammals. Comparisons of different mammalian species have revealed intriguing associations between gut microbiota composition and host diet, anatomy and phylogeny (Ley et al. 2008b). However, mammals constitute <10% of all vertebrate species, and it remains unclear whether similar associations exist in more diverse and ancient vertebrate lineages such as fish. In this issue, Sullam et al. (2012) make an important contribution toward identifying factors determining gut microbiota composition in fishes. The authors conducted a detailed meta-analysis of 25 bacterial 16S rRNA gene sequence libraries derived from the intestines of different fish species. To provide a broader context for their analysis, they compared these data sets to a large collection of 16S rRNA gene sequence data sets from diverse free-living and host-associated bacterial communities. Their results suggest that variation in gut microbiota composition in fishes is strongly correlated with species habitat salinity, trophic level and possibly taxonomy. Comparison of data sets from fish intestines and other environments revealed that fish gut microbiota compositions are often similar to those of other animals and contain relatively few free-living environmental bacteria. These results suggest that the gut microbiota composition of fishes is not a simple reflection of the micro-organisms in their local habitat but may result from host-specific selective pressures within the gut (Bevins & Salzman 2011).

Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks

PubMed Central

McGuire, Krista L.; Payne, Sara G.; Palmer, Matthew I.; Gillikin, Caitlyn M.; Keefe, Dominique; Kim, Su Jin; Gedallovich, Seren M.; Discenza, Julia; Rangamannar, Ramya; Koshner, Jennifer A.; Massmann, Audrey L.; Orazi, Giulia; Essene, Adam; Leff, Jonathan W.; Fierer, Noah

2013-01-01

In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg) compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs. PMID:23469260

Digging the New York City Skyline: soil fungal communities in green roofs and city parks.

PubMed

McGuire, Krista L; Payne, Sara G; Palmer, Matthew I; Gillikin, Caitlyn M; Keefe, Dominique; Kim, Su Jin; Gedallovich, Seren M; Discenza, Julia; Rangamannar, Ramya; Koshner, Jennifer A; Massmann, Audrey L; Orazi, Giulia; Essene, Adam; Leff, Jonathan W; Fierer, Noah

2013-01-01

In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg) compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.

Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia)

PubMed Central

Schneider, Dominik; Engelhaupt, Martin; Allen, Kara; Kurniawan, Syahrul; Krashevska, Valentyna; Heinemann, Melanie; Nacke, Heiko; Wijayanti, Marini; Meryandini, Anja; Corre, Marife D.; Scheu, Stefan; Daniel, Rolf

2015-01-01

Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations. PMID:26696965

Vegetation analysis for arid lands geobotany

NASA Technical Reports Server (NTRS)

Barbour, M. G.; Ustin, S. L.

1985-01-01

Three primary study sites were selected for measurement of plant phenological properties and spectral analysis. The sites selected represented typical sagebrush, creosote bush, and saltbush communities in Owens Valley, CA. Community composition was studied at these three sites plus five burned sites. Ten 50 m transects at each locality were measured for percent cover (over 10 cm) by a given species. On each transect two point quarter and five nearest neighbor analyses were conducted. These data provided percent cover, cover by area, plant size, tendency for association, and recolonization patterns after a disturbance. Plots representing percentage plant cover for six sites are included.

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities

Treesearch

Fei Cheng; Lin Hou; Keith Woeste; Zhengchun Shang; Xiaobang Peng; Peng Zhao; Shuoxin Zhang

2016-01-01

Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high...

Molecular characterization of soil bacterial community in a perhumid, low mountain forest.

PubMed

Lin, Yu-Te; Whitman, William B; Coleman, David C; Chih-Yu, Chiu

2011-01-01

Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.

Changes in the bacterial community of soybean rhizospheres during growth in the field.

PubMed

Sugiyama, Akifumi; Ueda, Yoshikatsu; Zushi, Takahiro; Takase, Hisabumi; Yazaki, Kazufumi

2014-01-01

Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.

Effects of climate change on plant population growth rate and community composition change.

PubMed

Chang, Xiao-Yu; Chen, Bao-Ming; Liu, Gang; Zhou, Ting; Jia, Xiao-Rong; Peng, Shao-Lin

2015-01-01

The impacts of climate change on forest community composition are still not well known. Although directional trends in climate change and community composition change were reported in recent years, further quantitative analyses are urgently needed. Previous studies focused on measuring population growth rates in a single time period, neglecting the development of the populations. Here we aimed to compose a method for calculating the community composition change, and to testify the impacts of climate change on community composition change within a relatively short period (several decades) based on long-term monitoring data from two plots-Dinghushan Biosphere Reserve, China (DBR) and Barro Colorado Island, Panama (BCI)-that are located in tropical and subtropical regions. We proposed a relatively more concise index, Slnλ, which refers to an overall population growth rate based on the dominant species in a community. The results indicated that the population growth rate of a majority of populations has decreased over the past few decades. This decrease was mainly caused by population development. The increasing temperature had a positive effect on population growth rates and community change rates. Our results promote understanding and explaining variations in population growth rates and community composition rates, and are helpful to predict population dynamics and population responses to climate change.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

PubMed

Wilkins, Laetitia G E; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-11-27

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area.

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures

PubMed Central

Wilkins, Laetitia G. E.; Rogivue, Aude; Schütz, Frédéric; Fumagalli, Luca; Wedekind, Claus

2015-01-01

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area. PMID:26611640

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

PubMed

Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

PubMed Central

Eldridge, David J; Woodhouse, Jason N; Curlevski, Nathalie J A; Hayward, Matthew; Brown, Mark V; Neilan, Brett A

2015-01-01

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance. PMID:25932616

Rhizospheric soil and root endogenous fungal diversity and composition in response to continuous Panax notoginseng cropping practices.

PubMed

Tan, Yong; Cui, Yinshan; Li, Haoyu; Kuang, Anxiu; Li, Xiaoran; Wei, Yunlin; Ji, Xiuling

2017-01-01

Rhizosphere and endophytic fungal communities are considered critically important for plant health and soil fertility. In response to continuous cropping, Panax notoginseng becomes vulnerable to attack by fungal pathogens. In the present study, culture-independent Illumina MiSeq was used to investigate the rhizospheric and root endophytic fungi in response to continuous Panax notoginseng cropping practices. The results demonstrated that fungal diversity is increased inside the roots and in rhizospheric. Ascomycota, Zygomycota, Basidiomycota and Chytridiomycota were the dominant phyla detected during the continuous cropping of Panax notoginseng. The fungal diversity in the rhizospheric soil and roots of root-rot P. notoginseng plants are less than that of healthy plants in the same cultivating year, thus showing that root-rot disease also affects the community structure and diversity of rhizospheric and root endophytic fungi. Similarities in the major fungal components show that endophytic fungal communities are similar to rhizospheric soil fungal community based on a specialized subset of organisms. Canonical correspondence analysis on the fungal communities in root-rot rhizospheric from both healthy plants and rotation soils reveals that the soil pH and organic matter have the greatest impact upon the microbial community composition during continuous cropping, whereas soil nutrition status does not significantly affect the fungal community composition in response to continuous cropping practices. In addition, the results suggest that the unclassified genera Leotiomycetes, Cylindrocarpon, Fusarium and Mycocentrospora are shown as the potential pathogens which are responsible for the obstacles in continuous cropping of P. notoginseng. Further exploration of these potential pathogens might be useful for the biological control of continuous cropping of P. notoginseng. Copyright © 2016 Elsevier GmbH. All rights reserved.

Assessment of Bacterial bph Gene in Amazonian Dark Earth and Their Adjacent Soils

PubMed Central

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry. PMID:24927167

Vertical stratification of bacterial communities driven by multiple environmental factors in the waters (0-5000 m) off the Galician coast (NW Iberian margin)

NASA Astrophysics Data System (ADS)

Dobal-Amador, Vladimir; Nieto-Cid, Mar; Guerrero-Feijoo, Elisa; Hernando-Morales, Victor; Teira, Eva; Varela-Rozados, Marta M.

2016-08-01

The processes mediated by microbial planktonic communities occur along the entire water column, yet the microbial activity and composition have been studied mainly in surface waters. This research examined the vertical variation in bacterial abundance, activity and community composition and structure from surface down to 5000 m depth following a longitudinal transect off the Galician coast (NW Iberian margin, from 43°N, 9°W to 43°N, 15°W). Community activity and composition changed with depth. The leucine incorporation rates decreased from the euphotic layer to the bathypelagic waters by three orders of magnitude, whereas prokaryotic abundance decreased only by one order of magnitude. The relative abundance of SAR11 and Alteromonas, determined by catalyzed reported deposition fluorescence in situ hybridization (CARD-FISH), decreased with depth. Meanwhile, the contribution of SAR 202 and SAR324 was significantly higher in the deeper layers (i.e. NEADW, North East Atlantic Deep Water and LDW, Lower Deep Water) than in the euphotic zone. Bacterial community structure, assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was depth-specific. A distance based linear model (DistLM) revealed that the variability found in bacterial community structure was mainly explained by temperature nitrate, phosphate, dissolved organic matter (DOM) fluorescence, prokaryotic abundance, leucine incorporation and to a lesser extent salinity, oxygen, CDOM absorbance and dissolved organic carbon concentration. Our results displayed a bacterial community structure shaped not only by depth-related physicochemical features but also by DOM quality, indicating that different prokaryotic taxa have the potential to metabolize particular DOM sources.

Assessment of bacterial bph gene in Amazonian dark earth and their adjacent soils.

PubMed

Brossi, Maria Julia de Lima; Mendes, Lucas William; Germano, Mariana Gomes; Lima, Amanda Barbosa; Tsai, Siu Mui

2014-01-01

Amazonian Anthrosols are known to harbour distinct and highly diverse microbial communities. As most of the current assessments of these communities are based on taxonomic profiles, the functional gene structure of these communities, such as those responsible for key steps in the carbon cycle, mostly remain elusive. To gain insights into the diversity of catabolic genes involved in the degradation of hydrocarbons in anthropogenic horizons, we analysed the bacterial bph gene community structure, composition and abundance using T-RFLP, 454-pyrosequencing and quantitative PCR essays, respectively. Soil samples were collected in two Brazilian Amazon Dark Earth (ADE) sites and at their corresponding non-anthropogenic adjacent soils (ADJ), under two different land use systems, secondary forest (SF) and manioc cultivation (M). Redundancy analysis of T-RFLP data revealed differences in bph gene structure according to both soil type and land use. Chemical properties of ADE soils, such as high organic carbon and organic matter, as well as effective cation exchange capacity and pH, were significantly correlated with the structure of bph communities. Also, the taxonomic affiliation of bph gene sequences revealed the segregation of community composition according to the soil type. Sequences at ADE sites were mostly affiliated to aromatic hydrocarbon degraders belonging to the genera Streptomyces, Sphingomonas, Rhodococcus, Mycobacterium, Conexibacter and Burkholderia. In both land use sites, shannon's diversity indices based on the bph gene data were higher in ADE than ADJ soils. Collectively, our findings provide evidence that specific properties in ADE soils shape the structure and composition of bph communities. These results provide a basis for further investigations focusing on the bio-exploration of novel enzymes with potential use in the biotechnology/biodegradation industry.

Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gacura, Matthew D.; Sprockett, Daniel D.; Heidenreich, Bess

Here, fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this studywe developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from40 fungal genomes. The primerswere used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senescedmore » tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communitieswere up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystemtype were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.« less

Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi

DOE PAGES

Gacura, Matthew D.; Sprockett, Daniel D.; Heidenreich, Bess; ...

2016-02-17

Here, fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this studywe developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from40 fungal genomes. The primerswere used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senescedmore » tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communitieswere up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystemtype were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.« less

Community Structure Comparisons of Hydrothermal Vent Microbial Mats Along the Mariana Arc and Back-arc

NASA Astrophysics Data System (ADS)

Hager, K. W.; Fullerton, H.; Moyer, C. L.

2015-12-01

Hydrothermal vents along the Mariana Arc and back-arc represent a hotspot of microbial diversity that has not yet been fully recognized. The Mariana Arc and back-arc contain hydrothermal vents with varied vent effluent chemistry and temperature, which translates to diverse community composition. We have focused on iron-rich sites where the dominant primary producers are iron oxidizing bacteria. Because microbes from these environments have proven elusive in culturing efforts, we performed culture independent analysis among different microbial communities found at these hydrothermal vents. Terminal-restriction fragment length polymorphism (T-RFLP) and Illumina sequencing of small subunit ribosomal gene amplicons were used to characterize community members and identify samples for shotgun metagenomics. Used in combination, these methods will better elucidate the composition and characteristics of the bacterial communities at these hydrothermal vent systems. The overarching goal of this study is to evaluate and compare taxonomic and metabolic diversity among different communities of microbial mats. We compared communities collected on a fine scale to analyze the bacterial community based on gross mat morphology, geography, and nearby vent effluent chemistry. Taxa richness and evenness are compared with rarefaction curves to visualize diversity. As well as providing a survey of diversity this study also presents a juxtaposition of three methods in which ribosomal small subunit diversity is compared with T-RFLP, next generation amplicon sequencing, and metagenomic shotgun sequencing.

Community Structure Analysis and Biodegradation Potential of Aniline-Degrading Bacteria in Biofilters.

PubMed

Hou, Luanfeng; Wu, Qingping; Gu, Qihui; Zhou, Qin; Zhang, Jumei

2018-07-01

Aniline has aroused general concern owing to its strong toxicity and widespread distribution in water and soil. In the present study, the bacterial community composition before and after aniline acclimation was investigated. High-throughput Illumina MiSeq sequencing analysis illustrated a large shift in the structure of the bacterial community during the aniline acclimation period. Bacillus, Lactococcus, and Enterococcus were the dominant bacteria in biologically activated carbon before acclimation. However, the proportions of Pseudomonas, Thermomonas, and Acinetobacter increased significantly and several new bacterial taxa appeared after aniline acclimation, indicating that aniline acclimation had a strong impact on the bacterial community structure of biological activated carbon samples. Strain AN-1 accounted for the highest number of colonies on incubation plates and was identified as Acinetobacter sp. according to phylogenetic analysis of the 16S ribosomal ribonucleic acid gene sequence. Strain AN-1 was able to grow on aniline at pH value 4.0-10.0 and showed high aniline-degrading ability at neutral pH.

Chemistry Simulations Using MERRA-2 Reanalysis with the GMI CTM and Replay in Support of the Atmospheric Composition Community

NASA Technical Reports Server (NTRS)

Oman, Luke D.; Strahan, Susan E.

2016-01-01

Simulations using reanalyzed meteorological conditions have been long used to understand causes of atmospheric composition change over the recent past. Using the new Modern-Era Retrospective analysis for Research and Applications, version 2 (MERRA-2) meteorology, chemistry simulations are being conducted to create products covering 1980-2016 for the atmospheric composition community. These simulations use the Global Modeling Initiative (GMI) chemical mechanism in two different models: the GMI Chemical Transport Model (CTM) and the GEOS-5 model developed Replay mode. Replay mode means an integration of the GEOS-5 general circulation model that is incrementally adjusted each time step toward the MERRA-2 analysis. The GMI CTM is a 1 x 1.25 simulation and the MERRA-2 GMI Replay simulation uses the native MERRA-2 approximately horizontal resolution on the cubed sphere. The Replay simulations is driven by the online use of key MERRA-2 meteorological variables (i.e. U, V, T, and surface pressure) with all other variables calculated in response to those variables. A specialized set of transport diagnostics is included in both runs to better understand trace gas transport and changes over the recent past.

Analysis of Lung Microbiota in Bronchoalveolar Lavage, Protected Brush and Sputum Samples from Subjects with Mild-To-Moderate Cystic Fibrosis Lung Disease

PubMed Central

Hogan, Deborah A.; Willger, Sven D.; Dolben, Emily L.; Hampton, Thomas H.; Stanton, Bruce A.; Morrison, Hilary G.; Sogin, Mitchell L.; Czum, Julianna; Ashare, Alix

2016-01-01

Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relationships between microbiota in samples taken directly from the lung and the microbiota in spontaneously expectorated sputum. In this initial study, nine stable, adult CF patients with an FEV1>50% underwent regional sampling of different lobes of the right lung by bronchoalveolar lavage (BAL) and protected brush (PB) sampling of mucus plugs. Sputum samples were obtained from six of the nine subjects immediately prior to the procedure. Microbial community analysis was performed on DNA extracted from these samples and the extent of damage in each lobe was quantified from a recent CT scan. The extent of damage observed in regions of the right lung did not correlate with specific microbial genera, levels of community diversity or composition, or bacterial genome copies per ml of BAL fluid. In all subjects, BAL fluid from different regions of the lung contained similar microbial communities. In eight out of nine subjects, PB samples from different regions of the lung were also similar in microbial community composition, and were similar to microbial communities in BAL fluid from the same lobe. Microbial communities in PB samples were more diverse than those in BAL samples, suggesting enrichment of some taxa in mucus plugs. To our knowledge, this study is the first to examine the microbiota in different regions of the CF lung in clinically stable individuals with mild-to-moderate CF-related lung disease. PMID:26943329

Variation in ectomycorrhizal fungal communities associated with Oreomunnea mexicana (Juglandaceae) in a Neotropical montane forest.

PubMed

Corrales, Adriana; Arnold, A Elizabeth; Ferrer, Astrid; Turner, Benjamin L; Dalling, James W

2016-01-01

Neotropical montane forests are often dominated by ectomycorrhizal (EM) tree species, yet the diversity of their EM fungal communities remains poorly explored. In lower montane forests in western Panama, the EM tree species Oreomunnea mexicana (Juglandaceae) forms locally dense populations in forest otherwise characterized by trees that form arbuscular mycorrhizal (AM) associations. The objective of this study was to compare the composition of EM fungal communities associated with Oreomunnea adults, saplings, and seedlings across sites differing in soil fertility and the amount and seasonality of rainfall. Analysis of fungal nrITS DNA (nuclear ribosomal internal transcribed spacers) revealed 115 EM fungi taxa from 234 EM root tips collected from adults, saplings, and seedlings in four sites. EM fungal communities were equally species-rich and diverse across Oreomunnea developmental stages and sites, regardless of soil conditions or rainfall patterns. However, ordination analysis revealed high compositional turnover between low and high fertility/rainfall sites located ca. 6 km apart. The EM fungal community was dominated by Russula (ca. 36 taxa). Cortinarius, represented by 14 species and previously reported to extract nitrogen from organic sources under low nitrogen availability, was found only in low fertility/high rainfall sites. Phylogenetic diversity analyses of Russula revealed greater evolutionary distance among taxa found on sites with contrasting fertility and rainfall than was expected by chance, suggesting that environmental differences among sites may be important in structuring EM fungal communities. More research is needed to evaluate whether EM fungal taxa associated with Oreomunnea form mycorrhizal networks that might account for local dominance of this tree species in otherwise diverse forest communities.

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem.

PubMed

Zhou, Jizhong; Deng, Ye; Zhang, Ping; Xue, Kai; Liang, Yuting; Van Nostrand, Joy D; Yang, Yunfeng; He, Zhili; Wu, Liyou; Stahl, David A; Hazen, Terry C; Tiedje, James M; Arkin, Adam P

2014-03-04

Unraveling the drivers of community structure and succession in response to environmental change is a central goal in ecology. Although the mechanisms shaping community structure have been intensively examined, those controlling ecological succession remain elusive. To understand the relative importance of stochastic and deterministic processes in mediating microbial community succession, a unique framework composed of four different cases was developed for fluidic and nonfluidic ecosystems. The framework was then tested for one fluidic ecosystem: a groundwater system perturbed by adding emulsified vegetable oil (EVO) for uranium immobilization. Our results revealed that groundwater microbial community diverged substantially away from the initial community after EVO amendment and eventually converged to a new community state, which was closely clustered with its initial state. However, their composition and structure were significantly different from each other. Null model analysis indicated that both deterministic and stochastic processes played important roles in controlling the assembly and succession of the groundwater microbial community, but their relative importance was time dependent. Additionally, consistent with the proposed conceptual framework but contradictory to conventional wisdom, the community succession responding to EVO amendment was primarily controlled by stochastic rather than deterministic processes. During the middle phase of the succession, the roles of stochastic processes in controlling community composition increased substantially, ranging from 81.3% to 92.0%. Finally, there are limited successional studies available to support different cases in the conceptual framework, but further well-replicated explicit time-series experiments are needed to understand the relative importance of deterministic and stochastic processes in controlling community succession.

When micro meets macro: microbial lipid analysis and ecosystem ecology

NASA Astrophysics Data System (ADS)

Balser, T.; Gutknecht, J.

2008-12-01

There is growing interest in linking soil microbial community composition and activity with large-scale field studies of nutrient cycling or plant community response to disturbances. And while analysis of microbial communities has moved rapidly in the past decade from culture-based to non-culture based techniques, still it must be asked what have we gained from the move? How well does the necessarily micro-scale of microbial analysis allow us to address questions of interest at the macro-scale? Several challenges exist in bridging the scales, and foremost is the question of methodological feasibility. Past microbiological methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. We describe the use of a modified lipid extraction method to generate microbial community data sets that allow us to match landscape-scale or long-term ecological studies with microbial community data. We briefly discuss the challenges and advantages associated with lipid analysis as an approach to addressing ecosystem ecological studies, and provide examples from our research in ecosystem restoration and recovery following disturbance and climate change.

Phylogenetic and functional potential links pH and N2O emissions in pasture soils.

PubMed

Samad, Md Sainur; Biswas, Ambarish; Bakken, Lars R; Clough, Timothy J; de Klein, Cecile A M; Richards, Karl G; Lanigan, Gary J; Morales, Sergio E

2016-10-26

Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N 2 O and N 2 emissions. Soil pH regulates the reduction of N 2 O to N 2 , however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N 2 O emission ratio (N 2 O/(NO + N 2 O + N 2 )) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N 2 O emission ratio and community changes. Soil pH was negatively associated with N 2 O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir &nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N 2 O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N 2 O emission ratio through more efficient conversion of N 2 O to N 2 .

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

NASA Astrophysics Data System (ADS)

Samad, M. D. Sainur; Biswas, Ambarish; Bakken, Lars R.; Clough, Timothy J.; de Klein, Cecile A. M.; Richards, Karl G.; Lanigan, Gary J.; Morales, Sergio E.

2016-10-01

Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.

Methyl Fluoride Affects Methanogenesis Rather than Community Composition of Methanogenic Archaea in a Rice Field Soil

PubMed Central

Daebeler, Anne; Gansen, Martina; Frenzel, Peter

2013-01-01

The metabolic pathways of methane formation vary with environmental conditions, but whether this can also be linked to changes in the active archaeal community structure remains uncertain. Here, we show that the suppression of aceticlastic methanogenesis by methyl fluoride (CH3F) caused surprisingly little differences in community composition of active methanogenic archaea from a rice field soil. By measuring the natural abundances of carbon isotopes we found that the effective dose for a 90% inhibition of aceticlastic methanogenesis in anoxic paddy soil incubations was <0.75% CH3F (v/v). The construction of clone libraries as well as t-RFLP analysis revealed that the active community, as indicated by mcrA transcripts (encoding the α subunit of methyl-coenzyme M reductase, a key enzyme for methanogenesis), remained stable over a wide range of CH3F concentrations and represented only a subset of the methanogenic community. More precisely, Methanocellaceae were of minor importance, but Methanosarcinaceae dominated the active population, even when CH3F inhibition only allowed for aceticlastic methanogenesis. In addition, we detected mcrA gene fragments of a so far unrecognised phylogenetic cluster. Transcription of this phylotype at methyl fluoride concentrations suppressing aceticlastic methanogenesis suggests that the respective organisms perform hydrogenotrophic methanogenesis. Hence, the application of CH3F combined with transcript analysis is not only a useful tool to measure and assign in situ acetate usage, but also to explore substrate usage by as yet uncultivated methanogens. PMID:23341965

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

PubMed Central

Samad, M. d. Sainur; Biswas, Ambarish; Bakken, Lars R.; Clough, Timothy J.; de Klein, Cecile A. M.; Richards, Karl G.; Lanigan, Gary J.; Morales, Sergio E.

2016-01-01

Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2. PMID:27782174

Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes ▿ †

PubMed Central

Will, Christiane; Thürmer, Andrea; Wollherr, Antje; Nacke, Heiko; Herold, Nadine; Schrumpf, Marion; Gutknecht, Jessica; Wubet, Tesfaye; Buscot, François; Daniel, Rolf

2010-01-01

The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the Acidobacteria, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, Firmicutes, and Bacteroidetes. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (H′) was higher in the A horizons than in the corresponding B horizons. In addition, the H′ was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the Actinobacteria, Bacteroidetes, Cyanobacteria, Fibrobacteres, Firmicutes, Spirochaetes, Verrucomicrobia, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria were derived from A horizons, whereas the majority of the sequences related to Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospira, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass. PMID:20729324

Response of periphyton fatty acid composition to supplemental flows in the upper Esopus Creek, Catskill Mountains, New York

USGS Publications Warehouse

George, Scott D.; Ernst, Anne G.; Baldigo, Barry P.; Honeyfield, Dale C.

2016-01-07

Fatty acid analysis of periphyton is an emerging tool for assessing the condition of a stream ecosystem on the basis of its water quality. The study presented in this report was designed to test the hypothesis that periphyton communities have a fatty acid profile that can detect excessive turbidity and suspended sediment. The fatty acid composition of periphyton was assessed during two seasons upstream and downstream from an underground aqueduct that provides supplemental flows, which are a potential source of turbidity and suspended sediment on the upper Esopus Creek, New York. These data were compared with measurements of periphyton standing crop, diatom community structure and integrity, and basic water-quality parameters. Periphyton standing crop and diatom community integrity indicated little evidence of impairment from the supplemental flows. The relative abundances of two physiologically important fatty acids, γ-linolenic acid (18:3ω6) and eicosapentaenoic acid (20:5ω3), were significantly lower downstream from the supplemental flows and multivariate analyses of fatty acid profiles identified significant differences between sites upstream and downstream from the supplemental flows. Individual fatty acids and summary metrics, however, were not significantly correlated with turbidity or suspended sediment. Together, these results indicate that the supplemental flows may cause some measurable effects but they do not constitute a major disturbance to the periphyton community on the upper Esopus Creek. Fatty acid analysis may have potential as a tool for monitoring changes in periphyton nutritional composition that may reflect water quality and ecosystem health but needs to be further evaluated around a more definitive source of water-quality impairment.

Jellyfish modulate bacterial dynamic and community structure.

PubMed

Tinta, Tinkara; Kogovšek, Tjaša; Malej, Alenka; Turk, Valentina

2012-01-01

Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.

Herpetofaunal Community Change in Multiple Habitats after Fifteen Years in a Southwest Florida Preserve, USA

PubMed Central

Cassani, John R.; Croshaw, Dean A.; Bozzo, Joseph; Brooks, Brenda; Everham, Edwin M.; Ceilley, David W.; Hanson, Deborah

2015-01-01

Herpetofaunal declines have been documented globally, and southern Florida, USA, is an especially vulnerable region because of high impacts from hydrological perturbations and nonindigenous species. To assess the extent of recent change in herpetofauna community composition, we established a baseline inventory during 1995-97 at a managed preserve in a habitat rich area of southwest Florida, and repeated our sampling methods fifteen years later (2010-11). Nine drift fence arrays were placed in four habitat types: mesic flatwood, mesic hammock, depression marsh, and wet prairie. Trapping occurred daily for one week during 7-8 sampling runs in each period (57 and 49 total sampling days, respectively). Species richness was maintained in mesic hammock habitats but varied in the others. Catch rates of several native species (Anaxyrus terrestris, Lithobates grylio, Anolis carolinensis, Nerodia fasciata) declined significantly. Other native species (Lithobates sphenocephalus, Siren lacertian, and Notophthalmus viridescens piaropicola) that were abundant in 1995-97 declined by greater than 50%. Catch rate of only two species (the nonindigenous Anolis sagrei and the native Diadophis punctatus) increased significantly. Hierarchical cluster analysis indicated similarity within habitat types but significant dissimilarity between sampling periods, confirming shifts in community composition. Analysis of individual species’ contributions to overall similarity across habitats shows a shift from dominance of native species in the 1990s to increased importance of nonindigenous species in 2010-11. Although natural population fluctuations may have influenced differences between the two sampling periods, our results suggest considerable recent change in the structure and composition of this southwest Florida herpetofaunal community. The causes are unknown, but hydrological shifts and ecological impacts of nonindigenous species may have contributed. PMID:26016475

Microbial diversity in hummock and hollow soils of three wetlands on the Qinghai-Tibetan Plateau revealed by 16S rRNA pyrosequencing.

PubMed

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world's highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1-10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem.

Microbial Diversity in Hummock and Hollow Soils of Three Wetlands on the Qinghai-Tibetan Plateau Revealed by 16S rRNA Pyrosequencing

PubMed Central

Deng, Yongcui; Cui, Xiaoyong; Hernández, Marcela; Dumont, Marc G.

2014-01-01

The wetlands of the Qinghai-Tibetan Plateau are believed to play an important role in global nutrient cycling, but the composition and diversity of microorganisms in this ecosystem are poorly characterized. An understanding of the effects of geography and microtopography on microbial populations will provide clues to the underlying mechanisms that structure microbial communities. In this study, we used pyrosequencing-based analysis of 16S rRNA gene sequences to assess and compare the composition of soil microbial communities present in hummock and hollow soils from three wetlands (Dangxiong, Hongyuan and Maduo) on the Qinghai-Tibetan Plateau, the world’s highest plateau. A total of 36 bacterial phyla were detected. Proteobacteria (34.5% average relative abundance), Actinobacteria (17.3%) and Bacteroidetes (11%) had the highest relative abundances across all sites. Chloroflexi, Acidobacteria, Verrucomicrobia, Firmicutes, and Planctomycetes were also relatively abundant (1–10%). In addition, archaeal sequences belonging to Euryarchaea, Crenarchaea and Thaumarchaea were detected. Alphaproteobacteria sequences, especially of the order Rhodospirillales, were significantly more abundant in Maduo than Hongyuan and Dangxiong wetlands. Compared with Hongyuan soils, Dangxiong and Maduo had significantly higher relative abundances of Gammaproteobacteria sequences (mainly order Xanthomonadales). Hongyuan wetland had a relatively high abundance of methanogens (mainly genera Methanobacterium, Methanosarcina and Methanosaeta) and methanotrophs (mainly Methylocystis) compared with the other two wetlands. Principal coordinate analysis (PCoA) indicated that the microbial community structure differed between locations and microtopographies and canonical correspondence analysis indicated an association between microbial community structure and soil properties or geography. These insights into the microbial community structure and the main controlling factors in wetlands of the Qinghai-Tibetan Plateau provide a valuable background for further studies on biogeochemical processes in this distinct ecosystem. PMID:25078273

The influences of canopy species and topographic variables on understory species diversity and composition in coniferous forests.

PubMed

Huo, Hong; Feng, Qi; Su, Yong-hong

2014-01-01

Understanding the factors that influence the distribution of understory vegetation is important for biological conservation and forest management. We compared understory species composition by multi-response permutation procedure and indicator species analysis between plots dominated by Qinghai spruce (Picea crassifolia Kom.) and Qilian juniper (Sabina przewalskii Kom.) in coniferous forests of the Qilian Mountains, northwestern China. Understory species composition differed markedly between the forest types. Many heliophilous species were significantly associated with juniper forest, while only one species was indicative of spruce forest. Using constrained ordination and the variation partitioning model, we quantitatively assessed the relative effects of two sets of explanatory variables on understory species composition. The results showed that topographic variables had higher explanatory power than did site conditions for understory plant distributions. However, a large amount of the variation in understory species composition remained unexplained. Forward selection revealed that understory species distributions were primarily affected by elevation and aspect. Juniper forest had higher species richness and α-diversity and lower β-diversity in the herb layer of the understory plant community than spruce forest, suggesting that the former may be more important in maintaining understory biodiversity and community stability in alpine coniferous forest ecosystems.

Modeling Pollinator Community Response to Contrasting Bioenergy Scenarios

PubMed Central

Bennett, Ashley B.; Meehan, Timothy D.; Gratton, Claudio; Isaacs, Rufus

2014-01-01

In the United States, policy initiatives aimed at increasing sources of renewable energy are advancing bioenergy production, especially in the Midwest region, where agricultural landscapes dominate. While policy directives are focused on renewable fuel production, biodiversity and ecosystem services will be impacted by the land-use changes required to meet production targets. Using data from field observations, we developed empirical models for predicting abundance, diversity, and community composition of flower-visiting bees based on land cover. We used these models to explore how bees might respond under two contrasting bioenergy scenarios: annual bioenergy crop production and perennial grassland bioenergy production. In the two scenarios, 600,000 ha of marginal annual crop land or marginal grassland were converted to perennial grassland or annual row crop bioenergy production, respectively. Model projections indicate that expansion of annual bioenergy crop production at this scale will reduce bee abundance by 0 to 71%, and bee diversity by 0 to 28%, depending on location. In contrast, converting annual crops on marginal soil to perennial grasslands could increase bee abundance from 0 to 600% and increase bee diversity between 0 and 53%. Our analysis of bee community composition suggested a similar pattern, with bee communities becoming less diverse under annual bioenergy crop production, whereas bee composition transitioned towards a more diverse community dominated by wild bees under perennial bioenergy crop production. Models, like those employed here, suggest that bioenergy policies have important consequences for pollinator conservation. PMID:25365559

Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.

PubMed

Kuehn, Joanna S; Gorden, Patrick J; Munro, Daniel; Rong, Ruichen; Dong, Qunfeng; Plummer, Paul J; Wang, Chong; Phillips, Gregory J

2013-01-01

Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified as causative agents of mastitis, many clinical mastitis cases remain culture negative, even after enrichment for bacterial growth. To understand the basis for this increasingly common phenomenon, the composition of bacterial communities from milk samples was analyzed using culture independent pyrosequencing of amplicons of 16S ribosomal RNA genes (16S rDNA). Comparisons were made of the microbial community composition of culture negative milk samples from mastitic quarters with that of non-mastitic quarters from the same animals. Genomic DNA from culture-negative clinical and healthy quarter sample pairs was isolated, and amplicon libraries were prepared using indexed primers specific to the V1-V2 region of bacterial 16S rRNA genes and sequenced using the Roche 454 GS FLX with titanium chemistry. Evaluation of the taxonomic composition of these samples revealed significant differences in the microbiota in milk from mastitic and healthy quarters. Statistical analysis identified seven bacterial genera that may be mainly responsible for the observed microbial community differences between mastitic and healthy quarters. Collectively, these results provide evidence that cases of culture negative mastitis can be associated with bacterial species that may be present below culture detection thresholds used here. The application of culture-independent bacterial community profiling represents a powerful approach to understand long-standing questions in animal health and disease.

16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria

PubMed Central

Oliveira, Cássia; Gunderman, Lauren; Coles, Cathryn A.; Lochmann, Jason; Parks, Megan; Ballard, Ethan; Glazko, Galina; Rahmatallah, Yasir; Tackett, Alan J.; Thomas, David J.

2018-01-01

The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa. PMID:29551950

Community Composition and Abundance of Anammox Bacteria in Cattail Rhizosphere Sediments at Three Phenological Stages.

PubMed

Zhou, Xiaohong; Zhang, Jinping; Wen, Chunzi

2017-11-01

The distribution of anammox bacteria in rhizosphere sediments of cattail (Typha orientalis) at different phenological stages was investigated. Results showed that the number of 16S rRNA gene copies of the anammox bacteria was considerably higher in the rhizosphere sediment than in the nonrhizosphere sediment and control sediment. The abundances of the anammox bacteria exhibited striking temporal variations in the three different cattail phenological stages. In addition, the Chao1 and Shannon H indexes of the anammox bacteria in cattail rhizosphere sediments had evident spatial and temporal variations at different phenological stages. Four anammox genera (Brocadia, Kuenenia, Jettenia, and a new cluster) were detected and had proportions of 34.18, 45.57, 0.63, and 19.62%, respectively. The CCA analysis results indicated that Cu, TN, Pb, and Zn were pivotal factors that affect anammox bacteria composition. The PCoA analysis results indicated that the community structure at the rhizosphere and nonrhizosphere sediments collected on July was relatively specific and was different from sediments collected on other months, suggesting that cattail can influence the community structures of the anammox bacteria at the maturity stage.

Chapter 11. Community analysis-based methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Y.; Wu, C.H.; Andersen, G.L.

2010-05-01

Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. Inmore » increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.« less

Molecular characterization of total and metabolically active bacterial communities of "white colonizations" in the Altamira Cave, Spain.

PubMed

Portillo, M Carmen; Saiz-Jimenez, Cesareo; Gonzalez, Juan M

2009-01-01

Caves with paleolithic paintings are influenced by bacterial development. Altamira Cave (Spain) contains some of the most famous paintings from the Paleolithic era. An assessment of the composition of bacterial communities that have colonized this cave represents a first step in understanding and potentially controlling their proliferation. In this study, areas showing colonization with uncolored microorganisms, referred to as "white colonizations", were analyzed. Microorganisms present in these colonizations were studied using DNA analysis, and those showing significant metabolic activity were detected in RNA-based RNA analysis. Bacterial community fingerprints were obtained both from DNA and RNA analyses, indicating differences between the microorganisms present and metabolically active in these white colonizations. Metabolically active microorganisms represented only a fraction of the total bacterial community present in the colonizations. 16S rRNA gene libraries were used to identify the major representative members of the studied communities. Proteobacteria constituted the most frequently found division both among metabolically active microorganisms (from RNA-based analysis) and those present in the community (from DNA analysis). Results suggest the existence of a huge variety of taxa in white colonizations of the Altamira Cave which represent a potential risk for the conservation of the cave and its paintings.

Mineral Control of Soil Carbon Dynamics in Forest Soils: A Lithosequence Under Ponderosa Pine

NASA Astrophysics Data System (ADS)

Heckman, K. A.; Welty-Bernard, A.; Rasmussen, C.; Schwartz, E.; Chorover, J.

2008-12-01

The role of soil organic carbon in regulating atmospheric CO2 concentration has spurred interest in both quantifying existing soil C stocks and modeling the behavior of soil C under climate change scenarios. Soil parent material exerts direct control over soil organic carbon content through its influence on soil pH and mineral composition. Soil acidity and mineral composition also influence soil microbial community composition and activity, thereby controlling soil respiration rates and microbial biomass size. We sampled a lithosequence of four parent materials (rhyolite, granite, basalt, limestone) under Pinus ponderosa to examine the effects of soil mineralogy and acidity on soil organic carbon content and soil microbial community. Three soil profiles were examined on each parent material and analyzed by X-ray diffraction, pH, selective dissolution, C and N content, and 13C signature. Soils from each of the four parent materials were incubated for 40 days, and microbial communities were compared on the basis of community composition (as determined through T-RFLP analysis), specific metabolic activity, biomass, δ13C of respired CO2, and cumulative amount of C mineralized over the course of the incubation. Soil C content varied significantly among soils of different parent material, and was strongly and positively associated with the abundance of Al-humus complexes r2 = 0.71; P < 0.0001, Fe-humus complexes r2 = 0.74; P = 0.0003, and crystalline Fe-oxide content r2 = 0.63; P = 0.0023. Microbial community composition varied significantly among soils and showed strong associations with soil pH 1:1 in KCl; r2 = 0.87; P < 0.0001, concentration of exchangeable Al r2 = 0.81; P < 0.0001, amorphous Fe oxide content r2 = 0.59; P < 0.004, and Al-humus content r2 = 0.35; P < 0.04. Mineralization rates, biomass and δ13C of respired CO2 differed among parent materials, and also varied with incubation time as substrate quality and N availability changed. The results demonstrate that within a specific ecosystem type, soil parent material exerts significant control over the lability and bioavailability of soil C and soil microbial community composition. We suggest that soil parent material and mineralogy are critical parameters for predicting soil C dynamics and recalcitrance of soil C stocks.

Microbial biogeography of arctic streams: exploring influences of lithology and habitat.

PubMed

Larouche, Julia R; Bowden, William B; Giordano, Rosanna; Flinn, Michael B; Crump, Byron C

2012-01-01

Terminal restriction fragment length polymorphism and 16S rRNA gene sequencing were used to explore the community composition of bacterial communities in biofilms on sediments (epipssamon) and rocks (epilithon) in stream reaches that drain watersheds with contrasting lithologies in the Noatak National Preserve, Alaska. Bacterial community composition varied primarily by stream habitat and secondarily by lithology. Positive correlations were detected between bacterial community structure and nutrients, base cations, and dissolved organic carbon. Our results showed significant differences at the stream habitat, between epipssamon and epilithon bacterial communities, which we expected. Our results also showed significant differences at the landscape scale that could be related to different lithologies and associated stream biogeochemistry. These results provide insight into the bacterial community composition of little known and pristine arctic stream ecosystems and illustrate how differences in the lithology, soils, and vegetation community of the terrestrial environment interact to influence stream bacterial taxonomic richness and composition.

Microbial Biogeography of Arctic Streams: Exploring Influences of Lithology and Habitat

PubMed Central

Larouche, Julia R.; Bowden, William B.; Giordano, Rosanna; Flinn, Michael B.; Crump, Byron C.

2012-01-01

Terminal restriction fragment length polymorphism and 16S rRNA gene sequencing were used to explore the community composition of bacterial communities in biofilms on sediments (epipssamon) and rocks (epilithon) in stream reaches that drain watersheds with contrasting lithologies in the Noatak National Preserve, Alaska. Bacterial community composition varied primarily by stream habitat and secondarily by lithology. Positive correlations were detected between bacterial community structure and nutrients, base cations, and dissolved organic carbon. Our results showed significant differences at the stream habitat, between epipssamon and epilithon bacterial communities, which we expected. Our results also showed significant differences at the landscape scale that could be related to different lithologies and associated stream biogeochemistry. These results provide insight into the bacterial community composition of little known and pristine arctic stream ecosystems and illustrate how differences in the lithology, soils, and vegetation community of the terrestrial environment interact to influence stream bacterial taxonomic richness and composition. PMID:22936932

Distribution of ether lipids and composition of the archaeal community in terrestrial geothermal springs: impact of environmental variables.

PubMed

Xie, Wei; Zhang, Chuanlun L; Wang, Jinxiang; Chen, Yufei; Zhu, Yuanqing; de la Torre, José R; Dong, Hailiang; Hartnett, Hilairy E; Hedlund, Brian P; Klotz, Martin G

2015-05-01

Archaea can respond to changes in the environment by altering the composition of their membrane lipids, for example, by modification of the abundance and composition of glycerol dialkyl glycerol tetraethers (GDGTs). Here, we investigated the abundance and proportions of polar GDGTs (P-GDGTs) and core GDGTs (C-GDGTs) sampled in different seasons from Tengchong hot springs (Yunnan, China), which encompassed a pH range of 2.5-10.1 and a temperature range of 43.7-93.6°C. The phylogenetic composition of the archaeal community (reanalysed from published work) divided the Archaea in spring sediment samples into three major groups that corresponded with spring pH: acidic, circumneutral and alkaline. Cluster analysis showed correlation between spring pH and the composition of P- and C-GDGTs and archaeal 16S rRNA genes, indicating an intimate link between resident Archaea and the distribution of P- and C-GDGTs in Tengchong hot springs. The distribution of GDGTs in Tengchong springs was also significantly affected by temperature; however, the relationship was weaker than with pH. Analysis of published datasets including samples from Tibet, Yellowstone and the US Great Basin hot springs revealed a similar relationship between pH and GDGT content. Specifically, low pH springs had higher concentrations of GDGTs with high numbers of cyclopentyl rings than neutral and alkaline springs, which is consistent with the predominance of high cyclopentyl ring-characterized Sulfolobales and Thermoplasmatales present in some of the low pH springs. Our study suggests that the resident Archaea in these hot springs are acclimated if not adapted to low pH by their genetic capacity to effect the packing density of their membranes by increasing cyclopentyl rings in GDGTs at the rank of community. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Using a trait-based approach to link microbial community composition and functioning to soil salinity

NASA Astrophysics Data System (ADS)

Rath, Kristin; Fierer, Noah; Rousk, Johannes

2017-04-01

Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared through 16S rRNA gene amplicon sequencing. Microbial community composition changed greatly along the salinity gradients. Using the salt-tolerance assessments to estimate bacterial trait-distributions we could determine substantial differences in tolerance to salt revealing a strong causal connection between environment and trait distributions. By constraining the community composition with salinity tolerance in ordinations, we could assign which community differences were directly due to a shift in community trait distributions. These analyses revealed that a substantial part (up to 30%) of the community composition differences were directly driven by environmental salt concentrations.. Even though communities in saline soils had trait-distributions aligned to their environment, their performance (respiration, growth rates) was lower than those in non-saline soils and remained low even after input of organic material. Using a trait-based approach we could connect filtered trait distributions along environmental gradients, to the composition of the microbial community. We show that soil salinity played an important role in shaping microbial community composition by selecting for communities with higher salt tolerance. The shift toward bacterial communities with trait distributions matched to salt environments probably compensated for much of the potential loss of function induced by salinity, resulting in a degree of apparent functional redundancy for decomposition. However, more tolerant communities still showed reduced functioning, suggesting a trade-off between salt tolerance and performance.

Using DGGE and 16S rRNA gene sequence analysis to evaluate changes in oral bacterial composition.

PubMed

Chen, Zhou; Trivedi, Harsh M; Chhun, Nok; Barnes, Virginia M; Saxena, Deepak; Xu, Tao; Li, Yihong

2011-01-01

To investigate whether a standard dental prophylaxis followed by tooth brushing with an antibacterial dentifrice will affect the oral bacterial community, as determined by denaturing gradient gel electrophoresis (DGGE) combined with 16S rRNA gene sequence analysis. Twenty-four healthy adults were instructed to brush their teeth using commercial dentifrice for 1 week during a washout period. An initial set of pooled supragingival plaque samples was collected from each participant at baseline (0 h) before prophylaxis treatment. The subjects were given a clinical examination and dental prophylaxis and asked to brush for 1 min with a dentifrice containing 0.3% triclosan, 2.0% PVM/MA copolymer and 0.243% sodium fluoride (Colgate Total). On the following day, a second set of pooled supragingival plaque samples (24 h) was collected. Total bacterial genomic DNA was isolated from the samples. Differences in the microbial composition before and after the prophylactic procedure and tooth brushing were assessed by comparing the DGGE profiles and 16S rRNA gene segments sequence analysis. Two distinct clusters of DGGE profiles were found, suggesting that a shift in the microbial composition had occurred 24 h after the prophylaxis and brushing. A detailed sequencing analysis of 16S rRNA gene segments further identified 6 phyla and 29 genera, including known and unknown bacterial species. Importantly, an increase in bacterial diversity was observed after 24 h, including members of the Streptococcaceae family, Prevotella, Corynebacterium, TM7 and other commensal bacteria. The results suggest that the use of a standard prophylaxis followed by the use of the dentifrice containing 0.3% triclosan, 2.0% PVM/MA copolymer and 0.243% sodium fluoride may promote a healthier composition within the oral bacterial community.

Census of the bacterial community of the gypsy moth larval midgut by using culturing and culture-independent methods.

PubMed

Broderick, Nichole A; Raffa, Kenneth F; Goodman, Robert M; Handelsman, Jo

2004-01-01

Little is known about bacteria associated with Lepidoptera, the large group of mostly phytophagous insects comprising the moths and butterflies. We inventoried the larval midgut bacteria of a polyphagous foliivore, the gypsy moth (Lymantria dispar L.), whose gut is highly alkaline, by using traditional culturing and culture-independent methods. We also examined the effects of diet on microbial composition. Analysis of individual third-instar larvae revealed a high degree of similarity of microbial composition among insects fed on the same diet. DNA sequence analysis indicated that most of the PCR-amplified 16S rRNA genes belong to the gamma-Proteobacteria and low G+C gram-positive divisions and that the cultured members represented more than half of the phylotypes identified. Less frequently detected taxa included members of the alpha-Proteobacterium, Actinobacterium, and Cytophaga/Flexibacter/Bacteroides divisions. The 16S rRNA gene sequences from 7 of the 15 cultured organisms and 8 of the 9 sequences identified by PCR amplification diverged from previously reported bacterial sequences. The microbial composition of midguts differed substantially among larvae feeding on a sterilized artificial diet, aspen, larch, white oak, or willow. 16S rRNA analysis of cultured isolates indicated that an Enterococcus species and culture-independent analysis indicated that an Entbacter sp. were both present in all larvae, regardless of the feeding substrate; the sequences of these two phylotypes varied less than 1% among individual insects. These results provide the first comprehensive description of the microbial diversity of a lepidopteran midgut and demonstrate that the plant species in the diet influences the composition of the gut bacterial community.

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

PubMed Central

Woodhouse, Jason Nicholas; Kinsela, Andrew Stephen; Collins, Richard Nicholas; Bowling, Lee Chester; Honeyman, Gordon L; Holliday, Jon K; Neilan, Brett Anthony

2016-01-01

The frequency of freshwater cyanobacterial blooms is at risk of increasing as a consequence of climate change and eutrophication of waterways. It is increasingly apparent that abiotic data are insufficient to explain variability within the cyanobacterial community, with biotic factors such as heterotrophic bacterioplankton, viruses and protists emerging as critical drivers. During the Australian summer of 2012–2013, a bloom that occurred in a shallow ephemeral lake over a 6-month period was comprised of 22 distinct cyanobacteria, including Microcystis, Dolichospermum, Oscillatoria and Sphaerospermopsis. Cyanobacterial cell densities, bacterial community composition and abiotic parameters were assessed over this period. Alpha-diversity indices and multivariate analysis were successful at differentiating three distinct bloom phases and the contribution of abiotic parameters to each. Network analysis, assessing correlations between biotic and abiotic variables, reproduced these phases and assessed the relative importance of both abiotic and biotic factors. Variables possessing elevated betweeness centrality included temperature, sodium and operational taxonomic units belonging to the phyla Verrucomicrobia, Planctomyces, Bacteroidetes and Actinobacteria. Species-specific associations between cyanobacteria and bacterioplankton, including the free-living Actinobacteria acI, Bacteroidetes, Betaproteobacteria and Verrucomicrobia, were also identified. We concluded that changes in the abundance and nature of freshwater cyanobacteria are associated with changes in the diversity and composition of lake bacterioplankton. Given this, an increase in the frequency of cyanobacteria blooms has the potential to alter nutrient cycling and contribute to long-term functional perturbation of freshwater systems. PMID:26636552

Microbial Community Biofabrics in a Geothermal Mine Adit▿ †

PubMed Central

Spear, John R.; Barton, Hazel A.; Robertson, Charles E.; Francis, Christopher A.; Pace, Norman R.

2007-01-01

Speleothems such as stalactites and stalagmites are usually considered to be mineralogical in composition and origin; however, microorganisms have been implicated in the development of some speleothems. We have identified and characterized the biological and mineralogical composition of mat-like biofabrics in two novel kinds of speleothems from a 50°C geothermal mine adit near Glenwood Springs, CO. One type of structure consists of 2- to 3-cm-long, 3- to 4-mm-wide, leather-like, hollow, soda straw stalactites. Light and electron microscopy indicated that the stalactites are composed of a mineralized biofabric with several cell morphotypes in a laminated form, with gypsum and sulfur as the dominant mineral components. A small-subunit rRNA gene phylogenetic community analysis along the stalactite length yielded a diverse gradient of organisms, with a relatively simple suite of main constituents: Thermus spp., crenarchaeotes, Chloroflexi, and Gammaproteobacteria. PCR analysis also detected putative crenarchaeal ammonia monooxygenase subunit A (amoA) genes in this community, the majority related to sequences from other geothermal systems. The second type of speleothem, dumpling-like rafts floating on a 50°C pool on the floor of the adit, showed a mat-like fabric of evidently living organisms on the outside of the dumpling, with a multimineral, amorphous, gypsum-based internal composition. These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments. PMID:17693567

Influence of Early XXth Century Plastic Culture on Russian Design Formation

NASA Astrophysics Data System (ADS)

Surina, L.

2017-11-01

The paper deals with the analysis of the experimental research conducted by A.M. Rodchenko and Ya.G. Chernikov who became the ancestors of the Soviet design and substantiated the theory of composition, its main terminology as the basis for professional activities of a designer. It is established that a designer working with traditional or post-traditional visual communication relies on the compositional activity which is at the intersection of science and art and therefore has a dual nature. The preference of various compositional techniques and graphic means by the professional community determines the development direction of avant-garde design.

Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow

PubMed Central

Thiele, Stefan; Fuchs, Bernhard M.; Amann, Rudolf

2014-01-01

Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter. PMID:25527538

Rapid Shifts in Soil and Forest Floor Microbial Communities with Changes in Vegetation during Secondary Tropical Forest Succession

NASA Astrophysics Data System (ADS)

Smith, A.; Marin-Spiotta, E.; Balser, T. C.

2012-12-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. In order to predict how disturbance affects belowground carbon storage, it is important to understand how the forest floor and soil microbial community respond to changes in land cover, and the consequences on SOM formation and stabilization. We are measuring microbial functional diversity and activity across a long-term successional chronosequence of secondary forests regrowing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Here we report intra- and interannual data on soil and litter microbial community composition (via phospholipid fatty acid analysis, PLFA) and microbial activity (via extracellular enzyme activity) from active pastures, secondary forests aged 20, 30, 40, 70, and 90-years, and primary forests. Microbial community composition and extracellular enzyme activity differed significantly by season in these wet subtropical ecosystems, even though differences in mean monthly precipitation between the middle of the dry season (January) and the wet season (July) is only 30mm. Despite seasonal differences, there was a persistent strong effect of land cover type and forest successional stage, or age, on overall microbial community PLFA structure. Using principal component analysis, we found differences in microbial community structure among active pastures, early, and late successional forests. The separation of soil microbes into early and late successional communities parallels the clustering of tree composition data. While the successional patterns held across seasons, the importance of different microbial groups driving these patterns differed seasonally. Biomarkers for gram-positive and actinobacteria (i15:0 and 16:0 10Me) were associated with early (20, 30 & 40 year old) secondary forests in the dry season. These younger forest communities were identified by the biomarker for anaerobic gram-negative bacteria (c19:0) in the wet season, which suggests the presence of anaerobic microsites in these very clayey Oxisols. Enzymatic activity did not differ with succession but was highest in the dry season. We expect this may be due to decreased turnover of enzymes with low soil moisture. Interannual sampling has revealed a very rapid microbial response to changes in aboveground cover. Within a year following woody biomass encroachment, we detected a shift in the soil microbial community from a pasture-associated community to an early secondary forest community in one of our replicate pasture sites. This very rapid response in the belowground microbial community structure to changes in vegetation has not been strongly documented in the literature. This data supports a direct link between aboveground and belowground biotic community structures and highlights the importance of long-term repeated sampling of microbial communities in dynamic ecosystems. Our findings have implications for predicting rapid ecological responses to land-cover change.

Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest

PubMed Central

Xiang, Xingjia; Shi, Yu; Yang, Jian; Kong, Jianjian; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Chu, Haiyan

2014-01-01

Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties. PMID:24452061

Bacterial Community Succession in Pine-Wood Decomposition.

PubMed

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Bacterial Community Succession in Pine-Wood Decomposition

PubMed Central

Kielak, Anna M.; Scheublin, Tanja R.; Mendes, Lucas W.; van Veen, Johannes A.; Kuramae, Eiko E.

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities. PMID:26973611

Metal oxides, clay minerals and charcoal determine the composition of microbial communities in matured artificial soils and their response to phenanthrene.

PubMed

Babin, Doreen; Ding, Guo-Chun; Pronk, Geertje Johanna; Heister, Katja; Kögel-Knabner, Ingrid; Smalla, Kornelia

2013-10-01

Microbial communities in soil reside in a highly heterogeneous habitat where diverse mineral surfaces, complex organic matter and microorganisms interact with each other. This study aimed to elucidate the long-term effect of the soil mineral composition and charcoal on the microbial community composition established in matured artificial soils and their response to phenanthrene. One year after adding sterile manure to different artificial soils and inoculating microorganisms from a Cambisol, the matured soils were spiked with phenanthrene or not and incubated for another 70 days. 16S rRNA gene and internal transcribed spacer fragments amplified from total community DNA were analyzed by denaturing gradient gel electrophoresis. Metal oxides and clay minerals and to a lesser extent charcoal influenced the microbial community composition. Changes in the bacterial community composition in response to phenanthrene differed depending on the mineral composition and presence of charcoal, while no shifts in the fungal community composition were observed. The abundance of ring-hydroxylating dioxygenase genes was increased in phenanthrene-spiked soils except for charcoal-containing soils. Here we show that the formation of biogeochemical interfaces in soil is an ongoing process and that different properties present in artificial soils influenced the bacterial response to the phenanthrene spike. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

[Microbial diversity of sediments from the coasts of Dalian Changshan Islands].

PubMed

Li, Jialin; Wang, Zhonghua; Qin, Song; Wang, Guangyi

2011-05-01

To understand the impacts of anthropogenic activities on structure and composition of bacterial communities and to evaluate how bacterial communities respond to environmental gradients at coastal sediments. The diversity of bacterial communities in sediments from tourist and mariculture zones at coastal area of Dalian Changshan Islands was assessed using terminal restriction fragment length polymorphism (t-RFLP) and denaturing gradient gel electrophoresis (DGGE) approaches. Meanwhile, 16S rRNA clone library was constructed to reveal the composition and structure of bacterial communities in the most seriously polluted site (D4). There were much higher values of richness, Shannon-wiener and evenness index at D4 site by the analysis of terminal restriction fragments (t-RFs). The clustering result on the t-RFs areas and DGGE patterns showed that the bacterial diversity of tourist zone were more similar, while the distinction was increased with pollution levels among the tourist and mariculture zones. The 16S rRNA clone of D4 revealed that the Proteobacteria were the dominant phylum, and gamma-proteobacteria was the main class within Proteobacteria. The study documented changes in bacterial community structure by human impacts of mariculture than geographical location.

Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality.

PubMed

Hautier, Yann; Isbell, Forest; Borer, Elizabeth T; Seabloom, Eric W; Harpole, W Stanley; Lind, Eric M; MacDougall, Andrew S; Stevens, Carly J; Adler, Peter B; Alberti, Juan; Bakker, Jonathan D; Brudvig, Lars A; Buckley, Yvonne M; Cadotte, Marc; Caldeira, Maria C; Chaneton, Enrique J; Chu, Chengjin; Daleo, Pedro; Dickman, Christopher R; Dwyer, John M; Eskelinen, Anu; Fay, Philip A; Firn, Jennifer; Hagenah, Nicole; Hillebrand, Helmut; Iribarne, Oscar; Kirkman, Kevin P; Knops, Johannes M H; La Pierre, Kimberly J; McCulley, Rebecca L; Morgan, John W; Pärtel, Meelis; Pascual, Jesus; Price, Jodi N; Prober, Suzanne M; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Standish, Rachel J; Virtanen, Risto; Wardle, Glenda M; Yahdjian, Laura; Hector, Andy

2018-01-01

Biodiversity is declining in many local communities while also becoming increasingly homogenized across space. Experiments show that local plant species loss reduces ecosystem functioning and services, but the role of spatial homogenization of community composition and the potential interaction between diversity at different scales in maintaining ecosystem functioning remains unclear, especially when many functions are considered (ecosystem multifunctionality). We present an analysis of eight ecosystem functions measured in 65 grasslands worldwide. We find that more diverse grasslands-those with both species-rich local communities (α-diversity) and large compositional differences among localities (β-diversity)-had higher levels of multifunctionality. Moreover, α- and β-diversity synergistically affected multifunctionality, with higher levels of diversity at one scale amplifying the contribution to ecological functions at the other scale. The identity of species influencing ecosystem functioning differed among functions and across local communities, explaining why more diverse grasslands maintained greater functionality when more functions and localities were considered. These results were robust to variation in environmental drivers. Our findings reveal that plant diversity, at both local and landscape scales, contributes to the maintenance of multiple ecosystem services provided by grasslands. Preserving ecosystem functioning therefore requires conservation of biodiversity both within and among ecological communities.

Differences in planktonic microbial communities associated with three types of macrophyte stands in a shallow lake.

PubMed

Mentes, Anikó; Szabó, Attila; Somogyi, Boglárka; Vajna, Balázs; Tugyi, Nóra; Csitári, Bianka; Vörös, Lajos; Felföldi, Tamás

2018-02-01

Little is known about how various substances from living and decomposing aquatic macrophytes affect the horizontal patterns of planktonic bacterial communities. Study sites were located within Lake Kolon, which is a freshwater marsh and can be characterised by open-water sites and small ponds with different macrovegetation (Phragmites australis, Nymphea alba and Utricularia vulgaris). Our aim was to reveal the impact of these macrophytes on the composition of the planktonic microbial communities using comparative analysis of environmental parameters, microscopy and pyrosequencing data. Bacterial 16S rRNA gene sequences were dominated by members of phyla Proteobacteria (36%-72%), Bacteroidetes (12%-33%) and Actinobacteria (5%-26%), but in the anoxic sample the ratio of Chlorobi (54%) was also remarkable. In the phytoplankton community, Cryptomonas sp., Dinobryon divergens, Euglena acus and chrysoflagellates had the highest proportion. Despite the similarities in most of the measured environmental parameters, the inner ponds had different bacterial and algal communities, suggesting that the presence and quality of macrophytes directly and indirectly controlled the composition of microbial plankton. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Signatures of the collapse and incipient recovery of an overexploited marine ecosystem

PubMed Central

Thompson, Patrick L.; Ball, R. Aaron; Fortin, Marie-Josée; Gouhier, Tarik C.; Link, Heike; Moritz, Charlotte; Nenzen, Hedvig; Stanley, Ryan R. E.; Taranu, Zofia E.; Gonzalez, Andrew; Guichard, Frédéric; Pepin, Pierre

2017-01-01

The Northwest Atlantic cod stocks collapsed in the early 1990s and have yet to recover, despite the subsequent establishment of a continuing fishing moratorium. Efforts to understand the collapse and lack of recovery have so far focused mainly on the dynamics of commercially harvested species. Here, we use data from a 33-year scientific trawl survey to determine to which degree the signatures of the collapse and recovery of the cod are apparent in the spatial and temporal dynamics of the broader groundfish community. Over this 33-year period, the groundfish community experienced four phases of change: (i) a period of rapid, synchronous biomass collapse in most species, (ii) followed by a regime shift in community composition with a concomitant loss of functional diversity, (iii) followed in turn by periods of slow compositional recovery, and (iv) slow biomass growth. Our results demonstrate how a community-wide perspective can reveal new aspects of the dynamics of collapse and recovery unavailable from the analysis of individual species or a combination of a small number of species. Overall, we found evidence that such community-level signals should be useful for designing more effective management strategies to ensure the persistence of exploited marine ecosystems. PMID:28791149

Influence of Peanut Cultivars and Environmental Conditions on the Diversity and Community Composition of Pod Rot Soil Fungi in China.

PubMed

Wang, Mian; Chen, Mingna; Yang, Zhen; Chen, Na; Chi, Xiaoyuan; Pan, Lijuan; Wang, Tong; Yu, Shanlin; Guo, Xingqi

2017-12-01

Peanut yield and quality are seriously affected by pod rot pathogens worldwide, especially in China in recent years. The goals of this study are to analyze the structure of fungal communities of peanut pod rot in soil in three peanut cultivars and the correlation of pod rot with environmental variables using 454 pyrosequencing. A total of 46,723 internal transcribed spacer high-quality sequences were obtained and grouped into 1,706 operational taxonomic units at the 97% similarity cut-off level. The coverage, rank abundance, and the Chao 1 and Shannon diversity indices of the operational taxonomic units were analyzed. Members of the phylum Ascomycota were dominant, such as Fusarium , Chaetomium , Alternaria , and Sordariomycetes , followed by Basidiomycota. The results of the heatmap and redundancy analysis revealed significant variation in the composition of the fungal community among the three cultivar samples. The environmental conditions in different peanut cultivars may also influence on the structure of the fungal community. The results of this study suggest that the causal agent of peanut pod rot may be more complex, and cultivars and environmental conditions are both important contributors to the community structure of peanut pod rot fungi.

Alterations in soil microbial community composition and biomass following agricultural land use change.

PubMed

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-04

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Alterations in soil microbial community composition and biomass following agricultural land use change

NASA Astrophysics Data System (ADS)

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-01

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Geobacteraceae Community Composition Is Related to Hydrochemistry and Biodegradation in an Iron-Reducing Aquifer Polluted by a Neighboring Landfill†

PubMed Central

Lin, Bin; Braster, Martin; van Breukelen, Boris M.; van Verseveld, Henk W.; Westerhoff, Hans V.; Röling, Wilfred F. M.

2005-01-01

Relationships between community composition of the iron-reducing Geobacteraceae, pollution levels, and the occurrence of biodegradation were established for an iron-reducing aquifer polluted with landfill leachate by using cultivation-independent Geobacteraceae 16S rRNA gene-targeting techniques. Numerical analysis of denaturing gradient gel electrophoresis (DGGE) profiles and sequencing revealed a high Geobacteraceae diversity and showed that community composition within the leachate plume differed considerably from that of the unpolluted aquifer. This suggests that pollution has selected for specific species out of a large pool of Geobacteraceae. DGGE profiles of polluted groundwater taken near the landfill (6- to 39-m distance) clustered together. DGGE profiles from less-polluted groundwater taken further downstream did not fall in the same cluster. Several individual DGGE bands were indicative of either the redox process or the level of pollution. This included a pollution-indicative band that dominated the DGGE profiles from groundwater samples taken close to the landfill (6 to 39 m distance). The clustering of these profiles and the dominance by a single DGGE band corresponded to the part of the aquifer where organic micropollutants and reactive dissolved organic matter were attenuated at relatively high rates. PMID:16204512

454-Pyrosequencing analysis of highly adapted azo dye-degrading microbial communities in a two-stage anaerobic-aerobic bioreactor treating textile effluent.

PubMed

Köchling, Thorsten; Ferraz, Antônio Djalma Nunes; Florencio, Lourdinha; Kato, Mario Takayuki; Gavazza, Sávia

2017-03-01

Azo dyes, which are widely used in the textile industry, exhibit significant toxic characteristics for the environment and the human population. Sequential anaerobic-aerobic reactor systems are efficient for the degradation of dyes and the mineralization of intermediate compounds; however, little is known about the composition of the microbial communities responsible for dye degradation in these systems. 454-Pyrosequencing of the 16S rRNA gene was employed to assess the bacterial biodiversity and composition of a two-stage (anaerobic-aerobic) pilot-scale reactor that treats effluent from a denim factory. The anaerobic reactor was inoculated with anaerobic sludge from a domestic sewage treatment plant. Due to the selective composition of the textile wastewater, after 210 days of operation, the anaerobic reactor was dominated by the single genus Clostridium, affiliated with the Firmicutes phylum. The aerobic biofilter harbored a diverse bacterial community. The most abundant phylum in the aerobic biofilter was Proteobacteria, which was primarily represented by the Gamma, Delta and Epsilon classes followed by Firmicutes and other phyla. Several bacterial genera were identified that most likely played an essential role in azo dye degradation in the investigated system.

Analysis and Characterization of Damage Utilizing an Orthotropic Generalized Composite Material Model Suitable for Use in Impact Problems

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Hoffarth, Canio; Rajan, Subramaniam; Blankenhorn, Gunther

2016-01-01

The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased usage in the aerospace and automotive communities. In order to address a series of issues identified by the aerospace community as being desirable to include in a next generation composite impact model, an orthotropic, macroscopic constitutive model incorporating both plasticity and damage suitable for implementation within the commercial LS-DYNA computer code is being developed. The plasticity model is based on extending the Tsai-Wu composite failure model into a strain hardening-based orthotropic plasticity model with a non-associative flow rule. The evolution of the yield surface is determined based on tabulated stress-strain curves in the various normal and shear directions and is tracked using the effective plastic strain. To compute the evolution of damage, a strain equivalent semi-coupled formulation is used in which a load in one direction results in a stiffness reduction in multiple material coordinate directions. A detailed analysis is carried out to ensure that the strain equivalence assumption is appropriate for the derived plasticity and damage formulations that are employed in the current model. Procedures to develop the appropriate input curves for the damage model are presented and the process required to develop an appropriate characterization test matrix is discussed

Analysis and Characterization of Damage Utilizing an Orthotropic Generalized Composite Material Model Suitable for Use in Impact Problems

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Hoffarth, Canio; Rajan, Subramaniam; Blankenhorn, Gunther

2016-01-01

The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased usage in the aerospace and automotive communities. In order to address a series of issues identified by the aerospace community as being desirable to include in a next generation composite impact model, an orthotropic, macroscopic constitutive model incorporating both plasticity and damage suitable for implementation within the commercial LS-DYNA computer code is being developed. The plasticity model is based on extending the Tsai-Wu composite failure model into a strain hardening-based orthotropic plasticity model with a non-associative flow rule. The evolution of the yield surface is determined based on tabulated stress-strain curves in the various normal and shear directions and is tracked using the effective plastic strain. To compute the evolution of damage, a strain equivalent semi-coupled formulation is used in which a load in one direction results in a stiffness reduction in multiple material coordinate directions. A detailed analysis is carried out to ensure that the strain equivalence assumption is appropriate for the derived plasticity and damage formulations that are employed in the current model. Procedures to develop the appropriate input curves for the damage model are presented and the process required to develop an appropriate characterization test matrix is discussed.

Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method

PubMed Central

Paz, Henry A.; Anderson, Christopher L.; Muller, Makala J.; Kononoff, Paul J.; Fernando, Samodha C.

2016-01-01

The rumen microbial community in dairy cows plays a critical role in efficient milk production. However, there is a lack of data comparing the composition of the rumen bacterial community of the main dairy breeds. This study utilizes 16S rRNA gene sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed the same diet by sampling the rumen microbiota via the rumen cannula (Holstein cows) or esophageal tubing (both Holstein and Jersey cows). After collection of the rumen sample via esophageal tubing, particles attached to the strainer were added to the sample to ensure representative sampling of both the liquid and solid fraction of the rumen contents. Alpha diversity metrics, Chao1 and observed OTUs estimates, displayed higher (P = 0.02) bacterial richness in Holstein compared to Jersey cows and no difference (P > 0.70) in bacterial community richness due to sampling method. The principal coordinate analysis displayed distinct clustering of bacterial communities by breed suggesting that Holstein and Jersey cows harbor different rumen bacterial communities. Family level classification of most abundant (>1%) differential OTUs displayed that OTUs from the bacterial families Lachnospiraceae and p-2534-18B5 to be predominant in Holstein cows compared to Jersey cows. Additionally, OTUs belonging to family Prevotellaceae were differentially abundant in the two breeds. Overall, the results from this study suggest that the bacterial community between Holstein and Jersey cows differ and that esophageal tubing with collection of feed particles associated with the strainer provides a representative rumen sample similar to a sample collected via the rumen cannula. Thus, in future studies esophageal tubing with addition of retained particles can be used to collect rumen samples reducing the cost of cannulation and increasing the number of animals used in microbiome investigations, thus increasing the statistical power of rumen microbial community evaluations. PMID:27536291

Temperature controls on aquatic bacterial production and community dynamics in arctic lakes and streams.

PubMed

Adams, Heather E; Crump, Byron C; Kling, George W

2010-05-01

The impact of temperature on bacterial activity and community composition was investigated in arctic lakes and streams in northern Alaska. Aquatic bacterial communities incubated at different temperatures had different rates of production, as measured by (14)C-leucine uptake, indicating that populations within the communities had different temperature optima. Samples from Toolik Lake inlet and outlet were collected at water temperatures of 14.2 degrees C and 15.9 degrees C, respectively, and subsamples incubated at temperatures ranging from 6 degrees C to 20 degrees C. After 5 days, productivity rates varied from 0.5 to approximately 13.7 microg C l(-1) day(-1) and two distinct activity optima appeared at 12 degrees C and 20 degrees C. At these optima, activity was 2- to 11-fold higher than at other incubation temperatures. The presence of two temperature optima indicates psychrophilic and psychrotolerant bacteria dominate under different conditions. Community fingerprinting via denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes showed strong shifts in the composition of communities driven more by temperature than by differences in dissolved organic matter source; e.g. four and seven unique operational taxonomic units (OTUs) were found only at 2 degrees C and 25 degrees C, respectively, and not found at other incubation temperatures after 5 days. The impact of temperature on bacteria is complex, influencing both bacterial productivity and community composition. Path analysis of measurements of 24 streams and lakes sampled across a catchment 12 times in 4 years indicates variable timing and strength of correlation between temperature and bacterial production, possibly due to bacterial community differences between sites. As indicated by both field and laboratory experiments, shifts in dominant community members can occur on ecologically relevant time scales (days), and have important implications for understanding the relationship of bacterial diversity and function.

Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

PubMed

Illeghems, Koen; De Vuyst, Luc; Papalexandratou, Zoi; Weckx, Stefan

2012-01-01

This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering?

PubMed

Moreno-Pino, Mario; De la Iglesia, Rodrigo; Valdivia, Nelson; Henríquez-Castilo, Carlos; Galán, Alexander; Díez, Beatriz; Trefault, Nicole

2016-07-01

Spatial environmental heterogeneity influences diversity of organisms at different scales. Environmental filtering suggests that local environmental conditions provide habitat-specific scenarios for niche requirements, ultimately determining the composition of local communities. In this work, we analyze the spatial variation of microbial communities across environmental gradients of sea surface temperature, salinity and photosynthetically active radiation and spatial distance in Fildes Bay, King George Island, Antarctica. We hypothesize that environmental filters are the main control of the spatial variation of these communities. Thus, strong relationships between community composition and environmental variation and weak relationships between community composition and spatial distance are expected. Combining physical characterization of the water column, cell counts by flow cytometry, small ribosomal subunit genes fingerprinting and next generation sequencing, we contrast the abundance and composition of photosynthetic eukaryotes and heterotrophic bacterial local communities at a submesoscale. Our results indicate that the strength of the environmental controls differed markedly between eukaryotes and bacterial communities. Whereas eukaryotic photosynthetic assemblages responded weakly to environmental variability, bacteria respond promptly to fine-scale environmental changes in this polar marine system. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Dynamic succession of substrate-associated bacterial composition and function during Ganoderma lucidum growth

PubMed Central

Li, Qiang; Zou, Jie; Tan, Hao; Tan, Wei; Peng, Weihong

2018-01-01

Background Ganoderma lucidum, a valuable medicinal fungus, is widely distributed in China. It grows alongside with a complex microbial ecosystem in the substrate. As sequencing technology advances, it is possible to reveal the composition and functions of substrate-associated bacterial communities. Methods We analyzed the bacterial community dynamics in the substrate during the four typical growth stages of G. lucidum using next-generation sequencing. Results The physicochemical properties of the substrate (e.g. acidity, moisture, total nitrogen, total phosphorus and total potassium) changed between different growth stages. A total of 598,771 sequences from 12 samples were obtained and assigned to 22 bacterial phyla. Proteobacteria and Firmicutes were the dominant phyla. Bacterial community composition and diversity significantly differed between the elongation stage and the other three growth stages. LEfSe analysis revealed a large number of bacterial taxa (e.g. Bacteroidetes, Acidobacteria and Nitrospirae) with significantly higher abundance at the elongation stage. Functional pathway prediction uncovered significant abundance changes of a number of bacterial functional pathways between the elongation stage and other growth stages. At the elongation stage, the abundance of the environmental information processing pathway (mainly membrane transport) decreased, whereas that of the metabolism-related pathways increased. Discussion The changes in bacterial community composition, diversity and predicted functions were most likely related to the changes in the moisture and nutrient conditions in the substrate with the growth of G. lucidum, particularly at the elongation stage. Our findings shed light on the G. lucidum-bacteria-substrate relationships, which should facilitate the industrial cultivation of G. lucidum. PMID:29915697

Impact of Long-Term Diesel Contamination on Soil Microbial Community Structure

PubMed Central

Maphosa, Farai; Morillo, Jose A.; Abu Al-Soud, Waleed; Langenhoff, Alette A. M.; Grotenhuis, Tim; Rijnaarts, Huub H. M.; Smidt, Hauke

2013-01-01

Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean samples showed higher diversity than contaminated samples (P < 0.001). Bacterial phyla with high relative abundances in all samples included Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, and Chloroflexi. High relative abundances of Archaea, specifically of the phylum Euryarchaeota, were observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific operational taxonomic units (OTUs; defined using a 97% sequence identity threshold) in contaminated samples together suggest that natural attenuation of contamination has occurred. OTUs with sequence similarity to strictly anaerobic Anaerolineae within the Chloroflexi, as well as to Methanosaeta of the phylum Euryarchaeota, were detected. Anaerolineae and Methanosaeta are known to be associated with anaerobic degradation of oil-related compounds; therefore, their presence suggests that natural attenuation has occurred under anoxic conditions. This research underscores the usefulness of next-generation sequencing techniques both to understand the ecological impact of contamination and to identify potential molecular proxies for detection of natural attenuation. PMID:23144139

Experimental analysis of the effects of consumer exclusion on recruitment and succession of a coral reef system along a water quality gradient in the Spermonde Archipelago, Indonesia

NASA Astrophysics Data System (ADS)

Plass-Johnson, Jeremiah G.; Heiden, Jasmin P.; Abu, Nur; Lukman, Muhammad; Teichberg, Mirta

2016-03-01

The composition of coral reef benthic communities is strongly affected by variation in water quality and consumer abundance and composition. This is particularly evident in highly populated coastal regions where humans depend on coral reef resources and where terrestrial run-off can change the chemical composition of the water. We tested the effects of grazing pressure and ambient water conditions along an established eutrophication gradient on the recruitment and successional development of benthic communities of the Spermonde Archipelago, Indonesia, through caging experiments with settlement tiles. Within 1 month, benthic community composition of the closest reef to land, near the city of Makassar, was significantly different from other sites further offshore, driven primarily by differences in recruitment of invertebrates or turf algae. In contrast to other caging experiments, consumer exclusion had no effect after 3 months, suggesting that larger, mobile consumers had little effect on the benthic communities of these reefs at all sites. Despite conditions that usually favour macroalgal development, this group was rarely observed on recruitment tiles even after 4 months of consumer exclusion. Furthermore, tiles from both the caged and open treatments retained high proportions of open space indicating the possible role of small-sized or non-fish consumers that were not excluded from the experiment. These results indicate that, unlike many other studies, benthic consumers in the Spermonde Archipelago had little effect on the recruitment and early succession of the reef habitat and that unexamined biota such as mesograzers may be significant in degraded systems.

On Growth and Form of the Zebrafish Gut Microbiome

NASA Astrophysics Data System (ADS)

Jemielita, Matthew; Taormina, Michael; Rolig, Annah; Burns, Adam; Hampton, Jennifer; Guillemin, Karen; Parthasarathy, Raghuveer

2014-03-01

The vertebrate gut is home to a diverse microbial community whose composition has a strong influence on the development and health of the host organism. Researchers can identify the members of the microbiota, yet little is known about the spatial and temporal dynamics of these microbial communities, including the mechanisms guiding their nucleation, growth, and interactions. We address these issues using the larval zebrafish (Danio rerio) as a model organism, which are raised microbe-free and then inoculated with controlled compositions of fluorophore-expressing bacteria. Live imaging using light sheet fluorescence microscopy enables visualization of the gut's entire microbial population over the first 24 hours of colonization. Image analysis allows us to quantify microbial populations that range from a few individuals to tens of thousands of microbes, and analyze the structure and growth kinetics of gut bacterial communities. We find that genetically-identical microbes can show surprisingly different growth rates and colonization abilities depending on their order of arrival. This demonstrates that knowing only the constituents of the gut community is insufficient to determine their dynamics; rather, the history of colonization matters.

[Community structure of soil meso- and micro-fauna in different habitats of urbanized region].

PubMed

Qin, Zhong; Zhang, Jia-en; Li, Qing-fang

2009-12-01

Investigations were made in May, June, and November 2007 and January 2008 to study the structural characteristics and their seasonal variations of soil meso- and micro-fauna communities in six habitats of three land use types (forest land, constructed grassland and farmland) in Tianhe District of Guangzhou City. The horizontal spatial distribution of soil fauna differed with habitat. During the investigation periods, the Botanical Garden of South China Agricultural University had the highest individual number (1286) of soil mesa- and micro-fauna, while the farmland, especially in the Fenghuang Street area, had the lowest number of individuals and groups. The seasonal variation of the individual number was in order of autumn (1815) > spring (1623) > winter (1365) > summer (1276). Hierarchical clustering and detrended correspondence analysis also showed that the community composition of soil meso- and micro-fauna in different habitats exhibited distinct seasonal variation. In the same seasons, the community structure and composition of soil meso- and micro-fauna in different habitats were correlated to the degrees of human interferences and the properties of soil environment.

Bacteria diversity and arsenic mobilization in rock biofilm from an ancient gold and arsenic mine.

PubMed

Tomczyk-Żak, Karolina; Kaczanowski, Szymon; Drewniak, Łukasz; Dmoch, Łukasz; Sklodowska, Aleksandra; Zielenkiewicz, Urszula

2013-09-01

In this paper we characterize the biofilm community from an ancient Złoty Stok gold and arsenic mine. Bacterial diversity was examined using a culture-independent technique based on 16S rRNA gene amplification, cloning and sequencing. We show that unexpectedly the microbial diversity of this community was extremely high (more than 190 OTUs detected), with the most numerous members from Rhizobiales (α-Proteobacteria). Although the level of rock biofilm diversity was similar to the microbial mat community we have previously characterized in the same adit, its taxonomic composition was completely different. Detailed analysis of functional arrA and aioA genes, chemical properties of siderophores found in pore water as well as the biofilm chemical composition suggest that the biofilm community contributes to arsenic pollution of surrounding water in a biogeochemical cycle similar to the one observed in bacterial mats. To interpret our results concerning the biological arsenic cycle, we applied the theory of ecological pyramids of Charles Elton. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression

PubMed Central

O’Callaghan, Maureen; Condron, Leo M.; Kowalchuk, George A.; Van Nostrand, Joy D.; Zhou, Jizhong; Wakelin, Steven A.

2018-01-01

Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity. PMID:29734390

Supplementing Blends of Sugars, Amino Acids, and Secondary Metabolites to the Diet of Termites (Reticulitermes flavipes) Drive Distinct Gut Bacterial Communities.

PubMed

Huang, Xing-Feng; Chaparro, Jacqueline M; Reardon, Kenneth F; Judd, Timothy M; Vivanco, Jorge M

2016-10-01

Although it is well known that diet is one of the major modulators of the gut microbiome, how the major components of diet shape the gut microbial community is not well understood. Here, we developed a simple system that allows the investigation of the impact of given compounds as supplements of the diet on the termite gut microbiome. The 16S rRNA pyrosequencing analysis revealed that feeding termites different blends of sugars and amino acids did not majorly impact gut community composition; however, ingestion of blends of secondary metabolites caused shifts in gut bacterial community composition. The supplementation of sugars and amino acids reduced the richness significantly, and sugars alone increased the evenness of the gut bacterial community significantly. Secondary metabolites created the most dramatic effects on the microbial community, potentially overriding the effect of other types of compounds. Furthermore, some microbial groups were stimulated specifically by particular groups of compounds. For instance, termites fed with secondary metabolites contained more Firmicutes and Spirochaetes compared to the other treatments. In conclusion, our results suggest that the termite (Reticulitermes flavipes) can be used as a simple and effective system to test the effects of particular chemical compounds in modulating the gut microbiome.

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

PubMed

Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

2015-01-01

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression.

PubMed

Dignam, Bryony E A; O'Callaghan, Maureen; Condron, Leo M; Kowalchuk, George A; Van Nostrand, Joy D; Zhou, Jizhong; Wakelin, Steven A

2018-01-01

Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity.

Integrating community assembly and biodiversity to better understand ecosystem function: the Community Assembly and the Functioning of Ecosystems (CAFE) approach.

PubMed

Bannar-Martin, Katherine H; Kremer, Colin T; Ernest, S K Morgan; Leibold, Mathew A; Auge, Harald; Chase, Jonathan; Declerck, Steven A J; Eisenhauer, Nico; Harpole, Stanley; Hillebrand, Helmut; Isbell, Forest; Koffel, Thomas; Larsen, Stefano; Narwani, Anita; Petermann, Jana S; Roscher, Christiane; Cabral, Juliano Sarmento; Supp, Sarah R

2018-02-01

The research of a generation of ecologists was catalysed by the recognition that the number and identity of species in communities influences the functioning of ecosystems. The relationship between biodiversity and ecosystem functioning (BEF) is most often examined by controlling species richness and randomising community composition. In natural systems, biodiversity changes are often part of a bigger community assembly dynamic. Therefore, focusing on community assembly and the functioning of ecosystems (CAFE), by integrating both species richness and composition through species gains, losses and changes in abundance, will better reveal how community changes affect ecosystem function. We synthesise the BEF and CAFE perspectives using an ecological application of the Price equation, which partitions the contributions of richness and composition to function. Using empirical examples, we show how the CAFE approach reveals important contributions of composition to function. These examples show how changes in species richness and composition driven by environmental perturbations can work in concert or antagonistically to influence ecosystem function. Considering how communities change in an integrative fashion, rather than focusing on one axis of community structure at a time, will improve our ability to anticipate and predict changes in ecosystem function. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Vertical zonation of soil fungal community structure in a Korean pine forest on Changbai Mountain, China.

PubMed

Ping, Yuan; Han, Dongxue; Wang, Ning; Hu, Yanbo; Mu, Liqiang; Feng, Fujuan

2017-01-01

Changbai Mountain, with intact montane vertical vegetation belts, is located at a sensitive area of global climate change and a central distribution area of Korean pine forest. Broad-leaved Korean pine mixed forest (Pinus koraiensis as an edificator) is the most representative zonal climax vegetation in the humid region of northeastern China; their vertical zonation is the most intact and representative on Changbai Mountain. In this study, we analyzed the composition and diversity of soil fungal communities in the Korean pine forest on Changbai Mountain at elevations ranging from 699 to 1177 m using Illumina High-throughput sequencing. We obtained a total 186,663 optimized sequences, with an average length of 268.81 bp. We found soil fungal diversity index was decreased with increasing elevation from 699 to 937 m and began to rise after reaching 1044 m; the richness and evenness indices were decreased with an increase in elevation. Soil fungal compositions at the phylum, class and genus levels varied significantly at different elevations, but with the same dominant fungi. Beta-diversity analysis indicated that the similarity of fungal communities decreased with an increased vertical distance between the sample plots, showing a distance-decay relationship. Variation partition analysis showed that geographic distance (mainly elevation gradient) only explained 20.53 % of the total variation of fungal community structure, while soil physicochemical factors explained 69.78 %.