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Title: Phylogenetic and functional biomarkers as indicators of bacterialcommunity responses to mixed-waste contamination

Abstract

Few studies have demonstrated changes in community structurealong a contaminant plume in terms of phylogenetic, functional, andgeochemical changes, and such studies are essential to understand how amicrobial ecosystem responds to perturbations. Clonal libraries ofmultiple genes (SSU rDNA, nirK, nirS, amoA, pmoA, and dsrAB) wereanalyzed from groundwater samples (n=6) that varied in contaminantlevels, and 107 geochemical parameters were measured. Principalcomponents analyses (PCA) were used to compare the relationships betweenthe sites with respect to the biomarker (n=785 for all sequences)distributions and the geochemical variables. A major portion of thegeochemical variance measured between the samples could be accounted forby tetrachloroethene, 99Tc, NO3, SO4, Al, and Th. The PCA based on thedistribution of unique biomarkers resulted in different groupingscompared to the geochemical analysis, but when the SSU rRNA genelibraries were directly compared (?Cxy values) the sites were clusteredin asimilar fashion compared to geochemical measures. The PCA based uponfunctional gene distributions each predicted different relationshipsbetween the sites, and comparisons of Euclidean distances based upondiversity indices for all functional genes (n=432) grouped the sites byextreme or intermediate contaminant levels. The data suggested that thesites with low and high perturbations were functionally more similar thansites with intermediate conditions, and perhaps captured the overallcommunity structure better than amore » single phylogenetic biomarker.Moreover, even though the background site was phylogenetically andgeochemically distinct from the acidic sites, the extreme conditions ofthe acidic samples might be more analogous to the limiting nutrientconditions of the background site. An understanding of microbialcommunity-level responses within an ecological framework would providebetter insight for restoration strategies at contaminated fieldsites.« less

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
OSTI Identifier:
922808
Report Number(s):
LBNL-60419
Journal ID: ISSN 0013-936X; ESTHAG; R&D Project: VGTLTH; BnR: KP1102010; TRN: US200803%%535
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Environmental Science and Technology; Journal Volume: 40; Journal Issue: 8; Related Information: Journal Publication Date: April 15,2006
Country of Publication:
United States
Language:
English
Subject:
59; 54; CONTAMINATION; DISTRIBUTION; ECOSYSTEMS; FUNCTIONALS; GENES; NUTRIENTS; PLUMES; Biomass Production Bioremediation Environmental GenomicsExtremophiles Stress Response Sulfate Reducers

Citation Formats

Fields, M.W., Bagwell, C.E., Carroll, S.L., Yan, T., Liu, X., Watson, D.B., Jardine, P.M., Criddle, C.S., Hazen, T.C., and Zhou, J. Phylogenetic and functional biomarkers as indicators of bacterialcommunity responses to mixed-waste contamination. United States: N. p., 2007. Web.
Fields, M.W., Bagwell, C.E., Carroll, S.L., Yan, T., Liu, X., Watson, D.B., Jardine, P.M., Criddle, C.S., Hazen, T.C., & Zhou, J. Phylogenetic and functional biomarkers as indicators of bacterialcommunity responses to mixed-waste contamination. United States.
Fields, M.W., Bagwell, C.E., Carroll, S.L., Yan, T., Liu, X., Watson, D.B., Jardine, P.M., Criddle, C.S., Hazen, T.C., and Zhou, J. Fri . "Phylogenetic and functional biomarkers as indicators of bacterialcommunity responses to mixed-waste contamination". United States. doi:.
@article{osti_922808,
title = {Phylogenetic and functional biomarkers as indicators of bacterialcommunity responses to mixed-waste contamination},
author = {Fields, M.W. and Bagwell, C.E. and Carroll, S.L. and Yan, T. and Liu, X. and Watson, D.B. and Jardine, P.M. and Criddle, C.S. and Hazen, T.C. and Zhou, J.},
abstractNote = {Few studies have demonstrated changes in community structurealong a contaminant plume in terms of phylogenetic, functional, andgeochemical changes, and such studies are essential to understand how amicrobial ecosystem responds to perturbations. Clonal libraries ofmultiple genes (SSU rDNA, nirK, nirS, amoA, pmoA, and dsrAB) wereanalyzed from groundwater samples (n=6) that varied in contaminantlevels, and 107 geochemical parameters were measured. Principalcomponents analyses (PCA) were used to compare the relationships betweenthe sites with respect to the biomarker (n=785 for all sequences)distributions and the geochemical variables. A major portion of thegeochemical variance measured between the samples could be accounted forby tetrachloroethene, 99Tc, NO3, SO4, Al, and Th. The PCA based on thedistribution of unique biomarkers resulted in different groupingscompared to the geochemical analysis, but when the SSU rRNA genelibraries were directly compared (?Cxy values) the sites were clusteredin asimilar fashion compared to geochemical measures. The PCA based uponfunctional gene distributions each predicted different relationshipsbetween the sites, and comparisons of Euclidean distances based upondiversity indices for all functional genes (n=432) grouped the sites byextreme or intermediate contaminant levels. The data suggested that thesites with low and high perturbations were functionally more similar thansites with intermediate conditions, and perhaps captured the overallcommunity structure better than a single phylogenetic biomarker.Moreover, even though the background site was phylogenetically andgeochemically distinct from the acidic sites, the extreme conditions ofthe acidic samples might be more analogous to the limiting nutrientconditions of the background site. An understanding of microbialcommunity-level responses within an ecological framework would providebetter insight for restoration strategies at contaminated fieldsites.},
doi = {},
journal = {Environmental Science and Technology},
number = 8,
volume = 40,
place = {United States},
year = {Fri Mar 30 00:00:00 EDT 2007},
month = {Fri Mar 30 00:00:00 EDT 2007}
}
  • Few studies have demonstrated changes in community structure along a contaminant plume in terms of phylogenetic, functional, and geochemical changes, and such studies are essential to understand how a microbial ecosystem responds to perturbations. Clonal libraries of multiple genes (SSU rDNA, nirK, nirS, amoA, pmoA, and dsrAB) were analyzed from groundwater samples (n = 6) that varied in contaminant levels, and 107 geochemical parameters were measured. Principal components analyses (PCA) were used to compare the relationships among the sites with respect to the biomarker (n = 785 for all sequences) distributions and the geochemical variables. A major portion of themore » geochemical variance measured among the samples could be accounted for by tetrachloroethene, {sup 99}Tc, NO{sub 3}, SO{sub 4}, Al, and Th. The PCA based on the distribution of unique biomarkers resulted in different groupings compared to the geochemical analysis, but when the SSU rRNA gene libraries were directly compared ({Delta}C{sub xy} values) the sites were clustered in a similar fashion compared to geochemical measures. The PCA based upon functional gene distributions each predicted different relationships among the sites, and comparisons of Euclidean distances based upon diversity indices for all functional genes (n = 432) grouped the sites by extreme or intermediate contaminant levels. The data suggested that the sites with low and high perturbations were functionally more similar than sites with intermediate conditions, and perhaps captured the overall community structure better than a single phylogenetic biomarker. Moreover, even though the background site was phylogenetically and geochemically distinct from the acidic sites, the extreme conditions of the acidic samples might be more analogous to the limiting nutrient conditions of the background site. An understanding of microbial community-level responses within an ecological framework would provide better insight for restoration strategies at contaminated field sites.« less
  • No abstract prepared.
  • Random community genomes (metagenomes) are now commonly used to study microbes in different environments. Over the past few years, the major challenge associated with metagenomics shifted from generating to analyzing sequences. High-throughput, low-cost next-generation sequencing has provided access to metagenomics to a wide range of researchers. A high-throughput pipeline has been constructed to provide high-performance computing to all researchers interested in using metagenomics. The pipeline produces automated functional assignments of sequences in the metagenome by comparing both protein and nucleotide databases. phylogenetic and functional summaries of the metagenomes are generated, and tools for comparative metagenomics are incorporated into the standardmore » views. user access is controlled to ensure data privacy, but the collaborative environment underpinning the service provides a framework for sharing databasets between multiple users. In the metagenomics RAST, all users retain full control of their data, and everything is available for download in a variety of formats. The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes. With built-in support for multiple data sources and a back end that houses abstract data types, the metagenomics RAST is stable, extensible, and freely available to all researchers. This service has removed one of the primary bottlenecks in metagenome sequence analysis--the available of high-performance computing for annotating the data.« less
  • Understanding the spatial patterns of organisms and the underlying mechanisms shaping biotic communities is a central goal in community ecology. One of the most well documented spatial patterns in plant and animal communities is the positive-power law relationship between species (or taxa) richness and area. Such a taxa-area relationships (TARs) are one of the principal generalizations in ecology, and are fundamental to our understanding of the distribution of global biodiversity. However, TARs remain elusive and controversial in microbial communities, especially in soil habitats, due to inadequate sampling methodologies. Here, we describe TARs, at a whole-community level, across various microbial functionalmore » and phylogenetic groups in a forest soil using a comprehensive functional gene array (FGA) with > 24,000 probes. Our analysis indicated that the forest soil microbial community exhibited a relatively flat taxa-area relationship (slope z = 0.0624), but the z values varied considerably across different functional and phylogenetic groups (z = 0.0475-0.0959), which are several times lower than those commonly observed in higher plants and animals. These results suggest that the turnover in space of microorganisms may be, in general, lower than that of plants and animals.« less