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Title: High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

Abstract

There is increasing interest in harnessing the functional diversity of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Understanding the response of communities to stimulation, including flanking taxa, presents important opportunities for optimizing remediation approaches. We used high-density PhyloChip microarray analysis to comprehensively determine community membership and abundance patterns amongst a suite of samples from U(VI) bioremediation experiments. Samples were unstimulated or collected during Fe(III) and sulfate reduction from an acetate-augmented aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Results showed the greatest diversity in abundant SRB lineages was present in naturally-reduced sediment. Desulfuromonadales and Desulfobacterales were consistently identified as the dominant Fe(III)- and sulfate-reducing bacteria (IRB and SRB) throughout acetate amendment experiments. Stimulated communities also exhibited a high degree of functional redundancy amongst enriched flanking members. Not surprisingly, competition for both sulfate and iron was evident amongst abundant taxa, but the distribution and abundance of these ancillary SRB (Peptococcaceae, Desulfovibrionales and Syntrophobacterales), and lineages containing IRB (excluding Desulfobacteraceae) was heterogeneous amongst sample types. Interesting, amongst the most abundant taxa, particularly during sulfate reduction, were Epsilonproteobacteria that perform microaerobic or nitrate-dependant sulfur oxidation, and a number of bacteria other than Geobacteraceae thatmore » may enzymatically reduce U(VI). Finally, in depth community probing with PhyloChip determined the efficacy of experimental approaches, notably revealing striking similarity amongst stimulated sediment (from drill cores and in-situ columns) and groundwater communities, and demonstrating that sediment-packed in-situ (down-well) columns served as an ideal method for subsurface biostimulation.« less

Authors:
; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1047981
Report Number(s):
PNNL-SA-79168
Journal ID: ISSN 0168-6496; FMECEZ; 16309; KP1702030; TRN: US1204062
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
FEMS Microbiology Ecology
Additional Journal Information:
Journal Volume: 81; Journal Issue: 1; Journal ID: ISSN 0168-6496
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; ABUNDANCE; ACETATES; AQUIFERS; BACTERIA; BIOREMEDIATION; COLORADO; COMMUNITIES; DISTRIBUTION; DRILL CORES; FUNCTIONALS; IRON; OXIDATION; REDUNDANCY; SEDIMENTS; STIMULATION; SULFATE-REDUCING BACTERIA; SULFATES; SULFUR; Proteogenomics; functional diversity; bioremediation; uranium; Environmental Molecular Sciences Laboratory

Citation Formats

Handley, Kim M, Wrighton, Kelly E, Piceno, Y M, Anderson, Gary L, DeSantis, Todd, Williams, Kenneth H, Wilkins, Michael J, N'Guessan, A L, Peacock, Aaron, Bargar, John R, Long, Philip E, and Banfield, Jillian F. High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. United States: N. p., 2012. Web. doi:10.1111/j.1574-6941.2012.01363.x.
Handley, Kim M, Wrighton, Kelly E, Piceno, Y M, Anderson, Gary L, DeSantis, Todd, Williams, Kenneth H, Wilkins, Michael J, N'Guessan, A L, Peacock, Aaron, Bargar, John R, Long, Philip E, & Banfield, Jillian F. High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment. United States. https://doi.org/10.1111/j.1574-6941.2012.01363.x
Handley, Kim M, Wrighton, Kelly E, Piceno, Y M, Anderson, Gary L, DeSantis, Todd, Williams, Kenneth H, Wilkins, Michael J, N'Guessan, A L, Peacock, Aaron, Bargar, John R, Long, Philip E, and Banfield, Jillian F. 2012. "High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment". United States. https://doi.org/10.1111/j.1574-6941.2012.01363.x.
@article{osti_1047981,
title = {High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment},
author = {Handley, Kim M and Wrighton, Kelly E and Piceno, Y M and Anderson, Gary L and DeSantis, Todd and Williams, Kenneth H and Wilkins, Michael J and N'Guessan, A L and Peacock, Aaron and Bargar, John R and Long, Philip E and Banfield, Jillian F},
abstractNote = {There is increasing interest in harnessing the functional diversity of indigenous microbial communities to transform and remediate a wide range of environmental contaminants. Understanding the response of communities to stimulation, including flanking taxa, presents important opportunities for optimizing remediation approaches. We used high-density PhyloChip microarray analysis to comprehensively determine community membership and abundance patterns amongst a suite of samples from U(VI) bioremediation experiments. Samples were unstimulated or collected during Fe(III) and sulfate reduction from an acetate-augmented aquifer in Rifle, Colorado, and from laboratory experiments using field-collected materials. Results showed the greatest diversity in abundant SRB lineages was present in naturally-reduced sediment. Desulfuromonadales and Desulfobacterales were consistently identified as the dominant Fe(III)- and sulfate-reducing bacteria (IRB and SRB) throughout acetate amendment experiments. Stimulated communities also exhibited a high degree of functional redundancy amongst enriched flanking members. Not surprisingly, competition for both sulfate and iron was evident amongst abundant taxa, but the distribution and abundance of these ancillary SRB (Peptococcaceae, Desulfovibrionales and Syntrophobacterales), and lineages containing IRB (excluding Desulfobacteraceae) was heterogeneous amongst sample types. Interesting, amongst the most abundant taxa, particularly during sulfate reduction, were Epsilonproteobacteria that perform microaerobic or nitrate-dependant sulfur oxidation, and a number of bacteria other than Geobacteraceae that may enzymatically reduce U(VI). Finally, in depth community probing with PhyloChip determined the efficacy of experimental approaches, notably revealing striking similarity amongst stimulated sediment (from drill cores and in-situ columns) and groundwater communities, and demonstrating that sediment-packed in-situ (down-well) columns served as an ideal method for subsurface biostimulation.},
doi = {10.1111/j.1574-6941.2012.01363.x},
url = {https://www.osti.gov/biblio/1047981}, journal = {FEMS Microbiology Ecology},
issn = {0168-6496},
number = 1,
volume = 81,
place = {United States},
year = {Wed Jun 13 00:00:00 EDT 2012},
month = {Wed Jun 13 00:00:00 EDT 2012}
}