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Title: Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

Abstract

To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion (>55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. Lastly, these results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.

Authors:
 [1];  [2];  [2];  [2];  [3];  [4];  [2];  [2];  [2];  [5];  [6];  [7];  [6];  [8];  [9];  [10];  [11]
  1. Univ. of Oklahoma, Norman, OK (United States); The Univ. of Rhode Island, Kingston, RI (United States)
  2. Univ. of Oklahoma, Norman, OK (United States)
  3. Arizona State Univ., Tempe, AZ (United States)
  4. Univ. of Oklahoma, Norman, OK (United States); Chinese Academy of Sciences (CAS), Beijing (China)
  5. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  7. Montana State Univ., Bozeman, MT (United States)
  8. Michigan State Univ., East Lansing, MI (United States)
  9. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  10. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  11. Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Tsinghua Univ., Beijing (China)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1327637
Alternate Identifier(s):
OSTI ID: 1255538; OSTI ID: 1407297
Grant/Contract Number:  
AC05-00OR22725; FG02-07ER64398; AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; metagenomics; bioremediation; groundwater microbiology

Citation Formats

Hemme, Christopher L., Tu, Qichao, Shi, Zhou, Qin, Yujia, Gao, Weimin, Deng, Ye, Nostrand, Joy D. Van, Wu, Liyou, He, Zhili, Chain, Patrick S. G., Tringe, Susannah G., Fields, Matthew W., Rubin, Edward M., Tiedje, James M., Hazen, Terry C., Arkin, Adam P., and Zhou, Jizhong. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. United States: N. p., 2015. Web. doi:10.3389/fmicb.2015.01205.
Hemme, Christopher L., Tu, Qichao, Shi, Zhou, Qin, Yujia, Gao, Weimin, Deng, Ye, Nostrand, Joy D. Van, Wu, Liyou, He, Zhili, Chain, Patrick S. G., Tringe, Susannah G., Fields, Matthew W., Rubin, Edward M., Tiedje, James M., Hazen, Terry C., Arkin, Adam P., & Zhou, Jizhong. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. United States. doi:10.3389/fmicb.2015.01205.
Hemme, Christopher L., Tu, Qichao, Shi, Zhou, Qin, Yujia, Gao, Weimin, Deng, Ye, Nostrand, Joy D. Van, Wu, Liyou, He, Zhili, Chain, Patrick S. G., Tringe, Susannah G., Fields, Matthew W., Rubin, Edward M., Tiedje, James M., Hazen, Terry C., Arkin, Adam P., and Zhou, Jizhong. Sat . "Comparative metagenomics reveals impact of contaminants on groundwater microbiomes". United States. doi:10.3389/fmicb.2015.01205. https://www.osti.gov/servlets/purl/1327637.
@article{osti_1327637,
title = {Comparative metagenomics reveals impact of contaminants on groundwater microbiomes},
author = {Hemme, Christopher L. and Tu, Qichao and Shi, Zhou and Qin, Yujia and Gao, Weimin and Deng, Ye and Nostrand, Joy D. Van and Wu, Liyou and He, Zhili and Chain, Patrick S. G. and Tringe, Susannah G. and Fields, Matthew W. and Rubin, Edward M. and Tiedje, James M. and Hazen, Terry C. and Arkin, Adam P. and Zhou, Jizhong},
abstractNote = {To understand patterns of geochemical cycling in pristine versus contaminated groundwater ecosystems, pristine shallow groundwater (FW301) and contaminated groundwater (FW106) samples from the Oak Ridge Integrated Field Research Center (OR-IFRC) were sequenced and compared to each other to determine phylogenetic and metabolic difference between the communities. Proteobacteria (e.g., Burkholderia, Pseudomonas) are the most abundant lineages in the pristine community, though a significant proportion (>55%) of the community is composed of poorly characterized low abundance (individually <1%) lineages. The phylogenetic diversity of the pristine community contributed to a broader diversity of metabolic networks than the contaminated community. In addition, the pristine community encodes redundant and mostly complete geochemical cycles distributed over multiple lineages and appears capable of a wide range of metabolic activities. In contrast, many geochemical cycles in the contaminated community appear truncated or minimized due to decreased biodiversity and dominance by Rhodanobacter populations capable of surviving the combination of stresses at the site. Lastly, these results indicate that the pristine site contains more robust and encodes more functional redundancy than the stressed community, which contributes to more efficient nutrient cycling and adaptability than the stressed community.},
doi = {10.3389/fmicb.2015.01205},
journal = {Frontiers in Microbiology},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {10}
}

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