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Front Microbiol. 2015 Oct 31;6:1205. doi: 10.3389/fmicb.2015.01205. eCollection 2015.

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.

Author information

1
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
2
The Biodesign Institute, Arizona State University, Tempe AZ, USA.
3
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA ; CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences Beijing, China.
4
Bioscience Division, Los Alamos National Laboratory, Los Alamos NM, USA.
5
United States Department of Energy, Joint Genome Institute, Walnut Creek CA, USA.
6
Department of Microbiology, Montana State University, Bozeman MT, USA.
7
Center for Microbial Ecology, Michigan State University, East Lansing MI, USA.
8
Department of Civil and Environmental Engineering, University of Tennessee-Knoxville, Knoxville TN, USA ; Department of Earth and Planetary Sciences, University of Tennessee-Knoxville, Knoxville TN, USA ; Department of Microbiology, University of Tennessee-Knoxville, Knoxville TN, USA ; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN, USA.
9
Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley CA, USA.
10
Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA ; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley CA, USA ; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University Beijing, China.

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. 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.

KEYWORDS:

bioremediation; groundwater microbiology; metagenomics

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