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. 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.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Hemme
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
authors.forename: Qichao
authors.initials: Q
authors.lastname: Tu
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Shi
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
authors.forename: Yujia
authors.initials: Y
authors.lastname: Qin
authors.affiliation: The Biodesign Institute, Arizona State University, Tempe AZ, USA.
authors.forename: Weimin
authors.initials: W
authors.lastname: Gao
authors.affiliation: 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.
authors.forename: Ye
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
authors.forename: Joy D Van
authors.initials: JD
authors.lastname: Nostrand
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.affiliation: Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA.
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos NM, USA.
authors.forename: Patrick S G
authors.initials: PS
authors.lastname: Chain
authors.affiliation: United States Department of Energy, Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: Susannah G
authors.initials: SG
authors.lastname: Tringe
authors.affiliation: Department of Microbiology, Montana State University, Bozeman MT, USA.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Fields
authors.affiliation: United States Department of Energy, Joint Genome Institute, Walnut Creek CA, USA.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing MI, USA.
authors.forename: James M
authors.initials: JM
authors.lastname: Tiedje
authors.affiliation: 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.
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.affiliation: Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley CA, USA.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.affiliation: 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.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
keywords: bioremediation; groundwater microbiology; metagenomics