title: Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.
abstract: Temporal variability complicates testing the influences of environmental variability on microbial community structure and thus function. An in-field bioreactor system was developed to assess oxic versus anoxic manipulations on in situ groundwater communities. Each sample was sequenced (16S SSU rRNA genes, average 10,000 reads), and biogeochemical parameters are monitored by quantifying 53 metals, 12 organic acids, 14 anions, and 3 sugars. Changes in dissolved oxygen (DO), pH, and other variables were similar across bioreactors. Sequencing revealed a complex community that fluctuated in-step with the groundwater community and responded to DO. This also directly influenced the pH, and so the biotic impacts of DO and pH shifts are correlated. A null model demonstrated that bioreactor communities were driven in part not only by experimental conditions but also by stochastic variability and did not accurately capture alterations in diversity during perturbations. We identified two groups of abundant OTUs important to this system; one was abundant in high DO and pH and contained heterotrophs and oxidizers of iron, nitrite, and ammonium, whereas the other was abundant in low DO with the capability to reduce nitrate. In-field bioreactors are a powerful tool for capturing natural microbial community responses to alterations in geochemical factors beyond the bulk phase.
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: King
authors.affiliation: Department of Environmental Health and Enginering, Johns Hopkins University , Baltimore, Maryland 21218, United States.
authors.forename: Sarah P
authors.initials: SP
authors.lastname: Preheim
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Bailey
authors.affiliation: Fish, Wildlife and Conservation Biology, Colorado State University , Fort Collins, Colorado 80523, United States.
authors.forename: Michael S
authors.identifier: 0000-0001-7119-6301
authors.initials: MS
authors.lastname: Robeson
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Taniya
authors.initials: T
authors.lastname: Roy Chowdhury
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Bryan R
authors.initials: BR
authors.lastname: Crable
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.|Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Hurt
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Tonia
authors.initials: T
authors.lastname: Mehlhorn
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Kenneth A
authors.initials: KA
authors.lastname: Lowe
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Tommy J
authors.initials: TJ
authors.lastname: Phelps
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Anthony V
authors.initials: AV
authors.lastname: Palumbo
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: Craig C
authors.initials: CC
authors.lastname: Brandt
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.|Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.|Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States.
authors.forename: Mircea
authors.initials: M
authors.lastname: Podar
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors.forename: Ping
authors.identifier: 0000-0002-9455-2265
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States.
authors.forename: W Andrew
authors.initials: WA
authors.lastname: Lancaster
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States.
authors.forename: Farris
authors.initials: F
authors.lastname: Poole
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.
authors.forename: David B
authors.identifier: 0000-0002-4972-4136
authors.initials: DB
authors.lastname: Watson
authors.affiliation: Department of Microbiology & Immunology, Montana State University , Bozeman, Montana 59717, United States.
authors.forename: Matthew
authors.identifier: 0000-0001-9053-1849
authors.initials: M
authors.lastname: W Fields
authors.affiliation: Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States.
authors.forename: John-Marc
authors.initials: JM
authors.lastname: Chandonia
authors.affiliation: Civil and Environmental Engineering and Biological Engineering, Massachusets Institute of Technology , Cambridge, Massachusetts 02139, United States.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Alm
authors.affiliation: Department of Microbiology and Plant Biology, University of Oklahoma , Norman, Oklahoma 73019, United States.
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States.
authors.forename: Michael W W
authors.initials: MW
authors.lastname: Adams
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.|Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States.
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.affiliation: Environmental Genomics and Systems Biology Division, Lawrence Berkley National Laboratory , Berkley, California 94720, United States.
authors.forename: Adam P
authors.initials: AP
authors.lastname: Arkin
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , P.O. Box 2008, MS-6036, Oak Ridge, Tennessee 37831-6036, United States.|Department of Civil and Environmental Engineering, University of Tennessee , Knoxville, Tennessee 37996, United States.
authors.forename: Dwayne A
authors.identifier: 0000-0002-4469-6391
authors.initials: DA
authors.lastname: Elias
mesh_terms: D001419:Bacteria / Q000235:genetics*; D019149:Bioreactors; D060587:Groundwater / Q000737:chemistry; D009573:Nitrites; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D009573:Nitrites; D012336:RNA, Ribosomal, 16S