title: Aquifer environment selects for microbial species cohorts in sediment and groundwater.
abstract: Little is known about the biogeography or stability of sediment-associated microbial community membership because these environments are biologically complex and generally difficult to sample. High-throughput-sequencing methods provide new opportunities to simultaneously genomically sample and track microbial community members across a large number of sampling sites or times, with higher taxonomic resolution than is associated with 16 S ribosomal RNA gene surveys, and without the disadvantages of primer bias and gene copy number uncertainty. We characterized a sediment community at 5 m depth in an aquifer adjacent to the Colorado River and tracked its most abundant 133 organisms across 36 different sediment and groundwater samples. We sampled sites separated by centimeters, meters and tens of meters, collected on seven occasions over 6 years. Analysis of 1.4 terabase pairs of DNA sequence showed that these 133 organisms were more consistently detected in saturated sediments than in samples from the vadose zone, from distant locations or from groundwater filtrates. Abundance profiles across aquifer locations and from different sampling times identified organism cohorts that comprised subsets of the 133 organisms that were consistently associated. The data suggest that cohorts are partly selected for by shared environmental adaptation.
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
authors: Laura A
authors: LA
authors: Hug
authors: Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
authors: Brian C
authors: BC
authors: Thomas
authors: Department of Plant and Microbial Biology, Berkeley, CA, USA.
authors: Christopher T
authors: CT
authors: Brown
authors: Department of Earth and Environmental Science, Columbia University, New York, NY, USA.
authors: Kyle R
authors: KR
authors: Frischkorn
authors: Geophysics Department, Earth Sciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA.
authors: Kenneth H
authors: KH
authors: Williams
authors: Metagenome Program, DOE Joint Genome Institute, Walnut Creek, CA, USA.
authors: Susannah G
authors: SG
authors: Tringe
authors: 1] Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA [2] Department of Environmental Science, Policy, and Management, Berkeley, CA, USA.
authors: Jillian F
authors: JF
authors: Banfield
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D003120:Colorado; D019015:Geologic Sediments / Q000382:microbiology*; D060587:Groundwater / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D054892:Metagenome; D012329:RNA, Bacterial / Q000032:analysis; D012336:RNA, Ribosomal, 16S / Q000032:analysis
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
references: Bioinformatics. 2006 Nov 1;22(21):2688-90
references: 16928733
references: MBio. 2013;4(5):e00708-13
references: 24149512
references: ISME J. 2014 Jul;8(7):1452-63
references: 24621521
references: BMC Microbiol. 2013;13:146
references: 23800252
references: BMC Bioinformatics. 2004 Aug 19;5:113
references: 15318951
references: Nat Rev Microbiol. 2014 Sep;12(9):635-45
references: 25118885
references: Bioinformatics. 2012 Jun 1;28(11):1420-8
references: 22495754
references: Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16213-6
references: 22927371
references: Microb Ecol. 1991 Dec;22(1):293-304
references: 24194344
references: Environ Microbiol. 2015 Mar;17(3):622-36
references: 24674078
references: Environ Sci Technol. 2005 Dec 1;39(23):9039-48
references: 16382923
references: J Contam Hydrol. 2007 Aug 15;93(1-4):216-35
references: 17442451
references: Appl Environ Microbiol. 2004 Oct;70(10):6037-46
references: 15466548
references: PLoS One. 2013;8(4):e62510
references: 23638103
references: Science. 2012 Sep 28;337(6102):1661-5
references: 23019650
references: Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1929-40
references: 17062412
references: Appl Environ Microbiol. 2009 Oct;75(20):6591-9
references: 19717633
references: Genome Res. 2015 Apr;25(4):534-43
references: 25665577
references: Nat Rev Microbiol. 2006 Feb;4(2):102-12
references: 16415926
references: BMC Bioinformatics. 2010;11:119
references: 20211023
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Nat Biotechnol. 2013 Jun;31(6):533-8
references: 23707974
references: PLoS One. 2010;5(6):e11147
references: 20593022
references: Appl Environ Microbiol. 2006 Apr;72(4):2756-64
references: 16597980
references: Nucleic Acids Res. 2004;32(5):1792-7
references: 15034147
references: Microbiome. 2013 Aug 05;1(1):22
references: 24450983
references: Nat Methods. 2012 Apr;9(4):357-9
references: 22388286
references: Nat Commun. 2013;4:2120
references: 23979677
references: Nat Commun. 2015;6:6372
references: 25721682
references: Nat Rev Microbiol. 2008 Jun;6(6):431-40
references: 18461076
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D109-14
references: 22080510
references: Bioinformatics. 2007 May 15;23(10):1282-8
references: 17379688
references: Genome Res. 2013 Jan;23(1):111-20
references: 22936250
references: Appl Environ Microbiol. 1992 Sep;58(9):3020-6
references: 1444415
references: Appl Environ Microbiol. 2000 May;66(5):1980-6
references: 10788370
references: Science. 2003 Aug 15;301(5635):976-8
references: 12881573
references: Science. 2007 Nov 30;318(5855):1449-52
references: 17947550
references: Environ Sci Technol. 2009 Jul 15;43(14):5429-35
references: 19708377
references: Genome Biol. 2008;9(10):R151
references: 18851752
references: Nucleic Acids Res. 1999 Jan 1;27(1):29-34
references: 9847135
references: Appl Environ Microbiol. 1984 Dec;48(6):1197-202
references: 6517587