title: Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.
abstract: The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors: Karthik
authors: K
authors: Anantharaman
authors: Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
authors: Christopher T
authors: 0000-0002-7758-6447
authors: CT
authors: Brown
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors: Laura A
authors: LA
authors: Hug
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors: Itai
authors: I
authors: Sharon
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors: Cindy J
authors: CJ
authors: Castelle
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors: Alexander J
authors: AJ
authors: Probst
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors: Brian C
authors: BC
authors: Thomas
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.
authors: Andrea
authors: A
authors: Singh
authors: School of Earth Sciences and Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA.
authors: Michael J
authors: MJ
authors: Wilkins
authors: Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors: Ulas
authors: U
authors: Karaoz
authors: Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors: Eoin L
authors: EL
authors: Brodie
authors: Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors: Kenneth H
authors: KH
authors: Williams
authors: Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors: Susan S
authors: SS
authors: Hubbard
authors: Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA.|Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors: Jillian F
authors: JF
authors: Banfield
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D002244:Carbon / Q000378:metabolism; D017753:Ecosystem; D064349:Genome, Microbial / Q000235:genetics*; D019015:Geologic Sediments / Q000382:microbiology*; D060587:Groundwater / Q000382:microbiology*; D056186:Metagenomics; D009584:Nitrogen / Q000378:metabolism; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013455:Sulfur / Q000378:metabolism
chemical_list: D012336:RNA, Ribosomal, 16S; D013455:Sulfur; D002244:Carbon; D009584:Nitrogen