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Nat Microbiol. 2018 Mar;3(3):328-336. doi: 10.1038/s41564-017-0098-y. Epub 2018 Jan 29.

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.

Author information

1
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
2
Group for Aquatic Microbial Ecology, Biofilm Center, Department of Chemistry, University of Duisburg-Essen, Essen, Germany.
3
Department of Geoscience, University of Calgary, Calgary, AB, Canada.
4
Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
5
Department of Plant Pathology, University of California, Davis, Davis, CA, USA.
6
Plant Development and Electron Microscopy, Department of Biology I, Biocenter LMU Munich, Planegg-Martinsried, Germany.
7
Department of Geoscience, University of Calgary, Calgary, AB, Canada. cryan@ucalgary.ca.
8
Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.

Abstract

An enormous diversity of previously unknown bacteria and archaea has been discovered recently, yet their functional capacities and distributions in the terrestrial subsurface remain uncertain. Here, we continually sampled a CO2-driven geyser (Colorado Plateau, Utah, USA) over its 5-day eruption cycle to test the hypothesis that stratified, sandstone-hosted aquifers sampled over three phases of the eruption cycle have microbial communities that differ both in membership and function. Genome-resolved metagenomics, single-cell genomics and geochemical analyses confirmed this hypothesis and linked microorganisms to groundwater compositions from different depths. Autotrophic Candidatus "Altiarchaeum sp." and phylogenetically deep-branching nanoarchaea dominate the deepest groundwater. A nanoarchaeon with limited metabolic capacity is inferred to be a potential symbiont of the Ca. "Altiarchaeum". Candidate Phyla Radiation bacteria are also present in the deepest groundwater and they are relatively abundant in water from intermediate depths. During the recovery phase of the geyser, microaerophilic Fe- and S-oxidizers have high in situ genome replication rates. Autotrophic Sulfurimonas sustained by aerobic sulfide oxidation and with the capacity for N2 fixation dominate the shallow aquifer. Overall, 104 different phylum-level lineages are present in water from these subsurface environments, with uncultivated archaea and bacteria partitioned to the deeper subsurface.

PMID:
29379208
DOI:
10.1038/s41564-017-0098-y
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