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

Probst, Alexander J.; Ladd, Bethany; Jarett, Jessica K.; Geller-McGrath, David E.; Sieber, Christian M.  K.; Emerson, Joanne B.; Anantharaman, Karthik; Thomas, Brian C.; Malmstrom, Rex R.; Stieglmeier, Michaela; Klingl, Andreas; Woyke, Tanja; Ryan, M. Cathryn; Banfield, Jillian F.

doi:10.1038/s41564-017-0098-y

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

Journal Article · Mon Jan 29 00:00:00 EST 2018 · Nature Microbiology

DOI:https://doi.org/10.1038/s41564-017-0098-y· OSTI ID:1436345

Probst, Alexander J. ^[1]; Ladd, Bethany ^[2]; Jarett, Jessica K. ^[3]; Geller-McGrath, David E. ^[1]; Sieber, Christian M. K. ^[4]; Emerson, Joanne B. ^[1]; Anantharaman, Karthik ^[1]; Thomas, Brian C. ^[1]; Malmstrom, Rex R. ^[3]; Stieglmeier, Michaela ^[5]; Klingl, Andreas ^[5];

^[3];

^[2];

^[1]

Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science
Univ. of Calgary, AB (Canada). Dept. of Geoscience
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science; USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Ludwig Maximilian Univ., Munich (Germany). Plant Development and Electron Microscopy. Dept. of Biology

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Sloan Foundation (United States); German Research Foundation (DFG); Natural Sciences and Engineering Research Council of Canada (NSERC)

Grant/Contract Number:: AC02-05CH11231; SC0010566; G-2016-20166041; PR 1603/1-1

OSTI ID:: 1436345

Journal Information:: Nature Microbiology, Vol. 3; ISSN 2058-5276

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 113 works

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