TY - JOUR
T1 - Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface
AU - Probst, Alexander J.
AU - Ladd, Bethany
AU - Jarett, Jessica K.
AU - Geller-Mcgrath, David E.
AU - Sieber, Christian M.K.
AU - Emerson, Joanne B.
AU - Anantharaman, Karthik
AU - Thomas, Brian C.
AU - Malmstrom, Rex R.
AU - Stieglmeier, Michaela
AU - Klingl, Andreas
AU - Woyke, Tanja
AU - Ryan, M. Cathryn
AU - Banfield, Jillian F.
N1 - Funding Information:
We thank J. Hinshaw for his contribution to fieldwork logistics and yearlong temperature monitoring. We also thank C. Brown, S. Spaulding, S. Clingenpeel, D. Barton, B. Rocha and D. Bethune for logistic support during fieldwork. C. Niemann provided technical assistance regarding scanning electron microscopy. D. Goudeau is acknowledged for help with singlecell lab work. We thank T. G. del Rio for handling of metagenomic samples at JGI. We are grateful to S. Gribaldo for discussion of the phylogenetic placement of bacterial and archaeal phyla. A.J.P. was supported by the German Science Foundation under DFG PR 1603/11 and by Lawrence Berkeley National Laboratory’s Sustainable Systems Scientific Focus Area funded by the US Department of Energy, Office of Science, Office of Biological and Environmental Research under contract DEAC0205CH11231. Work at UCB was funded by the Sloan Foundation (“Deep Life”, grant no. G201620166041). Funding for hydrogeological and geochemical analyses was provided by a Natural Sciences and Engineering Research Council of Canada Discovery Grant to M.C.R. Development of ggKbase was supported by the Office of Science, Office of Biological and Environmental Research, of the US Department of Energy Grant DOESC10010566. Work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DEAC0205CH11231. We thank DOE’s Emerging Technologies Opportunity Program “Development of a pipeline for highthroughput recovery of nearcomplete and complete microbial genomes from complex metagenomic datasets” for sequencing.
Publisher Copyright:
© 2017 The Author(s).
PY - 2018/3
Y1 - 2018/3
N2 - 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 CO 2 -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 N 2 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.
AB - 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 CO 2 -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 N 2 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.
UR - https://www.scopus.com/pages/publications/85041121836
U2 - 10.1038/s41564-017-0098-y
DO - 10.1038/s41564-017-0098-y
M3 - Article
C2 - 29379208
AN - SCOPUS:85041121836
SN - 2058-5276
VL - 3
SP - 328
EP - 336
JO - Nature Microbiology
JF - Nature Microbiology
IS - 3
ER -