A global perspective on bacterial diversity in the terrestrial deep subsurface

A. Soares, A. Edwards, D. An, A. Bagnoud, J. Bradley, E. Barnhart, M. Bomberg, K. Budwill, S. M. Caffrey, M. Fields, J. Gralnick, V. Kadnikov, L. Momper, M. Osburn, A. Mu, J. W. Moreau, D. Moser, L. Purkamo, S. M. Rassner, C. S. SheikB. Sherwood Lollar, B. M. Toner, G. Voordouw, K. Wouters, A. C. Mitchell

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

While recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12–20% of Earth’s biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8% in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the impor-tance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.

Original languageEnglish (US)
Article number001172
JournalMicrobiology (United Kingdom)
Volume169
Issue number1
DOIs
StatePublished - 2023

Bibliographical note

Funding Information:
The work was funded by a National Research Network for Low Carbon Energy and Environment (NRN-LCEE) grant to A.C.M. and A.E. from the Welsh Government and the Higher Education Funding Council for Wales (Geo-Carb-Cymru). Borehole samples from Nevada and California, USA (e.g. Nevares Deep Well 2 and BLM-1), were obtained with help in the field from Alexandra Wheatley, Jim Bruckner, Jenny Fisher and Scott Hamilton-Brehm, and technical assistance and funding from the US Department of Energy’s Subsurface Biogeochemical Research Program (SBR), the Hydrodynamic Group, LLC, the Nye County Nuclear Waste Repository Program Office (NWRPO), the US National Park Service, and Inyo Country, CA. Samples from a mine in Northern Ontario, Canada, were obtained with funding from the Natural Sciences and Engineering Research Council of Canada and the assistance of Thomas Eckert, and Greg Slater of McMaster University. The Census of Deep Life (CoDL) and Deep Carbon Observatory (DCO) projects are acknowledged for a range of studies used in this analysis, as well as the sequencing team at the Marine Biological Laboratory (MBL). Disclaimer: Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Funding Information:
The work was funded by a National Research Network for Low Carbon Energy and Environment (NRN-LCEE) grant to A.C.M. and A.E. from the Welsh Government and the Higher Education Funding Council for Wales (Geo-Carb-Cymru). Borehole samples from Nevada and California, USA (e.g. Nevares Deep Well 2 and BLM-1), were obtained with help in the field from Alexandra Wheatley, Jim Bruckner, Jenny Fisher and Scott Hamilton-Brehm, and technical assistance and funding from the US Department of Energy’s Subsurface Biogeochemical Research Program (SBR), the Hydrodynamic Group, LLC, the Nye County Nuclear Waste Repository Program Office (NWRPO), the US National Park Service, and Inyo Country, CA. Samples from a mine in Northern Ontario, Canada, were obtained with funding from the Natural Sciences and Engineering Research Council of Canada and the assistance of Thomas Eckert, and Greg Slater of McMaster University. The Census of Deep Life (CoDL) and Deep Carbon Observatory (DCO) projects are acknowl-edged for a range of studies used in this analysis, as well as the sequencing team at the Marine Biological Laboratory (MBL). Disclaimer: Any use of trade, firm or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Publisher Copyright:
© 2023 The Authors.

Keywords

  • 16S rRNA gene
  • bacterial
  • deep subsurface
  • meta-analysis

PubMed: MeSH publication types

  • Meta-Analysis
  • Journal Article
  • Research Support, Non-U.S. Gov't

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