Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities
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- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, USA, Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California, USA, Chan Zuckerberg Biohub, San Francisco, California, USA, Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
Candidate Phyla Radiation (CPR) bacteria and nanoarchaea populate most ecosystems but are rarely detected in soil. We concentrated particles of less than 0.2 μm in size from grassland soil, enabling targeted metagenomic analysis of these organisms, which are almost totally unexplored in largely oxic environments such as soil. We recovered a diversity of CPR bacterial and some archaeal sequences but no sequences from other cellular organisms. The sampled sequences include Doudnabacteria (SM2F11) and Pacearchaeota, organisms rarely reported in soil, as well as Saccharibacteria, Parcubacteria, and Microgenomates. CPR and archaea of the phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) were enriched 100- to 1,000-fold compared to that in bulk soil, in which we estimate each of these organisms comprises approximately 1 to 100 cells per gram of soil. Like most CPR and DPANN sequenced to date, we predict these microorganisms live symbiotic anaerobic lifestyles. However, Saccharibacteria, Parcubacteria, and Doudnabacteria genomes sampled here also harbor ubiquinol oxidase operons that may have been acquired from other bacteria, likely during adaptation to aerobic soil environments. We conclude that CPR bacteria and DPANN archaea are part of the rare soil biosphere and harbor unique metabolic platforms that potentially evolved to live symbiotically under relatively oxic conditions.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH)
- Grant/Contract Number:
- SCW1678; AC52-07NA27344; SC0020163; SC0016247; AC02-05CH11231; 18-ERD-041; DP2AI117984
- OSTI ID:
- 1813894
- Alternate ID(s):
- OSTI ID: 1834749; OSTI ID: 1860646
- Report Number(s):
- LLNL-JRNL-814549; e01205-20
- Journal Information:
- mSystems, Journal Name: mSystems Vol. 6 Journal Issue: 4; ISSN 2379-5077
- Publisher:
- American Society for MicrobiologyCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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