TY - JOUR
T1 - Life and death in the soil microbiome
T2 - how ecological processes influence biogeochemistry
AU - LLNL Soil Microbiome Consortium
AU - Sokol, Noah W.
AU - Slessarev, Eric
AU - Marschmann, Gianna L.
AU - Nicolas, Alexa
AU - Blazewicz, Steven J.
AU - Brodie, Eoin L.
AU - Firestone, Mary K.
AU - Foley, Megan M.
AU - Hestrin, Rachel
AU - Hungate, Bruce A.
AU - Koch, Benjamin J.
AU - Stone, Bram W.
AU - Sullivan, Matthew B.
AU - Zablocki, Olivier
AU - Trubl, Gareth
AU - McFarlane, Karis
AU - Stuart, Rhona
AU - Nuccio, Erin
AU - Weber, Peter
AU - Jiao, Yongqin
AU - Zavarin, Mavrik
AU - Kimbrel, Jeffrey
AU - Morrison, Keith
AU - Adhikari, Dinesh
AU - Bhattacharaya, Amrita
AU - Nico, Peter
AU - Tang, Jinyun
AU - Didonato, Nicole
AU - Paša-Tolić, Ljiljana
AU - Greenlon, Alex
AU - Sieradzki, Ella T.
AU - Dijkstra, Paul
AU - Schwartz, Egbert
AU - Sachdeva, Rohan
AU - Banfield, Jillian
AU - Pett-Ridge, Jennifer
N1 - Funding Information:
The authors thank the Lawrence Livermore National Laboratory (LLNL) Soil Microbiome Scientific Focus Area team for helpful discussions, and K. Georgiou and E. Whalen for providing comments on earlier drafts of the manuscript. This work was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research, Genomic Science Program (GSP) LLNL ‘Microbes Persist’ Soil Microbiome Scientific Focus Area SCW1632. Work at LLNL was performed under the auspices of the DOE, Contract DE-AC52-07NA27344. Part of this work was performed at Lawrence Berkeley National Laboratory funded under U.S. Department of Energy contract number DE-AC02-05CH11231.
Funding Information:
The authors thank the Lawrence Livermore National Laboratory (LLNL) Soil Microbiome Scientific Focus Area team for helpful discussions, and K. Georgiou and E. Whalen for providing comments on earlier drafts of the manuscript. This work was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research, Genomic Science Program (GSP) LLNL ‘Microbes Persist’ Soil Microbiome Scientific Focus Area SCW1632. Work at LLNL was performed under the auspices of the DOE, Contract DE-AC52-07NA27344. Part of this work was performed at Lawrence Berkeley National Laboratory funded under U.S. Department of Energy contract number DE-AC02-05CH11231.
Publisher Copyright:
© 2022, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.
PY - 2022/7
Y1 - 2022/7
N2 - Soil microorganisms shape global element cycles in life and death. Living soil microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter — Earth’s largest terrestrial carbon pool and the primary source of plant nutrients. Their metabolic functions are influenced by ecological interactions with other soil microbial populations, soil fauna and plants, and the surrounding soil environment. Remnants of dead microbial cells serve as fuel for these biogeochemical engines because their chemical constituents persist as soil organic matter. This non-living microbial biomass accretes over time in soil, forming one of the largest pools of organic matter on the planet. In this Review, we discuss how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. With recent omics advances, many of the traits that frame microbial population dynamics and their ecophysiological adaptations can be deciphered directly from assembled genomes or patterns of gene or protein expression. Thus, it is now possible to leverage a trait-based understanding of microbial life and death within improved biogeochemical models and to better predict ecosystem functioning under new climate regimes.
AB - Soil microorganisms shape global element cycles in life and death. Living soil microorganisms are a major engine of terrestrial biogeochemistry, driving the turnover of soil organic matter — Earth’s largest terrestrial carbon pool and the primary source of plant nutrients. Their metabolic functions are influenced by ecological interactions with other soil microbial populations, soil fauna and plants, and the surrounding soil environment. Remnants of dead microbial cells serve as fuel for these biogeochemical engines because their chemical constituents persist as soil organic matter. This non-living microbial biomass accretes over time in soil, forming one of the largest pools of organic matter on the planet. In this Review, we discuss how the biogeochemical cycling of organic matter depends on both living and dead soil microorganisms, their functional traits, and their interactions with the soil matrix and other organisms. With recent omics advances, many of the traits that frame microbial population dynamics and their ecophysiological adaptations can be deciphered directly from assembled genomes or patterns of gene or protein expression. Thus, it is now possible to leverage a trait-based understanding of microbial life and death within improved biogeochemical models and to better predict ecosystem functioning under new climate regimes.
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U2 - 10.1038/s41579-022-00695-z
DO - 10.1038/s41579-022-00695-z
M3 - Review article
C2 - 35228712
AN - SCOPUS:85126929164
SN - 1740-1526
VL - 20
SP - 415
EP - 430
JO - Nature Reviews Microbiology
JF - Nature Reviews Microbiology
IS - 7
ER -