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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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.
The authors declare no competing interests.
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- Microbial necromass
Dead cellular biomass (for example, cell envelopes) and extracellular products (for example, extracellular polymeric substances).
- Ecological succession
A consistent, distinct trajectory of community change through time.
The zone of soil under direct influence of a living plant root.
The zone of soil under direct influence of fungal hyphae.
The zone of soil under direct influence of decaying litter.
- Bulk soil
Soil that is not in the direct influence of living or dead roots; characterized by lower levels of microbial density and activity relative to high-resource habitats.
- Ecophysiological traits
Traits related to the physiology of a microorganism, as shaped by their biotic and abiotic ecological context.
- Mineral-associated organic matter
Soil organic matter that exists in some degree of association with soil minerals.
- Carbon-use efficiency
(CUE). Microbial biomass yield given a quantity of available substrate.
- Community assembly
Processes that shape the identity and abundance of species within a biological community.
A form of symbiosis where both partners benefit.
A process that regulates population size based on population density.
- Viral shunt
The theory that viral lysis of microbial cells returns labile organic matter to an available pool.
- Exploitative competition
Indirect competition for resources.
- Antagonistic competition
Direct competition involving combative interactions.
- Trophic transfer
The transfer of energy between trophic levels.
- Microbial loop
The flux of nutrients, energy and organic matter within microbial communities.
- Birch effect
The ephemeral pulse of CO2 following wetting of dry soil.
- Microbially explicit biogeochemical models
Models that represent the amount of microbial biomass as a dynamic variable that mediates biogeochemical transformation rates.
- Trait inference
Indirect trait quantification based on genomic data, as opposed to direct observation of microbial trait.
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Sokol, N.W., Slessarev, E., Marschmann, G.L. et al. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nat Rev Microbiol 20, 415–430 (2022). https://doi.org/10.1038/s41579-022-00695-z
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