Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems

Greenlon, Alex; Sieradzki, Ella; Zablocki, Olivier; Koch, Benjamin J.; Foley, Megan M.; Kimbrel, Jeffrey A.; Hungate, Bruce A.; Blazewicz, Steven J.; Nuccio, Erin E.; Sun, Christine L.; Chew, Aaron; Mancilla, Cynthia-Jeanette; Sullivan, Matthew B.; Firestone, Mary; Pett-Ridge, Jennifer; Banfield, Jillian F.

doi:10.1128/msystems.00417-22

Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems

Journal Article · Thu Oct 27 00:00:00 EDT 2022 · mSystems

DOI:https://doi.org/10.1128/msystems.00417-22· OSTI ID:2575211

Greenlon, Alex ^[1]; Sieradzki, Ella ^[1]; Zablocki, Olivier ^[2]; Koch, Benjamin J. ^[3]; Foley, Megan M. ^[3]; Kimbrel, Jeffrey A. ^[4]; ^[3]; Blazewicz, Steven J. ^[4]; Nuccio, Erin E. ^[4]; Sun, Christine L. ^[2]; Chew, Aaron ^[1]; Mancilla, Cynthia-Jeanette ^[1]; Sullivan, Matthew B. ^[2]; ^[1]; ^[5]; ^[1]

University of California, Berkeley, CA (United States)
The Ohio State University, Columbus, OH (United States)
Northern Arizona University, Flagstaff, AZ (United States)
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); University of California, Merced, CA (United States)

The growth and physiology of soil microorganisms, which play vital roles in biogeochemical cycling, are shaped by both current and historical soil environmental conditions. Here, we developed and applied a genome-resolved metagenomic implementation of quantitative stable isotope probing (qSIP) with an H₂¹⁸O labeling experiment to identify actively growing soil microorganisms and their genomic capacities. qSIP enabled measurement of taxon-specific growth because isotopic incorporation into microbial DNA requires production of new genome copies. We studied three Mediterranean grassland soils across a rainfall gradient to evaluate the hypothesis that historic precipitation levels are an important factor controlling trait selection. We used qSIP-informed genome-resolved metagenomics to resolve the active subset of soil community members and identify their characteristic ecophysiological traits. Higher year-round precipitation levels correlated with higher activity and growth rates of flagellar motile microorganisms. In addition to heavily isotopically labeled bacteria, we identified abundant isotope-labeled phages, suggesting phage-induced cell lysis likely contributed to necromass production at all three sites. Further, there was a positive correlation between phage activity and the activity of putative phage hosts. Contrary to our expectations, the capacity to decompose the diverse complex carbohydrates common in soil organic matter or oxidize methanol and carbon monoxide were broadly distributed across active and inactive bacteria in all three soils, implying that these traits are not highly selected for by historical precipitation.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 2575211

Report Number(s):: LLNL--JRNL-835074

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 6 Vol. 7; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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