Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils

Journal Article · 27 September 2023 · Nature Ecology and Evolution

DOI: https://doi.org/10.1038/s41559-023-02207-5 · OSTI ID:2283632

Santos-Medellín, Christian  ^[1]; Blazewicz, Steven J.  ^[2]; Pett-Ridge, Jennifer  ^[3]; Firestone, Mary K. ^[4]; Emerson, Joanne B.  ^[1]

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1. University of California, Davis, CA (United States)
2. Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
3. Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); University of California, Merced, CA (United States); University of California, Berkeley, CA (United States)
4. University of California, Berkeley, CA (United States)

As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. In this report we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for ‘Cull-the-Winner’ dynamics, whereby viruses infect and cull but do not decimate dominant host populations.

• 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); National Institutes of Health (NIH)
• Grant/Contract Number: AC52-07NA27344; SC0020163; SC0021198
• OSTI ID: 2283632
• Report Number(s): LLNL--JRNL-852843; 1080377
• Journal Information: Nature Ecology and Evolution, Journal Name: Nature Ecology and Evolution Journal Issue: 11 Vol. 7; ISSN 2397-334X
• Publisher: Nature Publishing GroupCopyright Statement
• Country of Publication: United States
• Language: English