Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands

Journal Article · Wed Nov 02 00:00:00 UTC 2022 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.2209132119 · OSTI ID:1896555

Santos-Medellín, Christian ^[1]; Estera-Molina, Katerina ^[2]; Yuan, Mengting ^[2]; Pett-Ridge, Jennifer ^[3]; Firestone, Mary K. ^[2]; Emerson, Joanne B. ^[1]

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1. Department of Plant Pathology, University of California, Davis, CA 95616
2. Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
3. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, Life &, Environmental Sciences Department, University of California, Merced, CA 95343

Viruses shape microbial communities, food web dynamics, and carbon and nutrient cycling in diverse ecosystems. However, little is known about the patterns and drivers of viral community composition, particularly in soil, precluding a predictive understanding of viral impacts on terrestrial habitats. To investigate soil viral community assembly processes, here we analyzed 43 soil viromes from a rainfall manipulation experiment in a Mediterranean grassland in California. We identified 5,315 viral populations (viral operational taxonomic units [vOTUs] with a representative sequence ≥10 kbp) and found that viral community composition exhibited a highly significant distance–decay relationship within the 200-m ² field site. This pattern was recapitulated by the intrapopulation microheterogeneity trends of prevalent vOTUs (detected in ≥90% of the viromes), which tended to exhibit negative correlations between spatial distance and the genomic similarity of their predominant allelic variants. Although significant spatial structuring was also observed in the bacterial and archaeal communities, the signal was dampened relative to the viromes, suggesting differences in local assembly drivers for viruses and prokaryotes and/or differences in the temporal scales captured by viromes and total DNA. Despite the overwhelming spatial signal, evidence for environmental filtering was revealed in a protein-sharing network analysis, wherein a group of related vOTUs predicted to infect actinobacteria was shown to be significantly enriched in low-moisture samples distributed throughout the field. Overall, our results indicate a highly diverse, dynamic, active, and spatially structured soil virosphere capable of rapid responses to changing environmental conditions.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDOE; USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC52-07NA27344; SC0020163
• OSTI ID: 1896555
• Report Number(s): LLNL--JRNL-835076; e2209132119
• Journal Information: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 45 Vol. 119; ISSN 0027-8424
• Publisher: Proceedings of the National Academy of SciencesCopyright Statement
• Country of Publication: United States
• Language: English