Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile

Abstract

Soil microbes play pivotal roles in global carbon cycling; however, the fundamental interactions between microbes and their infecting viruses remain unclear. This is exacerbated with soil depth, where the patterns of viral dispersal, ecology, and evolution are markedly underexplored. To investigate viral communities throughout the soil depth profile, we leveraged a publicly available metagenomic data set sampled from grassland soil in Northern California. In total, 10,196 non-redundant viral operational taxonomic units were recovered from soil between 20 cm and 115 cm below the surface. Viral prevalence was high throughout the soil depth profile, with viruses infecting dominant soil hosts, including Actinomycetia. Contrary to leading hypotheses, lysogeny did not dominate in the soil viral communities. Viral diversity was assessed at both the population level (i.e., macrodiversity) and strain level (i.e., microdiversity) to reveal diverse ecological and evolutionary patterns of virus-host interactions in surface and subsurface soils. Investigating viral microdiversity uncovered potential patterns of antagonistic co-evolution across both surface and subsurface soils. Furthermore, we have provided evidence for the potential of soil viruses to augment the remineralization of soil carbon. While we continue to yield a more comprehensive understanding of soil viral ecology, our work appeals to future researchers to further investigate subsurface viral communities.