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

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.IMPORTANCESoil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems. Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.

Automated summary

Soil microbes and viruses interact in playing crucial roles in the global carbon cycling. In this study, a publicly available metagenomic data set was used to investigate the interactions between viruses and their hosts in soil depth intervals. Contrary to previous assumptions, viruses were found to infect dominant soil hosts rather than being predominantly lysogenic. Additionally, evidence was provided for the potential of soil viruses to enhance the remineralization of soil carbon. This research emphasizes the need for further exploration of subsurface viral communities to improve our understanding of soil viral functions.