Beneath the surface: Unsolved questions in soil virus ecology

Soil virus ecology is an exciting but still nascent field of research in soil microbiology. While there has been a recent surge in soil virus research studies, many fundamental questions remain unanswered, and a range of technical and bioinformatic challenges need to be overcome. In this perspective article, we present a series of key questions that highlight fruitful research areas for ongoing and future efforts. These include describing the challenges involved in understanding soil viral abundance and activity, spatiotemporal dynamics, life strategy prevalence, virus-mediated biogeochemical impacts, viral protein function, host prediction, and soil RNA virus discovery. In the near term, combining approaches (e.g., cultivation-based, meta-omics, biogeochemical, experimental, and bioinformatic) will be key to assessing the ecological and biogeochemical impacts of soil viruses from the microscopic to the field and global scales. Still, we stress that results must be tempered by current methodological limitations and highlight knowledge gaps that are most pressing to fill via new methods or measurements, such as the prevalence of different viral replication strategies across soils, the fate of microbial necromass carbon after viral lysis, the frequency of virus-host encounters that do not lead to successful infections yet could be bioinformatically mistaken as infections, and the diversity and ecological impacts of RNA viruses in soil. • New approaches are needed to estimate viral infection, production, and decay rates • Soil viromics has revealed extreme spatiotemporal heterogeneity • Viral impacts on soil carbon turnover are likely substantial • Phage therapy shows promise but will be challenging to scale in soils • Bioinformatic hurdles remain for predicting protein function, hosts, and RNA viruses