UC Davis

Viruses are abundant in soil, and by infecting other soil biota, viruses have the potential to impact soil food webs, and carbon and nutrient cycling. While viruses are an important component of the soil microbiome, they are relatively understudied. To explore viral diversity and ecology in plants and natural and agricultural soil systems, in this thesis, I used a combination of total soil metagenomics, viral size-fraction metagenomics (viromics) and dsRNA metatranscriptomics to investigate the viral communities in Minnesotan peatland soils, various oak and conifer plant species, California wetland soils and agricultural bulk and rhizosphere soils. In chapter one of this thesis, we determined that viral communities are mainly structured by depth and water content in a Minnesota peatland. In Chapter two we found that the viral communities of oak and conifer species are predominantly structured by host tree phylogeny. In Chapter three, we uncovered that habitat characteristics, such as soil salinity and plant community, play an important role in structuring the soil virome in a California wetland ecosystem with a salinity gradient. In Chapter four, we determined that viruses are abundant in the rhizosphere microbiome, and that soil compartment, moisture content, and spatial location of the field all have significant impact on viral community composition. Moreover, we created a database for reference-based viral genome recovery, named Phages and Integrated Genomes Encapsidated Or Not (PIGEON), in order to explore viral biogeographical patterns. In conclusion, viruses are an important, diverse and understudied component of the soil microbiome, and here, we explored viral diversity and community structuring in a variety of habitats.