The ecology of soil viruses: abundance, distribution, diversity and impact on microbial community structure

Viruses as a critical biotic component in all ecosystems have exhibited pronounced ecological significance. The global abundance of viruses in the biosphere has been estimated at 1 x 1031, with 90-95% of these viruses residing in soil and/or sedimentary environments. Despite the apparent greater abundance and diversity, soil virology is under-investigated relative to other environments such as marine and freshwater habitats and soil viral genomic data are underrepresented in public repositories of genetic information. In this dissertation, we investigated the viral abundance, diversity, and virus-host interactions in natural soils and the simulated stimulated subsurface bioremediation environments. We used epifluorescence microscopy counting, mitomycin C-induction assays, viral metagenomics sequencing, random amplified polymorphic DNA technique, bacterial 16S rRNA gene amplicons sequencing, and bioinformatics tools and revealed the viral ecology in the soils. Viral abundance and virus-to-bacteria ratio decreased with soil depth in the natural Ultisol, Alfisol, and Mollisol. The bacterial community composition and diversity significantly correlated with viral abundance, virus-to-bacteria ratio, and lysogenic fraction. The inducible lysogenic fractions among bacterial hosts increased with soil depth, indicating lysogeny became the more dominant reproduction strategy for autochthonous soil bacteriophages in deeper soil. The surface soil viromes had higher relative abundances of Microviridae (ssDNA virus) compared with the subsurface soil virome. Meanwhile, subsurface soils had higher relative abundances of dsDNA viruses, auxiliary metabolic genes and genes potentially encoding proteins of bacteriophage structural components and replication machinery than surface soils. The results in the simulated subsurface bioremediation systems showed that acetate availability was important in influencing viral abundance, community composition and interactions with microbial hosts. The increased viral abundance coincided with an increase in relative abundance of Fe(III)-reducing bacteria in areas of the columns exhibiting the most Fe(III) reduction. The research in this dissertation furthers our understanding of microbial ecology and has broader implications as the nature of virus-bacteria interactions is of fundamental interest.