Investigating the Spatiotemporal Trends of Agricultural Soil Viral Communities via Paired Total Metagenomes and Viromes

Abstract:

Soil viruses can shape the composition of microbial communities and have substantial impacts on biogeochemical processes and soil productivity, yet their ecology is poorly understood. Here, we provide a detailed characterization of the viral diversity associated with agricultural soils at the pre-planting and harvesting stages of a tomato growing season. By comparing the performance of total metagenomes and viromes generated from the same set of samples, we show that size fractionation successfully depleted sources of non-viral DNA in viromes, facilitating the recovery of thirty times more viral populations (vOTUs) than total metagenomes. Accordingly, viromes captured substantially more taxonomic diversity and allowed access to the rare virosphere, whereas total metagenomes tended to recover only the most persistent and abundant vOTUs. We also report that both viral and microbial communities displayed coupled temporal shifts that coincided with rhizosphere recruitment processes and nitrogen amendments. Additionally, viral communities were exclusively affected by a spatial gradient along the sampled field, suggesting that viruses can be particularly sensitive to soil heterogeneity at a local scale. Overall, these results highlight the ability of viromes to explore soil viral diversity and the dynamic compositional trends of viral communities.