Data from: Host community activity, but not always composition, explains viral biogeography in bulk and rhizosphere soils over a tomato growing season

The soil microbiome is key to plant health and nutrient acquisition, and
viruses likely play important but largely unknown roles in these
processes. To interrogate bulk and rhizosphere soil viral biogeography, we
collected samples over a tomato growing season in California from an
experiment testing arbuscular mycorrhizal fungi (AMF) treatment. We
generated 78 viromes, 16S rRNA gene, and ITS1 amplicon datasets, and 33
rhizosphere metatranscriptomes. Of 67,038 DNA viral ‘species’ genomes
(vOTUs), 25% were previously identified, predominantly in agricultural
systems, suggesting habitat filtering and greater viral homogeneity across
agricultural compared to natural soils globally. Rhizospheres had
significantly higher DNA viral richness than bulk soils, whereas no
significant richness differences were observed for other biota. 60% of
vOTUs were shared between compartments, compared to only 21-23% of
bacterial and fungal taxa. Although bulk soil viral biogeography resembled
that of prokaryotes, with significant structuring by moisture content,
greater virome similarity between high-moisture bulk soils and
rhizospheres suggests that conditions with high host activity selected for
similar viral communities. In rhizospheres, while bacterial and fungal
communities differed most over time, DNA and RNA viral communities
differed most by sampling location, matching prokaryotic transcriptional
patterns and further implicating host activity in viral biogeography.
Similarly, AMF treatment induced changes in the prokaryotic transcriptome,
but across biota, only significantly affected DNA viral communities.
Overall, results indicate strong viral responses to spatiotemporally
localized conditions, with viral biogeography reflecting both dispersal
opportunities (high between neighboring bulk and rhizosphere soils, low
across fields) and selection via local host activity.