Fig. 1

Overview of sampling strategy and general features of East River Watershed (ERW) DNA and RNA viruses. A Visual schematic of the sampling strategy. Bulk soil samples were collected in the ERW, Colorado on four dates, starting first at peak winter snow depth (March 7, 2017), during the snowmelt period (May 9, 2017), following the complete loss of snow and the start of the plant growing season (June 9, 2017), and finishing in autumn after plant senescence (September 15, 2017), at three discrete depth increments; 0 to 5 cm, 5 to 15 cm, and 15 cm + below the soil surface (Supplementary Tables 1 and 2). During snow-free times of the year (i.e., September and June), soils were collected at the upslope and downslope while during periods of winter snow cover (i.e., March and May), snow-pits were dug down to the soil surface, eventually yielding 46 and 43 metagenomes and metatranscriptomes, respectively. B Length distribution of the different quality tiers of DNA (blue) and RNA (green) vOTUs, based on their estimated completeness assessed by CheckV. HQ high-quality (≥ 90% complete), MQ medium-quality (≥ 50% complete), and LQ low-quality (< 50% complete). The LQ RNA vOTUs appear to be uniquely associated with larger RNA virus genomes (Supplementary Table 4). C Completeness, global distribution, virus taxonomy, and host taxonomy for DNA vOTUs ≥ 10kbp. Global distribution is based on shared clusters from a vContact2 analysis using only DNA vOTUs ≥ 10kbp, and virus and host taxonomy are based on GeNomad and iPHoP, respectively (see the “Methods” section). Completeness, global distribution, virus taxonomy, and host taxonomy for all DNA vOTUs (including ones < 10kbp) are presented in Supplementary Fig. 4. The spaces between the different branches represent the transition (or connection) of each vOTU between categories. D Completeness, global distribution, virus taxonomy, and host taxonomy for RNA vOTUs. Global distribution is assessed by genome-based clustering, and virus and host taxonomy are based on GeNomad and iPHoP and refined using phylogenetic analyses of the RNA virus marker gene RdRP (RNA-dependent RNA polymerase, see the “Methods” section)