Additional file 2 of Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

Description

Additional file 2: Supplementary Table 1. Description of the 46 IMG metagenomes and 43 metatranscriptomes (related to Fig. 1A). Supplementary Table 2. Metadata for all the East River Watershed soil samples (related to Fig. 1A). Supplementary Table 3. DNA vOTU table with RPKM for each vOTU by sample, contig information, taxonomy and host prediction (related to Fig. 1C). Supplementary Table 4. RNA vOTU table with RPKM for each vOTU by sample, contig information, taxonomy and host prediction (related to Fig. 1D). Supplementary Table 5. Detailed information of RNA vOTUs linking RdRP Set 1 (related to Fig. 2). Viral taxonomy is based on Coat protein (CP) from Callanan et al., (2020) [80] and RdRP marker genes. "Putative_Viral_order", "Putative_Viral_family", "Putative_host" columns are based on predictions made with a custom script (See Materials). Supplementary Table 6. Detailed information of RNA vOTUs linking RdRP Set 2 (related to Suplementary Fig. 1). "Putative_Viral_order", "Putative_Viral_family", "Putative_host" columns are based on predictions made with a custom script (See Materials). Supplementary Table 7. Detailed information of RNA vOTUs linking RdRP Set 3 (related to Suplementary Fig. 1). "Putative_Viral_order", "Putative_Viral_family", "Putative_host" columns are based on predictions made with a custom script (See Materials). Supplementary Table 8. Detailed information of RNA vOTUs linking RdRP Set 4 (related to Suplementary Fig. 1)."Putative_Viral_order", "Putative_Viral_family", "Putative_host" columns are based on predictions made with a custom script (See Materials). Supplementary Table 9. Detailed information of RNA vOTUs linking RdRP Set 5 (related to Suplementary Fig. 1). "Putative_Viral_order", "Putative_Viral_family", "Putative_host" columns are based on predictions made with a custom script (See Materials). Supplementary Table 10. Output table generated by vConTACT2 analysis with all the taxonomic information to reference genomes, as well as all the clustering information (related to Fig. 1C). Supplementary Table 11. UNIFRAC distances between this study and environmental studies (related to Fig. 2C). “Hillary” dataset was described in Hillary et al., (2022) [14], “Starr” was described in Starr et al., (2019) [29], "Callanan" was described in Callanan et al., (2020) [80], and "Wolf" was described in Wolf et al., (2020) [79]. Supplementary Table S12. PERMANOVA testing of contribution of season, depth and location on total DNA and RNA viral community and active DNA and RNA viral community (related to Fig. 3BCD) Supplementary Table 13. Significance of changes in total and active DNA and RNA vOTU abundance between months by ANOVA and post-hoc tests (related to Fig. 3EFG). Supplementary Table 14. Functional annotation of protein families against PHROGS database (related to Fig. 4C). Supplementary Table 15. Information (RPKM for each vOTU by sample, contig information, taxonomy and host prediction) of active DNA vOTUs exhibiting significant changes in abundance (n = 144) determined by STAMP analyses presented in Table S13 (related to Fig. 5A). Supplementary Table 16. Ecological strategies assigned to archaeal and bacterial OTUs from Sorensen et al., (2020) [6].

Knowledge graph centered on Additional file 2 of Virus diversity and activity with 14 nodes and 87 connections. Top connected: snowpack persistence, E. L. Brodie, plant-pathogen interactions, community structure, Patrick O. Sorensen.

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