DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes.

The small genomes of most viruses make it difficult to fully capture viral diversity in metagenomes dominated by DNA from cellular organisms. Viral size fraction metagenomics (viromics) protocols facilitate the enrichment of viral DNA from environmental samples, and these protocols typically include DNase treatment of the post-0.2-μm-filtered viromic fraction to remove contaminating free DNA prior to virion lysis. However, DNase may also remove desirable viral genomic DNA (e.g., contained in virions compromised due to frozen storage or laboratory processing), suggesting that DNase-untreated viromes might be useful in some cases. In order to understand how virome preparation with and without DNase treatment influences the resultant data, here, we compared 15 soil viromes (7 DNase treated and 8 untreated) from 8 samples collected from agricultural fields prior to tomato planting. DNase-treated viromes yielded significantly more assembled viral contigs, contained significantly less nonviral microbial DNA, and recovered more viral populations (viral operational taxonomic units [vOTUs]) through read mapping. However, DNase-treated and untreated viromes were statistically indistinguishable in terms of ecological patterns across viral communities. Although the results suggest that DNase treatment is preferable where possible, in comparison to previously reported total metagenomes from the same samples, both DNase-treated and untreated viromes were significantly enriched in viral signatures by all metrics compared, including a 225-times-higher proportion of viral reads in untreated viromes compared to total metagenomes. Thus, even without DNase treatment, viromics was preferable to total metagenomics for capturing viral diversity in these soils, suggesting that preparation of DNase-untreated viromes can be worthwhile when DNase treatment is not possible.