DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes

Sorensen, Jackson W.; Zinke, Laura A.; ter Horst, Anneliek M.; Santos-Medellín, Christian; Schroeder, Alena; Emerson, Joanne B.

doi:10.1128/msystems.00614-21

Title: DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes

Journal Article · 07 September 2021 · mSystems

DOI: https://doi.org/10.1128/msystems.00614-21 · OSTI ID:1818999

Sorensen, Jackson W. ^[1]; Zinke, Laura A. ^[1]; ter Horst, Anneliek M. ^[1]; Santos-Medellín, Christian ^[1]; Schroeder, Alena ^[1]; Emerson, Joanne B. ^[2]

Univ. of California, Davis, CA (United States). Dept. of Plant Pathology
Univ. of California, Davis, CA (United States). Dept. of Plant Pathology; Univ. of California, Davis, CA (United States). Genome Center

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.

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Research Organization:: Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDA; National Institute of Food and Agriculture (NIFA; USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); USDOE

Grant/Contract Number:: SC0020163; 2021-67013-34815-0; 1S10OD010786-01

OSTI ID:: 1818999

Alternate ID(s):: OSTI ID: 1853476

Journal Information:: mSystems, Vol. 6, Issue 5; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Microbiology
DNase
relic DNA
viromics
metagenomics
soil
viruses

Title: DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes

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