Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

Trubl, Gareth; Hyman, Paul; Roux, Simon; Abedon, Stephen T.

doi:10.3390/soilsystems4020023

Title: Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

Journal Article · Tue Apr 21 00:00:00 EDT 2020 · Soil Systems

DOI:https://doi.org/10.3390/soilsystems4020023· OSTI ID:1660507

^[1];

^[2];

^[3]; Abedon, Stephen T. ^[4]

Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Ashland Univ., Ashland, OH (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
The Ohio State Univ., Columbus, OH (United States)

The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.

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Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC52-07NA27344; AC02-05CH11231

OSTI ID:: 1660507

Alternate ID(s):: OSTI ID: 1766494

Report Number(s):: LLNL-JRNL-793747; 988504

Journal Information:: Soil Systems, Vol. 4, Issue 2; ISSN 2571-8789

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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