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Review

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

1
Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
2
Department of Biology/Toxicology, Ashland University, Ashland, OH 44805, USA
3
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
4
Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
*
Authors to whom correspondence should be addressed.
Soil Syst. 2020, 4(2), 23; https://doi.org/10.3390/soilsystems4020023
Received: 25 February 2020 / Revised: 4 April 2020 / Accepted: 17 April 2020 / Published: 21 April 2020
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. View Full-Text
Keywords: bioinformatics; eDNA; gene transfer agent; isolate; metagenome; plasmid; ultrasmall microbes; virology; virome; virus-like particles bioinformatics; eDNA; gene transfer agent; isolate; metagenome; plasmid; ultrasmall microbes; virology; virome; virus-like particles
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MDPI and ACS Style

Trubl, G.; Hyman, P.; Roux, S.; Abedon, S.T. Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. Soil Syst. 2020, 4, 23. https://doi.org/10.3390/soilsystems4020023

AMA Style

Trubl G, Hyman P, Roux S, Abedon ST. Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics. Soil Systems. 2020; 4(2):23. https://doi.org/10.3390/soilsystems4020023

Chicago/Turabian Style

Trubl, Gareth, Paul Hyman, Simon Roux, and Stephen T. Abedon 2020. "Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics" Soil Systems 4, no. 2: 23. https://doi.org/10.3390/soilsystems4020023

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