Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

Trubl, Gareth; Solonenko, Natalie; Chittick, Lauren; Solonenko, Sergei A.; Rich, Virginia I.; Sullivan, Matthew B.

doi:10.7717/peerj.1999

Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient

Journal Article · Tue May 17 00:00:00 EDT 2016 · PeerJ

DOI:https://doi.org/10.7717/peerj.1999· OSTI ID:1506096

Trubl, Gareth ^[1]; Solonenko, Natalie ^[2]; Chittick, Lauren ^[2]; Solonenko, Sergei A. ^[3]; Rich, Virginia I. ^[4]; Sullivan, Matthew B. ^[5]

Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology; Ohio State University
Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Ecology, Evolution and Organismal Biology
Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology; Dept. of Ecology, Evolution and Organismal Biology; Dept. of Civil, Environmental and Geodetic Engineering

Permafrost stores approximately 50% of global soil carbon (C) in a frozen form; it is thawing rapidly under climate change, and little is known about viral communities in these soils or their roles in C cycling. In permafrost soils, microorganisms contribute significantly to C cycling, and characterizing them has recently been shown to improve prediction of ecosystem function. In other ecosystems, viruses have broad ecosystem and community impacts ranging from host cell mortality and organic matter cycling to horizontal gene transfer and reprogramming of core microbial metabolisms. Here we developed an optimized protocol to extract viruses from three types of high organic-matter peatland soils across a permafrost thaw gradient (palsa, moss-dominated bog, and sedge-dominated fen). Three separate experiments were used to evaluate the impact of chemical buffers, physical dispersion, storage conditions, and concentration and purification methods on viral yields. The most successful protocol, amended potassium citrate buffer with bead-beating or vortexing and BSA, yielded on average as much as 2-fold more virus-like particles (VLPs) g^–1of soil than other methods tested. All method combinations yielded VLPs g^–1of soil on the 10⁸order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g^–1of soil among the soil types. In conclusion, this research provides much-needed guidelines for resuspending viruses from soils, specifically carbon-rich soils, paving the way for incorporating viruses into soil ecology studies.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Arizona, Tucson, AZ (United States).

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: SC0010580

OSTI ID:: 1506096

Journal Information:: PeerJ, Journal Name: PeerJ Vol. 4; ISSN 2167-8359

Publisher:: PeerJ Inc.Copyright Statement

Country of Publication:: United States

Language:: English

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Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil Göller, Pauline C.; Haro-Moreno, Jose M.; Rodriguez-Valera, Francisco Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-0795-2	journal	February 2020
An Improved Method for Extracting Viruses From Sediment: Detection of Far More Viruses in the Subseafloor Than Previously Reported Pan, Donald; Morono, Yuki; Inagaki, Fumio Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00878	journal	April 2019
Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth Hyman, Paul Pharmaceuticals, Vol. 12, Issue 1 https://doi.org/10.3390/ph12010035	journal	March 2019
VIBRANT: Automated recovery, annotation and curation of microbial viruses, and evaluation of virome function from genomic sequences Kieft, Kristopher; Zhou, Zhichao; Anantharaman, Karthik https://doi.org/10.1101/855387	posted_content	November 2019
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing Trubl, Gareth; Jang, Ho Bin; Roux, Simon mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/msystems.00076-18	journal	October 2018
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences Kieft, Kristopher; Zhou, Zhichao; Anantharaman, Karthik Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00867-0	journal	June 2020
Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD) Narr, Anja; Nawaz, Ali; Wick, Lukas Y. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.01975	journal	October 2017
Uncovering a hidden diversity: optimized protocols for the extraction of dsDNA bacteriophages from soil Göller, Pauline C.; Haro-Moreno, Jose M.; Rodriguez-Valera, Francisco ETH Zurich https://doi.org/10.3929/ethz-b-000400872	text	January 2020
Optimizing de novo genome assembly from PCR-amplified metagenomes Roux, Simon; Trubl, Gareth; Goudeau, Danielle PeerJ, Vol. 7 https://doi.org/10.7717/peerj.6902	journal	January 2019
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils Trubl, Gareth; Roux, Simon; Solonenko, Natalie PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7265	journal	January 2019
Benchmarking protocols for the metagenomic analysis of stream biofilm viromes Bekliz, Meriem; Brandani, Jade; Bourquin, Massimo PeerJ, Vol. 7 https://doi.org/10.7717/peerj.8187	journal	January 2019

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54 ENVIRONMENTAL SCIENCES
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