Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
Abstract
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–1ofmore »
- Authors:
-
- 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
- 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 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
- Publication Date:
- Research Org.:
- Univ. of Arizona, Tucson, AZ (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1506096
- Grant/Contract Number:
- SC0010580
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PeerJ
- Additional Journal Information:
- Journal Volume: 4; Journal ID: ISSN 2167-8359
- Publisher:
- PeerJ Inc.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES; 58 GEOSCIENCES; viral diversity; viral ecology; soil viruses; phages; microbial ecology; humic-laden; permafrost; viral methods; active layer; Peatland; marine viruses; fresh-waters; population-dynamics; humic substances; climate-change; diversity; abundance; bacteria; bacteriophages; adsorption
Citation Formats
Trubl, Gareth, Solonenko, Natalie, Chittick, Lauren, Solonenko, Sergei A., Rich, Virginia I., and Sullivan, Matthew B. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. United States: N. p., 2016.
Web. doi:10.7717/peerj.1999.
Trubl, Gareth, Solonenko, Natalie, Chittick, Lauren, Solonenko, Sergei A., Rich, Virginia I., & Sullivan, Matthew B. Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient. United States. https://doi.org/10.7717/peerj.1999
Trubl, Gareth, Solonenko, Natalie, Chittick, Lauren, Solonenko, Sergei A., Rich, Virginia I., and Sullivan, Matthew B. Tue .
"Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient". United States. https://doi.org/10.7717/peerj.1999. https://www.osti.gov/servlets/purl/1506096.
@article{osti_1506096,
title = {Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient},
author = {Trubl, Gareth and Solonenko, Natalie and Chittick, Lauren and Solonenko, Sergei A. and Rich, Virginia I. and Sullivan, Matthew B.},
abstractNote = {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.},
doi = {10.7717/peerj.1999},
journal = {PeerJ},
number = ,
volume = 4,
place = {United States},
year = {Tue May 17 00:00:00 EDT 2016},
month = {Tue May 17 00:00:00 EDT 2016}
}
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Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils
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- Environmental Microbiology, Vol. 9, Issue 11
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method: Linker amplification for ultra-low DNA samples
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