Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient
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 character...
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ftosti:oai:osti.gov:1282053 2023-05-15T17:54:28+02:00 Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient Trubl, Gareth Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Natalie Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Chittick, Lauren Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Sergei A. 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 Rich, Virginia I. Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Sullivan, Matthew B. 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 2019-04-12 application/pdf http://www.osti.gov/servlets/purl/1282053 https://www.osti.gov/biblio/1282053 https://doi.org/10.7717/peerj.1999 unknown http://www.osti.gov/servlets/purl/1282053 https://www.osti.gov/biblio/1282053 https://doi.org/10.7717/peerj.1999 doi:10.7717/peerj.1999 54 ENVIRONMENTAL SCIENCES 58 GEOSCIENCES 2019 ftosti https://doi.org/10.7717/peerj.1999 2019-04-13T22:48:08Z 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 –1 of soil than other methods tested. All method combinations yielded VLPs g –1 of soil on the 10 8 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g –1 of 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. Other/Unknown Material palsa permafrost SciTec Connect (Office of Scientific and Technical Information - OSTI, U.S. Department of Energy) PeerJ 4 e1999 |
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54 ENVIRONMENTAL SCIENCES 58 GEOSCIENCES |
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54 ENVIRONMENTAL SCIENCES 58 GEOSCIENCES Trubl, Gareth Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Natalie Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Chittick, Lauren Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Sergei A. 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 Rich, Virginia I. Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Sullivan, Matthew B. 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 Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient |
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54 ENVIRONMENTAL SCIENCES 58 GEOSCIENCES |
description |
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 –1 of soil than other methods tested. All method combinations yielded VLPs g –1 of soil on the 10 8 order of magnitude across all three soil types. The different storage and concentration methods did not yield significantly more VLPs g –1 of 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. |
author |
Trubl, Gareth Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Natalie Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Chittick, Lauren Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Sergei A. 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 Rich, Virginia I. Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Sullivan, Matthew B. 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 |
author_facet |
Trubl, Gareth Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Natalie Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Chittick, Lauren Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Solonenko, Sergei A. 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 Rich, Virginia I. Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology Sullivan, Matthew B. 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 |
author_sort |
Trubl, Gareth Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology |
title |
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient |
title_short |
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient |
title_full |
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient |
title_fullStr |
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient |
title_full_unstemmed |
Optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient |
title_sort |
optimization of viral resuspension methods for carbon-rich soils along a permafrost thaw gradient |
publishDate |
2019 |
url |
http://www.osti.gov/servlets/purl/1282053 https://www.osti.gov/biblio/1282053 https://doi.org/10.7717/peerj.1999 |
genre |
palsa permafrost |
genre_facet |
palsa permafrost |
op_relation |
http://www.osti.gov/servlets/purl/1282053 https://www.osti.gov/biblio/1282053 https://doi.org/10.7717/peerj.1999 doi:10.7717/peerj.1999 |
op_doi |
https://doi.org/10.7717/peerj.1999 |
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PeerJ |
container_volume |
4 |
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e1999 |
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1766162221278167040 |