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Title: 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 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 » 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.« less
Authors:
 [1] ;  [2] ;  [2] ;  [3] ;  [1] ;  [4]
  1. Univ. of Arizona, Tucson, AZ (United States). Dept. of Soil, Water and Environmental Science; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
  2. Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology; Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
  3. 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
  4. 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:
OSTI Identifier:
1282053
Grant/Contract Number:
SC0010580
Type:
Accepted Manuscript
Journal Name:
PeerJ
Additional Journal Information:
Journal Volume: 4; Journal ID: ISSN 2167-8359
Publisher:
PeerJ Inc.
Research Org:
Univ. of Arizona, Tucson, AZ (United States).
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
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