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Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services

Trubl, Gareth
http://orcid.org/0000-0001-5008-1476
http://rave.ohiolink.edu/etdc/view?acc_num=osu1543425468999981

Abstract Details

2018, Doctor of Philosophy, Ohio State University, Microbiology.
Permafrost contains 30–50% of global soil carbon (C) and is rapidly thawing. While the fate of this C is unknown, it will be shaped in part by microbes and their associated viruses, which modulate microbial activities via mortality and metabolic control. To date, viral research in soils has been outpaced by that in aquatic environments due to the technical challenges of accessing soil viruses, compounded by the dramatic physicochemical heterogeneity in soils. The Stordalen Mire long-term ecological field site in Arctic Sweden encompasses a mosaic of natural permafrost thaw stages, and has been well characterized biogeochemically and microbiologically, making it an ideal site to characterize the soil virosphere and its potential impacts on the C cycle. A viral resuspension protocol was developed to generate quantitatively-amplified dsDNA viromes. The protocol yielded ~108 virus-like particles (VLPs) g-1 of soil across three thaw-stage habitats, and seven resulting viromes yielded 53 vOTUs. Viral-specific bioinformatics methods were used to recover viral populations, define their gene content, connect them to other related viruses (globally) and potential hosts (locally). Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ~30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. The vOTUs exhibited distinct ecology, with different distributions along the thaw gradient habitats, and a shift from soil-virus-like assemblages in the dry palsas to aquatic-virus-like assemblages in the inundated fen. Seventeen vOTUs were linked to microbial hosts (in silico), implicating viruses in infecting abundant microbial lineages from Acidobacteria, Verrucomicrobia, and Deltaproteobacteria, including those encoding key biogeochemical functions such as organic matter degradation. Thirty auxiliary metabolic genes (AMGs) were identified and suggested virus-mediated modulation of central carbon metabolism, soil organic matter degradation, polysaccharide binding, and regulation of sporulation. This pilot dataset suggested viral community structure changes with permafrost thaw, and that resident viruses impact ecosystem C processing via killing dominant microbial lineages & modulating several C metabolic pathways. We proceeded to optimize steps for generating quantitatively-amplified viromes for capturing both ssDNA and dsDNA viruses. Three different DNA extraction kits were tested and one yielded appreciable distinct communities (with ~1/3 novel viral populations), suggesting that different DNA extraction kits may bias the viral communities captured. The optimized protocol resulted in increased DNA yield and purity leading to the recovery of 299 vOTUs. Together, these findings suggest that these soil viruses have distinct ecology and impact host-mediated biogeochemistry via top-down (inferred from lysing dominant microbial hosts) and perhaps bottom-up (inferred from virally-encoded metabolic genes) controls. This optimized protocol could now be used to generate quantitatively-amplified viromes and in combination with the initial ecological insights provided here, these data can now guide future research in confirming and predicting viral impacts on soil ecosystem services.
Virginia Rich (Advisor)
Matthew Sullivan (Committee Co-Chair)
Kelly Wrighton (Committee Member)
Matthew Anderson (Committee Member)
165 p.
Biogeochemistry; Climate Change; Ecology; Environmental Science; Microbiology; Soil Sciences; Virology
Arctic, carbon cycling, environmental microbiology, microbial ecology, peatlands, permafrost, soil microbiology, soil viromics, viral ecology, viromes, metagenomics, climate, biogeochemistry, Stordalen Mire

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Citations

  • Trubl, G. (2018). Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543425468999981

    APA Style (7th edition)

  • Trubl, Gareth. Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services. 2018. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1543425468999981.

    MLA Style (8th edition)

  • Trubl, Gareth. "Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services." Doctoral dissertation, Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1543425468999981

    Chicago Manual of Style (17th edition)

osu1543425468999981
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This open access ETD is published by The Ohio State University and OhioLINK.