Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Journal Article · Fri Nov 26 00:00:00 EST 2021 · Microbiome

DOI:https://doi.org/10.1186/s40168-021-01156-0· OSTI ID:1832662

ter Horst, Anneliek M. ; Santos-Medellín, Christian; Sorensen, Jackson W.; Zinke, Laura A.; Wilson, Rachel M.; Johnston, Eric R.; Trubl, Gareth; Pett-Ridge, Jennifer; Blazewicz, Steven J.; Hanson, Paul J.; Chanton, Jeffrey P.; Schadt, Christopher W.; Kostka, Joel E.; Emerson, Joanne B.

Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH₄ and CO₂ concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

• Research Organization: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: SC0021198; SC0020163; SC0007144; SC0012088; SCW1478; Microbiome SFA SCW1632; LLNL LDRD 18-ERD-041; GI Community Sequencing Award #2017; AC05-1008 00OR22725; AC05-00OR22725
• OSTI ID: 1832662
• Alternate ID(s): OSTI ID: 1833930; OSTI ID: 1845648
• Report Number(s): LLNL-JRNL-818141; 233; PII: 1156
• Journal Information: Microbiome, Journal Name: Microbiome Vol. 9 Journal Issue: 1; ISSN 2049-2618
• Publisher: Springer Science + Business Media
• Country of Publication: United Kingdom
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
viral ecology
viromics
soil viruses
soil microbial ecology
peat
metagenomics
biogeography
virome