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

Abstract

Background 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. Results 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. Conclusions 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.

Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench

“…Next, the selected viral scaffolds were run through DRAM-v using default parameters, and those genes with gene descriptions and auxiliary scores of <4 were considered putative AMGs. As suggested previously ( 44 , 105 ), to be conservative, we did not consider the genes related to glycosyltransferases, ribosomal proteins, organic nitrogen, and nucleotide metabolism as viral AMGs. For all putative AMGs annotated by VIBRANT and DRAM-v and to avoid false-positive results for selected AMGs caused by possible pollution of host sequences, only the putative AMGs located between two viral hallmark genes or virus-like genes and those located alongside the viral hallmark genes or virus-like genes were considered high-confidence viral AMGs for further analysis.…”

Eco-evolutionary response of soil viral communities to land use changes

“…Viral metagenomics has greatly expanded the viral ecology of aquatic ecosystems and mammalian guts, yet, knowledge about soil viruses lag behind. There were approximately a hundred of reported soil viromes derived from Arctic permafrost 8 , agricultural soils 9,10 , mangrove sediment 4 , peat 11 and Antarctic soils 12 , providing insights into the niche partitioning of viral populations 11 , their response to climate change and environmental stress 8 , and phage mediated horizontal gene transfer 3 . However, none of these viromes was from forest, urban park and road verge soil, the macrodiversity and microdiverisity of viral communities in soils with varied land use types have not been fully explored.…”

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

“…Following the publication of the original article [ 1 ], the co-author reported that Funding section was not included. Below is the Funding section.…”

“…Correction to: Microbiome 9, 233 (2021) https://doi.org/10.1186/s40168-021-01156-0 Following the publication of the original article [1], the co-author reported that Funding section was not included. Below is the Funding section.…”