Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome

Denison, Elizabeth R.; Pound, Helena L.; Gann, Eric R.; Gilbert, Naomi E.; Weston, David J.; Pelletier, Dale A.; Wilhelm, Steven W.

doi:10.1186/s40793-025-00719-0

Identification of shared viral sequences in peat moss metagenomes reveals elements of a possible Sphagnum core virome

Journal Article · Thu Jun 05 00:00:00 EDT 2025 · Environmental Microbiome

DOI:https://doi.org/10.1186/s40793-025-00719-0· OSTI ID:3012433

Denison, Elizabeth R. ^[1]; Pound, Helena L. ^[1]; Gann, Eric R. ^[1]; Gilbert, Naomi E. ^[2]; Weston, David J. ^[3]; Pelletier, Dale A. ^[3]; Wilhelm, Steven W. ^[1]

University of Tennessee, Knoxville, TN (United States)
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Viruses are an understudied component of plant microbiomes. Identifying viruses that are shared between individual plants, or members of the “core virome”, could reveal stable viral populations with the potential to modulate the composition and function of the microbiome. Here, we examined the virome associated with Sphagnum mosses, a keystone species that has direct influence over the fate of peatland carbon stores. We analyzed bulk metagenomes and metatranscriptomes generated from Sphagnum field samples collected over a ten-month period to identify virus-like sequences shared among plants. Individual Sphagnum samples harbored distinct DNA and RNA viromes where only a small percentage (< 1%) of the total number of identified viral contigs were shared among all samples. Based on taxonomic classification, the shared viral contigs represent bacterial viruses, or phage (Caudoviricetes), as well as viruses of eukaryotes, namely nucleocytoplasmic large DNA viruses (Nucleocytoviricota) and RNA viruses (Riboviria). We linked the shared phage-like contigs to viral regions within sequenced genomes of bacterial taxa that are members of the Sphagnum core microbiome, suggesting that these contigs represent temperate phage or degraded prophage. The putative nucleocytoplasmic large DNA viruses and RNA viruses were phylogenetically diverse and showed sequence similarity to viruses associated with a broad range of hosts and environmental sources. The identification of shared viral contigs suggested that, despite the compositional heterogeneity between samples, Sphagnum mosses may harbor a core virome. Future work validating the presence of the core virome is warranted as it may aid in understanding how persistent viruses impact microbiome ecology and symbiont evolution within this climatically relevant keystone species.

View Accepted Manuscript (DOE)

Research Organization:: Duke University, Durham, NC (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0020362; AC05-00OR22725

OSTI ID:: 3012433

Alternate ID(s):: OSTI ID: 2575250
OSTI ID: 2998446

Journal Information:: Environmental Microbiome, Journal Name: Environmental Microbiome Journal Issue: 1 Vol. 20; ISSN 2524-6372

Publisher:: Springer Science and Business Media LLCCopyright Statement

Country of Publication:: United States

Language:: English

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