Ecology of active viruses and their bacterial hosts in frozen Arctic peat soil revealed with H₂¹⁸O stable isotope probing metagenomics

Abstract

Winter soil processes are critical to the carbon balance of northern ecosystems, yet the microbial ecology governing biogeochemical cycling in frozen soils is largely unknown. We used stable isotope probing targeted metagenomics to reveal the genomic potential of active microbial populations, with an emphasis on viruses, in soils. Peat soils were incubated under simulated winter conditions (subzero and anoxic) with H218O or natural abundance water for 184 and 370 days. Isotope incorporation revealed 46 active bacterial populations (MAGs; spanning 9 bacterial phyla) and 243 active viral populations (vOTUs). Active hosts were predicted for 33% of the active vOTUs and were some of the most abundant MAGs, having capacity for fermentation and carbohydrate utilization. Additionally, almost one-third of vOTUs carried auxiliary metabolic genes spanning five functional categories, highlighting the potential impact of viruses in microbial biogeochemistry. CO2 production throughout the incubation supports our evidence of microbial activities under winter conditions. Our results revealed a multi-trophic and changing microbial community in tandem with a changing viral community targeting dominant active bacteria consistent with the “kill-the-winner” hypothesis. These data have important implications for low-temperature soil processes in northern peatlands and reveal active host-linked soil viral ecology, with potential multifaceted biogeochemical impacts.

Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems

“…Many studies have documented viruses in soil (e.g. Williamson et al, 2017, Trubl et al, 2021, ter Horst, et al, 2021, but as viruses can be deactivated in soil through multiple mechanisms (e.g., by sorption to minerals), a grand challenge is to assess what fraction of viruses is active. We identified potential phage sequences in metagenomic assemblies (total of 119,253 viral contigs across all all-fraction assemblies; clustered into 8,617 viral populations), and examined patterns of activity measured by AFE, focusing on phage contigs for which we confidently predicted hosts.…”

Integrating Viral Metagenomics into an Ecological Framework

“…Stable isotope probing (SIP) combined with metagenomics has become a popular technique to characterize specific microbes (or link individuals to specific functions) and the viruses that infect them (90)(91)(92)(93) or to label organisms and viruses active in a sample (94). This technique involves incubating samples with isotopically labeled substrate(s), separating labeled and unlabeled nucleic acid via CsCl-density centrifugation, and sequencing the different fractions.…”

“…of methods to distinguish actively replicating populations from dormant or dead biomass (e.g., SIP) and their use in combination with viral metagenomics should be more widely adopted (for an example, see 94). Alternatively, metatranscriptomes paired with metagenomes can reveal not only RNA viruses but also transcriptional activity of DNA viruses, although the small amounts of mRNA and lack of correlation between transcription and actual translation and virion production do require care in interpreting such data.…”