Host-linked soil viral ecology along a permafrost thaw gradient

Abstract

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling.

Demographic and environmental drivers of metagenomic viral diversity in vampire bats

“…Although we did not test the ecological and evolutionary consequences of variation in viral diversity in this study, it is probable that some members of the vampire bat viral community identified here have functional importance. For example, viral metagenomics has identified specific viral taxa associated with disease (Duerkop et al, 2018;Hannigan, Duhaime, Ruffin, Koumpouras, & Schloss, 2018;Ly et al, 2014;Norman et al, 2015) and the critical contributions of certain viral groups to overall ecosystem function (Emerson et al, 2018;Sunagawa et al, 2015;Thurber, Payet, Thurber, & Correa, 2017). Follow-up analyses could include targeting individual viral taxa that are linked with health or disease in other systems, examining associations between variation in viral diversity and host fitness, or testing interactions between viral communities and other components of the host microbiome.…”

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

“…Recent advances in metagenome sequencing have enabled high-throughput exploration of the virosphere, leading to a >200-fold increase in viral genomes available in databases, and uncovering >1,000 new genus-level viral groups (Emerson et al, 2018;Paez-Espino et al, 2016;Roux et al, 2016;Suttle, 2007). While these data provide new insights into viral genome diversity, 40 most of these uncultivated viral genomes are not associated with any host.…”

Untapped viral diversity in global soil metagenomes

“…Emerson et al 12 predicted 14 viral glycoside hydrolase (GH) enzymes in these sequences with projected functions for breaking glycosidic linkages in pectin, hemicellulose, starch, and cellulose molecules; one of these was confirmed to express an endomannanase enzyme 12 .…”