Response of soil viral communities to land use changes

Abstract

Soil viruses remain understudied when compared to virus found in aquatic ecosystems. Here, we investigate the ecological patterns of soil viral communities across various land use types encompassing forest, agricultural, and urban soil in Xiamen, China. We recovered 59,626 viral operational taxonomic units (vOTUs) via size-fractioned viromic approach with additional mitomycin C treatment to induce virus release from bacterial fraction. Our results show that viral communities are significantly different amongst the land use types considered. A microdiversity analysis indicates that selection act on soil vOTUs, resulting in disparities between land use associated viral communities. Soil pH is one of the major determinants of viral community structure, associated with changes of in-silico predicted host compositions of soil vOTUs. Habitat disturbance and variation of soil moisture potentially contribute to the dynamics of putative lysogenic vOTUs. These findings provide mechanistic understandings of the ecology and evolution of soil viral communities in changing environments.

Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem

“…In the ERW soils, lytic infection of active hosts seemed favored in spring and early summer (May / June), consistent with KtW interactions. This model is expected to occur under favorable conditions, such as a nutrient enrichment or wetting soils, generating high bacterial diversity 32 and favoring lytic over lysogenic infections 60 , which is consistent with conditions during the plant-growing season in ERW soils. Conversely, the temporal delay between the activity of phages and the growing period of their hosts under snow conditions or upon snowmelt associated to the low diversity of hosts may be best described by a third model, recently proposed: "Piggyback-The-Loser" (PtL) 61 or "Piggyback-The-Persistent" (PtP) 62 , that suggests the opposite of the PtW model.…”

Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

“…Nucleotide diversity of cold seep viral populations ranged from zero to 3.06×10 -3 , and were on-average 1.29×10 -4 (median 3.38×10 -5 ) for viruses detected in both active and extinct cold seep sediments ( Figure 4a ). This viral nucleotide diversity is significantly lower than that observed for viral populations in seawater sampled from throughout the world’s oceans (on-average 3.78×10 -4 ) 22 and in soils having various land uses (on-average 6.54×10 -3 ) 51 . Low SNP frequencies were also observed in Haima cold seep viral populations (0.33 SNP per 1000 bp on average, median 0.076; Figure 4b ), e.g., compared to those detected in the SARS-CoV-2 coronavirus, in 25 uncultivated virophage populations in North American freshwater lakes, and in 44 dsDNA viral populations dominating the oceans, based on various approaches for the extraction of viral genomes 52–54 .…”

Australian terrestrial environments harbour extensive RNA virus diversity

“…A relationship between virome composition and land use has been previously observed for both DNA viruses (Narr et al ., 2017; Liao et al ., 2022) and RNA viruses (Hillary et al ., 2022) in soil on other continents. Likewise, local sampling environment has been shown to be associated with viral abundance and diversity (Chen et al ., 2022; Durham et al ., 2022).…”