Dynamics of autochthonous soil viral communities parallels dynamics of host communities under nutrient stimulation

Abstract

Viruses are highly abundant in soils with their numbers exceeding those of cooccurring bacterial cells by 10- to over 1000-fold. Water and organic matter content influence the magnitude of the viral-to-bacterial ratio in soils; thus, ecosystem type and land use shape interactions between viral and host microbial communities in soils. Less understood are the shorter term interactions between viral and host communities that ultimately maintain the large viral standing stock within soils. This study examined short-term dynamics of viral and bacterial communities in soils to determine whether the growth of soil bacterial communities results in the production of soil viruses, and if viral community responses occur within specific populations. In microcosms amended with different carbon sources, increases in viral abundance (VA) accompanied increases in bacterial abundance (BA) and bacterial respiration rate (BRR). The timing and intensity of increases in BA, VA and BRR were different across C sources suggesting differences in the predominant mode of viral replication within growth-stimulated bacterial populations. Moreover, compositional changes occurred in soil bacterial and viral communities indicating that new viral production arose from a subset of host populations. To our knowledge, these are the first observations of soil viral populations responding to short-term changes in soil bacterial communities.

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

“…Compositional differences between April and August samples were significant for both viral and microbial communities (Fig 4A), and a Mantel test revealed that the Bray-Curtis dissimilarity matrices of viral and microbial communities were significantly correlated (R = 0.59, P = 0.0003). Unsurprisingly, due to the reliance of viruses on their hosts for replication, viral and microbial communities have been previously observed to correlate in soil (14,18), and results here suggest that viruses and their bacterial and archaeal hosts had coupled temporal responses to the same variables and/or to each other.…”

“…Viral replication depends on the successful infection of suitable hosts. As such, the abundances of viral populations and, consequently, the structure of viral communities are inherently linked to the compositional trends of coexisting host communities (18)(19)(20). In agricultural soils, rhizosphere processes can alter microbial diversity by actively promoting or inhibiting the recruitment of select taxa (21,22).…”

Untapped viral diversity in global soil metagenomes

“…We also investigated the impact of agriculture on soil viral AMGs. We predicted that cultivation would shift the composition of soil viromes due to shifts in soil properties such as pH, total nitrogen content, and fertilizer application, as previously demonstrated 5,6,13,35,36 .…”

“…A global meta-analysis of viral distribution revealed that the vast majority of viruses are clearly habitat-specific 3 . The soil virome in particular is poorly characterized in terms of its size and composition, but limited evidence shows that soil viruses are more abundant and diverse than viruses from other ecosystems 4,5,6 . This high viral diversity may be a result of the heterogeneous physical matrix of soil where spatial structuring generates a plethora of environmental niches 7,8 .…”

Soil Viral Communities Vary Temporally and along a Land Use Transect as Revealed by Virus-Like Particle Counting and a Modified Community Fingerprinting Approach (fRAPD)

“…Virus abundances in soil have been reported to range between 10 7 and 10 9 virus like particles per g of soil (Williamson et al, 2003 , 2005 ; Swanson et al, 2009 ; Srinivasiah et al, 2015 ) and exceed in some cases (e.g., Antarctic soils) the abundance of co-occurring bacteria by up to 8,200-fold (Williamson et al, 2007 ). So far it is unclear, if, to which degree, and how environmental conditions affect viral numbers and viral community composition in soils.…”