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)

Abstract

Environmental surveys on soil viruses are still rare and mostly anecdotal, i. e., they mostly report on viruses at one location or for only a few sampling dates. Detailed time-series analysis with multiple samples can reveal the spatio-temporal dynamics of viral communities and provide important input as to how viruses interact with their potential hosts and the environment. Such surveys, however, require fast, easy-to-apply and reliable methods. In the present study we surveyed monthly across 13 months the abundance of virus-like particles (VLP) and the structure of the viral communities in soils along a land use transect (i.e., forest, pasture, and cropland). We evaluated 32 procedures to extract VLP from soil using different buffers and mechanical methods. The most efficient extraction was achieved with 1× saline magnesium buffer in combination with 20 min vortexing. For community structure analysis we developed an optimized fingerprinting approach (fluorescent RAPD-PCR; fRAPD) by combining RAPD-PCR with fluorescently labeled primers in order to size the obtained fragments on a capillary sequencing machine. With the concomitantly collected data of soil specific factors and weather data, we were able to find correlations of viral abundance and community structure with environmental variables and sampling site. More specifically, we found that soil specific factors such as pH and total nitrogen content played a significant role in shaping both soil viral abundance and community structure. The fRAPD analysis revealed high temporal changes and clustered the viral communities according to sampling sites. In particular we observed that temperature and rainfall shaped soil viral communities in non-forest sites. In summary our findings suggest that sampling site was a key factor for shaping the abundance and community structure of soil viruses, and when site vegetation was reduced, temperature and rainfall were also important factors.

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 viruses are underexplored players in ecosystem carbon processing

“…Soils’ heterogeneity in texture, mineral composition, and OM content results in significant inconsistency of yields from standard virus ‘capture’ methods (36–39). While many soils contain large numbers of viral particles (10 7 –10 9 virus particles per gram of soil; 37, 40–42), knowledge of soil viral ecology has come mainly from the fraction that desorb easily from soils (<10% in 43) and the much smaller subset that have been isolated (44).…”

Soil microbial diversity drops with land‐use change in a high mountain temperate forest: a metagenomics survey

“…It is still unclear how soil characteristics and ecosystem management practices affect viral communities. Fertilizer application has been reported to increase the abundance of viruses (Chen et al, 2014) and temporal variability in forest and arable soils (Narr et al, 2017). Viral communities are very dynamic as viruses have extreme evolutionary capacities and high genetic diversity that have allowed them to parasitize all known groups of organisms and to rapidly adapt to numerous host species.…”