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.
Highlights
The first description of abundant virus-like particles (VLP) in environmental samples in the late 80s of the last century has substantially changed our view on the distribution and ecological relevance of viruses (Bergh et al, 1989)
The most efficient extraction of VLP was achieved with 1× saline magnesium buffer (SM buffer) in combination with vortexing, which was used for all further samples
In order to validate and confirm land use as a relevant factor shaping viral communities, future studies with more land use replicates are required. To our knowledge this is the first time-series study over 1 year that analyzes both the viral abundance and community structure and puts these data into the context of several environmental parameters
Summary
The first description of abundant virus-like particles (VLP) in environmental samples in the late 80s of the last century has substantially changed our view on the distribution and ecological relevance of viruses (Bergh et al, 1989). Viruses have been found in most environments (Paez-Espino et al, 2016), many ecosystems are still grossly undersampled which keeps us from fully understanding the stability and dynamics of viral communities in a spatio-temporal context. The temporal dynamics of viruses have so far been mainly investigated in marine and freshwater systems (Larsen et al, 2001; Laybourn-Parry et al, 2007; Needham et al, 2013). The abundance of free viruses in marine systems follows a seasonal cycle, with overall peak abundances in summer and fall (Jiang and Paul, 1994; Sandaa and Larsen, 2006; Parsons et al, 2012; Payet and Suttle, 2013). The temporal variability of soil viruses has only sporadically been addressed with the exception of studies with a rather epidemiological or agronomic focus (El-Didamony and AbdelFattah, 1998; Fuxa et al, 2001)
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