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).

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.

Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies.

Pseudoalteromonas phage vB_PspS-H40/1 is a lytic phage that infects Pseudoalteromonas sp. strain H40. Both, the phage and its host were isolated in the 1970s from seawater samples collected from the North Sea near the island of Helgoland, Germany. The phage particle has an icosahedral capsid with a diameter of ~43 to 45 nm and a long non-contractile tail of ~68 nm in length, a typical morphology for members of the Siphoviridae family. The linear dsDNA genome of Pseudoalteromonas phage vB_PspS-H40/1 has a sequence length of 45,306 bp and a GC content of 40.6%. The genome has a modular structure and contains a high proportion of sequence information for hypothetical proteins, typically seen in phage genome sequences. This is the first report of the complete genome sequence of this lytic phage, which has been frequently used since the 1990s as biological tracer in hydrogeological transport studies.