A reservoir of genetic diversity and key players in geochemical processes

Soil viruses are of great importance as they may influence the ecology of soil biological communities through both an ability to transfer genes from host to host and as a potential cause of microbial mortality. Consequently, viruses are major players in global geochemical cycles, influencing the turnover and concentration of nutrients and gases.

Despite this importance the area of soil virology is understudied. To explore the role of the viruses in plant health and soil quality, we are studying virus diversity and abundance in different geographic areas (ecosystems) using classical methods of virus purification, electron microscopy and next generation sequencing (metagenomic studies).

We have recently isolated and characterised virus-like particles from soils in the Dundee area of Scotland. Different virus morphotypes including tailed, polyhedral (spherical), rod-shaped, filamentous and bacilliform particles were detected in the soil samples. We have also characterised viruses from different soil functional domains surrounding wheat roots (rhizosheath and rhizosphere), and bulk soil.

We have found that viruses are highly abundant in all the domains. Moreover, in spite of the differences in the abundance of bacterial communities in these domains, no significant variations in viral population structure in terms of morphology and abundance were found. Typically there were ~ 1.1 – 1.2 x 109 virions g-1 dry weight of soil, revealing remarkable differences in virus-to-bacteria ratios in domains close to roots (~ 0.28 – 0.29) compared to bulk soil (~ 4.8).

Soils probably harbour many absolutely novel viral species that together may represent a large reservoir of genetic diversity. For example, we have recently isolated a novel bacteriophage from Antarctic soils. The phage, that we have named SpaA1, is morphologically similar to phages of the family Siphoviridae. The 42,784 bp genome of the phage encodes 63 genes which cluster within three regions of the genomes, each of apparently different origin, in a mosaic pattern.

Remarkably, one of the regions contains an almost complete genome of a distinct bacteriophage, MZTP02. These data suggest that MZTP02 can be exchanged between genomes of other bacteriophages, leading to the formation of chimeric genomes. The insertion of a complete phage genome into the genome of another phage has not been described previously and might represent a novel ’fast track’ route for virus evolution and horizontal gene transfer.

Investigating this largely unexplored diversity of soil viruses has the potential to transform our understanding of the role of viruses in global ecosystem processes and the evolution of microbial life itself.