Marker gene analysis reveals novel viral genetic diversity in unsaturated soils

Despite significant advances in knowledge regarding phages in aquatic systems, viruses in soil remain poorly characterized. Particularly, little is known regarding the presence and distribution of various phage families in unsaturated soil environments. Marker genes, which are indicative of a specific viral group, are an established, efficient, and cost-effective method of investigating phage diversity in environmental samples. This study utilized three marker genes to study the genetic diversity of viruses in 42 different soil samples. Two of the marker genes, the major capsid protein of the Gokushoviruses, and DNA polymerase of the T7-like phages failed to amplify in any of the soil samples. The third marker gene, g23, successfully amplified in 15 of the 42 soil samples (35.7%), and positive samples were selected for further analysis. Amplicon sequencing produced 335 amplified sequence variants from 7 soils. Amplified g23 sequences from unsaturated soils were compared to sequences from local freshwaters, as well as previous studies in freshwater, marine, paddy field, and upland black soil environments. Our results suggest that geographic distance may be more important than environmental source in explaining sequence-based differences across samples. Further, our analysis revealed novel genetic diversity within the T4-like phage family in temperate, unsaturated soils from this study.

Automated summary

Despite limited knowledge about viruses in soil, this study utilized marker genes to investigate the genetic diversity of viruses in 42 soil samples. The results suggest that geographic distance may be more important than environmental source in explaining sequence-based differences across samples.