Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community

Although metagenomics reveals that natural virus communities harbor vast genetic diversity, the spatiotemporal dynamics of viral diversity in the wild are seldom tested, especially across small geographic scales. This problem is usefully examined in the above-ground phyllosphere, because terrestrial plants are frequently infected by taxonomically-diverse RNA viruses, whose elevated mutation rates generate abundant allele diversity. Here, we studied the problem by comparative analysis of RNA virus samples over time from three spatially-separated patches of a common perennial legume, white clover (Trifolium repens L.), growing in a grassy lawn in Woods Hole Village (Falmouth, MA, USA). We predicted that clover samples would show similarly high levels of virus species (alpha) diversity across space, but differing among-patch diversity of non-dominant virus taxa over time (4 samples spanning 6 weeks). Results showed that recognizable alpha diversity in clover patches was consistently dominated by RNA virus family Alphaflexiviridae across space, but that all patches showed inconsistent spatiotemporal presence of a diversity of minority virus families. Also, we observed that white clover mosaic virus (WClMV) dominated all patches across space and time. The high coverage of WClMV fostered an haplotype analysis, which revealed that two strains of the virus consistently infected clover plants during the 6-week period.