Spatiotemporal dynamics of RNA virus diversity in a phyllosphere microbial community

Abstract

24Although metagenomics reveals that natural virus communities harbor vast genetic diversity, the 25 spatiotemporal dynamics of viral diversity in the wild are seldom tested, especially across small 26 geographic scales. This problem is usefully examined in the above-ground phyllosphere, because 27 terrestrial plants are frequently infected by taxonomically-diverse RNA viruses, whose elevated 28 mutation rates generate abundant allele diversity. Here, we studied the problem by comparative 29 analysis of RNA virus samples over time from three spatially-separated patches of a common 30 perennial legume, white clover (Trifolium repens L.), growing in a grassy lawn in Woods Hole 31 Village (Falmouth, MA, USA). We predicted that clover samples would show similarly high 32 levels of virus species (alpha) diversity across space, but differing among-patch diversity of non-33 dominant virus taxa over time (4 samples spanning 6 weeks). Results showed that recognizable 34 alpha diversity in clover patches was consistently dominated by RNA virus family 35 Alphaflexiviridae across space, but that all patches showed inconsistent spatiotemporal presence 36 of a diversity of minority virus families. Also, we observed that white clover mosaic virus 37 (WClMV) dominated all patches across space and time. The high coverage of WClMV fostered 38 an haplotype analysis, which revealed that two strains of the virus consistently infected clover 39 plants during the 6-week period. 40 41 43 Viruses numerically dominate biological entities on Earth and may represent the majority 44 of its genetic diversity as well [1, 2]. Viruses can alter microbial community structure [3] and 45 colonization [4] and impact food webs. Their effects also scale up, driving global geochemical 46 cycles [5, 6]. However, virus sampling across different natural environments is uneven. Marine 47 systems are perhaps the best studied to date [7], making it crucial to examine non-marine and 48 terrestrial communities (but see [4, 8]). Understanding the viral communities of the phyllosphere 49 (above-ground terrestrial plant biomass) has important implications for food safety, e.g. 50 outbreaks of food-borne human pathogens, such as hepatitis A virus and norovirus, have been 51 associated with fresh produce [9]. Furthermore, the broadscale ecological and evolutionary 52 implications of plant viruses is largely unknown, even though viral infections have been detected 53 in a variety of wild plants [10]. Even a seemingly basic question about the nature of viral 54 communities associated with plants remains unknown: will the same viruses be observed today 55 as they will tomorrow, the next week, et cetera? 56 Plant viruses face unique challenges when infecting their hosts, which can potentially 57 drive the ecological and evolutionary dynamics of their microbial communities. The plant cell 58 wall is particularly difficult to breach; viruses can avoid this issue either through vertical 59 transmission, or by relying on passive, mechanical damage to plant cell walls, m...

Discovery of Brassica Yellows Virus and Porcine Reproductive and Respiratory Syndrome Virus in Diaphorina citri and Changes in Virome Due to Infection with ‘ Ca . L. asiaticus’

“…The extent of these multiple infections and their interactions with each other and with their insect hosts is slowly being revealed due to the development of new molecular tools, especially next generation sequencing ( 7 ). After long-term, continuous interactions, once these viruses can colonize an insect’s gut, there is the possibility of phyllosphere transmission by insect vectors ( 8 , 9 ).…”