Cotton farming affects ileal virome in a sedentary wild passerine

Although a few studies have focused on avian gut virome variation in response to environmental stressors, none have assessed virome in relation to the production of chemically intensive crop-based agriculture that alters food resources and detrimentally affects various aspects of avian health and fitness. In this study, we used shotgun metatranscriptomics to assess whether exposure to cotton (Gossypium spp.) production had a deleterious effect on the ileal virome of sedentary northern mockingbirds (Mimus polyglottos) sampled from two cotton-producing areas (16 birds in total) and one uncultivated area (7 birds) in Texas, USA. We recovered 43 viruses representing 13 virus families, which included two viruses that appear to be potential vertebrate pathogens. Individual sample richness varied from 25 to 33 viruses. Both virome richness (Adj. r2 = 0.247, F(2, 20) = 4.615, P = 0.022) and composition (r2 = 0.370, F(2, 20) = 5.883, P = 0.001) differed among three sampling regions. Cotton production was associated with the increase of virome richness (Adj. r2 = 0.283, df = 22, P = 0.005). Pesticide occurrence data collected using silicone bands at the three sites suggest that virome compositional changes are not only associated with total pesticide exposure but are also particularly sensitive to the pesticide combinations detected at each location.