Northern mockingbird ileal virome variation in Texas

A few studies have focused on avian gut virome variation in response to environmental stressors, but none have assessed virome in relation to chemically intensive crops, the production of which effects various aspects of avian health and fitness, and deleteriously alters available food resources. In this study we used shotgun metatranscriptomics (2 x 150bp; Illumina HiSeq 4000 with median 64,008,420 bidirectional sequences/sample) to assess whether exposure to agriculture (specifically cotton production) had a detrimental effect on the ileum virome of sedentary northern mockingbirds (Mimus polyglottos) sampled from two cotton-producing areas (16 birds) and one uncultivated area (7 birds) in Texas, USA. We recovered 43 viruses, 41 of which were assigned to 14 families and two to unclassified Riboviria. The majority of viruses (36 of 43) represented families associated with arthropods, plants, or fungi. Two of the remaining six viruses are host-associated and another one is associated with Avian Haemosporidia. The last three viruses are of unknown association. Individual sample richness varied from 25 to 33 strains. Virome richness differed among localities (Adj. r2 = 0.247, F(2, 20) = 4.615, P = 0.022) and was related to the proportion of cultivated area in the sampling region. Virome composition differed among localities (r2 = 0.370, F(2, 20) = 5.883, P = 0.001) and was affected by both the proportion of cultivated area (Spearman rho = 0.184, n permutations = 9999, P = 0.013) and even stronger by pesticide profiles (Spearman rho = 0.522, n permutations = 9999, P < 0.001).