Cotton farming pesticides affect ileal microbiota activity expressions of virulome but not resistome or metabolic pathways in a sedentary wild passerine

The increased use of agrochemicals to enhance crop production has had detrimental environmental effects including implication in the sharp decline of North American farmland-breeding birds. Here, using a combination of deep shotgun metatranscriptomics and pesticide exposure data, we sought to assess whether exposure to cotton (Gossypium spp.) production had a differential effect on ileum multi-kingdom microbial activity, metabolism, anti-microbial resistance, and virulence factors 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. Both Shannon Index values (Adj. r² = 0.174, F_(1,21) = 5.633, p = 0.027) and a Mantel test (Spearman ρ = 0.184, p = 0.013) supported a relationship between metabolically active microbiota Bray–Curtis dissimilarities and differences in pesticide mixtures among study areas. Virulence factor richness (Adj. r² = 0.182, F_(1,21) = 5.890, p = 0.024), Shannon Index (Adj. r² = 0.231, F_(1,21) = 7.612, p = 0.012), and load (sum of virulence factor abundances; Adj. r² = 0.160, F_(1,21) = 5.194, p = 0.033) were related to total pesticide load (total quantity of pesticides). We found no pesticide effects on expression of either antimicrobial resistance genes or metabolic pathways.