Cotton Farming Pesticides Affect Ileal Microbiota Activity and Expression of Virulome but Not Resistome or Metabolic Pathways in a Sedentary Wild Passerine

ABSTRACT 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. r 2 = 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. r 2 = 0.182, F (1,21) = 5.890, p = 0.024), Shannon Index (Adj. r 2 = 0.231, F (1,21) = 7.612, p = 0.012), and load (sum of virulence factor abundances; Adj. r 2 = 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.