Northern mockingbird ileal microbiota activity and expression of antimicrobial resistance genes, virulence factors, and metabolic pathways in Texas cotton producing and uncultivated areas

The increased use of agrochemicals to enhance crop production has had detrimental environmental effects. Indeed, pesticides and their deleterious environmental effects have been implicated in the sharp decline in 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 (Adj. r2 = 0.160, F(1, 21) = 5.194, p = 0.033) were related to total pesticide loads. We found no pesticide effects on expression of either antimicrobial resistance genes or metabolic pathways.