Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse

Chemically intensive crop production depletes wildlife food resources, hinders animal development, health, survival, and reproduction, and it suppresses wildlife immune systems, facilitating emergence of infectious diseases with excessive mortality rates. Gut microbiota is crucial for wildlife's response to environmental stressors. Its composition and functionality are sensitive to diet changes and environmental pollution associated with modern crop production. In this study we use shotgun metagenomics (median 8,326,092 sequences/sample) to demonstrate that exposure to modern crop production detrimentally affects cecal microbiota of sharp-tailed grouse (Tympanuchus phasianellus: 9 exposed, 18 unexposed and greater prairie chickens (T. cupido; 11, 11). Exposure to crop production had greater effect on microbiota richness (t = 6.675, P < 0.001) and composition (PERMANOVA r(2) = 0.212, P = 0.001) than did the host species (t = 4.762, P < 0.001; r(2) = 0.070, P = 0.001) or their interaction (t = 3.449; r(2) = 0.072, both P = 0.001), whereas sex and age had no effect. Although microbiota richness was greater in exposed (T. cupido chaol = 152.8 +/- 20.5; T. phasianellus 115.3 +/- 17.1) than in unexposed (102.9 +/- 15.1 and 101.1 +/- 17.2, respectively) birds, some beneficial bacteria dropped out of exposed birds' microbiota or declined and were replaced by potential pathogens. Exposed birds also had higher richness and load of virulome (mean +/- standard deviation; T. cupido 24.8 +/- 10.0 and 10.1 +/- 5.5, respectively; T. phasianellus 13.4 +/- 6.8/4.9 +/- 2.8) and resistome (T. cupido 46.8 +/- 11.7/28.9 +/- 10.2, T. phasianellus 38.3 +/- 16.7/18.9 +/- 14.2) than unexposed birds (T. cupido virulome: 14.2 +/- 13.5, 4.5 +/- 4.2; T. cupido resistome: 31.6 +/- 20.2 and 13.1 +/- 12.0; T. phasianellus virulome: 5.2 +/- 4.7 and 1.4 +/- 1.5; T. phasianellus resistome: 13.7 +/- 16.1 and 4.0 +/- 6.4).

Automated summary

Chemically intensive crop production has detrimental effects on wildlife, including depletion of food resources, hindrance of animal development and health, suppression of immune systems, and facilitation of infectious diseases. This study shows that exposure to modern crop production significantly impacts the gut microbiota of sharp-tailed grouse and greater prairie chickens, leading to changes in composition and potential pathogen overgrowth.