Antibiotics and Pesticides Enhancing the Transfer of Resistomes among Soil-Bayberry-Fruit Fly Food Chain in the Orchard Ecosystem

While substantial amounts of antibiotics and pesticides
are applied
to maintain orchard yields, their influence on the dissemination and
risk of antibiotic resisitome in the orchard food chain remains poorly
understood. In this study, we characterized the bacterial and fungal
communities and differentiated both antibiotic resistance genes (ARGs)
and virulence factor genes (VFGs) in the soil, Chinese bayberry (matured
and fallen), and fruit fly gut, collected from five geographic locations.
Our results showed that fruit fly guts and soils exhibit a higher
abundance of ARGs and VFGs compared with bayberry fruits. We identified
112 shared ARGs and 75 shared VFGs, with aminoglycoside and adherence
factor genes being among the most abundant. The co-occurrence network
revealed some shared microbes, such as Bacillus and Candida, as potential hosts of ARGs, highlighting the vector
risks for both above- and below-ground parts of the orchard food chain.
Notably, the elevated levels of antibiotics and pesticide residues
in orchard soils increase ARGs, mobile genetic elements (MGEs), and
VFGs in the soil-bayberry-fruit fly food chain. Our study highlighted
that agricultural management, including the overuse of antibiotics
and pesticides, could be the key factor in accumulating resistomes
in the orchard food chain.