Sheep and rapeseed cake manures promote antibiotic resistome in agricultural soil

The application of manure in agriculture caused the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in soil environments. However, the co-occurrence pattern and host diversity of ARGs and MGEs in soils amended with animal and green manures remains unclear. In this study, metagenomic assembly and binning techniques were employed to comprehensively explore the effects of sheep manure and rapeseed cake manure on soil microbiome, antibiotic resistomes, and ARG hosts. both sheep manure and rapeseed cake manure increased the abundance and diversity of ARGs, especially those resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB) antibiotics. Metagenomic analysis revealed that mobile genetic elements (MGEs), such as plasmids, transposases, and integrases, preferentially enhanced the potential mobility of some ARGs subtypes (i.e. sul2, aadA, qacH, and folp). The application of sheep manure and rapeseed cake manure resulted in distinct co-occurrence pattern of ARGs-MGEs, and the co-occurrence network in the sheep manure treatment had higher complexity and could facilitate ARGs dissemination more conveniently. Additionally, manure application reshaped the bacterial community structure and composition, and the potential ARG hosts mainly belonged to the phyla Pseudomonadota, Actinobacteria, and Bacillota. ARG hosts exhibited specificity in all manure treatments, and some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant after the application of sheep manure. It is concluded that animal and green manures increased the co-occurrence of ARGs and MGEs, enriched the potential hosts (including pathogens) of ARGs, and promoted the dissemination of ARGs in agricultural soils.