Sheep and rapeseed cake manure 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 green manure on soil microbiome, antibiotic resistomes, and ARG hosts. Sheep manure increased the abundance and diversity of ARGs, especially those resistant to multidrug, quinolone, rifampicin, and macrolide-lincosamide-streptogramin (MLSB) antibiotics. 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), facilitating the spread of ARGs. Additionally, sheep manure reshaped the bacterial community structure and composition as well as ARG hosts, some opportunistic pathogens (i.e. Staphylococcus, Streptococcus, and Pantoea) acquired antibiotic resistance and remained recalcitrant. It is concluded that sheep manure increased the co-occurrence of ARGs and MGEs, enriched the potential ARG hosts, and promoted the dissemination of ARGs in agricultural soils.