Assessment of Extracellular Antibiotic Resistance Genes (Eargs) and Intracellular Antibiotic Resistance Genes (Iargs) in the Commercial Organic Fertilizers

Compost-based organic fertilizers made from animal manures often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). However, whether ARGs and MGEs are present intracellularly or extracellularly remains unclear. In the present study, we quantified extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) in 51 commercial organic fertilizers derived from different raw material types by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results from qPCR showed that eARGs and eMGEs accounted for 11 - 56% and 4 - 45% of the total ARGs and MGEs, respectively. Metagenomic analyses showed comparable diversity, mobility and host compositionsbetween eARGs and iARGs. Twenty-four percent of ARGs were present in plasmids, while 56.7% of potentially mobile ARGs were found to be associated with plasmids. Risk patterns were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7% and 8.2% of the total abundances, respectively. Variation partitioning analysis indicated that raw material type and their interactions with environmental factors and bacterial community significantly affected the composition of eARGs (67.3%) and iARGs (67.2%), indicating that the composition of ARGs was largely driven by deterministic mechanisms, which was further substantiated by the null model and neutral community model. Taken together, eARGs are an important reservoir of ARGs in manure composts. More attention should be paid to the contribution of eARGs to the dissemination of antibiotic resistance into the general environment and the corresponding mitigation strategies.