Uncovering the potential relationship between the prevalence of antibiotic resistance genes and nitrous oxide emissions in vegetable soils amended with bio-organic fertilizers

Although organic fertilizer application may affect the prevalence of antibiotic resistance genes (ARGs) and nitrous oxide (N 2 O) emissions, the knowledge regarding the potential linkages between ARG profiles and N 2 O emissions in agricultural systems remains limited. Here, a pot experiment was conducted to investigate the soil resistome characteristics and N 2 O emission dynamics under organic fertilizer (OF) and bio-organic fertilizer (BOF) applications using a SmartChip PCR platform and a static opaque chamber method. The results revealed distinct soil resistome profiles under different fertilization regimes. BOF treatment significantly reduced the abundance of soil ARGs and mobile genetic elements, while increasing cumulative N 2 O emissions. Planctomycetota , Gemmatimonadota , and Bdellovibrionota , which are key taxa shaping ARG profiles, were markedly reduced under BOF treatment, and this reduction was associated with decreased ARG abundance. The increase in N 2 O emissions under BOF was primarily associated with the reduction of ARG-hosting bacteria, which may have indirectly contributed to an increase in the abundance of AOB- amo A and nir K genes. Key fungal species identified within the co-occurrence network had a limited impact on N 2 O emissions and related functional genes. Additionally, OF and BOF markedly increased vegetable yield, thereby reducing yield-scaled N 2 O emissions compared with the no fertilizer applied. Collectively, these findings highlight that the soil resistome and greenhouse gas emissions induced by organic fertilizers should be jointly considered in comprehensive ecological risk assessments to inform and optimize sustainable fertilization strategies. • Bio-organic fertilizer reduced ARG abundance in vegetable soils. • Bio-organic fertilizer increased N 2 O emissions and vegetable yield. • Key microbial taxa shaped ARG profiles were linked to N 2 O emissions. • Lower ARG hosts were associated with higher amo A and nir K gene abundances.