Permeability decides the effect of antibiotics on sedimentary nitrogen removal in Jiulong River Estuary

•Antibiotics inhibited potential sedimentary N removal and increased N2O yield.•Antibiotics had different effect on in situ sedimentary N removal along estuary.•Permeability of sediment determines the effect of antibiotics on N removal.•ARGs can't resist the inhibition of antibiotics on microbe related to N removal. Sedimentary denitrification takes place beneath the oxic layer at the sediment-water interface, where nitrate and antibiotics need to diffuse through the overlying water. However, the antibiotics’ effect on sedimentary N removal and associated N2O production has not been adequately investigated under in situ conditions. Here, isotope pairing techniques, including slurry incubations (potential) and intact core incubations (in situ), combined with metagenomic analysis were applied to investigate the impacts of two protein-inhibiting antibiotics (oxytetracycline and thiamphenicol) on sediment nitrogen removal in a subtropical estuary. Slurry incubations showed that the two antibiotics significantly inhibited denitrification (67–98%) and anammox (49–99%), while intact core incubations presented no antibiotic effect at upstream but significant inhibition (23%-52%) at downstream. Meanwhile, N2O yields were stimulated up to 20 folds in slurry incubations yet showing insignificant response in intact cores. Such contrasting results between up- and down-stream and between slurry and intact core incubations strongly indicated that permeability, which determines diffusion of antibiotics to microbes, is the key to exert the effect of antibiotics on in situ sedimentary nitrogen removal processes regardless the existence of antibiotics resistance genes. This diffusive obstruction may mitigate the toxic effect of antibiotics on nitrogen removal related microbes in natural environments. [Display omitted]