How do different antibiotic residues in manure change soil N2O emissions and soil N-cycling microbial communities?

Circular agriculture aims to close nutrient cycles, thereby increasing dependence on recycled resources such as animal manure. Yet, the prevalent use of veterinary antibiotics often results in manure contaminated with antibiotic residues, and little is known about the effects of antibiotic residues in manure on soil microbial functions. Here, we studied the effects of antibiotic residues on soil nitrogen (N) cycling, including emissions of nitrous oxide (N2O). We hypothesized that the impact varies based on the specific antibiotic used. We conducted an incubation experiment using cattle manure spiked with four different veterinary antibiotics (flumequine, oxytetracycline, sulfadiazine, and tylosin), along with antibiotic-free manure. The spiked manure was mixed with sandy grassland soil and incubated for 31 days, during which fluxes of soil N2O were measured. Soil N pools and N-cycling functional genes were quantified on day 13 and day 31. In a separate incubation experiment, we studied the persistence and bioavailability of the four antibiotics in soil over time after manure application. Both sulfadiazine and oxytetracycline in manure substantially reduced cumulative soil N2O emissions compared to antibiotic-free manure, by 78 % and 72 %, respectively, but the inhibitory mechanisms of these two compounds were potentially different. Compared to antibiotic-free manure, sulfadiazine in manure significantly increased soil AOA/AOB, whereas oxytetracycline increased the relative abundance of nosZII-carrying bacteria. Flumequine remained persistent in the soil but did not have significant effects on N cycling. Similarly, tylosin did not change the soil N cycling significantly. In summary, the impacts of antibiotics in manure on soil N cycling are type-dependent. Persistent antibiotics may not have substantial impacts, but non-persistent compounds could still affect soil microbes even after a single manure application. Studying the effects of repeated antibiotic exposure through manure application is essential in understanding how circular agricultural practices impact nutrient cycling and soil health.