Emerging Microbial and Enzymatic Approaches for Sustainable Antibiotic Biodegradation in Livestock Manure to Mitigate Water Pollution Risks

Abstract

The extensive use of antibiotics in animal husbandry leads to the release of unmetabolised residues and the dissemination of antimicrobial resistance genes (ARGs) in manure, posing environmental and public health challenges. Conventional treatment technologies, including hydrolysis, photodegradation, and phytoremediation, are often constrained by incomplete mineralisation, high cost, and environmental variability. Biocatalytic and microbially mediated processes are increasingly recognised as sustainable alternatives. Enzymes, which in clinical contexts confer resistance, can, in environmental matrices, catalyse the dismantling of antibiotic scaffolds, attenuating bioactivity and promoting detoxification. Catalytic classes such as hydrolases, transferases, and oxidoreductases mediate diverse transformations, including hydrolytic cleavage, functional group transfer, and oxidative modification. Microbial consortia and bioaugmentation further enhance biodegradation, while biochar and other amendments reduce ARG persistence. Advances in multi-omics, enzyme engineering, and immobilisation have expanded catalytic repertoires, improved stability, and enabled integration with composting, anaerobic digestion, and hybrid bioprocesses. Nonetheless, incomplete degradation, recalcitrant intermediates, and horizontal gene transfer remain challenges. Importantly, since degradation products may leach into soils and aquatic systems, optimising these processes is critical to prevent residues from entering the water cycle. This review synthesises advances in microbial and enzymatic degradation strategies, highlighting opportunities for sustainable manure management while mitigating water pollution risks.