Antimicrobial resistance in plant-associated microbial communities: mechanisms, ecology, and one health implications

Antimicrobial resistance (AMR) has emerged as a major global challenge threatening human, animal, plant and the environment health. Although AMR has been extensively studied in clinical and veterinary sectors, its emergence and dissemination in plant-based agricultural systems remains comparatively underexplored despite of the widespread use of antibiotics, fungicides and other antimicrobial compounds in crop production. These practices exerts selective pressure on plant associated microbial communities, promoting the evolution and dissemination of antimicrobial resistance genes (ARGs) across interconnected environmental compartments including soil, water, plants and food systems highlighting the importance of one health. This review synthesizes current knowledge on the occurrence, mechanisms and ecological drivers of AMR in plant associated microbial communities. It discusses resistance mechanism in bacterial and fungal plant pathogens, the role of soil, rhizosphere, and phyllosphere microbiomes as reservoirs and transmission hubs for ARGs and evidence from global and regional studies illustrating the complexity of AMR in agricultural ecosystems. The review also evaluates emerging sustainable alternatives to conventional antimicrobial use including phage therapy, microbiome engineering, RNA-based biopesticides, CRISPR-based technologies, and nanotechnology based approaches, which have the potential to reduce chemical reliance and mitigate selection pressure for resistance. Overall, integrating plant health into one health governance frameworks, strengthening AMR surveillance in agricultural systems, and promoting sustainable disease management strategies are essential for limiting the spread of resistance and safeguarding agricultural productivity, ecosystem integrity and public health.