Microbiota Composition Shaped by Seasonal Variation and Environmental Compartments Affects the Abundance of Antimicrobial‐Resistant Bacteria in Indonesian Aquaculture

ABSTRACT Antimicrobial use in aquaculture can drive antimicrobial‐resistant (AMR) bacteria, but the ecological factors shaping their emergence and persistence across environmental compartments remain unclear. We investigated these factors through laboratory experiments and field surveys in Indonesia. In zebrafish aquaria, oxytetracycline exposure promoted the emergence of resistant bacteria and mainly affected the gut microbiota. In field surveys, gene‐based analyses identified tetG ‐ and ribosomal protection protein‐associated taxa across sample types. Bacterial community analysis revealed seasonal contrasts: dry‐season samples frequently clustered into a “main group” enriched in AMR‐associated taxa, whereas wet‐season samples showed fewer members and greater heterogeneity. Mapping of resistant taxa indicated higher proportions of resistant bacteria in the main group and during the dry season. The median relative abundance of potential tet‐resistant bacteria was higher in the main group than in other samples (3.52% vs. 1.34%) and in the dry season than in the wet season (3.34% vs. 1.80%). Quantitative comparisons among environmental compartments suggested that the gut functions as a primary site for the emergence of AMR bacteria, while water serves as a medium for their accumulation and dispersal. These findings indicate that seasonal variation and compartment‐specific microbial structure jointly shape the abundance and distribution of AMR bacteria in aquaculture environments.