High‐Resolution Metabarcoding Reveals the Microbiome Dynamics of Mangrove Oysters ( <i>Crassostrea gasar</i> ) and Their Habitat

ABSTRACT The mangrove oyster ( Crassostrea gasar ) plays a key ecological role in Amazonian estuaries by filtering suspended organic particles, microalgae, phytoplankton, and bacteria, contributing to water quality and nutrient cycling. Its gut microbiota is shaped by complex interactions with the surrounding aquatic environment, reflecting the ecological conditions of its habitat. We applied a high phylogenetic resolution metabarcoding approach to investigate the richness, structure, and dynamics of bacterial communities associated with C. gasar and their environments. Samples were collected from four Amazonian farming sites—Santo Antônio de Urindeua (SAU), Nova Olinda (NO), Pereru de Fátima (PF), and Lauro Sodré (LS)—during both rainy and dry seasons. Total microbial DNA was extracted from water, sediment and oyster gut samples, and full‐length 16S rRNA genes were sequenced using the PromethION 2 Solo platform (Oxford Nanopore Technologies). The microbiomes of oysters and water are both significantly influenced by abiotic factors. Redundancy analysis identified salinity and pH as the primary environmental drivers structuring bacterial communities. Seasonal decreases in these parameters during the rainy season led to increased alpha diversity, while their temporal fluctuations drove beta diversity patterns, resulting in distinct bacterial assemblages between rainy and dry periods across all sampling sites. The pan‐microbiome encompassed 5409 taxa, with a core bacteriome of 2330 taxa dominated by Actinomycetota, Pseudomonadota, Mycoplasmatota, and Bacillota. Ecologically significant genera included Sphaerochaeta (organic matter fermentation), Crinalium (nitrogen fixation), Corynebacterium (pathogen defense), and Enterobacter (nutrient cycling), reflecting functional diversity in oyster‐associated microbial communities. The presence of Salmonella during low rainfall underscores potential ecological risks. These findings reveal that oyster‐associated microbiomes exhibit taxonomic shifts in response to seasonal environmental variation, with potential implications for ecosystem functioning. The detection of functionally important taxa (nitrogen fixation, organic matter degradation, pathogen defense) across environmental gradients provides insights into microbial ecological dynamics in Amazonian estuarine oyster farming.