Growth-Associated Reorganization of Gill and Skin-Mucus Microbiota in Cultured Decapterus maruadsi: Contrasting Occurrence–Abundance Patterns

Abstract

Simple Summary Fish gills and skin mucus are continuously exposed to surrounding water, but they provide different biological surfaces for microbial colonization. We examined the gill and skin-mucus microbiota of cultured Decapterus maruadsi at three successive growth stages from the same cohort. The two mucosal habitats changed differently during growth. In the gill, a small group of microorganisms that occurred widely across the complete dataset contributed an increasingly large fraction of community abundance from the early to middle stage and remained important at the late stage. Skin mucus followed a different, non-linear pattern: the middle-stage community was strongly dominated by microorganisms with intermediate occurrence frequencies, before high-prevalence microorganisms again became abundant at the late stage. Broad bacterial groups remained similar among samples, but extensive differences emerged at the genus and amplicon sequence variant (ASV) levels. These findings show that gill and skin-mucus microbiota undergo distinct patterns of growth-associated reorganization rather than a uniform developmental process.