Environmental drivers of pathogen and annelids interactions in oyster farming systems of a subtropical estuary

Abstract Oyster aquaculture is growing worldwide, but biofouling and pathogen infestations remain major challenges. Cultivation systems differ in hydrodynamic and substrate conditions, which may influence pathogen prevalence and shell-boring annelids such as Polydora spp. In the Paranaguá Estuarine Complex (southern Brazil), Crassostrea oysters are farmed in longline, mud-bottom, and grown in natural mangrove habitats, yet the effects of these environments on host–parasite interactions are still poorly understood. In this study, we evaluated the occurrence of Vibrio parahaemolyticus , Perkinsus spp., and annelid assemblages across culture types, bays, and seasons. Annelid communities associated with oyster shells were quantified, pathogens were detected in gill and rectum tissues, and oyster condition index (CI) was assessed. Multimodel inference was applied to test the effects of pathogens and fouling organisms on CI and to identify the main drivers of infestation patterns. Pathogens and Polydora spp. were widespread across all environments, but no consistent negative effects on CI were detected. Instead, environmental conditions and cultivation context were more important in explaining variation in oyster condition. In contrast, Polydora infestation was strongly associated with farming practices, with higher loads consistently observed in mud-bottom systems, indicating that these environments may act as reservoirs of shell-boring pests. From a management perspective, our results support the implementation of integrated monitoring programs that combine pathogen detection with environmental variables and farming practices. Reducing sediment accumulation in culture areas, avoiding prolonged use of mud-bottom systems, and limiting the translocation of oysters from infested sites may help control the spread of Polydora . Additionally, routine surveillance of Perkinsus spp. and V. parahaemolyticus should be incorporated into farm management to ensure product quality and sanitary safety. These actions can contribute to improving the sustainability and resilience of oyster aquaculture in subtropical estuarine systems.