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¹ Aquaculture and Sea-Ranching, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany DOI : 10.4194/AQUAST2395 Viewed : 128 - Downloaded : 90 The bacterial community of a flow-through aquaculture farm with cultured rainbow trout in northern Germany was analysed in summer and autumn 2020. Water samples were taken when entering (inflow) and leaving (outflow) the fish raceways. The study was based on bacterial counts to estimate the heterotrophic bacterial load and on isolation of bacterial strains by using selective growth media. Strain identification was performed by sequencing the V3-V4 hypervariable region of the 16S rDNA gene fragment. Heterotrophs abundance showed high variability and temporal variation between sampling points, which was related to water temperature changes. It tended to be higher in the outflow water compared to the inflow water during the warm period, associated with the observation of skin ulcerations, fin necrosis or exophthalmia. The opposite was observed during the cold period. Potentially fish pathogenic bacteria and fungi were detected in both periods regardless of heterotrophic bacterial loads, although fish diseases were only reported during the warm period. The method presented allows the rapid identification of bacterial pathogens that may potentially infect fish, and serves as a guide or indicator to anticipate disease events during the most problematic season of the year. Keywords : Microorganisms Bacterial load Environmental interactions Disease prevention Freshwater aquaculture Pathogens