Characterization of the marine aquaculture microbiome: A seasonal survey in a seabass farm

Vibriosis is a recurrent disease in marine aquaculture environments. Monitoring the dynamics of bacterial populations in several compartments of the aquaculture infrastructure is of paramount importance to understand the occurrence of the disease. In the present study, the fish farm, located in the north of France, is a flow-through system where the tanks are supplied by two water inlets. Water from breeding tanks, and inlets and the biofilms in the tanks were sampled weekly in a seabass farm for 7 months. DNA was extracted from 477 samples to sequence the variable V4-V5 region of the 16S rRNA gene and analyze the sequences using the QIIME2 platform. Proteobacteria (54.52%) and Bacteroidetes (26.85%) composed more than 80% of the phylum diversity. Alpha- and beta-diversity indicators showed that bacterial communities were more diverse in samples from biofilms and tanks than in samples from water inlets. Some families were specific to one compartment, e.g. ammonium-oxidizing bacteria in biofilms, whereas Vibrionaceae family isolates were mostly found in tank water samples. Taxa were determined up to the species level for the Vibrionaceae. Besides, all six determined genera of Vibrionaceae were identified, with mostly Vibrio and Photobacterium isolates detected in almost all samples. Vibrionaceae persisted over time in the biofilms. Our results suggest that biofilms may be a potential reservoir in case of dysbiosis. This study helps better understand microbial interactions, especially with Vibrionaceae in aquaculture environments. •A weekly sampling campaign was conducted for 7 months in an aquaculture farm.•16S rRNA gene amplicons were sequenced to monitor bacterial communities.•Biofilm samples were highly diverse and may be considered a Vibrionaceae reservoir.•Vibrionaceae family isolates were most frequently found in tank water samples.•Planctomycetes, Chloroflexi and Thaumarchaeota phyla were specific to biofilm samples.