In depth comparative microbiome analysis of Mediterranean fish hatcheries

The importance of the fish hatcheries' microbial communities to fish health and welfare has been long recognized, and several studies have been conducted to map these communities during healthy rearing conditions but also during disease outbreaks. Most studies focus on the intestinal and epidermal microbiome of the developing fish, which is mainly shaped by the live feeds (microalgae, rotifers and copepods) used in the rearing process. The microbiome of live feeds, however, has not been investigated thoroughly so far. In this work, we analyzed the microbiome of one research and two commercial fish hatcheries producing Mediterranean fish species, with emphasis on their live feed sectors. The aim was to compare the microbiomes of hatcheries with different characteristics (water source, production intensity and practices) and provide baseline information about their structure with focus on putative pathogenic bacteria. The hatcheries were sampled seasonally over one year. Sampling involved 5 stations: inlet, microalgae, rotifers, Artemia and outlet. 16S rRNA amplicon Novaseq sequencing was conducted in a total of 129 samples. The bioinformatics analysis conducted inferred, 46.745 taxonomically annontated ASVs. The genera of Vibrio and Tenacibaculum were abundant and diverse in all hatcheries, with the incoming water contributing significantly to the presence of important taxa that constitute presumptive pathogens. Alpha diversity analysis (Spearman correlation plots) revealed a relatively stable microbiome between seasonal samplings for every hatchery. Nevertheless, a diverse microbiome between sampling stations was discovered. A core microbiome for every hatchery was cataloged, which included significant putative fish pathogens belonging to Vibrio and Tenacibaculum genera. Mapping of the microbiome in the live feeds through metagenomics is the first step towards an efficient microbial control in the fish hatcheries.