sole microbiome in a hatchery life cycle. sole microbiome in a hatchery life cycle

Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in the RAS environment as in the host (in this case, Solea senegalensis). Our goal was to determine how much of the microbiome of the fish is inherited from the brooding stock, and how much is acquired during the fish life cycle in an aquaculture production batch, especially regarding potential probiotic and pathogenic groups. Our work comprises fish tissue samples from -2 days after hatching (DAH) and up to 145 DAH, and includes the live feed introduced in the first stages (from larvae to weaning). Total DNA was isolated from the different tissues, 16S rRNA gene was sequenced (V6-V8 region) using the Illumina MiSeq® platform. The output was analysed with the DADA2 pipeline, and taxonomic attribution with SILVAngs version 138.1. In non-metric multidimensional scaling analysis (NMDS) distribution of the Bray-Curtis dissimilarity index, both age and life cycle stage appeared to be drivers of the bacterial community dissimilarity. However, only life cycle stage was significant with homogeneity of dispersion in the Adonis test. To try to distinguish the inherited (present since the egg stage) from the acquired (detected at some later stage in the production) community, different tissues were analysed at 49, 119 and 146 DAH (gill, intestine, fin and mucus). Only a few genera were inherited (when compared with the egg and larvae community), but those that were inherited accompany the fish microbiome through the life cycle. Determining the inherited and acquired community can have direct impact in husbandry strategies and we highlight the need for these types of study in commercial aquacultures. Two genera of potentially probiotic bacteria (Bacillus and Enterococcus) are already present in the eggs, others are acquired later, in particularly when feed is introduced. The potential pathogenic genera Tenacibaculum and Vibrio are inherited in the eggs, Photobacterium and Mycobacterium seem to be acquired at 49 and 119 DAH respectively. Significant co-occurrence was found between Tenacibaculum and both Photobacterium and Vibrio. Significantly negative correlations exist between Vibrio and Streptococcus, Bacillus, Limosilactobacillus and Gardnerella. Our work reinforces the importance of these types of life cycle studies (with samples from different stages in production for a temporal dynamic). We still need more information on this topic as repetition of patterns in different settings is essential to confirm our findings, and to find new patterns. Aside from this, works like ours can make scientific advancements while providing improvements in production husbandry strategies.