Prokaryotic interactions in recirculating aquaculture systems (RAS) environmental communities may play a crucial role in driving their functional potential. However, these interactions are often neglected. The aim of this work is to detect prokaryotic interactions in a Solea senegalensis RAS, through the definition of relevant taxa and cluster identification using co-variance and co-occurrence tools. Amplicon sequence variants (ASV) were obtained from the water, tank biofilm, and biofilters of two systems, pre-ongrowing and weaning, and the study focuses on two microbial target groups, the potentially pathogenic and the nitrifying prokaryotes. No significant negative correlations were found with any target ASVs, indicating a mostly cooperative environment. As expected, ammonia oxidizing bacteria (Nitrosomonas) and archaea (Candidatus Nitrosopumilus) were found to be positively interacting with the nitrite oxidizing bacteria Nitrospira. However, no interactions were found between them, and results hint at a niche differentiation based on ammonia competition. Nitrospira also showed subcommunities with no ammonia oxidizing archaea or ammonia oxidizing bacteria correlations, hinting at a separate functional role of complete ammonia oxidation to nitrate for some Nitrospira ASVs. Two taxa commonly associated with pathogenic outbreaks, Tenacibaculum and Vibrio, had a significant positive correlation in one of the systems. With no outbreaks reported, this association may prove relevant in disease preventions and to improve outbreak predictions. Future studies may further elucidate this interaction, as cumulative evidence is still needed to better understand this correlation.
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 and in the host (in this case, Solea senegalensis). Our goal was to determine how much of the sole microbiome is inherited from the egg stage, and how much is acquired during the remainder of the sole life cycle in an aquaculture production batch, especially regarding potentially probiotic and pathogenic groups. Our work comprises sole tissue samples from 2 days before hatching and up to 146 days after hatching (−2 to 146 DAH), encompassing the egg, larval, weaning, and pre-ongrowing stages. Total DNA was isolated from the different sole tissues, as well as from live feed introduced in the first stages, and 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. Using the Bray–Curtis dissimilarity index, both age and life cycle stage appeared to be drivers of bacterial community dissimilarity. To try to distinguish the inherited (present since the egg stage) from the acquired community (detected at later stages), different tissues were analysed at 49, 119 and 146 DAH (gill, intestine, fin and mucus). Only a few genera were inherited, but those that were inherited accompany the sole microbiome throughout the life cycle. Two genera of potentially probiotic bacteria (Bacillus and Enterococcus) were already present in the eggs, while others were acquired later, in particularly, forty days after live feed was introduced. The potentially pathogenic genera Tenacibaculum and Vibrio were inherited from the eggs, while Photobacterium and Mycobacterium seemed to be acquired at 49 and 119 DAH, respectively. Significant co-occurrence was found between Tenacibaculum and both Photobacterium and Vibrio. On the other hand, significantly negative correlations were detected between Vibrio and Streptococcus, Bacillus, Limosilactobacillus and Gardnerella. Our work reinforces the importance of life cycle studies, which can contribute to improve production husbandry strategies. However, we still need more information on this topic as repetition of patterns in different settings is essential to confirm our findings.
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