Microbial community dynamics in a hatchery recirculating aquaculture system (RAS) of sole (Solea senegalensis)

Abstract

Recirculating aquaculture systems (RAS) have been developed to reduce the aquaculture environmental impact and control rearing conditions. They allow water reuse by managing waste and nutrient recycling, consequently making intensive fish production compatible with environmental sustainability. A key aspect of these systems is the water treatment performed by the beneficial bacterial community of the biofilter. In this study we aim to investigate the dynamics of the prokaryotic community of a sole (Solea senegalensis) hatchery RAS in relation to the variability of water physical-chemical parameters. Samples from different matrices (water, biofilter and tank wall biofilm) were collected from several compartments of a commercial RAS. Total DNA was isolated from the different matrices and the V4-V5 region of the 16S rRNA gene was sequenced using Illumina MiSeq® platform and the output analyzed in the DADA2 pipeline using the SILVAngs database. Overall, the prokaryotic communities were dominated by Proteobacteria (12–89%) and Bacteroidetes (8–86%) and a total of 58 genera contributed with more than 3% of the relative abundance across the different samples. The most abundant genera were Tenacibaculum, Sulfitobacter, Leucothrix, Novosphingobium, Marinicella, Pseudoalteromonas, Polaribacter_2, Schleiferia and Algibacter. The prokaryotic community shifts were found to be modelled by water parameters such as salinity and pH. This study provides new knowledge on the prokaryotic community composition in different units of recirculating systems, essential for the understanding of the microbial community balance in aquaculture and represents an important tool for overall aquaculture system management.