A molecular and multivariate approach to the microbial community of a commercial shallow raceway marine recirculation system operating with a Moving Bed Biofilter

Information on commercial aquaculture systems bacterial communities is scarce. The present study was performed in a turbot shallow raceway recirculating aquaculture system throughout 221 days after initial fish stocking. The dynamics of bacteria attached to a Moving Bed Biofilm Reactor and the distribution of the system culturable planktonic heterotrophic bacteria were assessed. Different levels of free heterotrophic bacteria were found over time: ≤2.6 × 104 CFU mL−1 in incoming and ozonated water and ≥1.5 × 106 CFU mL−1 in raceway and biofilter water. 16S rRNA gene sequencing of nine strains persistently isolated from the system affiliated with Bacteroidetes, α‐Proteobacteria or γ‐Proteobacteria. Polymerase chain reaction‐denaturating gradient gel electrophoresis (PCR‐DGGE) data showed temporal and spatial segregation of attached biofilter community. The first 32 days were the most important for bacterial establishment with higher culturable bacteria biomass loadings and higher community diversity. Multivariate canonical correspondence analysis of PCR‐DGGE showed that the most common aquaculture water quality descriptors explained 70% of the DGGE pattern variability.We acknowledge the fish farm manager and the fish farm staff for permission and assistance. This work was funded by EC project ‘Raceways – a hyperintensive fish farming concept for lasting competitiveness and superior production’ (COOP‐CT/016869/2006–2008). This work was also supported by a post‐doc grant by Fundação para a Ciência e Tecnologia to I. Henriques (BPD/21384/2005).publishe