Changes in rearing water microbiomes in RAS induced by membrane filtration alters the hindgut microbiomes of Atlantic salmon (Salmo salar) parr

An important step in water treatment in recirculating aquaculture systems (RAS) is the removal of particulate organic matter. While commonly applied treatment technologies remove most of the particles, fine particulate organic matter typically accumulate in RAS, and serve as substrate for heterotrophic bacteria in the system. Membrane ultrafiltration has been shown to reduce the concentrations of total organic carbon and to counteract blooms of opportunistic bacteria in periods with high organic loading. The potential influence of such opportunistic bacteria on the fish microbiomes and fish welfare is poorly understood. In this study, we investigated the effects of high organic loading on the water and hindgut microbiomes in RAS with Atlantic salmon parr. Two pilot-scale RAS, one with membrane ultrafiltration of a 10–15% side-stream (mRAS), and one without (cRAS), were operated in periods with low and high organic loadings, and the water and hindgut microbiomes were characterized by Illumina sequencing of 16S rDNA amplicons. At the end of the experiment, after a period of high organic loading, two OTUs representing Mycobacterium and Spartobacteria dominated the water microbiomes in cRAS, with relative abundances as high as 24 and 17%, respectively. In the mRAS water they were rare (relative abundances of 1.9 and 0.1%). The membrane ultrafiltration stabilized the water microbiota and efficiently prevented the growth of these bacterial populations in RAS. The parr hindgut microbiomes were generally highly distinct from the RAS water microbiomes and were dominated by the bacterial phyla Bacilli and Firmicutes. Furthermore, an OTU probably representing Carnobacterium inhibens, originally isolated from the gut of adult salmon, was highly abundant in the gut microbiomes, with relative abundances reaching over 30%. However, for the cRAS fish after a period with high organic loading, the relative abundance of this Carnobacterium OTU was reduced, and an increased similarity between the gut and the water microbiomes was observed. The Mycobacterium and Spartobacteria OTUs that were abundant in the cRAS water were also abundant in the cRAS hindgut samples. This indicates a direct influence of the water microbiomes on the gut microbiomes, and that high organic loading in the cRAS resulted in growth of opportunistic bacteria that were able to colonize the fish gut. The present study shows that membrane filtration is an applicable strategy to counteract growth of opportu