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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 opportunistic bacteria in RAS and to promote positive fish – microbe interactions.

The selection pressure can be used to reduce the opportunities for proliferation of potentially harmful bacteria. Hypothetically the chance of proliferation of opportunistic bacteria in the fish tank can be minimized by microbial maturation of the incoming water at a microbial carrying capacity similar to that in the rearing tanks. In a start feeding experiment with Ballan wrasse (Labrus bergylta) we compared the bacterial environment in two flow through systems: a microbially matured system (MMS), where the water presented to the fish was matured in a biofilter, and a fed microbially matured system (F-MMS), where the biofilter was fed organic matter to increase the microbial carrying capacity. As predicted, the MMS showed a more variable and often high microbial growth potential in the tank water. The microbial community composition of the tank water was more stable, diverse and species rich in the F-MMS than in the MMS. The results are promising for controlling the microbiota of the rearing water by competent use of water treatment and selection regimes. Statement of relevance The experiment shows that small changes in management (organic load and maturation of water) of water treatment give significant different microbiota in fish tanks. The experiment also shows that by increasing the microbial carrying capacity in a maturation unit to the level of the tank microbial carrying capacity, the microbial community in the fish tank becomes more stable and less open for opportunistic proliferation. This work reveals promising possibilities for controlling the microbiota of the rearing water in land based aquaculture by competent use of water treatment and selection regimes. Improved control and understanding of microbial control is very relevant for the aquaculture industry.

An Atlantic cod larva (Gadus morhua) feeding experiment was carried out to compare three different live feed enrichment products for Brachionus ibericus and Artemia salina: 1) Nannochloropsis sp. microalgal concentrate (frozen) (N), 2) Pavlova viridis microalgal concentrate (frozen) (P), and 3) Larviva Multigain (R) (BioMar, Denmark)-formulated commercial product (CP). Over the experimental period of 42 days larvae of groups P and CP showed significantly higher instantaneous growth rates (G: 0.074 +/- 0.001 d(-1) and 0.079 +/- 0.009 d(-1)) than larvae of group N (G: 0.04 +/- 0.0 d(-1)). Survival at the end of the trial of group CP was highest (20 +/- 8%), whereas significantly lower survival was observed for groups P (7 +/- 2%) and N (

The use of probiotic bacteria is a strategy suggested to overcome microbial problems during early stages of farmed animals, including fish. However, few studies have investigated the efficiency in the establishment of probiotics in the fish and how lasting such treatments are. The objective of this study was to evaluate whether the microbiota of Atlantic cod larvae Gadus morhua L can be steered by introduction of selected probiotic candidates, and if there are particular developmental stages where this is more easily obtained. Cod larvae were given a mixture of 4 candidate probiotic strains (Microbacterium (ID3-10), Ruegeria (RA4-1), Pseudoalteromonas (RA7-14) and Vibrio (RD5-30)) through the live feed and the water during a treatment period of 24 h. The strains originated from reared cod larvae and are proven to have probiotic properties. The larvae were treated at seven different ages, namely days 0, 2, 4, 8, 16, 30 and 45 post-hatching, with one new experimental group started each time. A real-time PCR strategy was developed to quantify the relative amounts of the four added bacterial strains in live feed, and in water and cod larvae during 10 days after exposure. Only ID3-10 was measured to constitute considerable fractions of the larval microbiota for most of the treatments, despite the fact that all the probiotic candidates originated from cod larvae intestines. In most cases, the amounts of the added strains decreased to approximately background levels after a maximum of 4 days, indicating only a transient presence in the larvae. The results indicate that probiotic treatment aiming for colonization with new strains in the cod larvae is difficult, and challenges the probiotic concept for the larval stage unless continuous or repeated addition to the fish larvae is used.

A high share of opportunistic and fast-growing microbes is generally negative for the performance of marine fish larvae. It is hypothesised that larvae that are reared in water dominated by K-strategists (mature microbial communities) will perform better, because they are less likely to encounter opportunistic (r-selected) microbes and develop detrimental host–microbe interactions. K-selection can be set up by securing competition for resources by maintaining a low nutrient supply per microbe in a maturing biofilter in a flow through system or in a recirculation system without disinfection. In an experiment with Atlantic cod larvae (Gadus morhua L.) the development of the microbial community in the inflowing water to tanks as well as in the tank water was studied in a conventional flow through system (FTS) and two hypothesised K-selective systems: a microbially matured flow through system (MMS) and a recirculation aquaculture system (RAS). As predicted, the K-selective treatments resulted in a significantly more mature and stable microbial community composition in the water going in to the fish tanks compared to the FTS. The larvae in the K-selective treatments showed 72% higher survival than the larvae in the FTS. In K-selective systems where the inflowing water to the fish tanks is matured at a microbial carrying capacity that is significantly lower than the carrying capacity in the rearing tank (i.e. MMS) there is hypothetically an opening for proliferation of opportunists to match the higher carrying capacity in the tank water. As predicted, the RAS showed K-selection of the incoming water at a carrying capacity similar to that of the tank water, which resulted in a significantly more stable microbial community composition in the tank water of the RAS than in the MMS and FTS. The results of this experiment showed a high potential for increasing fish survival by using K-selection of bacteria, which is a cheap and easy method that can be used in all kinds of new or existing aquaculture systems.

Particle accumulation in recirculating aquaculture systems (RAS) are generated from uneaten food and feces, and bacteria tends to proliferate. Small organic particles act as substrate for bacterial growth and may by direct interference with gills cause stress and reduce disease resistance for the cultivated species. Most diseases in aquaculture of marine fish larvae are caused by opportunistic microorganisms that become pathogenic when the fish is under stressed conditions. The present study investigated the potential of using a membrane bioreactor (MBR) as a part of the water treatment in a RAS for production of marine fish larvae, since the small pore size (50 nm) efficiently removes organic particles including the colloidal fraction in the system. The experiment was a 50 day start-feeding experiment with Atlantic cod ( Gadus morhua L.), comparing water quality and larval performance in a conventional RAS (cRAS) with a membrane filtrated RAS (mRAS). In mRAS, 8.5% of the water flow was at any time membrane filtrated. The present study showed that the MBR improved water quality significantly by reducing turbidity and by lowering the total number of bacteria in the rearing water (up to 80% reduction). Microbial communities in water samples were significantly different between cRAS and mRAS already on 5 days post-hatching (dph) and throughout the experiment. The microbial community composition of the rearing water was significantly different from the composition of the larval microbiota during the experiment, although differences between larval samples were different only on 50 dph. The present study showed the potential of using MBR to lower the bacterial carrying capacity (CC) by efficiently removing organic particles and bacteria. In average a 13% higher cod larval growth (weight, %) at 40 dph and a 3.0% higher survival rate at 50 dph were measured in the mRAS scheme.