Microbial Community Dynamics and Host-Microbe Interactions in Cultivation Systems for Atlantic Cod Larvae (Gadus morhua)
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The roles of host associated bacteria have been given increasingly more attention during the last decade, and we now know that the microbiota is essential for digestion, development of the immune system and the gut function. In aquaculture, research has shown that host-microbe interactions play major roles in the health and welfare of the fish, and traditionally the focus has been on avoiding pathogens entering the systems. However, many researchers now believe that instead of eradicating the microbes in the system, one should aim at improving the microbial communities present, and the use of microbial ecology has been proposed as a tool for managing the microbiota in aquaculture systems. The rapid technological development in studying fish larvae-microbe interactions during the last decade, now allows us to study old questions with new tools, and hopefully get closer to the correct answers. By amplicon sequencing of the 16S rRNA gene (454 pyrosequencing and Illumina sequencing), we have characterised water, feed and cod larval microbiota in different rearing systems; traditional flow through systems, microbially matured aquaculture systems and recirculation aquaculture systems (FTS, MMS and RAS, respectively). Small-scale gnotobiotic fish experiments have been used to investigate effects of the presence of bacteria. Host responses were investigated by microarray analyses. We have shown that different water treatments yield distinct microbial communities in the incoming water. However, differences in the carrying capacity of the incoming water and the tank water in FTS and MMS, lead to uncontrolled bacterial growth in the fish tanks in these systems. In RAS, the carrying capacities of the incoming water and the tank water are similar and this reduces the uncontrolled bacterial growth in the fish tanks. We believe that the observed higher survival and growth of fish reared in RAS systems, is due to the microbial conditions. However, the microbial maturation in the MMS clearly has a biological effect on the fish, as survival in such systems is also higher than in FTS. In a study comparing RAS and FTS, we see that the immune system is more highly activated in cod larvae from FTS, than cod larvae from RAS, and we speculate that this is due to a higher amount of potentially detrimental bacteria and host-microbe interactions in the FTS. Many studies, including two studies comparing different aquaculture systems included in this thesis, show that the water microbiota affects the composition of the fish microbiota. However, the fish microbiota is always highly distinct from the water microbiota. This indicates strong selection within the fish. However, little is known regarding which ecological processes determines the microbial community assembly in newly hatched cod larvae. In our second study, we quantified the relative importance of ecological processes under action by calculating nearest taxon indices (NTI) and β-NTI and elucidated the relationship between the water microbiota and the fish microbiota. This showed that the microbial community assembly was dominated by homogenous selection within the fish, and that drift became increasingly important with age and created inter-individual variations. We also showed that some bacteria can persist both in water and in fish, and that relatively rare bacteria in the water may have large effects on the community structure of the fish microbiota. In our experiment using gnotobiotic husbandry we showed that the presence of bacteria down-regulate certain immune responses in cod larvae. We speculate that specific parts of the innate immune system in the Atlantic cod is turned on by default, and that non-pathogenic bacteria modulate the immune response of the cod larvae. Sequencing results also showed that the microbial water quality in the conventional rearing bottles were possibly detrimental for the cod larvae. Opportunistic bacteria were detected in the rearing water and associated with the fish, and gene expression analysis showed that genes related to inflammation and signalling were up-regulated in conventionally reared fish.