Microbial community assembly in Atlantic cod larvae (Gadus morhua): Contributions of ecological processes and metacommunity structure. Community assembly in cod larvae

In this study we investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed at quantifying ecological processes influencing community assembly in cod larvae and at elucidating the complex relationship between the microbiota of the environment and the fish. The primary experimental variable in this study was the use of three different water treatments systems to create three distinct microbial communities entering the rearing tanks. These systems were a flow through system (FTS), a microbial maturation system (MMS), and a recirculation aquaculture system (RAS). Each system had three replicate rearing tanks (of 160 L) and were maintained from hatching to 30 days post hatching (dph). Thereafter all rearing tanks received the same microbial water quality (i.e. MMS water) until 46 dph. The larvae were fed rotifers from day 3 – 26 dph, Artemia nauplii from day 22 – 32 dph, and formulated feed from day 31-46 dph. Samples for characterization of microbial communities associated with cod larvae, live feed, rearing water, and incoming water were taken at 4, 8, 17, 30 and 46 dph. Amplicons representing the variable regions 3 and four of the bacterial 16S rRNA gene were sequenced on a Illumina MiSeq run.