Molecular and culture-based bacterial ecology in a zebrafish (Danio rerio) housing system during set-up and equilibration

Zebrafish are an emerging model system for many applications in biomedical and toxicological research. As an aquatic species, zebrafish are intimately connected to, and dependent on, their environment. In research settings, zebrafish are typically maintained in commercial housing systems with a circulating water supply and multiple levels of filtration. Recirculating aquaculture systems (RAS) rely on the microbiome present in the system, typically enriched in a biofiltration substrate, to remove the harmful ammonia generated by fish via oxidation. For these reasons, systems are allowed to equilibrate prior to population, and population should occur gradually. There is little, if any, information available regarding the bacterial community structure in commercial zebrafish housing systems, or the time-point at which the system or biofilter reaches a microbiological equilibrium. To address these knowledge gaps, a commercial zebrafish housing system was monitored at multiple different system sites, from pre-population through 18 weeks post-population, using both molecular and culture-dependent methods. We demonstrate a rich and dynamic community in tank water, dominated by Cutibacterium and Staphylococcus spp., which reaches a stable richness by approximately three to four weeks post-population, but continues to slowly evolve in composition throughout the study duration. The microbiomes of the fluidized bed biofilter (FBB) and water leaving the ultraviolet (UV) disinfection unit were distinct from water at all other system sites. Core taxa in the system detected using molecular methods comprised 36 amplicon sequence variants from eight phyla, 15 of which represented Proteobacteria including multiple members of the families Burkholderiaceae and Sphingomonadaceae. Culture-based screening yielded 36 distinct isolates, 33 of which could be identified reliably to the level of genus or better, and showed moderate agreement with sequencing data.