Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flow through (FT) hatcheries require more water than Recirculating-Aquaculture-Systems (RAS) which enable up to 99% of water to be recycled thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS n=2, FT n=1). Gill, skin, and digesta from six juvenile fish along with tank biofilms and water were sampled from tanks in each of the hatcheries (60 fish across 10 tanks) to assess the built environment and mucosal microbiota using 16S rRNA gene sequencing. The water and tank biofilm had more microbial richness than fish mucus while skin and digesta from RAS fish had 2x the richness of FT fish. Body sites each had unique microbiomes (P<0.001) and were influenced by hatchery system type (P<0.001) with RAS systems more similar. A strong association between the tank and fish microbiome was observed. Water and tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin and digesta communities were more similar to the origin tank biofilm vs. all other experimental tanks suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. Lastly, microbial diversity and mucous cell density was positively associated with fish growth and length. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome with the skin microbiome as an important intermediate. IMPORTANCE Atlantic salmon, Salmo salar, is the most farmed marine fish worldwide with an annual production of 2,248 million metric tonnes in 2016. Salmon hatcheries are increasingly changing from flow through towards RAS design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies on hatcheries have focused either on the fish mucosal microbiota or the built environment microbiota, but have not combined the two to understand interactions. Our study evaluates how water and tank biofilm microbiota influences fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and furthermore how this can influence fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for beneficial phenotypes.

Amoebic gill disease (AGD) is a significant health issue for Atlantic salmon farmed in a marine environment. While the disease is currently managed using freshwater or hydrogen peroxide baths, there is a need to develop other treatments. The aims of this study were to examine the effect of salinity (0 ppt and 35 ppt) and temperature (3 °C and 15 °C) on attachment and survival of Neoparamoeba perurans in vitro over short exposure times (15 min and 2 h) and to assess the efficacy of reduced temperature (3 °C) as treatment for Atlantic salmon affected by AGD. In vitro freshwater 3 °C was at least as effective as freshwater 15 °C and the attachment was significantly lower after 2 h in freshwater 3 °C than freshwater 15 °C. In vivo there was no difference between the fish treated with freshwater 15 °C for 2 h or freshwater 3 °C. This study showed that despite exposure to low temperature reducing attachment of N. perurans to their substrate in vitro, 15 min cold-water bath treatment was not more effective at reducing AGD in Atlantic salmon than current commercial 2 h freshwater bath.

To investigate the relationship between microbial community profiles and gill pathology during a production cycle of Atlantic salmon in two commercial hatcheries. Relationships between gill histology, environmental conditions and microbiome were determined using high-throughput data including 16S rDNA amplicon sequencing data, histopathology data and water quality parameters. Hatchery A used riverine water and operated a mixed system of recirculation aquaculture system (RAS) and flowthrough. Hatchery B was used bore water and operated a RAS. Melanin deposits, hyperplastic, inflammatory lesions were observed histologically in the gills. A higher prevalence of melanin deposits was detected and correlated to a change in beta diversity of bacterial communities in early time points (fingerling and parr stages). High abundance of Sphaerotilus sp., Pseudomonas sp., Nitrospira sp., Exiguobacterium sp., Deinococcus sp., and Comamonas sp. was correlated with high prevalence of melanin in filaments. Bacterial diversity increased as the fish cohort transitioned from RAS to flowthrough in hatchery A. Under commercial conditions, the commensal community of gill bacteria was related to melanin prevalence.

The increasing exploratory efforts in the Greenland mineral industry, and in particular, the proposed rare earth element (REE) mining projects, requires an urgent need to generate data on baseline REE concentrations and their potential environmental impacts. Herein, we have investigated REE concentrations in anadromous Arctic char (Salvelinus alpinus) and shorthorn sculpins (Myoxocephalus scorpius) from uncontaminated sites in Northwest Greenland, along with the relationships between the element concentrations in gills and liver, and gill histology and serum biochemical parameters. Concentrations of arsenic, silver, cadmium, cerium, chromium, copper, dysprosium, mercury, lanthanum, neodymium, lead, selenium, yttrium, and zinc in gills, liver and muscle are presented. No significant statistical correlations were observed between element concentrations in different organs and gill histology or serum biochemical parameters. However, we observed positive relationships between age and histopathology, emphasizing the importance of including age as a co-variable in histological studies of fish. Despite no element-induced effects were observed, this study is considered an important baseline study, which can be used as a reference for the assessment of impacts of potential future REE mine sites in Greenland.