Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.
Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
Appl Environ Microbiol. 2020 Jun 2;86(12). doi: 10.1128/AEM.00411-20.
Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, commercial fishing through wild stock enhancements, and aquaculture production. Flowthrough (FT) hatcheries require more water than recirculating aquaculture systems (RAS), which enable up to 99% of their water to be recycled, thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of three Atlantic salmon hatcheries (RAS = 2, FT = 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 2 times the richness of FT fish. Body sites each had unique microbiomes ( < 0.001) and were influenced by hatchery system type ( < 0.001), with RAS being 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 that in the origin tank biofilm than those in 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 were 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. Atlantic salmon, , is the most farmed marine fish worldwide, with an annual production of 2,248 million metric tons in 2016. Salmon hatcheries are increasingly changing from flowthrough toward recirculating aquaculture system (RAS) design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies of hatcheries have focused either on the fish mucosal microbiota or on the built environment microbiota but have not combined the two to understand their interactions. Our study evaluates how the water and tank biofilm microbiota influences the 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.
成功地在孵化场中养殖鱼类对于保护、娱乐性捕鱼、通过野生种群增强进行商业捕鱼以及水产养殖生产都至关重要。流水式（FT）孵化场比循环水养殖系统（RAS）需要更多的水，因为 RAS 可以回收高达 99%的水，从而显著减少对环境的影响。在这里，我们评估了三个大西洋鲑鱼孵化场（RAS=2，FT=1）的生物和物理微生物组相互作用。从每个孵化场的水箱中采集了 6 条幼鱼的鳃、皮肤和消化物，以及水箱生物膜和水，以使用 16S rRNA 基因测序评估养殖环境和黏膜微生物组。水和水箱生物膜的微生物丰富度高于鱼类黏液，而 RAS 鱼类的皮肤和消化物的丰富度是 FT 鱼类的两倍。身体部位都有独特的微生物组（<0.001），并且受到孵化场系统类型的影响（<0.001），RAS 更为相似。观察到水箱和鱼类微生物组之间存在很强的关联。水和水箱生物膜的丰富度与皮肤和消化物的丰富度呈正相关。引人注目的是，鳃、皮肤和消化物群落与原始水箱生物膜中的群落更相似，而与所有其他实验水箱中的群落更不相似，这表明水箱生物膜对鱼类相关微生物群落有直接影响。最后，微生物多样性和黏液细胞密度与鱼类生长和长度呈正相关。本研究的结果为水箱微生物组与鱼类微生物组之间存在联系提供了证据，皮肤微生物组是一个重要的中间环节。大西洋鲑鱼是全球养殖量最大的海水鱼类，2016 年的年产量为 2248 万吨。由于对水消耗的影响较低，孵化场越来越多地从流水式向循环水养殖系统（RAS）设计转变，以更好地控制生产并提高环境可持续性。迄今为止，孵化场的微生物组研究要么集中在鱼类黏膜微生物组上，要么集中在养殖环境微生物组上，但尚未将两者结合起来以了解它们的相互作用。我们的研究评估了水和水箱生物膜微生物组如何影响三种黏膜环境（鳃、皮肤和消化物）中的鱼类微生物组。本研究的结果强调了养殖环境是鱼类黏液中微生物定植的独特来源，此外，这如何影响鱼类健康。进一步的研究可以利用这些知识来设计养殖环境，以调节鱼类微生物组，从而产生有益的表型。
