Understanding Microbiomes in Salmon Hatcheries

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By Milthon Lujan

By Chase Martin*
USA.- Researchers at Scripps Institution of Oceanography at UC San Diego and the University of Tasmania have found that different hatchery systems for salmon greatly influence the microbial communities of the fish, which in turn may influence their overall health. These findings, published April 17 in the journal Applied Environmental Microbiology, could have impacts that determine which hatchery methods produce healthier and greater volumes of salmon.


Aquaculture is the fastest growing agriculture system, producing over half of the seafood the world eats. Atlantic salmon (Salmo salar) is the most farmed marine fish in the world, with production in 2019 around 2.6 million metric tons. While native to the North Atlantic, the majority of Atlantic salmon are now farmed, some of which are reared outside of their natural range, in places such as British Columbia, Chile, and Australia. The fry – or juveniles – are born and reared in land-based freshwater fish hatcheries, before moving to ocean net pens to mature for harvesting.

Fish hatcheries can take two primary forms: flow through (FT) hatcheries and recirculating aquaculture systems (RAS). The former requires new water to continuously flow through the system, while RAS recycle up to 99 percent of the water used. FT hatcheries take in and release relatively large volumes of water, usually from natural surface waters, and require water treatment and settlement systems. RAS systems have the potential to significantly reduce freshwater requirements and thereby lower environmental impacts.

Jake Minich, a PhD student at Scripps Oceanography, traveled to Tasmania as part of the Australia Americas Internship/Exchange for PhD students funded by the Australian Academy of Science. There, he worked with three hatcheries, one FT and two RAS, to understand how fish microbiomes differ between the two systems, and which may ultimately be best suited for fish health and growth.

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“Australia is a leader in sustainable aquaculture, and I wanted to see and experience this first hand,” said Minich.


Minich analyzed the microbiomes of the gills, skin, and fecal matter of 60 fish across ten tanks, while also looking at the microbial makeup of the water the fish were reared in. He found that fish in RAS tanks had twice the microbial richness than those in FT tanks, with RAS tanks also boasting greater microbial diversity in the water as well. He discovered this increased microbial diversity in fish skin and stool corresponded to larger fish sizes. This suggests that the environment in which the fish are raised greatly influences their health and could be a new way to manipulate and promote growth.

In general, increased microbial diversity is associated with greater stability. Maintaining a diversity of microbial populations allows for functional partitioning of activities leading to an overall more stable ecosystem. This general phenomenon has been documented throughout multi-scale ecological systems, from macro to micro.

According to Minich, this study is one of the first to describe how the microbes in the built environment (tanks and water) are potentially seeding the fish microbiomes, and furthermore how in turn these microbiomes may explain differences in growth performance of the fish.

“The next decade will see continued expansion of fish aquaculture worldwide and the optimization of the fish microbiome is one sustainable approach to improve aquaculture yield,” said Eric Allen, professor of marine biology at Scripps and Minich’s advisor. “Continued research to connect microbiome composition with fish performance will take an increasingly prominent role in this industry and the current report is a right step in this direction.”

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Jeremiah J Minich, Greg D Poore, Khattapan Jantawongsri, Colin Johnston, Kate Bowie, John Bowman, Rob Knight, Barbara Nowak, Eric E. Allen. Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota. Applied and Environmental Microbiology Apr 2020, AEM.00411-20; DOI: 10.1128/AEM.00411-20 https://aem.asm.org/content/early/2020/04/15/AEM.00411-20.abstract 

*Source: Scripps Institution of Oceanography, UC San Diego

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