To grasp the wide-ranging impacts of our industrial food systems, take a peek inside a salmon’s ear. That’s what marine biologist Tormey Reimer did when, in 2013 at the University of Melbourne, she began to investigate deformities that were developing on the structures that salmon use to hear.

Bony fish species have structures called otoliths in their ears, small crystals that they use to detect sound. Biologists have for decades relied on otoliths to age fish, using them like rings on a tree. But what Reimer saw was an altogether larger, lighter, and more transparent crystal called a vaterite, growing into the otolith and obstructing the fish’s ability to hear. “I did a bit of digging and found it was much more common in farmed salmon than wild,” she says. And, she began to suspect it had something to do with the accelerated growth rates in fish farms.

Now, in a recent paper, she’s confirmed that hunch. By surveying groups of farmed salmon, Reimer discovered that the biggest feature underpinning a salmon’s likelihood of developing vaterites – beyond diet, and genetics – was their growth speed. “The fastest-growing fish were three times more likely to have vaterites than the slow-growing fish,” Reimer says. Farmed fish typically get high-nutrient feed, and are exposed to longer light conditions than they would experience in the wild. Because salmon will eat whenever it’s light, this system creates constantly guzzling fish that grow faster and more efficiently.

Reimer still doesn’t know precisely why faster growth leads to vaterite formation; one theory is that it might have something to do with rapid skeletal growth, which could usurp resources intended for the proper development of otoliths. But she does know that fish afflicted with vaterites will have impaired hearing for life. “I see this as one of many puzzle pieces in animal welfare,” she says. “What’s surprising is that we’ve known about most of the issues in aquaculture for a really long time, but this is a brand new one that’s just popped up.”

Aquaculture has reached such a scale and degree of efficiency that hearing-impaired fish have simply become an artefact of its success. Crowded conditions and disease outbreaks are already problems that the industry has to tackle; adding a human-caused disability to that list takes the concern to a new high. And it’s only likely to intensify.

Aquaculture is now the fastest-growing sector of food production. Roughly half –probably more – of the fish we produce worldwide comes from farms. All this is set against a backdrop of globally dwindling and stagnating wild fisheries, which also increases aquaculture’s desirability on a global stage. What does this mean for the industry’s future, and the welfare of the farmed fish we’ll come to rely on more and more?

“There’s only so much wild fish you can pull from the ocean, and it’s not going to grow. We need more fish and it’s going to come from aquaculture,” says Rebecca Gentry, a marine ecologist at the University of California, Santa Barbara. She’s the author on another recent study that explored a different concern in aquaculture: productivity. In the research she found that every coastal country on the planet technically could meet its seafood needs – and do so sustainably – via offshore fish farming in only a small portion of its coastal waters.

By identifying only the most suitable habitat for aquaculture globally – areas of ocean with the right depth for fish farms, and which exist outside marine protected areas and busy shipping lanes – Gentry proved that we could produce 100 times our current seafood needs. Crucially, she showed that in countries whose populations experience serious food insecurity, aquaculture can provide a cheap and reliable source of protein. The limits on the success of marine aquaculture aren’t space, which is in abundance, the study concluded. Instead, it’s economics, and governance, that will determine aquaculture’s future.

Facebook Twitter Pinterest Salmon farming in Hitra Bay, west of Trondheim in Norway. Each circular net contains some 120,000 salmons. Photograph: Celine Serrat/AFP/Getty Images

Another major limitation is aquaculture’s poor reputation, marred by problems like the persistent outbreaks of viral disease, which spread rapidly in the close quarters and often beyond the farm enclosures to infect wild fish. The antibiotics and pesticides used to control these outbreaks in turn often pollute the surrounding waters. But as Gentry’s study shows, aquaculture also has the power to solve some of our most pressing food security concerns, because by creating an abundant supply of farmed fish, it lessens the pressure on overfished stocks. “It’s not black and white. Aquaculture has, and hasn’t, done really well. I mean, mowing down mangroves for shrimp farms – that’s so red hot, sustainably,” Gentry says. “We need to step back and think, what is sustainable aquaculture?”

And, how does the welfare of of salmon – and other fish – slot into that goal? The problem is big enough to consider seriously. In another previous study, Reimer was part of a team that sampled Norwegian hatchery-raised salmon, and discovered that almost all of the fish in the sample were afflicted with vaterites. When she compared the results with studies on other farmed fish, she found that the rate was similarly high. “Vaterite has been found in other farmed fish species: in carp, eel, red drum. So I do believe that really any fish that has an otolith and is farmed in a way that maximises growth rate, should be looked at to see if this is affecting them,” Reimer says.

At such a scale, this should push us to examine the ethics of fish farming as we expand aquaculture, the same way we might do for cattle, poultry, and pigs. “It may not seem like a big deal to say that many farmed fish are hearing impaired. But if you were to say to someone that a high proportion of the cows you eat are blind in the field, there would be an uproar,” Reimer says.

It’s true that fish hardly inspire the same degree of affection as the mammals we farm. But it’s more than a question of emotion; it’s also a practical issue that aquaculture companies can’t ignore. Many countries, including the UK, demand the “Five Freedoms” for all farmed animals, including fish. One of these requires that animals be capable of expressing normal behaviours. That’s a freedom that Reimer and colleagues assume that hearing-impaired salmon do not enjoy.

None of this is intended to undermine aquaculture, she says. “Farmers want to grow fish as quickly as possible and get them to market. I wouldn’t expect aquaculture companies to reduce growth rates.” Instead Reimer hopes for further research to illuminate what’s really going on, perhaps hitting on a way to reduce the risk of vaterites, maybe via diet, while still keeping growth rates intact. “It’s a good opportunity to put the resources into that research and to get it solved as quickly as possible. Through ignorance, we have let it go on for quite some time.”

Certainly, as aquaculture continues its global spread, we’ll need to find creative and varied solutions to the challenges that will inevitably arise. The case of the deafened salmon is omen-like, crystallising some of the biggest concerns about aquaculture’s future growth. It brings to our plates an uncomfortable awareness about the huge scope of damage that our food systems can create.

And yet, if we do it well, aquaculture could also become an invaluable tool for fixing some of the damage we’ve wrought through our traditional fisheries. Pragmatically, Reimer says: “While they’re both doing terrible things to the environment, one can be improved. The other cannot.”