Under drizzly skies on the west coast of Norway, Thor Halvor Nygaard surveys the fish in the pens floating in the country’s largest fjord. “It’s a good place for the fish,” says Mr Nygaard, the site manager on the Skredstivik farm for the past 15 years, pointing to the fiord’s strong current, which provides oxygen and helps disperse waste.

The Sognefjord is best known for its breathtaking scenery, with steep mountains plunging into a flooded valley. But the fjord is also one of the best examples of the rise in fish farming, or aquaculture. Norway’s Marine Harvest, the world’s largest producer of salmon and trout, owns the farm. In a few months, the salmon in Skredstivik’s nine pens will be shipped to supermarkets and grocery freezers in the US and Europe.

In the process, they will contribute to a turning point in the global food supply: for the first time, consumption of farmed fish and seafood this year is set to exceed that of wild fish, according to the UN’s Food and Agriculture Organisation. Three decades ago, only 11 per cent of the fish and seafood consumed was cultivated. This shift ensures a more stable supply of fish for a growing world population, but it also has environmental risks.

“The agricultural revolution meant that people no longer needed to hunt,” says Alf-Helge Aarskog, chief executive of Marine Harvest. “That is the same as we are doing [in fishing].”

Fish cultivation spans centuries – manuscripts show that the Chinese grew carp around the 5th century BC. The ancient Egyptians also attempted farming fish, and there are indications that Mediterranean civilisations cultivated oysters. But it has been over the past half century that aquaculture developed into an industry.

Farmed fish production has grown by 13 times since 1980, with the industry producing $144bnworth of salmon, shrimp, trout, scallops and many other species in 2012. The amount of captured wild fish has remained stagnant since the 1990s at around 90m tonnes a year as a result of the depletion of key grounds and the introduction of quotas.

The steady rise in demand for seafood catapulted farmed fish production above global beef output in volume terms in 2010. Shrimp and salmon, species where farming has boosted production, top the list for the total global seafood trade, which was worth $136bn in 2013.

Industry executives say farming has brought two crucial changes that have underpinned growth: consistency of supply and much lower consumer prices.

The buoyant outlook has attracted new investors. Mitsubishi, the Japanese trading house, recently bought Norwegian salmon farmer Cermaq for $1.4bn, suggesting that multinationals have woken up to the financial potential of the sector.

But after two decades of strong performance, the seafood farming industry is facing growing pains. Dubbed the “blue revolution” in the mid-20th century, fish farming was initially seen as an environmentally friendly way to produce food using limited resources and agricultural waste.

No longer. In the 1980s, it came under pressure for the overuse of antibiotics in fishfeed and environmental issues such as destruction of mangroves and pollution from wastewater.

Thousands of miles from the fjords of Norway, a flight over Surat Thani, in the southern part of Thailand, reveals the most acute challenges facing the farming industry.

In the South China Sea, the devastating impact of the so-called early mortality syndrome hitting shrimp is clear. The disease has ravaged Thailand’s shrimp industry since 2012. But it is only a sign of a much bigger problem: high-intensity farming pollutes and can foster the spread of disease.

Audun Lem, a seafood expert at the FAO in Rome, says that while farming has worked hard to improve its environmental record, “the problems from the 1980s and 1990s still stain the industry”.

Once the largest producer of shrimp in the world, Thailand’s production is set to drop by a third to about 200,000 tonnes. The disease has also hit neighbouring Malaysia, Vietnam and China and has spread as far as Mexico. The result is a sharp fall in shrimp supplies, which have pushed up prices by 35 per cent over the past five years.

“Since the disease hit, survival has fallen by half,” says Daniel Gruenberg,
a consultant in Thailand.

This epidemic, along with the white spot disease that hit shrimp farms in the 1990s and the salmon anaemia that devastated Chile’s salmon industry four years ago, has helped make fish health a priority. But while the challenge of disease has grown, veterinary science – still in its infancy in the fish industry compared with agriculture – has struggled to cope.

Frank Asche, a marine economist and professor at Norway’s University of Stavanger, argues that the fish farming industry is still learning ways to deal with disease. “Like agriculture, we need to prevent and cure.”

Science is starting to help. In Japan, genetic information and classic breeding methods are being combined to develop strains of fish less susceptible to disease.

Takashi Sakamoto, a researcher at the Tokyo University of Marine Science and Technology, has developed a flounder immune to some viral infections. “Using genetic information we can create more disease-resistant fish,” he says. “That is where the world is going.”

Aaron McNevin, director of aquaculture at the World Wildlife Fund, says efforts to fight disease have eased pollution because healthy fish require fewer chemicals. “Pollution is still ubiquitous but improving. Biosecurity has facilitated lower pollution loads,” he says.

Industry executives and conservationists worry that a move to countries where there is less regulation could hurt the industry. Myanmar has become a new production centre for shrimp. India’s industry is expanding fast, while farmed tilapia, a firm freshwater fish, has proved popular in Brazil and several African countries.

Along with disease and pollution, the other big problem facing the seafood industry is rising costs.

Rick Barrows, a researcher at the US agriculture department, has been studying alternative fish feeds to move away from the traditional, and increasingly expensive, feed: other fish.

Farmed fish typically are fed the wild variety – mainly anchovies caught off the coasts of Chile, Peru and elsewhere. Salmon farmers, for example, use 1.4kg of fish feed to produce a single kilogramme of salmon, which has come down from a 3:1 ratio in 2000. Mr Barrows’ trial diets include organisms such as yeast, bacteria and algae.

When the sector was in its infancy, supplies of fishmeal were abundant and prices relatively low. But in recent years, as aquaculture consumption jumped, the price of fishmeal in producers such as Peru has also hit record highs.

The sharp price increase has accelerated efforts to replace proteins from fish with plants, such as soyabean and sunflower seeds. But there is a catch. While companies have managed to lower the fish content to about a quarter of the total used in the feed, they still rely on wild fish for the Omega-3 fatty acids that are beneficial to human health. Mr Barrows calls a substitute for fish oil “the holy grail” for the industry.

The experience of the agriculture and livestock sectors shows that the challenges are solvable. But the easy years of growth, when output boomed and prices declined, are firmly behind the seafood industry. The sector has entered uncharted waters.

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