The following is a script from "Salmon in the Sea" which aired on May 11, 2014. Dr. Sanjay Gupta is the correspondent. Peter Klein, producer.
Salmon is the most popular fish on American dinner plates, but most of it is no longer fished out of the sea. Close to three quarters of our salmon is farmed - grown in cages suspended in the open ocean in places like South America, Europe and Canada. It's a multibillion dollar industry now, but many environmental organizations are concerned these farms could be spreading diseases into the wild. And they've issued a red-label warning for farmed salmon, urging consumers to avoid buying the product because of its potential environmental impact. Salmon farmers say the industry has improved over the years, and they're actually helping to save the last remaining wild salmon in the sea.
Ian Roberts: So we're arriving to the farm now.
Sanjay Gupta: That's it, right?
Ian Roberts: Yeah, yeah.
Ian Roberts has been farming salmon in Canada for more than 20 years. He works for Marine Harvest. They're the biggest salmon farming company in the world, and he took us to see one of their farms in British Columbia.
Sanjay Gupta: Pretty spectacular.
Ian Roberts: This is the office.
This farm is about 150 miles north of Vancouver.
Sanjay Gupta: When you come out here, it is so beautiful. And the argument is that these farms threaten the pristine nature of this beauty. Is that a fair argument?
Ian Roberts: No. While there is a local impact, and let's be honest, when you farm anything, whether it's vegetables or animals on land, you have an impact. But you're also taking pressure off wild stocks. By raising fish in the ocean, we're actually conserving what we have left in the ocean.
What's left in the ocean is in trouble. The number of wild salmon in both the Atlantic and Pacific oceans has been on a steady decline over the past century while the demand for salmon just keeps rising. So Ian Roberts says he sees it as almost his duty to farm fish.
Ian Roberts: We farm everything we eat. All our vegetables are farmed. All our meats are farmed. The ocean is the last place where we hunted and gathered. The problem is there is seven billion of us now on this planet. And the oceans can't give us any more fish. We owe it to our oceans to make sure that we're providing an alternate to just capturing the last wild fish.
"While there is a local impact, and let's be honest, when you farm anything, whether it's vegetables or animals on land, you have an impact. But you're also taking pressure off wild stocks."
Marine Harvest owns about 30 farms just like this one in British Columbia. Each farm is about the size of a couple football fields, built in calm ocean inlets where farmed salmon can thrive.
Ian Roberts: Here, I'll get you just to grab his tail there and see how he kicks.
Sanjay Gupta: OK. Am I being hazed? Is that what that was?
Ian Roberts: That's exactly what it is.
Ian Roberts: That's a nice lookin' fish.
While these fish appear normal...
Sanjay Gupta: You're free, into the pen.
...the environment they live in is anything but normal.
Salmon - which are naturally white in color - get their pink color from eating shrimp and other creatures in the wild that have chemicals called carotenoids.
Sanjay Gupta: So this is the feed? Let's talk a look.
These farmed salmon get synthetic versions of the chemical added to their food - which give them that classic pink color consumers expect.
Ian Roberts: We can adjust the amount of carotenoids in the diet to adjust the color.
Ian Roberts: That's the oxygen alarm.
Sanjay Gupta: So does that mean the oxygen has just gone down--
Ian Roberts: Too low, yeah.
Sanjay Gupta: Is that a limitation of a farm? Because if they were in the wild, they would swim deeper or go to a different place.
Ian Roberts: Sure. Yeah, you need to manage the environment where your animals live. That's farming.
Each of these pens holds 60,000 fish, and one of the concerns about these farms is that this tight concentration can lead to otherwise harmless viruses mutating into superbugs, and then spreading.
Sanjay Gupta: One of the things that happens in humans is if they live in close quarters, what might otherwise be a relatively harmless infection can spread very quickly. Is that an issue here?
Ian Roberts: Well, we have to be aware of that because it is intensive culture. It is something that we take into consideration.
So farmers vaccinate salmon against known viruses but the vaccines don't always work.
Every year there are outbreaks on salmon farms, and some scientists are concerned those diseases could spread to wild salmon.
Alexandra Morton: Salmon farming cannot be done in the ocean in net pens without destroying the environment around it.
That's a strong statement, but it's one Alexandra Morton, a prominent environmental activist and scientist, has been trying to prove for the past two decades.
Sanjay Gupta: The idea of farming is something that most people are familiar with, cows and chickens and things like that. Why should salmon farming be different?
Alexandra Morton: These are not farms. These are feed lots. They're growing as many animals as possible, as fast as possible, in as small a space as possible.
What worries her is what happened five years ago, when salmon farms in Chile made news...
[CBS News report: In Chile's Northern Patagonia, the salmon are dying...]
A highly communicable, and deadly, virus called Infectious Salmon Anemia, or ISA, broke out on the farms in Chile, and wiped out most of the farmed salmon there.
Alexandra Morton: The story in Chile's interesting because the virus they think got in there 10 years before it actually went viral. And they were kinda fooling around with it. Maybe it's here. Maybe it's not. No, it's not here. And then whammo, the thing just ignited.
Sanjay Gupta: How bad did it get in Chile and how bad could it get here?
Alexandra Morton: They could not believe how many fish it killed. It caused $2 billion of damage. But they don't have wild salmon. Nobody knows what's gonna happen here. This salmon farming experiment, this is the only place it's going on amongst abundant wild salmon. Here we are risking everything on this coast.
So Morton tests wild salmon in British Columbia for the virus, ISA - the one that caused so much trouble in Chile.
Sanjay Gupta: What are you looking for right now?
Alexandra Morton: Right now I'm looking for a freshly dead fish.
"Nobody knows what's gonna happen here. This salmon farming experiment, this is the only place it's going on amongst abundant wild salmon. Here we are risking everything on this coast."
She combs the riverbanks for wild salmon that are dying during the natural spawning cycle.
She's looking for evidence of viruses she believes are being passed from farmed salmon to the wild fish.
Alexandra Morton: You open up a fish and it's like a book.
Sanjay Gupta: This-- I mean, you're doing an autopsy?
Alexandra Morton: I am doing an autopsy, yes.
She sends off tissue samples to labs around the world, including the one that diagnosed the problem in Chile.
Alexandra Morton: And let's see what the liver looks like.
So far her tests have shown genetic markers for the ISA virus - indication, she says, that the virus is already present in these waters.
Sanjay Gupta: There are salmon farmers who will say, "Look-- these viruses don't cause a problem. There's a difference between the presence of a virus and infection and a fish actually getting sick. And it's important to distinguish these things?"
Alexandra Morton: Yes. They have no idea. There's nobody actually looking at the wild fish carefully. So that remains an open question.
Sanjay Gupta: So we don't know for sure that they're causing a problem. But we don't know that they're not?
Alexandra Morton: That's right. So we're gambling.
Sanjay Gupta: One of the things you hear is that these fish could have an impact on the wild fish that swim through this area. Why not just put these farms somewhere where they're not in that kind of proximity?
Ian Roberts: We have relocated farms over the past, identifying that they're not in the best areas, perhaps and they're in sensitive habitat. But I don't believe that aquaculture in British Columbia is having an effect on the wild fish. If it was, I wouldn't be a part of the business.
Farmers and environmentalists have their differences, but Ian Roberts acknowledges Alexandra Morton's role in raising legitimate concerns about the effect on ecosystem in the early days of salmon farming.
Sanjay Gupta: Wow, look at-- that's-- that's so beautiful.
While dolphins and other sea mammals may be a stunning part of this landscape they can be a nuisance to salmon farms, stealing fish and damaging nets.
So, Morton says, the farms used to blast loud sounds under water to scare the mammals away.
Alexandra Morton: Humpback whale.
Sanjay Gupta: Just like that!
But those devices could hurt the animals, and they disrupted migratory patterns of some whales.
Alexandra Morton: There she goes.
Sanjay Gupta: There's the tail.
In response to pressure from Morton and other environmentalists, the farms stopped using the underwater noise devices and instead built better fences around the farms.
Ian Roberts: Seals and sea lions have been a problem in the past. But the technology we use today and the thickness of the nets and the way we anchor the nets really keeps them away from the farm. This farm hasn't had any issues.
Sanjay Gupta: I'm curious, you've got 600,000 fish. What does it look like below here?
Ian Roberts: It looks like a muddy bottom, but it's got nutrients on top, which is the fish waste.
Sanjay Gupta: I've heard the term "dead zone." It's called the-- that doesn't sound good when you hear "dead zone" underneath these farms. Is that a fair assessment?
Ian Roberts: No. No, not at all. There's-- added nutrients below the farms. Added nutrients bring in life. Prawns come to the farm to feed on those nutrients. But there is an impact to the bottom of the ocean, but that's only temporary.
Farms are sometimes left fallow between harvests because studies show the impact to the bottom of the ocean can be significant - with trace metals and organic waste polluting the ocean floor.
Morton says it can take years for the ocean bottom to recover, and she took us outside a fallowed farm to show us what it looks like below.
She dropped a special underwater camera 300 feet down.
Sanjay Gupta: So, what do we have?
Alexandra Morton: You see the brown waste of the farm.
Sanjay Gupta: So, that mushy, spongy stuff -- is that just an accumulation or layer of waste?
Alexandra Morton: That is farmed salmon poop.
There are 125 salmon farms along the coastline of British Columbia, and the Canadian government plans to allow more. But just up the coast, in Alaska, salmon farms simply don't exist.
George Eliason: There's no room for farmed salmon in Alaska.
George Eliason is a third generation fisherman in Alaska...which has the largest wild salmon fishery in the world. Twenty-five years ago, Alaska banned salmon farming out of concern that the farming industry could harm the lucrative fishing trade.
Eliason's father was the state senator who drafted the legislation to outlaw salmon farming.
Sanjay Gupta: What was the concern back then?
George Eliason: Disease. Pollution.
Sanjay Gupta: The concerns that your father had about what it might do to the wild salmon population, was he right?
George Eliason: He was right. We've got a great fishery up there now. Why take the chance? Why even try it?
Instead of farming fish, the Alaskan government set up hatcheries where young salmon are grown and then released - not into cages - but into the wild to boost the population of wild salmon in the ocean.
George Eliason: We call it ocean ranching.
Sanjay Gupta: Should they still be called wild salmon or has that become a misnomer at this point?
George Eliason: They're wild. They're wild.
Ocean ranching, combined with careful regulations, has created a thriving wild salmon population in Alaska, a stark contrast to the situation in western Canada. In 2009, when sockeye salmon numbers on a major river in British Columbia hit a historic low, the Canadian government launched an ambitious two-year-long Commission to finally explore the causes of the decline.
Brian Wallace, senior counsel to the Commission, says they examined more than a half million documents, including Alexandra Morton's research.
Sanjay Gupta: She makes a claim that ISA virus has been found in the waters and the fish of British Columbia. Is that true?
Brian Wallace: I don't know whether that's true or not.
Sanjay Gupta: How can we not know if that's true? I mean, we're not talking about opinion or conjecture; we're talking about science here.
Male voice: We don't have the answer.
Sanjay Gupta: You looked at 600,000 documents, and you spent $26 million. We should have some sort of answer here, shouldn't we?
Brian Wallace: This is a very complex subject. Somebody said, you know, "This isn't rocket scientist-- science, it's much more complicated than that."
Sanjay Gupta: So we don't know that the virus is not here, and we don't know if it is here?
Brian Wallace: I think that's correct.
The Commission determined that climate change and other environmental factors were likely causes of the decline in wild salmon in western Canada, but said disease transmission from farms could be a factor as well.
So the Commission recommended a moratorium on any new farms built along the most sensitive sockeye salmon migration routes... and it gave farmers eight years to prove... there was no significant risk of passing viruses... to wild fish.
Sanjay Gupta: It sounds like until the virus actually gets out of these farms and into the wild population that's gonna establish the risk.
Brian Wallace: That's one way to establish it.
Sanjay Gupta: That sounds like it'd be too late.
Brian Wallace: I hope not.