Aquaculture is widely recognised as the world's fastest growing food sector, worth around US$200 billion by some estimates.

As the world's population grows by an estimated 1.6 billion people over the coming three decades, so will the demand for protein.

In Western countries it is seen as an ethical alternative, but the established aquaculture process has a fatal flaw — it's aiding in the depletion of ocean stocks, because many farmed fish have long been fed on fishmeal made from their wild counterparts.

It's a practice Jason Drew, the chief executive of a South African business called AgriProtein, describes as "sheer madness".

"The fish-in to fish-out ratio is negative," he says.

Alternative forms of fish food have been developed in the past and some, like the CSIRO-engineered Novaq, are being used by Australian prawn farmers to not only sustain the animals, but also increase their growth weight.

But a major problem with many alternatives remains the cost.

Turning maggots into fish food

Watching the livestock graze at AgriProtein's Cape Town facility doesn't exactly fill one with splendoured visions of bucolic serenity.

The polite name for what they raise is larvae. The vernacular is maggot.

At this factory in Cape Town, maggots are processed to become fishmeal. ( Supplied: AgriProtein )

Dubbed the world's first industrial-scale insect recycling site, the new facility takes more than 250 tonnes of organic waste a day and uses it to produce around 50 tonnes of MagMeal — a food source for fish made from dried maggots.

The process is driven by more than 8.5 billion black soldier flies.

Mr Drew said it took eight years of experimentation and "abject failure" before they hit on the perfect breeding process.

"You can go out to almost any university bookshop and find theses on how to kill flies," he says.

"But very few people have actually wanted to make them survive and thrive, apart from ourselves."

Some of AgriProtein's funding has come through the Australian Government's aid and development programme, and the company plans to open seven more maggot factories in the next year — three in Saudi Arabia alone.

MagMeal might be food for animals, but the farmed fish it supports soon end up in kitchens around the world, helping to meet the exponential demand for protein that's resulted from the growth in prosperity of the new middle class in Asia and Africa.

Fears of antibiotic overuse

One of the problems associated with industrial-scale fish-farming is how to control disease.

By some estimates, around 5 per cent of the world's farmed fish stocks are lost each year to pathogens.

Outbreaks are currently dealt with either by the use of antibiotics or vaccination.

The sustainability of large-scale fish farming in Hobart came under scrutiny last year. ( ABC News: Sophie Zoellner )

Antibiotic overuse is problematic, because it can lead to an increase in viral resistance which, in turn, poses a danger to human health.

But the method is favoured by aquaculture operators because of the difficulties involved in hand-vaccinating fish.

Biotechnology developer Simon Porphy estimates around $US10 billion is lost to disease every year.

"Ten billion dollars worth of fish stock is equal to feeding 90 million people," he says. "That's the size of the population of Vietnam."

Mr Porphy's Irish-based company MicroSynbiotiX has been working on a form of oral vaccination, using natural materials and designed to be environmentally friendly.

"We realised that microalgae are a natural part of the fish diet and they're typically used in the hatcheries. What we are doing is basically genetically modifying the microalgae to encapsulate the vaccine," he said.

"Vaccines get destroyed in the stomach of fish since they are quite acidic, so we wanted to come up with an oral delivery mechanism that can overcome this particular challenge.

"The digestion process of the fish will unlock the vaccine and the vaccine will get absorbed in the hindgut of the fish, thereby eliciting a desirable immune response."

Scaling down to help the poor

In many parts of the developing world families have traditionally raised fish in basic ponds to supplement their diet.

Aquaponics can provide a modern alternative, but building small household systems can be expensive and difficult to maintain.

Aquaculture can work on a small scale — such as in this facility in regional Victoria. ( ABC RN: Jeremy Story Carter )

Last year, Michigan-based inventor Michelle Leach was recognised for her work in developing a more resilient, low-cost aquaponic system by the Australian Government's Blue Economy Challenge, which seeks to reengineer aquaculture practice.

Ms Leach's inflatable aquaponic food production system was piloted in rural El Salvador with the assistance of non-profit organisations, and is just about to be trialled in Tanzania in East Africa.

Aquaponics involves the growing of vegetable and fish in a single recirculating biofilter-based system.

"Essentially the fish produce waste, and there's beneficial bacteria living in the system that break that waste down into a form of nitrogen, which plants can absolve," Ms Leach said.

Aquaponic systems use nutrients from fish activity to grow vegetables. ( Getty Images: Rhonda Gutenberg )

"The fish are essentially fertilising the plants and the plants are cleaning the water for the fish. It's a way to grow a lot of food in a very small area using little water."

The current version, dubbed "The Oasis", costs around $US200 and resembles a small blow-up swimming pool.

"If you are in the tropical world you can grow 12 months out of the year, so that's two crops of 100 tilapia per year, and probably around 600 pounds of tomatoes," Ms Leach said.

"A person should be very easily able to pay back their loan within the first two years."

For many impoverished families, $US200 can prove to be a lot of money, so Ms Leach hopes micro-finance institutions will help make the technology available to as many people as possible.

While the system has been deliberately scaled down, she said it doesn't always have to be that way.

"We've focused on making it suitable to really improve the diet of a family of four to six members, with just enough to sell so that they have money to purchase the crop inputs, more fish and seeds for the next crop cycle," she said.

"That doesn't mean once a person understands how to do aquaponics, they couldn't have two systems and start increasing their income."