HIGH FLYERS THINK TANK

Biotechnology and the future of Australian agriculture

The Shine Dome, Canberra, 26 July 2005

Biotechnology: Aquaculture
by Professor Bernie Degnan, School of Integrative Biology, University of Queensland

My brief today is to outline the interface between biotechnology and aquaculture, specifically in how it deals with production of seafood. While I am going to do that, I would also like to, at the end, think about it in terms of interfacing with biopharming and biofabrication systems. This is a place where we can really exploit the novel biodiversity that we have in the oceans around us.

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Aquaculture biotechnology is a broad church. It spans from natural products, chemistry, on through vaccine development, on to genetics. As such, it is a very difficult field to define, and as such there is no one expert in aquaculture biotechnology.

As far as background goes, aquaculture is of interest, I think, because – and this is probably why it is included today – it is a massively growing sector of our food production, both in Australia and worldwide. In the past 50 years it has grown about five-fold, and is now expected to be producing 40 per cent of the world's seafood in 15 years or so. This is largely because we seem to have plateaued as far as our ability to procure food from the oceans from wild stocks is concerned.

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It is recognised that aquaculture, unlike what we have been hearing about all day, is still in its early phases. We don't really have a 'chicken', although salmon and tilapia are grown that way. There are still close to 150 species that are being developed, at various stages, from basically backyard enterprises through to industrial-scale production, such as in the case of salmon. Nonetheless, in order for this field to grow further, there are a few things that need to be done.

So we are in an interesting situation, where we are trying to infuse biotech solutions at the same time as actually figure out how to grow these things, which is very different from most of the things that we have heard about today. Nonetheless, there is still a lot of overlap and we can see that managing the health of these animals, figuring out what to feed them – how to do that in a sustainable way – and also trying to understand how they actually operate at a molecular and cellular level, at a physiological and anatomical level.

Basically, success is contingent upon having all these things run in parallel to generate environmentally sustainable production systems.

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On a world scale, Australia is a small producer of seafood. Most of the seafood that is produced occurs to the north of us, in Asia, in terms of both wild catch and aquaculture production. Australia, as a place in this market, basically exports high-quality material – tuna, abalone, pearls, things like that. So all our high-value products tend to be exported.

In Australia we are a little bit different again from Asia, in that we have this fantastic environment that surrounds our coastline and is highly prized by the community, basically our oceans. And so we are living under very tight environmental constraints, certainly rightly so, and we are also a fairly expensive place to grow seafood as compared with Asia.

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So where do we fit in the scheme of things? Basically, we are trying to develop biotech solutions to the main problems that exist not only within Australia but throughout the world. These fall into three basic categories: disease diagnostics and treatments, production of environmentally sustainable nutritional products, and defining and improving genetic stocks.

One of the issues on the local scene is that these goals are often linked to the development of aquaculture production systems within the country, and in order for this field of aquaculture biotechnology to grow within Australia there has to be a dissociation to some extent. That is, the biotechnology is much bigger than the local industries in a lot of cases.

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There are some very clear examples of how we should be going forward, and probably the case study as far as aquaculture goes is the salmon industry, in the sense that the salmon industry has made every mistake possible but now has come out on top. We have industrial-scale production and we have now what would be considered a fairly green production system, for an animal that eats a lot of protein.

What the graph here shows is basically the weaning of the industry from the use of antibiotics through the production of vaccines. Vaccine programs in aquaculture are actually quite advanced, probably as advanced as any other aspect of the industry itself. So here is a case of production increasing massively in Scotland at the same time as a complete lack of use of antibiotics over that time. So some new technologies have been developed and there are a number of DNA vaccines that have been quite successful; also, just currently, RNAi and single-chain antibody expression systems are being introduced and trialled.

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There is a huge need to increase the knowledge that we have on what these animals eat. This is a particularly big challenge when you have many different species, all with different nutritional requirements. There is no one feed for fish, one feed for shellfish, et cetera – each one requires a species-specific diet development to facilitate growth. And we are at a point now where a lot of the species that we attempt to grow, we can't match what happens in nature or come even close to nature, never mind [inaudible].

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[inaudible] species that we culture, and as such have an impact immediately on what is happening in these environments. So there are a number of genome sequences or large EST projects that now are associated with cultured species, and these in the short term are being used to inform selective breeding programs and desired stocks, particularly with desired traits and biosecurity.

This is interesting, because in a lot of cases we don't even have the basic physiological, developmental cellular biology to superimpose these genomics on, so we are in a situation where we have to do everything simultaneously – which makes things a bit tricky, as compared with what is happening in other systems.

The problems are very similar: we are looking for commercially desirable traits, trying to find the genes that are underpinning those; we are trying to have a level of biosecurity – a lot of animals go to market as live animals, and so being able to inhibit sex determination or maturation is crucial to maintain commercial integrity – and there is the need to identify large-effect genes in a lot of systems.

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That said, there are a whole bunch of full-scale genome projects that are currently in place – that have either occurred or are slated to occur – largely with community sequencing projects run out of NIH or the US Department of Energy Joint Genome Institute (JGI). You see here an abbreviated list, largely from JGI, of some of the genomes that have been sequenced and are going to be sequenced. You can see that they aren't commercial species, with the exception maybe of catfish. Nonetheless, this information is going to provide us with a greater understanding of the types of genes that are required to do various things.

Of particular interest might be how these genomes might interface with biopharming and biofabrication pathways. For example, the sponge Reniera shown on that list is a local species, of which there is four-fold coverage at the moment. It will be eight-fold by September. And so this will probably be the first full genome from a marine organism in Australia. Having this information will allow us to look very closely at the biosynthetic pathways that underlie the production of secondary metabolites in this sponge, along with a whole bunch of other sponges. It also provides a system to truly get into metagenomics. Sponges are communities which have animals and microbes, and by having an animal genome you can then start to tease out the microbial genomes and look at the biosynthetic pathways that underlie this production.

The other thing that is of interest as far as biofabrication is concerned is that marine organisms are increasingly informing engineers and biophysicists on how to produce novel structures. So there are now laboratories in the University of California system and Caltech that have sponge biologists working next to biophysicists and engineers on how to actually build glass skeletons. They are producing bioconductors and semiconductors next to understanding how a skeleton is built in a sponge. A good example of that appeared on the cover of Science 2 weeks ago.

So we have all these systems in addition to producing foodstuffs that should be exploited in our production systems in marine organisms.

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In summary: we are fairly well positioned to be a central driver in the future development of aquaculture worldwide, as a community of fairly well-educated individuals, and one of the key features of doing this is to develop systems in our training, probably at the university level, where we start to interface between traditional marine sciences and aquaculture, and the types of areas where we need people to work – genetics, biochemistry et cetera.