CSTFA Our Research Aquaculture Research

Aquaculture Research

As the human population rapidly approaches 9 billion, finding the means to supply sufficient animal protein in a sustainable and economic way to feed this burgeoning population is one of the most important challenges humanity will face in the immediate future. With the majority of the population growth occurring in the tropics - from southeast Asia, Latin America, to Africa - farming of aquatic species is the most efficient and healthy way to produce animal protein.

The Aquaculture team within the CSTFA are world-leaders in tropical aquaculture research and development, with a particular focus on genetics, nutrition, aquatic animal health, physiology, hatchery production, algae, husbandry, post-harvest processing and sustainable practices. Researchers directly partner with the aquaculture industry to solve real world problems and mainly work with tropical species including barramundi, marine shrimp, pearl oysters, tropical abalone, sea cucumbers, freshwater crayfish, micro- and macroalgae and ornamental fish.

Aquaculture research banner.

Researchers from the CSTFA have experience and expertise in all biological and industry aspects of tropical aquaculture, including hatchery and nursery techniques, aquatic animal health, nutrition and feed development, bioremediation, sustainable livelihoods, seafood quality and human health, reproductive control and domestication, and the application of advanced selective breeding techniques. Recent examples of leading and industry-impactful research includes:

  • development and implementation of genomic-based breeding programs for barramundi, pearl oysters and marine shrimp (Pacific white shrimp, black tiger shrimp)
  • identification and prevalence of commercially important pathogens
  • situational analysis of northern Australian aquaculture
  • feed development using plant-based and alternative protein sources
  • bioremediation of waste nutrients using macroalgae
    influence of microbial communities for health and productivity of marine shrimp

Prof Dean Jerry

E dean.jerry@jcu.edu.au P +61 7 4781 5586

The Aquaculture Genetics team is focused on developing the knowledge and tools required by the aquaculture industry to understand genetic processes affecting culture success and in the conduct of efficient selective breeding programs. With over 15 year’s expertise delivering services to the global aquaculture industry, JCU and the CSTFA have been instrumental in the design and conduct of breeding programs for many important tropical species, including barramundi, marine shrimps, pearl oysters and freshwater crayfish.

The aquaculture genetics team works directly with the aquaculture industry to develop the tools and knowledge required for them to commence selective breeding programs. As examples of some of these partnerships we currently work with global companies involved in breeding programs for marine shrimp (Global Gen Inc, Seafarms Ltd), barramundi (Mainstream Aquaculture), tilapia (Worldfish), redclaw crayfish (NQFA), pearl oyster (Atlas South Sea Pearl) and abalone. There is a particular focus on improvement of important aquaculture species in Australia and Asia.

Researchers have access to a fully-equipped, modern genetics laboratory, including an Illumina Mi-Seq sequencer, flow cytometers, robotics, quantitative PCR and high throughput PCR capabilities. Given its strengths in quantitative statistics and genomics, it also has the high-performance computing capability necessary to link phenotypes with the genome and develop genomic selection algorithms. JCU also has the largest tertiary aquaculture aquaria research infrastructure in Australia for the conduct of genetic related experiments and training.

Prof Kyall Zenger

E kyall.zenger@jcu.edu.au P +61 7 4781 6532

The Aquaculture Nutrition team  has been influential in developing and implementing applied solutions across these fields for several important tropical species, including barramundi, grouper, tilapia, freshwater crayfish, tiger prawn and sea cucumbers. The university also boasts a world-leading comprehensive teaching program in aquaculture physiology, nutrition, and propagation, with specific applications to commercial aquaculture and hands-on training in up-to- date relevant production techniques.

The group is recognised as being at the forefront of R&D in these respective areas and provides a full complement of expertise, including methods for determining nutritional requirements of species, evaluating the use of sustainable plant based ingredients to replace marine ingredients as well as of novel and functional dietary ingredients to improve intestinal health, molecular characterisation of the physiological response to dietary and environmental changes, resolving the drivers of egg and larval quality, and measurement of metabolism and energetics in aquaculture species.

Dr Leo Nankervis

E leo.nankervis@jcu.edu.au  P +61 7 4781 6524

The aquarium trade is a multi-billion dollar industry worldwide, and it is growing at a rapid pace. However, unlike freshwater ornamentals, of which 98% are captive bred, it is estimated that currently over 95% of marine ornamental s are collected directly from the wild, mainly from coral reefs, a practice that negatively impacts biodiversity of the fragile reef ecosystems. Moreover, in developing countries where the bulk of marine ornamentals are sourced, the collection is often done via reef damaging methods, e.g. using explosives and cyanide, which contributes to reef destruction.


In order to be sustainable, highly sought-after marine aquarium species must be bred in captivity to supply the trade and to further expand the industry. The Marine Ornamentals Captive Breeding Group are developing captive breeding techniques for a range of popular marine ornamentals, including crustaceans and fish. The Group have so far successfully bred more than 30 species, several of which are world firsts, and work on multiple other species is ongoing.

The aquaculture department at JCU is a world-leader for the research and development of captive breeding techniques for various marine ornamental fish and crustaceans, as well as intensive culture methods for tropical copepods, the key prey for larviculture of many marine ornamentals. The data and knowledge generated through R&D are being used to improve the economic and environmental sustainability of the multi-billion dollar marine ornamental trade industry while fostering an emerging marine ornamental aquaculture industry.

A/Prof Chaoshu Zeng

E chaoshu.zeng@jcu.edu.au P +61 7 4781 6237

Culture systems provide the ability to develop a wide range of novel products for human, animal and plant use. This includes the ability to utilise waste streams from industrial and agricultural systems to provide remediation and access to resources. Researchers from the Novel Aquatic Products and Applications Program are world leaders in the development of novel products using both micro and macro algae for food, energy and health products.

James Cook University has been a world leader in the research and development of macroalgae for more than 14 years and over this period has been a leading international source of high-quality research for the integrated production of macroalgae for the bioremediation of wastewaters.

Both marine and freshwater macroalgae are bio-resources that can be produced through an integrated process with the treatment of waste waters from aquaculture, agriculture, municipal water treatment, and industrial, mining and mineral processing. Our research and development focuses on the integrated production of macroalgae with existing industries for bioremediation (treating waste streams), utilising carefully selected marine and freshwater species. Subsequently, we focus on the development and delivery of valuable bio-products and biotechnologies, based on the unique biochemistry and properties of macroalgae. Our ultimate goal is to develop and commercialise marine and freshwater macroalgae for products ranging from human food and food ingredients (phycocolloids) through to nutraceuticals, animal feeds, fertilisers, biochar and bioenergy.

Dr Andrew Cole

E andrew.cole3@jcu.edu.au P +61 7 4781 5250

  • ARC Research Hub for advanced breeding to transform prawn aquaculture.
  • Genetic diversity audit of farm held stock of greenlip and blacklip abalone.
  • Development of advanced reproductive techniques to characterize infertility in Barramundi.
  • ARC Linkage, Deciphering the molecular and environmental determinants of sex-change in barramundi.
  • Growing a profitable, innovative, collaborative Yellowtail Kingfish industry: bringing 'white' fish to the market - RnD4Profit.
  • ARC Linkage, Advanced animal breeding in aquaculture: using genome-wide molecular breeding values for rapid animal improvement in the Silver-lipped pearl oyster.
  • ARC Linkage, High-throughput DNA sequencing facility at James Cook University.
  • Expanding spiny lobster aquaculture in Indonesia.
  • Eliminate factors inhibiting redclaw farming from reaching its full potential.
  • Direct age determination with validation for commercially important Australian lobster and crab species (western, eastern, southern and ornate rock lobster, and crystal, Tasmanian giant and mud crab).
  • Dietary Protein and Energy Requirements of Group: Assessing SBM and SPC Utilization by Tiger Grouper and Establishing Baseline Nutritional Requirements for Humpback Grouper.
  • Development of Soy Aquafeeds for Grouper.
  • Review of Grouper Production Approaches and development of Targeted Soy-Optimized Diets For Key Grouper Species in Asia.
  • Evaluation of Local and Imported Pacific Island Aquafeeds for Tilapia.