People and projects
The lab works on many topics within sustainable aquaculture and fisheries, and more broadly in aquatic and terrestrial ecology. Within aquaculture, we try to solve the environmental and animal welfare problems aquaculture creates by working both inside and outside aquaculture systems.
- ecological effects of aquaculture on surrounding ecosystems
- fundamental aspect of fish welfare
- techniques and technologies to prevent parasite infection on farmed fish
- short and long term effects of parasite treatments on farmed fish
- preventing and reducing the effects of escaped fish in the wild
- understanding the nature and extent of critically low periods of dissolved oxygen in fish farms
- using macro-algae to mop up nutrients in coastal ecosystems
- sea urchin aquaculture
Marine, freshwater and terrestrial ecology
- preventing cane toad invasions
- effects of cane toads on freshwater crocodiles
- freshwater fishes of northern Australia
- sea turtle ecology
Creating more disease resistant and productive stock for aquaculture
Fish products not only provide high-value protein but are also important sources of a wide range of essential micronutrients such as iron, zinc, and vitamins such as vitamin A. Many countries are struggling to provide enough food for their growing populations. Aquaculture is an efficient way of producing animal protein, can play an important role in reducing poverty and can alleviate pressures on wild fishery stocks. But expansion of aquaculture is often limited by a lack of knowledge about simple farming practices (including feed and feeding) and the availability of good genetic stocks. Areas available for aquaculture are limited, so we need to make the fish and production more efficient so that more of this healthy food source can be produced per unit area.
My research focuses on making fish and shellfish more productive for aquaculture by developing technologies that can be used to speed genetic improvement with selective breeding. My focus has been on improving the resilience of fish in the aquaculture environment, including:
- genomic selection for improving the disease resistance of rohu carp and tiger shrimp in India
- resilience to summer mortality for abalone in Australia
- design of selective breeding programs for barramundi, abalone and seaweeds
- epigenetic programming to produce robust Atlantic salmon for aquaculture in Norway
- genes associated with cardiovascular fitness (swimming performance) of Atlantic salmon in Norway
- assisting the development of aquaculture to alleviate poverty
- using the latest high throughput sequencing technologies and bioinformatics methodologies to better understand how particular genetic variants or changes in gene expression affect the resilience of fish
Sea urchin roe enhancement and tracing escapees from aquaculture
Aquaculture is the new frontier for the global expansion of fish production for human consumption. However, developing our oceans as a seafood buffet comes with environmental costs, for example the complex interactions between farmed and wild fish. During my PhD, I developed stable isotope marking methods to detect farmed fish in the wild and thus better assess their impacts. In my post-doc, I am researching sustainable roe enhancement of the sea urchin Heliocidaris erythrogramma using capture-based aquaculture.
The Kimberley freshwater fish fauna is the least studied in Australia; its true biodiversity and evolutionary history are unknown. The aim of my project is to assess the true freshwater fish biodiversity in the Kimberley using a combination of genetic and morphological approaches, and to investigate the influence of past and present geological and climatic processes on the evolution of these communities and their distributions.
Current PhD students
Daniel Wright (now a post-doc at the Institute of Marine Research, Norway)
Sea lice and amoebae causing amoebic gill disease are top parasites of Atlantic salmon, the most farmed marine fish. Their increasing co-occurrence in major production regions has sparked interest in parasite control techniques targeting both. Though, current reliance on treatments (mostly chemicals) leaves few options and drives treatment resistance evolution in parasite populations. This thesis explores the applicability of a more preventative and chemical-free approach to tackle multiple parasites: fish behaviour and cage environment manipulations.
Samantha Bui (now a post-doc at the Institute of Marine Research, Norway)
The expansion of Atlantic salmon (Salmo salar) aquaculture systems has led to the success and proliferation of the ectoparasitic sea louse, Lepeophtheirus salmonis. Mediating infestation should have a biological basis, and this PhD investigates the fundamental behavioural interaction between host and parasite. It focuses on salmon behavioural defence and susceptibility, and effect of infestation on performance. Behaviour should be in the toolbox against pathogens in aquaculture, and this project has provided baseline knowledge of host-parasite interactions that will also help drive the development of biological tools.
Environmental transmission and connectivity of sea lice in marine ecosystems
Large-scale epidemics are affecting important marine species. For the most widely produced marine fish, salmon, parasitic ‘sea lice’ are the most significant problem. These external parasites cause major environmental and economic impacts. Understanding its epidemiology is crucial for management of infestations. I am investigating the environmental transmission of sea lice Lepeophtheirus salmonis in marine ecosystems with intensive salmon aquaculture. For this, I integrate empirical and modelling methodologies to dissect the processes involved in parasite dispersal and build connectivity models to design strategies to prevent lice outbreaks. My project will build fundamental knowledge on lice epidemiology and will allow informed management actions to minimize lice infestations on both farmed and wild salmonid populations.
Occurrence and implications of hypoxia in Atlantic salmon aquaculture
Despite declining capture fisheries, in 2014 world per capita fish supply reached a record high of 20 kg per year as a result of the rapid and steady expansion of aquaculture. The largest single aquaculture commodity by value is salmonids, representing 16.6% of world trade, with demand for Atlantic salmon steadily increasing. The industry, however, is constrained by environmental challenges. Hypoxia, which can occur naturally, is exacerbated in marine cages due to restricted water movement and locally increased biomass. Even apparently minor reductions in dissolved oxygen concentration can result in decreased growth, appetite, immune function and fish welfare. The aim of my project is to improve our understanding of the dynamics of dissolved oxygen fluctuation in salmon cage aquaculture so that managers can focus mitigation efforts and minimize risk as the industry continues to expand.
Camille White (now a post-doc at the University of Tasmania)
Aquaculture outputs and trophic subsidies: Trade-offs in consuming an anthropogenic resource.
Aquaculture is an increasingly common trophic subsidy in coastal marine ecosystems, with waste feed, faecal material and nitrogenous wastes potential food sources for marine consumers. As modern aquafeeds are increasingly high in terrestrial lipids and oils, the biochemical composition of the aquaculture-derived subsidy is relatively alien in the marine environment. Using terrestrial fatty acids as a tool, I investigated dispersal and uptake of the aquaculture subsidy, in both laboratory and field scenarios. I was able to demonstrate that aquaculture outputs are widely dispersed in marine systems and assimilated by marine consumers. Using marine amphipods and sea urchins as model species, I examined maternal and multi-generational effects of increased terrestrial lipids in the diet of marine consumers. I found that consuming waste could alter both biochemical composition and reproductive outputs in invertebrate fauna. When applied to a field scenario, where aquaculture outputs have been linked to increases in sea urchins, I found that broader-scale effects will be a trade-off between energetic benefits of consuming a lipid-rich subsidy, versus any negative effects that a high terrestrial diet may have on reproductive outcomes.
Linking habitat selection and fitness consequences in novel marine ecosystems
It is assumed that animals either choose the best available habitat or don’t choose at all. Despite this, there is evidence that almost all animals do make habitat selection decisions, and that they don’t always choose wisely. This is because rapid environmental change can outpace the evolution of decision-making tools, causing animals to prefer attractive but nonetheless unsuitable habitats (‘ecological traps’). I am studying several marine ecosystems altered by invasive species and aquaculture activities, to discover whether (a) native fauna are willing to inhabit these unfamiliar environments, and (b) whether these decisions are likely to lead to good fitness outcomes.
Bioremediation of nitrogen enriched aquatic environments by macroalgae.
Coastal activities that involve the discharge of nutrients can result in deleterious environmental impacts, with harmful effects on marine biodiversity. My thesis will focus on the potential uses of freshwater and marine macroalgae as bioremediation agents. The first part of the thesis will focus on sampling and testing of production and competition of local freshwater species and their ability to remove nutrients from wastewater. The second part will focus on the link between nutrient discharges and drift algal production and the environmental costs and benefits of algal drift harvesting for nutrient management.
Triple jeopardy in the tropics: assessing extinction risk in Australia’s freshwater biodiversity hotspot
Northern Australian is home to many poorly known, range-restricted and potentially vulnerable freshwater fishes. Species with small ranges, low abundances and narrow ecological niches have a ‘triple jeopardy’ extinction risk. I identify fishes with smaller ranges and lower abundances than expected across Australia. In the diverse, highly endemic Kimberley region, I investigate the dietary, habitat and physiological specialization of range-restricted fish. I show that northern Australia contains many potentially vulnerable species, with the Kimberley a hotspot of freshwater conservation concern.
I am testing whether harvesting purple sea urchins from barrens can be made commercially viable through roe enhancement. Specifically, I aim to (1) determine if the gonad index of urchins from barrens increases faster and to a higher level compared to urchins from kelp beds after reconditioning on a high quality diet; and (2) evaluate the effects of temperature manipulation on the gonad index and quality of post-spawned sea urchins. This work will be the foundation for a potential sea urchin aquaculture industry in Port Phillip Bay that will provide new economic opportunities while simultaneously solving the pressing environmental problem of urchin barrens.
Hydrogen peroxide is a widely used agent in salmon aquaculture to remove parasites. However, some of the effects it can have in this host-parasite relationship are unclear. I will determine how varying concentrations of hydrogen peroxide treatment influence salmon mortality, pre-adult lice removal, salmon lice re-infection and the mucous cells of salmon. I will also try to create a new treatment method by reducing water temperatures during hydrogen peroxide treatments to minimise negative effects of the treatment upon fish. My results will be used by farmers to reduce salmon mortality.
Past PhD and MSc students
Tormey Reimer (now working in the U.S.A.)
Ella Kelly (now a PhD student at the University of Melbourne)
Cathy Cavallo (now a PhD student at Monash University)
Kristal Sorby (now a PhD student at Deakin University)
Michael Sievers (now a PhD student at the University of Melbourne)