Modern aquaculture is an innovative enterprise. Techniques and technologies are often rapidly developed and implemented by industry for production gain, improvements to biosecurity and disease control, the securing of animal welfare and minimizing environmental impacts. Our lab works across all of these issues to solve some of the big issues in modern aquaculture. We target problems, work to understand them, then test innovative techniques and technologies. We work across traditional discipline boundaries to construct approaches that have best chance of practical effect, and can be scaled-up to be used on farms.
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
I started out with a strong interest in ecological and evolutionary theory, writing an Honours thesis on sexual selection and a PhD thesis on the fitness consequences of habitat selection decisions (e.g. ecological traps). I’ve since turned to various applied topics relating to sustainable use of the coastal marine environment, especially aquaculture-environment interactions. As a postdoctoral researcher, I currently split my time between the SALTT lab and the Norwegian Institute of Marine Research (https://www.hi.no/en), studying, among other things:
- New strategies to prevent and control sea lice within salmon farms
- Environmental benefits arising from aquaculture, such as habitat provision and nutrient remediation at shellfish and seaweed farms (including some work in collaboration with The Nature Conservancy)
- Conservation and restoration of temperate reef ecosystems, especially solutions to overabundant sea urchin populations
Aquaculture is one of the fastest growing primary food production areas globally and fish farming has now surpassed wild catch fisheries in terms of annual tonnage of product produced. As a Research Fellow in the SALTT lab, my research focuses on improving aquaculture production through rigorously testing of new and innovative production techniques that strive to make aquaculture more environmentally sustainable and improve the health and welfare of fish produced in commercial production facilities. My main research areas focus on:
- Test trialling submerged sea cage salmon farming as an alternative farming method to enable salmon farms to move further offshore to areas of the ocean that have more stable and optimal environmental conditions.
- Researching the use of tag technology to enable the use of sentential fish as bio-indicators of fish health and welfare in commercial aquaculture.
- Investigating the potential use of sea urchin roe enhancement aquaculture to create a commercial driver to incentivise the removal of overabundant urchins from barrens in Port Phillip Bay as a method to drive cost neutral restoration of kelp forest reefs.
CURRENT PhD STUDENTS
I’m interested in the ecology of parasites and how they evolve in response to novel conditions. Salmon aquaculture is a fascinating system to study these processes – the rapid growth of aquaculture has dramatically altered the ecology and epidemiology of salmon parasites such as sea lice. For my PhD, I will explore how sea lice might evolve in response to modern pest control strategies. My research will focus on whether lice can become resistant to these controls, which could have huge environmental, welfare and commercial implications.
I am interested in how aquaculture can be harnessed beyond food production to help repair and restore habitats and ecosystems we have degraded through various activities. For my PhD, I will first explore how different aquaculture activities can achieve environmentally beneficial and conservation outcomes, before diving into putting some of this theory into action by conducting field trials.
CURRENT MSc STUDENTS
I am assessing the current state of salmonid aquaculture in the top producing farming regions. Using Google Earth satellite images, we are able to see what technology is in use and where it is positioned within the landscape. These factors have a major influence on fish welfare, biosecurity and production levels. In addition, I am also looking at historical images to see how the industry has changed over the past decades.
Shellfish aquaculture is a valuable source of both commercial and ecological services. My research focuses on the potential for the industry to provide ecosystem benefits outside of those we already know, particularly in the area of coastal defence. I’m exploring whether the offshore floating structures used to grow shellfish can reduce the impact of waves on shorelines to reduce coastal erosion. This potential expansion of the understood ecosystem benefits of shellfish aquaculture could inform the construction and placement of economically valuable leases that might also help mitigate the global issue of coastal erosion.
Southern Australia is a prominent biodiversity hotspot for species of red and brown seaweeds used for a variety of food and biomedical applications. While these seaweeds are commonly cultured globally, very little is currently cultured in Australia. My research focuses on attempting to integrate these seaweeds with established land-based abalone aquaculture to provide new methods of production in a growing industry.
Past PhD, MSc and Honours students
Several new depth-focused cage designs have been developed to inhibit physical interactions between the positively phototactic sea lice and surfacing sea-cage Atlantic salmon (Salmo salar). As these cages become implemented at the commercial scale, sea-caged salmon are faced with a suite of new rearing environments and systems to adapt to. My PhD explores how (1) depth-modified cages will affect salmon buoyancy, and (2) whether we can utilise the learning capacity of salmon to facilitate their adaptation to novel environments. Georgia is now employed by PIRSA as an Aquatic Animals Health Officer.
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 focussed on sampling and testing of production and competition of local freshwater species and their ability to remove nutrients from wastewater. The second part focussed on the link between nutrient discharges and drift algal production and the environmental costs and benefits of algal drift harvesting for nutrient management. Juanma returned to southern Spain to work as a post-doc at the University of Alicante.
My research investigated salmon lice and their vertical migration in different light intensities. This will provide more information about how environmental cues influence where salmon lice distribute in the water column. The data collected will improve Norway’s Salmon Lice Dispersal Model which model’s estimated salmon lice populations. This information will be used by farmers to reduce salmon lice infections across the Norwegian coast. Aylah now works as a laboratory assistant for Agriculture Victoria Research.
My research focuses on cleaner fish used as a biological control on salmon farms in Norway. I’m trying to understand and improve cleaner fish welfare in sea cages, as well as their parasite removal efficiency. More broadly, I’m fascinated by the pull between ecology and economy that both drive decision-making in aquaculture, and how we can make aquaculture a more sustainable and ethical industry. Kat now works at Stile Science where she will educate the next generation of Australian scientists with style and panache.
My research focuses on determining the effect of salinity and temperature preferences on the vertical distribution of salmon lice larvae through column experiments. Understanding salinity and temperature preferences of lice larvae is important, as my results will help improve models determining how larvae can disperse and also how infections can be prevented.
Cleaner fish are used extensively to remove sea lice in the Norwegian salmon aquaculture. These fish are removed from their natural habitat and placed into fish farms where environmental conditions may be outside of their normal ranges. This has raised concern about their welfare within sea cages. My research aims to measure the effect of temperature on physiological performance in the Ballan wrasse (Labrus bergylta). My results will be used to produce welfare guideline for their use in aquaculture. Jeffrey moved to Norway as a research assistant at the Institute of Marine Research.
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.
Tina was enrolled at UTas and co-supervised by Barbara Novak. She is now a researcher at the Institute of Marine Research, Norway.
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.
Francisca did a 3 year post-doc at CSIRO working on the epidemiology of pilchard orthomyxovirus, before taking up a position as a Senior Lecturer in the vet school at the University of Sydney.
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.
Danny did a 3 year post-doc at the Institute of Marine Research, Norway, before returning to Australia to work as a research scientist at the NSW Department of Primary Industries. He is now a Fisheries Scientist with ABARES.
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.
Sam is now a researcher in the Animal Welfare Group at the Institute of Marine Research, Norway.
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.
Camille is now a lecturer at the University of Tasmania.
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.
James was a post-doc at the University of Melbourne writing a field guide to the freshwater fishes of the Kimberley, was a freshwater ecologist at NIWA, New Zealand for 2 years, then moved to the Arthur Rylah Institute in Victoria as a freshwater ecologist.
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.
Matt is now an environmental consultant.
Cassie completed her Master of Science in 2017, was a research assistant in the SALTT laboratory, and has since moved to the Department of Agriculture and Water Resources in Canberra where she works on commercial fisheries policy and indigenous engagement.
Tormey completed her Master of Science in 2015, became a fisheries technician at The Pacific States Marine Fisheries Commission in the U.S.A. before moving back to Australia to start a PhD at the University of Tasmania.
Ella completed a PhD at the University of Melbourne on quoll behaviour and conservation. She now works for the Victorian Department of Environment, Land, Water and planning as a Conservation Biologist.
Cathy completed a PhD student at Monash University on penguin biology. She now works for Remember the Wild.
Kristal is now a PhD student at Deakin University.
Michael is now a post-doctoral researcher at Griffith University in Queensland. In 2021, was awarded a prestigious DECRA grant by the recent Australian Research Council round to work on the project Redefining success in marine ecosystem restoration. Using automated monitoring via artificial intelligence, Michael’s new project aims to improve evaluations of marine ecosystem restoration and how animal data can improve future restoration projects.