My research career began with larval fish ecology and biological oceanography before shifting towards the ecology of pelagic fish and the effects of fisheries during my PhD at the University of Sydney. During a post-doc at SINTEF Fisheries and Aquaculture, Norway, I began to research the ecological effects of aquaculture. My research interests have now converged to a common theme: basic ecological research, to ensure fishing, aquaculture and other anthropogenic practices are developed and conducted sustainably. While this theme has an applied angle, it draws strongly on fundamental principles of ecological theory.
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
My PhD thesis concerned animal habitat selection decisions and their consequences for fitness in marine environments modified by invasive species or aquaculture infrastructure. Now I’m working primarily on sustainability and animal welfare in marine aquaculture, with a focus on developing and validating new methods to prevent, monitor and control ectoparasitic louse infestations on Norwegian salmon farms (together with the Norwegian Institute of Marine Research and industrial partners).
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.
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.
CURRENT MSc STUDENTS
PAST PhD, MSc AND Hon. STUDENTS
Kathy completed an MSc working on the effects of parasite treatments in aquaculture before working as a research assistant in the lab. She now works as a research entomologist for CESAR Australia, a company that provides solutions to pest control for Australia agriculture.
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 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.
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.
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.
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.
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 at the University of Melbourne, I researched sustainable roe enhancement of the sea urchin Heliocidaris erythrogramma using capture-based aquaculture.
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 post-doctoral 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 is now a post-doc at CSIRO working on the epidemiology of pilchard orthomyxovirus.
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.
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 research fellow 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.
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 is now a PhD student at the University of Melbourne.
Cathy is now a PhD student at Monash University.
Kristal is now a PhD student at Deakin University.
Michael is now a post-doctoral researcher at Griffith University in Queensland.