Current PhD Projects

We have many exciting PhD projects already approved in our QAS, QMS and RHD programs.

If you don't see something that fits your interest or passion, please explore our find a supervisor tool, and get in touch with a supervisor who may be able to help you.

Acoustic characteristics of Antarctic krill in relation to their biochemical composition

Supervision Team

Dr Patti Virtue (supervision contact)

Dr Olav Rune Godø (Institute of Marine Research, Norway)

Dr Peter Nichols (CSIRO)

and others

Funding for a PhD student scholarship has been obtained through an ARC Linkage grant. This research will be done jointly through the IMAS and Institute of Marine Research, Norway. Antarctic krill are an important species in the Southern Ocean supporting most of the Antarctic birds and mammals. A sustainable krill fishery is developing with krill products used in aquaculture and increasingly for human consumption. A new omega 3 krill oil industry has emerged and is rapidly expanding. Our aim is to understand and predict the factors governing oil levels and the biochemical composition in krill in an ecological perspective, including impacts of distribution, growth, reproduction and recruitment.

The scientific elements of this PhD will include:

1. Experimental work over four seasons to investigate how the acoustic characteristics of krill are affected by oil content, maturation status, and behavioural characteristics

2. Investigation of the relative contribution of krill oil levels, krill shape sex and size to their acoustic characteristics

3. Investigation of krill distribution and stratification in the Antarctic over four seasons in relation to the conclusions from item 1 and in relation to krill lipid studies

There is a possibility that the student will join a krill acoustic survey team this summer (January 2016) to Antarctica aboard the RS James Clark Ross.

The PhD student will be involved in collecting acoustic and biological data during commercial fishing and scientific surveying of krill. The student will receive training in acoustics which will be the main tool for mapping krill density distributions in space and time. Uncovering acoustic backscattering properties of krill throughout their life cycle will be done in controlled laboratory experiments as well as through in situ observation, with an emphasis on utilising the potential of broadband acoustic techniques. The student will work together with two other PhD students in the project to link acoustic properties and behavioural characteristics to the observed variation in lipid contents or other physiological and biochemistry properties of the krill. The students will have access to krill experimental facilities and various sophisticated acoustic field equipment.

The PhD student will be based at the Institute of Marine Research (IMR) in Bergen, Norway and IMAS. They will be supervised by a research team as part of the ARC Linkage. The student will spend time in Bergen and Hobart and take courses both at University of Bergen and at UTAS.

Skills needed selection criteria of candidates:

First Class Honours (or equivalent) or Master's degree in a relevant discipline (eg physics, statistics, cybernetics and biological sciences).  Some basic knowledge in acoustics is desirable, and an interest to develop and apply acoustic technology to address biological questions. Ability to work at sea as part of an interdisciplinary team. Strong written and oral communication skills.

An evaluation of vertical nutrient fluxes and biological demand in the ocean (QMS)

Supervision team:

Peter Strutton

Helen Phillips

Predicting the trajectory of ocean productivity into the future requires that we understand the controls on that productivity in the present day ocean. Among the processes that contribute to vertical nutrient fluxes are vertical advection or upwelling, turbulent mixing and internal waves. To evaluate the importance of these processes it is necessary to compare their contribution to total nutrient fluxes with the biological demand.

This project will compare the importance of the major nutrient flux pathways across at least three contrasting environments: The Southern Ocean, Tasman Sea and tropical Pacific. Existing isotope-based measurements of biological nitrogen consumption will be combined with data on vertical nutrient gradients, thermocline displacement and vertical mixing. The outcome will be a better understanding of the major drivers of primary productivity in significant and contrasting ecosystems.

The PhD supervisors have partially assembled the necessary in situ data sets. The PhD student would analyse these data in the context of satellite productivity climatologies and seasonal to interannual variability. This could incorporate CMIP model projections to evaluate changes in nutrient fluxes, primary productivity and the ocean carbon cycle.

Assessing options for enhanced utilisation of Australia’s EEZ (Centre for Marine Socioecology)

This PhD project is available through the Centre for Marine Socioecology, an IMAS partnership with CSIRO and the Australian Government.

Supervision Team:

Stewart Frusher
Marcus Haward
Joanna Vince, UTas
David Smith, CSIRO
Tony Smith, CSIRO

The world's requirements for food, energy, recreation and transport are changing as our population rapidly increased to an expected 11 billion by 2050. The marine domain will be expected to play an increasing role to meet the needs of society. Already we are seeing discussion about offshore energy and food production systems in the Northern Hemisphere:

Australia has the third largest EEZ globally and thus there are opportunities to develop our offshore regions although this may require changes in policy and legislation.

The project addresses an identified need to develop transparent and equitable frameworks for the management of Australia's marine domain.

Current discussion on ocean management arises against a background of changing and expanding pressures on marine ecosystems – population growth, demand for seafood, impacts on marine systems, and changes in global biophysical and economic systems. A crucial challenge is the ability of governance arrangements to simultaneously achieve acceptable resource use across a range of resource futures and maintain the sustainability and resilience of communities.

This PhD project will initially provide a synthesis of current global activity in the (proposed) development of the offshore marine domain. This will also include the policy and legislation being developed and implemented by countries pursuing offshore development. A small number cases eg Australia, USA, Canada, Norway and the Netherlands are potential countries that can be examined as part of the the focus of the study

Norway and the Netherlands are chosen as non federal systems to provide a counterfactual to the effects of federalism, recognising that while Australia, USA, Canada are federal polities they have different ways of responsibility sharing within their political systems. The cross country comparison will provide a framework of analysis to be utilised during work in the second component of the study.

The second component of the project will be to evaluate the options for Australia including what legal, jurisdictional and governance issues may have to be altered to enable future development. This component will develop from and complement the works done in the first component.

Phase 1: Identify the requirements for a resilient and sustainable resource management regime by: an initial specification of requirements through literature study, document analysis and qualitative work with key informants.

Phase 2: Assessment of current arrangement against these requirements and identification of areas where reform or improvement is needed.

Phase 3: Assessment of potential regime reforms against the requirements for effective resource allocation will be undertaken

(i) Using participative scenario planning, which will again involve stakeholder input. Scenario planning is a tool that is used to develop three to four plausible futures in which to examine alternative resource allocation regimes and tools. Working with multiple scenarios allows consequences and appropriate responses to be examined under different circumstances. A variety of qualitative and quantitative data – social, institutional, economic and environmental – will be incorporated into the scenarios.

(ii) Application of Bayesian Belief Networks to allow modelling of the drivers, constraints and key variables identified in the workshops.

Phase 4 The results from the analysis will include recommendations for resilient and sustainable allocation regimes, tailored for the various Australian jurisdictional, resource and environmental contexts .

Find out more.

Biophysical modelling of Antarctic krill: key habitats, ocean transport and dependent marine predators

Supervision Team:

Dr Stuart Corney (supervision contact)

Dr Sophie Bestley

Krill play a central role in Southern Ocean foodwebs, and have a unique life cycle that utilises fundamentally different habitats at different life stages. This project will use biophysical modelling approaches to model krill habitat use at larval, juvenile and adult stages and to explore interactions with krill predators. The project will use output from a sea ice model and expand upon a set of recently developed algorithms to identify key areas for under-ice larval krill habitat, based on both food availability and habitat complexity. Transport modelling approaches will then be used to identify key locations for recruitment of juvenile krill to the adult population, and to relate these to large-scale patterns of krill flux, focusing in particular on the Indian Sector of the Southern Ocean. Evaluation and interpretation of these spatio-temporal predictions may utilise both ship-based observations of Antarctic marine predators (whales and flying seabirds) as well as available electronic tracking datasets (seals and penguins). These models will be used to evaluate potential responses of krill populations under IPCC climate change scenarios, and the associated implications for krill-dependent predators. Here there may also be scope to develop specific habitat suitability models for key CCAMLR indicator species such as Adelie penguins. Modelling approaches to represent habitat use by larval, juvenile and adult krill will help to inform our understanding of krill population responses to environmental change. These models will also contribute to informing management of the Southern Ocean krill fishery, and to interpreting interactions between krill prey and their dependent predators.

Calibration and application of radionuclide proxies of ocean productivity and circulation


Dr Zanna Chase  (supervision contact)

The long-lived naturally-occurring radionuclides, 231Pa and 230Th, are used in paleoceanography to reconstruct particle flux (productivity) and circulation, two key components of the climate system. Yet our understanding of the behaviour of these isotopes in the modern ocean is incomplete. To increase understanding of these and other elements, the international community launched GEOTRACES, a comprehensive study of the oceanic cycling and distribution of trace elements and their isotopes. The Australian GEOTRACES leg in the South West Pacific forms the basis of this PhD project. Additional samples may be collected in the Southern Ocean as opportunities arise. These measurements will be used to inform pale-reconstructions of productivity and circulation in the region from marine sediment cores. Measurements of 231Pa and 230Th will be made by isotope dilution ICP-MS.

Climate change and flows of energy and nutrients through polar microbial foodwebs

Supervision team:

Philip Boyd (IMAS, ACE CRC)

Andrew McMinn (IMAS, ACE CRC)

The project will use a combination of lab-based experimental chambers and field-based (shipboard) incubators to investigate the interplay between different tropic levels within the microbial foodweb. The following will be measured: uptake of DOC and bacterial secondary production, grazing on heterotrophic bacteria by a range of different microzooplankton grazers. This will enable the flows of energy to be estimated through the microbial foodweb. A parallel suite of rate measurements will be conducted to determine patterns of nutrient recycling by the microbes. The findings of this research will link with ecological modelling experiments to place the altered role of the microbial foodweb into a wider ecological context.

Climate variability influences on shy albatross populations and conservation under climate change

Supervision team:

Associate Professor Mary-Anne Lea

Rachael Alderman

Dr Alistair Hobday

This project will allow the student to develop a range of skills important for career development in marine science and address an important area of marine science – performance of biological systems under climate variability and change. While the focus is on a single species, the shy albatross, the methods and conceptual framework will allow extension to a broad range of species and contexts. The quantitative nature of this PhD is evidenced in the application of formal meta-analysis techniques, quantitative population models, and development and analysis of performance metrics (sensu Management Strategy Evaluation). The student will use historical data, generate new data from fieldwork on animals and humans (via surveys), and integrate these in decision-frameworks for use by conservation managers.

Climate-driven variability in tropical Pacific productivity (QMS)

Supervision Team:

Assoc Prof Peter Strutton

Richard Matear

(One other co-supervisor to be appointed with expertise in bio-optics and ocean remote sensing)

The tropical Pacific spans a quarter of Earth’s circumference and is the origin of the most globally influential mode
of climate variability: El Nino. Under normal conditions, upwelling leads to moderate productivity but also a large flux of CO2 to the atmosphere. During El Nino, upwelling, productivity and CO2 flux can be weakened or shut down entirely.

It is important that we understand not only the total variability in tropical Pacific primary productivity, but also the changes in phytoplankton community composition. These changes have consequences for the food web, and for export of carbon to depth.

This project would suit someone with an interest in large scale ocean variability at time scales spanning seasons to decades. The student will use a combination of the following data sets to understand changes in the tropical Pacific ecosystem:

  • output from global models that seek to simulate phytoplankton productivity and nutrient dynamics;
  • archival in situ measurements of nutrients and phytoplankton pigments;
  • profiling bio-optical observations of chlorophyll fluorescence, particulate backscatter and attenuation;
  • satellite estimates of total chlorophyll, particulate carbon and phytoplankton community composition.

There is also scope to develop regionally-tuned satellite algorithms.The goal of the project is to develop a more detailed understanding of the relationship between large scale climate modes and ecosystem function, including future changes.

Conceptual models and data science approaches for ingesting multiple data streams for ecosystem based management

Supervision team:

Professor Mark Hindell

Dr. Chris Wilcox

Management of human uses of the marine environment is increasing moving from a single sector and impact basis to a more integrated approach. The recent move to integrated spatial planning, such as Australia’s Marine Bioregional Plans or the global push to implement Ecosystem Based Fisheries Management are clear examples of this shift. While these new integrated approaches promise better outcomes, both for the environment and the users, they suffer from significant challenges. The availability and cost of data to underpin management is a particularly significant challenge.

In the context of ecosystem based management of fisheries one approach to this issue has been to balance coverage and resolution in data collection across multiple methods, in an attempt to get synthetic information across the system but at an affordable cost. For instance, vessel movements can be monitored from tracking systems, which provide high levels of coverage at very low costs. However, these data only provide indirect information on fishing effort and potentially catches. Sampling vessels returning to port allows measurement of a subset of catches, improving the resolution of the data. However the cost of this activity necessitates a lower level of coverage. The highest level of detail comes from observers on vessels, where all fishing activities and catches are directly recorded in real time. These efforts are typically very limited due to cost and logistics, generally covering 5% or less of the total fishing effort.

This project will develop a conceptual model, and linked statistical models, that can be used to unify these disparate data sets. Concepts from animal foraging theory will be used to interpret vessel movement data in the context of likely fishing success, allowing linkage to landings and observer data. Observer and landings data will be interpreted from the perspective of sampling theory, using heterogeneity in movement behaviours based on VMS to identify strata across fisheries, companies and vessels and to identify appropriate methods for scaling sampling data from these sources up to cover the fisheries as a whole.

Determining and understanding changes in sea level over the last century

Supervision Team:

Professor Richard Coleman (supervision contact)

Dr John Hunter (CSIRO)

Dr John Church (CSIRO)

Global average sea level rose 10-20 cm over the past century and could rise as much as 80 cm during the present century, due primarily to global warming (from the Third Assessment Report of the Intergovernmental Panel on Climate Change (IPCC), 2001). While we are quite confident about the historic rate of rise of global sea level, we know little about the regional variation of that rise, especially in the Southern Hemisphere where there is a dearth of observational data. We also know little about changes in extreme sea level heights (e.g. due to storm surges) during the last century. It is, however, important that we understand what happened in the last century if we are to predict what will happen during the present century.

There exists, both in Australia and overseas, a large and relatively unexplored data set, originating from coastal tide gauges. However, many of these data sets are not presently referenced to standard vertical height datums, some contain errors (which are, in many cases, correctable), and a significant number are not yet in digital form. This represents a considerable problem of resource allocation, in the sense that there will probably never be sufficient resources to satisfactorily analyse all existing tide gauge records. We therefore have to select the most appropriate historic records (i.e. those that will provide useful data in a required region, and for which there is a reasonable chance that reliable datum information will be found).

Over the past decade, sea-level height has also been monitored by a number of orbiting satellites, using radar altimeters. The near-global coverage allows us to make good estimates of global sea-level rise, although the limited time-span precludes estimation of sea-level rise prior to about 1990. A recent analysis by researchers from the ACE CRC has used the satellite data to infer the spatial variability of sea level rise, and the tide gauge data to infer the time history. Such a combination of tide gauge and satellite data has yielded a reconstruction of sea level at high spatial resolution over the globe, covering much of the 20th century.

We are therefore gaining a quite good understanding of the way in which sea level varied during the 20th century. We do, however, have a significant problem in accounting for the observed rise in terms of the water budget and thermal expansion. For example, the IPCC Third Assessment Report could only account for around one half of the observed sea level rise. There is therefore a concerted international effort to improve our understanding of the various contributions to the observed sea level rise.

The project would seek to both quantify and understand one or more of the aspects of historic sea level rise noted above. Possible projects would include:

  1. The analysis of historic Australian and regional tide gauge records in order to improve the coverage of sea level data in this data-sparse part of the world.
  2. The development of techniques to synthesise sea level records from different sources (e.g. tide gauge records from a number of locations and satellite observations) in order to generate global and regional reconstructions.
  3. The analysis of tide gauge records in order to improve our understanding of extreme sea levels and of how, and why, they have changed during the past century.

The analysis of the results of numerical models of the ocean/atmosphere system in order to improve our understanding of various contributions to sea level rise.

Developing biomarkers of salmon farming: tracing feeds in the environment

Supervision Team:

Dr Louise Adams

Dr Catriona Macleod

Prof Chris Carter

FRDC has approved a three-year, $900,000 project to assess the impact of sediments from Tasmanian salmon farms on adjacent or nearby rocky reef systems and the potential for interactions with other marine industries. The study will provide information to help managers provide for the sustainability and future expansion of fish farming, and will describe existing impacts on other commercial and recreational users. 

For many months now commercial and recreational fishers and farmers have complained publicly about sediments, referred to as dust, which they believe have come from salmon farms impacting important productive reef systems in southern Tasmania. Tasmania's coastal reef systems support significant fisheries for a range of species that include trumpeters, morwongs, wrasse, rock lobster and abalone.  

A key concern is whether there may be adverse effects on reef health (i.e. off-site interactions) as a result of increased aquaculture activities. Therefore a key element of the main FRDC study will be to provide a better assessment of the potential risk to reef systems from sediment deposition and nutrient dispersion from fish farms directly. Whilst the study will use modelling to predict the risk associated with the deposition of farm derived sediments to the ecology of reef habitats in new farming regions, and will seek to identify cost-effective and risk appropriate approaches for assessment of reef health, it is not within the scope of the study to evaluate effects on abalone directly. Consequently, this PhD project is proposed in association with the main study to provide a better understanding using biomarker accumulation rates of how waste feed/ faeces from salmon farming might directly influence abalone, and to what extent abalone might take up nutrients resulting from fish farming. The study will also compare these laboratory derived accumulation rates with loadings in fish collected from the wild (FRDC study areas) to assess natural loadings and the influence of trophic interactions.

Development of culture techniques for the native oyster, Ostrea angasi, to maximise farm production and restore reef habitat.

Supervision team:

Dr Christine Crawford

Dr Jeff Ross

Dr Sarah Ugalde

In recent years there have been various attempts in Tasmania and South Australia to culture the native (flat) oyster, Ostrea angasi, but they have never developed into a major industry, largely because Pacific oysters have been easier and faster to grow. However, with the recent outbreak of OsHV-1 virus causing Pacific Oyster Mortality Syndrome (POMS), a number of oyster farmers have expressed interest in culturing Angasi oysters. Research is needed to support this developing industry, including determining the best husbandry techniques, influence of different environmental conditions, and disease management (such as Bonamiosis). In addition, this project will investigate methods, such as modified atmospheric packaging, to extend the current short shelf life (2- 3 days) of 0. angasi, which has severely limited market potential. 

Additionally, over the last decade there has also been increasing interest in restoring natural O.angasi reef habitat in estuaries and bays of southern Australia. Before European colonisation, this oyster formed extensive and dense reef habitat; however, early settlers indiscriminately overfished these reefs and this habitat is now considered to be functionally extinct in Australia. In Tasmania small and patchy low relief O.angasi reefs (beds) exist close to several Pacific oyster farms and farmers are keen to restore these reefs in conjunction with efforts to develop the O.angasi aquaculture industry. These two activities can support one another as the same resources are required, such as a source of 0. angasi spat that can be ongrown under different semi-controlled husbandry and environmental conditions. This project will add to existing knowledge of O.angasi reproduction, seed collection, predation, disease management and husbandry techniques under different conditions.

Dynamical downscaling of near-shore marine climate, extremes, and biogeochemistry around Southeast Australia (QMS)

Supervision Team:

Dr Eric C. J. Oliver (supervision contact)

Assoc Prof Neil J. Holbrook

Dr Mark Baird (CSIRO)

The surface waters of southeast Australia are warming at almost four times the global average rate (Holbrook & Bindoff, 1997; Ridgway, 2007), and this warming is associated with the multi-decadal intensification of the South Pacific gyre and southward extension of the nutrient-poor East Australian Current (EAC). This warming is projected to increase under anthropogenic-driven climate change (Matear et al, 2013) and may lead to dramatic changes to extreme ocean temperature events off southeast Australia, not only in terms of their increased frequency, but also their persistence – known as "marine heat waves" (Oliver et al., 2014). Much effort has focussed on understanding the offshore warming and forcing mechanisms (e.g., Cai et al., 2005; Cai, 2006; Sun et al., 2012; Oliver and Holbrook, 2014). However, comprehensive investigations of the coastal effects of this warming have been limited due to the paucity of coastal oceanographic observations and absence of high-resolution model data across the continental shelf.  The large-scale warming of Australia's southeast region is nevertheless expected to have implications for biological productivity and, by extension, human interests in the region such as fisheries and species conservation.  In particular, the impact of this warming on coastal marine heat waves, which are poorly understood in this region, are of great interest.  It is important to understand how this dramatic change in Australia's southeast regional marine waters is related to, and affects, the shallow waters of the continental shelf.

High-resolution predictions of ocean variability on Australia's continental shelf are essential for characterising how the complex near-coastal marine climate (e.g., circulation, temperature, salinity) and ecology will change in the coming decades.  Existing observations are too sparse in time and space to adequately characterise the ocean variability that define the relevant coastal oceanographic processes at the scales of ecological importance. Efforts to provide reanalysed ocean variability using data-assimilative numerical models have had success in predicting the large-scale ocean circulation but the model designs have limited the accuracy of predictions of ocean variability on the continental shelf (e.g., Bluelink ReANalysis, or BRAN). Some regions have employed high-resolution regional models to address this limitation through dynamical downscaling (e.g., using: SAROM in South Australia; SEAPOM in New South Wales; eReefs for the waters of the Great Barrier Reef) but there has not been a regional-scale downscaling effort for the continental shelf around Tasmania.  We intend to develop and implement a high-resolution regional model for southeast Australia (focused at first on Tasmanian waters) to downscale BRAN and future marine climate projections onto the continental shelf.  This will enable questions to be answered regarding changes in marine climate on the continental shelf at scales and locations that are in line and more consistent with the biological changes that have been observed, and are of concern into the future.

Skills Needed to Complete Project:

First Class Honours (or equivalent) or Master's degree in physical oceanography, physics or mathematics required. Desirable skills include familiarity with computer programming languages (C, FORTRAN, MATLAB), ocean dynamics, and time series analysis.

Ecophysiology and ichthyotoxicity of the dinoflagellate Noctiluca scintillans


Professor Gustaaf Hallegraeff

Noctiluca scintillans red tide frequency and distribution has increased in Tasmanian waters, Australia since the first sighting in 1994 and severely threatened Tasmanian aquaculture farms in 2002. We seek to identify key prey items for this phagotrophic dinoflagellate in Tasmanian waters from combined culture and field studies, as well as aim to elucidate the production of anoxia, ammonia or polyunsaturated fatty acids as the mechanism for fish morbidity and mortality.

Ecosystem Reflexivity and the Effectiveness of Marine Governance (Centre for Marine Socioecology)

This PhD project is available through the Centre for Marine Socioecology, an IMAS partnership with CSIRO and the Australian Government.

Supervision Team:

Jeffrey McGee
Julia Blanchard
Marcus Haward
Aysha Fleming, CSIRO
Tony Smith, CSIRO

This PhD project aims to develop and test cutting edge theory for improving the design of institutions for marine governance at an international, regional and/or national scale.

Our current era is considered by many as 'The Anthropocene', which is dominated by human impacts on the Earth's ecosystems pushing us past physical, biological and human limits. The effective management of changes in human activities in the face of extreme events and ecosystem change requires resilience in governance and institutions. Dryzek (2014) therefore recently proposed 'ecosystem reflexivity' as key component of institutions that are required in the Anthropocene. However, to date research on the ecosystem reflexivity of institutions has been primarily theoretical and conceptual and would benefit from further empirical testing.

Adopting a socio-ecological systems perspective and building on methods that have been used for the analysis and modeling of marine ecosystems, this PhD project will develop a framework for exploring Dryzek's recent work on ecosystem reflexivity of environmental institutions for the Anthropocene. The project will combine use of the international environmental regimes database (Breitmeier, Young and Zürn 2006) with in-depth case study analysis of institutions relating to marine governance such as the Convention for the Conservation of Antarctic Living Marine Resources, Agreement on the Conservation of Albatrosses and Petrels or regional fisheries institutions.

The project will combine insights from the above qualitative and quantitative approaches to address the following key questions on the design, operation and effectiveness of institutions for the governance of marine resources and environments in the Anthropocene:

* How might ecosystem reflexivity be measured and used in the design of institutions for marine governance?

* How does ecosystem reflexivity contribute to the effectiveness of institutions for marine governance?

* Does the impact of ecosystem reflexivity on effectiveness change with the scale of the institution involved?

* What are the policy implications of designing for ecosystem reflexivity? What lessons can be learnt from the case-study institutions in this regard?

Find out more.

Ecosystem service 'offsets' and aquaculture: determining equivalence and acceptability of environmental and social impacts and benefits

Supervision Team:

Dr Emily Ogier

Associate Professor Catriona Macleod

Dr Dugald Tinch

Dr Karen Alexander

The concept of offsets, though well developed and applied in terrestrial resource-based and energy sectors, has not been tested in marine-based aquaculture. This project examines the applicability of offsets as an instrument to achieve optimal social, economic and environmental returns from marine ecosystem services from marine-based aquaculture activity. Using a case study of Integrated Multi Tropic Aquaculture in Tasmania, this project will develop and test ecological, economic as well as social criteria for determining the equivalence and acceptability of impacts and benefits generated by proposed offsets. It will compare the outcomes of combinations of public policy settings and proposed offset strategies in order to inform both marine spatial planning and ecosystem-based management processes, and models of sustainable and socially-supported aquaculture production.

Effect of ocean acidification on physiology and growth of Antarctic krill

Supervision Team:

Dr So Kawaguchi (supervision contact)

Dr Kerrie Swadling

Researchers at the AAD have recently shown that early embryonic development of krill is inhibited by ocean acidification caused by increased CO2 levels (Kawaguchi et al. 2011, 2013). This project aims to assess the sensitivity of Antarctic krill to ocean acidification using laboratory-based experiments. This information will then be used to identify how factors such as CO2 level, temperature, and food affect growth and metabolic parameters of krill, and to refine existing krill growth models.

Effects of ecomoorings for habitat restoration and threatened species management.

Supervision team:

Dr Rick Stuart-Smith

Dr Jeff Ross

Dr Tim Lynch

Balancing coastal development and conservation of benthic ecosystems and endangered species

There is an increasing demand for mooring infrastructures for recreational boats. Most moorings are currently based on the traditional block and chain or“swing” design, which utilised a heavy chain and have direct mechanical impacts on the benthos. Not only do swing moorings have widespread impacts on seagrass and soft sedminent systems worldwide, but in south-east Tasmania, these also reduce microhabitat complexity for the critically endangered spotted handfish (Brachionichthys hirsutus). New mooring desigs exist which should theoretically reduce impacts on the benthos, and handfish, such as the taut ecomooring, which utilise a bungee component to absorb the forces, However, the ecological, socioeconomic and conservation benefits opf these have not been assessed.

This project will focus on investigating the effect of taut ecomooring deployment on benthic ecosystem and assessing the effectiveness of taut ecomooring on restoring critical habitat in soft sediment system. This project will include field survey near moorings in Tasmania to survey changes in epibenthic community and benthic geomorphology, as well as investigate potential synegestic effect between biofouling, mechanical disturbance and marine pests. Using the field data, this project will also construct species disturubiton and disturbance/recovery model for epibenthic community over various spatial and temporal scales to support the population viability analysis on the B. hirsutus population.

Feedbacks between the Antarctic Ice Sheet and the global ocean circulation

Supervision team:

Steven Phipps (click here to email Steven for more information)

Zanna Chase

Taryn Noble

Ben Galton Fenzi (AAD, ACE CRC)

The nature of the relationship between the Antarctic Ice Sheet (AIS) and the global ocean circulation remains uncertain. Proxy evidence suggests that cooling oceans lead to reduced melting of the AIS, increased formation of Antarctic Bottom Water (AABW) and a colder and saltier deep ocean; in contrast, warming oceans lead to increased melting of the AIS, reduced formation of AABW and a warmer and fresher deep ocean. These changes in ocean circulation have important implications for the global carbon cycle. Understanding of these processes is critical if we are to be able to predict future changes in the AIS, the global ocean and the nature of ocean-climate coupling.

This project will use the history of Antarctica and the Southern Ocean over the past glacial cycle to explore the feedbacks between the AIS and the global ocean circulation. State-of-the-art models will be used to simulate ice-ocean interactions, with a particular emphasis on ice shelf dynamics, and to test dynamical hypotheses. Proxy data from the Southern Ocean will be used to inform the experimental design and to validate the model simulations.

The researcher will use the Parallel Ice Sheet Model (PISM) to simulate the response of the Antarctic Ice Sheet to changes in ocean temperatures. During the first year, targeted regional experiments will be performed. The magnitude and distribution of the ocean temperature anomalies used to drive PISM will be guided by proxy data. Sensitivity experiments will also be performed to explore uncertainty arising from model parameterisations. During the second year, the CSIRO Mk3L climate system model will then be used to study the effects of the simulated Antarctic meltwater fluxes on the global ocean circulation. The proxy data will be used to validate these experiments. Finally, during the third year of the project, additional experiments using PISM and/or CSIRO Mk3L will be used to test dynamical hypotheses.

This project will suit candidates with a physical science/engineering background and well-developed numerical analysis skills. Experience in compiling and running scientific software will be highly advantageous for the purpose of completing the model experiments.

Generating 3D structures of seabed biota from cross-shelf marine environments using autonomous underwater vehicle imagery to examine temperate biodiversity

Supervision team:

Dr Neville Barrett

Dr Jacquomo Monk

Dr Vanessa Lucieer

Reef habitats face a diverse array of threats, from eutrophication and overfishing to climate change.  Reefs below water depths of 40m, host sponges and corals that provide the majority of biological 3D structure and are potentially critical in maintaining productivity through pelagic-benthic coupling. If these organisms are destroyed through anthropogenic or natural disturbances, the structural complexity and productivity of these reefs decline. This may have important consequences for the survival and growth of reef fish as these complex habitats mediate predator-prey interactions, provide food, and influence competition through the provision of refugia. Yet, measuring the biogenic structural complexity of the seabed at biologically meaningful scales is not trivial.

Structural complexity of the seabed is measured in a variety of ways; with a recent focus on photogrammetry and structure-from-motion (SfM) techniques. These techniques use a series of overlapping images, taken from multiple perspectives to reconstruct the 3D structure of the seabed including the associated habitat-forming organisms at high resolution and accuracy.

This project will explore how stereo imagery from autonomous underwater vehicles can to provide novel 3D structural information on deep-water temperate marine reefs.

Getting the right combination of controls and nudges to address complex compliance problems in high value fisheries

Supervision team:

Professor Caleb Gardner

Dr Emily Ogier

Dr Ingrid van Putten

Dr Suadi

This project involves refining wild fisheries regulations for a specific (although common) situation where large numbers of loosely regulated fishers target small individual catches of high value species for recreational, cultural, or commercial purposes. Examples of this situation include Australian recreational harvests of bluefin tuna, abalone, and lobster; Australian indigenous harvests of tropical rock lobster; and Indonesian artisanal commercial harvests of rock lobster respectively. 

Regulation of fishery with small quantities but high value catches is especially challenging regardless of whether the catch is sold or not. The high desirability of the target species combined with the enforcement challenge posed by numerous fishers creates a complex management problem. Fishers will continue to target these species even when stocks are depleted and catch rates are low. The economics of this situation (including for recreational fishers) means that normal market processes will fail to protect the stock. Given this recipe for stock depletion, management controls are critical but enforcement is difficult when there are numerous (sometimes dispersed) participants. For example, Indonesian artisanal fishers find loopholes to avoid enforcement and land undersize lobsters, while in Australia recreational fishers circumvent daily bag limits by doing multiple daily trips and catch sharing with friends. 

A modern approach to improve outcomes in these difficult resource management problems is to incorporate human behavioural response into the design of regulations. That is, try to create systems that nudge people towards more responsible fishing practices through positive reinforcement and indirect suggestion and thus changing the fisher's decision making environment. For example, people can be fined for littering (regulations) but the more effective deterrent to littering has been the creation of social norms that nudge behaviour - so few people litter nowadays even when there's zero risk of detection. This approach is used in numerous aspects of public policy but is under-explored in fisheries although appears to have great potential. This would seem especially the case in fisheries where regulations are currently in place but perceived ineffective or prone to non-compliance. For these fisheries, that may have distinct fisher characteristics and stock attributes, different combinations of fisheries regulations and nudges can be explored.

Gill necrosis in farmed Atlantic salmon

Supervision team:

Professor Barbara Nowak

Dr James Wynne

This is an exciting opportunity to work on a salmon industry related project in Tasmania with worldwide applications. Gill health is essential for fish performance. There are a range of gill conditions affecting Atlantic salmon while in grow out cages. One of the less investigated but not uncommon pathologies Is gill necrosis. The project will focus on potential causes of gill necrosis and risk factors including environmental factors (for example hydroids, other biofouling, plankton, temperature), effect of gill health in hatcheries and the presence of pathogens and other microorganisms on the gills at the time of necrotic changes. The outcomes will include improved understanding of the gill necrosis including potential management strategies based on the risk factors. 

The research addresses an important issue in salmon farming, includes both laboratory analysis (histology, transcriptomics, proteomics) and field work as well as analysis of large data sets.

High resolution modeling of the retreat of the East Antarctic Ice Sheet since the Last Glacial Maximum

Supervision Team:

Professor Matt King (supervision contact)

Dr Ben Galton-Fenzi

There is great uncertainty surrounding the degree to which the Antarctic Ice Sheet has contributed to sea level since the Last Glacial Maximum (LGM). The vast East Antarctic ice sheet is particularly poorly understood. This PhD project will use a high resolution ice stream/ice shelf model in order to better understand the retreat history of one of East Antarctica's major drainage basins, the Amery Ice Shelf/Lambert Glacier system. Model runs will be performed in order to best-fit geological and geodetic constraints, examining the response of the ice sheet to changes in ice-shelf basal melting, accumulation and relative sea level change. Extensions to this work include application to other major glacier/ice shelf systems and incorporation of the results in a model of Earth's response to ice-ocean loading changes, known as glacial isostatic adjustment. The project will use published ice history data and other publicly available data. Simulations will be performed using grants and allocated resources within the National Computing Infrastructure and the Tasmanian Partnership for Advanced computing.

Holocene variability of the Totten Glacier, East Antarctica

Supervision Team:

Dr Taryn Noble

Associate Professor Zanna Chase

Associate Professor Ashley Townsend

Current projections of future sea level rise suggest only modest increases in the mean global sea level by the end of the twenty-first century, but with large uncertainties. One source of uncertainty arises because current sea level projections do not include ice sheet-ocean dynamic feedbacks, whereby a warming ocean accelerates the rate of ice-sheet melting. Recent evidence suggests this mechanism may result in level rise of 40 cm by 2100 with a future commitment of up to 10 m if global air temperatures continue to increase to greater than 2o C above pre-industrial values. Ocean-forced instability of the Antarctic ice sheet has been observed in marine sediment cores  and ice sheet modelling, and recent evidence suggests an inter-hemisphere atmospheric control on ice-ocean feedbacks. Furthermore, recent work indicates that the Antarctic ice sheet experienced much greater variability during the Holocene period than previously thought.

There is growing evidence for on-going changes in Southern Ocean and atmospheric circulation, which may have already contributed to accelerated melting of ice shelves buttressing Antarctic glaciers. Given the large potential impact on sea-level, there is an urgent need to understand the mechanism of ice-ocean feedbacks, and the stability of the Antarctic ice sheet. This project will address these needs using recently collected sediment cores from the continental slope adjacent to the Totten Glacier, East Antarctica. Multiple geochemical proxies will be used to reconstruct millennial-scale ocean and ice sheet dynamics to understand the East Antarctic’s ice sheet response to climate change.

Impact of climate change on Australia's climate drivers and water resources (QMS)

Supervision Team:

Assoc Prof Neil Holbrook

Dr Peter McIntosh (CSIRO)

The response of climate variability to climate change forcing is one of the most important issues in climate research. Australia's highly variable climate is influenced by climate drivers such as El Nino - Southern Oscillation (ENSO), the Indian Ocean Dipole (IOD), the Southern Annular Mode (SAM) and the mid-latitude long-wave pattern and related atmospheric blocking. Climate-change induced modifications to the characteristics of these modes may result in significant changes to the variability and extremes in Australia's temperature, rainfall and evaporation. These changes may require substantial adaptation by climate-sensitive sectors such as agriculture, water resources and the urban environment.

Coupled ocean-atmosphere climate models are being used to make predictions of climate change and climate variability. These models explicitly represent climate processes on all timescales, from long-term climate change, through interannual climate variability down to daily weather systems. It is important that we understand how accurately climate models represent these processes in the past in order to gain confidence in their predictions. Where dynamical processes are not modeled well in comparison to observations, there is an opportunity to diagnose the causes and improve the models.

To inform planning and management decisions in climate-sensitive industries, it is imperative that climate models give accurate predictions, and that the level of accuracy is known for climate variables that are of most importance for the sector. For example, in rain-fed agriculture the rainfall distribution during the growing season is just as important as the rainfall total.

The main climate model used in this study will be ACCESS, the Australian Community Climate and Earth-System Simulator. The ability of this model to simulate the key drivers of Australian climate variability will be assessed. Are the model representations of ENSO, IOD, SAM and atmospheric blocking sufficiently accurate? If so, how do these climate modes change as the climate changes? What model deficiencies are revealed by these studies? Is it possible to improve the representation of key climate features in ACCESS?

For many industries in Australia the important climate variables are rainfall, temperature and evaporation, and their variability on daily, monthly, seasonal and annual timescales. The ability of ACCESS to make predictions about these key variables will be assessed. For example, does the model represent accurately the daily distribution of rainfall, and the way in which this varies from year-to-year? How does rainfall variability change due to climate change, and what are the implications for agriculture, water resources and other sectors dependent on climate?

Impact of nutritional and environmental factors on the proteome and gene expression in Atlantic salmon

Supervision team:

Professor Chris Carter

Dr Andrew Bridle

Dr Richard Wilson

Dr Waldo Ortin-Nuez

This is an exciting opportunity to link in with international research on salmonids, Atlantic salmon, rainbow trout and chi nook salmon, and to gain skills and experience in forward looking technology around molecular biology and recirculation aquaculture systems. The research will focus on understanding the impact of nutrition and environmental change under controlled conditions on large Atlantic salmon. Environmental variables include temperature, salinity and pH because these impact on industry performance and sustainability. Nutritional variables include feed formulation and ration. Feed formulation will be done in consultation with industry partners.

Your research will advance fundamental knowledge about the Atlantic salmon proteome and how proteomics can be used to understand drivers of growth and growth efficiency. The project will develop proteomic based methods and relate this to gene expression based approaches. The research will contribute to sustainable aquaculture by understanding what happens to salmon when exposed to various situations that may be encountered in aquaculture. It will equip you with a range of new skills from maintenance of fish to advance molecular analyses.

Impact of nutritional and environmental factors on the proteome and gene expression in chinook salmon

Supervision team:

Professor Chris Carter

Dr Andrew Bridle

Dr Richard Wilson

Dr Matthew Miller

This is an exciting opportunity to link in with international research on salmon id species (Atlantic salmon, rainbow trout and chi nook salmon) and to gain skills and experience in forward looking technology around molecular biology and recirculation aquaculture systems. The research will focus on understanding the impact of genome (family) and environmental change under controlled conditions on chi nook salmon. Environmental variables include temperature, salinity and pH because these impact on local NZ industry performance and sustainability. Your research will advance fundamental knowledge about the chinook salmon proteome and how proteomics can be used to understand drivers of growth and growth efficiency. The project will develop proteomic based methods and relate this to other molecular based approaches. The research will contribute to sustainable aquaculture by understanding what happens to salmon when exposed to various situations that may be encountered in aquaculture. It will equip you with a range of new skills from maintenance of fish to advance molecular analyses.

Improved ice flow relations for ice sheet modelling: laboratory and model studies

Supervision Team:

Adam Treverrow (ACE CRC, UTAS)

Jason Roberts (AAD, ACE CRC)

Roland Warner (ACE CRC), AWI Collaborators (Alfred Wegener Institute, Germany)

The numerical relation describing the flow properties of ice is a fundamental component of models used to predict the dynamic evolution of the Antarctic Ice Sheet. In this project a comprehensive program of laboratory ice deformation experiments, combined with microstructural analyses will be used to improve the numerical relationship governing ice flow rates in ice sheet models. In particular, the effects of complex flow configurations and temperatures close to the melting point will be investigated experimentally with results used to develop an improved flow relation which will be evaluated using a regional-scale ice sheet model.

Improving environmental management to protect nature’s fish hatcheries: identifying risk factors for mercury bioaccumulation in seagrass beds and estuarine wetlands.

Supervision Team:

Dr Catriona Macleod

Dr Jeff Ross

Dr Sean Riley

Prof Bill Maher (University of Canberra)

Metal contamination is a feature of many urbanised estuaries. Mercury (Hg) is of particular concern because it readily bioaccumulates up food chains, with potentially critical consequences for the health of ecosystems. It is primarily the methylated form of mercury (MeHg) that has implications for wildlife and human health. Most MeHg is produced in sediments, where the less toxic inorganic Hg is methylated by bacteria into a highly toxic species, MeHg (Ekstrom et al., 2003). This process can be influenced by a range of environmental factors that either directly affect the methylation process or the availability of Hg species for transformation. It is well documented that certain areas within estuaries can be mercury methylation "hotspots"; areas such as wetlands and seagrass beds. Anaerobic conditions tend to underpin the sediment biogeochemistry in these areas, which results in enhanced microbial sulfate reduction (an anaerobic process that is a key driver of mercury methylation). These areas also tend to be significant nursery habitats for estuarine and coastal fish species and as such, represent an important, but poorly understood, risk pathway for trophic bioaccumulation and a threat to fish stocks.

Mercury contamination is a key issue for the Derwent estuary, with current levels detected in sediments and biota being well above nationally recommended environmental and human health guidelines. While some heavy metals in the most heavily contaminated areas of the Derwent are declining in response to industry regulation/mitigation activities, Hg remains a significant concern due to its persistence and bioavailability. A public health warning issued in 2011 advised against eating fish from the catchment area based on research showing that mean Hg concentrations of key recreationally caught fish species exceeded the FSANZ guidelines (Verdouw et al., 2011). Recent research has shown that Hg levels in fish species within the estuary are inherently tied to the background environmental loadings, but that other biogeochemical processes can influence bioavailability and toxicity (Jones et al., 2013a,b).

This PhD project will explore Hg cycling in methylation "hot spots" in the Derwent estuary. The project will investigate methylation processes and biological transfer pathways with a view to identifying the environmental conditions that both promote and moderate mercury bioavailability (toxicity), in such areas. Changes to the sediment biogeochemistry either as a result of natural ecosystem dynamics or as a result of specific interventions (i.e. active remediation or management strategies) will influence the mercury methylation potential and as such, the mercury bioaccumulation risk for juvenile fish species that populate these habitats.

This project will inform understanding of the pathways for mercury bioaccumulation and link the chemistry and biology in these "hotspots" to identify those environmental conditions that present the greatest risk to juvenile fish. This information will be used to model the key interaction and risk pathways, which will in turn allow testing of potential management strategies for these habitats. This will ensure more effective management and remediation actions. Worldwide, many estuaries face a similar fate to the Derwent, and the lessons learnt here will be useful additions to the knowledge base as authorities elsewhere try to find the best way to monitor, manage and minimise the impacts of Hg contamination.

A key component will be the development of a qualitative (and potentially semi-quantitative) model identifying the relationships between sediment biogeochemistry, biology, and environmental conditions in these "hotspots". This research will underpin management strategies for these areas specifically, and will provide much needed information to support management of Hg contamination in temperate estuaries more broadly. The Derwent Estuary Program strongly supports this project and is willing to provide resources to support the research. The study is well aligned with their strategic management objectives for the overall remediation of the estuary. The project outcomes will provide valuable scientific input for ongoing management and the implementation of effective mitigation strategies for Hg contamination in the Derwent estuary.

Investigating subglacial hydrological meltwater production, distribution, and flow in East Antarctica

Supervision Team:

Felicity Graham (click to email Felicity for further information)

Jason Roberts (AAD/ACE CRC)

Leo Peters (IMAS)

The flow of ice is very strongly controlled by conditions at the base of the ice sheet, including the type of rock or sediment and the presence of liquid water. This has large implications for not only the flow of the ice sheet, but the mass balance of the ice sheet, and hence impacts on both sea-level change and circulation in the oceans. This project will explore the subglacial hydrological environment beneath the little studied East Antarctic Ice Sheet. The candidate will make use of new airborne geophysical data and numerical modelling to quantify the production, distribution, and flow of sub-glacial water in East Antarctica.

Investigation of changes in atmospheric storm tracks and East Antarctic surface accumulation

Supervision Team:

Dr Petra Heil (supervision contact)

Dr Jason Roberts

The Antarctic ice sheets are a critical component of the dynamic link that couples the spatially and temporally varying components of the Earth system. Recent ice-shelf break-up (e.g. the Larsen and Wilkins ice shelves) and glacier tongue disintegration has increased the exposure of the Antarctic ice sheet and may lead to changes in the mass and geometry of high Antarctic ice masses. This project will focus on quantifying the processes that affect moisture flux onto the East Antarctic ice sheet, and their subsequent effects on the East Antarctic surface mass balance and geometry. Data will include meteorological data from automatic weather stations and manned observatories (station, vessels), and remotely-sensed parameters. Numerical models will be used to characterize the effects of these parameters on the surface accumulation of the ice sheets.

Isochrones in the ice sheet: Internal layer structure of the East Antarctic ice sheet from ice penetrating radar

Supervision Team:

Jason Roberts (AAD, ACE CRC)

Duncan Young (U Texas at Austin, USA)

Adam Treverrow (ACE CRC, UTAS)

Changes in atmospheric acidity, for example from volcanic eruptions, are captured by falling snow which is subsequently buried by additional snow falls and is advected into the interior of the ice sheet. These changes in acidity cause changes in the dielectric properties of the ice, and can therefore be detected by ice penetrating radar, and the layers may extend for hundreds to thousands of kilometres and reflects the current location of what was the surface at some time in the past. This project will use the spatial distribution of such isochrones and depth dating from ice cores to study palaeo-accumulation, basal melt and ice dynamics.

Key drivers of Antarctic ice edge blooms (QMS)

Supervision team:

Associate Professor Peter Strutton

Dr Richard Matear

Associate Professor Andy Hogg

Retreating sea ice can trigger extensive accumulations of phytoplankton biomass (blooms) in spring and summer, by stratifying the surface ocean and releasing sea ice algae and nutrients. This is one of the classic ocean examples of light and nutrients occurring in the same place at the same time to stimulate ocean productivity. Other prominent examples include the temperate spring blooms like the North Atlantic, and coastal upwelling systems. These high productivity events are sites of significant carbon uptake and potential export to sediments, and they are ecological hotspots of enormous ecological and economic importance.

Around Antarctica, ice edge blooms are temporally and spatially patchy and ephemeral. Their physical and biological drivers remain unclear. The objective of this project is to quantify the importance of several different processes in triggering ice edge phytoplankton blooms. The project will use a combination of satellite observations and model output to determine when and where ice edge blooms occur, how variable they are, and the physical drivers of that variability.

Linking tracking data and foraging theory to understand the behaviour of fishermen and identify suspicious activities.

Supervision team:

Professor Mark Hindell

Dr. Chris Wilcox

Satellite-based vessel monitoring systems (VMS) were designed for fishery control and surveillance, but they provide potentially valuable source information on spatial and temporal patterns of fishing vessels activity (Craig et al, 2007). By analysing the movement of fishing vessels during fishing trips, we can understand how fishermen conduct fishing activities, using theory from foraging ecology as a unifying paradigm. The insights from statistical models of these space-time patterns can help us understand key features of the foraging strategies used by fishermen, and link those behaviours with relevant fisheries management measures.  Together these linkages can be used to identify pending management failures and identify priorities for surveillance and enforcement.

Marine heat waves in the southeast Indian Ocean (QMS)

Supervision team:

Dr Helen Phillips

Prof Nathan Bindoff

Dr Ming Feng (CSIRO)

Although the concentration of atmospheric greenhouse gases has been increasing at an accelerating rate for the past decades, the average rate of global surface air temperature rise has remained constant since the start of the 21st century. This apparent inconsistency was termed the global warming hiatus and was highlighted in the IPCC Fifth Assessment Report. England et al. (2014) suggested that a persistent la Nina state, in conjunction with intensified trade winds, caused enhanced heat uptake in the Pacific Ocean, accounting for the “missing” heat in the atmospheric climate system. Despite having absorbed additional heat, the heat content of the upper Pacific Ocean has not increased over the past decades. Rather, the absorbed heat has been transported into the Indian Ocean via the Indonesian Throughflow. This export stimulated the redistribution of heat to depths (> 50), making it unavailable for the atmospheric climate system and therefore contributing to the slower rise in surface air temperatures. The local changes in distribution of heat and salt associated with this heat export remains unknown. In particular, the impact of these watermasses modifications on Indian Ocean currents is yet to be studied. There has been increasing trend of marine heatwaves (MHWs) in the southeast Indian Ocean during this climate change hiatus period.

As a result of global ocean warming, MHW have been increasingly observed around the world oceans (Hobday et al. 2016). MHWs have dramatic impacts on local climate and biological systems. For example, a MHW event along Western Australia in 2011 resulted in +5oC sea surface temperature anomalies in the Leeuwin current, causing widespread coral bleaching and increased fish mortality. Such extreme events are driven by intense strengthening of the poleward Leeuwin current, which transports warmer water farther south. This atypical eastern boundary current is maintained by a strong meridional pressure gradient partly forced by intrusions of fresher and warmer waters through the ITF. There are likely to be significant changes in the Indian Ocean under climate change, such as an increase of salinity gradients in the eastern Indian Ocean due to global warming would increase the meridional pressure gradient and strengthening currents near the eastern boundary. It is uncertain how these large scale changes would impact on the MHW frequency and intensity.

This project will investigate the following key questions for Australia and the Eastern Indian Ocean region:
1) Based on Hobday et al. (2016) characterisations of MHW, what is the impact of the decadal climate variations such as the climate change hiatus on the frequency and intensity of MHWs?
2) How does the Leeuwin current respond to a warming Indian Ocean?
3) How will the likelihood of MHWs in the southeast Indian Ocean change under climate change?

Metrics for phytoplankton physiological status in the Southern Ocean

Supervision team:

Professor Philip Boyd

Dr Christina Schallenberg

Professor Tom Trull

Dr Robert Strzepek

A key limitation to confident estimates of global ocean productivity, and thus its contribution to food security, is lack of information regarding the physiological status of phytoplankton. Assessment of their photosynthetic competency in time and space is a crucial requirement for improved estimates and models of oceanic productivity. This is especially true for areas such as the Southern Ocean, where excess nutrients open the possibility of enhanced productivity, and production is currently limited by lack of the trace element iron (Fe). This project will focus on developing metrics for the status of phytoplankton health, with emphasis on Southern Ocean species and physiological stress due to iron limitation. In particular, the project will involve the use of optical techniques that offer the possibility of rapid, non-invasive assessment, including via robotic profiling sensors and satellite remote sensing. The student is expected to conduct a diverse mix of oceanographic field work and laboratory incubations. The experimental results will inform efforts to extend existing models of phytoplankton physiology to simulate fluorescence characteristics, including their expected responses to light and iron stress. In addition, working with satellite and autonomous float observations, and developing/improving biogeochemical and ocean circulation models are also encouraged.

Metrics for phytoplankton physiological status in the Southern Ocean (QMS)

Supervision team:

Professor Philip Boyd

Dr Christina Schallenberg

Professor Tom Trull

Dr Robert Strzepek

A key limitation to confident estimates of global ocean productivity, and thus its contribution to food security, is lack of information regarding the physiological status of phytoplankton. Assessment of their photosynthetic competency in time and space is a crucial requirement for improved estimates and models of oceanic productivity. This is especially true for areas such as the Southern Ocean, where excess nutrients open the possibility of enhanced productivity, and production is currently limited by lack of the trace element iron (Fe). This project will focus on developing metrics for the status of phytoplankton health, with emphasis on Southern Ocean species and physiological stress due to iron limitation. In particular, the project will involve the use of optical techniques that offer the possibility of rapid, non-invasive assessment, including via robotic profiling sensors and satellite remote sensing. The student is expected to conduct a diverse mix of oceanographic field work and laboratory incubations. The experimental results will inform efforts to extend existing models of phytoplankton physiology to simulate fluorescence characteristics, including their expected responses to light and iron stress. In addition, working with satellite and autonomous float observations, and developing/improving biogeochemical and ocean circulation models are also encouraged.

Microscope PAM fluorometry as a predictive phytoplankton tool


Professor Andrew McMinn (supervision contact)

Professor Gustaaf Hallegraeff

Recent technological advances in PAM (pulsed amplified modulated) fluorometry now allow us to characterize photosynthetic parameters of single algal cells viewed under a light microscope. This project seeks to apply this new toll to monitoring seasonal phytoplankton succession in the Derwent River with the aim to predict blooms of individual species and identify critical environmental variables.

Mining information on historic plankton records over long time scales: sediment depth cores assessed by microfossil and ancient DNA approaches

Supervision team:

Professor Gustaaf Hallegraeff

Professor Andrew McMinn

An exciting PhD research opportunity is open for a talented graduate student to assemble how Australia’s coastal plankton ecosystems have fluctuated over the past 50 to 1000 years with respect to algal and jellyfish blooms, impacts from introduced species, climate change and increased human utilisation of coastal resources. This PhD research program will analyse dated sediment cores from New South Wales and Tasmanian coasts and estuaries, using a combination of traditional microfossil and cutting edge ancient DNA technology. In pilot studies we were able to newly detect aDNA of very numerous taxa that do not produce microscopic fossils.

The project is funded by the Australian Research Council and supervised by Professors Gustaaf Hallegraeff and Andrew McMinn. It is based at the Institute for Marine and Antarctic Studies (IMAS) of the University of Tasmania, and conducted in collaboration with the Australian Centre for Ancient DNA (ACAD) of the University of Adelaide and Australian Nuclear Science and Technology Organisation (ANSTO).

Graduates with a strong academic record in Earth or Biological Sciences, and strong microscopic and computing skills are encouraged to apply. Experience in molecular genetics is desirable but not essential. Applications for this PhD position are open to domestic and international students, provided the latter are competitive when applying for fee waiver scholarships.

Modelling the cycle of iodine: sea to air, air to land surface

Supervision Team:

Dr Edward Butler (CSIRO) (supervision contact)

Dr Andrew Seen

Dr Jill Cainey (CGBAPS)

Dr Ole Hertel (NERI, Denmark)


Iodine is decisively a marinogenic element; its delivery to the land (and to terrestrial life) depends on the efficiency of its transport from the sea to the land surface via the atmosphere. The deficiency of iodine in many regions of the global land-mass remains a pivotal issue for human health, as it does for agriculture—especially that of raising livestock.
The sea-air transfer of iodine is enhanced proportionately over the other halogens chlorine and bromine by volatile forms of iodine (organic and inorganic) formed in surface seawaters by biological and photochemical processes. These iodine volatiles in the atmosphere are extremely reactive. They are not only capable of catalytic decomposition of ozone, but they also form very fine aerosols that can influence global climate.

Delivery of iodine to land surfaces is either by wet or dry deposition, but a third pathway also exists with the uptake of gaseous iodine (e.g. methyl iodide) by plants and soils. The extent of retention of iodine is determined by the nature of the soils and the physiology of the plants. Regardless of the importance of either soils or plants in intercepting iodine, neither can be considered as lasting repositories for the halogen. Iodine's reactivity ensures that it is either volatilised back to the atmosphere, or solubilised in surface run-off to enter again into the hydrologic cycle.
For the reasons touched on above—iodine's role in key atmospheric processes (cloud-condensation nuclei, albedo, and ozone destruction) and the efficiency of its transfer to land surfaces that ultimately underpins the nutrition of all higher terrestrial animals—it is critically important to be able to predict and understand the pathways, cycling and ultimate distribution of iodine throughout Earth's ecosphere.


The broad goal of this project is to develop a predictive, numerical model to describe the sea-air flux of iodine, its reactions and cycling in the atmosphere, and deposition to/emission from land surfaces. It is expected that the model will be calibrated and validated against relevant Tasmanian environmental data on iodine.

The PhD study can either involve: The development of a broadly based model to cover the full path (sea to air to land), or focus on development of a more detailed module (or nested model) for the full model—e.g. evasion of iodine from the sea, and its entry and cycling in the 'reactive iodine pool' in the atmosphere.

An associated task will include participation in the collection of atmospheric iodine data, relevant to the model, at the Cape Grim Baseline Atmospheric Pollution Station in North-West Tasmania.

The focus for this study will be the island of Tasmania and its surrounding seas. The reason for this is that a useful data set has been, and continues to be, obtained for the distribution and the biogeochemistry of iodine in the regional sea through the collaboration of Institute of Antarctic and Southern Ocean Studies (University of Tasmania), CSIRO Marine and Atmospheric Research and the Antarctic Climate and Ecosystems Cooperative Research Centre. This is importantly complemented by the measurements of atmospheric iodine compounds by the Cape Grim Baseline Air Pollution Station (joint Bureau of Meteorology/CSIRO Facility) on the north-western tip of Tasmania. Furthermore, records exist in Tasmania relating to iodine deficiency in the island's landscape (e.g. state-wide distribution of goitre among livestock). This complete database on iodine provides the basis for calibrating and validating the model.

The development of the model is vitally dependent upon the modelling expertise (and model code) of the Danish National Environmental Research Institute—a principal partner in this project. For example, their DEHM-REGINA long-range transport model is seen as a likely key tool in the project. Local expertise, such as that involved with oceanic transport and biogeochemical models, and the resources of the CSIRO Atlas of Regional Seas, will also be required to construct the iodine model. It is also conceivable that satellite data (e.g. estimated chlorophyll) will contribute to this work.

Given the key role of the National Environmental Research Institute at Roskilde in Denmark, the PhD student is expected to make a number of short-term visits to this facility during their candidature.

New and improved environmental surrogates for the Southern Ocean and their utility for quantifying and predicting biological patterns

Supervision Team:

Dr Nicole Hill (supervision contact)

Professor Philip Boyd

The Southern Ocean and Antarctica are vast and remote and collecting in situ physical and biological data is challenging. Information from satellites, oceanographic floats, and other remotely sensed data provide synoptic information about the physical environment of the Southern Ocean that can be integrated into numerical or statistical models and validated with in situ data. This is an effective approach to maximising the utility of sparse biological data. The aim of the project is to improve the variety, coverage and/or resolution of key physical variables currently available for the Southern Ocean and Antarctica, evaluate their usefulness for describing biological patterns and to use these variables, in conjunction with other variables, to enhance our understanding of the distribution of benthic and pelagic organisms. The broad objectives are to (a) utilise existing physical datasets and numerical or mechanistic models to extend the spatial coverage of and, in certain regions, downscale estimates of key ocean variables (for example carbon flux and pH) (b) contribute to the development of new physical variables to characterise the biologically-relevant properties of the Southern Ocean at a range of spatial scales and resolutions, and (c) evaluate and apply these surrogates for describing and predicting patterns in the distribution of zooplankton and benthic invertebrate organisms.

Optimisation of water quality parameters to model recirculation aquaculture system (RAS) performance

Supervision Team:

Professor Chris Carter (supervision contact)

Dr Mark Adams

Associate Professor John Purser

Dr David Wright (PanLogica Pty Ltd)

Recirculation Aquaculture Systems (RAS) use recirculation technology to maintain water quality through physical, chemical and biological treatment in order to reduce water exchange and address issues such as biosecurity, production costs and nearness to market. RAS are increasingly important in aquaculture including Atlantic salmon farming ( ; Carter 2015). RAS can be used across the Atlantic salmon life-cycle: eggs and young animals are maintained in freshwater and then transferred to seawater. In Tasmania, the salmon farming industry uses and continues to develop more sophisticated freshwater hatcheries based, however the salmon are then on-grown in the sea. However, the University of Tasmania is building an experimental facility (EAF) that will employ RAS technology for research on large salmon in seawater. IMAS also runs several freshwater RAS.

RAS employ various types of software and models and the aim of this PhD is to understand the characteristics of input and output data required for optimisation software. The optimisation software is provided by PanLogica, a world leading supplier of optimisation software to the global aquaculture industry,  and the student will work with PanLogica and IMAS on both freshwater and seawater RAS production optimisation.    

Project outline, objectives and methods

This research aims to develop an understanding of how to optimise the use of freshwater recirculation systems according to the proprietary optimisation models developed by Panlogica. Research will first focus on collecting and assessing the importance of different model parameters that relate to inputs such as volume of water used, water quality measurements, characteristics of salmon used, fixed costs and running costs. These data will be used to improve the optimisation model, improved versions of the model will be tested and further improvements made (and to reduce the amount of data collected). The last experiment will be designed to test the optimisation model. 

The proposed research will be organised in the following sequence and to complete four experiments (Chapters 2 to 5). The approach and direction of the research is likely to change in relation to information from the first two experiments and to take advantage of any opportunities to work with commercial operations.

Chapter One. Literature review of software and modelling used for RAS. (first publication)

Chapter Two. Data collection and analysis of usefulness for developing optimisation models for freshwater RAS.

Chapter Three. Improved modelling for freshwater RAS based on identification of critical data characteristics.

Chapter Four. Modelling a comparison of two or more different design features for a freshwater RAS.

Chapter Five. Testing software and manipulation of systems. Final benchmarking and independent comparison of predicted against datasets.

Chapter Six. General Discussion

Optimise data collection and develop robust tag-based assessment strategies for exploratory fisheries (QMS)

Supervision team:

Paul Burch

Klaas Hartmann

Philippe Ziegler (AAD)

Rich Hillary (CSIRO)

The Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) is responsible for the sustainable management of Antarctic and Sub-Antarctic fisheries. Toothfish fisheries around South Georgia, on the Kerguelen Plateau and in the Ross Sea are assessed with integrated stock assessment models that use tag-recapture data as their main indices of abundance. In addition, many exploratory fisheries are in development within the CCAMLR Convention area for which integrated assessment models have not been developed yet due to insufficient data.

Assessing these exploratory fisheries is challenging due to their relatively low catch levels and paucity of data, as well as spatial issues such as fish movement and annual variability in access of fishing grounds due to sea ice. This project will use simulation modelling to optimise data collection and develop robust assessment strategies for these fisheries.

Perspectives in Marine Conservation: CCAMLR as a Case Study for Marine Resource Management Strategies (Centre for Marine Socioecology)

This PhD project is available through the Centre for Marine Socioecology, an IMAS partnership with CSIRO and the Australian Government.

Supervision Team:

Dirk Welsford, AAD
Marcus Haward

There is increasing movement towards evidence-based management for marine resources around the globe. However, the requirement for scientific evidence of human impacts to inform and enable decision-making is somewhat at odds with the precautionary approach to management, which calls for preventive actions in the face of uncertain information about risks. The Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) is regularly cited as an example of a management organization that has successfully applied the precautionary approach to achieve conservation objectives for marine environments1 . Indeed the 2011 Deep Sea Conservation Coalition (DSCC) named CCAMLR as one of the only fisheries management organizations to have implemented resolutions put forth in 2009 by the United Nations General Assembly (UNGA)2.

This project will assess current strategies for management of marine resources in the CCAMLR convention area as a case study to examine the relationship between evidence based management, CCAMLR's precautionary approach, and the growing need for adaptive decision making in the context of climate change impacts on marine social-ecological systems.

Find out more.

Predictability of the interaction between El Nino Southern Oscillation and the tropical Indian Ocean (QMS)

Supervision team:

Assoc Prof Neil Holbrook

Dr Terry O'Kane

Dr Peter McIntosh

El Nino Southern Oscillation (ENSO) is a global, seasonal climate anomaly controlled by ocean-atmosphere interaction in the central and eastern equatorial Pacific Ocean . Climate anomalies in the monsoon systems of Australia , Asia and Africa are also modulated by ocean-atmosphere interaction in the tropical Indian Ocean , where the dominant pattern is the recently discovered Indian Ocean Dipole (IOD) or zonal mode. ENSO can influence IOD by an atmospheric tele-connection but IOD also is able to grow on its own. This study will assess the mechanisms that control IOD and its predictability.

Protein turnover in Chinese perch

Supervision Team

Professor Chris Carter

Associate Professor Greg Smith

Dr Louise Adams

Professor Zhong-Yang HE

Professor Qing-Jun SHAO

The research aims to understand the protein metabolism of Chinese perch or Mandarin fish (Siniperca chuatsi) through linking nutrient requirement experiments to amino acid flux and aspects of protein turnover. Mandarin fish is a valuable aquaculture species in China and annual production is approximately 300000 tonnes. The development of formulated pelleted feeds remains challenging and provides an opportunity to conduct nutrient requirement research on protein, energy and essential amino acids. This information will provide a basis for increasing the efficiency of protein use and improve commercial feeds. Protein turnover combines two energetically expensive systems, protein synthesis and protein degradation. The quantity and quality of dietary protein have major impacts on protein turnover and therefore the efficiency of using protein. The PhD will combine nutrient requirement experiments with measuring components of amino acid and protein metabolism.

Practical components of the research will be carried out at the Zhejiang Provincial Ocean and Fisheries Bureau and the student will conduct field work in Hangzhou, Zhejiang at the Zhejiang Technical Extension Centre. This is an excellent opportunity to contribute to the development of an important aquaculture species and experience aspects of Chinese aquaculture (which accounts for 2/3 of the world's aquaculture production).

Quantify the impact of glacial melt water on Antarctic bottom water formation

Supervision Team:

Dr Ben Galton-Fenzi (supervision contact)

Dr Guy Wiliams

John Hunter (ACE CRC)

Dr Steve Rintoul (CSIRO)

The Antarctic ice sheet is formed by the accumulation of snow over millennial timescales. The accumulated ice flows, under gravity, to the ocean as glaciers where they may begin to float as ice shelves. Ice is added to an ice shelf by inflowing glaciers and net snowfall on the upper surface, while ice is lost by melting at the ice-shelf base and iceberg calving from the front. The ice flux from Antarctica into the ocean is thus strongly influenced by the mass loss processes occurring beneath the ice shelves and through iceberg calving. These processes are important for the formation of deep water (e.g. Antarctic Bottom Water or AABW), which occurs in the shelf seas around Antarctica and ventilates the abyssal oceans.

AABW has been observed over the past few decades to be freshening. One hypothesis for the freshening is the increased melting of ice shelves in response to global warming. However, we do not yet fully understand the processes that link coastal Antarctic ocean processes to ice-shelf melting and dense water formation. The research project will seek to answer the following questions:

  1. What are the oceanographic processes that govern the production of glacial melt water?
  2. What role does glacial melt water have on the formation and export of AABW?
  3. How is production of glacial melt water and AABW likely to change in the future?

Outline, Objectives and Methods:

Of particular relevance to the project is the role of coastal latent heat polynyas as a source of dense water in the region of the Mertz Glacier Tongue (MGT). Water that circulates onto the continental shelf is modified through sea ice formation processes and interaction with the base of the MGT. It is known that the resulting water mass has sufficient density to become Antarctic Bottom Water (AABW) as it flows into the deep abyssal ocean. Buoyant glacial melt water that is released during the melting process rises along the underside of the ice shelf and is transformed to Ice Shelf Water (ISW). The glacial melt water can become locally supercooled at a shallower depth, leading to the formation of frazil ice and basal accretion of marine ice.

The interaction of the atmosphere with the MGT/ocean system is currently being investigated at ACE CRC using a modified version of the Rutgers version of the Regional Ocean Modeling System (ROMS). Initial results suggest that the circulation on the shelf region is seasonally controlled by the production of dense water from polynyas. The dense water also acts to block warmer waters from the open ocean moving onto the shelf region, leading to lower melt rates of the MGT during winter. The project would seek to both quantify and understand one or more of the aspects of the interaction processes that occur between the Antarctic ice sheet and the oceans. Focussing on the region of the Mertz glacier tongue, projects could include:

  1. The analysis of historic oceanographic observations in conjunction with the development and evaluation of a numerical ocean model, in order to better understand how glacial melt water can modify the production of AABW, on annual and inter-annual time scales.
  2. Determination of the sensitivity of AABW production to mixing with glacial melt water, using numerical models forced by various climate scenarios.
  3. Quantification of the production rate of glacial melt water from Antarctica and determination of the way in which it manifests as ISW.
  4. Examination of the exchange of heat and mass flux between the open ocean and the sub ice-shelf cavity.
  5. Examination of the impact of iceberg calving on glacial melt water production and dense water formation, with a particular focus on the recent calving event of the Mertz Glacier tongue.

Skills needed to undertake this project:

  • Essential: An undergraduate degree in mathematics/physics or related disciplines
  • Desirable: Familiarity with numerical code

Quantitative analysis of phytoplankton populations using pigment markers

Supervision Team:

Dr Simon Wotherspoon (supervision contact)

Dr Simon Wright

Photosynthetic pigments (chlorophylls and carotenoids) are widely used as biomarkers to determine the abundance and taxonomic composition of phytoplankton populations. However, interpretation of pigment data is difficult because of the great diversity of pigment patterns in algae, and because the pigment content of each taxon can be variable. The CHEMTAX software, developed by CSIRO and the AAD, is the prime analytical tool for pigment-based marine ecology worldwide. This project will study recent developments in this field, including Bayesian methods (van den Meersche et al. 2008, Whiten et al. 2011), develop new software for use by the world's oceanographic and limnological communities, and study methods to improve analysis where ecological gradients (e.g. latitude or time) cause changes in the pigment ratios or communities.

Relationship between gut microbiome and health in chinook salmon

Supervision team:

Professor Barbara Nowak

Associate Professor John Bowman

Professor Chris Carter

Dr Jane Symonds

This is an exciting opportunity to link in with an international team focussed on improving the performance, feed conversion efficiency and health of chi nook salmon farmed in New Zealand.

The research is centred on assessing the relationship between gut rnicrobiome and health in chinook salmon and how they are related to fish performance. Initially the research will focus on gut microbiome in salmon farmed in sea cages and on freshwater farms to compare gut microbiome from commercially farmed Atlantic salmon growout stage at two different environments as well as investigate any relationship between gut microbiome and other health markers and fish performance. The next step will be to compare gut microbiome and health markers in a number of families held under the same environmental conditions to evaluate the effect of family on gut microbiome and the relationship between the gut microbiome,other health markers, gut capacity and fish performance. The methods will be assessed to determine their suitability as diagnostic tools for fish health and welfare, both on the farm and within experimental tank based trials. 

The microbiome investigation will be applied in trials to compare the bacteria in the gut in feed efficient and inefficient salmon of known genetics. All microbiome research will be supported by gut histology, Including morphometry and other assessments of gut performance. This will provide a comprehensive picture of the health and performance of each salmon investigated and identify the influences of gut health on feed conversion efficiency. The research will advance fundamental knowledge about chinook salmon health, in particular gut health (microbiome and histology), and develop important analytical tools that can be used on farm to improve husbandry and welfare and in trials to understand how health influences fish performance. It will equip the student with a range of new skills to advance fish health management and will contribute to sustainable aquaculture.

Response of the Larsen C Ice Shelf system to changes in grounding line forcing from numerical modelling

Supervision team:

Matt King

Sue Cook (ACE CRC)

Felicity Graham

One of the most intriguing glacier observations of the last decade or so has been that the velocity of many large glaciers varies substantially from its long-term mean due to tidal variation in the zone where the glaciers begin to flow – their grounding zone (Anandakrishnan et al. 2003; Gudmundsson et al. 2006, 2011; Winberry et al. 2011; Rosier et al. 2015). Such changes in motion have been observed using GPS on large West Antarctic glaciers, with the changes propagating tens of kilometres upstream. Combined with modelling, they provide unique insights into the interaction of the ice and its bed, the role of subglacial water, and the sensitivity of glaciers to modest changes in forcing (e.g., Rosier et al. 2015).

In parallel the floating extension of entire glacier systems, the ice shelves, have also been observed to experience tidal modulation of their flow (Doake et al. 2002; King et al. 2011; Makinson et al. 2011). These include the large Ross and Ronne ice shelves, fed by large ice streams tens of kilometres wide, alongside the smaller Larsen C Ice Shelf (King et al. 2011) fed by relatively small glaciers by Antarctic standards. The precise link between the modulation of flow of grounded and floating ice is yet to be fully established.

The Larsen C Ice Shelf system's response to tidal forcing is little studied to date, in particular the upstream glaciers, and this PhD will focus on modelling the response of the Larsen C system to tidal forcing in an attempt to understand the characteristics of the glaciers feeding the ice shelf and their sensitivity to changes in forcing in their grounding zone.

The candidate will construct a viscoelastic finite element model of the Larsen C system. Modelling will commence with the creation of an idealised model of a single glacier being forced in its grounding zone, followed by the extension to a larger floating ice shelf. The role of subglacial water will be considered. The model will then be extended to 3D with realistic 3D geometry, created using existing airborne geophysical data which provide ice elevation and bedrock geometry. Spatially continuous ice velocity data are also available for model tuning. GPS data from the floating and grounded ice sheet provide both the tidal forcing and the surface velocity response, the latter acting as model validation. The final model will yield new insights into the sensitivity of this relatively northern glacier system to changes in forcing in its grounding zone.

Salmon farm nutrients: can production conditions change environmental loadings and impacts?

Supervision Team:

Dr Catriona Macleod

Dr Jeff Ross

Professor Chris Carter

Provide the context of the project that demonstrates the reason for doing the work and its relevance to IMAS research priorities.  The statement should clearly illustrate the relationship between this proposal, work done previously and other work in progress. Bear in mind that this will be used in the description of the project on the Web.

The Salmon industry in Tasmania seeks to double production by 2030, but achieving this will require both new farm production approaches and expansion into new areas. Maintaining high environmental performance (a priority for both the industry and its regulators) requires an understanding of how farming in new areas might affect the environment. To ensure that management remains best practice, and farms continue to be efficient and sustainable, a reliable understanding of the local and broader scale impacts and potential interactions with other resource users are required. A research project funded by the FRDC has just commenced that will undertake a mix of modelling, field based studies and targeted experiments, with a view to characterising the extent of farming impact and identifying indicators that can be used to monitor for near and far-field impacts. The identification of suitable assessment sites will largely be based on modelling outputs, with targeted experimental studies then located at sites to assess environmental conditions before and after farming.  This study will be undertaken in all of the current salmon farming regions (Lower Huon/ Channel, Storm Bay, Macquarie Harbour).

  • In Macquarie Harbour the emphasis will be on validating local scale monitoring approaches (on-site focus)
  • In the Southern regions a key element of the research will be identifying the potential for cost-effective and risk appropriate approaches for assessment of reef health (off-site interactions). 
  • Models will provide an important predictive tool for determining risk to the ecology of both soft sediment and reef habitats in new farming regions.

Dispersion modelling will be used to link off-site assessments to local scale studies, specifically to identify exposure to nutrients and sediments from fish farms.  Ultimately, the deposition and dispersion models will provide an important predictive tool for determining risk to the ecology of soft sediment and reef habitats in areas where salmon farming occurs.

Dispersion modelling is used to identify the "footprint" of the farms either in terms of actual sediment deposition or the extent of nutrient dispersion. This estimate relies on accurate evaluation of the initial nutrient content of the feed/ waste material source. The leaching and degradation rates in these models are currently based on values from studies undertaken over 10 years ago and, whilst potentially quite conservative, these values would benefit from validation based on a more accurate and recent assessment based on diets currently in use.

Sensitivity of the ocean's overturning circulation to changes in climate (QMS)

Supervision Team:

Dr Maxim Nikurashin (supervision contact)

Dr Steve Rintoul (CSIRO)

Dr Andy Hogg (ANU)

The meridional overturning circulation (MOC) is a planetary-scale oceanic flow which is of direct importance to the climate system: it transports heat meridionally and regulates the exchange of CO2 with the atmosphere. The MOC is forced by wind and heat/freshwater fluxes at the surface and turbulent mixing in the ocean interior. The MOC is closely tied to the distribution of water masses in the ocean and consists of two overturning cells: the upper cell, corresponding to sinking of dense water mass in the North Atlantic, and the lower cell, corresponding to sinking of the densest water mass around Antarctica. Paleoclimate reconstructions suggest that the MOC was quite different in past climates: the boundary between the two overturning cells was substantially shallower and the strength of the MOC was likely weaker during the Last Glacial Maximum than in the present climate. Various studies suggest that variations in the MOC may have been responsible for the low CO2 in the atmosphere in glacial climates.

While being crucially important for the climate system, the dynamics of the MOC remain poorly understood. A number of conceptual theories have been developed and tested with idealized numerical simulations. However, the relevance of simple conceptual theories to the MOC simulated with higher complexity models or observed in nature still remains unclear. The overall goal of this project is to test and further improve our understanding of the dynamics that governs the MOC in the ocean. The project will focus on the sensitivity of the MOC to changes in forcing conditions across models with various complexities, ranging from simple theoretical models to realistic ocean and/or coupled general circulation models (GCMs). A few specific objectives of the project are:

  • Design an idealized numerical simulation of the MOC with a GCM and carry out sensitivity experiments with different ocean geometry, physical parameters, and forcing conditions
  • Simulate the MOC with realistic ocean and/or coupled GCM and explore its sensitivity to changes in forcing conditions
  • Analyze the results from both sets of simulations and compare them to theoretical predictions

Results of this project will improve our understanding of the response of the ocean's overturning circulation to changing climate and hence the role of the ocean in past and future climates.

First potential publication: "The impact of the non zonally-symmetric wind and buoyancy forcing on the overturning circulation of the ocean".

The student will need an undergraduate Mathematics and/or Physics Degree.

Submesoscale Physics and Iron Biogeochemical Modelling (QMS)


Prof. Philip Boyd at IMAS

Dr Richard Matear at CSIRO

For more details please contact Philip Boyd (

The biogeochemistry of trace elements in the Australian sector of the Southern Ocean: GEOTRACES-SR3 repeat section from Tasmania to Antarctica

Supervision team:

Associate Professor Andrew Bowie

Dr Pier van der Merwe

Dr Melanie East

Dr Kathrin Wuttig

The Southern Ocean influences climate, sea level, biogeochemical cycles and marine productivity on global scales. Observations suggest that rapid change is already underway in the Southern Ocean, but the measurements are sparse and hence the nature, causes and implications of Southern Ocean change are not yet understood. This project will contribute to a multi-disciplinary observational program measuring a comprehensive suite of physical and biogeochemical variables along a full‐depth repeat hydrographic section extending from Australia to the Antarctic sea ice edge.

The candidate will join a research team on a 42 day voyage of the Marine National Facility’s Research Vessel ‘Investigator’ in early 2018 that will study the marine biogeochemistry of trace elements and their isotopes (TEIs) along the SR3 section (~140oE), a signature field program of the ACE CRC. Following the fieldwork, the candidate will participate in laboratory analyses and experiments using state-of-the-art facilities and instrumentation to determine the distributions, physico-chemical form and sufficiency of micronutrient trace elements in the Southern Ocean, and their relationships to changing environmental conditions. In the latter stages, this project will feed vital information on the prevalence and flux of trace elements into biogeochemical and ecosystem models of the region.

The ecological role of Squalus acanthias in Macquarie Harbour and its relationship with marine farming

Supervision Team:

Dr Jeremy Lyle

Dr. Justin Bell

Associate Professor Jayson Semmens

Squalus acanthias is a common, small, demersal shark that inhabits cool temperate waters throughout the world. They are long-lived, slow growing, have a low reproductive output and have been shown to be vulnerable to anthropogenic impacts.

A discrete population of S acanthias appears to be resident in Macquarie Harbour, a large estuarine system in western Tasmania that is also the location of large-scale salmonid aquaculture operations. The species has apparently thrived in Macquarie Harbour and, because of their opportunistic feeding behaviour, now feed predominantly on aquaculture-derived sources. These include fish pellet overfeed and fauna that is displaced from aquaculture cages when they are cleaned. However, there has been a marked decline in dissolved oxygen concentrations throughout much of Macquarie Harbour in recent years, the impact of this change on the native fauna, including S acanthias is largely unknown.

Given the unique characteristics of this S. acanthias population, this project will aim to investigate the ecological role of the speciesinMacquarie Harbour. In particular, it will investigate the physiological tolerances of S. acanthias with respect to the environmental conditions encountered in the Harbour and the role the species plays in removing aquaculture-derived sources of organic matter.

The global importance of benthic-pelagic coupling for the ecosystem function of coastal reefs

Supervision team:

Dr Rick Stuart-Smith

Associate Professor Julia Blanchard

Dr Asta Audzijonyte

Although the world’s major fisheries mostly occur in temperate zones and are driven by pelagic primary productivity, the largest biodiversity, tropical fish biomass (and food for coastal communities in the tropics) is found in shallow reef habitas. Yet it still remains unclear whether coastal reefs act as largely self-sustained systems or strongly depend on primary productivity from pelagic areas. In order to improve management of reef resources and predict impacts of habitat loss (corals in the tropics and kelp in the temperate zone) on ecosystem dynamics it is essential to understand the importance of alternative primary production pathways supporting coastal reef systems.

This project will focus on investigating the relative importance of pelagic versus different types of benthic primary production (coral, macroalgal, microphytobenthos) on shallow reefs. It will use a combination of chemical tissue analyses from reef organisms, field data on biomass partitioning across trophic groups and benthic cover estimates from the Reef Life Survey global database. The project will include field work from Tasmania up to the tropics to collect samples and record local habitat characteristics, laboratory work for stable isotope analyses and statistical analyses to interpret results and extrapolate the findings across other reefs in the global Reef Life Survey database.

The impact of atmospheric drivers on ice shelf basal melting

Supervision team:

Ben Galton-Fenzi (AAD, ACE CRC)

David Gwyther

Jason Roberts (AAD, ACE CRC)

Sea level rise originating from Antarctica is difficult to quantify. Mass loss occurs through iceberg calving and ice shelf basal melting. While calving can be observed from satellite, large-scale surveys of basal melting are logistically impossible. Yet, ice shelf basal melting is thought to be the most important driver of sea level rise, as relatively warm ocean waters can melt deep grounded ice and therefore accelerate the flow the Antarctic Ice Sheet into the ocean.

Numerical modelling is an optimum tool for investigating basal melting. Using a state-of-the-art numerical model, modified for ice shelf-ocean interaction, the successful applicant will investigate basal melting of several ice shelves, with a particular focus on East Antarctica. Atmospheric interaction will be explored through coupling of sea ice - atmosphere - ocean models, with a focus on quantifying drivers of basal melt.

The successful applicant for this project will ideally have numerical experience and/or a background in physics, mathematics or oceanography.

The importance of individual quality in determining population trajectories in a long-lived seabird

Supervision team:

Professor Mark Hindell

Dr Clive McMahon

Associate Professor Mary-Anne Lea

Persistence of animal populations is determined by the balance of new individuals (thorough birth or emigration) and individuals leaving the population (through death or immigration). For many years it was assumed that broadly speaking all individual contribute more or less equally to the birth/recruitment part of this equation, but recent research suggests that in fact a disproportionate number of animals recruited are from a small number of high quality individuals. This has important ramifications for understanding the dynamics and viability of animal populations.

This study uses long-term demographic data from the Fisher Island short-tailed shearwater study population to quantify the importance of individual quality to the population trajectory of the long-lived and abundant species of seabird. Short-tailed shearwater are a trans-hemispheric migrant, spending the austral winter in the Bering Sea and feeding in the Southern Ocean during the summer breeding season. This means that ocean condition in both the north and south of their range may influence adult foraging success and therefore breeding success. We hypothesis that high quality individuals will be better at finding food in this challenging environment and therefore produce more offspring than poorer quality individuals.

The importance of reef context in species-habitat relationships across temperate shelf marine seascapes

Supervision team:

Dr Neville Barrett

Dr Jacquomo Monk

Dr Vanessa Lucieer

Reef structure and spatial distribution plays an important role in species-habitat relationships. With increasing pressures on reef species there is a heightened need for improved knowledge on the status of key relationships between species and the benthos for sound management. Understanding how species select their habitat based on the extent and complexity of reef systems, is a key element in developing an understanding of species distributions and overall abundance estimates. To date the best-documented relationship between reef structure and species is for coral reefs and tropical reef fish assemblages. Fish abundance has been able to be predicted by coral reef structure at scales ranging from individual coral colonies to 100’s of metres. In temperate water ecosystems however, the importance of the reef environment in understanding key species associations is limited and varies by species. Some studies have found no effect or mixed responses among taxa, however, in many cases this apparent lack of response may be due to a mismatch between the spatial scales of the observations of both species and reef habitat. In addition to fish, the importance of reef bio-structures for preferred fish habitat such as sponges, algae and mobile invertebrate communities, is understudied and even less understood.

This project aims to explore the importance of reef structure and spatial assemblage in influencing  cross-shelf, temperate water organisms abundance and distribution. This will be undertaken using the extensive underwater imagery datasets collected by through researchers within NESP Marine Biodiversity Hub.

The influence of marine ice on ice shelf dynamics and stability

Supervision Team:

Adam Treverrow (ACE CRC, UTAS)

Sue Cook (ACE CRC, UTAS)

Roland Warner (ACE CRC)

Layers of marine accreted ice represent a significant proportion of many large Antarctic ice shelves and are thought to enhance their stability; however, little is known of the flow properties of these layers. This project will involve a combination of laboratory ice deformation experiments on ice samples from the Amery Ice Shelf and 3-dimensional modelling of ice shelf dynamics. Experimentally determined parameterisations of ice flow properties will be used in the development of a regional ice shelf model which will be used to assess the influence of marine ice layers on ice shelf dynamics and stability.

The missing link: meso-pelagic prey field prediction for Southern Ocean marine predators

Supervision team:

Dr Rowan Trebilco

Dr Sophie Bestley

Prof. Mark Hindell

Dr Patrick Lehodey

Dr Ben Raymond

Dr Martin Cox

Dr Andrew Constable

Provide the context of the project that demonstrates the reason for doing the work and its relevance to IMAS research priorities. The statement should clearly illustrate the relationship between this proposal, work done previously and other work in progress. Bear in mind that this will be used in the description of the project on the Web.
The migrations of many marine top predators (e.g. whales, seabirds, seals and penguins) are driven by the spatio-temporal distribution and abundance of prey (krill and other micronekton). Important vertical migrations may occur in the water column in addition to large-scale horizontal migrations between different regions and water masses. However, the dynamics of the key mid-trophic levels (prey) remain a gap in developing an integrated understanding of marine ecosystems. 

The structuring of the food chain can have important implications for the transfer of energy to higher trophic levels, and consequent structuring of marine community composition. For example, one current working hypothesis is that physical controls can regulate primary production via diatoms versus micro-phytoplankton, and lead to alternative system states: krill or salp dominated. Similarly, there is evidence for a north-south gradient leading from krill-dominated cold waters in the south to warm copepod and fish based communities in the north. 

Over the past 15 years, a spatial ecosystem and population dynamics model (SEAPODYM) has been developed to represent key functional communities, including epi- and mesa-pelagic layers, and predict spatio-temporal structure of marine resources for ecological and economical management. This study aims to extend an implementation of SEAPODYM in the Southern Indian Ocean, connecting the Australian (Macquarie, Heard and McDonald) and French (Kerguelen) subantarctic islands. 

It should provide an integrative framework for exploring the physical and biological processes governing alternative energy pathways and the consequences for marine predator populations as well as important international fisheries.

The Ocean’s Biological Pump (Mesozooplankton controls on particle export)

Supervision Team

Prof Phil Boyd
Dr Kerrie Swadling

Any person expressing an interest in this project should email both Prof Boyd and Dr Swadling during December and January due to leave.

This position will be part of the interdisciplinary team investigating and ARC-funded project “Geoengineering the Southern Ocean? A Transdisciplinary assessment”. The role will focus on the holistic evaluation of what drives the efficiency of the ocean’s biological pump. This will include desktop studies, laboratory and field based research, along with mathematical modelling simulations.

The ocean’s biological pump is a key conduit for the transfer of biogenic carbon into the oceans interior and for the replenishment of nutrients via remineralisation in the deep ocean. In the geological past, changes in the efficiency of the pump have been invoked as a candidate mechanism to account for about 1/3 of the observed 80 ppmv reduction in atmospheric carbon dioxide concentrations. Consequently, geoengineering of the biological pumps has been proposed as a potential mitigation strategy to alleviate increasing anthropogenic CO2 emissions.

Mesozooplankton and particle-attached microbes play key roles in the biological pump via particle transformations (solubilisation, grazing), building blocks for heterogeneous particles (faecal pellet carbon and other elements), and hence have a strong influence on the magnitude and efficiency of carbon export. This post-graduate research fellowship will explore how different mesozooplankton taxa contribute to particle transformations which in turn help to set the magnitude of the downward export flux, and hence how they help to modify the efficiency of the pump.

Essential Requirements

  1. A BSc (Hons) or Masters or equivalent in a relevant field.
  2. Experience in invertebrate physiology.
  3. Keen to work at sea and in the laboratory.
  4. Interested in being part of a research team.
  5. Well-developed written and oral communication skills.

Desirable Attributes

We are looking for a candidate to focus on a project that centres on the following topics:

  1. Environmental controls/forcing of mesozooplankton with different feeding strategies (respiration, clearance rate, growth vs temperature etc.) – on local and subantarctic species.
  2. Influence of prey concentration and quality feeding strategies on local and subantarctic species.
  3. Linking the time-series distributions of subantarctic mesozooplankton at Southern Ocean Time-Series (SOTS) site to environmental conditions at the SOTS site.

The role of incentives, regulation, and nudges in influencing compliance behaviour of marine resource users (Centre for Marine Socioecology)

This PhD project is available through the Centre for Marine Socioecology, an IMAS partnership with CSIRO and the Australian Government.

Supervision Team:

Ingrid van Putten, CSIRO
Sarah Jennings, UTas
Sean Pascoe, CSIRO
Hugh Sibly, UTas

Understanding compliance behaviour of commercial and recreational fishers has been a topic of research for some time. Understanding compliance is important because if a failure to comply occurs at sufficiently high levels it may affect the environmental sustainability of the resource. The impacts of non-compliance on marine resources occurs in many different management situations including highly regulated, cooperatively managed, self regulated, or guided by guidelines only. Compliance in the marine environment is no longer exclusively concerned with the extractive activities of fishers but it is a multi sectoral problem and includes, for instance, tourists and tourism operators, transport, industrial users (oil & gas, renewable) and aquaculture.

Economic assessments of compliance tend to assume rational economic behaviour. In this type of economic assessment the decision to infringe or break the rules is based on the expected return, taking into account the direct returns and costs of different behaviours, and the risk of detection and punishment. However, if everyone behaved rationally this would suggest that there should be high levels cheating on, for instance, declaring taxes. After all, the likelihood of getting caught is low but payoff can be very high.  Similarly in the context of marine resources, compliance behaviour may also not be as expected from simply weighing the payoff against the probability of being caught. The difference between expected marine resource user compliance (in terms of classical economics) and what is observed in reality may be a measure of (lack of – or high) social capital.

Measuring actual non-compliance is not easy as there are strong incentives to keep actual behaviour a secret. It is not at all clear that people will reveal their real behaviour or even their preferences in hypothetical situations. However, where observational studies have measured compliance (particularly in fisheries research) a number of studies have outlined that rational economic principles do in fact explain compliance decisions but importantly, that normative and social factors also explain compliance. Perceived legitimacy of regulations, the norms to which fishers respond with respect to illegal action, or the perceived behaviour and response of peers also explain compliance behaviour.

There are departures from "rational behaviour" revealed by behavioural economics and previous fisheries specific studies have illustrated that compliance can also be explained by culture, norms and social factors. This study builds on previous fisheries work but focuses beyond fisheries to include the other marine sectors mentioned above. This study will not identify a new class of non-rational phenomena (or behaviour) but instead focus on analysing if and why different marine resource users are not behaving "rationally" in terms of compliance. The primary aim is to inform the debate around policy on compliance, and resource management more generally.

Given the extant knowledge around departures from rational behaviour and all that has been learned from behavioural economics –this project will identify potential incentives for compliance behaviour and understand how policies can be best adjusted. In identifying incentives, the interactions between traditional incentive and regulatory based management and nudges are of particular interest. Nudges are different from traditional incentives in that they appeal to motivations of human behaviour other than material rewards and costs. Nudges modify the context in which decisions are made to change behaviour (for instance by framing the choice differently). Changing behaviour by nudging may be a costs effective way of achieving marine user compliance which may be useful if enforcement of traditional economic incentives and regulations is high.

Overall the study will consider social, psychological and economic explanations of behaviour and choices around compliance in the marine environment. The study will use this knowledge to investigate the role of incentives, regulation, and nudges in influencing compliance behaviour of marine resource users. The best mix of traditional incentives, regulations, and nudges will be linked to the broader context: the resource use (including property rights characteristics), the users, the resource, and the risk.

The objectives of the project are to:

1. Determine the compliance aspects/problems of different marine uses
2. Estimate expected compliance of marine uses and users (using an experimental approach)
3. Assess actual compliance (based on revealed preferences study or a proxy observational measure)
4. Assess differences and model expected and actual compliance behaviour and determine if social, behavioural economics (psychological) or economic explanations can be found
5. Determine a mix of traditional incentives, regulations and nudges to achieve optimal compliance for the different marine uses and users
6. Develop a set of policy options to help achieve desirable levels of compliance behaviour.

Find out more


The role of sea ice kinematics on the state of Antarctic sea ice

Supervision Team:

Dr Petra Heil (supervision contact)

Dr Rob Massom

Sea ice is a crucial component of the Earth system due to its roles in controlling energy and moisture transfer between the ocean and atmosphere, ice-albedo feedback connected to polar amplification, and in marine ecosystems and bio-geochemical activity. This project will seek to quantify and characterize sea ice motion and deformation in the Southern Ocean, with a view to determining the drivers of these processes and to estimate their susceptibility to change under predicted atmospheric and/or oceanic change. The methods used for this project will include time-series analysis of Lagragian data, image cross-correlation of satellite-based swath data, and optimal interpolation to determine the baseline of Antarctic ice kinematics. Statistical analysis, including linear models and multi-variable correlation analysis will be used to determine the effect of external forcing on the sea ice.

The Southern Ocean spring bloom

Supervision team:

Associate Professor Peter Strutton

Dr Joan Llort

Professor Philip Boyd

In 1953, Sverdrup explained the spring greening of the North Atlantic in terms of changes in light availability and ocean stratification. Sixty years later this idea has become hotly debated with several papers claiming that, particularly at high latitudes, the oceans are not completely dormant in winter. On the contrary, it has been argued that phytoplankton biomass begins to increase soon after the winter solstice, and that phytoplankton growth and grazing mortality actually become more closely coupled in spring. It seems that the mechanisms underlying the spring bloom are far from resolved, and have recently been the topic of an entire special issues of a peer-reviewed journal and other high profile papers.

This debate was stimulated by conclusions largely drawn from satellite data on chlorophyll and particle concentrations. Since then, in situ subsurface data have also been brought to bear on the problem, but emerging data sets make this the right time to evaluate these competing ideas in the Southern Ocean.

This project will use autonomous floats from the Southern Ocean to look at the initiation of the spring bloom from the point of view of simultaneous changes in ocean physics, chlorophyll, biogenic particles, nitrate and carbon. The result will be an improved understanding of the genesis of the Southern Ocean spring bloom, its regional variability and sensitivity to climate change.

The under-utilisation of Australia’s living marine fisheries resources

Supervision Team:

Prof Caleb Gardner (contact)

Dr Klaas Hartmann

Dr Sean Tracey

Australia has the world's third largest EEZ, whether this is measured by total area or by the size of the more productive continental shelf region.  Total area of the EEZ is around 8.5 million square kilometres (or even 10.5 million square kilometres including Australia's Antarctic Territory, although this is recognised by only four other countries!). 

Despite this large area, fisheries production is very low with Australia harvesting only slightly over 100 kg from each square km of continental shelf.   This is the second lowest level of national production globally.  Eritrea is the only country that produces less and they contend with severe problems like piracy, which don't affect production in Australia. 

This low level of production in Australia is not only of social and economic interest but also has political implications.  Debate around issues like overfishing, aquaculture subsidies, marine parks, resource allocation splits between commercial and recreational fishers, and seafood imports often reference Australia's low fisheries production.  For example, a paper in the Australian Medical Journal in 2014 made the extraordinary claim that Australians should be discouraged from eating seafood, despite acknowledged benefits to public health, because our EEZ was unproductive and that current consumption could not be sustained.  These type of arguments rely on the claim that Australia's EEZ is vastly less productive than other EEZs.  That is, our low production is a consequence of our lack of glaciation and large river outflows and fisheries are simply limited by the unproductive Australian ecosystem.

The argument that Australia's low production of seafood production is limited purely by ecology doesn't hold up under scrutiny.  Many countries without large river outflows and primary production far less than that of Australia sustain harvests more than 20 times greater per square km than Australia (for example Morocco, Turkey, Maldives, Yemen, Italy, Sudan).  All countries adjacent to Australia have production many times higher, including even East Timor, which has double the production despite recent political turmoil and limited infrastructure.  Solomon Islands has 10x Australia's rate of production despite political turmoil and severe infrastructure challenges. We share the productive Coral Sea ecosystem with Papua New Guinea.  Australia takes no tuna catch from this region while PNG harvests 200,000 tonnes.

Australia's fisheries production is clearly limited by more than an unproductive ecosystem with factors at play such as: (i) trade and competitive advantage of production (high labour costs); (ii) the political power of the conservation movement; (iii) political power of the recreation fishing lobby; (iv) regulatory barriers.

This project will explore the causes of under-utilisation, trends in under-utilisation, and the opportunity cost for the Australian community including access to seafood and public health.

Tidal melting of Antarctic ice shelves since Last Glacial Maximum

Supervision Team:

Professor Matt King (supervision contact)

Dr Ben Galton-Fenzi

This PhD project will use a numerical ocean model to examine the role of tidal currents in the retreat of the Antarctic ice sheet since the Last Glacial Maximum. Model runs will be performed in order quantify ice shelf basal melt rates for a series of LGM and post-LGM ice sheet configurations. Extensions to this work include application to a time-stepping coupled ice-ocean model to quantify the total effect of tidally-driven basal melt on post-LGM ice sheet retreat. The student will have access to appropriate computer models as part of a larger modelling effort within UTAS / ACE CRC. Simulations will be performed using grants and allocated resources within the National Computing Infrastructure and the Tasmanian Partnership for Advanced computing.

Tides and barotropic oceanic signals around Australia (QMS)

Supervision team:

Professor Richard Coleman

Dr Benoit Legresy

Dr Mark Hemer

2021 should see the launch of a game changer satellite for oceanography, SWOT. A key limitation to interpret the high resolution ocean topography in the coastal regions will be the barotropic signals (tides and response to wind and atmospheric pressure). To overcome this limitation, we need to get a pan-Australian operational model which can run at the necessary resolution and accuracy. The tides and barotropic signals are the main energetic signals in the ocean at short time scales. They are also a prominent source of renewable energy in the ocean. Available global ocean barotropic models are now good enough to picture the sea surface height and barotropic currents appropriately. However, they are less reliable when approaching the coast, mainly due to their lack in resolution and associated poor representation of the bathymetry and coastline. The topic of this work will be to develop the regional barotropic model for Australia which can reach the level of detail and accuracy to deliver to various applications. The main application is for satellite coastal altimetry correction and interpretation. The model should be useful to a number of topics using sea surface height and currents.

Towards understanding recreational fisher behaviour - supporting resource management and stock assessment.

Supervision Team:

Dr Jeremy Lyle

Dr Sean Tracey

Dr Klaas Hartmann

IMAS has conducted surveys of recreational fishing activities for more than two decades, covering a period of significant management changes, variability in the abundance of some key species and changing fisher preferences.  These surveys represent a rich dataset that includes detailed information about individual fishing activities as well as profiling information about the fishers themselves which can be linked directly to the fishing behaviour. 

Characterising the heterogeneity of the recreational fishing population and how this links to fisher choices (as revealed by fishing behaviour) has important implications in understanding how the sector responds to changing resource availability and management intervention.  Furthermore, societal changes, including an aging population, increasing urbanisation and cultural diversity, are factors that are having an influence on the nature and scale of the recreational fishery in Tasmania and globally.

Transnational Environmental Campaigns in the Australia-Asian Region: The Case of Seafood, Fisheries and Target Markets (Centre for Marine Socioecology)

This PhD project is available through the Centre for Marine Socioecology, an IMAS partnership with CSIRO and the Australian Government.

Supervision Team:

Elizabeth Lester, UTAS
Emily Ogier, UTas
Jeff McGee, Utas
Ingrid van Putten, CSIRO

This PhD project is part of a larger ARC project that examines transnational media flows of environmental concern in the Australia-Asian region. Investigating a number of cases across Australia's resource-based industries, the ARC project aims to develop a deep understanding of media roles and practices in the interaction between claims-makers and decision-makers. Led by Professor Libby Lester ( and collaborating with leading international scholars, the project deploys an original approach for the study of transnational politics and communications. It will provide new knowledge into how environmental conflict is produced, conducted and resolved. As this knowledge has real consequences for industries, communities and environments, the project will contribute to policy negotiations, environmental and corporate decision-making, and Australia's strategic research goals.

The ARC project addressed two key questions:
1. How are mediated environmental campaigns formulated, carried and understood between Australia and Asia?
2. How do they influence Australia's agenda to strengthen regional relations and trade?

Specifically, it aims to:
* identify emerging forms of transnational environmental campaigns such as those run by Markets for Change and Greenpeace;
* analyse pressure group, industry and government communication and political strategies in Australia;
* investigate Asian corporate and activist responses to these communications and politics;
* examine how environmental activism operates across complex media and political networks and systems, and seeks to change political and consumer behavior;
* assess industry, government and public diplomacy attempts to manage these impacts.

This PhD project will specifically focus on fisheries and marine farming, investigating social and environmental interaction with local communities at the sites of production through supply chains and into target markets.

Find out more.

Understanding energy pathways through Southern Ocean mesopelagic communities

Supervision team:

Dr Rowan Trebilco

Dr Andrea Walters

Prof Mark Hindell

Dr Andrew Constable

Dr Ben Raymond

Dr Anton Van de Putte

Provide the context of the project that demonstrates the reason for doing the work and its relevance to IMAS research priorities. The statement should clearly illustrate the relationship between this proposal, work done previously and other work in progress. Bear in mind that this will be used in the description of the project on the Web.

Mesopelagic fish are the most abundant vertebrate in the biosphere, accounting for more biomass than any other group of fish. In the Southern Ocean, mesopelagic fish and squid dominate mid- trophic levels, comprising the pathways by which energy from primary producers is made accessible to higher-order predators including whales, seals, penguins, flying seabirds, and large (often commercially valuable) fish. The short, krill- dominated food chains are well studied and relatively well represented in ecosystem models. However, squid and mesopelagic fish are far less well studied and represent a key area of uncertainty in current ecosystem modelling efforts. In particular, key areas of uncertainty include: (i) whether mesopelagic communities constitute a single or multiple distinct energy pathways to higher trophic levels; (ii) the environmental factors that drive variation and differentiation of mesopelagic energy pathways; and (iii) more broadly, the factors that drive the distribution, abundance and biomass of key mesopelagic groups. This uncertainty is compounded by the fact that different sampling gears give very different pictures of mesopelagic distribution and abundance. 

Recognition of both the importance of mid- trophic levels, and the current lack of knowledge of their trophodynamics, has recently motivated several major national and international research initiatives focused on these groups.

Understanding how the microbiome of host and pathogen affects AGD pathogenesis

Supervision team:

Dr Mark Adams

Dr James Wynne

This project represents an exciting opportunity for a student to conduct novel research on the association between bacteria and Amoebic gill disease (AGD) in Atlantic salmon. While AGD remains a major issue for the Tasmanian Atlantic salmon industry, little research has been conducted to understand how bacteria affect AGD progression. In this project the student will use a combination of approaches, including antibiotic treatment, metagenomic 165 sequencing and bacteriology to characterise the role of bacteria in AGD. This project will lead to a greater understanding of the factors affecting gill health and may ultimately inform new treatment strategies.

Understanding the drivers of Antarctic climate over the past 2,000 years

Supervision team:

Steven Phipps

Jason Roberts (AAD/ACE CRC)

Tessa Vance (ACE CRC)

The response of the Antarctic Ice Sheet (AIS) is one of the key uncertainties in projections of future global sea level rise. Changes in the volume of the AIS are driven, in part, by changes in air temperature, ocean temperature and precipitation. An understanding of the drivers of the Antarctic climate is therefore critical if we are to be able to generate reliable projections of future changes in global sea level. Thanks to the availability of high-resolution palaeoclimate proxy data, the past 2,000 years provides us with a valuable opportunity to improve our understanding of climatic drivers.

This project will combine novel climate modelling approaches with proxy data from natural archives in order to reconstruct and understand changes in the climate of Antarctica over the past 2,000 years. A global climate model will be used to simulate the response to natural and anthropogenic forcings, include greenhouse gases, the sun and volcanoes. Simple proxy system models will be developed, alleviating potential problems with the interpretation of proxy records by allowing for a direct comparison between the climate model simulations and palaeoclimate proxy records. Through data assimilation and the application of techniques for detection and attribution, it will then be possible to reconstruct changes in the climate of Antarctica over the past 2,000 years and to identify the drivers that are responsible.

This project will use the CSIRO Mk3L climate system model to generate multiple ensembles of simulations. Each ensemble will simulate the response of the climate system to a single forcing (orbital, greenhouse gases, solar and volcanic) over the past 2,000 years. These simulations will be used in conjunction with an existing ensemble of simulations, in which all of these forcings were applied simultaneously.

The candidate will then develop simple forward models for key Antarctic proxy systems, including sea salt and stable isotopes. By driving these forward models using data from the climate model simulations, it will be possible to simulate the responses ("fingerprints") of Antarctic proxy systems to natural and anthropogenic forcings.

Through the application of techniques for offline data assimilation, this will enable the direct assimilation of Antarctic and Southern Ocean proxy records into a climate modelling framework. The assimilation will generate a reanalysis of the Antarctic climate spanning the past 2,000 years, including air temperature, ocean temperature and precipitation. Through the application of techniques for detection and attribution, the fingerprints generated using the forward models will also be used to quantify the roles of natural and anthropogenic forcings in driving the Antarctic climate.

In addition to the scientific outputs, this project will generate a number of significant and high-value products:

  • A suite of climate system model simulations that can be used for detection and attribution studies.
  • Novel forward models for key Antarctic proxy systems.
  • A reanalysis of the Antarctic climate spanning the past 2,000 years, providing critically-needed boundary conditions that are required to drive models of the Antarctic Ice Sheet.

This project will suit candidates with a physical science/engineering background and well-developed numerical analysis skills. Experience in compiling and running scientific software will be highly advantageous for the purposes of completing the model experiments.

Using thorium isotopes to quantify lithogenic inputs to the Southern Ocean

Supervision team:

Associate Professor Zanna Chase

Professor Philip Boyd

Associate Professor Ashley Townsend

Associate Professor Andrew Bowie

The scarcity of iron limits biological productivity in the nutrient rich surface waters of the Southern Ocean. This in tum limits the biological uptake of atmospheric carbon dioxide. Lithogenic iron sources such as dust, bottom sediments, and glaciers are important to support biological activity, but quantifying these inputs remains a challenge. A method based on the isotopes of thorium (Th) has recently been developed. This method relies on the fact that the long-lived thorium isotope, 232Th, is derived exclusively from lithogenic sources, and is not removed biologically. The shorter-lived Th isotope, 230To, has a well-constrained rate of input from uranium decay. The paired analysis of 230To and 232Th concentrations thus enables a calculation of the rate of input of lithogenic material, once the 232Th content and fractional solubility of 232Th in lithogenic particles is known. 

This project will apply these methods to three oceanographic voyages around Australia that form part of the GEOTRACES programme (, an international study of the biogeochemistry of trace elements and their isotopes.

Using variational methods to investigate ice shelf basal melting

Supervision team:

Ben Galton-Fenzi (AAD, ACE CRC)

David Gwyther

Terry O'Kane (CSIRO)

Sea level rise originating from Antarctica is difficult to quantify. Ice-ocean interaction at the base of ice shelves, such as basal melting, is critically important for determining the Antarctic contribution to sea level rise. Numerical ocean models present an ideal tool for investigating this interaction. Model runs are typically forecast or hindcast solutions for modelling realistic ice shelves or idealised process-oriented studies.

An under-explored option is inverse models. Variational methods allow the assimilation of observations and exploration of model sensitivities. The Regional Ocean Modelling System is a commonly used numerical ocean model, has been modified for ice shelf interaction, includes an inverse model. Using a newly-developed extension to the inverse modelling framework, the successful applicant will apply inverse methods to ice shelf-ocean interaction; initially focussing on sensitivity of cross-shelf exchange of oceanic heat to uncertainties in the primary forcings.

The successful applicant will ideally have inverse modelling experience and/or a background in mathematics/physics.

Authorised by the Executive Director, Institute for Marine and Antarctic Studies
October 30, 2015