Centre for Freshwater Ecosystems - Honours and Graduate Research 2020
Centre for Freshwater Ecosystems - Honours and Graduate Research 2020
The Centre for Freshwater Ecosystems (CFE) brings together a wealth of expertise to understand and solve signiﬁcant challenges to support the sustainable management of freshwater ecosystems.
Our work directly supports decision-making regarding maintenance and restoration of the long-term health of rivers, catchments, ﬂoodplains and wetlands.
Our mission is to lead the way for healthy and sustainable freshwater ecosystems through innovation and excellence in research and education. Research themes pursued by the centre include:
- Ecosystem monitoring and assessment
- Environmental biogeochemistry and contaminants
- Environmental and social policy
- Fish ecology and management
- Genetics and conservation
- Invertebrate community ecology
- Quantitative modelling and forecasting
- Spatial modelling and GIS analysis
- Water management
- Wetland and floodplain ecology
Further information available at www.latrobe.edu.au/centre-for-freshwater-ecosystems
Nancy Millis Building 8
The primary focus of an Honours year is research training. Your course will involve a mix of advanced theory, research training and a research project leading to a thesis.
The minimum entry requirement is a three-year Bachelor's Degree and a B-grade average (marks of 70-79%) in subjects relating to your Honours degree. Application forms are available at: http://www.latrobe.edu.au/study/undergrad/how-to-apply/direct/honours
Information on scholarships is available at https://www.latrobe.edu.au/scholarships
Masters and Doctor of Philosophy (PhD) Research Programs
A Masters or Doctor of Philosophy (PhD) allows you to pursue an independent and sustained investigation into a research problem (of your own design) that makes a significant and original contribution to knowledge in the context of professional practice.
Before you apply for graduate research candidature you must identify a potential supervisor and receive in-principle approval for your research project. You can search for a suitable supervisor by browsing the research and training scholars at La Trobe at https://scholars.latrobe.edu.au/
Once you have in-principle approval from your supervisor you should then submit an application. Further information on the application process is available at https://www.latrobe.edu.au/research/future/apply
Full details on the eligibility and application process is available at https://www.latrobe.edu.au/study/apply/research
Graduate Research Scholarships
The Centre for Freshwater Ecosystems has available one LTU Research Training Program (RTP) Stipend Scholarship or LTU Postgraduate Research Scholarship (LTUPRS) AU$27,082, plus a AU$15,000 industry top-up scholarship funded by the Department of Environment, Land, Water and Planning (DELWP) connected to a PhD on ‘The effects of climate change on the ecology of unregulated rivers’ (CCDF1), for a suitable candidate.
To find out further information on the types of scholarships you can apply for as a graduate researcher at La Trobe please go to https://www.latrobe.edu.au/research/future/costs-scholarships
Applications for International scholarships close 30th September 2019
Applications for domestic scholarships close 31st October 2019
Potential Research Topics (Honours, Masters and PhD)
Please note: Each topic listed below can be adapted for either honours, masters or PhD studies.
Environmental Chemistry and Contaminants
Research topic ECC1: The link between dissolved organic carbon (DOC) characteristics and algal blooms
Harmful algal blooms (HABs) cost the global economy billions of dollars annually and are a major concern to human health, the health of the environment and the economy. Our understanding of what triggers such blooms and their associated toxicity is limited. Recently the formation of harmful algal blooms was linked to increased inputs of organic carbon (DOC) into waterways. DOC may also be utilised by some species of harmful algal species as a direct food source, stimulating growth and leading to the proliferation of these algae. Direct effects are likely to be related to the type of DOC present with differences in the bioavailability of terrestrially derived, highly aromatic DOC of a high molecular weight compared with autochthonous derived DOC, less aromatic and of a lower molecular weight likely. Our current understanding of the role of DOC in bloom formation is currently lacking. This is of great concern given that DOC concentrations and quality within freshwaters have been predicted to change in the future due to climate change and HAB are increasing in prevalence. Therefore, this project proposes to explore the role of DOC in harmful algal bloom formation and toxicity within the Murray Darling Basin by conducting both field and laboratory trials.
Research topic ECC2: Dissolved organic carbon (DOC) and influence on metal toxicity
This project aims to characterize the types of dissolved organic carbon (DOC) found within Australian freshwaters
and investigate how these influence metal toxicity to aquatic organisms. DOC has the ability to decrease the toxicity of metals to organisms in natural waters, and the intensity of the decrease is related to the type of DOC. Information
the impact of Australian DOC on metal toxicity to Australian biota is limited. This project will investigate the influence of different types of DOC’s on toxicity of metals such as Zn, with an ultimate goal to incorporate data on
DOC quality into predictive models to improve their performance.
Research topic ECC3: Hydrology and DOC in alpine peatlands during extreme events
Alpine and sub-alpine peatlands are the source of many headwater streams in the Australian Alps, and have an important role in controlling the chemical composition of these streams over both seasonal and event timescales. Our previous work has shown that peatlands strongly regulate stream composition under storm flow conditions, with the major perturbation to stream chemistry being the export of a dissolved organic carbon (DOC) ‘pulse’ (Karis et al., 2016). This DOC pulse is likely important in the provisioning of energy for downstream processes, and also the delivery of chemical cues for stream biota. This project will combine hydrology and chemistry to understand the relative contributions of rain water, groundwater and peatland storage water in the storm pulse (using isotopic tracers) and the characteristics of the DOC exported. In particular we are interested in understanding the biogeochemical processes that occur within the peat profile, and the mobilisation of organic molecules with changes in peatland water table and antecedent peat soil condition. Climate change predictions for the Australian Alps are for more frequent and intense storm events; as part of this work we will look at storm frequency and how this affects the regulation capacity of these systems.
Academic background required: Environmental chemistry, geochemistry or hydrology. Previous experience with computer coding and device control would be an advantage. [Note: this project involves working in alpine environments under sometimes challenging conditions].
Research topic ECC4: Dissolved organic nitrogen in natural waters as a source of bioavailable nitrogen
Dissolved organic nitrogen (DON) in natural waters (river, lakes and wetlands) is likely an important source of bioavailable nitrogen for microbes, algae and biofilm communities in these ecosystems. DON is part of the wider pool of dissolved organic carbon (DOC), a group of large and poorly-characterised macromolecules, present in freshwaters and formed through decomposition of natural biomolecules. Characterisation techniques for DOC and DON tend to be global (non-specific) methods that do not provide detailed speciation, limiting our understanding of nutrient uptake from these sources. In this project we will investigate the association of identifiable organic nitrogen compounds (e.g. amino acids, N-acetyl glucosamine, nucleic acids) with DOC, over a range of DOC size classes, using DOC from a variety of natural and reference sources. The analytical methods developed in this work will be used to investigate a natural aquatic disturbance (e.g. storm and/or flood) to determine the relative mobility of DON compounds during the event. Such data will be invaluable to understanding the contributions of different hydraulic components to stream flow and the interpretation of landscape-scale processes.
Fish Ecology and Management
Research topic FEM1: Floods, chemical cues and fish movement
The regulation of river flow through placement of dams and other structures has changed annual flow patterns in many rivers worldwide. Dams are well recognised as environments where significant nutrient transformation takes place such that water released from dams may differ not only in timing, but also in composition compared to natural flow. Research in our laboratory has shown that the magnitude of lateral movements by river-floodplain fishes may be greater during natural connection events than during managed ones (e.g. opening of a regulator). The causal mechanisms underlying the responses to natural versus managed flood events are not understood, but are likely due to managed flows not delivering appropriate chemical cues that activate fish movement onto the floodplain. This project will involve field and laboratory experiments that examine various types of flooding events (natural/artificial) and how these floods affect the quality and quantity of potential molecular cues for fish movement. This is the first project in a research theme that tackles potential mechanisms that may differentiate fish response to natural versus managed flows and would comprise a powerful mix of fish ecology and environmental chemistry. The final design of the project will be developed strongly in conjunction with a successful candidate.
Research topic FEM2: Quantifying productivity and fish growth rates across different habitats
Many fish species have a short critical period after hatching when appropriate food densities must be available to allow survival. With increasing pressure on water-managers to use limited volumes of water wisely for the environment, environmental water is increasingly being used to manipulate water levels in channels and in wetlands to support fish recruitment. This project will investigate what habitats need to be inundated to maximise zooplankton production and associated productivity to support of fish-recruitment. This will quantify the relationship between flow and zooplankton emergence from channels, perennial wetlands and intermittent wetlands sediments. Without this information, river managers will be unable to ensure there is sufficient larval fish-food to support recruitment following spawning under differing environmental flows.
Research topic FEM3: What do Australian fish get out of accessing floodplain habitats?
A critical question in Australian river management—and indeed river management around the world—is: how does allocating water to floodplains affect the mean fitness of aquatic animal populations? Dominant theoretical frameworks of freshwater science contend that many fishes of river-floodplain ecosystems have evolved dependencies on floodplain access, but anecdotal evidence indicates that there is much uncertainty concerning the role floodplain habitats play in the population dynamics of freshwater fishes. The PhD project will focus on deciphering the significance of floodplain habitats to fish populations of the Murray-Darling Basin. This project will involve melding field and laboratory studies to compare and contrast the relative effects of floodplain and channel habitats on individual- and population-level fitness.
Research topic FEM4: Can eDNA identify the fish waterbirds feed on?
Fish are thought to be important prey items for many waterbird species; however, little is known about the prevalence of waterbird predation on fish species. This project aims to quantify the presence of fish species in the diets of water birds through DNA metabarcoding. This project will link with existing and recent research projects both at La Trobe and CSIRO.
Research topic FEM5: Do flow conditions in rivers influence food choice and condition of young fish?
The early life of fishes is a period of high natural mortality, with
Industry link: Jason Thiem (NSW Fisheries, DPIR)
Research topic FEM6: How important are carp as a food source in aquatic ecosystems?
A carp herpesvirus has been proposed as a biological control to significantly reduce the abundance of invasive common carp (Cyprinus carpio) from Australian waterways. While scientific literature on specific effects of carp on food webs is scarce (King et al. 1997; Robertson et al. 1997), carp removal could potentially influence food availability for consumers (birds and fish) that prey on carp. This project aims to quantify the value of carp as a food resource and compare them with other potential fish species that may take their place in the food web if carp are reduced or removed from our waterways. This project will link with existing and recent research projects both at La Trobe and CSIRO.
Industry link: Heather McGinness (CSIRO)
Research topic FEM7: Drivers of fish migration
Individual variation in the movement behaviour of animals is emerging as a key theme in current ecological research. Despite this, the environmental and biological factors that drive individual differences in movement behaviour remain poorly understood. Populations of migratory fish in Australian rivers face a range of threats and there is an urgent need for better understanding of migratory behaviour to support conservation and management. This project will combine innovative techniques, including otolith (earstone) chemistry and biochronology, to examine the drivers of migration for important inland and coastal fish species. The project has both theoretical and applied outcomes, and provides the opportunity for close collaboration with staff from State fisheries agencies.
Research topic FEM8: Habitat use and dispersal of Murray crayfish
Murray crayfish (Euastucus armatus) is a large, iconic freshwater crayfish occurring in the rivers of southern Murray-Darling Basin. The species has undergone significant declines in both abundance and range in recent years due to overfishing, drought and blackwater events. Restoration efforts are currently underway to improve populations throughout their range. However, basic information on key life history characteristics, including adult habitat use, activity patterns and early life stage dispersal, is urgently needed. This project will use acoustic tracking and other novel techniques in collaboration with staff from State Fisheries agencies to provide information to guide future conservation and management of the species.
Industry link: Jason Thiem (NSW Fisheries, DPIR)
Research topic FEM9: Genetics of fish resilience, movement and recolonization
Freshwater fishes living in the Murray-Darling Basin (MDB), Australia, have evolved under one of the most variable natural flow regimes in the world. Fish in the MDB must contend with highly variable flow conditions, including long periods of drought, which have become exacerbated since European arrival due to climate change and large-scale water extraction to support agriculture. The ability to withstand periods of low flow or to recolonise rivers following cease-to-flow events or hypoxic black water events is therefore critical to the long-term survival of many native fish species in the MDB. This PhD project will address knowledge gaps around the genetic basis of hypoxia tolerance and dispersal behaviour for a range of freshwater fish species (including the iconic Murray cod and golden perch). This project will link with existing research projects at La Trobe and the Arthur Rylah Institute and utilise a combination of field-based methods (including otolith microchemistry, mark-recapture, radiotelemetry) and genomic methods. The final design of the project will be developed strongly in conjunction with a successful candidate.
Wetlands and Floodplains Ecology
Research topic WFE1: Environmental DNA can be a useful tool for conducting freshwater bio-assessments.
Conventionally, universal probes, designed to capture genetic material from many taxa, have been used for eDNA -based community analyses. However, many of the organisms traditionally targeted in freshwater bio-assessments are often missed when using universal probes on eDNA. This is primarily due to the abundance of, and bias towards detecting, non-target organisms. What is required is a suite of probes that target selected groups of freshwater organisms. This project would investigate, develop and test taxa-specific probes for use on Australian freshwater fauna.
Climate Change, Drought and Freshwater ecosystems
Research topic CCDF1: The effects of climate change on the ecology of unregulated rivers.
The periodic loss of flow in non-perennial streams can act as a major ecological disturbance, reducing survival rates of aquatic biota and restricting surviving individuals to localised refuge habitats (e.g. deep pools, local groundwater seeps etc.) While we have a fair understating of the ability of many species to survive in these local refuges, knowledge of recovery cycles from drying events (i.e. their resilience), is less well understood. This includes how historical patterns of resilience may be compromised by increases in flow stress. Conceptually, the recovery potential, or the resilience, of different species, can be strongly linked to aspects of biology and life-history (such as fecundity, and dispersal ability). However there are few examples from Victorian waterways where these concepts have been tested empirically to better understand the threats associated with different patterns of drying. This PhD project will broadly address questions related to the ecological risks associated with increased hydrologic stress in unregulated rivers. The proposed area of focus is on factors that influence population persistence in unregulated rivers affected by stream drying. There is scope to apply a range of novel approaches, including spatial modelling, genetic methods, capture- recapture studies, and/or other suitable techniques to improve our understanding of the risks to population persistence in non-perennial streams. The project will also align with several other PhD projects currently underway, which are similarly focussed on unregulated streams, but with a stronger focus on hydrology and hydrologic change.
The Centre for Freshwater Ecosystems has available one LTU Research Training Program (RTP) Stipend Scholarship or LTU Postgraduate Research Scholarship (LTUPRS) AU$27,082, plus a AU$15,000 industry top-up scholarship funded by the Department of Environment, Land, Water and Planning (DELWP) connected to a PhD on research topic for a suitable candidate.