Plant Functional Biology and Climate Change Cluster

2013 PhD Project List

Research Groups Aquatic Processes

Remote Sensing and Ecological Modelling

Terrestrial Ecohydrology

Aquatic Processes Group

Title: Molecular ecology and evolution of paralytic shellfish toxins

Supervisors: Dr Shauna Murray

Project Description: Paralytic shellfish toxins are a major group of marine biotoxins produced by certain species of phytoplankton, with

potentially severe impacts on humans, marine mammals, birds and other invertebrates. This project will examine

relevant genes involved in toxin production in species of the harmful dinoflagellate genus Alexandrium, and study their

expression under relevant environmental conditions.

Title: Molecular ecology of coral-dinoflagellate symbioses

Supervisors: Dr Shauna Murray This project will use molecular genetic techniques to determine the impact on coral-dinoflagellate symbiosis of toxins

produced by dinoflagellates (microalgae). In this project, the candidate will: sequence relevant genes associated with

toxin production from coral symbionts, determine their evolution in relation to other toxin-production genes, and

determine their expression under a variety of ecological parameter

Desirable skills and qualifications: Students interested in these projects will be required to have a first class honours or MSc degree, and/or published work or research experience. A strong grounding in molecular genetic techniques, microbiology, phytoplankton research and/or chemistry is an advantage.

Funding: ARC Future Fellow

Biotoxins from HABs are

transferred throughout the food

web when toxic algal cells are

eaten by zooplankton, fish, and

shellfish that are, in turn, eaten by

other animals and humans. (G.

Wikfors)

http://www.whoi.edu/redtide/impacts/ecosystems

Title: Determining the effects of anthropogenic stress on marine macrophyte interactions Supervisors: Dr. Paul Gribben and Professor Peter Ralph

Project Description:

The coastline in NSW is experiencing the loss of some macrophytes but the potential expansion of others. Because of the high conservation value of marine macrophytes, the replacement of some species by others may have wide ranging implications for biodiversity if the macrophytes are functionally different. This project will investigate the role of coastal anthropogenic stressors in determining the apparent rapid spread of the native green alga, Caulerpa filiformis in NSW and how these stressors alter the outcomes of interactions of Caulerpa with other macrophytes. The successful student will combine physiological ecology and disturbance ecology with experimental lab and field studies to address these issues. The project is part of multidisciplinary team involves the UTS:C3 (P. Gribben and P. Ralph), NSW Department of Primary Industries (B. Creese) and the Office of Environment and Heritage (P. Scanes).

Desirable Skills and qualifications:

The student must have a 1st Class Honours or MSc degree expertise in plant physiology and a strong background in

experimental ecology.

Caulerpa filiformis is found on exposed rocky reefs in central New South Wales from Sydney to Port Stephens.

This species is prolific on many rocky reefs and is the most dominant marine plant displacing many other species. (Photo: David Harasti)

Title: Screening and optimisation of microalgae for biofuel production Supervisor: Professor Peter Ralph and Dr Martin Schliep

Project Description: We are seeking applications from potential PhD candidates to join our algal biofuel research team and to contribute to the on-going biofuel research program. The candidate will utilise UTS’ cutting-edge photobioreactor matrix technology for photobioanalytic screening and adaptational optimisation of natural isolates from various Australian sampling sites. The goal is to accelerate discovery and commercialisation of suitable microalgal strains for the Australian algal biofuel industry. Promising new strains will be examined comprehensively in collaboration with experts from CSIRO. The successful applicant will i) screen natural isolates for high lipid yielding microalgal strains (bio-prospecting), ii) biochemically and photobiologically characterise these strains, iii) optimise culture conditions for maximum lipid production, and iv) test identified potential biofuel strains under simulated field conditions.

Desirable skills and qualifications: Applicants should have First Class Honours (or Masters Degree) in plant/algal physiology, photobiology or a relevant discipline. Australian and New Zealand applicants preferred. The successful candidate may be eligible for top up scholarship funding; however this is dependent upon the calibre of applicant and the project.

The microalgae Nannochloropsis oculata is ‘glowing’ in the Phenometrics photobioreactor/s at UTS: Algal Biofuels Group. (Photo: J.Saad)

Title: Pelagic carbon production in coastal habitats

Supervisors: Dr Martina Doblin and Prof Peter Ralph

Project Description: Quantitative models of carbon are required for Australian coastal areas to improve global carbon estimates, which are

predominately biased towards American and European environments. Currently, our knowledge of coastal carbon

stocks in Australia and estimates of coastal carbon flux are very limited.

Phytoplankton are the engines of marine pelagic production1, and the amount of carbon they produce is strongly

influenced by light and nutrient availability—environmental factors that are changing due to human activities.

This project will make direct estimates of pelagic community productivity and metabolism in coastal habitats. It will

implement multiple methods (oxygen, fluorescence, carbon isotopes) and examine the regulation of primary

productivity by environmental factors. The data will lead to better parameterisation of carbon pools and fluxes, and

improve productivity models needed to build coastal carbon budgets.

Desirable skills and qualifications: The student must have a first class Honours or MSc degree, and/or published work or research experience. Experience in phytoplankton culture and willingness to conduct field research would be an advantage.

Funding: UTS in association with CSIRO Marine and coastal carbon biogeochemistry cluster

An example of a coastal phytoplankton species, Thalassiosira sp., photographed under a microscope.

(Image: M. Doblin)

1 Primary Production is the production of organic compounds from atmospheric or aquatic carbon dioxide, principally through the process of photosynthesis. Primary production is a key indicator of ecosystem health and carbon cycling and this can have a strong influence on the economic, social and physical health of the human population living in the coastal zone.

Title: Integrating remote sensing with in situ measurements to understand the impacts of

climate on the marine foodweb

Supervisors: Dr Martina Doblin, Dr Jason Everett, Professor Alfredo Huete

Project Description: Phytoplankton form the base of the marine foodweb and are key indicators of climate change, amplifying

environmental signals such as changes in ocean temperature, pH and oxygen content. This project will examine

shifts in phytoplankton distribution and composition around Australia using a national dataset of in situ

measurements and remotely sensed satellite imagery.

Desirable skills and qualifications: The student must have a first class Honours or MSc degree, and/or published work or research experience. Experience in remote sensing/GIS and spatial analysis would be an advantage.

Funding: UTS in association with the CSIRO Marine and coastal carbon biogeochemistry cluster, with additional support from Australia’s Integrated Marine Observing System.

Variation of marine phytoplankton on the NSW shelf during 2007 and 2008. (Image: J. Everett)

Title: Emergence of stress-induced diseases in marine ecosystems: effect of environmental

changes on bacteria-host interactions

Supervisors: Dr Martina Doblin, Dr Olivier Laczka

Project Description: Marine diseases are a major concern worldwide and affect a large range of organisms and industries such as aquaculture and tourism. Bacteria-host interactions are influenced by their surrounding environment, and changes in bacterial communities generated by ecosystem perturbations often lead to the emergence of pathogens. While extensive research is being carried out to study the composition of bacteria communities within marine hosts, the early detection and mechanisms governing the appearance and distribution of pathogenic microorganisms are yet to be discovered.

This project will study model marine hosts under stressful conditions and examine changes in the distribution and pathogenic properties of associated microbial communities. The research will involve an extended range of analytical methods such as fluorometry and spectroscopy, flow cytometry and advanced microscopy imaging. The work will also include the use of molecular biology tools ranging from Polymerase Chain Reaction (PCR) to bio-informatic analysis of sequence data. Bacterial, algal and coral culturing will be performed on a regular basis.

Desirable skills and qualifications: The student must have a first class Honours or MSc degree, and/or published work or research experience. Experience in microbiology, molecular genetic techniques and culturing would be an advantage.

Funding: Chancellor’s post-doctoral fellowship

Seawater aquarium showing diversity of corals affected by marine diseases.(Image: www.lostmymarblz.com)

Terrestrial Ecohydrology Research Group Title: Examination of causes of drought-induced mortality: C starvation or hydraulic

failure?

Supervisors: Professor Derek Eamus Project Description: Over the past 30 years there has been increasing awareness that large-scale (regional) and long-term (one to several years duration) droughts were occuring more frequently and that this was associated with large rates of mortality (forest die-back). Large-scale mortality of forests changes the albedo of terrestrial land surfaces and alters the feedbacks amongst landscapes, vegetation function, climate and vegetation-atmosphere interactions. This project will investigate the relative importance of hydraulic failure and C starvation as causes of mortality in trees using a combination of glasshouse experiments, field manipulations and modelling.

Desirable Skills and Qualifications: Applicants should have interests in plant physiology, plant ecophysiology or experimental ecohydrology at Hons degree level (1st class or upper second).

Funding: There is some extra funding available to support this project.

An estimated 75% of River Red Gums have been affected by drought ( Photo: Ann Wilson)

Remote Sensing and Ecological Modelling Research Group Title: Integrating remote sensing, landscape flux measurements, and phenology to understand the impacts of climate change on Australian landscapes Supervisors: Professor Alfredo Huete, Dr Natalia Restrepo-Coupe, Dr Mark Broich Project Description: The accurate representation of the spatial and seasonal patterns of vegetation functioning is a key requirement to drive ecosystem productivity and hydrologic models and predict future trends and changes resulting from climate change and land use impacts. Satellite remote sensing generate consistent and systematic observations of the land surface and provide a powerful tool in characterization of vegetation structure, measurement of ecosystem processes, and estimation of primary production and evapotranspiration (ET). In this project we aim to integrate satellite time series with eddy covariance tower flux measurements to more accurately project the seasonal and spatial distributions of water and carbon fluxes across Australian landscapes. The expected outcomes would provide independent assessments of ecosystem fluxes for comparison with and constraining of models, such as CABLE, and improve our understanding of the controls on phenological aspects of function from the major biomes in Australia. Specific goals include,

Desirable skills and qualifications: Relevant prior course degree in either ecology or remote sensing. Some knowledge of image analysis, data processing, or programming Funding: ARC Discovery, AusCover-TERN

The coupling and upscaling of ground- and tower based in-situ biophysical

measurements to satellite imagery. Courtesy of Bigfoot validation site.

Title: Spatio-temporal patterns in vegetation productivity -rainfall relationships and biome resilience with climate variability Supervisors: Professors Alfredo Huete and Derek Eamus Project Description: Large-scale, warm droughts have recently occurred in North America, Africa, Europe, Amazonia, and Australia resulting in major impacts on terrestrial ecosystems, carbon balance, and food security. Understanding how changes in rainfall variability and future climate change impact on regional and continental-scale carbon and water balances are required for policy, planning, management of land and water resources, and assessments of ecosystem health and functioning. In this project, spatio-temporal vegetation responses and sensitivities to changing precipitation patterns in Australia will be examined with high temporal frequency satellite data sets and site level meteorological and flux data information. Water availability generally limits plant growth and production in the landscapes of Australia. However, such biomes may differ greatly in their sensitivity of net productivity to interannual variations in rainfall. The overall aim is to assess broadscale ecological controls of vegetation responses to climate variability across Australian biome types (arid regions to tropical savannas and forests) with satellite data sets. Rain use efficiencies (RUE= annual above ground NPP/annual rainfall) and water use efficiencies (WUE= GPP/Transpiration) will be used to characterize vegetation productivity- water cycle relationships across biomes and climate regimes.

Desirable skills and qualifications: Relevant prior course degree in either ecology or remote sensing. Some knowledge of image analysis, data processing, or programming

Funding: ARC Discovery

Recent drought and flood events in Australia observed with satellite MODIS enhanced vegetation index (EVI) anomalies in 2009-2010.

Title: Interactions of vegetation canopy bio-optical properties with leaf chemistry, structure, and phenology Supervisors: Dr Natalia Restrepo-Coupe and Professor Alfredo Huete Project Description: How plants interact with sunlight is central to the functioning of ecosystems and provides a basis for remote sensing of biogeochemical cycles of carbon and water fluxes at biome scales. Remote sensing data from satellite and in situ spectral cameras capture ecosystem phenological cycles described by vegetation greening or browning, where greening, is generally related to increasing photosynthetic activity. In this project, we aim to investigate biophysical interactions between complex tree-grass plant canopies and incident radiation with an innovative integration of in situ digital spectral cameras, spectral sampling radiometers, and intense measures of a host of leaf and canopy level traits on a continuous diurnal through seasonal basis. This includes investigations of leaf spectral changes diurnally and seasonally as well as relationships between leaf optical properties and leaf traits to assess their seasonal dependencies

Desirable skills and qualifications: Relevant prior course degree in either ecology or remote sensing. Some knowledge of image analysis, data processing, or programming

Funding: AusCover-TERN

Natalia Restrepo-Coupe of C3 group mounts continuous measuring spectral cameras at

Chowilla OzFlux tower site.

Title: On-Farm Adaptation Options in Dealing with Climate Change Risk Supervisors: Dr Qunying Luo and Professor Qiang Yu

Project Description: This project aims to evaluate on-farm adaptation options in dealing with climate change risk. To achieve this aim, both participatory research approach (PRA) and system modelling approach will be utilised. The PhD candidate will directly work with farmer representatives or farmers groups to attain local knowledge about possible adaptation options in the face of climate change. The Agricultural Production System sIMulator (APSIM) crop models will then be used to evaluate the effectiveness of a range of nominated management options in dealing with adverse climate change impact. Cost-benefit analysis will be conducted to help the identification of effective adaptation options. The proposed research is in line with the National Climate Change Adaptation Research Plan: Primary Industries facilitated by the National Climate Change Adaptation Research Facility (NCCARF).

Desirable Skills and Qualifications: The candidate should have strong communication skills in engaging farmers and farmers group and have crop modelling skills including bio-economic modelling.

NCCARF research aims to ensure that Australia’s primary industries will continue to be sustainable by taking advantage

of opportunities and benefits and reducing unavoidable climate change impacts.