TropWATER’s Dr Ian McLeod wins 2020 Eureka Prize for Applied Environmental Research

James Cook University scientists are celebrating two wins at last night’s ‘Oscars of Australian science’, the Eureka Prizes.

A team of scientists led by the ARC Centre of Excellence for Coral Reef Studies at JCU has won the 2020 Eureka Prize for Excellence in Interdisciplinary Scientific Research.

Social-Ecological Research Frontiers is led by Professor Josh Cinner. The international team includes scientists from seven Australian institutions, with Dr Michele Barnes, Dr Jacqui Lau and Dr Georgina Gurney rounding out the Coral CoE at JCU team.

“We study coral reefs bucking the trend and thriving despite climate change, over-fishing and pollution,” Prof Cinner said. “Some coral reefs have surprisingly high amounts of fish despite high human pressures. We call these reefs ‘bright spots’.”

Studying bright spots can help inform new solutions to tackle the decline of reefs worldwide. The team used a blend of social science, ecology and other disciplines to identify and learn more about these unique areas.

Rebuilding Australia’s Lost Shellfish Reefs has won the 2020 Eureka Prize for Applied Environmental Research.

This collaboration between JCU, The Nature Conservancy, and the Universities of Adelaide and Tasmania has documented the decline of Australia’s once-extensive shellfish reefs and identified what needs to be done to repair and conserve them.

“Early maritime explorers such as Cook and Flinders regularly referred to extensive shellfish reefs, formed by dense aggregations of oysters and mussels,” said Dr Ian McLeod, Principal Research Scientist at JCU’s TropWATER.

From early European settlement of Australia, vast quantities of oysters and mussels were harvested for food and as a source of lime for mortar, until less than one per cent of Australia’s shellfish reefs remained.

“These reefs, which once stretched around our southern coastline, provide food, clean water, boost fish populations and protect our shorelines,” Dr McLeod said.

“Bringing our shellfish reefs back from the brink will reinstate those vital ecosystem services, benefitting the marine and coastal environments and all who rely on them.

“The Australian Government’s recent $20 million Reef Builder commitment to rebuild reefs at 13 locations around Australia is a giant step towards recovering this lost ecosystem and puts Australia and JCU at the forefront of underwater marine restoration.”

Dr McLeod and Adjunct Associate Professor Chris Gillies led the team, with collaborators from The University of Adelaide and the University of Tasmania. The research is supported by the Australian Government’s National Environmental Science Program Marine Biodiversity Hub.

JCU Provost Professor Chris Cocklin congratulated all the researchers involved, along with their collaborating institutions.

“The Eureka Prizes are independently judged, and recognize the very best in Australian Science,” Professor Cocklin said. “To bring home two such awards at the end of a tough year is a great achievement and a well-earned tribute to all involved.”

New marine science scholarships as JCU extends deal with NQBP

James Cook University will have a leading role in safeguarding the reef as it begins a new $5 million, five-year partnership with North Queensland Bulk Ports Corporation (NQBP).

The environmental monitoring agreement expands the current three-year partnership JCU has to track the health of the marine environment around NQBP’s ports at Mackay, Hay Point, Abbot Point and Weipa and will enable new PhD and BSc scholarships based on the work.

Associate Professor Michael Rasheed from JCU’s Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) is co-director of the project.

Dr Rasheed said NQBP’s operational footprint offered a one-of-a-kind opportunity for marine science research and student learning as the government-owned corporation has three ports adjacent to the Great Barrier Reef.

It is the only port authority in the world with three priority ports located on the shores of a World Heritage Area; facilitating $40bn of trade globally, while supporting 27,000 Queensland jobs in agriculture and mining.

“They take their environmental responsibilities very seriously. To this end, JCU provides scientifically robust and credible information on key port marine environmental assets for government agencies, stakeholders and the community,” said Dr Rasheed.

He said that over the next five years, JCU researchers will introduce remote camera systems to replace divers, trial next generation photomosaicing, use Under Water Automated (UAVs) and bring in Remote Operated Vehicles (ROVs) and improved sensors and data loggers.

Professor Marcus Lane JCU’s Deputy Vice Chancellor said the partnership will introduce new scholarships for two PhD and five Bachelor of Science students to work on science relevant to applied management in the port industry.

He said NQBP will provide five $5,000 per annum scholarships for Bachelor of Science (Marine Science) students for three years, a total commitment of $75,000. NQBP and JCU will also fund one PhD scholarship each, worth a combined $200,000 over three years. In addition 10 internships for undergraduate students will be offered.

“This partnership aligns with JCU’s commitment to making sure marine science graduates are some of the best prepared in Australia for employment opportunities in their field,” said Professor Lane.

Dr Nathan Waltham, from TropWATER, is a co-director of the project, and Deputy Director of JCU’s Marine Data Technology Hub. He said the monitoring program is conducted year-round and includes ongoing site visits across NQBP’s Queensland port facilities.

“The program’s footprint is extensive and continually provides our researchers with marine water quality, seagrass and coral monitoring data.  We are also embracing new technology in marine monitoring, as part of our continual improvement and integration of 21st Century technology and learning,” Dr Waltham said.

He said the experience of NQBP’s sustainability and environment team will also make an impact in the lecture hall by way of guest appearances.

“Since 2017, JCU students have worked directly with NQBP staff learning valuable insights about the important marine habitat management in the Great Barrier Reef World Heritage Area. NQBP staff also share their knowledge by presenting at guest lectures for our students,” Dr Waltham said.

Dr Rasheed said other opportunities were also on the horizon for JCU students.

“Looking ahead, while this partnership is built on marine environmental science there are also good opportunities to expand into other areas where NQBP and JCU share interests such as engineering, safety and commerce,” said Dr Rasheed.

JCU Vice Chancellor Professor Sandra Harding said it was an important partnership that stretched back over 25 years.

“Both JCU and NQBP have an enduring commitment to and expertise in the north – the new agreement is a perfect match of capabilities and experience that will benefit the university and its students, the ports and their employees and the environment we enjoy here in the tropics,” she said.

Data collected by the partnership, available on dashboards via NQBP’s website, is used to inform local marine health and reef reporting information.

NQBP CEO Nicolas Fertin says the partnership will build on the “exceptional success” of the three years of the previous arrangement which commenced in 2017.

“The vision is to be the world’s leading university and port industry partnership – and the work we’ve done already has laid some integral foundations,” Mr Fertin said.

“We want to deliver best practice science, monitoring and management of port marine environments while training the next generation of industry and job-ready science graduates.”

Mr Fertin said the work with JCU was key to NQBP’s world-leading environmental approach.

“Extensive ambient marine environmental monitoring of water quality, coral and seagrass by JCU is used to assist NQBP to ensure risks to the environment are managed and ships continue to flow in and out of our ports,” Mr Fertin said.

“The protection of the reef and local environment is of paramount importance to us. The environment is central in our planning, everyday operations and other important activities such as maintenance dredging which ensures trade keeps flowing to service the Queensland economy.”

Video of JCU environmental monitoring operations in the port of Weipa available here

Please see accompanying media alert for details of a media call at JCU Townsville, 10.15am tomorrow, Friday 25 September.


Dr Nathan Waltham (JCU Townsville)
M: 0411 161 161

Dr Michael Rasheed (JCU Townsville)
M: 0400 715 097

Tom Davis (NQBP)
M: 0450 325 047


The seagrass monitoring program covers 30,000 hectares across NQBP’s four trading ports.

Measurements are taken by high frequency water quality loggers which record water depth, root mean square water depth (RMS), temperature, turbidity and photosynthetically active radiation (PAR) every 10 minutes.

With 17 permanent loggers across the four ports, there are almost 900,000 individual marine water quality records collected every year.

Pandora’s box: aquatic biosecurity challenges associated with the freshwater aquarium trade and northern Australian ecosystems

Most of us are familiar with pests and weeds causing problems in freshwater ecosystems. In northern Australia, more notable troublemakers include pigs, tilapia and salvinia. However, a recent report commissioned by the Department of Agriculture, Water and the Environment through the Environmental Biosecurity Project Fund, examines the issue of the many low-profile animals such as small fish, shrimps and snails as well as plants and microbiota that also pose potential to risk aquatic ecosystems in Northern Australia. The report explores challenges and opportunities associated with the global aquarium trade and northern Australian freshwater ecosystems, considering the range of mechanisms by which aquatic ecosystems are being invaded or could become established from a banquet of alien species.

The report contains broad thinking and recommendations that considers agriculture, urban development and remote areas at national and regional scales and is not merely of relevance to those operating within the aquarium trade itself. As a consequence, a broad theme of the report is supportive of translational ecology principles. Translational ecology is a solution focused practice based on regional communities working together with scientists to coexist within ecosystems. The report is based on a relatively wide authorship group of individuals that are active in Northern Australian settings.

For further Information contact Brendan Ebner (E) (P) 0457 925 768

Ebner, B.C., Millington, M., Holmes, B.J., Wilson, D., Sydes, T., Bickel, T.O., Power, T., Hammer, M., Lach, L., Schaffer, J., Lymbery, A. and Morgan, D.L. (2020). Scoping the biosecurity risks and appropriate management relating to the freshwater ornamental aquarium trade across northern Australia. Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) Publication 20/17, James Cook University, Cairns, (97 pp).

Project update: Assessing sea turtle health using bio-electrical impedance analysis

A project update from PhD Candidate Sara Kophamel.

We finished data collection!

After several challenging field trips to the Great Barrier Reef and around Magnetic Island, we managed to examine enough turtles for our project. We have been testing a device called “Bioelectrical Impedance Analyser” (BIA) on over 150 juvenile green turtles to estimate body composition.

The BIA measures Impedance, which can be related to the amount of whole-body fat. Fat is a very good indicator of an individual’s fitness. However, the BIA has never been used on this species, so we had to validate it first. For doing so, we conducted computed tomography scans (CTs), which allowed us to non-invasively measure fat. CT scans help to easily identify fat, as fat has got a lower density than surrounding tissues, such as muscle or organs. Our preliminary data indicate that our validation process is promising, and in a next step we will link the findings from the CT scans to the BIA Impedance measurements.

With our approach, we hope to improve green turtle population assessments by providing a useful, accurate and portable device for measuring body composition.

Figure 1. Ingram Island, North Queensland
Figure 2. BIA measurement on a juvenile green turtle (Chelonia mydas) captured on Ingram Island, North Queensland
Figure 3. BIA measurement on a two-year old juvenile green turtle (Chelonia mydas)
Figure 4. Computed tomography scan of a juvenile green turtle (Chelonia mydas)
Figure 5. Fat analysis on CT scan of a juvenile green turtle (Chelonia mydas)



Using eDNA in the tropics to effectively identify invasive, elusive and rare species

TropWATER researchers have led a new review describing how to better use a revolutionary DNA technique in the tropics, so scientists can more effectively identify invasive, elusive and rare species.

PhD candidate Madalyn Cooper (supervised by TropWATER staff) led the study examining how the collection of environmental DNA (eDNA) differed under tropical conditions.

“It’s no exaggeration to say that eDNA sampling is a revolutionary technology, it’s completely opened up the field of biology and is a massive boost to those working in biodiversity conservation,” she said.

The technique involves taking a sample (usually filtering water from a stream, river or the sea) and analysing it for trace elements of the DNA shed by living creatures. Scientists are able to accurately tell, from a single sample, which fish live in a waterhole or which terrestrial animals have visited it.

“There are some special challenges to using eDNA analysis in the tropics and we wanted to explain what they were and suggest ways to overcome them,” said Ms Cooper.

She said tropical scientists faced logistic challenges in tropical and remote locations, including high heat, UV levels and humidity, high microbial activity, and the impacts of monsoonal events.

“All of this has a detrimental effect on the use of eDNA techniques. What we have done is lay the groundwork for how this might be overcome,” she said.

JCU researcher Dr Cecilia Villacorta Rath said there was still a place for traditional detection methods.

“The eDNA samples generally do not capture data for age, size, and reproductive status, so if we want this information we still need to use traditional visual assessment methods.”

Dr Villacorta Rath said one of the crucial uses of the technology was in combating the spread of invasive species.

“Detection programs are only successful when detection is early. Environmental DNA is a great tool, but it has to be used properly. Early detection of invasive species still requires constant monitoring and rigorous surveillance over large areas,” she said.

Ms Cooper said biodiversity research and conservation management would be transformed in the tropics if eDNA methods and traditional biodiversity field studies were successfully blended.

Main recommendations of the research:

  • Improved understanding of how the complex set of environmental conditions unique to the tropics influence eDNA dispersal, degradation, and detection.
  • Concerted effort to expand sequence databases, not only by haphazard submission of sequences, but a targeted effort to increase sequencing information for tropical species.
  • Established best practice eDNA protocols appropriate for field work conducted under tropical conditions and subsequent laboratory methods that ensure the reliability of the obtained results.



OZFish North Queensland works to improve the health of local waterways

TropWATER Member and OzFish Unlimited project manager for north and far north QLD, Dr Geoff Collins has been working with the Cairns OzFish Chapter, as well as local government and other community groups to improve the health of local waterways. This includes delivering community education and citizen science projects. OzFish recently ran two community events that were well attended by the local communities and resulted in the successful removal of invasive fish species from urban waterways. Both events were well supported by local councils (Cassowary Coast Council and Townsville City Council).

OzFish Unlimited is an Australian charity dedicated to supporting recreational fishers make local fishing grounds healthy, vibrant and more productive. Their active work includes habitat restoration such as resnagging, riverbank planting, fishways, shellfish reef restoration, giant kelp restoration and other projects such as monitoring river health and habitat mapping – anything that can improve, revitalise and protect fish habitat across Australia.

Locally in north Queensland things are progressing – Dr Collins has recently been working with community group NQ Dry Tropics to monitor the movement of fish through vertical slot fishways in the lower Burdekin. Fish monitoring was undertaken in February and captured the period of high flow that occurred immediately after high rainfall. Dr Collins will soon be calling on local fishers to help with further fish surveys in tropical urban systems, in an effort to better understand how fish use modified urban waterways and to identify how they can be better managed to meet the requirements of urban runoff while still providing valuable fish habitat.

OzFish is on the lookout for new members locally to support their project work. To find out more go to: or get in touch with Dr Collins directly on or 0427 992 567.

New paper – using jellyfish to monitor herbicide runoff

Herbicides are an integral part of global agricultural activity but can be advected into local drainages that can discharge to coastal marine systems. Herbicide runoff can impact coastal marine organisms, including those associated with coral reefs and coastal mangrove forests. In this study, the symbiotic sedentary jellyfish Cassiopea maremetens were exposed to analytical grade hexazinone to determine their sensitivity and potential for recovery after exposure to a press herbicide event of 14 days followed by a recovery period of matching duration. Bell surface area, photosynthetic yield (i.e. effective quantum yield, EQY), statolith count and zooxanthellae density were analyzed. Most metrics demonstrated significant decreases when exposed to higher concentrations of hexazinone, while EQY was significantly decreased at exposure concentrations from 31 μg/L hexazinone and above. In contrast, zooxanthellae density (cells/mm2) increased in the highest concentrations compared to control animals. At the end of the exposure period the EC50 for bell surface area, EQY, and statolith count were 176 μg/L, 81.96 μg/L, and 304.3 μg/L, respectively. Jellyfish were able to recover to similar start values for all measured metrics at the end of the 14-day recovery period, with EQY showing recovery by Day 7 of the recovery period. This study demonstrated that statolith counts as an estimate of age were not affected by herbicides. We conclude that the depressed metrics from herbicide related impacts of C. maremetens are effective indicators of a relatively recent herbicide perturbation in that the recovery timeframe for these jellyfish is relatively short.

Full paper here: McKenzie, M.R., Templeman, M.A., Kingsford, M.J., 2020. Detecting effects of herbicide runoff: the use of Cassiopea maremetens as a biomonitor to hexazinone. Aquatic Toxicology, doi:


Citizen science water quality monitoring project in the Whitsunday Region

TropWATER researchers Dr Nathan Waltham and Dr Jordan Iles are engaged with tourism operators to initiate a citizen science water quality monitoring project in the Whitsunday Region. This citizen science project brings together partners from a cross section of the Whitsunday community, the Partners include Reef Catchments, the Mackay-Issac-Whitsunday Healthy Rivers to Reef Partnership, North Queensland Bulk Ports, TropWATER (Centre for Tropical Water and Aquatic Ecosystem Research) at James Cook University (JCU), and Whitsunday Tourism Operators – Whitsunday Bareboat Operators Association, Whitsunday Charter Boat Industry Association.

Find out more Email Us Phone 07 4781 4262