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.

New global database to guide coral restoration

James Cook University researchers say a massive new research database will help experts make better decisions about the restoration of coral reefs.

“It’s critical to learn from past mistakes and adapt methods and techniques, to ensure more effective and science-based restoration,” said lead author Dr. Lisa Boström Einarsson, from JCU’s Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER).

Attempts to restore coral reefs have been controversial, but the popularity of coral restoration projects has been growing in recent decades, in response to growing threats to reefs worldwide. 

“Until now it has been difficult for managers, practitioners and researchers to get an overview of global restoration projects, and to assess what methods and techniques may be most suitable for their area and reef type,” said Dr Boström-Einarsson. 

Coral restoration projects typically focus on reintroducing coral to areas where coral reefs are degraded or lost. Common strategies include attaching small fragments of coral, reintroducing baby coral, or stabilising the material coral grows on. 

Dr Boström-Einarsson was part of an international team of scientists that looked at 362 case studies on active coral restoration spanning four decades in 56 countries. The researchers developed a database to document case studies of coral restoration from around the world. 

Dr Boström-Einarsson said on average, survival in restored corals was relatively high, between 60 and 70 per cent, demonstrating that it was possible to successfully grow corals at smaller scales. 

The researchers were surprised at the diversity of corals included in the data set, with over 200 different species of corals studied.  

“It was important to us that the data we collected be widely available to managers and practitioners as well as coral reef researchers,” said Dr Boström Einarsson. “So we developed an interactive tool to explore the database and made the data and the review available online.” 

The research team also identified common issues in programs around the world.

“We found a lack of clear and achievable objectives or appropriate, standardised monitoring and reporting of active restoration projects, along with many projects that were poorly designed in relation to their stated objectives,” said Dr Boström-Einarsson.

Dr Ian McLeod, a Principal Research Scientist at TropWATER, said almost half of the projects did not evaluate any metrics relevant to judging their success. 

“The case studies were dominated by short-term projects, with a median monitoring period of 12 months: far less than the length of time required for a reef to form,” said Dr McLeod.  

Dr McLeod said critics of coral restoration argued it detracted focus from mitigating climate change and other threats to the marine environment and was pointless unless it could restore reefs at the ecosystem scale, but ‘recent research has shown that optimal conservation outcomes should include both habitat protection and restoration’. 

“Restoration is a common and accepted practice for wetlands and shellfish reefs,” he said. “For it to be effective, the trick is to choose methods that match your objectives and set aside funding for appropriate monitoring and adaptive management”. 

Dr Boström-Einarsson said it was critical not to view restoration as a replacement for meaningful action on climate change.

“The increased frequency, intensity and severity of mass coral bleaching is diminishing the time and capacity for recovery between events,” she said. “Well-designed and managed restoration projects have an important role to play, but there is only so much they can do if radical action on the climate is not taken almost immediately.” 

An interactive database of the report can be found here.

This project was jointly funded by the Australian Government through the Reef Restoration and Adaptation Program ( and the National Environmental Science Program.

Boström-Einarsson L, Babcock RC, Bayraktarov E, Ceccarelli D, Cook N, Ferse SCA, Harrison P, Hein M, Shaver E, Smith A, Stewart-Sinclair PJ, Vardi T, McLeod IM. (2020). Coral restoration – A systematic review of successes, failures and future directions. PlosOne. DOI: 10.1371/journal.pone.0226631



Content (infographic, video): here

Photo library:


One size fits none: Tailoring messages to communicate environmental threats

A new publication led by TropWATER postgraduate student Madelyn Pardon describes a more targeted approach to the communication of environmental threats, such as drought, with the aim of increasing the sustainability of the natural resource.

This research aimed to understand peoples’ perceptions of environmental threats to inform threat message construction and branch away from the previous “one size fits all” approach to environmental campaigns. The study used a health decision making model (Extended Parallel Process Model) to cluster individuals based on common cognitive characteristics. The research focused on the context of water security in the drought declared region of Townsville, North Queensland (Australia), where water use was monitored and restricted. A sample of 363 participants was recruited from this region. Participants completed an online survey which asked questions relating to water usage behaviours, perceptions relating to how the water restrictions were communicated, as well as the concerns regarding water security at the time and in the future. Three cluster groups were constructed based on EPPM variables (perceived self-efficacy, perceived response-efficacy, and perceived threat). Each group was significantly different in terms of levels of water-saving behaviour. This research informs a more targeted approach to the communication of environmental threats, such a drought, with the aim of increasing the sustainability of the natural resource.

Link to the published article –

Competitive Summer Internship and Industry Placement with $2,000 bursary – Cairns/Townsville/Mackay

How would you like to join forces with the 2019 national award winners for “Outstanding University and Business Collaboration for National Benefit” for a unique career-enhancing opportunity in marine science and environmental management?

James Cook University’s TropWATER and North Queensland Bulk Ports Corporation (NQBP) are offering a one-of-a-kind opportunity for just two JCU undergraduate and honours students who are interested in pursuing a post-graduate career in marine science or postgraduate research.

What’s on offer

  • A four-week industry-research placement with JCU and NQBP
  • A bursary of $2,000 to help fund flights, and other costs required to undertake the internship
  • Guidance from JCU and NQBP staff during a research and industry application experience over four weeks during the semester two and three breaks between November 2019 and February 2020.

The good stuff

Applicants will gain:

  • Invaluable knowledge in field, laboratory, desktop and administrative skills within a research environment with the Seagrass and Coastal Ecology Group in Cairns and the Coastal Catchments and Water Quality Group in Townsville. These placements will take place over three weeks, with timing and location flexible depending on student location.
  • A one-week placement with NQBP in Mackay
  • Experience for a research and management career or a higher degree in marine biological sciences, as well as offering a unique opportunity to see how results of research are applied in management and operations within industry.

Who can apply:

You must be enrolled in either a second or third year undergraduate course or an honours program at James Cook University.

I’ve heard enough, how do I apply?

Applications close 25 October 2019. To apply, submit a cover letter (maximum one page) describing why you want to participate in the program and what skills you can bring to TropWATER and NQBP Attach your resume (maximum two pages), a copy of your academic transcript and two academic referees Students will be selected based on their academic credentials and application letters. Applicants will be notified of outcomes by 1 November 2019.

Submit your application to Dr Michael Rasheed or

Dr Nathan Waltham

More information:            


Clever little fish

Sometimes animals surprise us. We are familiar with dogs catching frisbee, parrots talking and the cat that ninja-grabs at twine, but fish performing party tricks. Mmmmm what’s going on here?

A quirky behaviour exhibited by a freshwater fish has recently been reported in the Journal Pacific Conservation Biology by a TropWATER researcher and colleagues. A population of coal grunters (Hephaestus carbo) has been found to turn objects over when hunting for hidden bugs and small shrimps. A researcher from TropWATER first noticed the behaviour when taking underwater photos of coal grunters on his weekend. Even TropWATER staff deserve a break from time to time.

Further investigation revealed the fish behaviour to be relatively common at the particular stream where ‘coal grunters were frequently using their snout and nape (top of the head) to flip wood, pieces of bark and large seed pods in search of tiny prey that cling to such objects’ commented the ever shy Dr Ebner. A neat little video clip is available on the TropWATER YouTube channel (

The research team also found it interesting that other species of grunter were present in the stream but did not exhibit the ‘object flipping’ behaviour. The short (2 page) and simple observation based report is authored by Brendan Ebner, James Donaldson and Danswell Starrs, and is available in online-first from the Journal website.

Find out more Email Us Phone 07 4781 4073