Sediment hotspots: Improving confidence in our catchment models

New research suggests the effectiveness of water quality catchment models – used to identify sediment hotspots in Great Barrier Reef catchments – can be enhanced by incorporating river sediment tracing and independent water samples.

Led by James Cook University TropWATER, in collaboration with CSIRO, Queensland Department of Environment and Science and Griffith University, the research highlights how multiple lines of evidence are critical in improving confidence in model outputs for both policymakers and managers.

Lead author TropWATER’s Dr Zoe Bainbridge said while the spatial model has been continually refined over the past two decades, local field data from the catchment helps to validate the model and accurately identify sediment hotspots.

Using this integrated approach, the four-year study identified the Little Bowen River, Rosella and Pelican Creeks as the largest sources of sediment in the Bowen River catchment. The finding contradicted early estimates of the model, highlighting the importance of using multiple lines of evidence when identifying sediment hotspots.

“There are significant investment opportunities to target remediation at eroding gully and riverbank sites to reduce sediment run-off,” Dr Bainbridge said.

“By adopting these multiple lines of evidence approach, landholders and managers can have confidence that remediation sites chosen are going to result in the best investment outcomes and improved water quality for downstream wetlands, seagrass and coral reefs.”

The landholder monitoring, a collaborative between North Queensland Dry Tropics, landholders and TropWATER scientists will continue this wet season. These additional samples, capturing catchment runoff during different size flow events will provide further confidence in the field data.

The research was carried out in the Bowen-Broken-Bogie tributaries of the Burdekin River catchment, which has been identified as a major contributor of fine sediments to the Great Barrier Reef lagoon.

The study is part of the Landholders Driving Change (LDC) project managed by the NQ Dry Tropics Natural Resource Management body, funded through the Queensland Government (Major Integrated Project) and the partnership between the Australian Government’s Reef Trust and Great Barrier Reef Foundation.

This research was published in Science of The Total Environment under a CSIRO-JCU Catchment Water Quality Science Partnership, and an Advance Queensland Research Fellowship.


Dr Zoe Bainbridge with landholders Mick and Natalie Comerford
Dr Zoe Bainbridge with landholders Mick and Natalie Comerford









Restoring lost seagrass meadows in the Great Barrier Reef

The first meadow-scale seagrass restoration project in Tropical Australia is set to breathe new life into two vital seagrass areas of the Great Barrier Reef World Heritage Area.

Led by James Cook University’s TropWATER Centre, the project will restore crucial seagrass habitats within the Wet Tropics region that suffered substantial losses due to repeated flood events leading up to 2011. The meadows have not recovered since these floods.

Project lead Associate Professor Michael Rasheed said the project would establish targeted seagrass restoration techniques and assess the impacts to seagrass Blue Carbon and the resurgence of fisheries functions in the restored seagrass.

“This project builds on three years of local trials that have developed effective restoration techniques ready to be rolled out on a large scale,” he said.

“We are really excited to partner with four Traditional Owner groups on whose sea country the work will take place as well as recreational fishing volunteers and world leading science teams from three universities, conservation NGOs and industry to deliver this project,” he shared.

“Results of the project will provide critical information toward developing a seagrass restoration methodology for Blue Carbon application in future seagrass restoration programs throughout tropical Australia and importantly leave a legacy of empowered Traditional Owners and Community for long-term stewardship of the restored seagrass areas.”

The project is funded under BHP’s Blue Carbon grant program, which aims to provide funding and support to emerging blue carbon projects.

Girringun lead drone-based dugong surveys with JCU scientists

Hinchinbrook Island historically boasts extensive seagrass meadows and a thriving dugong population, but the region is still recovering from the devasting impacts from Cyclone Yasi more than a decade ago.

In a new program, Girringun Traditional Owners are leading a new high-tech seagrass and dugong monitoring program around Hinchinbrook Island – focusing on fine-scale monitoring to map the elusive dugongs in connection to their seagrass habitats.

The program has TropWATER scientists equipping Indigenous rangers with the skills to utilise small drones for dugong surveys, while undertaking helicopter and boat-based surveys to generate “digital maps” of seagrass habitats.

Funded by the Great Barrier Reef Foundation’s Healing Country Grant, the initiative is driving strong Sea Country management while enriching scientific knowledge. The program is in partnership with JCU, Charles Darwin University and the Girringun Aboriginal Corporation.

Empowering Indigenous-led sea country management  

Girringun Aboriginal Corporation represents the interests of nine tribal groups and six saltwater Traditional Owner groups in the Cardwell and Hinchinbrook region, in North Queensland, with groups holding profound cultural ties and a wealth of ancestral wisdom that spans their respective traditional areas.

Girringun have worked closely with TropWATER scientists for decades in connecting western science and Indigenous knowledge to better manage and protect these habitats.

Jade Pryor, coordinator of Girringun Traditional Use of Marine Resources Agreement (TUMRA), said there had been a growing focus on gathering data on the dugongs and seagrass habitats in the region.

“This program has provided a new generation of Indigenous rangers and Traditional Owners with an opportunity to connect and look after their Sea Country, while actively contributing to building the scientific data required for managing dugong and seagrass,” she said.

Jade said the program has allowed for the continuing growth for employment opportunities for Traditional Owners, and given elders the opportunity to connect with Country and share knowledge with younger generations.

“This has immense value in supporting our People spiritually and emotionally,” she said.

“Our vision is for our People to be self-sufficient in sea country monitoring.”

Hinchinbrook: An important dugong hotspot in the Great Barrier Reef 

Dugongs’ main food source is seagrass – making the health of the seagrass meadows crucial for the survival of the local dugong population.

While seagrass surveys have shown large meadows in the northern Hinchinbrook region, these habitats are vulnerable to the impacts of cyclones and floods, and are still recovering from seagrass loss caused by Cyclone Yasi in 2011.

TropWATER’s seagrass ecologist Dr Alex Carter said despite Hinchinbrook’s reputation as a dugong hotspot, there was limited data on seagrass in the area.

“We hope this ranger-led monitoring program can track the condition of key meadows over time, especially in the face of growing climate-related pressures.”

Alex said the Indigenous-led monitoring was also zooming in to understand the important relationship between seagrass and dugong health in the region.

“That’s the exciting part of this project. We’re gaining a unique insight into how and when dugongs use seagrass habitats, and that’s never been done in this region before.”

To allow recovery of seagrass habitats and dugongs, Girringun have also banned traditional hunting of dugongs, with regular patrols undertaken by Girringun Rangers in partnership with Great Barrier Reef Marine Park Authority Compliance Team and Queensland Department of Agriculture and Fisheries.

Drones, AI and genetics: the emerging technologies

Drones, genetic analysis, artificial intelligence, and animal-borne tracking tags are emerging technologies that can drive robust community monitoring programs – and enable fast collection of scientific data.

TropWATER dugong expert Dr Chris Cleguer said the high-tech program gives Traditional Owners the opportunity to monitor both ecological and cultural important habitats.

“Girringun monitoring program has set an incredible benchmark for future Indigenous-led monitoring programs,” he said.

“We finally have tools that enable rangers and members of the wider community to be a lot more involved and lead their own monitoring programs with remote support from scientists.

“We’re seeing new generations reconnect and care for country, while providing unique data and information that scientists just can’t collect on a frequently bases like sea rangers can.”

The team hope to expand the seagrass and dugong project across northern Australia.

Scientists track one of the world’s most invasive ants in waterways

As yellow crazy ants invade habitat across Queensland, James Cook University researchers have developed a world-first environmental DNA (eDNA) method that can detect infestations of the highly invasive species.

The breakthrough research is the first time scientists have successfully isolated the genetic material of terrestrial invertebrates in waterways.

Lead author, JCU’s Dr Cecilia Villacorta-Rath, said devising a method to detect yellow crazy ants using eDNA was a challenging puzzle.

“eDNA methods work by detecting a species’ genetic material that’s left behind in the environment – but extracting genetic material for non-aquatic species is difficult because you can’t reliably detect the species in the soil,” she said.

“We knew the invasive ant often colonise creek banks, and we knew high amounts of genetic material surrounded these nests, like decomposing ants and larvae. What we didn’t know was how much of their genetic material would make it into waterways.

“This led us to not only develop eDNA methods capable of detecting the ants’ genetic material in the water, but also to detect their presence even when the infestation was 300 metres away from the creek edge”.

Dr Villacorta-Rath said the technology could give management authorities another tool to pinpoint locations of infestations before they become uncontrollable.

“Water samples can potentially tell us whether the ants are present in an entire small stream catchment, meaning we can effectively survey large areas for their presence.”

Yellow crazy ants are considered one of the world’s most invasive species, with outbreaks found in Queensland, and more broadly in Australia and the Indo-Pacific. Left untreated, the acid-spraying ants can increase in density to resemble a moving carpet consisting of millions of workers.

Co-author and Associate Professor Lori Lach said the eDNA technology could help with early detection or tracking the progress of eradication programs.

The big problem with controlling invasive species, like yellow crazy ants, is finding them before they settle into new areas,” she said.

“Detecting infestations early on will reduce threats to native ants, lizards, birds, and other fauna. Human health and agriculture can also be affected if infestations are not detected and treated early.”

JCU’s TropWATER Centre Director and co-author, Professor Damien Burrows, said eDNA analysis was known for monitoring aquatic systems, but terrestrial monitoring was less explored.

“Our research is critical on several fronts. Not only have we found a method to target one of the most invasive species, but we’re also paving the way to fast-track detection of other land-based species,” he said.

“Australia has some of the most biodiverse habitats in the world, which makes biosecurity measures incredibly important in protecting our environment.

“The developments our team is making in eDNA technology have significant benefits for invasive species eradication and detection programs.”

eDNA detection provides another method to detect invasive yellow crazy ants alongside existing methods including luring, trapping, detection dogs, or sightings.

This project is jointly funded through the Australian Government’s National Environmental Science Program through the Northern Australia Environmental Resources Hub and the Established Pest Animals and Weeds Management Pipeline Program – Advancing Pest Animal and Weed Control Solutions.

The Australian Government is committed to the fight against Yellow Crazy Ants and has pledged $24.8 million to address the highly invasive species across Queensland.

This funding is supporting the Queensland Government through the Wet Tropics Management Authority’s Yellow Crazy Ant Eradication Program, as well as through direct funding for eradication efforts in the Townsville Region.

Invasive terrestrial invertebrate detection in water and soil using a targeted eDNA approach, was published in the journal NeoBiota and is freely available here.

TropWATER-led program wins National Award

A TropWATER-led water quality monitoring project has won the Agriculture and Regional Development award at the 34th Banksia National Sustainability Awards.

Under the project, scientists work with growers in the Russell-Mulgrave catchment to monitor water quality and detect runoff ‘hotspots’ at local catchment scales.

The project sees scientists working with growers to understand local water quality processes and find water quality solutions that are relevant to their farms.

Developed through the National Environmental Science Program’s Tropical Water Quality Hub and administered through the Cairns-based Reef and Rainforest Research Centre (RRRC), TropWATER’s Project 25 outstanding success has led to significant further investment and works in the catchment.

New PhD opportunity – Dugongs & drone-based photogrammetry

PhD project opportunity
James Cook University, Australia 

Assessing the body size and body condition of dugongs using drone-based photogrammetry

Assessments of individual animal health and condition can signal early signs of population level effects in wildlife from environmental and anthropogenic factors. Animal health assessments relying on wild animal captures can be challenging, hindering our understanding of the wellbeing of populations. In marine mammals, photogrammetry techniques have been applied broadly for measuring body size and estimating body condition of several taxa including manatees. These methods produce reliable body length and nutritional health estimates and can be used to investigate trends in growth and survival, and to identify regional differences in morphometric patterns.

This project will test and validate photogrammetry methods using small aerial drones for accurate morphometric measurements of dugongs’ body size and condition. The student will also utilize this tool in the field to answer different ecological questions relating to nutritional health in dugongs. The student and his supervisory team will work with multiple partners including academics, NGOs, and Traditional Owners and indigenous and non-indigenous land & sea rangers to collect dugong imagery data to identify regional differences in morphometrics of dugongs in places of high dugong conservation value. In return, partners may be trained to conduct drone-based body condition assessment themselves.

The student will be based in the at James Cook University, Townsville, Queensland, Australia, under the supervision of Dr Christophe Cleguer (JCU) and Associate Professor Fredrik Christiansen (Aarhus University). Travel to Europe (Denmark) may be necessary during the course of the PhD.


The successful applicant will have a First Class Honours (or equivalent) in biological science or a related field and will pick up extra points in the scoring system if they have a first authored paper. Preference will be given to those applicants with previous experience in marine mammals’ biology/bioenergetics and evidence of strong bio-statistical and programming skills. Proven experience in working with Indigenous communities is preferred. Journal publications in these fields are desirable but not essential.  Applicants must apply by 25th April, 2023.

Applicants will need to be familiar with the JCU Higher Degree by Research Requirements.

Funding: A 3.5 year stipend scholarship co-funded by JCU and National Environment Science Program (NESP) is provided ($29,900 pa for 3.5 years, tax exempt).  Funds are available to support equipment purchase and initial field implementation.

Contact: Interested applicants should send their 1) CV, 2) academic transcript and 3) a short (max. 1 page) letter outlining their suitability and interest in the project to Dr Christophe Cleguer (

Inshore reef habitats of Great Barrier Reef islands

From coral trout and snapper to wrasses, butterfly fish and damselfish – the inshore reef habitats of Great Barrier Reef islands are known for their complex and rich fish communities.

This month our scientists are conducting visual surveys of reef fishes and benthic habitats of eight inshore island groups in the Great Barrier Reef, building on a 20-year long-term monitoring program at four of the island groups and four new monitoring sites.

The island reefs surveyed are high-value and high-use for tourism and recreational fishing, with areas monitored in no-take marine reserves and zones open to fishing – making the data highly valuable in understanding how fish communities change over time and how they benefit from marine reserves.

Lead researcher Dr Maya Srinivasan said while some reefs were degraded due to past impacts such as cyclones and coral bleaching, many reefs were in great condition with a variety of live coral and fish species.

The inshore fringing reef monitoring seeks to uncover important insights into fish communities in a range of different habitats, including nursery habitats such as mangroves and seagrasses, island fringing reefs, and deeper areas between reefs.

The program is part of the IMR Reef Fish Monitoring Project, funded by the partnership between the Australian Government’s Reef Trust with the Great Barrier Reef Foundation. This is a joint program managed by the Australian Institute of Marine Science, with support from TropWATER, University of the Sunshine Coast, Great Barrier Reef Marine Park and Queensland Agriculture.


eDNA to improve waterway monitoring of invasive and native fish

TropWATER is working with OzFish and the Townsville City Council to use environmental DNA (eDNA) methods to improve waterway monitoring in the Australian tropics.

The project aims to understand what invasive and native species are in key waterways, to help monitor the health of our aquatic systems and improve management.

Lead researcher Dr Cecilia Villacorta-Rath said eDNA was an innovative and cost-effective technique to identify key species without the need of sighting them.

“eDNA analysis can capture the ‘DNA footprint’ that is left in the water – we don’t need to see the species to detect its presence,” she said.

“By collecting water samples and running an analysis in our lab, we can determine what fish species live in the creeks.”

“Long-term eDNA data will give an insight into the fish communities inhabiting these sampled creeks and how these fish communities change through time.”

Citizen science led programs like OzFish and Creekwatch have monitored the health of local creeks in Townsville using methods such as traps and nets in the past, which are labour-intensive and selective, and not able to capture the whole fish biodiversity present in a waterbody.

Dr Villacorta-Rath said eDNA was a valuable tool for these community programs to gain a more comprehensive understanding of the fish species found in these waterways.

“We have run multiple workshops in Townsville, to train community groups on how to take water samples for eDNA analysis.”

“Anyone can take water samples for analysis and it’s great to see so many members of the public get involved.”

More fieldtrips are planned for the Townsville, Herbert, and Burdekin regions. To participate in the next OzFish eDNA sampling event (being held in the Burdekin), please visit:

This project is funded by the partnership between the Australian Government’s Reef Trust and the Great Barrier Reef Foundation and is being delivered in partnership with OzFish Unlimited, James Cook University (TropWATER) and Townsville City Council.




The benefits of converting flood-prone cane paddocks into melaleuca plantations

The common melaleuca ‘paper-bark’ tree could be a powerhouse in not only storing carbon but filtering farm runoff – and farmers and scientists are teaming up to understand how big of an impact these native trees have.

James Cook University’s (JCU) TropWATER Centre’s Dr Adam Canning is working with Ingham farmer John Cardillo and Greening Australia in a project that’s converted 15 acres of flood-prone cane farm into melaleuca plantations.

The project investigates the amount of carbon stored by these plantations compared to non-restored areas, and their role in capturing nutrients from farm run-off mobilised during high rainfall.

Lead researcher Dr Adam Canning said the research looks at how restoration can fit in with the agricultural landscape, where there are benefits for both farmers and the environment.

“Planting melaleuca plantations on flood-prone farms has dual benefits – they are powerful carbon sinks and can help improve water quality,” he said.

“But if agricultural land is restored, it could be at a production loss to farmers, so we need to think about how restoration can have co-benefits for farmers.

“This project is finding the best way to use these flood-prone paddocks to support the long-term success of the agricultural economy by leveraging emerging ecosystem service markets.”

The research involved buring resin bags in the soil for 12 months to measure the nitrate leaching to aquatic ecosystems, as well as assessing soil carbon and microbiome levels.

Canefarmer John Cardillo, who has been involved in various revegetation projects, said the low-lying paddocks were wasted on cane because they were flood prone.

“Revegetating these paddocks is a good way to use this land,” he said.

“These paddocks are so close to the coast – the planted trees are great for holding sediment and it helps with erosion during floods.

“It might seem like a drop in the ocean, but this all adds up.”

Greening Australia’s Sean Hoobin said, “Land which isn’t good for cane can be converted to carbon farming both from vegetation and blue carbon methods – bringing additional income to landholders.”

“Greening Australia’s work with JCU to measure the water quality benefit of melaleuca wetlands, means that farmers may also be able to receive a Reef Credit payment to increase the overall value of restoration.”

Canning said there’s likely many flood-prone cane paddocks in Queensland that can be converted to melaleuca wetlands, and the results from this project could play big role in future restoration initiatives in the agricultural landscape.

“We have also been scoping the potential for planting over 120 other water-tolerant native tree species in locations across the Great Barrier Reef catchment to support carbon sequestration, nutrient runoff treatment and biodiversity.”

This article appeared in Wet Tropic’s Reef and Rivers magazine:



Seagrass restoration project spans two oceans

James Cook University scientists will lead seagrass restoration research spanning tropical Australia’s two oceans.

Researchers from JCU’s Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) will investigate restoration techniques for key tropical seagrass species, from Queensland’s Great Barrier Reef across to the north of Western Australia.

Their aim is to develop a blueprint for coastal managers to rapidly restore seagrass meadows in high-priority regions.

TropWATER’s Associate Professor Michael Rasheed said future-proofing highly diverse seagrass meadows is crucial to reversing the global downward trend in tropical seagrasses.

“Seagrasses are critical ecosystems,” he said. “They provide habitat for fish, they power coastal marine productivity, and they sequester carbon to help combat climate change – but they’re under increasing pressure from extreme weather events, coastal development and declining water quality.”

Associate Professor Rasheed said climate models predict that future conditions will see more frequent seagrass loss in tropical Australia, making it essential to have tools at hand for effective intervention and restoration.

“We’re investigating the most effective ways to restore different seagrass species, and developing the tools needed for rapid restoration on local and regional levels,” he said.

Professor Rasheed said the project would focus on tropical seagrasses, as most previous seagrass restoration projects have occurred in temperate regions.

Tropical seagrasses can be very different to temperate seagrasses. They have different growth strategies, and they have the potential for much faster recovery once established.

“Some restoration methods applied in temperate systems may not be applicable or transferable to tropical seagrass meadows, which makes our work all the more valuable.

“We’ll investigate methods such as using seeds and cuttings, and new ways they can be used in the field, much the same as many land plants and nurseries operate.”

“We’re going to develop new techniques for tropical seagrass restoration, a blueprint for seagrass-friendly marine infrastructure, and restoration decision tools that can be applied at local and regional scales.”

The project builds on a long-term collaboration with industry partners Ports North and North Queensland Bulk Ports Corporation (NQBP).

“We are proud to support this ground-breaking research that aims to provide practical solutions to safeguard seagrasses and the Reef,” said Simona Trimarchi, NQBP’s Senior Manager of Sustainability and Environment.

The research is a significant next step in TropWATER’s long-term partnership with industry and will benefit from the decades of data already gathered.

“We take our environmental responsibilities seriously,” said Paul Doyle, Ports North’s General Manager of Corporate Affairs and Sustainability. “Together with JCU’s TropWATER Centre we’ve supported seagrass monitoring and research for almost three decades across the ports of tropical Queensland.”

The project is funded by a more than $450,000 Linkage grant from the Federal Government’s Australian Research Council.

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