Large-scale seagrass restoration takes root in Tropical Australia

Tropical Australia’s first large-scale seagrass restoration project begins this week in Cairns and Mourilyan, aiming to replenish more than 400 hectares of seagrass habitat devasted by cyclones and La Nina weather events more than a decade ago.

Led by James Cook University’s TropWATER, the initiative will see scientists and volunteers planting thousands of seagrass fragments and sowing more than half a million seeds over the next four years.

The project is a collaboration with four Traditional Owner groups, OzFish Unlimited and local community groups, with funding support from BHP’s Blue Carbon Grants program.

JCU TropWATER’s Associate Professor Michael Rasheed, who leads the team, said the project was built on years of rigorous research and trials.

“This is the first time seagrass restoration has been attempted at this scale in tropical Australia. We’ll be working in partnership with community in partnership with communities and leading researchers in the field.

“For more than a decade, the loss of these seagrass meadows has set off a ripple effect, robbing these ecosystems of their remarkable benefits – as a food source for dugongs and green turtles, and as essential nurseries for prawns and fish.

“It’s critical these habitats are restored, not just for the sake of the marine life they sustain, but for the resilience of our coastal communities.”

Seagrasses are coastal marine powerhouses, capable of capturing carbon from the atmosphere up to 35 times faster than tropical rainforests.

Along with re-establishing the seagrass meadows the team will measure these “blue carbon” storage gains, and will monitor the return of fish.

The initiative brings together Traditional Owner partner groups, including Gimuy Walubara Yidinji, Dawul Wuru, Goondoi and Mandubarra, in safeguarding their Sea Country estates.

The donor seagrass for the program comes from Gimuy Walubara Yidinji country in Cairns.

“We’re pleased to extend assistance and share our resources with our neighbouring communities, including Mandubarra and Goondoi in Mamu country to our south,” Gimuy Walubara Yidinji Elder Gudju Gudju said.

“This collaboration will help restore their lost seagrasses while enhancing our understanding of safeguarding our own,” he said.

“Our Rangers are building strong relationships with JCU scientists and creating valuable opportunities for mutual learning. These partnerships empower our community, rangers, and scientists to exchange knowledge. They foster the protection of our remarkable marine ecosystem for generations to come.”

The team needs help from the community for the project to succeed. OzFish Unlimited’s Dr Geoff Collins is in charge of coordinating community and volunteer engagement for the project.

“Preparing seagrass shoots for deployment takes a lot of time and we value the contribution our volunteers have made to this program to date,” Dr Collins said.

“As we continue to expand this work there’ll be an increasing role for volunteers to help improve seagrass meadows, which are important for the health of our coastal fish stocks.

“We’ll be posting regular notifications and events to let the community know when you can come down to the Marina in Cairns, or the Mourilyan Harbour boat ramp, to help prepare the seagrasses for sowing out on site during September.”

The team will restore five hectares of meadows wiped out a decade ago. They will also work to speed the recovery of 425 hectares of meadows that are struggling to recover from cyclone damage and consecutive years of heavy wet season impacts leading up to 2011.

Associate Professor Rasheed said seagrass habitats are interconnected with the health of the Great Barrier Reef, and the loss of meadows can have cascading effects on the entire Reef ecosystem.

“Climate change is causing more frequent and widespread impacts on seagrass meadows, and we need to take steps to future-proof these ecosystems,” he said.

“This project will show effective restoration methods that can be used throughout tropical Australia and a blueprint for measuring their effectiveness at combating climate change and we’re excited to get cracking on the work this week.”

A gateway to understanding manta rays in the central Great Barrier Reef

James Cook University scientists are studying a previously unknown manta ray aggregation at Holbourne Island – capturing photographs of the mantas’ distinct markings and deploying satellite and acoustic tracking tags.

It’s the first satellite and acoustic tag to be deployed on a manta ray in the central area of the Great Barrier Reef, uncovering valuable insights on how mantas travel and connect with neighbouring habitats.

Funded by North Queensland Bulk Ports Corporation (NQBP), the JCU team will continue to work with Dr Adam Barnett and Ingo Miller from Biopixel Oceans Foundation (BOF) to uncover critical information about these elusive creatures.

The data from the tracking tags will feed into BioTracker and into a broader national research program ‘Project Manta’, which seeks to uncover manta behaviour, movement patterns and population dynamics in Australia.

The manta aggregation discovery was first made by Tony and Avril Ayling, experienced reef monitors and JCU alumni.

Researching the elusive gentle giants

Manta rays, known as the world’s largest rays, boast impressive wing spans of up to 7 meters and are often referred to as the gentle giants of the ocean.

Each manta ray has distinct markings on their underbelly, similar to a fingerprint. By capturing images of mantas’ underbelly, researchers can track individual mantas these unique identifiers.

Lead scientist of the JCU-NQBP coral monitoring program, JCU’s Dr Katie Chartrand, said with limited data on manta populations within the central Great Barrier Reef, the newly identified site offers a valuable opportunity to capture images of mantas and track population movements in the region.

“We know this manta aggregation at Holbourne Island is attributed to a cleaning station. This is where smaller fish species diligently remove dead skin, bacteria, and parasites from manta rays and other larger marine animals,” she said.

“These cleaning stations are fixed to where the cleaning fish set up shop, meaning we will be able to reliably document animals visiting over a long period of time.”

It’s the first satellite and acoustic tag to be deployed on a manta ray in the region, and will invaluable insight s on how mantas travel and connect with neighbouring habitats.

Research support research programs ‘Project Manta’ and ‘BioTracker’

Project Manta has over 1500 individuals recorded in the east coast database, with over 9000 photo-ID sightings. Through its comprehensive photo-ID sightings database and satellite and acoustic tracking tags, Project Manta will be able to fill key knowledge gaps about mantas in Australia.

BioTracker follows sharks and rays using satellite transmitters to learn more about movement and migration patterns, which helps to identify habitats key to their survival, their relationship with other marine animals, population dynamics, and their vulnerability to threats. A network of acoustic underwater receivers feedback additional information on finer-scale megafauna movements.

The Holbourne Island discovery, supported by the long-standing partnership between NQ Bulk Ports and JCU, enhances the research efforts of Project Manta and BioTracker.

NQBP’s has a long-standing marine monitoring partnership with JCU, with scientists undertaking extensive ambient marine environmental monitoring of water quality, coral and seagrass for more than two decades.

Surveying mangrove forests along the southern Great Barrier Reef coastline

Mangroves are nature’s blue carbon powerhouses – capable of capturing and storing significant amounts of carbon – making them a vital tool in mitigating the climate crisis.

They’re also biodiversity hotspots that provide essential breeding grounds for native fish, while stabilising coastline ecosystems and reducing erosion.

But the state of mangrove habitats along the Great Barrier Reef coastline is a growing concern, and until now, knowing if and where we can restore lost forests has remained unanswered.

Funded through Greening Australia’s Reef Aid program, as part of the Blue Carbon Initiative, a team of James Cook University TropWATER scientists have taken to the skies, conducting helicopter shoreline surveys from Cairns to Gladstone.

With a bird’s-eye view, the team assessed the health of these vital shoreline ecosystems, including both forest loss and gain and their continued threats. At the same time, they identified potential sites for restoration and registration as Carbon Projects under the Clean Energy Regulator’s recently released Tidal Restoration of Blue Carbon Ecosystems method.

Shoreline transformation: the condition of mangrove forests along the Great Barrier Reef coastline

Over 80,000 high-resolution geo-referenced photographs were captured during the surveys, providing a crucial baseline of the Great Barrier Reef shoreline condition and a profound insight into what’s being lost.

Lead JCU researcher Professor Norm Duke said the stretch of coastline, with its distinctive blend of wet and dry tropic climatic areas, had not been surveyed to this extent before and early results show vast damage.

“Our observations provide clear, unequivocal and quantifiable evidence of changes to this increasingly dynamic shoreline,” he said.

“We can see the impact of severe tropical cyclones that have battered the region over the past four decades. We can also see extensive shoreline tree loss from erosion, coupled with scouring erosion of salt pans, and retreat of terrestrial shorelines.

“These are thought to be widespread evidence of rising sea levels.”

Dr Duke said observations were consistent with local records of sea level rise over the last half century of at least 4mm per year.

“We believe these changes must be monitored on a regular basis so that we can both manage the impacts, improve the resilience of shoreline marine ecosystems, and guide effective adaptation to the inevitable altered coastal areas.”

Can we restore mangrove habitats along the Great Barrier Reef coastline?

While it’s possible to restore some parts of coastal shorelines, Dr Duke says it’s not the complete answer to the climate crisis for shorelines.

“This project is allowing us to identify locations for restoration of tidal wetland habitats and their capacity to sequester and store carbon – which could help reduce one of the key drivers of global climate change,” he said.

“But our assessments reveal forces at play are far more widespread and active, and simply planting mangroves is not the answer to the climate crisis.”

Dr Duke said there needs to be greater effort into building greater resilience into shorelines, including the repair of damaged areas, and targeted planning for coastal zones to adapt and retreat.

“The complexity of such a response cannot be underestimated, but if we don’t anticipate the inevitable and predictable changes coming our way, then we will be faced with one damaging shoreline disaster after another.”

“As a smart society, if we move quickly, we can be climate change entrepreneurs instead of its ignorant victims.”

Dr Duke said building resilience allows mangroves to migrate upland to survive. This includes providing supratidal buffer zones for the upland migration of mangrove seedlings by controlling things like fires along shoreline edges, removal of smothering weeds, eradication of routing feral pigs, combined with targeted mitigation like the removal of non-essential constructed bund barriers.

Greening Australia’s Director of Reef Aid Dr Lynise Wearne said the project is an exciting opportunity to understand the priorities and opportunities for coastal restoration across the Reef Catchments as Greening Australia pioneers innovative nature-based solutions that benefit communities, economies and the environment.

The shoreline surveys were conducted in May 2023, and scientists will produce a detailed report later this year.


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.


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