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.

Requirements:

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 25^th 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 (Christophe.cleguer@jcu.edu.au).

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.

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:  https://ozfish.org.au/event/edna-sample-collection-ws-burdekin-qld-march-2023/

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 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: https://wettropicswaterways.org.au/wp-content/uploads/2022/08/Reef-and-Rivers-Issue-2_final_spreads_small.pdf

Indigenous rangers and scientists team up to drive coral growth on the Great Barrier Reef during spawning season and beyond.

A team of scientists, First Nations Rangers, tourism operators and conservationists have collected millions of coral sperm and egg bundles at Moore Reef on Gunggandji Sea Country, 50 kilometres offshore from Cairns.

After a week of incubating in custom-designed pools, the coral babies have been  settled out at nearby Hastings Reef, on Yirrganydji Sea Country, in the hope of repairing patches of degraded reef.

The larval delivery project is part of the newly launched reef conservation collective called ‘The Reef Cooperative’, a partnership between Citizens of the Great Barrier Reef, Dawul Wuru Aboriginal Corporation, James Cook University (JCU), Reef Recruits, Mars Sustainable Solutions, GBR Biology and funded by Cotton On Foundation.

The coral larvae project is led by JCU TropWATER and Reef Recruits, who bring years of experience with raising and settling coral larvae and managing complex marine field operations.

JCU’s Dr Katie Chartrand says climate-related disturbances are increasing and the windows for reefs to recover are getting shorter and shorter.

“By using the Great Barrier Reef’s most reproductive time of year – the annual synchronised spawning – we have the potential to significantly boost reef recovery at targeted reef sites,” she said.

“Key to this project is that it’s being delivered with traditional custodians who hold a wealth of knowledge about their local reefs while the research team provides the scientific tools to train those involved.

“This project has been an opportunity to work hand in hand with two local Traditional Owner groups. Sharing our knowledge on spawning and larval rearing is building local capacity to drive conservation outcomes for First Nations peoples across the Great Barrier Reef in the future.”

The team will release 30 million larvae in the project over the next 3 years and build capacity within the community and The Reef Cooperative.

“The transfer of coral larvae from Gunggandji Sea Country to Yirrganydji Sea Country for settling on Hastings Reef is an important opportunity to engage Traditional Owner groups and tell our story about the Great Barrier Reef. Through The Reef Cooperative, we can focus on the Aboriginal cultural heritage dimensions of the Great Barrier Reef, which have not historically been known or told across Australia and the world,” Gavin Singleton, Dawul Wuru Aboriginal Corporation.

These larvae will increase coral coverage over more than 200 square metres of strategically selected degraded reef. The baby corals will have lots of natural predators, but at least 15,000 of them should survive to maturity.

”It’s a privilege to work on this project in collaboration with Traditional Owners. It’s also exciting to be trialling new methods to increase the coverage of high-density larval delivery,” said Dr Kerry Cameron, Reef Recruits.

This project spans two different sea countries, which is only possible thanks to the support and collaboration of the Gunggandji and Yirrganydji people. Gunggandji Elders say Moore Reef has long been known to them as a source reef and they have a strong spiritual connection with it.

“The fusion of Traditional Owner Ecological Knowledge with modern science for the whole world to see and be part of is what the mutually beneficial partnership of the Reef Cooperative is all about, and provides hope for the World Heritage Great Barrier Reef for generations to come,” said Eric Fisher, GBR Biology.

Tim Diamond, GM of Cotton On Foundation says, “Through our partnership with Citizens of the Great Barrier Reef, we are proud to be the founding funders of The Reef Cooperative and supporting the important cultural and conservation milestones for Hastings Reef on Yirrganydji Sea Country. The Reef Cooperative is a unique conservation model in action, driven by innovation and knowledge sharing between Traditional Owners, scientists and conservationists that can help protect and conserve the Great Barrier Reef. We’re looking forward to mobilising our customers and supporters in reef conservation over the next three years of The Reef Cooperative journey.”

Yirrganydji rangers have supported the fieldwork to prepare the delivery site at Hastings Reef and rangers from both groups will help with the collection of coral spawn and raising of the larvae.

The Women Warriors of the Torres Strait – an all-female crew of Traditional Owners, rangers and scientists led by the Torres Strait Regional Authority (TSRA) Sea Team and James Cook University – has set sail as part of the Great Reef Census to survey the northernmost section in the Torres Strait, northern Australia.

The five-day voyage to Mer (Murray Island) by the Women Warriors of the Torres Strait is the first time the Great Reef Census – led by Citizens of the Great Barrier Reef – has ventured beyond Cape York.

TSRA Senior Natural Resource Management Officer and Marine Biologist Madeina David, 24, said the trip served as ‘ethical science’ in the Torres Strait, with researchers and Traditional Owners working together to monitor the Great Barrier Reef, collect data and share findings with island communities to support local decision making.

“Our voyage sets a new course for science to value, respect and incorporate the traditional ecological knowledge of custodians who have cared for land and sea for centuries,” Ms David said.

“We will connect ancient knowledge and modern science to assess the condition of the northern Great Barrier Reef, including water temperatures, coral conditions and even explore the potential for a future turtle sanctuary.”

TSRA Sea Team Manager Moni Carlisle said checking conditions, including marine habitat at Mer, would provide critical insight into the future of the Great Barrier Reef.

“The Torres Strait is the northern tip of the Great Barrier Reef and known as the seagrass capital of the world. As home to globally important marine migratory species, including dugong and sea turtles, it is proving to be vital to the future of the Great Barrier Reef for both corals and sanctuary for species recovery,” she said.

JCU TropWATER’s Dr Katie Chartrand said the expedition was a valuable opportunity to work in partnership with Traditional Owners and rangers to paint a clearer picture of this hotspot of reef biodiversity.

“Using the Great Reef Census, we can rapidly collect thousands of reconnaissance images of remote reefs that have rarely or never before been formally surveyed,” she said.

Dr Chartrand said concerns have been raised of potential outbreaks of crown-of-thorns starfish, flagging the importance to survey this pristine region of the Great Barrier Reef.

“This Census gives TSRA and the local Meriam community a snapshot of the health of the reef habitats – and that’s a powerful strategy in taking steps to protect these extraordinary reefs.”

The Women Warriors of the Torres Strait Great Reef Census voyage is funded by the TSRA and supported by partners including the Citizens of the Great Barrier Reef and James Cook University.