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Barretts Lagoon – wetland system repair partnership

Coastal wetlands provide habitat for many plants and fauna.  However, many wetlands are under pressure from nutrient, sediments, invasive aquatic plants and fish, changed hydrology and generally experience challenging water quality conditions.  Management is desirable, but is challenging because it is expensive, access is limited and the task in on-going and it works best when all partners participate.

Barretts Lagoon is located on the Tully floodplain, in the wet tropics of northern Queensland.  The lagoon is owned by local farmers and holds important agricultural, community and cultural values, and, like many other coastal waters, its water and habitat quality are important.

Dr Nathan Waltham (TropWATER, James Cook University), funded through the National Environment Science Programme – Tropical Water Quality Hub (Project 3.3.2) recently visited the wetland and met local farmers that have taken a lead in protecting the lagoon by spraying out invasive aquatic plant species with approved best practice methods, and generally ensuring the lagoon is kept clean and looking healthy.

Terrain NRM organised the meeting, which was also attended by Gulnay Traditional Owners, Girringun Aboriginal Corporation, Queensland Parks and Wildlife Service, and Cassowary Coast Regional Council, where a broader plan to wetland and connectivity was discussed.  This partnership will meet again early in  2018 to plan out wetland and waterway restoration actions, scientific data needed, data sharing with landholders, and funding opportunities to build on the already great work completed by local farmers in protecting this lagoon system.

For more information, contact Dr Nathan Waltham (

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JCU’s TropWATER experts support a global gathering to tackle coral reef problems

James Cook University (JCU), in collaboration with Australia Awards, the Department of Foreign Affairs and Trade (DFAT), the Great Barrier Reef Marine Park Authority (GBRMPA), the International Union for the Conservation of Nature (IUCN), and other agencies, has sponsored Reef Ecologic’s International Coral Reef Management and Leadership program, which runs from 6 November to 26 November 2017.
JCU’s TropWATER experts support a global gathering to tackle coral reef problems

Australia Award Fellows snorkelling on the Great Barrier Reef

Current and emerging leaders converged on the Great Barrier Reef to learn and share ideas for tackling the crucial challenge of protecting coral reefs as part of the 2017 International Coral Reef Management and Leadership Program.

Coral reefs are facing unprecedented pressures, threatening globally important biodiversity and compromising opportunities for sustainable economic development.

Fifteen reef managers from seven coral reef nations gathered in Australia to learn from industry experts, many of them JCU scientists. Fellows attended lectures from prominent JCU scientists on topics such as Marine Protected Area (MPA) management, sustainability, reef physiology, emerging threats to coral reefs, and the importance of communications.

TropWATER scientist Dr Ian McLeod provided an engaging presentation on communication strategies, a skill recognised as increasingly important in the world of coral reef management.

“Australia is recognised as a world leader in coral reef management. We have a long history of development assistance from Australia, and this coral reef management program is another example of the wonderful support Australia can provide us in the Maldives,” said Mr Ibrahim Naeem, Director General of the Environmental Protection Agency (EPA) in the Maldives.

“Coral reefs are in crisis, but they are too precious to lose. What we need is a reef revolution. This program of learning has inspired me to work with my government and our stakeholders to find new ways to help coral reefs, which are so vital to the people and economy of Saint Lucia, in fact to all of the eastern Caribbean,” said Mr Thomas Nelson, Deputy Chief Fisheries Officer in Saint Lucia.

Involving an exciting schedule of expert presentations, immersive learning and the memorable personal experiences of snorkeling on the Great Barrier Reef, the program provided a unique opportunity for coral reef managers from across the globe to strengthen their leadership skills and form alliances that can underpin national and regional actions that will help coral reefs.

The program included a field trip to JCU’s Orpheus Island Research Station (OIRS), a distinctively academic and adventurous setting, where Fellows snorkelled amongst giant clams and tropical fish and undertook leadership challenges providing crucial skills for when they return home.

“It’s an immersive project that provides unique opportunities for the Fellows to share ideals and exchange knowledge. We go on a journey together to improve the capacity of people throughout the world with the outcome that they are better prepared to manage coral reefs in their own countries,” said Dr Adam Smith, director of Reef Ecologic.

Each is hoping to take lessons learnt in Australia home to their respective countries, implementing effective coral reef management in their own contexts.

“The people of Fiji are coral reef people. They all want to help coral reefs cope with climate change. The things I have learned in Australia will help me empower Fijians to be strong and proud stewards of their coral reefs. That is the future for conservation in my home,” said Tomasi Tikoibua, from Fiji’s Institute of Applied Sciences, the University of the South Pacific.

This is the third year of the International Coral Reef Management and Leadership Program. Australia is privileged among coral reef nations to have such globally-significant expertise and to be able to help other nations who share a strong dependence on these majestic and productive ecosystems.

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$3 million ports partnership to benefit JCU tropical marine research

A new research and monitoring partnership between James Cook University and North Queensland Bulk Ports (NQBP) worth more than $3 million over 3 years will be signed today in Mackay.

Green Turtle_$3M Ports Funding_2017
Green turtle
JCU’s Vice Chancellor, Professor Sandra Harding said the agreement brings together JCU’s world leading expertise in applied tropical marine science and provides a pathway for student engagement with industry.

“This partnership epitomises JCU’s commitment to ensure its research is focused on creating a brighter future for the tropics and towards promoting student programs that create excellent post degree job opportunities,” she said.

NQBP General Manager Engineering and Development Dr Rochelle Macdonald said the partnership was part of the company’s program to ensure its environmental monitoring programs and stewardship are truly world class.

“NQBP is the only port authority in the world to manage three priority ports located on the shores of a World Heritage Area. As such, it is vital to us that we lead the way in monitoring and research within the port environments we manage,” she said.

Scientists from JCU’s Tropical Water & Aquatic Ecosystem Research Centre (TropWATER) will be responsible for keeping an eye on the marine environment at four of NQBP’s sites.

Dr Michael Rasheed, the TropWATER co-director of the partnership, said the centre will monitor water, seagrass and coral at the ports of Mackay, Hay Point and Abbot Point, all adjacent to the Great Barrier Reef, as well as water and seagrass quality at the Port of Weipa in the Gulf of Carpentaria.

“What we do is provide them with independent environmental data collected in a scientifically rigorous manner,” he said.

“We’ll be watching what happens to water quality at 18 separate points, and checking on seagrass at 23 meadows. We’ll also be monitoring six different sites to keep an eye on the coral.”

Dr Rasheed said established methods such as helicopter surveys, divers and boat-based camera sleds will also be used as part of long term assessments of seagrass and coral health.

Dr Nathan Waltham, co-director of the research program, said the scientists’ equipment will be state-of-the-art.

“For instance, we have a device, custom built at TropWATER, that uses optical backscatter to monitor sediment deposits. These instruments also continually record turbidity, temperature, depth, wave energy and photosynthetically active radiation at 10-minute intervals.”

“These high frequency water quality loggers will be located next to important marine habitats, including seagrass and coral, to assist in tracking changes,” he said.

TropWATER currently monitors all four ports, (as well as six other Queensland ports for other port authorities), in an arrangement stretching back more than 20 years.

NQBP Senior Manager Environment and Planning Kevin Kane said the agreement built on the already long-standing relationship between the two organisations that has been delivering world-leading research.

“The partnership with JCU will provide NQPB with an integrated and scientifically rigorous marine water quality and sensitive marine habitat program that will assist port operations, as well as meet community expectations for high standards of environmental stewardship and management.”

He said the new agreement will see the current monitoring regime extended to other areas of the environment.

“The integration and expansion of our current programs and sites under this partnership will result in significant gains to the effectiveness and value of the science and information collected.”

Link to images and video here.


Dr Michael Rasheed.

North Queensland Bulk Ports Corporation: Kirsty Mugridge | Media and Community Engagement Advisor
07 4969 0772 |

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Eric Wolanski has been appointed on the European Union DANUBIUS-PP Scientific and Technical Advisory Board

Eric Wolanski has been appointed on the European Union DANUBIUS-PP Scientific and Technical Advisory Board (STAB; see;

DANUBIUS-RI will be a pan-European distributed research infrastructure dedicated to interdisciplinary studies of large river–sea systems. It will enable and support research addressing the conflicts between society’s demands, environmental change and environmental protection in river–sea systems worldwide. The DANUBIUS-PP Consortium comprises 29 partners from 16 countries, and includes representatives of 2 ERICs (ICOS & EMSO). The partners include universities, research institutes, and specialized government bodies.

The committee members are:

  •  Professor Vanda Brotas (University of Lisbon)
  • Dr Deborah Chapman (University College Cork)
  • Peter Heininger (retired from German Federal Institute of Hydrology)
  • Professor Jesus Marco de Lucas (Spanish National Research Council)
  • Professor Eric Wolanski (James Cook University)

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Burdekin Water Futures – TropWATER presenters

The Burdekin Water Futures Group was established in 2006 to facilitate a more strategic approach to water management in the Burdekin River catchment. Burdekin Water Futures is a consortium of Government, community, industry, businesses, farmers and scientists working together, sharing information and knowledge, for the long term management and protection of the Burdekin catchment.

A forum was held this week where presentations from Government, industry, scientists and community were heard covering a range of important environmental topics and new information relating to water delivery/storage, irrigation management, cane production, ground and surface water, and aquatic ecosystems. TropWATER's Dr Stephen Lewis and Jane Waterhouse presented an overview of data and information relating to the Burdekin catchment.

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Call to stop African eco-disaster in the making

A James Cook University scientist has warned of an environmental catastrophe in Africa’s world-famous Serengeti if planned new dams are built.

JCU’s Professor Eric Wolanski is an internationally recognised expert on interactions between water and ecosystems. 

He collaborated in this study with top level managers from the Tanzania National Parks organisation, culminating in an article published last week in the scientific journal Oryx published by Cambridge University Press - The Serengeti will die if Kenya dams the Mara River.

Professor Wolanski said the proposed dams in Kenya are a disaster in the making.

“The Serengeti ecosystem has only one year-round river, the Mara. If these dams are built there will be insufficient water to support the ecosystem in a drought year.”

The Serengeti hosts an annual wildlife migration of up to 2 million animals - mainly wildebeest, zebra and other species that live on the plains.

Dr Wolanski said seven dams are in the planning stages.

“The proposed Norera dam is 30 kilometres upstream from the Serengeti ecosystem, and the recommended minimum flow to support the environment is 300 litres per second, but the dam would release just a third of that.

“On top of that, all that water would be used by irrigators downstream of the dam before the river enters the Serengeti ecosystem. If that dam is built, the Serengeti will almost certainly face ecological collapse during the next major drought,” he said.  

Dr Wolanski said if the more than 1.2 million wildebeest involved in the migration cannot use the Mara River in a dry year, modelling suggests that 80 % would die.  

He said water diverted for hydropower in Kenya would also flood the nesting sites of three-quarters of Africa's lesser flamingos around Lake Natron in Tanzania.

Dr Wolanski said the dams are an international issue, as they would be built in Kenya, and the river flows from there into the Serengeti in Tanzania. He said that Kenya gets all the economic benefits, while Tanzania gets all the environmental problems.

“In a dry year, the Kenyan operator has either to release water for the Serengeti and kill the Kenyan irrigation fields or retain the water for irrigation and kill the Serengeti. This becomes a local political decision, with Tanzania having no say.”

Dr Wolanski said it was no exaggeration to say an international effort was needed to save the Serengeti.

“Tanzania has to be involved as an equal partner with Kenya in the decision-making about managing the Mara and Ewaso Ngiro Rivers. If that’s not possible, then the financing of these dams must be stopped.”

Contacts: Professor Eric Wolanski, FTSE


P: 07 4781 5453

M: 0408 89 71 07

Images here.

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3 post-doc positions going at TropWATER, JCU

TropWATER @JCU has 3 post-doctoral level positions available. These vacancies are now open and candidates can apply online via Jobs@JCU.  Applications will close at Midnight on Sunday 22 October 2017.  These positions will also be advertised in various online sources (Water Jobs, Uni Jobs, seek etc.). 

These are Academic level A or B positions (depending on experience):

  1. Position 16146 will mainly work on wetland systems repair in the GBR catchments and Torres Strait, plus coastal ecology, habitat enhancement/restoration, coastal water quality in ports and aquatic ecology projects in Gulf of Carpentaria/Cape York.  Good all round ecology skills required.  Lots of variety in this position.
  2. Position 16147 will work on eDNA.  The position will focus on answering ecological questions about the abundance and distribution of various rare and exotic aquatic animal and plant species in northern Australia, using eDNA as the tool for these investigations.  The person should have at least some genetics background but if not strong, they will be working as part of a team of post-docs that possess considerable lab genetic skills.
  3. Position 16148 will work on freshwater ecology.  Like 16146, this position will cover water and sediment quality, fish, invertebrate and riparian vegetation study so a wide variety of ecology skills is required.  This position will mostly work on projects related to mining and industrial impacts on freshwater environments.

For enquiries contact Prof. Damien Burrows:
P: 07-47814262

Also see our website at for some ideas on the range of projects we work on.

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PhD opportunity: Environmental DNA for the management of aquatic biodiversity of northern Australia (PhD top up scholarship available)

JCU is home to a team of eDNA researchers who are developing rapid and cost-effective technology for monitoring aquatic species in Northern Australia with practical monitoring and assessment applications.  We are looking for enthusiastic, dedicated and passionate PhD candidates to join our team.

To appropriately manage the aquatic biodiversity of northern Australia, especially in the face of pressure for development of water resources, there is a requirement to have a greater understanding of faunal distribution, abundance and occurrence patterns, especially for key species of high conservation status or other special interest (e.g. exotics species, cryptic species).  There is a need for an approach that can rapidly increase data on the occurrence of aquatic fauna to more effectively manage their populations and to further our understanding of key drivers of population vulnerability/resilience. Being able to conduct more frequent and widespread survey/sampling/monitoring of key aquatic species of importance in northern Australia would greatly assist decisions around appropriate development of northern resources and the current discourse about northern development.

This project will take advantage of the rapidly growing field of eDNA.  Organisms constantly shed DNA into their environment (eDNA) and this can be utilised to determine their presence in place of traditional sampling methods. eDNA field sampling can involve as little as collecting water samples and subsequent laboratory analyses. Consequently, the method offers the potential for research and monitoring programs to be conducted rapidly, at lower cost, across a large array of locations, and to involve the participation of non-specialists.  

This PhD project will develop and employ eDNA technology for species of conservation and/or management significance. The project can be shaped to the students interests, but may focus on:

  • Development and validation of probes for species of conservation and/or management importance in Northern Australia.
  • Development of a metabarcoding approach to target a range of species of interest.
  • Investigation of the relationship between water quality parameters, sampling procedures, sample transport time and DNA degradation and detection rates.

The student will be based at James Cook University, Townsville, Australia (under the supervision of Prof. Damien Burrows and Assoc Prof Jan Strugnell). The student will receive expert training in fieldwork and laboratory and bioinformatics skills and work as part of a team of 3 post-docs working on eDNA, and other leading aquatic researchers.

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. Applicants must be eligible for an Australian Postgraduate Award (APA). Preference will be given to those applicants with previous experience in genetics and/or evidence of strong technical and laboratory skills. Journal publications in these fields are desirable but not essential. A top-up ($10,000) per year for three years is available for this project.  Operating funds are also available.

Enquiries are welcome. Please submit a short cover (1 page max.) letter detailing your suitability and interest, academic transcript and a CV with contact details for two referees by email to:

Prof Damien Burrows and Assoc Prof Jan Strugnell


Also visit

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Deadly fish pathogen detected in the Tully River catchment

Erin and Sue processing eel-tailed catfish in North Queensland
Erin and Sue processing eel-tailed catfish in North Queensland
A dangerous pathogen, which caused devastating losses in the aquaculture industry in the United States, has been detected in wild Australian catfish for the first time. Murdoch University researchers from the Centre for Fish and Fisheries Research who made the discovery, say the bacterium causes a potentially fatal disease called enteric septicaemia of catfish. The bacterium, known as Edwardsiella ictaluri is considered one of the most significant pathogens of farmed catfish in the United States and has also caused mortalities in farmed and wild fishes in many other parts of the world. It has previously been detected in imported fish and aquarium facilities in Australia but wild species had not been surveyed for the disease until this recent study.

The researchers say more investigation is required to determine the susceptibility and tolerance of native fish species to the bacterium. They also want to clarify whether E ictaluri is a recently introduced or a native strain. Lead researcher Associate Professor Alan Lymbery said if the pathogen affects Australian fish species in a similar way to cultured catfish in the USA, the delicate freshwater biodiversity of Australia’s rivers could be impacted.

Murdoch University researchers, Erin Kelly and Sue Gibson-Kueh made the trek to the east coast to process the specimens, and TropWATER’s Brendan Ebner and James Donaldson were the field crew responsible for collecting catfish from several of the east coast river sites. Erin and Sue discovered the pathogen in eight of 20 wild catfishes (Tandanus tropicanus) caught from the Tully River catchment. Catfish caught in 14 other locations across northern Australia were not found to carry E. ictaluri, but Professor Lymbery said the presence of the pathogen could not be ruled out from other rivers because sample sizes were small.

The ornamental fish industry in Australia has been valued at $350 million, with up to 15 million fishes imported and 700,000 exported per year. If Australia can no longer claim pathogen-free status, this trade may be affected. Aquaculture, currently Australia’s one of fastest growing primary industries, may also be impacted.

Although catfish species are particularly susceptible to the disease, E. ictaluri has affected an increasing number of non-catfish species, including salmonids and barramundi and thus may represent a threat to cultured fishes as well as Australia’s unique freshwater fish species. Infection with E. ictaluri results in acute, often fatal septicaemic disease or a chronic infection. Those that survive infection may become carriers for up for 200 days, serving as a reservoir of infection. Affected fish often swim in tight circles, chasing their tails or hang in the water with the head up and tail down. Professor Lymbery said more sampling was required to determine the geographic range of E. ictaluri in Australia, and to inform management actions.

Dr Ebner also commented that it is totally unknown what these means for the fish fauna of the Tully catchment and the nearby rivers of the Wet Tropics. What we do know is that the local endemic species of catfish Tandanus tropicanus is a host for the pathogen and so at least one of our highly localized endemic species is potentially affected negatively.

Due acknowledgment goes to Associate Professor, David Morgan for networking to assemble a wider team of fish ecologists for collect specimens across the breadth of Northern Australia. The study was funded by Fisheries Research and Development Corporation through the Aquatic Animal Health Subprogram. The study was a collaborative venture between Murdoch University, the Department of Primary Industries and Regional Development, CSIRO, TropWATER James Cook University, Charles Darwin University, the Museum and Art Gallery of the Northern Territory and the Queensland Department of Agriculture and Fisheries.

The research was published in the Journal of Fish Diseases.

Kelly, E., Martin, P. A. J., Gibson-Kueh, S., Morgan, D. L., Ebner, B. C., Donaldson, J., Buller, N., Crook, D. A., Brooks, S., Davis, A. M., Hammer, M. P. Foyle, L. Hair, S. and Lymbery, A. J. (On-line first). First detection of Edwardsiella ictaluri (Proteobacteria: Enterobacteriaceae) in wild Australian catfish. Journal of Fish Diseases DOI: 10.1111/jfd.12696

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