Near shore coral reefs are at the intersection of multiple environmental changes. Some of the changes are driven by human activities at a local scale, while others are driven by human activities at a global scale. Understanding how the local changes modify the impact of the global changes will help guide management designed to mitigate their impacts, and restore coastal ecosystems.

Local stressors, such as eutrophication, habitat modification and destruction, overfishing and pollutant runoff have a substantial cumulative environmental effect in their own right. However, when these overlay increasing global stressors, such as warming of surface waters and ocean acidification, near shore ecosystems can be stressed beyond critical thresholds.

Tropical Ecosystems Hub researchers from Project 5.2 ‘Experimental and Field Investigations of Combined Water Quality and Climate Effects on Corals and other Organisms’ are investigating individual and synergistic effects of water quality and global change on reproduction, larval development and settlement of key coral reef invertebrates, including corals, bryozoa, molluscs and crustose coralline algae.

Experiments undertaken include investigating the effects of light reduction and ocean acidification on seagrass species; the influence of ocean acidification on the thermal bleaching susceptibility of corals; and the effect of sedimentation, temperature and organic nutrient enrichment on the early life history stages of coral species.

Results from these studies will have direct implications for determining environmental thresholds in coastal waters and will inform prioritisation of investment in remediation works. Results may also have direct implications for the management conditions that apply, for example, to dredging operations on the Great Barrier Reef coast.

The findings of the project team endorse those from other projects, including Project 4.1, Project 4.2 and Project 5.3, that improving light availability in coastal marine habitats by reducing the turbidity associated with land-runoff will provide more resilience to future climate change. The project also has strong linkages to, and collaboration with, the Reef Marine Monitoring Program.

Contact Dr. Sven Uthicke ( for more information.




Tropical Ecosystems Hub researchers from the Great Barrier Reef water quality program came together recently with managers and people from industry who are working specifically on pesticide (including herbicide) research, monitoring and management in the Great Barrier Reef for the third meeting of the Pesticides Working Group.

Organisations in attendance included Sugar Research Australia, CANEGROWERS, Davco Farming, Burdekin Productivity Services, Terrain Natural Resource Management, Great Barrier Reef Marine Park Authority, QLD Dept. Agriculture, Fisheries & Forestry, QLD Dept. Environment & Heritage Protection, James Cook University, Australian Institute of Marine Science, University of Queensland, University of Technology Sydney, CSIRO and WWF.

The Pesticides Working Group is a forum for participants to outline and update the latest information from various projects. The scope is not limited to outputs of the NERP and includes other programs such as Reef Rescue R&D, the Paddock to Reef Program and the Reef Protection Package Science Program and the associated policy initiatives.

The expected outcomes of the third meeting were to inform a wide audience on recent activities and changes in managing, monitoring and regulating pesticides; update stakeholders on recent research and knowledge gaps; and determine what we need to know about emerging pesticides for risk assessments.

The meeting of the group heard presentations on current management strategies, including perspectives from the Great Barrier Reef Marine Park Authority; and updates from the Marine Monitoring Program and reforms to chemical reviews from Australian Pesticides and Veterinary Medicines Authority.

Other presentations related to recent research outcomes, including chronic and acute effects of Photosystem II herbicides on seagrass; persistence of herbicides in tropical waters; an update on the load monitoring program; the main outcomes of the integrated Reef Rescue research program; and emerging herbicides.

The working group heard that existing Water Quality Guidelines contained trigger values for toxicants that assisted management but that the management was constrained by an absence of predictability. Emphasis was given to gaining a clear picture of what type of pesticides are in use, where they are coming from, how much is being used and by whom. Workshop attendees were eager to see this type of usage data incorporated into the pesticide registration process, which would help ongoing research and monitoring activity.

It was noted that there is still much to learn about the environmental behavior of pesticides. However, the Pesticides Working Group and ongoing research assimilation and integration will be key activities to facilitate a coherent discussion on the role of pesticides in the condition of the Great Barrier Reef.

Contact Dr Michelle Devlin ( or Andrew Negri ( for more information.




In this issue of the Tropical Ecosystems Hub newsletter, Fiona McDuie and Brad Congdon from JCU provide the first conclusive proof that wedge-tailed shearwaters from the Great Barrier Reef over winter far away in the Northern Hemisphere adding a significant complication to the local management of this species.

Katharina Fabricius from AIMS reports on the first long-term tracking of turbidity in the GBR Lagoon linking the sediments and nutrients in river discharges with water clarity up to 80km from the coast. The positive finding from this research is the ability of the coastal system to sequester these materials and return to clearer conditions, which implies that reducing such contaminants at the source should produce rapid and widespread benefits for water quality.

John Brodie and Jane Waterhouse from JCU have completed an assessment of threats to water quality in the Torres Strait, which is not necessarily influenced by major flood plumes. Their finding that a big risk to regional water quality is the number of vessels transiting through the Straits driven by demand from outside the region reminds us of the broad-scale connectivity of coastal systems and activities.

Bob Pressey and his team from JCU extend this perspective to conservation planning for a changing coastal zone and highlight the cumulative impacts arising from multiple and interacting pressures. In a second project, Bob and others ask how best to invest limited resources in conservation management.

Cathy Dichmont from CSIRO asks whether local communities can find solutions for managing inshore coastal biodiversity. Finally Colin Simpfendorfer of JCU highlights the variable nature of inshore shark nurseries as one example of the multiple values that we are trying to conserve in these coastal systems.

I hope you find something new and interesting in this sample of outputs from the Tropical Ecosystems Hub and that it will make you want to learn more about all 39 projects in the program. As always, the best place to do this is the Hub website:

Dr. Peter Doherty, AIMS

For more information, contact Dr. Peter Doherty at:



2014 is the final year of operation of the NERP Tropical Ecosystems Hub. Research activities in the Hub are due to be concluded by the third quarter of this year and the focus of most Hub researchers has already shifted from research to communication. The importance of communication is because the TE Hub is built on a partnership between a broad range of research-users interested in the ecosystems of north Queensland and the major regional research providers.

In 2011, this partnership provided a forum for translating the Priority Questions from the Australian Government into a portfolio of 39 tasks for the marine and terrestrial ecosystems of the Torres Strait, and World Heritage properties of rainforest and reef. All of these tasks were selected and funded on the basis of their potential to yield new knowledge of relevance to one or more research-user.

The Australian Government requires knowledge to evaluate national policy settings and change them as necessary in the light of new evidence. Regional management authorities (GBRMPA, TSRA, and WTMA) are both portals to others and consumers of information for their own operations. Regional industries, local governments, NRM bodies, and other NGO’s may ask different questions about the same ecosystems.

With the breadth of this client base this in mind, it is satisfying to see the range of new knowledge being delivered by the projects covered by this update. Collectively, they deliver to local, regional, state, and national interests. I invite you to find these connections and I also acknowledge the special endeavours of one project to leave a lasting legacy in the region by building new capacity in our Indigenous partners.

Dr. Peter Doherty, AIMS

For more information, contact Dr. Peter Doherty at:



The NERP TE Hub is now entering its third year of operation. In the last month, milestone reports from every project have been presented to the four Hub Implementation Groups forming the basis for dialogue with our research users around mechanisms for effective knowledge transfer and uptake of results.

It was pleasing to see the richness of outputs emerging from these portfolios. Most projects produced peer-reviewed publications during the period and the strongest performers had multiple papers accepted by the very best journals in their field. There were new discoveries such as the first hard evidence that animals in the Wet Tropics rainforest are responding to climate change in predictable ways, that wedge-tailed shearwaters nesting on the Great Barrier Reef are trans-equatorial migrants that overwinter in Micronesia, that flooding from extreme events affects clarity of the GBR Lagoon long after the freshwater has dispersed as fine sediments are remobilised by the wind, and that the cost of more sediments in the water is slower growth and lower survival of corals.

It was rewarding to see some of these results being taken up by managers with immediate effect. Examples that come to mind include the close collaboration with QDEHP to protect the sole known population of a threatened and endangered frog, the creation of referral guidelines under the EPBC Act for future developments that may impact on turtles and dugongs, the consideration by the DSEWPaC Chemical Assessments Unit of new information on the toxicity and persistence of residual pesticides influencing water quality guidelines, and the provision of expert advice to governments, NGOs and community groups on how to deal with flying foxes in a managed landscape.

It was satisfying to hear about higher levels of engagement with Indigenous stakeholders so soon after the Hub released its Strategy and Implementation Plan. Examples that come to mind are collaborations with Traditional Owners in north Queensland to survey snubfin dolphins, with rangers from the Torres Strait Regional Authority Land and Sea Management Unit to assess the health of coastal vegetation and coral reefs, the employment of Girrigun Indigenous rangers in prescribed burns by Queensland Parks and Wildlife Service of forest habitat supporting endangered mahogany gliders, and the employment of Indigenous research assistants to connect some of the social and economics projects with their communities.

Finally I have been impressed by the work of the communications team at the RRRC to make this new information available quickly and to disseminate multiple messages about the NERP TE Hub program including syntheses and the latest series of Research Snapshots. All of this material can be found on our website ( and I encourage you to visit it on a regular basis. From there you can follow the link to the allied e-Atlas (, which I believe is now one of the largest online compilations of map services in Australia. It is a free public resource that has something useful for nearly everyone.

For further information contact:



A workshop was held on the 5th August, exploring the impact of cumulative pressures on the Great Barrier Reef. The workshop was facilitated by Britta Schaffelke, AIMS, and summarized the outputs from all NERP water quality projects including 4.1, 4.2 and 5.2. The day focused on the measurement of the accumulation of impacts on reef organisms from simultaneous and sequential pressures which are diminishing the ability of the reef to recover to previous states (i.e. impaired resilience).

All stressors/pollutants currently measured on the GBR are interacting through complex responses and processes and require a management response that is aware of how these pressures are working cumulatively across GBR ecosystems.

The main objectives of this workshop were to inform stakeholders about relevant NERP water quality outcomes. In addition and in collaboration with stakeholders, the workshop began a process of developing a GBR-relevant description of cumulative impacts and identified information needs of the research-users. Finally, the workshop identified future research focus areas for experimental ecology/modelling in engaged discussions between researchers and research-users.

Discussion focused on the need to develop cumulative impact assessment policies, accounting for the multiple use of the GBR and the numerous pressures that it faces. The tools available are monitoring, experimentation, models and scenarios built from the outcomes of the driver-response data collected in the NERP water quality projects.

The day was well attended, with researchers and research-users representing Australian Institute of Marine Science (AIMS), RRRC, James Cook University, University of Queensland, Department of Environment and Heritage Protection, Great Barrier Reef Marine Park Authority, World Wildlife Fund, Australian Marine Parks Tourism Operators, Reef Catchments and NQ Dry Tropics.

For more information, contact Dr Sven Uthicke from AIMS at




Understanding the status and trends of the human dimensions within communities of the Great Barrier Reef and adjacent catchments enables better integration into planning and management. Afterall, more than 940,000 people live, work and play in Great Barrier Reef coastal areas, islands, and waters; and the Reef provides employment for about 69,000 people.

Tropical Ecosystems Hub researchers from Project 10.1 ‘Social and Economic Long Term Monitoring Program for the Great Barrier Reef’ have undertaken comprehensive surveys of national residents, local residents, tourists, tourism operators and commercial fishers. And they haven’t finished. The team is currently engaging Traditional Owners, ports and shipping, catchment industries and mining.

The project team engages Great Barrier Reef managers and other research users at all stages of the research process. Consequently, SELTMP represents a significant collaboration between government, industry, community and researchers.

The SELTMP has been designed to describe conditions and trends of the human dimension of the Great Barrier Reef. It is produced on an ongoing basis so that planners and managers are informed of the shifting patterns of use, vulnerability to change, level of well-being and a range of contextual indicators, such as perceptions, attitudes, values, experiences and behaviours.

The SELTMP offers an opportunity to understand and monitor the growing threat of human actions on the Reef and its catchment and the corresponding capacity of industries and communities to face challenges such as climate change, environmental degradation, regulatory change and cultural change, and to better support ecosystem resilience. The monitoring of conditions and trends can alert Reef managers and other decisions-makers to changes in the system, impacts associated with planned or unplanned interventions, levels of public support, and the social and economic trade-offs associated with decision-making.

Better incorporation of the human dimension into Reef management is likely to lead to lower transaction costs, decrease uncertainty associated with decision making, increase public support for management decisions, increase the effectiveness of Reef management strategies, maximise the benefits that people derive from the Reef, and reduce the social and economic impacts associated with management.

To date, the project team has synthesized available data and collected much needed primary data to construct a 2013 snapshot of the social and economic dimension of the Great Barrier Reef and its catchments. The findings are not only valuable information for the GBRMPA Outlook Report and for the GBR Strategic Assessment but may also be useful for regional natural resource management bodies currently assembling regional plans.

Contact Dr. Nadine Marshall ( for more information. Read the 2013 report and an array of supporting information at:



Dr Dan Metcalfe has been named Runner-up in the 'Ecosystems and Communities' category in the 2013 British Ecological Society (BES) Photographic Competition. Dr Metcalfe (Project 7.1 Fire and Rainforests) is Research Program Leader for Ecology in CSIRO’s Ecosystem Sciences Division, based in Brisbane.

The photo was taken at Halloran’s Hill, Atherton, Far North Queensland and shows a fallen pink bloodwood (Corymbia intermedia) and blady grass (Imperata cylindrica) re-sprout, reinvigorated, two weeks after a dry season forest fire cleared the system of the wet season’s accumulation of vines, litter and cyclone debris.

Halloran’s Hill is an extinct volcano on the western fringe of the Wet Tropics of Queensland World Heritage Area.  Fire is a natural part of the dynamics of much of the Australian continent, but rainforest or vine thicket can survive in areas of the tropics where communities are protected from regular fire. The crater of Halloran’s Hill is one such protected area, the rocky rim helping to slow the progress of fire, and the crater keeping the local environment cooler and more humid than the surroundings. This community, named Mabi forest, after the Indigenous name for the Lumholtz Tree-kangaroo which thrives there, is listed as critically endangered with only 4% of its former extent remaining.  Fire is perceived as a threatening process and actively excluded, but Traditional Owners of the area recognise fire as a tool for landscape management, and evidence from pollen and charcoal records demonstrates the resilience of rainforest in the landscape in the presence of infrequent fire. The image was captured about 100 m from the rainforest/woodland boundary, effectively part of the ecotone, and Dr Metcalfe was walking through the fire scar, looking to see what impact the fire had made on any rainforest plants that had recruited under the eucalypt canopy, and whether any rainforest seedlings were recruiting along with the native grasses.

The announcement was made at INTECOL, the International Congress of Ecology, the World’s largest ecology meeting; running in London from the 18th to the 23rd of August and hosted by BES.

Click here to see a full-sized version of Dan's picture.

For further information contact:

Project: 7.1 Fire and rainforests


Tropical Ecosystems Hub researchers have drawn chilling conclusions for the future of specialist rainforest vertebrate species in the Wet Tropics region in a changing climate.

In its fifth Assessment Report, the Intergovernmental Panel on Climate Change (IPCC AR5) adopted four Representative Concentration Pathways (RCPs) for estimating the trajectory of greenhouse gas concentration in the atmosphere. The four pathways, RCP 2.6, RCP 4.5, RCP 6 and RCP 8.5, are effectively measures of the extent to which the Earth’s energy budget will be out of balance in the year 2100 relative to pre-industrial values.

The team from Project 3.1 Rainforest Biodiversity have concluded that, under a low emission scenario (RCP 4.5), about 10% of endemic rainforest vertebrates in the Wet Tropics are expected to be critically endangered by 2085. However, under a high emission scenario (RCP 8.5), similar to what we are currently tracking, nearly 60% of these species will be critically endangered.

Whilst the big challenge is to reduce global greenhouse gas emissions, the challenge for local land use managers and planners is to determine which areas provide refuge for species in a changing environment to maximise conservation of biodiversity.

Identifying areas with high species richness, species turnover or species endemism is an important first step in determining likely refugia both now and in the future. By using conservation prioritisation software, the team ensure that the areas of highest priority incorporate complementarity across both species and sites.

The project team’s analysis included 202 species across taxonomic groupings of birds, reptiles, amphibians and mammals from the Centre for Tropical Biodiversity and Climate Change long term monitoring database. The team assessed climate change impacts on individual species and biodiversity as a whole against the RCP emission scenarios for decadal time steps from present to 2085.

The modelling produced a suite of predictive metrics for use in understanding future impacts on species distributions and the ecology of the animals of the Wet Tropics. The project team focused on two variables from the models, “change in abundance” and level of future “habitat fragmentation”.

The results largely paint a grim picture for the survival of the endemic vertebrates of the rainforests of North Queensland if global greenhouse gas emissions continue to rise rapidly.

The results indicate that, with the “business-as-usual” worst-case scenario (RCP 8.5), great losses in species are predicted to occur by 2085. Coupled with these predicted losses in vertebrate populations in the future, results indicate that populations will be highly fragmented.

Mitigating greenhouse gas emissions and increasing carbon sequestration on a global scale is necessary to avert the worst of the scenarios modelled under IPCC AR5. However, the results of the current research emphasise the importance of identifying local, critical climate change refugia early and maintaining or enhancing connectivity between sites in anticipation of future climate scenarios.

To this end, the Queensland government is now using the methodology developed through this research to identify climate change refugia in the Wet Tropics region with the intention of purchasing land where necessary.



Managers of the Great Barrier Reef’s 900 islands face difficult decisions when it comes to investing in conservation management. So where should they invest limited resources to achieve the best outcomes for management problems?

These conservation decisions must be made in the face of spatially heterogeneous and dynamic threats, including invasive plants and animals and inappropriate fire regimes, and within a constrained budget. NERP Tropical Ecosystems Hub researchers from James Cook University are assembling a decision-making framework for such a purpose.

Project 9.3 works closely with GBRMPA and the Queensland Government to develop a cost-effective approach to prioritising management actions across GBR islands. More specifically, the project’s goal is to maximize conservation outcomes defined by specific objectives for diverse natural features, including native plant and animal species, vegetation assemblages and breeding aggregations.

A decision-support tool with GIS capability will help managers to identify management priorities within and between islands. The project will deliver results that are useful to a range of stakeholder organisations, including state and Australian government bodies, the tourism sector, and conservation planners and managers.

The project covers both Queensland and Commonwealth Islands in the southern sector of the GBR from Mackay to Bundaberg. This region was chosen based on the national and international significance of these islands in relation to vulnerable and endangered species, tourism value, and the likely threats presented by expanding industrial development.

For the initial development of the decision-support tool, 13 islands have been chosen as a representative sample of the southern GBR islands. These islands differ in size, geomorphology, species assemblages, regional ecosystems, threats and commercial and recreational uses. As a result, the selected islands encapsulate the varied challenges for management.

After the initial number of islands has been enlarged, the main project outputs will be:

  1. A compilation of all available data, including quantified expert judgements on islands to set parameters for key variables to be used in the management prioritization.
  2. A novel, cost-effective, transparent, and accountable approach to prioritizing management actions for multiple objectives across islands, designed and understood by GBR managers.
  3. An interactive, spatially explicit decision-support tool for day-to-day use that will allow managers to identify action-specific management priorities within and between islands.

Amelia Wenger, JCU

For more information, contact Amelia Wenger at:

Project 9.3: Prioritising management actions for Great Barrier Reef islands





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