Australia's tropical coastline is being encroached upon daily by human development. The complexity of the ecosystems where land meets sea, and of the multiple environmental impacts colliding in the coastal zone, requires a skilled multidisciplinary approach to problem solving. This project will identify and quantify the impact of various human activities (agricultural run-off, pesticides, freshwater diversion, aquaculture effluents, oil) on the ecology and biogeochemistry of coastal habitats along key areas of the north Queensland, Pilbara and Kimberley coasts. The research will address the deep underlying need to understand how subtle shifts in ecosystems can and do impact biota and the chemical balance of tropical coastal waters. Our findings will be shared with, and used by, a broad range of clients developing strategies to regulate or mitigate human impacts.

• Program 1 Objective 4 To improve understanding of the principal physical and chemical oceanographic processes in Australia's coastal and open ocean waters
• Program 1 Objective 7 To understand the dynamics of Australia's marine habitats and ecosystems
• Program 2 Objective 1 To ensure the maintenance of healthy and properly functioning ecosystems, through the development and application of effective monitoring and assessment procedures and sustainable management practices
• Program 2 Objective 2 To improve understanding of the impact of land-based human activities on the marine environment
• Program 2 Objective 3 To provide the scientific basis for the planning and implementation of sustainable multiple use practices in our marine environment
• Program 2 Objective 4 To apply knowledge of the ocean's variability and change, including interaction with the atmosphere and sediments, to the management of marine and terrestrial industries and environmental issues
• Program 2 Objective 7 To improve the sustainability, productivity and environmental performance of aquaculture

• Mangrove communities and estuarine food webs. AIMS does fundamental research into mangroves (and their rehabilitation) because these saline forests export significant energy and materials to coastal ecosystems; providing food and shelter for the juveniles of edible prawns and fishes. Mangrove-lined estuaries are also being studied for their capacity to assimilate and recycle contaminants from land-based sources, including greenhouse gases.
• Strategic basic research into water and sediment biogeochemistry. Biogeochemical signatures and processes inform studies of human impacts in the coastal zone, which range from point source pollution up to major modification of catchments.
• Marine pollution studies. The best technology is being applied to detect trace contaminants in the marine environment. Biochemical responses are also being studied in marine biota in order to monitor sublethal stress levels as an early warning system of chronic pollution.

• To quantify contaminant levels (nutrients, organic compounds, trace elements) in biota, water and sediments in the coastal zone
• To quantify the impact of nutrients and other contaminants derived from coastal catchments on marine biota, particularly with respect to growth rates, abundance, productivity and ecophysiology
• To produce mass balance estimates for nutrients (and some selected trace elements) within the coastal zones of northern Australia and PNG, in order to identify natural and anthropogenic loads
• To provide mass balance and bioindicator information to regulatory bodies in order to encourage policy and practices to mitigate human impacts in Australia's coastal zones

Key clients and stakeholders
ACIAR, CALM, CRC (CZWM), CRC (GBRWHA), CRC (Sugar), EA, Fisheries WA, FRDC, Fuchs (Australia), GBRMPA, QDPI, QEPA, WA DEP, agricultural representative bodies, coastal zone managers, local governments

Funding base (2000-01 figures)
$2,647,432 (Appropriations)$405,371 (External contracts at 1 July 2000)

Contact
Dr Daniel Alongi
Ph: (07) 4753 4314. 
Fax: (07) 4772 5852. 
Email: d.alongi@aims.gov.au

A current public debate suggests that coastal ecosystems and some inshore sections of the Great Barrier Reef World Heritage Area are being impacted by excess levels of dissolved and particulate nutrients derived from terrestrial run-off. This Subproject will examine the ecology and nutrient cycles of selected coastal ecosystems to quantify the nutrient supply in waters adjacent to modified catchments compared with control areas adjacent to unmodified catchments. Other elements of the research program will probe the biological consequences of elevated nutrients upon individuals, species and communities.

• To quantify the effects of run-off on the status of coastal reefs, pelagic food chains and biogeochemical cycles within inshore sections of the northern and central GBRWHA
• To identify mineral elements limiting mangrove nutrition and how these may affect mangrove litterfall and production, including rates of photosynthesis
• To identify and quantify physiological stress responses and tolerance thresholds of selected reef species which can be used as bioindicators of excess nutrients

• To improve knowledge of coastal biogeochemical cycles, especially the fluxes and transformations of nutrients and contaminants through salinity gradients

• Informed public debate about current water quality issues in the GBRWHA
• Identification of a suite of sublethal indicators of stress from excess nutrients that could be used to provide sensitive measures of chronic stress in coastal ecosystems and early warning systems of undesirable changes
• Production of a suite of ecosystem models incorporating biogeochemical fluxes of key nutrients and contaminants through the coastal zone that will allow scenario modelling and contribute to integrated catchment management

ACIAR, CRC (GBRWHA), FRDC, GBRMPA, QDPI, QEPA

Daniel Alongi, Barry Clough, Otto Dalhaus, Paul Dixon, Samantha Duggan, Katharina Fabricius, Laurence McCook, David McKinnon, Lindsay Trott

Dr Daniel Alongi
Ph: (07) 4753 4314. 
Fax: (07) 4772 5852. 
Email: d.alongi@aims.gov.au

Although there is public debate about trends in the water quality of some inshore sections of the GBRWHA, there is little evidence of any gross and/or acute pollution. It is more likely that any human impacts will have been expressed as incremental creep in baseline levels accompanied by subtle shifts in community parameters. Such changes are very difficult to detect by surveys and/or monitoring based upon abundance. It is logical, however, that chronic environmental stress causing ecological change will manifest itself first as physiological changes in vulnerable organisms. Thus this Subproject will first seek sensitive biomarkers for such change. Once available, a suite of suitable biomarkers will be used to survey marine organisms from riverine, lagoonal and coastal reef habitats along the north Queensland coast seeking any evidence of sublethal stress from land-based pollution. Such surveys may be repeated at appropriate intervals to provide a new form of monitoring more suited to the detection of chronic change.

• To develop appropriate biomarkers for organic contaminants that can be applied to tropical coastal fishes

• To extend research on biomarkers into non-traditional taxa such as reef corals and macroalgae

• To survey inshore regions of the GBRWHA for biomarker concentrations in key biota

• More appropriate and/or sensitive methods for detecting sublethal stress in tropical marine ecosystems

• Baseline surveys on biomarker levels that can be used as the basis for monitoring future change in inshore water quality

• Informed public debate about water quality issues within the GBRWHA

Key clients and stakeholders
CALM, CRC (GBRWHA), CRC (CZWM), CRC (Sugar), FRDC, Fuchs (Australia), GBRMPA, QDPI, QEPA

Research team
Wickramasinghe Bandaranayake, Kathy Burns, Sue Codi, Craig Humphrey, David Klumpp, Phil Mercurio (PGS), Diane Brinkman

Contact
Dr David Klumpp 
Ph: (07) 4753 4232. 
Fax: (07) 4772 5852. 
Email: d.klumpp@aims.gov.au

The ecology and biogeochemistry of tropical estuaries is poorly understood. This is a problem because the initial entry point for contaminants into the coastal ocean is estuarine outflow. This Subproject focuses on the processes controlling the fate of contaminants from river catchments to the edge of the coastal zone, and their links with food chains, especially within the central GBRWHA.

A special focus for this research will be the wetlands surrounding Bowling Green Bay (BGB), which are located near the Institute's Cape Ferguson laboratories. The coastal margins around this bay include a broad mixture of developments (cattle grazing, sugar cane, cropping, and sand mining) and a national park of international significance (RAMSAR-listed wetland). The area provides in microcosm a perfect case study for examining the impacts and interactions of mixed developments upon each other as well as individually and collectively upon the natural ecosystems. In addition to the observational study of the whole system and its components, support will be given to land holders interested in wetland restoration and rehabilitation projects.

• To understand processes controlling the chemical fate of natural and contaminant substances in wetlands, estuaries and the continental shelf

• To link these processes to geology and hydrology with ecological impacts on key planktonic and fish communities

• To produce validated models of these processes in order to provide practical information to relevant environmental management authorities

• To test these models by providing scientific advice in support of land holder-initiated lagoon restoration/rehabilitation projects

• Original knowledge about the complex chemical transformations of dissolved and particulate materials as they pass through salinity gradients

• Original knowledge about fundamental but poorly described connections between the land and the sea (e.g. groundwater discharge)

• Scientific information and practical models that will inform management practices within coastal catchments and provide some degree of control over the quality of riverine water flowing into coastal seas

Key clients and stakeholders
CALM, CRC (CZWM), CRC (GBRWHA), Fisheries WA, FRDC, GBRMPA, QDPI, QEPA, WA DEP, agricultural representative bodies, coastal zone managers

Research team
Gregg Brunskill, Kathy Burns, Mike Cappo, Sue Codi, Samantha Duggan, David McKinnon, Diane Brinkman, John Pfitzner, Irena Zagorskis

Contact
Dr Gregg Brunskill 
Ph: (07) 4753 4218. 
Fax: (07) 4772 5852. 
Email: g.brunskill@aims.gov.au

In the Kimberley region of Western Australia, the Ord River catchment is a tropical macrotidal estuary that is being modified by human activity. The most obvious change is that the Ord River has been dammed and the freshwater diverted into a massive irrigation scheme. The impact of reduced environmental flows in the lower Ord can be seen in the siltation of the East Arm of Cambridge Gulf, and the generation of a new tidal bore. Other changes can be expected but there is no history of observations from this remote estuary near the WA/NT border.

As part of its research into estuaries across northern Australia, AIMS will conduct baseline studies in 2000/01 into the sediments, mangroves and nutrient cycles in the East Arm of Cambridge Gulf. Comparable measurements will be made in the West Arm, which offers an unmodified control that retains its natural flows. These initial surveys will be done in collaboration with the CSIRO proponents of a proposed large multi-agency study (the Ord-Bonaparte Program); the AIMS work will become part of that study if the OBP can attract sufficient investment to meet its needs. If this occurs, the AIMS research on nutrient cycles and food webs will link with CMR research on prawn nurseries and links to the prawn fishery in adjacent Joseph Bonaparte Gulf (JBG).

• To measure differences in turbidity, sediments and water circulation between modified and unmodified segments of Cambridge Gulf (CG)
• To map the mangrove communities in Cambridge Gulf and measure their production
• To measure net autotrophy and net heterotrophy in CG and its river arms
• To compile a mass balance estimate of carbon and nitrogen flow in CG in the wet and dry seasons to estimate net transport of nutrients between CG and Joseph Bonaparte Gulf

• A quantitative understanding of historical changes in the sedimentation rates in the Cambridge Gulf since the damming of the Ord River
• A validated model of the hydrodynamics in Cambridge Gulf, including modified and unmodified river channels, that can be used to model sediment transport
• Baseline descriptions of mangrove communities in CG with estimates of production
• Quantification of the human impacts upon mangrove growth and production

Process models for nutrient cycling and material transfers between Cambridge and Joseph Bonaparte Gulfs, showing the relative importance of CG to the productivity of the larger system where there is a significant prawn harvest

Key clients and stakeholders
CALM, Fisheries WA, Ord-Bonaparte Consortium, NT Government

Research team
Daniel Alongi, Barry Clough, Otto Dalhaus, Paul Dixon, Katie Moore, William Skirving, Simon Spagnol, Frank Tirendi, Lindsay Trott, Eric Wolanski