Backgrounder: Climate change and the tropical marine environment

Coral reefs and mangrove forests contribute greatly to tropical coastal productivity and provide habitat for myriad fish and other species. These important ecosystems are under unprecedented pressure around the world due to declining water quality, over-exploitation and climate change.

Australia has some of the healthiest coral reefs on the planet due to our low population density and strong environmental management. The best-known systems are the Great Barrier Reef in Queensland and the Ningaloo Reef in Western Australia.

Corals thrive in locations that also happen to be near their physiological limits, making them sensitive to stresses caused by sea temperature anomalies resulting in the phenomenon known as coral bleaching.

Corals are also potentially threatened by ocean acidification linked to rising carbon dioxide (CO2) in the atmosphere, which impairs the ability of calcifying organisms to build their skeletons.

AIMS contributes to understanding the implications of a changing climate by monitoring, reconstructing and modelling the changing ocean climate, assessing impacts of climate change on coral reef and other organisms, identifying potential adaptation mechanisms, and identifying characteristics and locations that may provide refuges for marine species in a rapidly changing world.

What we know

Carbon dioxide

  • Atmospheric levels of CO2, the main greenhouse gas, which is measured at many locations around the world, have been rising steadily for decades and the rate of increase is accelerating. Measurements taken for CSIRO Gaslab from the AIMS headquarters site at Cape Ferguson in north Queensland show the level of atmospheric CO2 has risen from 355 ppm (parts per million ) in 1992 to 385 ppm in 2009. This is a steady increase of approximately 1.7 ppm per year and consistent with the 40 per cent increase since the late 18th century (World Data Centre for Greenhouse Gases).
  • The amount of CO2 in the atmosphere is increasing and about 30 per cent of the extra CO2 dissolves into the ocean. Consequently, the chemistry of the oceans is changing and becoming more acidic.
  • A growing body of experimental evidence shows that seawater acidified to mimic potential future scenarios significantly affects the health of some fish and coral species. There are many millions of species in the ocean and each has particular sensitivities to acidification and will respond in different ways. No single species lives in isolation and we don’t yet know how the effects on individual species translate to an ecosystem response. It is likely that acidified seawater will alter the makeup of marine ecosystems (as recently demonstrated by AIMS’s research in a naturally high CO2 environment) and weaken coral reef structures.


  • The long-term average surface water temperature of the Great Barrier Reef has increased by about 0.5 oC since the 19th century. The Reef system has experienced two mass coral bleaching events (in 1998 and 2002) caused by long periods of exposure to unusually warm seawater. Significant coral bleaching was also observed in early 2011, due to thermal stress, on Ningaloo Reef in Western Australia.
  • Warming waters along Australian tropical coastal regions have already resulted in southward shifts in climate zones, which are especially obvious in northern Tasmania.
  • Sea surface temperatures have been increasing over the past century and climate models predict this trend will continue. The full implications for coral reefs will only be understood with more research and monitoring but it is highly likely that the makeup of ecosystems will change. It seems likely that reefs will continue to exist, but with a loss of diversity and changes in community composition. We are also likely to see shifts in species to different parts of reefs, depending on how they adapt, or otherwise, to the changing conditions.


  • During the 1998 coral bleaching event, 42 per cent of shallow water coral reefs on the Reef bleached, and an estimated 2 per cent died that year. This equates to approximately 400 square kilometres of reef area.
  • In 2002, the largest bleaching event on record, an even greater proportion of the Reef bleached (55 per cent) and an estimated 5 per cent died. This equates to approximately 1000 square kilometres of reef area.
  • While these percentages may seem small, more frequent disturbances will increasingly compromise our coral reef ecosystems.
  • Coral bleaching was again observed in the 2006 summer in the southern Reef, where local water temperatures reached around 1–2 oC above the seasonal average.
  • Coral reefs may take 10 to 20 years to recover from serious bleaching events, which can cause coral death or sublethal effects that result in one or two years of reduced growth and no breeding.
  • Heat stress causes corals to expel the symbiotic algae they host in their tissues. What is not sufficiently understood are the numerous mechanisms that may let corals adapt to new, warmer and potentially more acidic conditions. Theoretically, there are no barriers to this adaptation but whether the rate of adaptation will be sufficiently fast is unknown.
  • Coral reef ecosystems depend on the interaction of microbes with each other and with their hosts, such as the central relationship between coral and its symbiotic algae and bacteria. Microbes are centrally involved in the physical processes concerned with phenomena such as the carbon cycle, where they convert CO2 into nutrients.

Extreme climate

  • Tropical cyclones are an occasional source of physical disturbance to coral reefs and, although tropical cyclones may not become more frequent, when they do occur in a warmer world they are likely to be more intense.
  • The El Niño–Southern Oscillation (ENSO) is the major source of yearly variability in tropical climates. It has a major influence on Australian weather, with drier conditions across northern Australia in El Niño years and wetter conditions during La Niña events. How ENSO frequency and intensity may change in a warming world is still unclear but any change would have significant impacts for Australia.
  • Potential changes to ocean currents and circulation patterns are also likely and there is already evidence that the East Australian Current is strengthening and penetrating further south. Such changes will affect reef connectivity, which, for example, influences recruitment of larvae on reefs. Precise projections are not available yet.
  • More extreme rainfall and river flows have been predicted and may lead to greater flows of freshwater and terrestrial runoff into reef systems. Recent evidence from proxy climate records in coral cores from the Reef suggest this is already happening.
  • AIMS’s latest research indicates that tropical rainfall has already become more variable, which is consistent with a warming world where extreme wet and dry events occur more often. Using AIMS’s coral cores—Australia’s most comprehensive library of coral cores from long-lived Porites corals—researchers were able to reconstruct northeast Queensland summer rainfall back to the late 17th century, providing over 300 years of records to examine past climate variability and change. View more on this topic.
  • Even without changes in total rainfall, warmer air temperatures (as already observed for Australia) will enhance the intensity of drought conditions. This may have a secondary effect where loss of vegetation due to the drought may lead to increased terrestrial runoff when droughts break. Declining water quality from drought-breaking floods can reduce coral diversity and increase seaweed cover on inshore reefs.
  • Global sea level has already risen approximately 20 cm since the late 19th century and is observed to be rising around Australia's coast.
  • Ecosystems operate in a complicated environment and while there is a growing body of data about how marine organisms respond to warmer seawater temperature, or increased acidity, far less is known about how these organisms will function and respond when both of these parameters change.
  • Of key concern for sustaining our valuable tropical marine ecosystems is the current rapid (and accelerating) rates of change in their environment. We need to understand the capability of marine organisms and ecosystems to successfully respond.

AIMS research

AIMS does research that underpins our current understanding of how a changing climate associated with global warming and increased acidity of the ocean may affect coral reef ecosystems.

AIMS bases its assessment of current conditions and likely future scenarios on verifiable data gained in the field, from a range of laboratory-based experiments, and from its unrivalled collection of coral cores dating back hundreds of years.

The consequences of increasing atmospheric carbon dioxide

CO2 in the atmosphere has risen to 394 parts per million (ppm) in 2011 from about 270 ppm before the industrial revolution started in the mid-18th century. Measurements of atmospheric CO2 taken from AIMS headquarters outside Townsville agree with this global figure.

Under current Intergovernmental Panel on Climate Change projections, and assuming no measures are adopted to reduce CO2 emissions, atmospheric CO2 concentrations are likely to reach 500–750 ppm in the second half of this century. Then global temperature averages may increase by at least 2 oC.

Coral reefs figure prominently in our national identity. The Great Barrier Reef contributes more than $5 billion annually to the Australian economy. Ningaloo Reef in Western Australia is growing in economic and environmental importance, as are the Kimberley Coast and Oceanic Shoals off Western Australia's north-west. While Australia's coral reefs are well managed, they are not isolated from global atmospheric and ocean changes.

Coral bleaching

Coral bleaching is not a new phenomenon—the coral animal is sensitive to a variety of stresses and bleaching is a natural response. Since the first recorded global mass coral bleaching episode in 1998, which was caused by unprecedented thermal stress, the phenomenon has been under intense scientific scrutiny.

The stress induced by higher temperatures causes a breakdown in the fundamental relationship that is at the heart of all coral reefs: the mutually beneficial relationship between the coral animal and its symbiotic algae, the zooxanthellae. The fragile equilibrium of this relationship operates within a finely tuned sea surface temperature range.

A key question is whether corals can enter into new symbioses with temperature-tolerant zooxanthellae, without losing some other benefits from their symbiotic association. Some zooxanthellae are more tolerant of higher temperatures than others, but they may not allow corals to grow as fast as they would with their usual symbionts.

Another key question is whether southward migration of larvae of the more warm water–adapted northern corals will be fast enough to ameliorate population losses from warming.

Finally, and perhaps of most importance, we don’t know whether corals will be able to adapt to the changing conditions at a fast enough rate to survive in the changing environment

Ocean acidification

Ocean acidification is a consequence of increasing atmospheric CO2, the main greenhouse gas. About 30 per cent of the extra CO2 from the atmosphere has so far dissolved in the oceans, causing their alkaline/acid balance to shift more towards acidic (their pH to decrease).

If the oceans had not absorbed a large proportion of that extra atmospheric carbon, we would have experienced more global warming than we have already. Oceans are naturally slightly alkaline, which is conducive to the calcifying process at the heart of tropical coral reefs.

If projections are correct that pH could decrease by up to 0.4 pH units by the end of this century, this would be well outside the realms of anything organisms have experienced over many millions of years. While 0.4 pH units might not seem like a lot, because pH is measured on a logarithmic scale this equates to a 2.5-fold increase in the concentration of hydrogen ions.

Coral reefs are built from the carbonate skeletons of corals. Corals are calcifying organisms—they take dissolved material from the surrounding sea water to grow their calcium carbonate skeleton. Corals are not alone in doing this—many marine plants and animals build calcareous crusts, skeletons or shells, contributing to reef growth.

This process is linked to the pH of seawater. As seawater heads down the pH scale to become slightly more acidic, the growth (calcification) of many coral species is likely to be increasingly compromised.

Scientists are still determining what this means for coral reefs and the multitude of organisms that live in and on reefs and other tropical marine environments.

Many processes, such as deposition of the marine cements that attach benthic organisms to surfaces and fertilisation of eggs by sperm, only function properly in an environment within a certain range of pH. Acidification may therefore affect the number of larvae produced by organisms that release their gametes into the ocean.

Absorption of CO2 by seawater will not only result in changes to seawater pH, but also change the composition of the dissolved gases available for animals to ‘breathe’ through their gills. Absorbing more CO2 into their bodies may affect their health and behaviour and may alter the pH of their body fluids.

Possible reef responses to climate change

Physiological acclimatisation and/or genetic adaptation are needed for corals to cope with higher temperatures and more acidic oceans. If the current rate of climate change continues, corals will have to acclimatise or adapt within the next few decades rather than over millennia.

Whether corals can adapt quickly enough to cope with climate change is a subject of much research. Are corals able to pass genes on to their offspring to enable them to tolerate higher temperatures in a short time span? With conditions changing rapidly, their capacity to do this within only a few generations may be crucial.

AIMS is examining whether and how the community of algae within corals might ‘shuffle’ to become dominated by more heat-tolerant strains. This phenomenon was first observed by AIMS scientists in corals from the Keppel Islands group after the 2006 bleaching event and is now being extensively investigated.

Corals in the waters around the Keppel Islands now have a much higher proportion of two more thermally tolerant strains of symbiotic algae than they did before the bleaching event, and they are better able to cope with higher sea surface temperatures.

However, this is just one species at one location and it is not yet known whether this can be extrapolated to the rest of the Great Barrier Reef or to other reef systems.

Also, research shows that corals with more heat-tolerant symbionts grow more slowly than others under average conditions.

The combined effects of seawater warming and acidification are only now starting to be studied. Ideally such studies may be done at naturally occurring sites that exhibit conditions akin to those forecast for future oceans. This includes organisms that live naturally in warm and acidic environments such as those found around undersea volcanic CO2 vents.

AIMS led a research expedition to one of these natural sites occurring in Milne Bay, Papua New Guinea. It is the only known cool CO2 seep site in tropical waters containing coral reef ecosystems.

The research showed the number and types of corals making up coral reefs are much reduced the closer they are to the natural CO2 seeps. Diversity of corals drops by 40 per cent and the reef becomes dominated by one form of corals, massive Porites.

The natural CO2 seeps have given scientists rare insights into what tropical coral reefs could look like if human-induced atmospheric CO2 concentrations continue to rise unabated. View more on this topic.

Controlled experiments in laboratories are also essential to assess causality. The range of marine species that can be experimentally investigated in the laboratory is, however, a tiny fraction of the number of species that live in the ocean. 

AIMS research on climate change

While supporting moves to reduce CO2 emissions globally, and making significant cuts to AIMS’s own energy consumption, the Institute is investing in research to understand the significance of climate change for tropical marine ecosystems including the Great Barrier Reef.

AIMS scientists have monitored decadal changes in coral cover on reefs of the Great Barrier Reef using two methods. The first involves divers estimating coral cover around the whole perimeters of reefs using manta tows and has been used to survey coral on many reefs along and across the Reef since the mid-eighties.

Secondly, coral communities have been studied more intensively in marked sites on the north-east slopes of 47 reefs using photographic methods. A recent analysis of manta tow data from 1985 to 2004 showed that coral cover fluctuated in an unsynchronised manner in different subregions of the Reef, but on average coral cover for all reefs declined by 0.21 per cent per year over this period.

Analysis of coral cover on the fixed photographic sites showed average declines of 0.27 per cent per year over 15 years between 1995 and 2009. While the two rates of coral loss are similar, the greater number of reefs that were sampled over a longer time by manta tows meant that the loss of coral cover estimated by this method showed a significantly significant decline. The net loss of cover estimated by the photographic methods on intensive survey sites has not yet reached statistical significance.

However, the gross result disguises a significant decline over time of the non-acroporid corals, which recover more slowly after disturbance than the fast growing Acropora species.

In Western Australia, AIMS has also monitored since 1993 the status and trends of fish and coral populations on Scott Reef (just over 400 kilometres northwest of Broome in the Indian Ocean). In 1998, when mass bleaching was observed on 70 per cent of reef systems worldwide, severe bleaching conditions killed more than 80 per cent of the corals on Scott Reef. Ongoing monitoring shows that coral and fish communities are still recovering from this major disturbance.

AIMS’s monitoring of the physical ocean environment through satellite observations and moored oceanographic instruments has shown that most coral bleaching is caused by a combination of high light and heat stress (that is, seawater that is warmer than the average seasonal cycle).


Q-IMOS is a geographic node of the Australian Integrated Marine Observing System (IMOS), managed by AIMS on behalf of a number of partners. Q-IMOS is an observation network that seeks to understand the influence of the Coral Sea on continental shelf ecosystems in Queensland, including the Great Barrier Reef Marine Park.

In the next decade, Q-IMOS will monitor the effect of rising ocean temperatures on the incidence of coral bleaching, and on the frequency of regional upwelling that fuels productivity in sections of the Reef. In the longer term, Q-IMOS will monitor the impact of global climate change upon ocean chemistry that threatens the survival of calcifying organisms, such as coral.

Q-IMOS consists of a number of sub-systems that together provide a picture of the main ocean features and the impact these have on coastal marine systems with a focus on coral reefs.

The core sub-system is an array of moorings located at key locations along the reef to detect and monitor the impact of ocean circulation events on coastal waters, especially the movement of offshore water onto the Great Barrier Reef such as during upwelling events.

Q-IMOS also monitors the main current system, the East Australian Current, that flows down the eastern Australian seaboard, and looks at how changes in ocean patterns are linked to changes in primary ocean productivity.

The mooring array is supported by an enhanced satellite observation system that collects daily images from a range of satellites showing patterns of surface temperature, ocean productivity and coastal runoff.

At the reef scale, seven reefs are being intensively monitored using innovative wireless sensor network technology that gives real-time data about water movement and ecosystem health at the scale of a single head of coral or a coral ‘bommie’ structure.

These networks link into the larger scale mooring arrays and satellite imagery to allow ocean phenomena to be tracked down to the scale of sections of the reef through the mooring array and then down to individual reefs and even reef areas through the wireless sensor networks.

This linkages across scales will allow, for the first time, a better understanding of how large-scale changes in the oceans, such as seen in El Niño and La Niña events, affect down to individual corals and how these corals, in response, adapt and sustain themselves.

An understanding of how the oceans affect the coast, and real-time observations of basic parameters such as temperature and salinity, can allow scientists to better understand events such as coral bleaching. Through rigorous aquarium and laboratory testing, this also allows for the development of an index of bleaching risk, based on cumulative heat stress (degree-heating days), making possible the forecast of major bleaching events.

Linking observation systems and models opens up new possibilities in forecasting events such as coral bleaching and the impact of events such as tropical cyclones.


About a quarter of AIMS’s research effort is now directed at marine microbes and symbiosis using advanced genetic and molecular approaches. This reflects the importance of microbial life to all major biogeochemical cycles and disease.

The symbioses of sponges, giant clams and corals all involve specialised microbes, and all of these symbioses are disrupted by sudden variations in sea temperatures. More detailed studies of coral symbiosis have shown that one species of coral can host multiple genetic strains of the photosynthetic zooxanthellae symbionts and that different combinations vary widely in tolerance to heat.

More heat-tolerant combinations trade off better survival in warmer water with slower colony growth under average conditions, raising the possibility that reef-building corals can persist in a warming ocean through selection for more heat-tolerant symbioses.

Answers to this crucial question are being pursued through a combination of controlled experiments in aquaria and reciprocal transplant experiments in natural populations to assess the viability of different symbioses in different thermal environments.

Theoretical models of coral bleaching implicate water quality as an extra factor modifying bleaching risk. The models predict that higher levels of dissolved nitrogen in the environment raises the risk of bleaching for any given combination of light and temperature.

This important idea requires testing through controlled experiments and, if supported, will provide a strong rationale for the current attempts to halt and reverse the decline of water quality in coastal seas caused by terrestrial runoff from agricultural landscapes.

At the ocean boundary, some locations experience the upwelling of deep water to the surface. These intrusive waters have the potential to both raise and lower the risk of coral bleaching because they contain higher levels of key dissolved nutrients but are also colder, coming from deeper levels.

The trade-off between these influences seems likely to explain some of the spatial variations in bleaching among offshore reefs during seasons of heightened risk. To incorporate such variations, AIMS and CSIRO are building the most accurate three-dimensional model of water circulation yet developed for the continental shelf of Queensland. Once validated, this model will be used to forecast regional risk for different parts of the Reef under different climate scenarios downscaled from global climate models.

AIMS scientists recently detected a two-decade decline in calcification rates by massive corals on the Reef that is unprecedented in at least the past 400 years. The reduction in growth rates is probably due to the increased frequency of thermal stress events, potentially worsened by progressive ocean acidification. Controlled experiments are required to establish the cause of this decline in the rate of calcification.

National Sea Simulator

AIMS’s ability to conduct the required experiments was boosted by new resources approved in the 2009–2010 Commonwealth Budget. Recognising the importance of climate change in the marine environment, the Australian Government provided $35 million for the construction of an advanced experimental seawater facility at AIMS’s headquarters in Townsville.

This large facility provides controlled environment spaces and is available to external scientists by application. The ability to manipulate multiple factors (temperature, salinity, nutrients and pH) independently in complex experimental designs allows scientists to test the responses of marine organisms to the range of hypothetical environments anticipated from different degrees of climate change and to predict the future for marine systems under various climate scenarios.

AIMS is also increasing its investment in monitoring natural marine systems across tropical northern Australia. This has been made possible by new investments by the Commonwealth and Queensland Governments in integrated marine observing systems.

This will include the first direct monitoring of carbonate saturation levels in complex reef systems to understand how water chemistry cycles affect reef construction rates by calcareous organisms.

Research on the impact of climate change on the marine environment and marine processes will inform a new generation of spatial and process models predicting the relative vulnerability of areas to climate change. In turn, these models will inform decision-making by natural resource managers, policy formulation and the exploration of potential mitigation strategies.

Improved understanding will also assist in providing refuge strategies for sensitive marine species in a rapidly changing environment.