Water quality and climate change: Managing for resilience

Full text

MTSRF Synthesis Report
Water quality and climate change:
Managing for resilience
Compiled by Johanna Johnson and Katherine Martin
Supported by the Australian Government’s
Marine and Tropical Sciences Research Facility

© Reef & Rainforest Research Centre Ltd, 2011
ISBN 978-1-921359-67-5
This report should be cited as:
Johnson, J. and Martin, K. (Compilers) (2011) Water quality and climate change: managing for resilience.
Synthesis Report prepared for the Marine and Tropical Sciences Research Facility (MTSRF). Reef & Rainforest
Research Centre Ltd, Cairns (42pp.).
Published by the Reef and Rainforest Research Centre on behalf of the Australian Government’s Marine and
Tropical Sciences Research Facility.
The Australian Government’s Marine and Tropical Sciences Research Facility (MTSRF) supports world-class,
public good research. The MTSRF is a major initiative of the Australian Government, designed to ensure that
Australia’s environmental challenges are addressed in an innovative, collaborative and sustainable way. The
MTSRF investment is managed by the Department of Sustainability, Environment, Water, Population and
Communities, and is supplemented by substantial cash and in-kind investments from research providers and
interested third parties. The Reef and Rainforest Research Centre Limited (RRRC) is contracted by the
Department to provide program management and communications services for the MTSRF.
This publication is copyright. The Copyright Act 1968 permits fair dealing for study, research, information or
educational purposes subject to inclusion of a sufficient acknowledgement of the source.
The views and opinions expressed in this publication are those of the authors and do not necessarily reflect those
of the Australian Government or the Minister for Sustainability, Environment, Water, Population and Communities.
While reasonable effort has been made to ensure that the contents of this publication are factually correct, the
Commonwealth does not accept responsibility for the accuracy or completeness of the contents, and shall not be
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contents of this publication.
Cover photographs courtesy of David Souter, Richard Pearson and Hayley Gorsuch.
This report is available for download from the
Reef and Rainforest Research Centre Limited website:
http://www.rrrc.org.au/publications/synthesis_reports.html
July 2011

Water quality and climate change: managing for resilience
i
Acknowledgements
The compilers gratefully acknowledge the researchers who contributed to this report.
Outstanding work by Ken Anthony, Ove Hoegh-Guldberg, Andrew Negri, Scarla Weeks,
Terry Hughes, Martijn van Grieken, Jeff Maynard, Ray Berkelmans, Katharina Fabricius,
Scott Wooldridge, Madeleine van Oppen, Michelle Devlin and their research teams has been
instrumental in advancing our knowledge of climate change and water quality impacts and
how they potentially interact.
Thanks are also extended to the then Commonwealth Department of the Environment,
Water, Heritage and the Arts (DEWHA) for funding the MTSRF, and the Reef and Rainforest
Research Centre (RRRC) for supporting this program over the past four years. The ongoing
involvement of primary end users in this research, including DEWHA, the Great Barrier Reef
Marine Park Authority (GBRMPA), WWF, the Queensland Department of the Premier and
Cabinet (DPC) and regional Natural Resource Management (NRM) groups has focused the
research outputs, such that they are already being applied to management activities.

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Contents
Acknowledgements ................................................................................................................... i
List of Figures ........................................................................................................................... iii
List of Tables ............................................................................................................................ iii
Acronyms and Abbreviations ................................................................................................... iv
About this Report ...................................................................................................................... v
Executive Summary .............................................................................................................. vi
1. Introduction ..................................................................................................................... 1
2. The effects of climate change on the Great Barrier Reef ............................................ 3
2.1 Coral bleaching susceptibility ................................................................................... 4
2.2 Coral bleaching mortality risk ................................................................................... 7
2.3 Ocean acidification ................................................................................................... 8
3. The effects of declining water quality on the Great Barrier Reef ............................. 10
3.1 Pollutant sources .................................................................................................... 11
3.2 Exposure to pollutants ............................................................................................ 12
3.3 Pollutant interactions .............................................................................................. 15
4. Linking water quality and resilience to climate change ............................................ 17
4.1 Water quality as a driver of resilience to climate change ....................................... 17
4.2 Modelling resilience of inshore reefs ...................................................................... 19
4.3 Managing water quality for resilience ..................................................................... 20
5. Conclusions and management applications .............................................................. 22
5.1 Conclusions ............................................................................................................ 22
5.2 Management applications ...................................................................................... 22
5.3 Future directions .................................................................................................... 23
6. References ..................................................................................................................... 24

Water quality and climate change: managing for resilience
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List of Figures
Figure 1: Links between carbon emissions and factors reducing coral reef resilience
due to ocean acidification, warming, tropical cyclones and sea level .................... 2
Figure 2: Observed (1871 to 2009) and projected (to 2100 for A2 and B1 emission
scenarios) annual sea surface temperatures for the GBR ..................................... 4
Figure 3: Genetic diversity of clade C symbionts in a widely distributed soft coral on
offshore and inshore reefs of the GBR .................................................................. 6
Figure 4: Modelled effects of the size of initial lipid stores before bleaching (top
arrow), rate of heterotrophy (left arrow), bleaching rate as a percent of
maximum chlorophyll a content (y-axis), and days since the onset of
bleaching for a three-month bleaching event (x-axis) on the risk of coral
mortality ................................................................................................................. 7
Figure 5: Relationship between the maximum depth of coral reef development and
the water quality index in the Whitsunday Islands, central GBR.......................... 10
Figure 6: Analysis of a coral core from Magnetic Island showing increased bulk
sediment and topsoil erosion in the Burdekin River since European
settlement from the 1850s ................................................................................... 12
Figure 7: Satellite image (Landsat 5 TM) of the Whitsunday Islands showing a flood
plume from the Proserpine and O’Connell Rivers, 28 January 2005 ................... 13
Figure 8: Monthly climatologies of euphotic depth for the southern GBR for March
2007 (left) and September 2002-2009 (right) ...................................................... 14
Figure 9: The effect of dissolved inorganic nutrients, particulate organic matter,
turbidity, and sedimentation on coral growth (y-axis) and survival along a
hypothetical environmental gradient from coastal to oceanic conditions
(x-axis) ................................................................................................................. 15
Figure 10: Coral colour changes substantially along a gradient from coastal to offshore
regions of the GBR, with corals significantly darker in coastal waters ................. 18
Figure 11: Modelled output postulating the interaction between DIN delivery and
bleaching thresholds of corals ............................................................................. 20
List of Tables
Table 1: Climate change projections for the GBR region under low (B1) and high
(A2) emissions scenarios ....................................................................................... 4
Table 2: Synthesis of direct effects of the four major components of terrestrial run-off
on adult corals ..................................................................................................... 11

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Acronyms and Abbreviations
COTS ................ Crown-of-thorns Starfish
DEWHA ............. Commonwealth Department of the Environment, Water, Heritage and the
Arts (now Sustainability, Environment, Water, Population and Communities)
DIN .................... Dissolved Inorganic Nitrogen
DIP .................... Dissolved Inorganic Phosphorus
DON .................. Dissolved Organic Nitrogen
DPC ................... Queensland Department of the Premier and Cabinet
GBR .................. Great Barrier Reef
GBRMPA .......... Great Barrier Reef Marine Park Authority
MODIS ............... Moderate Resolution Imaging Spectroradiometer
MTSRF ............. Marine and Tropical Sciences Research Facility
NRM .................. Natural Resource Management
RRRC ................ Reef and Rainforest Research Centre
SST ................... Sea Surface Temperature
WWF ................. World Wide Fund for Nature

Water quality and climate change: managing for resilience
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About this Report
This report provides a synthesis of the key findings of research conducted under the
Australian Government’s Marine and Tropical Sciences Research Facility (MTSRF) relevant
to understanding interactions between water quality and climate change, and how best to
manage for resilience. The report summarises the findings of projects supported by the
MTSRF. Some of the information in this report is extracted from these project reports with the
permission of the authors.
A key achievement of the MTSRF has been strong cooperation and collaboration between
research institutions in project development and implementation. The findings presented in
this report were derived from collaborative projects funded from several sources including the
MTSRF, and the research institutions have also contributed significant in-kind resources. It
should be noted that supporting information external to the MTSRF is included in this report
to provide context or to complete the discussion. Publications generated specifically by the
MTSRF are identified in the References section.
This synthesis report is one product in a series of informative reports that summarise MTSRF
research findings relevant to the GBR. Other products include:
 ‘Managing Great Barrier Reef water quality: MTSRF research overview’, compiled by J.
Waterhouse and M. Devlin (Waterhouse and Devlin 2011).
 ‘Improved understanding of biophysical and socio-economic connections between
catchment and reef ecosystems: Wet and Dry Tropics case studies’, compiled by M.
Devlin and J. Waterhouse (Devlin and Waterhouse 2011).
 ‘Optimising water quality and impact monitoring, evaluation and reporting programs’,
compiled by J. Waterhouse (Waterhouse 2010a).
 ‘Thresholds of major pollutants with regard to impacts on instream and marine
ecosystems’, compiled by J. Waterhouse (Waterhouse 2010b)
 ‘Identification of priority pollutants and priority areas in the Great Barrier Reef catchments’,
compiled by J. Waterhouse and J. Brodie (Waterhouse and Brodie 2011).
 ‘Managing for GBR resilience: Socio-economic influences’, compiled by J. Johnson and K.
Martin (Johnson and Martin 2011).
 ‘Review of MTSRF research advancing our understanding of the source, transport and
impacts of pesticides on the Great Barrier Reef and associated ecological systems’,
compiled by M. Devlin and S. Lewis (Devlin and Lewis 2011).

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Executive Summary
Climate change has been recognised as one of the greatest threats to coral reefs around the
world, including the Great Barrier Reef (GBR). A reduction in global carbon emissions is the
only long-term solution to the problems caused by climate change. However, effective
management and strategic investment in enhancing reef resilience, such as improvements to
water quality, will help mitigate some of the risks in the short term, giving natural
communities time to adapt or acclimatise to a changing environment.
Research funded by the Australian Government’s Marine and Tropical Sciences Research
Facility (MTSRF) has increased our understanding of the response of GBR ecosystems to
predicted increases in the atmospheric concentration of greenhouse gasses (mainly CO2),
such as increasing sea surface temperature, ocean acidification and secondary influences of
increasing incidents of coral disease. In addition, the complex interactions between climate
change, ocean acidification and water quality, and the mechanisms behind how water quality
influences reef resilience have been examined closely and new knowledge has emerged.
Collectively, this new information has been used by MTSRF researchers to develop models
that can deal with the complex nature of these relationships to predict how reefs might
respond to increasing severity of thermal events, increasing incidents of coral disease, ocean
acidification and ultimately the interactions between ecosystem health, water quality and
resilience.
While many questions still remain unanswered, findings to date have provided important
direction and tools for management to prioritise and target effort, such as knowledge to
identify the features of resilient areas of the GBR as possible future refugia that may facilitate
recovery of less resilience reefs. This knowledge also provides further impetus to strengthen
and implement strategies already aimed at improving GBR water quality, as this remains a
significant area where intervention can have tangible effects on resilience to future climate
change.
It is also recognised that any decline in the health of inshore GBR habitats will have social
and economic implications for coastal communities and reef-dependent industries. There is
therefore a need to engage with GBR communities to increase awareness of the issues and
continue to address land management practices that improve inshore water quality and
enhance resilience of the GBR ecosystem (see the companion report ‘Managing for GBR
resilience: Socio-economic influences’ by Johnson and Martin, 2011).

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1. Introduction
The Great Barrier Reef (GBR) is likely to experience increasing frequency and intensity of
disturbances under future global change, driven by increasing sea surface temperature
(SST), ocean acidification, changing ocean circulation, storm intensity and sea level rise. The
GBR Outlook Report (GBRMPA 2009) states that the “... overall outlook for the Great Barrier
Reef is poor and catastrophic damage to the ecosystem may not be averted”. Climate
change was assessed as the dominant factor influencing the future prospects for the GBR.
Fundamental ecological processes on the GBR are already being affected by climate
change; higher SSTs have resulted in three major bleaching events in the last decade, and
increasing ocean acidity has been identified as affecting calcification rates in reef-building
species (GBRMPA 2009). The extent and persistence of damage to the ecosystem will
depend to a large degree on the rate and magnitude of future change, and the resilience of
the GBR ecosystem (GBRMPA 2009). While influencing the rate of change of the world’s
climate is beyond the scope of local or regional management, research funded through the
Marine and Tropical Sciences Research Facility (MTSRF) has shown that management can
influence the resilience of reef ecosystems, with the goal of reducing the likelihood of the
system changing to an undesirable state.
Ecological resilience is the “capacity of an ecosystem to resist, recover or regenerate from
disturbances or damage without a change in state, so as to maintain key functions and
processes” (Nyström et al. 2000). The health of the GBR depends on the integrity of its
ecological processes, and may be characterised by high diversity and species richness or its
resilience to anthropogenic and natural disturbance.
Declining water quality, particularly in the inshore GBR, is one pressure that undermines reef
resilience and is likely to be exacerbated by ocean warming and acidification (Anthony et al.
2011). Agricultural, urban and industrial development in the GBR catchment has significantly
increased the sediment, nutrient and pesticide run-off from rivers draining into coastal and
inshore waters (Rayment and Neil 1997, Furnas 2003, McCulloch et al. 2003, Fabricius
2005, Brodie et al. 2008). Numerous field observations and laboratory studies have shown
that nutrient enrichment, turbidity, sedimentation and pesticides all affect the resilience of the
GBR ecosystem, degrading coral reefs and seagrass meadows at local and regional scales
(e.g. Fabricius 2010, Waycott and McKenzie 2010).
MTSRF-funded research has contributed significantly to the general view that GBR
ecosystems decline in species richness and diversity with increasing exposure to nutrients,
sediments and pesticides, compromising their ability to maintain essential ecosystem
functions with increasing frequency of disturbances. Inshore ecosystems are most at risk
from pollutants delivered during small to medium flood events, with risk related to the
predominant land-use of the catchment. For example, areas with significant fertiliser use
have been identified as regions associated with urban development and high intensity land-
uses, such as fertilised crops in coastal areas of the Wet Tropics, Lower Burdekin, Mackay
Whitsunday and Burnett Mary catchments (Brodie et al. 2008, 2009a, b). Most sediment
entering the GBR comes from catchments with large pastoral areas such as the Burdekin
and Fitzroy Rivers (Brodie et al. 2009b). Pesticides from agricultural activities are present in
the GBR lagoon in both wet and dry seasons (see Prange et al. 2009, Johnson et al. 2010,
Johnson et al. 2011), and recent monitoring data suggest that pesticides have become
ubiquitous contaminants throughout the GBR (Bartkow et al. 2008, McKenzie et al. 2010,
Lewis et al. 2009, Bainbridge et al. 2009a, Packett et al. 2009, Shaw et al. 2010).
The targeted, solutions-based research conducted under MTSRF means that the responses
of GBR coral reef communities to turbidity and nutrients from terrestrial run-off are now
relatively well understood (Fabricius 2005, De’ath and Fabricius et al. 2009, Thompson and
Dolman 2010, Thompson et al. 2010, Uthicke et al. 2010), and responses to pesticide

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exposure have been documented in controlled laboratory experiments (e.g. Negri et al. 2005,
Magnusson et al. 2008). Synergistic effects between pollutants are relatively poorly
understood as yet but likely to be significant, and must be considered when assessing the
impact of pollutants on ecological processes. For example, chronic exposure to elevated
nutrient or sediment concentrations can increase susceptibility to thermal stress and reduce
coral survival and recovery (Anthony et al. 2007, Hoegh-Guldberg et al. 2007a), and
exposure of corals to herbicides has been shown to increase sensitivity to thermal stress
(Negri et al. 2011). The severity of responses is often a combined function of the magnitude
and duration of exposure, and further depends on species-specific levels of sensitivity to the
pollutant. For example, differences in sensitivity to nutrient enrichment and sedimentation
between species of adult coral can lead to changes in community composition (Fabricius et
al. 2007b). Over time, chronic sub-lethal stress may decrease the resilience of reef
organisms to other pollutants or environmental stress (Hughes et al. 2003, Wooldridge
2009a, Anthony et al. 2011); however, the potential risks from chronic exposure to multiple
contaminants remain unclear (van Dam et al. 2011).
Increasing carbon emissions into the Earth’s atmosphere are having a range of effects on
global climate and the chemistry of oceans. These changes have been shown to impact on
coral reefs with potential implications for resilience to future disturbances (Figure 1).
Figure 1: Links between carbon emissions and factors reducing coral reef
resilience due to ocean acidification, warming, tropical cyclones and sea
level. Adapted from Anthony and Marshall (2009).
This report summarises the key findings of MTSRF research related to the interactions
between water quality, ocean warming and ocean acidification in the GBR, and the
implications for ecosystem resilience. Sections 2 and 3 provide an overview of the effects of
water quality and climate change in the GBR, respectively and Section 4 provides a
summary of evidence generated through MTSRF of the links between water quality and
resilience to climate and ocean chemistry projections. Finally, conclusions, management
applications and future research directions are presented in Section 5.

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2. The effects of climate change on the
Great Barrier Reef
Projected increases in atmospheric concentrations of carbon dioxide are predicted to
increase sea surface temperatures (SSTs) on the GBR by 1-3°C above the present average
temperature, while waters will become more acidic, the sea level will continue to rise, and
weather events will become more extreme by the year 2100 (Lough 2007, Ramasamy 2010;
Table 1). The projected effects of climate change (including ocean acidification) on GBR
species, habitats and industries were assessed by the Great Barrier Reef Marine Park
Authority (Johnson and Marshall 2007) and formed the foundation for the ‘Great Barrier Reef
Climate Change Action Plan 2007-2012’ (GBRMPA 2007). MTSRF-funded research has
aimed to build on these efforts to contribute to the understanding of the impacts and
interactions between climate variables, and other stressors on the ecosystem. As identified in
the publication ‘Climate Change and the Great Barrier Reef’ (Johnson and Marshall 2007)
and the ‘Great Barrier Reef Outlook Report 2009’ (GBRMPA 2009), climate change poses a
major threat to the survival of coastal habitats, in particular coral reefs, with flow-on effects
for other organisms in the GBR. At present, coral bleaching is episodic rather than chronic.
However, in the last fifty years, an increase in the baseline temperature of reef waters is
narrowing the gap between a regular summer and a coral bleaching season, with a +0.41°C
warming observed in the twenty year average (1980-2009) compared to the previous century
(1871-1900) (Figure 2). In addition, the decline in ocean pH is likely to have affected
calcification rates in marine organisms, particularly corals, and rising sea-levels and
increasing incidence of extreme weather events compromise the resilience of reef
ecosystems to cope with other stressors (GBRMPA 2009). For example, recent MTSRF-
funded research suggests that coral diseases like ‘white syndrome’ are more prevalent
following above average summer SSTs (Hughes 2010).
Coral bleaching occurs in response to physiological stress, and is the result of the symbiotic
zooxanthellae (Symbiodinium) being expelled by the coral host. For example, sudden
changes in salinity, irradiance or temperature can cause corals to bleach (Gleason and
Wellington 1993, Glynn and D’Croz 1990, Hoegh-Guldberg and Smith 1989, Jokiel and
Coles 1990). Exposure to chemicals such as pesticides may also trigger bleaching,
particularly if corals are exposed to poor water quality (Jones and Hoegh-Guldberg 1999,
Hoegh-Guldberg et al. 2007a, b, van Dam et al. 2011). All species of reef-building coral have
‘thermal thresholds’, the temperature threshold above which bleaching occurs. Thermal
thresholds vary spatially and temporally, reflecting adaptation or acclimatisation to local
conditions and intrinsic differences in susceptibility to bleaching (Berkelmans and Willis 1999,
Baker 2003). Bleaching events can affect individual polyps, an entire colony, or large areas
of reef consisting of many different colonies. Bleaching can result in decreased reproductive
capacity, increased vulnerability to disease, decreased growth and calcification rates, and
ultimately coral death (Done et al. 2003, Fabricius et al. 2007a). Whether bleaching leads to
coral mortality depends on a number of factors. Key findings of MTSRF-funded research
(Hoegh-Guldberg and colleagues) have shown that the risk of coral mortality after a
bleaching event is related to a combination of several factors, such as the rate of loss of
photopigments, duration of the bleaching event, degree of heterotrophy, and the energy
reserves of the corals (Hoegh-Guldberg 1999, Eakin et al. 2009, Wilkinson and Hodgson
1999).

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Figure 2: Observed (1871 to 2009) and projected (to 2100 for A2 and B1 emission
scenarios) annual sea surface temperatures for the GBR. Central black line is
observed average annual SST, 1871 to 2009. Data sources: HadlSST and
CSIRO. Source: J. Lough, Australian Institute of Marine Science.
Table 1: Climate change projections for the GBR region under low (B1) and high (A2) emissions
scenarios. Temperature and rainfall projections are relative to the twenty-year 1980-1999 baseline.
Projections represent the range of model predictions (10th to 90th percentile). Data adapted from
Lough 2007, Lough et al. in press, Ramasamy 2010.
Variable 2030 2070 (B1) 2070 (A2)
Air temperature (°C) +0.6 to +1.2 +1.1 to +2.0 +2.0 to +4.0
Sea surface temperature (°C) +0.4 to +1.0 +0.6 to +2.0 +1.0 to +3.0
Annual rainfall (% change) -8 to +8 -14 to +13 -25 to +25
Sea level (cm)a +13 to +20 +49 to +89b
Ocean pH -0.1 -0.2 -0.3
a Relative to 1990 baseline.
b Does not include the melting of the polar ice sheets as significant uncertainty exists regarding
melting rate, which will influence the magnitude of sea level rise.
2.1 Coral bleaching susceptibility
Susceptibility and response to bleaching varies geographically between coral colonies, and
between and within coral species (Marshall and Baird 2000), indicating that corals may, to
some extent, be able to acclimate or adapt to rising SSTs. Indeed, emerging evidence from
studies on the molecular basis of resilience suggests that corals with prior exposure to high
temperatures are more resilient to future increases in temperature (Done et al. 2003, Smith
2008, Hoegh-Guldberg 2010). Hence, variations in bleaching tolerance may be the product
of the prior thermal history of the coral, and genetic differences in coral and zooxanthellae
physiology (Berkelmans and van Oppen 2006).
In corals, acclimation to an altered thermal regime can occur through a change in the
physiology of the host (Coles and Brown 2003), physiology of the symbiont (e.g. photo-
protective mechanisms), and a change in the relative proportion of symbiont types within
colonies, from endogenous or exogenous pools of symbionts (Baker 2003, Coles and Brown
2003, Anthony and Hoegh-Guldberg 2003). Adaptation, however, can provide a genetic
basis for a change in tolerance through differential reproductive success or selective
mortality of less thermally tolerant individuals. Major coral-bleaching events are likely to

Water quality and climate change: managing for resilience
5
impose strong selective pressures on coral populations and potentially trigger mechanisms of
community shifts, adaptation, physiological acclimation or changes in genotype-phenotype
interactions in the surviving coral symbioses. For example, thermal tolerance of three coral
genera (Acropora, Pocillopora and Porites) was investigated following the 1998 global mass
bleaching event and during the subsequent, more severe event in the GBR in 2002 (Maynard
et al. 2008a). In 2002, bleaching severity in the three genera was 30-100% lower than
predicted from the relationship between severity and thermal stress in 1998, despite higher
solar irradiances (Maynard et al. 2008a). Interestingly, coral genera most susceptible to
thermal stress (Pocillopora and Acropora) showed the greatest increase in tolerance. It
appears that the heating rate and the productivity of symbionts are key factors in determining
the flexibility of thermal thresholds in reef-building corals (Hoegh-Guldberg 2010). Thus, even
over relatively short time-frames (four years), a major bleaching event can lead to community
shifts and possibly enhanced thermal tolerance of surviving coral assemblages without
extensive mortality. However, the extent to which acclimation or adaptation is possible in all
species is unknown.
Different corals and different symbionts exhibit a range of specificities from ‘generalist’ to
‘specialist’; however, host corals generally appear more specific than symbionts (Baker
2003). Symbionts of scleractinian (reef-building) corals are composed of several clades: A,
B, C, D and G, and a host may contain a combination of clades (Tonk et al. in press). In
Pacific corals, symbionts are predominantly from the C and D clades, with A, B and G being
found only occasionally at subtropical or temperate latitudes (Baker 2003). For example,
90% of corals sampled from the GBR contained clade C, 9 % clade D and 1% clades A, B
and G. The occurrence of clade D appears to be higher in more northerly locations of the
GBR as well as inshore locations within the central Mackay/Capricorn section. The wide
range of interactions suggests the symbiosis confer evolutionary and ecological flexibility on
both the coral and zooxanthellae.
Molecular studies have shown that the coral host-symbiont partnership can shift
phenotypically in response to thermal stress, with the up- and down-regulating of different
symbiont clades possible. For example, in the Keppel Islands, a severe bleaching event in
2006 affected approximately 95% of corals, resulting in 40% mortality (Maynard et al. 2010,
GBRMPA 2008), however by 2009 many of the affected areas had recovered (Hoegh-
Guldberg 2010). In the short period of recolonisation following bleaching, it appears that the
dominant symbiont changed from the light and heat sensitive clade C2 to the more thermally
robust clade C1 and D, which has been shown to occur in laboratory experiments (van
Oppen et al. 2005, Berkelmans and van Oppen 2006). However, when SSTs returned to
average values, the clade C1 and D were down-regulated and the clade C2 was up-
regulated. Studies have suggested that this is due to lower growth and reproductive rates in
corals with clade C1 and D (Little et al. 2004); hence, in favourable conditions the clade C2
provides corals with a competitive advantage. Clade D appears to be an opportunistic taxon
that up-regulates in recently stressed or marginal habitats, and/or bleached corals in the
process of recovering (Baker 2003, van Oppen 2001). Clade D may therefore be a useful
indicator species for inclusion in monitoring programs to detect early signs of stress or to
assess the impact of chronic stressors on ecosystem health. Declining water quality and
projected increases in SST suggest that clades C1 and D may become more dominant;
indeed, changes in symbiont phenotype may be occurring in affected ecosystems such as
inshore reefs subject to significant terrestrial impacts (van Oppen 2001).
A number of factors may determine the genetic diversity and connectivity of Symbiodinium
populations including regional differences in population history and hydrodynamic regimes,
the mode of host-symbiont acquisition, and variation in free-living ecology among
Symbiodinium types. For example, patterns of population structure of clade C symbionts in a
widely distributed soft coral reflected longshore circulation patterns and limited cross-shelf
mixing, which suggests that passive transport by currents is the primary mechanism of
dispersal (Howells et al. 2009). In addition, the genetic diversity of clade C symbionts on
inshore reefs was lower than on offshore reefs (Figure 3), which may reflect patterns of
bleaching or migration (Howells et al. 2009). To limit the extent of long-term and irreversible

MTSRF Synthesis Report
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decline in ecosystem health, effective management needs to incorporate the spatial scales at
which genetic material is exchanged into management models (Section 5) (Palumbi 2003,
Sale 2004, Ridgway and Gates 2006).
Figure 3: Genetic diversity of clade C symbionts in a widely
distributed soft coral on offshore and inshore reefs of the GBR.
Genetic diversity is measured by Shannon’s Index (H) averaged
(+/- SE) across microsatellite loci. Abbreviated reef names:
Dungeness Reef (Du), Orpheus Island (Or), Great Palm Island (Pa),
Hook Island (Ho), Deloraine Island (De), Escape Reef (Es), Pickersgill
Reef (Pi), Agincourt Reef (Ag), Undine Reef (Un), Trunk Reef (Tr), Rib
Reef (Ri) (Howells et al. 2009).
The spatial resilience of coral reefs may be significantly increased by the diverse and flexible
nature of the symbioses. The genotype of symbiotic dinoflagellates appears to be highly
diverse and plays an important role in determining environmental tolerance ranges of the
coral host (Tonk et al. in press). However, the genotype of Symbiodinium is not the only
determinant of the thermal tolerance of corals. Connectivity within and between coral
populations is an important component of reef resilience, because connectivity promotes
flexibility in response to environmental variability. Exchange of larvae creates and maintains
high levels of genetic diversity, which enables populations to potentially adapt to
environmental change and facilitates reseeding of damaged reefs (Reed and Frankham
2003, van Oppen and Gates 2006). In addition, the spread of selectively advantageous
alleles involved in physiological responses such as bleaching resistance is a potentially
important consequence of larval migration. Furthermore, gene flow increases local effective
population sizes, thereby enhancing the resistance of populations to rapid random changes
in allele frequencies from one generation to the next through genetic drift. Highly specialised
symbionts with low dispersal potential are likely to be susceptible to losses of genetic
diversity in the face of increased disturbances unless they are able to adapt, which could
impact on the fitness and recruitment success of the host (Howells et al. 2009) with flow-on
effects for ecosystem health. Furthermore, as the climate becomes more variable and
bleaching events become more frequent, research into whether recovery from bleaching
events occurs predominantly from exogenous or endogenous sources becomes increasingly
relevant. Therefore, the challenge may be how well environmental managers can maintain
connectivity between reefs.

Water quality and climate change: managing for resilience
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Box 1: Predictive models of coral adaptation
Differences in bleaching susceptibility of different symbiont taxa may be applied to predict future
incidences and severity of bleaching. To date, the ability to assess the vulnerability of the GBR to
increases in SSTs has been limited by a lack of knowledge about the capacity for coral symbioses
to acclimate or adapt to thermal stress over ecologically realistic time-frames (Hoegh-Guldberg
2004). What fraction of symbionts is susceptible to bleaching and does community structure of
symbionts remain constant over time? The range of bleaching tolerances among corals inhabiting
different thermal niches suggests that some coral symbionts have the capacity to adapt to higher
SSTs than those currently experienced (Coles and Brown 2003). MTSRF-funded research has
investigated whether bleaching sensitivity between geographically distinct, con-specific coral
populations growing along a natural thermal gradient was caused by differences in gene expression
(reflecting either local adaptation or acclimatisation), and/or by the presence of distinct alleles (due
to selection and local adaptation) (Hughes 2010). Experimental results will be used to develop a
theoretical model to describe the potential for corals to adapt to climate change and the likelihood of
changes in community structure or localised extinctions.
2.2 Coral bleaching mortality risk
Energy acquisition by the coral-algal symbiosis is determined by the rate of photosynthesis
and energy transfer by symbionts (Muscatine 1990) and heterotrophy by the host (Anthony
and Fabricius 2000). The energy status of corals has implications for survival and fitness,
and is a function of total energy intake and loss, and energy allocation between
maintenance, growth and reproduction (reviewed by Koiijman 2000). Energy status and
reserves, therefore, influence whether bleaching increases the risk of mortality depending on
the duration and severity of the event (Anthony et al. 2009). Consequently, highly
heterotrophic coral species in plankton-rich environments may be less critically affected by
loss of symbionts than species that are predominantly phototrophic. In addition, the plasticity
of the heterotrophic response influences the risk of mortality, with some species increasing
rates of heterotrophy during bleaching and recovery, fully compensating for reductions in
photosynthetically acquired carbon (Grottoli et al. 2006). Indeed, models showed high rates
of heterotrophy and large lipid reserves delay the onset of mortality during bleaching events
(Figure 4) and promoted survivorship (Anthony et al. 2009).
Figure 4: Modelled
effects of the size of
initial lipid stores
before bleaching (top
arrow), rate of
heterotrophy (left
arrow), bleaching rate
as a percent of
maximum chlorophyll
a content (y-axis), and
days since the onset
of bleaching for a
three-month bleaching
event (x-axis) on the
risk of coral mortality
(Anthony et al. 2009).

MTSRF Synthesis Report
8
The implications of these results are that corals unable to increase their feeding rates and
that are not recolonised by zooxanthellae in the critical period following bleaching will deplete
lipid stores to critically low levels, leading to higher mortality. Other stressors that negatively
influence lipid stores prior to a bleaching event (e.g. anomalous spring temperatures, Weeks
et al. 2008; terrestrial pollutants from flood events, Devlin and Brodie 2005) will influence the
severity of bleaching. In addition, the availability of resources during a bleaching event may
differentially affect coral mortality along eutrophication gradients (e.g. from inshore to
offshore reefs), and the timing of the bleaching event relative to seasonal cycles in lipid
levels is also likely to be a determinant of coral mortality under future events.
Box 2: Secondary effects of climate change
The cost of not adequately managing for reef resilience could result in increases in the severity and
frequency of disease outbreaks with increasing thermal stress. MTSRF research contributed to the
development of a predictive tool for outbreaks of ‘white syndrome’, a serious disease affecting
corals of the GBR (Hughes 2010). Average white syndrome abundances were much higher
following the exceptionally warm 2001/02 summer than in any other year that reefs have been
surveyed (Australian Institute of Marine Science (AIMS) Long-term Monitoring Program). Modelling
showed that white syndrome outbreaks require both a high heating rate and high cover of corals in
the genus Acropora, which is consistent with monitoring data showing 100% incidence of outbreaks
at sites with these features. The predictive tool based on the model identifies regions approaching
thermal thresholds known to have caused outbreaks of white syndrome in the past. Spatially
mapping areas of past and potential future outbreaks of white syndrome will enable researchers to
answer the following questions:
1. Is white syndrome induced by pathogens or caused by programmed cell death?
2. What percent of cases result in mortality, and is mortality spatially variable?
3. Is there a correlation between spatial variation in outbreaks and other factors such as host cover
and summer max SSTs?
Knowledge in the above areas will assist management to implement actions to influence processes
driving the susceptibility to and recovery from white syndrome. The production of a web-based
predictive tool for coral diseases compatible with the Google EarthTM platform will inform
management and provide an early warning system for coral disease outbreaks. Such a predictive
tool has broader applications, and investigations are underway into the transferability to the Pacific
and other coral reef regions globally.
2.3 Ocean acidification
Another threat to the GBR ecosystem is the declining pH of the ocean, or ocean acidification,
caused by carbon dioxide (CO2) from the atmosphere dissolving into solution. The world’s
oceans currently absorb approximately 25% of CO2 generated by humans, with about 40% of
this occurring in the Southern Ocean (Global Carbon Project 2008, Levitus et al. 2005,
Raven et al. 2005). Research shows that ocean acidification decreases the ability of reef-
building corals, marine plants and other marine organisms to build calcium carbonate
skeletons or shells. A lowering in pH leads to a reduction in the saturation state of aragonite,
the chemical building block of reef corals. Projections by MTSRF researchers indicate that
ocean acidification may lead to increased levels of severe bleaching, thus becoming a
significant concern by mid-century (Hoegh-Guldberg 2010).

Water quality and climate change: managing for resilience
9
Box 3: Linking oceanographic patterns, bleaching events and predictions of coral mortality
MTSRF-funded research has investigated the influence of mesoscale oceanographic patterns on
mass coral bleaching. Remote sensing data of chlorophyll and SST at high resolution (1 km) has
revealed distinct ‘biogeographic provinces’ across the GBR region. The data will be used to
investigate how broad-scale climate change phenomena and key environmental variables translate
into changes within the GBR ecosystem and impact on reefs at the meso- and local-scale. The
spatio-temporal variability in physical dynamics will be linked to biological response to determine
whether particular reef systems may be heated or cooled (flushed) and hence the degree of
exposure to thermal stress that causes coral bleaching and mortality. This approach was trialed in
the southern GBR where local environmental and biological features were used to assess bleaching
patterns and resilience at the reef-scale to future thermal events (Maynard et al. 2010).
Environmental stress, physiological response and mortality are inter-related (Gurney et al.
1996). Models that integrate the effect of key environmental factors on the coral stress
response and the extent to which this is influenced by historical adaptation and potential
acclimatisation, will improve the ability to predict risk of coral mortality and project future
changes in reefs with increasing SSTs. For example, models that build on multiple, nested
layers of biological and ecological information have more power to accurately predict
sublethal stress, the risk of mortality during and following a bleaching event, and the
subsequent probability of population and community recovery (Hoegh-Guldberg 2010).
Enhanced predictions of broad-scale mortality would enable management to understand
potential shifts in community composition and develop a response strategy to facilitate
recovery following bleaching events.

MTSRF Synthesis Report
10
3. The effects of declining water quality on the
Great Barrier Reef
Coral reefs usually form in oligotrophic waters (Hoegh-Guldberg 1999, Wilkinson 2004) and
natural gradients from coastal to oceanic conditions in temperature, light, nutrients and
trophic interactions combine to create a functioning reef ecosystem. Research suggests that
cross-shelf gradients in water quality are more persistent in regions with high agricultural run-
off than in more remote areas of the GBR (Brodie et al. 2007, Furnas et al. 1997, Fabricius
and De’ath 2004). Changes in water quality are known to influence the physiology, trophic
structure and ecology of benthic coral reef assemblages (van Woesik et al. 1999, Fabricius
2005, Fabricius et al. 2005, De’ath and Fabricius 2010). For example, the maximum depth
for reef-building coral growth is closely linked to an index of water quality that increases from
turbid to clear-water based on gradients of nutrients, sediment, irradiance and coral reef
development (Figure 5; Cooper et al. 2007). However, it is often difficult to establish causal
relationships between terrestrial run-off and reef health along natural gradients, because
many co-occurring contaminants plus reduced salinity interact to affect the ecological
balance of the GBR ecosystem.
Figure 5: Relationship between the
maximum depth of coral reef
development and the water quality
index in the Whitsunday Islands,
central GBR (Cooper et al. 2007).
In a comprehensive review of the effects of terrestrial run-off on the ecology of corals and
coral reefs, Fabricius (2005) identified four main factors driving responses to changing
coastal water quality: (i) increased dissolved inorganic nutrients, (ii) increased particulate
organic matter, (iii) decreased light availability due to turbidity, and (iv) increased
sedimentation. The review evaluated the effects of these factors on important ecological
processes such as the growth and survival of hard corals, coral reproduction and
recruitment, and organisms that interact with corals (Table 2). Building on this review, recent
MTSRF-funded studies focus on the effect of run-off on the growth, survival, reproduction
and recruitment processes of reef-building corals (see the companion report by Devlin and
Waterhouse (2011) for a more detailed overview of these studies).

Water quality and climate change: managing for resilience
11
Table 2: Synthesis of direct effects of the four major components of terrestrial run-off on
adult corals. The arrows indicate the relative strength and direction of the response; a
dash indicates that a response is unlikely; POM = particulate organic matter; DIN =
dissolved inorganic nitrogen; DIP = dissolved inorganic phosphorus (Fabricius 2005).
DIN DIP POM Light reduction Sedimentation
Calcification
Tissue
thickness – –
Zooxanthellae
density –
Photosynthesis
Adult colony
survival – –
3.1 Pollutant sources
Catchments adjacent to the GBR have undergone extensive modification over the past 150
years (Furnas 2003). This has led to the receiving waters of the GBR experiencing a six- to
nine-fold increase in the input of nutrients (depending on the nutrient species, Kroon et al.
2009), a five-fold increase in the amount of sediment (Kroon et al. 2009) and an increase in
the zone of influence of nutrient enrichment (Wooldridge et al. 2006, Devlin et al. 2010). The
delivery of contaminant loads to the GBR lagoon is typically episodic and dependent on
factors such as fertiliser and pesticide application, geography, geology, and spatial and
temporal changes in climate and rainfall across the catchments. The outputs of individual
rivers vary, from multiple discharges each year (e.g. Tully River), to one major annual
discharge event (e.g. Herbert and Pioneer Rivers), to one major flow every four to ten years
(e.g. Burdekin River) (Furnas 2003). The extent of area affected by run-off is greatest for
large rivers with intermittent flows such as the Fitzroy, Burdekin and Herbert Rivers, although
rivers that have frequent discharges (e.g. Tully River) have a chronic influence on coastal
ecosystems (e.g. Devlin et al. 2001, Packett 2007, Schaffelke et al. 2008). Most of the
terrestrial run-off affecting inshore reefs occurs during episodic flood events, predominately
during the monsoonal wet season between December and May (Devlin and Brodie 2005).
Recent research has enabled clearer identification of the sources of land-based sediment
and nutrients. Many of these findings are summarised in the companion report by
Waterhouse and Brodie (2011). Establishing relationships between pesticide use and run-off
is not as advanced due to challenges in characterising site-specific transport processes and
lack of usage data (see the companion report ‘Review of MTSRF research advancing our
understanding of the source, transport and impacts of pesticides on the Great Barrier Reef
and associated ecological systems’, by Devlin and Lewis, 2011). There is a strong
relationship between fertilised land uses (e.g. sugarcane, banana) and loss of nitrate, nitrite
and sometimes ammonia in the wet tropical catchments (Mitchell et al. 2006, Faithful et al.
2006, Rhode et al. 2006, Bainbridge et al. 2009b) and Fitzroy basin (Packett et al. 2009). In
contrast, sediment loss is not as high due to improved soil management measures in place
for over a decade in areas of sugarcane cultivation, such as green cane harvesting, trash
blanketing and reduced tillage (Bainbridge et al. 2006b, Rhode et al. 2006, Faithful et al.
2006). However, large sediment losses are associated with rangeland beef grazing lands
(Brodie and Waterhouse 2009, Bainbridge et al. 2006a) despite efforts to reduce erosion by
improving vegetation cover (Coughlin et al. 2007). Hence, the primary pollutants of concern
differ between wet and dry catchments, depending on catchment land uses.

MTSRF Synthesis Report
12
Given the high degree of spatial and temporal variability of the GBR and its catchments,
modelling is essential in the interpretation of short-term empirical monitoring data. The
SedNet and ANNEX model group has been used at the catchment and sub-catchment scale
to predict sediment and nutrient generation, transport and delivery to the GBR lagoon (e.g.
Brodie et al. 2003, Cogle et al. 2006, Armour et al. 2007, Kinsey-Henderson et al. 2007).
Once the sources of key pollutants are identified, pollutant loads can be accurately quantified
and as indicated above, have been progressed through MTSRF research (see Waterhouse
and Brodie 2010 for a summary; Brodie et al. 2009a, b, Brodie and Waterhouse 2010, Kroon
et al. 2009).
MTSRF-funded research has used innovative techniques to identify sources of sediment
from GBR sub-catchments through the analysis of coral cores from inner and mid-shelf reefs
using laser ablation analyses (Figure 6). Further, the contribution of different catchment
erosion processes to sediment loads was quantified using analyses of trace elements and
isotopes (Brodie et al. 2009a). This is combined with information on the type and quantity of
sediment produced by gully, scald, riverbank, hillslope and sheet erosion processes to assist
in identifying management practice changes that will be most effective in reducing sediment
loads. Further information on MTSRF research on the cost effectiveness of management
practices in sugar cane, bananas and grazing (undertaken by van Grieken and others) is
summarised in the companion report ‘Managing for GBR resilience: Socio-economic
influences’ by Johnson and Martin (2011).
Figure 6: Analysis of a coral core from Magnetic Island showing increased
bulk sediment and topsoil erosion in the Burdekin River since European
settlement from the 1850s (Lough, 2007).
3.2 Exposure to pollutants
Inshore reefs vary considerably in their resistance to the negative effects of pollutants in run-
off and their tolerance of future exposure (e.g. Thompson et al. 2011). The exposure
(concentration and duration) of the GBR ecosystem to pollutants depends on many factors,
including the (i) downstream distance from major discharge sources, (ii) mean annual
pollutant load, and (iii) dispersal of flood plumes within the GBR lagoon (Devlin and Brodie
2005, Devlin et al. 2010). Concentrations of contaminants in flood plumes are generally
diluted with increasing distance from the river mouth, although chemical and biological

Water quality and climate change: managing for resilience
13
processes occurring in the plume may influence patterns of retention and removal of some
compounds (Devlin et al. 2001, Devlin and Brodie 2005, Rhode et al. 2006, Packett 2007,
Lewis et al. 2009, Devlin and Schaffelke 2009). Flood plumes tend to disperse northwards
along the coastline, under the influence of south-east winds and Coriolis forcing (Wolanski
1994, Devlin et al. 2001) with most terrigenous sediment confined to inshore coastal waters
(Packett 2007, Wolanski et al. 2008, Devlin and Schaffelke 2009, Devlin et al. 2010; Figure
7). MTSRF-funded research has focused on identifying the dispersal of fine sediments as
vehicles for pollutants and plume extent (see Wolanski et al. 2008, Bainbridge et al. 2010).
Figure 7: Satellite image (Landsat 5 TM) of the Whitsunday Islands showing a
flood plume from the Proserpine and O’Connell Rivers, 28 January 2005. Areas of
elevated suspended solids are visible near the river mouths, with areas of
increased phytoplankton abundance indicative of nutrient enrichment that extends
to the islands. Red circles indicate some of the sampling locations (Cooper et al.
2007).
Intensifying human use of the coastal zone and predicted changes to rainfall patterns and
storm intensity are likely to increase the variety and quantity of pollutants delivered from the
land to the inshore GBR. Inshore ecosystems are most likely to be exposed to pollutants in
run-off from small to medium flood events (Fabricius and De’ath 2004, Maughan and Brodie
2009, Brodie and Waterhouse 2009). However, predictions of areas most at risk of
degradation are complicated by biological, chemical and physical processes of retention and
removal of pollutants, which are not well understood. Cycling of nutrients and local circulation
also influence exposure of reefs to pollutants, with reefs in poorly flushed areas, surrounded
by shallow seafloor, or subject to frequent disturbances likely to be more exposed and less
resilient to pollutant effects (Fabricius et al. 2009).
To effectively manage for ecosystem resilience and assess the impacts of improvements in
land management, monitoring needs to be able to accurately quantify loads of key pollutants
transported by river systems to the GBR lagoon and measure ecosystem response. The
companion report by Waterhouse (2010a) provides an overview of optimal techniques
developed under the MTSRF Program.

MTSRF Synthesis Report
14
Intensifying human use of the coastal zone and predicted changes to rainfall patterns and
storm intensity are likely to increase the variety and quantity of pollutants delivered from the
land to the inshore GBR. Inshore ecosystems are most likely to be exposed to pollutants in
run-off from small to medium flood events (Fabricius and De’ath 2004, Maughan and Brodie
2009, Brodie and Waterhouse 2009). However, predictions of areas most at risk of
degradation are complicated by biological, chemical and physical processes of retention and
removal of pollutants, which are not well understood. Cycling of nutrients and local circulation
also influence exposure of reefs to pollutants, with reefs in poorly flushed areas, surrounded
by shallow seafloor, or subject to frequent disturbances likely to be more exposed and less
resilient to pollutant effects (Fabricius et al. 2009).
To effectively manage for ecosystem resilience and assess the impacts of improvements in
land management, monitoring needs to be able to accurately quantify loads of key pollutants
transported by river systems to the GBR lagoon and measure ecosystem response. The
companion report by Waterhouse (2010a) provides an overview of optimal techniques
developed under the MTSRF program.
Box 4: Early warning of high risk bleaching areas
MTSRF-funded research led by Dr Scarla Weeks (University of Queensland) is collaborating with
the NASA Ocean Biology Processing Group and members of the US Naval Research Laboratory to
generate maps of spatial and temporal variation in euphotic depth for GBR waters. Euphotic depth
(Zeu%) is a measure of water clarity (Lee et al. 2007) with, for example, Zeu1% reflecting the depth
where only 1% of the surface photosynthetic available radiation (PAR) remains. GBR Secchi Depth
data have been regressed against the 10% euphotic depth level (Zeu10%), to generate a GBR-
validated euphotic depth algorithm. Utilising MODIS satellite data, select monthly mean images of
euphotic depth have been generated for GBR waters (Figure 8) however, optically shallow waters
require further refinement of the water quality clarity algorithm using GBR-specific in situ data.
Detecting changes in the transparency of the water column is critical for estimating spatial and
temporal variation in exposure of reefs to pollutants that are implicated in coral bleaching events, or
are involved in flood dynamics. Coupled with maps of thermal stress reflecting the long-term mean
pattern in seasonal variation (Weeks et al. 2008, Maynard et al. 2008b), data on euphotic depth will
provide an early warning assessment of reefs at high risk of bleaching following rapid changes in
irradiance, and assist agencies to target management actions that reduce pollutant loads and
enhance resilience.
Photic Depth vs. Physical Depth
Figure 8: Monthly climatologies of euphotic depth for the southern
GBR for (a) March 2007 (left), and (b) September 2002-2009 (right)
(Weeks et al. 2010).

Water quality and climate change: managing for resilience
15
3.3 Pollutant interactions
The effect of terrestrial run-off on inshore GBR communities depends on the predominant
contaminant in the run-off, however interactive effects are likely to be important drivers of
community structure. For example, crustose coralline algae are more sensitive to fine
sediment when diuron is present and combined exposure to sediment and diuron retarded
recovery of photosynthesis (Harrington et al. 2005). Data from MTSRF-funded research
shows that exposure to the herbicides diuron, atrazine and hexazinone reduces the ability of
coral and foraminifera symbionts to photosynthesise and that this effect is more severe in
elevated SSTs (Negri et al. 2011, van Dam 2011). Combining environmentally relevant
concentrations of diuron or atrazine with SSTs above 30°C can also lead to a synergistic
damage to photosystem II in coral symbionts (Negri et al. 2011). Another recent study
showed that protecting coral larvae from copper pollution can significantly improve the ability
of coral larvae to settle at elevated SSTs (Negri and Hoogenboom 2011). In addition, a
recent study by Humphrey et al. (2008) confirmed that environmentally relevant levels of
suspended sediments, salinity and dissolved inorganic nutrients interact to suppress
fertilisation and development in corals. Interestingly, low concentrations of each contaminant
alone had no effect on fertilisation rates, highlighting the complex nature of changing water
quality on coral ecology. Moderate levels of particulate organic matter may benefit growth of
some coral species (Figure 9). However, at higher levels feeding saturation occurs and the
associated reduction in light, sedimentation and dissolved inorganic nutrients negatively
affect rates of calcification, photosynthetic compensation points, recruitment success,
species richness, community structure, and may result in the proliferation of macroalgae and
Crowns-of-thorns starfish (COTS). If coral recruitment is negatively affected, any reduction in
fertilisation rates will have profound consequences for the recovery of coral reefs from
disturbances (Humphrey et al. 2008).
Figure 9: The effect of dissolved inorganic nutrients, particulate organic matter,
turbidity, and sedimentation on coral growth (y-axis) and survival along a
hypothetical environmental gradient from coastal to oceanic conditions (x-axis).
Grey shaded area approximates species-specific differences in response (normal
font) and local environmental conditions (bold italic font) (Humphrey et al. 2008).

MTSRF Synthesis Report
16
Similarly, low levels of sediment that alone would not reduce coral recruit survival, kill newly
settled recruits when combined with polysaccharides (marine snow) (Fabricius et al. 2003).
Collectively, these results demonstrate the need to further investigate interactions between
contaminants on reefs, especially those adjacent to catchments with a high sediment load,
such as the Burdekin River. While some of the specific mechanisms remain unknown, it is
clear that the combined effects of terrestrial contaminants will reduce coral reef resilience to
increasing frequency of disturbances in a changing climate.
Intrinsic differences in the sensitivity and susceptibility of inshore reefs to the effects of
terrestrial run-off may underpin spatial variation in resistance and resilience to climate
change (Cloern 2001), together with physical processes governing local exposure to
contaminants (Devlin et al. 2003, Devlin and Brodie 2005, Fabricius et al. 2007b). Increases
in SSTs can have acute, chronic, sub-lethal or lethal effects on species with narrow
temperature ranges, and different species within an ecosystem can respond in subtly
different ways to changes in water quality (Anthony et al. 2007). The health of GBR
ecosystems depends on the integrity of ecological processes, rather than the health or
abundance of individual species or groups of species. Measures of ecosystem health,
therefore, require an approach that provides a quantifiable measure of the integrity of
ecological processes (Sheaves et al. 2007). Assessing the effects of climate change on
ecological processes is complicated by the multitude of possible interactions between reef
organisms. The impact of bleaching on productivity and species diversity is not well known.
Variation in SSTs, ocean currents and upwelling events may individually or collectively
adversely affect key ecological processes that flow on to affect the whole ecosystem.

Water quality and climate change: managing for resilience
17
4. Linking water quality and resilience to climate
change
Considerable MTSRF research effort has been directed towards improving understanding of
the interactions between climate change and declining water quality on the GBR ecosystem
in order to generate practical management options that can be used to build and maintain
resilience. Under present carbon emissions projections, increasing SSTs will shift the
frequency of bleaching events from episodic to annual, storms will become more intense,
and ocean acidification will undermine calcification and reef structures. The persistence of
hard coral dominated reef-scapes beyond 2050 will therefore depend on their ability to
maintain essential ecosystem functions (Hoegh-Guldberg et al. 2007a, Veron et al. 2009).
Even in areas of relatively good water quality, field data suggest that an average recovery
interval of greater than five years is required between major disturbance events to maintain
present reef conditions (Wakeford et al. 2008). However, in the last decade, the nature and
heightened frequency of major disturbances such as coral bleaching, COTS outbreaks and
severe storms have exceeded the capacity of many reefs around the world to recover
(Wilkinson 2004). For example, in 1998, more than 16% of the world’s tropical coral reefs
were seriously degraded by a global bleaching event, with 50-90% mortality in some regions
(Wilkinson 2004). The GBR fared comparatively well, which has been attributed to greater
reef resilience from lower population pressure, targeted ecosystem management and,
relatively good water quality (GBRMPA 2009). However, more significant thermal events in
2002 and 2006 in the GBR and southern GBR respectively, resulted in greater coral mortality
and highlighted the increasing frequency (or reduced return interval) of these disturbances.
Given that water quality continues to decline and the overall outlook for the GBR is ‘poor’
(GBRMPA 2009), it is likely that the additional pressure of climate change will result in a shift
in reef productivity, community structure, ecosystem function, and the provision of ecosystem
goods and services. The situation facing management agencies is the problem of how to
minimise the magnitude of this shift by managing for resilience, through maintaining and
improving water quality, improvements in land management and coastal development. As a
consequence, considerable MTSRF-funded effort has focused on research projects aimed at
increasing understanding of the spatial and temporal connections between pollutant run-off
and the thermal bleaching susceptibility and mortality of corals.
4.1 Water quality as a driver of resilience to climate change
The complex, and often seemingly contradictory, effects of climate change and
eutrophication on coral reefs reveals the challenges of managing for ecosystem resilience.
On one hand, even though the extent to which corals are able to acclimate or adapt to
temperature perturbations is unclear, there is evidence that prior exposure to extreme
temperatures enhances the resilience of inshore corals to future exposures (Section 2.1).
Further, the risk of coral mortality during a bleaching event and subsequent recovery phase
decreases with increasing energy reserves and degree of plasticity in heterotrophic response
(Section 2.2). Dissolved inorganic nutrients such as nitrogen, which are rapidly converted
into particulate organic matter within hours or days, may have a beneficial effect on the
growth and energy reserves of heterotrophic coral species at moderate levels (Section 2.2).
Heterotrophy may account for spatial differences in bleaching-induced stress and mortality
between reefs with varying trophic resources. Hence, it would appear that reefs with previous
exposure to high temperatures and terrestrial run-off can be more resistant and resilient to
climate-change related disturbance in the short term.
However, while specific communities of coral are likely to incur some benefit from increased
nutrient availability, the interactive effects of contaminants in run-off and increases in SSTs
on reef heath are overwhelmingly negative. For example, MTSRF-funded research (Negri et

MTSRF Synthesis Report
18
al. 2011) showed elevated SSTs enhanced the negative effect of low concentrations of three
commonly detected photosystem-II herbicides on photosynthetic efficiency in corals (additive
effect), with a greater effect on chronic photoinhibition (synergistic effect) (Negri et al. 2011).
At high levels of particulate organic matter, the associated reduction in light negatively affects
rates of calcification, photosynthetic compensation points, and community structure and
function in corals, and increases susceptibility to bleaching (Section 2.1). Hence, exposure to
terrestrial run-off can increase the sensitivity of reef ecosystems to elevated SSTs that have
already been experienced in GBR areas during previous summers.
Further experiments investigating interactions between water quality and climate change
suggest that for at least one foram species, additive effects of the two stressors exist, with
foram growth rates negatively affected by increased nutrient concentrations and increased
temperature (Uthicke et al. 2010). At temperatures greater than 32°C, herbicides had a lethal
effect on diatom-bearing species of foraminifera (van Dam et al. 2011). Foram species were
also tested for susceptibility to thermal stress, and showed responses at temperatures only
slightly above current summer maxima, allowing identification of thermal thresholds for
several foraminiferan species. The development of a FORAM index provides an effective
bioindicator for the assessment of turbidity and light regimes and organic enrichment of
sediments on coral reefs (Uthicke et al. 2010).
Understanding properties of reefs or regions that contribute to their resilience could generate
practical management options, for example by enabling prioritisation of protection of reefs
that have the greatest chance of withstanding degradation, or targeting management actions
to increase the resilience of ecologically significant vulnerable areas. For example, the colour
darkness of coral communities increases along a gradient from offshore to coastal waters in
response to elevated concentrations of nitrate, particulate nutrients and suspended
sediments (Figure 10) (Fabricius 2005). The darker pigmentation of coastal corals results in
greater thermal absorption and therefore greater sensitivity to thermal stress under
conditions of high temperature and irradiance, compared to lighter offshore corals. However,
water flow alleviates surface warming in corals, such that high flow reef environments will
have a lower likelihood of bleaching than reefs or embayments under low flow conditions
(Nakamura and van Woesik 2001, West and Salm 2003).
Figure 10: Coral colour changes substantially
along a gradient from coastal to offshore regions
of the GBR, with corals significantly darker in
coastal waters (Fabricius et al. 2007b).
In addition, colony geometry and tissue characteristics of corals may, to some extent,
modulate internal light environments and alleviate light stress. Experiments showed the
surface temperature of darker corals in turbid water was significantly greater than that of
paler corals in clear water environments at comparable sea temperatures, light and flow
conditions, and concluded that surface warming of darkly pigmented corals in coastal
environments is sufficiently high to exceed bleaching thresholds (Fabricius et al. 2007b).
Hence a better understanding of the interactions between factors such as flow, irradiance,
pigmentation, colony geometry and water quality on the microenvironment of corals may

Water quality and climate change: managing for resilience
19
assist in interpreting some of the spatial and temporal variability in coral bleaching across the
GBR, and improve identification of vulnerable reefs (Fabricius et al. 2007a).
Recent modelling efforts funded by the MTSRF have focussed on linking regional water
quality and climate change variables to provide a framework for management agencies to
target investments under Reef Rescue to improve reef resilience (Wooldridge 2010).
However, the complex interactions between contaminants co-occurring in run-off complicate
predictions of spatial and temporal resilience to climate change, and consequently models
have generally focussed on only one water quality variable (e.g. sediment or nutrients;
Section 3.1). These models, whilst presenting a simplistic assessment of water quality
factors underpinning reef resilience, enable management to assess the potential effect of
various land-use scenarios or changes in land management practices on water quality. With
further development to include factors such as synergistic effects of stressors (Section 3.3),
non-linearity of responses (Section 2.2), species-specific thermal thresholds (Section 2.1),
spatial differences in thermal histories of reefs (Box 3), community composition (Section 2.3),
the effect of pulsed versus chronic exposure to contaminants (Section 3.2), and remote
sensing data of spatial variation in physical and hydrodymamic characteristics of reefs (Box
4), the capacity of models to identify specific effects of changes in water quality on reef
resilience will improve.
4.2 Modelling resilience of inshore reefs
Corals flourish in clear, nutrient-limited water; hence studies of eutrophication effects on
corals have often focused on enrichment with dissolved inorganic nutrients (e.g. Stambler et
al. 1994, Dubinsky and Stambler 1996, Koop et al. 2001, Szmant 2002). MTSRF-funded
researchers tested the theory that dissolved inorganic nitrogen (DIN) is an important driver of
coral response to elevated temperature (Wooldridge 2009a, b). This theory was postulated
on there being direct effects of DIN on coral physiology at high concentrations in poorly
flushed locations, and indirect effects from incorporation into benthic food webs and
conversion into particulate form (Alongi and McKinnon 2005, Fabricius 2005). Although there
is currently no direct experimental evidence of the effect of DIN on thermal sensitivity of
corals, the model provides a mechanism for testing interactions between water quality and
coral bleaching, and can eventually be used with empirical data inputs.
Wooldridge (2009a) modelled the possible future risk of coral bleaching at inshore reefs
located within the region influenced by flood plumes from the Burdekin River under a range
of land management scenarios. The exposure of inshore reefs to high concentrations of DIN
(using chlorophyll a as a proxy) was predicted to lower bleaching thresholds of corals
compared to reefs in waters with lower exposure, although the synergistic effects of
suspended sediment and associated reductions in light were not considered. The study
identified land management actions that lower the delivery of DIN to the reef as potentially
enhancing reef resilience to elevated SSTs (Wooldridge 2009b) (Figure 11). Similarly, in the
Tully-Murray catchment, it was proposed that a reduction in DIN outputs may influence
bleaching-induced mortality compared to no reduction in DIN (Wooldridge 2008).
Further simulations of projected increases in thermal tolerance of corals under a range of
climate change scenarios proposed that integrating reductions in DIN with the stabilisation of
atmospheric CO2 below 450 ppm would assist in maintaining coral dominated reefs beyond
2100 (Wooldridge 2010). At present, rates of adaptation are unlikely to be sufficiently fast for
corals to acquire increased resistance to increasing SSTs and declining pH even under
modest climate change scenarios (Wooldridge and Done 2009). Further research to
elucidate the effect of improved land management practices on thermal sensitivity and
building and maintaining coral reef resilience are imperative (Bellwood et al. 2004, Diaz-
Pulido et al. 2009, Hughes et al. 2010, Marshall and Schuttenberg 2006, Marshall and
Johnson 2007).

MTSRF Synthesis Report
20
Figure 11: Modelled output postulating the interaction between DIN delivery
and bleaching thresholds of corals (Wooldridge 2009b).
4.3 Managing water quality for resilience
MTSRF-funded research has made significant progress in linking research on the delivery
and impacts of pollutants on inshore GBR ecosystems and the resilience of reef communities
to changes in SSTs and other climate-related disturbances (Sections 2 and 3). This
knowledge is critical to inform the design and prioritisation of effective management
strategies that aim to enhance the resilience of the GBR to future climate change.
The form of nutrients in run-off has implications for management actions targeting sources of
pollutants. For example, floodwaters tend to contain higher concentrations of dissolved
organic nitrogen (DON) compared to in-river concentrations, while river waters tend to
contain higher concentrations of dissolved inorganic nitrogen (DIN). Using the results of
MTSRF modelling that postulated that reducing DIN delivery may improve coral resistant to
thermal stress (Wooldridge 2009b) allows for management to consider the minimisation of
DIN through improved agriculture practices, such as N-replacement approaches (Wallace et
al. 2009a).
Soils of fine texture have a high surface area and hence a greater sorption area for pollutants
providing a major transport mechanism for phosphorus and other elements to reach the GBR
(McCulloch et al. 2003, Packett et al. 2009, Bainbridge et al. 2010). Therefore, reducing fine
texture soils will reduce the impact of sedimentation as well as nutrients on inshore
ecosystems, with the potential to increase their resilience to thermal stress (Fabricius et al.
2009). In addition, quantifying the link between water quality and bleaching risk, together with

Water quality and climate change: managing for resilience
21
a spatially explicit model exploring patterns of land use and changes in land management
across a range of industries (Henderson and Kroon 2009), will enable management to target
areas to focus effort and cost-effective solutions to achieving water quality targets.
Predicting changes in the state of reef communities in response to climate change is
complicated by uncertainty concerning the processes driving post-disturbance recovery of
coral reefs operating under different levels of environmental and ecological degradation.
Uncertainty concerning the potential for the coral-symbiont partnership to adjust or adapt to
warming conditions, and uncertainty about the cumulative effects of other stressors on
ecosystem health. Managing a complex natural resource such as the GBR requires an
understanding of the different pressures on the system and their interactions, as there are
likely to be more than one ‘driver’ of reef resilience. Overly simplistic modelling of links
between water quality variables and reef resilience may produce negative flow-on effects
(maladaptation) that require additional strategies to manage. It is important to quantify how
these sources of uncertainty affect the accuracy of predicting shifts in ecosystem structure
and function with climate change, especially when comparing alternative policies and
management interventions for achieving desired system water quality outcomes.

MTSRF Synthesis Report
22
5. Conclusions and management applications
5.1 Conclusions
In summary, the interactive effects between water quality and climate change has
implications for the susceptibility of corals to thermal stress (i.e. bleaching), disease
virulence, the risk of widespread coral mortality, and recovery rates post-disturbance.
Effective management for GBR resilience requires integration across disciplines and an
understanding of the complexity of factors that influence spatial and temporal differences in
vulnerability to climate change. For example, resilience to bleaching may vary depending on
a reef’s thermal history, the frequency and nature of prior disturbances, and its exposure,
sensitivity and resilience to pollutants. To date, the development of models that predict
bleaching likelihood on the basis of one environmental variable represent a step forward in
understanding the complex mechanisms underpinning bleaching susceptibility of reefs to
increasing SSTs. With further development, such models can potentially simplify the complex
array of biological and physical interactions to deliver solutions to environmental managers
seeking to protect and conserve the biodiversity of the GBR.
The information generated through MTSRF has also contributed to an emerging community
consensus that water quality is one of the high-priority management issues for the GBR,
particularly in the face of climate change. Further empirical data is needed to quantify this
relationship and to identify specific actions that will sustain coral reef resilience (Hughes et al.
2010). Despite improvements in land management practices through government initiatives
such as the Reef Water Quality Protection Plan (Reef Plan; DPC 2009) and Reef Rescue
(Australian Government 2007), a long time-lag is expected before any improvement in GBR
water quality will translate into measureable changes in the ecosystem (Bainbridge et al.
2009a).
5.2 Management applications
Achieving sustainable loads of pollutants and developing mixtures of effective policy
instruments and governance arrangements for managing water quality and climate change
remain significant challenges at the catchment, regional and GBR scales. It is not known
whether current management and policy efforts will be sufficient to achieve water quality
improvement that will protect and enhance the resilience of the GBR ecosystem. Part of this
uncertainty relates to the fact that climate projections for the region have their own
uncertainty making most measures of resilience relative. Improving regional climate
projections and the understanding of the links between water quality, ecosystem resilience
and future change will assist management. Researchers funded by the MTSRF have made
significant progress in furthering understanding of the complex processes and interactions
between water quality and resilience to climate change, and developing models that can deal
with this complexity, and provide predictive tools for management.
The advanced models developed through the MTSRF can link changes in reef resilience with
changes in land management practices, and can provide management with spatial and
temporal mapping of exposure to pollutants in run-off, overlayed with areas where poor water
quality influences resilience (or lack of) to thermal stress. By showing that coral mortality is
related to bleaching severity, thermal event duration, and size of initial energy reserves, reef
areas that are most vulnerable to future thermal events can be identified and prioritised for
management. Conversely, by using MTSRF-funded results showing that corals that survived
prior exposure to high SSTs are more resilient to future thermal events through mechanisms
of tolerance and adaptation, management can make informed decisions to protect or
enhance this natural resilience as a seed bank for future recovery of less resilience reefs.

Water quality and climate change: managing for resilience
23
MTSRF models that can provide predictions of coral mortality following a bleaching event or
future implications of ocean acidification will improve understanding of community
composition shifts, which will be important information for monitoring community changes
due to climate and again identifying suitable reef areas for protection. This information also
has applications for industries that depend on the GBR, in particular tourism operators who
rely on healthy coral communities. Being able to predict how reef communities might change
under increasing SSTs or ocean acidification can inform future planning for reef-dependent
industries. Similarly, MTSRF research that has identified a strong link between temperature
anomalies and coral disease and developed a predictive tool linking thermal stress and
increased severity and frequency of coral disease, can be used to understand future spatial
patterns of coral disease and inform management and industry planning decisions.
Ultimately, GBR ecosystem resilience to future climate change will depend on the rate and
magnitude of change, and the effectiveness of improvements in water quality, which has
been shown to significantly undermine reef resilience. MTSRF research has provided
improved conceptual and empirical understanding of the effects of water quality variables on
changes in coral reef community structure, an increased understanding of the negative
interactive effects of different contaminants and climate change on ecosystem health, and
improved knowledge of the effects of water quality on the resilience of reef organisms to
climate change. Collectively, this information can be applied to strengthen existing water
quality improvement initiatives in the GBR catchment, provide information on which
ecosystems are most at risk and therefore require management focus, as well as inform
decisions to prioritise protection of specific reefs and locations as refugia to facilitate future
recovery of reefs in the face of climate change.
5.3 Future directions
Scientific information that informs effective management of the GBR must take a holistic
approach that considers interactions between multiple stressors, co-occurring environmental
factors, and the flow-on effects for ecosystem health. There is an urgent need to integrate
monitoring, modelling and experimental knowledge from catchments to the GBR, and to
experimentally define the direct effects of water quality parameters on thermal sensitivity,
bleaching threshold and recovery after disturbance. In addition, the mechanism by which
water quality influences calcification also needs to be understood to predict how the structure
of coral reefs may change under future ocean acidification. Ultimately, a single model that
predicts spatial and temporal vulnerability to the combined effects of ocean warming, ocean
acidification and climate change is critical. Such an integrated model will facilitate the
implementation of targeted management strategies by linking GBR ecosystem health with
water quality in the lagoon and catchments.
The development of new management practices and the modelling of future changes in land
use on water quality remain critical requirements to effectively target resources for water
quality improvement in a changing climate. Understanding the transport and trapping of
contaminants from the ‘source-to-sea’ has improved greatly however, current monitoring and
modelling methods significantly underestimate pollutant loads, and there is likely to be a
considerable lag in detection of any effect of changes in land use or land management
practices on marine water quality (Bainbridge et al. 2009, Bainbridge and Brodie 2009,
Brodie et al. 2009, Wallace et al. 2009b). Hence, improvements under the Reef Plan and
Reef Rescue initiative are likely to take years to detect change in ecosystem function. The
development of a single model linking transport process across the land-sea continuum is
required to provide a framework for linking land management to changes in water quality and
ecosystem health (see Webster et al. 2008)

MTSRF Synthesis Report
24
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