Annual Report
Coral Reef Targeted Research &
Capacity Building for Management Program
Acknowledgements
This report was developed and collated by Melanie King (Executive Officer) and Kristen Sampson (Project Officer) of
the CRTR Project Executing Agency, with significant contributions from the following CRTR Program members:
Professor Ove Hoegh-Guldberg, Chair Bleaching Working Group
Professor Peter Sale, Chair Connectivity Working Group
Professor Drew Harvell, Chair Disease Working Group
Professor Peter Mumby, Chair Remote Sensing Working Group
Dr Alasdair Edwards, Chair Restoration & Remediation Working Group
Professor Roger Bradbury, Chair Modelling & Decision Support Working Group
Professor Ed Gomez, Chair Southeast Asian Centre of Excellence
Dr Roberto Iglesias-Prieto, Chair Mesoamerican Centre of Excellence
Dr Maggie Kyelawanga, Chair East African Centre of Excellence
Dr Christopher Muhando East African Centre of Excellence
Mr Andy Hooten, Synthesis Panel Executive Secretary & US Coordinator
Mr Mark Paterson, Communication Coordinator Currie Communications
Ms Gabrielle Sheehan, Communication Officer Currie Communications
Contributions have also been received from Working Group and Centre of Excellence members through their
individual reports.
Further Information
Information used in this report has been collated from the individual Working Group and Centre of Excellence
2009 annual reports, and from communication activities during the reporting period. Additional information has
been produced with the input of the Management Team.
For further information regarding this report and/or to request copies of the individual Working Group and Centre
of Excellence reports, please contact the Executive Officer, Melanie King at m.king4@uq.edu.au.
Coral Reef Targeted Research & Capacity Building for Management Program, c/- Centre for Marine Studies,
Gerhmann Building, The University of Queensland, St Lucia, Queensland 4072, Australia
Tel: +61 7 3346 9942 Fax: +61 7 3346 9987 Email: info@gefcoral.org Internet: www.gefcoral.org
Published November 2009
2
2009 Annual Report
1
Contents
2
Acknowledgements
2
- Further Information
2
Executive Summary
4
Component 1
7
Addressing Knowledge and Technology Gaps
8
- Coral Bleaching and Local Ecological Responses
9
- Connectivity and Large-Scale Ecological Processes
11
- Coral Disease
13
- Modelling and Decision Support
15
- Coral Restoration and Remediation
16
- Remote Sensing
19
3
Component 2
21
Promoting Scientific Learning and Capacity Building
22
- Australasian Centre of Excellence
23
- East African Centre of Excellence
25
- Southeast Asian Centre of Excellence
27
Component 3
29
Linking Scientific Knowledge to Management and Policy
30
- `Common Sampling' Project
30
- GEF International Waters Conference
31
- 2009 Annual Synthesis Panel Meeting
31
- Publications
32
4
- Events
32
Component 4
33
Program Management
34
- Disbursements
34
- Procurement
35
- Sub-grants
35
- Communication
35
- Information Dissemination
37
Abbreviations
38
3
Executive Summary
As the Coral Reef Targeted Research & Capacity Building for Management (CRTR) Program comes towards the
end of Phase One in 2009, it sees the completion of almost five years of research from six Working Groups and
four Centres of Excellence, comprising over 70 researchers. In addition to the research, the Program members
have produced, or been involved in the production of, over 600 publications including peer-reviewed scientific
literature, books, conference presentations, electronic products, grey literature articles and media articles, and
participated in over 200 events. These activities have also led to the production of a number of communication
and outreach outputs for research, management, policy and local community audiences.
In 2004 the CRTR Program commenced its research activities designed to address fundamental information gaps
in our understanding of coral reef ecosystems, so that management options and policy interventions could be
strengthened globally. The research undertaken over the past five years has encompassed coral bleaching and
local ecological effects; coral disease; connectivity; restoration and remediation; remote sensing, and; modelling
and decision support. The results and information produced from this research is now being accumulated into an
impressive array of findings relevant to the scientific, management and policy communities at the global, regional
and local levels.
Marine Protected Area, Apo Island, The Philippines. Photo: Gidi Levi
With increasing calls to further protect coral reef ecosystems and the life-forms they sustain, the research from
the CRTR Program can assist in improving management and policy interventions, and future strategies. Key to
this has been the work undertaken to understand the causes and stresses caused by mass coral bleaching events
and coral disease. Research into the impacts of stress events on coral reefs has led to an improved understanding
of how coral reefs respond or adapt to the impacts of different stress events. Observations have demonstrated
that mild thermal stress events show different responses compared with extreme events during extreme events,
small colonies do better than larger colonies, while during mild events, colony size does not influence bleaching.
Furthermore, separate studies from the Bleaching and Disease Working Groups have revealed that thermal stress
plays a key role in increasing the incidence and susceptibility of corals to disease.
Additionally, the development of the "Lab in a Box" by the Disease Working Group will enable cutting-edge real-
time advanced microscopy and molecular microbiology in coral disease research in remote field settings. This
capability of working with fresh material and in tightly iterative mode has dramatically changed the depth and
quality of data and observations that can be made in field-based coral microbiology. Given the limited resources
that most remote island and reef managers have at their disposal, this toolkit could serve as a model for field coral
microbiology.
4
2009 Annual Report
Research from across the scientific working groups
has also led to valuable information for the improved
establishment of Marine Protected Areas (MPAs),
and their value in protecting coral reef systems
from environmental and anthropological impacts.
For example, work undertaken into the resilience
to disease through the establishment of MPAs has
found lower disease prevalence within MPAs than the
adjacent fished areas, which was strongly correlated
with fish functional diversity.
Equal y important in determining zoning such as
MPAs, or understanding which reefs are replenished
from what sources is the understanding of the
connectivity of larvae both from coral and fish
species. Research under the CRTR Program into
the development of immunogenetic tags to identify
coral planulae to species, and the development of
a novel `magnetic particle' technique for measuring
movement of water and particles away from spawning
sites of corals, has led to an extension in knowledge
of coral genetics in the Mesoamerican region, and
advanced knowledge of coral larval biology and
behavior that could be important in developing new
models of coral dispersal. The work undertaken by
the Connectivity Working Group has now resulted
in connectivity issues being more firmly based in
management decisions.
Habitat survey, Lingayan Gulf.
A new technique developed by members of the Remote Sensing Working Group has also led to the ability to
identify areas of the coastal zone that have particularly benign physical conditions in terms of coral bleaching.
The method also includes important new advances to the design of marine reserves such that connectivity and
different reserve design criteria can be incorporated explicitly into the algorithm. The methods have now been
showcased for the Bahamas and Belize.
Practical on-ground information for managers has also being developed. With the increasing emphasis on
aquaculture as a source of food and income for many communities throughout areas such as Asia, members of the
CRTR Program made some breakthrough discoveries in determining that potentially pathogenic microorganisms
such as Roseobacter spp. and Disulfovibrio spp., are likely moving from fish pens onto the reef. This discovery
necessitates that "Best Practices Guidelines" be established for aquaculture adjacent to reefs in order to preserve
the ecosystem for fisheries and the other life-forms it sustains.
Research into coral restoration techniques has demonstrated a number of successes with various cost-effective
methods of coral restoration being explored.
Much of this work is being undertaken in Bolinao,
Philippines, whereby the research team has been
exploring methods including coral fragment
transplantation techniques and larvae rearing before
being transplanted out onto the reef. Recent work
has included col aborations with local communities
on the transplantation of corals and the work has
shown good results and much promise with the
potential for scaling up. Using principally a locally
available resilient species, Porites cylindrica, local
volunteers transplanted more than a thousand second
generation transplants and local y available `corals
of opportunity' successful y, with a high degree of
survival. The activity used no scuba and no adhesives,
strictly volunteer time, and generated much interest
for future expansion.
Remote sensing tools developed over the five years Community volunteers transplant coral using low cost methods, with
will also assist in management and policy decision- goggles as their only equipment.
5
making at the regional and local scales. The creation of the Reef Observer software tool uses a state-of-the-art
model of radiative transfer, together with a large spectral library of coral reef substrata, to quantify the feasibility of
any coral reef remote sensing project. Reef Observer also has a capacity to identify whether particular changes in
coral reef state can be detected using remote sensing. The user can specify the type of change (% substrata), the
depth, the clarity of the water, and type of sensor. The radiative transfer software used to power Reef Observer is
now complete and is being disseminated free of charge.
The online Reef Remote Sensing Toolkit was extended to help practitioners match their remote sensing objectives
to the appropriate technologies (this toolkit covers a wide range of mapping problems and essentially stops short
of making prescriptive predictions for more detailed remote sensing problems for which Reef Observer is used).
The upgraded Toolkit is due for release on the website in December 2009.
These findings, amongst others, play an important role in assisting to develop mitigation and adaptation strategies
and provide the basis for identifying the least/most vulnerable reefs and predicting the spatial distribution of
future coral reefs and developing management priorities that are most appropriate for their future.
In addition to the research element, the Program has continued to make strong in-roads into building the capacity
of scientists and managers in developing countries through student scholarships, training workshops and courses
and the release of new information. Following the success of the Future Leaders Forum in 2007 and a follow-
up meeting at the International Coral Reef Symposium in 2008, the scholars' network of Masters, PhDs and
Post-doctoral researchers now extends to approximately 60 students from 17 countries around the world.
Cementing the success of this group, the network will release an anthology of their work under the CRTR Program
in early 2010.
Importantly in the final stages of Phase One, the CRTR Communication Team have continued to work with the
Working Groups and Centres of Excellence in producing relevant products adapting their research outputs for
target audiences. Information produced and packaged during the year has included products ranging from
advisory briefs and guides, to reports and case-study analyses.
Products developed from the research outputs will continue into early 2010 with the release of connectivity and
remote sensing handbooks, a coral reef restoration manual, a report on the role of indigenous knowledge in
the management of fish stocks and coral reefs in Tanzania, and an anthology of the CRTR scholars' work from
Phase One.
The East African COE produced a handbook to document the traditional fish stock management techniques of Zanzibar fishers.
Photo: Assaf Zvuloni
Phase One has seen a culmination of high-level, synthesised research information, information outputs and
capacity building activities being undertaken with the networks generated now spanning 70 senior scientists and
60 scholars from 23 countries. The success from the first five years has been seen in the numerous research
findings, many of which have been published in over 600 research publications, and in the large number of training
workshops, information exchanges, conferences, media events and meetings that have been participated in or
organised by Program members. Additional y, there have been management and policy successes with local
practices under review or changes already being made.
Whilst the planning for Phase Two is underway, it will be important to maintain the momentum gained under the
first Phase and to use the information still forthcoming from the science projects, to guide the future management
of and policy decision-making for coral reefs.
6
2009 Annual Report
1
Addressing Knowledge
and Technology Gaps
1
Component
7
Addressing Knowledge
and Technology Gaps
Despite an increasing awareness of the importance of coral reef ecosystems to human populations around the
world in terms of ecosystem goods and services including food security, livelihoods, tourism, and coastal defence,
there are still many gaps in the scientific knowledge regarding the forms and functions of these ecosystems.
To address these knowledge gaps, the CRTR Program is organised around six key scientific themes under
Component One, which address the scientific gaps pertaining to:
· Coral bleaching and local ecological responses
· Connectivity and large-scale ecological processes
· Coral disease
· Remote sensing
· Coral restoration and remediation
· Modelling and decision support
Highlights of progress over the reporting period are outlined below, with detailed progress available from the
Working Group Annual Reports.
8
2009 Annual Report
Coral Bleaching and Local Ecological Responses
1
Working Group Members:
Prof Ove Hoegh-Guldberg, Chair Centre for Marine Studies, The University of Queensland, Australia
Prof Yossi Loya, Co-Chair Department of Zoology, Tel Aviv University, Israel
Prof Robert van Woesik Department of Biological Sciences, Florida Institute of Technology, USA
Dr Tim McClanahan The Wildlife Conservation Society, Kenya
Dr Roberto Iglesias-Prieto Instituto de Ciencias del Mar y Limnologia,
Universidad Nacional Autonoma de Mexico
Dr Ruth Gates Hawaii Institute of Marine Biology, University of Hawaii, USA
Dr Michael Lesser Department of Zoology, University of New Hampshire, USA
Dr John Bythell Department of Marine Sciences & Coastal Management, University of Newcastle, UK
Dr Christian Wild University of Munich, Germany
The Bleaching Working Group (BWG) has
focused on key gaps in our understanding
of mass coral bleaching and related
ecological phenomena, and has pursued
research projects that range from
establishing a better understanding of
why corals bleach and get diseased, to the
impacts of coral mortality on fish populations
and human dependents. The associated
research has been conducted across the
four Centres of Excel ence: Heron Island
(Australia), Zanzibar (Tanzania), Bolinao
(Philippines) and Puerto Morelos (Mexico).
In addition to producing over 230 peer-
reviewed papers, the BWG has trained 17
postgraduate students and has supported
many more through its regional workshops
and research projects.
Fishermen in Mtwara, Tanzania. Photo: Tim McClanahan
Whilst focusing on the key gaps in understanding mass coral bleaching, the BWG has made significant progress
through increasing the understanding of the geographical and functional diversity of Symbiodinium (single-celled
aglae which live in a symbiotic relationship with coral reefs), and played a significant role in the establishment of a
worldwide database of Symbiodinium genetics. The results indicate there are marked regional differences in the
diversity and ecological dominance of symbiotic algae, with the patterns probably influenced by long-standing
environmental conditions and/or from historical changes in climate during transitions between geological periods.
Coral-algal symbioses are highly responsive to change through partner recombination but these processes may
require time scales of centuries or more in duration.
Furthermore, recent genetic studies have
identified large differences between Symbiodinium
occupying different host species, indicating
potential y hundreds of different species. At the
outset of this project the understanding of the
differences between species of Symbiodinium was
confined to a number of non-coding sequences
such as 18S, 28S and ITS ribosomal sequences.
This project made a major contribution to fil ing
this particular gap in understanding Symbiodinium
by expanding the number of sequenced genes
from a little over 10 to over 1450.
The results of these projects have established
an important platform for exploring the major
responses of Symbiodinium to stresses such Bleached versus normal Acropora near Great Keppel Island Southern
as those arising from climate change, and for Great Barrier Reef in January 2006. Photo: Ove Hoegh-Guldberg
9
exploring the underlying differences between reef-
building corals in their response to environmental
stress. They wil also be instrumental in improving
management strategies to adapt to changes in the
environment of coral reefs.
Understanding of the interactions of reef-building
corals and Symbiodinium, with the broader range
of symbiotic organisms associated with them, is
critical to understanding not only the basic biology
of corals, but also their response to stress and
disease. Research undertaken by BWG members
set out to describe host symbiont mutualism
between corals, dinoflagel ates and bacteria, and
resulted in a large number of new observations and
discoveries. The research identified the critical role
of the mucus layer on corals as a barrier to microbial
invasion, and concluded after extensive studies that
bacteria are rare within the tissues of corals.
Amphiprion-Maldives. Photo: Tim McClanahan
Members of the group also explored the potential role of bacteria in causing bleaching, discovering that Vibrio
and other bacterial infections are most likely secondary rather than primary causes of bleaching and disease.
It became clear that thermal stress increases the incidence and susceptibility of corals to disease, which echoes
results discovered within the Disease Working Group of the CRTR Program.
Research undertaken on the effects of bleaching on coral and fish communities in the Western Indian Ocean
compiled approximately 2000 site-time combinations of coral cover for the whole Western Indian Ocean
(WIO) for the period 1958-2005 and analysed regional patterns and identified the 1998 climatic oscillation as
the most significant factor in affecting regional variation
in coral cover. Further analysis of change in coral cover
and community structure, and their relationship with
environmental properties, indicated that the impact
of the disturbance was variable in space in association
with region-specific environmental properties; primarily
the background temperature, light condition and water
current. This has been mapped and provides the basis
for identifying least and/or most vulnerable reefs and
predicting the spatial distribution of future coral reefs
and developing management priorities that are most
appropriate for their future.
Ful details of the research findings and achievements
of the Bleaching Working Group can be found in the
report "Bleaching and Related Ecological Factors: CRTR
Working Group Findings 2004-2009" (www.gefcoral.org). Photo: D. Thornhill
10
2009 Annual Report
Connectivity and Large-scale Ecological Processes
1
Working Group Members:
Prof Peter Sale, Chair Biological Sciences, University of Windsor, Canada
Dr Carmen Ablan Molecular Genetics Laboratory, The WorldFish Center, Malaysia
Dr J Ernesto Arias Lab. Ecologica de Ecosistemas de ArrecifesCoralinos, CINVESTAV-U, Mexico
Prof Mark Butler IV Department of Biological Sciences, Old Dominion University, USA
Prof Robert Cowen Rosenstiel School of Marine and Atmospheric Science, University of Miami, USA
Dr Bret S. Danilowicz Paulson College of Science & Technology, Georgia Southern University, USA
Dr Geoff Jones School of Marine Biology & Aquaculture, James Cook University, Australia
Dr Serge Planes Centre National pour la Recherche Scientifique, Universite de Perpignan, France
Prof Barry Ruddick Department of Oceanography, Dalhousie University, Canada
Dr Yvonne Sadovy Society for the Conservation of Reef Fish Aggregations, The University of Hong Kong
Prof Robert Steneck School of Marine Sciences/Darling Marine Center, University of Maine, USA
Prof Alina M. Szmant Coral Reef Research Group, Center for Marine Science,
University of North Carolina at Wilmington, USA
Dr Simon Thorrold Biology Department, Woods Hole Oceanographic Institution, USA
Dr Mary Alice Coffreth Department of Biological Sciences, State University of New York, USA
Dr Ken Lindeman Environmental Defense, Miami, USA
Dr Enric Sala Center for Marine Biodiversity and Conservation, Scripps Institute of Oceanography, USA
Coral reefs are patchily distributed ecosystems potentially connected by ocean currents. `Connectivity' is the flux of
items between locations. The complexity of water movement in and around coral reef systems makes the building
of detailed information on connectivity patterns challenging and requires large teams and simultaneous field
observations and/ or collections over relatively large regions. Much of the work undertaken by the Connectivity
Working Group (CWG) has focused on demographic connectivity. The research undertaken by the CWG over the
past five years has resulted in connectivity issues now being more firmly based in management decisions. This is
also being reflected in the tone of the Connectivity Handbook, which will be available in early 2010.
The final year of Phase One, has seen the CWG focusing its efforts on (i) the final analysis and publication of research
results for the sub-projects, (i ) further developing thinking on the application of the science of connectivity into
MPA design, and (iii) effectively transferring knowledge of connectivity science to the management community.
Priority questions for the CWG centred on developing ways to measure connectivity in reef species including fish,
corals and lobster.
Whilst the CWG's five-year
workplan was very ambitious
there has been some major
outputs including a number
of
important
technical
achievements (published in
peer-reviewed literature), and
the
biophysical
modeling
framework developed by Claire
Paris and others, partly with
CRTR funding, now being made
available to the community via
the web (initial y in a password
protected mode, but ultimately
as freeware).
In addition to the research
undertaken, the CWG has also
been involved in discussions
concerning inappropriate coastal development, and has been responsible for the production of an advisory
brief on this issue. The arguments against inappropriate coastal development all relate to the need to maintain
connectivity both among populations and between habitats used by different life stages of coral reef species.
The need to ensure firm policy decisions are taken to protect these habitats has been highlighted in Belize where
11
legislation has been passed to ban the landing of fish fillets as a way of preventing fishing for parrotfishes and
other grazers. This legislative change has come about as a direct consequence of interactions between managers
and members of the connectivity and remote sensing programs.
Research findings from the CWG have included the advances made in testing approaches to explore connectivity
in a common, sedentary reef fish with demersal eggs, through the use of natural otolith tags (trace elements). It
has been found that genetic approaches, particularly assignment techniques that relate individual recruits to likely
natal populations were more useful, although the need for relatively large samples of adults and recruits, collected
over a large region demonstrated the logistical demands of these approaches. The project has provided new
detail on the scale of connectivity in this common species.
Work on the development of immunogenetic tags
to identify coral planulae to species has continued.
This project has now developed a novel `magnetic
particle' technique for measuring movement of water
and particles away from spawning sites of corals. It
also extended knowledge of coral genetics in the
Mesoamerican region, and advanced knowledge
of coral larval biology and behaviour that could be
important in developing new models of coral dispersal.
Whilst the research components have provided
new information for use in understanding the
connectivity between species and habitats, the CWG
has also continued to make important advances in
communicating the science to management audiences.
Along with the activities mentioned earlier, the CWG
has also produced a number of training workshops and
written products for managers. Attempts have been
undertaken to educate the management community
in the Mesoamerican region concerning issues of
connectivity as they relate to coral reef management.
The challenge of linking science to management,
Barracudas. Photo: Ernesto Weil
and of having a real impact on management actions,
has been met with some success with long-term connections between scientists and managers forged.
In particular, managers in the Mesoamerican region are now comfortable with contacting members of the Working
Group for advice on a broad range of topics, some of which concern connectivity.
Of particular note in linking the science to management actions, the CWG held a workshop at the CRIOBE facility,
Moorea, French Polynesia, 7-11 March, 2009, immediately following the Pacific Science Congress meeting in Tahiti.
Titled "Connectivity in Coral Reef Systems Lessons to Date and Goals for the Future", this meeting brought
together 10 members of the CWG `family' and six scientists with no prior contact with the CRTR Program, but
working on issues in connectivity at Pacific locations.
Planning is also now complete for the final workshop to be held with managers in the Mesoamerican region, in
Belize City, 9-11 November. Belize Department of Fisheries and The Nature Conservancy are collaborating with
the CWG in delivering the workshop.
12
2009 Annual Report
Coral Disease
1
Working Group Members:
Prof C. Drew Harvell, Chair Section of Ecology and Evolutionary Biology, Cornell University, USA
Prof Bette Willis, Co-Chair School of Marine Biology and Aquaculture, James Cook University, Australia
Dr Garriet Smith, Co-Chair Department of Biology and Geology, University of South Carolina-Aiken, USA
Dr Eric Jordan Dahlgren Instituto de Ciencias del Mar y Limnologia,
Universidad Nacional Autonoma de Mexico
Prof Farooq Azam Scripps Institution of Oceanography, University of Southern California, USA
Dr Laurie Raymundo Marine Laboratory, University of Guam, USA
Prof Eugene Rosenberg Department of Molecular Microbiology and Biotechnology,
Faculty of Life Sciences, Tel Aviv, Israel
Prof Ernesto Weil Department of Marine Sciences, Universidad de Puerto Rico Mayaguez, Puerto Rico
Photo: Ernesto Weil
Photo: Andy Hooten
As disease plays an increasing role in changing the structure and function of some coral reefs, we need to consider
how management actions influence outbreaks. Exploring even basic questions is hampered by (i) the global
nature of the problem; (ii) overall lack of resources; and (iii) a lack of expertise and technology in developing
countries where many reefs are located. In response to these gaps, the goal of the coral disease program is to fill
critical information gaps about coral reef disease to assist in the development of management and conservation
strategies that protect reef ecosystems from damage due to disease.
During the past five years of research, the Coral Disease Working Group (DWG) has made significant advances
in all five-priority areas of its work program, and the DWG will continue working on products even after the
completion of the Phase. The DWG's three most significant accomplishments of 2009 are (i) the Pan-Pacific Coral
Health and Disease Workshop, (ii) publication of the study in PNAS showing that coral disease prevalence is
lower in some types of Philippines MPAs than adjacent fished areas, and (iii) publication of research documenting
the transportation of aquaculture-associated bacteria onto the adjacent reefs and recovery of coral-associated
bacterial communities following exposure to aquaculture effluent in Bolinao.
The Group's three most important projects under development are (i) analysis of the global prevalence data, (ii) linking
coral disease with water quality in Mexico, and (iii) developing forecasting models of coral disease with temperature
anomalies. The initial manuscript submission of all three of these projects is expected in January 2010.
One of the primary goals of the year was to complete the final year of coral disease monitoring, and organise data
management and analysis for the Group's long-term sites under its global assessment of coral disease project. The
Pan-Pacific Coral Health and Disease Workshop facilitated discussions on the development and implementation
of coral disease management techniques and resulted in significant advances in data sharing and plans for future
col aboration. A clear indication of uptake was the fol ow-up meeting hosted by NOAA in August in Hawai to
advance forecasting approaches to coral disease in the Pacific.
A framework for development of a global coral disease prevalence database to facilitate data analysis is now
underway following these workshops, with the database being compiled and developed with analysis of the global
spatial and temporal patterns of disease now taking place. Additionally, the development of a model to forecast
future disease prevalence based on environmental factors for the Caribbean region is underway.
13
Furthermore, Jeff Maynard from the Great Barrier Reef
Marine Park Authority (GBRMPA) is col aborating with
New tools to
Dr Bette Willis to develop "Reef Temp," a disease-
predict disease outbreaks
forecasting program for Australia. These data are
currently being incorporated into three papers: a global
New tools continue to be developed, including
coral disease prevalence paper; a Pacific coral disease
a model ing tool which predicts white syndrome
prevalence paper; and a paper on the spatio-temporal
outbreak likelihood on the Great Barrier Reef. The
patterns of prevalence and severity of disease along
tool uses satellite SSTs to identify areas of high-
the Yucatan Peninsula.
accumulated heat stress and produces outbreak
likelihood maps in Google Earth. The website for
The impacts of coral disease on coral diversity,
this tool is scheduled to be launched late in 2009.
communities and populations have also been a key
focus for the DWG throughout the past five years. To
determine the impacts of coral disease on coral diversity, community structure and populations, temporal trends
need to be followed in a long-term data set. The main goal for this project in the past year was to commence
data analysis and manuscript preparation for several of the Centres of Excel ence. This has resulted in several
publications now in preparation based on the comprehensive monitoring program established in the Yucatan. The
publications include (i) Deriving Yucatan yellow band disease incidence values from prevalence values; (ii) Coral reef
community shifts from diseases; (iii) The relationship between partial mortality and size structure in Montastraea
annularis species complex; and (iv) The differential effects of hurricane Deane and coral disease patterns.
In addition to this monitoring and data analysis work, researchers have completed a large modelling effort based on
a decade of monitoring the Caribbean sea fan aspergillosis epizootic which is currently in review. This demographic
model is useful for investigating questions about the evolution of resistance and recovery time in populations
experiencing varying levels of disease impact.
Several fine scale temporal assessments of coral disease
outbreaks in the Great Barrier Reef (GBR) and Indo-
"Lab in a Box"
Pacific have also taken place. On the Great Barrier Reef,
The DWG has developed the proposed "Lab in a
researchers tracked lesion growth rates and disease
Box" enabling cutting-edge real-time advanced
spread for a black band disease (BBD) outbreak in the
microscopy and molecular microbiology in coral
Palm Islands and found that BBD affected 10% of the
disease research in remote field settings. This
population and was positively correlated with seasonal
capability of working with fresh material and in
temperature fluctuations. White syndrome and black
tightly iterative mode has dramatically changed
band disease outbreaks in Palau and Indonesia have
the depth and quality of data and observations
also been monitored for the past two years. With these
able to be made in field-based coral microbiology.
long-term data sets, the DWG has been able to assess
Given the limited resources that most remote
the genera-specific disease susceptibility across
island and reef managers have at their disposal,
geographic regions within the Great Barrier Reef and
this toolkit could serve as a model for field
the Caribbean.
coral microbiology.
The resilience of coral reefs to disease continues to be
studied in the Philippines by members of the DWG in
collaboration with the Southeast Asian Centre of Excellence. This work into the impacts of fish farm effluent on the
nearby coral reefs has found an unexpected degree of resilience in coral-associated bacterial communities that
was previously completely under the detection limits of any established disease survey method or "coral health
monitoring" effort. The discovery was enabled by the emphasis on hypothesis testing at timeframes that are short
enough to resolve time-varying microbial community responses to environmental stress.
Resilience of coral reefs to disease has also been connected to the establishment of MPAs. During the past three
years, DWG researchers have found lower disease prevalence within MPAs than the adjacent fished areas, which
was strongly correlated with fish functional diversity. This work continues to be communicated to local community
leaders and fisherman in the Philippines to assist local communities with the establishment of effective MPAs.
Lastly, the flagship products developed by the DWG, A Coral Disease Handbook: Guidelines for Assessment,
Monitoring and Management and the Underwater Cards for Assessing Coral Health continue to be in high
demand, and have been applied by the DWG to obtain a baseline level of coral disease in many regions worldwide.
These data will be invaluable as a benchmark against future disease outbreak events.
Furthermore, the collection of data, and corresponding workshops with the local scientists, helped to develop
a worldwide network of researchers that have been trained at the CRTR Centres of Excellence. Many managers
now have the tools in place to study future outbreaks and contact information for coral disease experts wil ing to
provide assistance.
14
2009 Annual Report
Modelling and Decision Support
1
Working Group Members:
Prof Roger Bradbury, Chair Research School of Pacific and Asian Studies,
Australian National University, Australia
Dr Pascal Perez, Co-Chair Research School of Pacific and Asian Studies,
Australian National University, Australia
Dr Porfirio Alino Marine Science Institute, University of the Philippines, Philippines
Dr Ernesto Arias Lab. Ecologia de Ecosistemas de Arrecifes Coralinos, CINVESTAV-U, Mexico
Dr Peter Campbell Advanced Computer Applications Center, Argonne National Laboratory, USA
Dr Bohdan Durnota Tjurunga Pty Ltd, Australia
Prof Rob Seymour University College London, UK
In the final year of the Program's Phase One, the Modelling & Decision
Support Working Group (MDSWG) has continued to maintain the
momentum from previous years. One of the major strengths of the MDSWG
lies in its PhD and Masters students, and the network is continuing to work
effectively and productively. One student has submitted his doctoral thesis,
another his masters thesis, while another is preparing her doctoral write-up.
A new doctoral and a new honours student have also begun to undertake
research within the Group's auspices.
Work on the local and regional models has continued over the reporting
period with instantiation, calibration and validation of regional models for
Mexico and the Philippines now completed. The local models have been
fully parameterized and ported to user-friendly environments. The post-
hurricane Dean survey of the Costa Maya has been completed, the data
analysed, and a report prepared. These new regional models for Mexico
and the Philippines allow realistic policy-relevant scenarios to be tested at
the regional scale. The models are uniquely realistic (being validated for
each region), and general (being built from fundamental ecological and
economic process models rather than empirically fitted to data). No other
models available today match their performance or scientific power. The Models and tools from the MDSWG can
local models allow users to explore prognoses for their reefs based on predict the impact of coastal developments
current and expected future conditions. Both regional and local models and climate change on coral reefs.
will be available as interactive online tools in March 2010.
Tulum, Mexico Bathers near Mayan Ruins. Photo: Mark Paterson
15
Coral Restoration and Remediation
Working Group Members:
Dr Alasdair Edwards, Chair School of Biology, University of Newcastle, UK
Emeritus Prof Ed Gomez, Co-Chair Marine Science Institute, University of the Philippines, Philippines
Dr Richard Dodge National Coral Reef Institute, Nova Southeastern University, USA
Dr Richard Speiler National Coral Reef Institute, Nova Southeastern University, USA
Dr Aileen Morse Marine Biotechnology Center, Marine Science Institute,
University of California-Santa Barbara, USA
Dr Buki Rinkevich National Institute of Oceanography, Haifa, Israel
Dr Makoto Omori Akajima Marine Science Laboratory, Japan
Dr Tadashi Kimura Japan Wildlife Research Center, Japan
Dr Andrew Heyward Australian Institute of Marine Science, Australia
Dr James Guest University of Singapore
Prof Loke Ming Chou University of Singapore
The worldwide degradation of coral reefs has
prompted greater attention to restoration and
remediation activities. During the past five years,
the Restoration & Remediation Working Group
(RRWG) has focused its efforts on: (i) integrated long-
term monitoring of natural recovery processes and
selected restoration interventions on standardised
substrates; (i ) enhancing coral larval recruitment, and
(i i) enhancing recovery by culture and transplantation
of corals.
Within the Phase One work program the RRWG is
now collating data and results, and finalising the Reef
Rehabilitation Manual, which is to be companion-
piece to the 2007 Reef Restoration Concepts and
Guidelines. In addition to the research outputs, the
RRWG has been involved in a number of capacity
10 month Favites halicora. Photo: James Guest
building and communication projects. For example,
a Coral Reef Restoration and Remediation Training Course in Eastern Africa was held at the East African CoE
from 27-31 July 2009 with trainees from Kenya, Tanzania, Seychelles and Mauritius, among others. This greatly
benefited from inputs from colleagues from the European Union REEFRES project. A regional reef restoration
network was set up and the RRWG has received requests for assistance from Nature Seychel es with respect to
rehabilitating a 30 hectare area of reef in the Cousin Island MPA that has not recovered from the 1998 bleaching
and appears to have shifted into a macroalgal-dominated state. This request is being considered as part of a
Phase Two integrated project for the region.
Under the work program, research has continued into
the monitoring of the Standardised Modules (SMs
pal et bal s) used in the long-term experiments
at Palau and Bolinao in the Pacific, and at Puerto
Morelos and Akumal in the Caribbean. Al surveys
planned for 2009 were successful y completed, with
the data from Palau and Bolinao entered into the
project databases and analysis of the data underway.
Journal articles for the peer-review literature have
been submitted and published in Coral Reefs,
Restoration Ecology, Marine Pol ution Bul etin and
Marine Ecology Progress Series. One paper on self-
attachment rates of transplants, largely derived from
the REEFRES work but partly supported by CRTR,
Floating reefball. Photo: Kirk Kilfoyle
was also published in Restoration Ecology.
16
2009 Annual Report
Under the coral larval recruitment program, the "larval
flypapers" research by Dr Morse at Palau was completed
1
in April 2009. The final surveys revealed that survival of
5000 sexual recruits outplanted on artificial reefs (pallet
bal s) was poor (1.5% after one year), although there
was good natural recruitment to the same pallet balls.
However, much better survival (up to 80%) was found for
asexual fragments of Acropora digitifera outplanted to
the natural reef and growth was found to be positively
correlated with mean water velocity. Comparisons of
survival of fragments of six species of Acropora between
natural reef and pal et bal s indicated 50% lower survival
on the pallet balls.
A dedicated coral larval rearing facility has now been
constructed at the Bolinao Marine Laboratory (BML)
of the Southeast Asian CoE and is ful y functional. The Favites halicora spawning. Photo: James Guest
facility will be used for further larval rearing work planned for 2010 and beyond by students and other researchers.
Another major attempt at spawning corals for larval rearing for restoration was made in May 2009 with a focus
on two faviid species (Favites halicora, Montastrea colemani). Spawning and larval rearing for both species was
successful despite a major typhoon hitting Bolinao just a few days before the spawning event. The majority of
coral spat are currently being reared in the newly constructed tanks at the hatchery facility at BML and some
will be outplanted to in situ nurseries in November 2009. Corals reared in 2009 are being co-reared ex situ with
juvenile topshells (Trochus niloticus) fol owing the
methods developed by Prof. M. Omori and co-workers
in Okinawa. An experiment to test the effect of surface
refugia on coral spat survival was also carried out with
`grooved' and `smooth' coral plug-ins transplanted to
an in situ nursery at Malilnep channel approximately one
month after fertilisation in 2009.
The efficacy of the "coral peg" as a substrate for culture
of sexually reared coral spat was tested at the Akajima
Marine Science Laboratory in Okinawa with corals on
the pegs being transplanted to the reef at Akajima.
Again, nibbling by fish was a serious problem for survival
of colonies, particularly during the first month after
transplantation. Separately from the CRTR research at
Palau, many juvenile colonies of Acroporatenuis that Floating nursery. Photo: Gidi Levi
had been cultured from eggs in June 2005 at Akajima were transplanted onto bommies in December 2006. About
ten 4-year and 5-year old colonies spawned for the first time on June 8, 2009. This is the first record of successful
rearing of reef-building corals from gamete to spawning adult and demonstrates the potential of using the present
culturing technique to assist local reef restoration. A note entitled "A novel substrate (the "coral peg") for deploying
sexually propagated corals for reef restoration" has been published in Galaxea, Journal of Coral Reef Studies.
The final component of the RRWG's five-year workplan,
enhancing recovery by culture and transplantation
of corals, has continued to progress with the year
seeing the completion of the single and mixed species
experiments and the piloting of transplantation of corals
involving the local communities. The latter showed
good results and much promise with the potential for
scaling up. Using principally a locally available resilient
species, Porites cylindrica, local volunteers transplanted
more than a thousand second generation transplants
and locally available `corals of opportunity' successfully,
with a high degree of survival. The activity used no scuba
and no adhesives, strictly volunteer time, and generated
much interest for future expansion. A prototype agent-
based model for single species transplantation has
been completed. It incorporates coral recruitment and
interactions between transplants of the same species, Montastrea colemani spat. Photo: James Guest
17
algae and gastropod (Drupella) predation.
There is good agreement between model
output and results of field experiments.
The model wil be extended to include
interactions among transplants of different
species as wel as effects of environmental
factors.
RRWG members continued to maintain
the nurseries at Bolinao and at Zanzibar
and Mafia Island in Tanzania and it is clear
that the techniques for nursery rearing at
a significant scale are now well-developed.
Most of these coral colonies, upon
reaching sizes suitable for transplantation,
have been transplanted onto study reefs. A
new approach for transplanting the corals
reared in rope nurseries was tested. This
involved towing the entire nursery and
submerging it onto the substrate where
it was attached using masonry nails. Initial
results have not been encouraging partly
Col ection of coral slicks at Aka Harbour for use in coral restoration research
Photo: M Hatta
due to a typhoon.
The results of the last five years suggest that coral nurseries are central to achieving active reef restoration at any
meaningful scale and that farming of thousands of coral colonies is achievable by local communities. Unfortunately,
methods of transplantation have lagged behind the fast development of nursery methodologies. However, the
last three years have seen achievements in transplantation. Almost 20,000 colonies of more than a dozen coral
species had been transplanted using several novel attachment methodologies (power drilling into substrates,
hand-drilling, gluing, etc.) in various transplantation protocols (monocultures, polycultures, randomly arranged
colonies, aggregates of same species/genotypes vs. mixed species/genotypes, and more), coral colony sizes and
locations.
18
2009 Annual Report
Remote Sensing
Working Group Members:
Prof Peter Mumby, Chair Marine Spatial Ecology Lab, School of Biological Sciences,
Hatherly Laboratory, University of Exeter, UK
Dr Laura David, Co-Chair Marine Science Institute, University of the Philippines, Philippines
Prof Stuart Phinn School of Geography, Planning and Architecture, The University of Queensland, Australia
Prof Ellsworth LeDrew Faculty of Environmental Studies, University of Waterloo, Canada
Dr Mark Eakin Marine Applications Science Team, Coral Reef Watch Project, NOAA, USA
Dr William Skirving Coral Reef Watch Project, NOAA, Australia
Dr Alan Strong Marine Applications Science Team, Coral Reef Watch Project, NOAA, USA
Over the past five years, the Remote Sensing Working Group (RSWG) has been developing and testing a wide
range of remote sensing tools, including satellite, airborne, acoustic and in-field methods. The Group has
quantified the limitations of coral reef remote sensing by combining modelling and field experiments. The final
year of the project has witnessed the realisation of the RSWG goals: (i) creation of a decision-support and analysis
software for monitoring the health of coral reefs using remote sensing; (ii) development of methods to detect
changes in coastal environments; (iii) application of remote sensing to the inventory, monitoring and management
of biodiversity, and; (iv) creation of an Ocean Atlas and tools to manage coral bleaching.
In achieving the first goal, the Working Group has created the Reef Observer software tool that uses a state-of-
the-art model of radiative transfer, together with a large spectral library of coral reef substrata, to quantify the
feasibility of any coral reef remote sensing project. The radiative transfer software used to power Reef Observer is
now complete and is being disseminated free of charge.
The Group's online Reef Remote Sensing Toolkit has
Impacts on Belize Policy
also being extended to help practitioners match their
remote sensing objectives to the appropriate
CRTR-sponsored research has informed the
technologies (the Toolkit covers a wide range of
legislation to ban herbivore exploitation in Belize
mapping problems and essential y stops short of
by providing a compelling report to Government
making prescriptive predictions for more detailed
on the drastic decline of parrotfish over the last
remote sensing problems for which Reef Observer is
seven years and corresponding rise in macroalgae.
used). The upgraded Toolkit is due for release on the
website in December 2009.
Under the `tools to detect change in coastal areas'
component of the Group's workplan, RSWG members
have recently published the results of a simulation
model in Remote Sensing of Environment (RSE) and
revealed that 1m resolution imagery is about optimal
for detecting changes in coral reef environments. In the
paper, researchers have shown that coral reef habitat
mapping can be improved significantly by combining
acoustic sonar with optical satellite data. The sonar
provides data on depth and rugosity whereas the
The dominant spotlight parrotfish is targeted by Belize
satel ite data provides continuous data on spectral
fishermen. Photo: B. Steneck
properties of the seabed.
Furthermore, the Reef Observer software tool also has a capacity to identify whether particular changes in coral
reef state can be detected using remote sensing. The user can specify the type of change (% substrata), the depth,
the clarity of the water, and type of sensor. The third goal of mapping of biodiversity and resource management
has also been achieved with a new technique developed to identify areas of the coastal zone that have particularly
benign physical conditions in terms of coral bleaching. The method also includes important new advances to the
design of marine reserves such that connectivity and different reserve design criteria can be incorporated explicitly
into the algorithm. The methods have been showcased for the Bahamas and Belize.
The RSWG has also demonstrated that acoustic remote sensing methods can be used to map benthic habitat
structure and reliably predict patterns in the density and biomass of many reef fish. Further, acoustic remote
sensing can be used to discriminate coral reef microhabitats and used to predict the distribution of juveniles for
many reef fish species. Lastly, the work on mapping the physical environments of coral reefs has demonstrated
19
Coral bleaching. Photo: Kathryn Rosell
Image: Iliana Chollett
that rates of warming of ocean temperature vary strikingly across the Coral Triangle region. These results have
recently been published in Coral Reefs, and are now beginning to inform conservation considerations in the Coral
Triangle.
Additionally, the RSWG has created a new suite of online products that provide levels of solar insulation.
An algorithm to combine data on sunlight with that of sea temperature in order to predict coral bleaching is at an
advanced stage through collaboration with the Bleaching Working Group.
20
2009 Annual Report
2
Promoting Scientific Learning
and Capacity Building
2Component21
Promoting Scientific Learning
and Capacity Building
Component Two of the Program is aimed at capacity building outcomes through the promotion of scientific
learning and linking scientific knowledge to management and policy. Sound management and policy tools will
shape and change the way policy and decision-makers view and approach coral reef management. The Program
is achieving this aim through:
· Building or enhancing the capacity of institutions across four regions to serves as regional Centres of
Excellence (CoEs); and
· Developing information, products and networks from the research that can lead to better management and
strengthened policies regarding coral reefs in the regions.
The four Centres of Excellence are based in major coral reef regions (three are in developing countries) around
the world, and are hosted by leading research institutions in those regions:
· Southeast Asia: Marine Science Institute / Bolinao Marine Laboratory, University of the Philippines.
· East Africa: Institute of Marine Sciences, University of Dar es Salaam, Tanzania.
· Western Caribbean/Mesoamerica: Unidad Academia Puerto Morelos, Instituto de Ciencias del Mar y
Limnologia, Universidad Nacional Autonoma de Mexico (UNAM).
· Australasia/South Pacific: Centre for Marine Studies / Heron Island Research Station, The University of
Queensland, Australia.
Southeast Asian CoE Chair Professor Ed Gomez and CRTR scholars inspecting the nets, Bolinao. Photo: M King
22
2009 Annual Report
Australasian Centre of Excellence
Centre for Marine Studies and Heron Island Research Station, The University of Queensland
Rarotonga, Cook Islands Agriculture and tourism create pressure on delicate coastal ecosystems. Photo: Melanie King
The Australasian Centre of Excel ence has used the past year as a consolidation of its research projects - (refer to
the Bleaching Working Group report), and its capacity building activities. Work has been completed on the Local
Government Initiative project in the Makira Province in the Solomon Islands. The project consisted of surveys and
information collected through on-site observations, discussions with Kahua Association (KA) members, and
community meetings on the present state of the coastal and marine environment. Following the survey, the project
team made up of Centre for Marine Studies experts determined indicators of present environment stresses and
identified potential future changes to the natural environment as a result of present and projected human
development. Recommendations were then developed for future activities to be undertaken and implemented by
the KA.
The recommendations included the development and implementation of `no-take' zones for shellfish and the
provision of educational materials to schools and communities. Materials on coastal and marine resources have
been provided to the Kahua Association for distribution, and the local communities have also agreed to establish
`no-take' zones for shellfish in the region. The communities are now working together to implement the zones with
technical advice from the project team.
Progress is also continuing on the `Planning for
Ecosystem-based Management: Managing the
Environment in Smal Island States' course and
Pacific Leadership Forum to be held in
Rarotonga, Cook Islands in January 2010, as
the final CoE activity. The 12-day interactive
course involving a number of external experts
and Pacific Island counterparts in seminars,
case-study and fieldwork scenarios wil explore
the issues facing the Pacific Islands and
how an ecosystem-based management (EBM)
approach can be implemented to improve the
management of these issues. The main aim is
to provide decision-makers and practitioners
with the tools and information to gain a better
understanding of the elements required in
the modern concept of integrated coastal
Local fisherman-Kahua Province Makira, Solomon Islands.
Photo: Geoff Dews
management.
23
Village children Kahua Province, Makua, Solomon Islands. Photo: Geoff Dews
The elements covered will provide participants with the knowledge and tools to develop and implement EBM
Plans into their coastal communities. In conjunction with the Planning for Ecosystem-based Management course,
the Pacific Leadership Forum will be conducted concurrently for Heads of the environment and fisheries
departments from Pacific countries. The Forum: `Policy & Planning for Ecosystem-based Management', is an
intensive, interactive three-day program to address the integrated policy approaches and options for achieving
the technical competencies and support needed to plan and implement EBM for coastal areas. It is aimed at high-
level senior executives that are in a position to implement changes, develop and implement effective policy and
policy processes, and to ensure future sustainable development of these critical resource bases. The intention is
that Heads of Departments will be better placed to empower and support implementation of EBM in their own
country.
The Australasian Centre of Excellence will continue to develop relationships and projects in the Pacific region and
beyond through the Global Change Institute (GCI) at the University of Queensland.
24
2009 Annual Report
East African Centre of Excellence
Institute of Marine Sciences, University of Dar es Salaam, Zanzibar
The East African Centre of Excel ence has
continued to serve as a research hub for
capacity building and information outreach
for users in the East African region during the
final year of the Program. During the reporting
period the CoE has continued to act as a
support-base for local and visiting researchers
and students; organised training workshops;
and completed the local research projects.
Visiting researchers have been involved in
the monitoring of spatial patterns in coral
population; rates of recruitment, partial
mortality and mortality; relationships between
processes and state variables; and the effect of
macro-processes on coral populations, under
the `Common Sampling' project, and the
results of this can be viewed in the Bleaching
Working Group report. Further to acting as
support centre for visiting researchers, the
CoE has also continued to provide scholarship
support to three PhD students whose studies
are focusing on coral restoration, disease and
bleaching. These students were supported
to travel abroad to analyse their samples in
specialised laboratories and to assist with their
specific research requirements. Mohammed
Suleiman and Leonard Jones are currently
finalising fieldwork whilst N.E. Mbije has
completed his fieldwork and is now finalising
and writing up his research findings.
Fishing harbour, Stone Town. Photo: Mark Paterson
Training workshops on the latest research techniques into impacts on coral reefs have always played an important
role in the region. The CoE collaborated with experts in the field of remote sensing and GIS as well as experts in
biological connectivity, restoration and remediation to learn new emerging techniques that will better equip them
with the skills to assist with coral reef research and management in the region. In July 2009, the CoE also played a
critical role in organising a major regional training workshop on coral reef restoration.
Regionally-relevant coral reef research has continued in the region with all aspects relating to nutrient analysis,
sedimentation rates, primary productivity, ocean current measurements and the recording of fish landed have
progressed well with some results have been published and presented at the 6th WIOMSA conference.
The CoE has also continued to maintain and develop
new links with policy and management decision makers,
with research information being provided to various
forums for inclusion into decisions. Examples of this
include:
· Coral health data from coral assessment (Sub-Project
A) has contributed in determining the status of coral
reefs in Tanzania, which has had a positive impact
on coral reef management in Tanzania. Some of this
information was included in the Status Report of
Coral Reefs of the World.
· Coral reef research results were used in deciding the
boundaries of two new marine conservation areas in
Zanzibar (Tumbatu and Changuu-Bawe Conservation
Institute of Marine Sciences Laboratory, Zanzibar
Photo: Mark Paterson
Areas) this year.
25
· CoE research activities have raised the
level of coral reef knowledge in many
sectors in Tanzania and the Western Indian
Ocean through presentation of results at
Government, local authority and
community meetings.
· CoE staff are being consulted and
contribute directly to integrated coastal
management policy and management
decisions.
· Results from pol ution studies have raised
awareness within the community on all
levels which has caused positive
behavioural changes and consciousness
toward marine conservation issues.
The Centre of Excel ence has also continued to
strengthen its links with the Marine Parks and
Reserve Unit in Tanzania, which is responsible
for managing marine parks, reserves and
conservations in the region, and continues
to make an active contribution in ongoing
preparations toward the declaration of the
Tanga Coelacanth Marine Protected Area.
Dhow boats, Zanzibar. Photo: Mark Paterson
26
2009 Annual Report
Southeast Asian Centre of Excellence
Marine Science Institute / Bolinao Marine Laboratory, University of the Philippines
The Southeast Asian Centre of Excel ence
has gone from strength to strength over the
past five years and has continued to make
substantial progress on its local research
projects and outreach activities, as wel as
instigating new investigations into issues that
have arisen out of the scientific studies of the
Working Groups, and the local projects.
Following incidences of mortality on the
Restoration & Remediation Working Group's
coral transplant sites on the reef flats off
Santiago Island at Bolinao, Pangasinan, the
Centre of Excellence and RRWG collaborated
on a new research activity to understand
submarine groundwater discharge, which
was believed to be the cause of the coral
mortality. This work was also part of research
being undertaken to better understand the
land sea connectivity of water and pollutants.
The spatial variability of the submarine
groundwater discharge (SGD) was mapped
using radon measurements, electrical resistivity
(ER) survey, CTD (conductivity, temperature, Bolinao Marine Laboratory.
depth) profiling, and water sampling for nutrient analysis. The results of the study revealed widespread occurrence of
SGD within the reef flat. Nitrate and radon in sites with potentially high SGD have values that are two to three orders
higher than typical seawater values. Seepage rates determined through radon flux and manual measurement were
higher for the dry season than the wet season, which may be due to the pumping effect of waves. Manuscripts are
currently being prepared for publication or presentation at conferences detailing the findings of this research.
In addition to the new research activity, the three local CoE Projects have continued to achieve results over the final
year. Project A (Taxonomy) conducted three coral taxonomy training sessions during this period with participants
from academe, local government units, government agencies and non government organisations attending. The
training was aimed at coral identification, survey methodology, coal disease identification and molecular techniques.
Photo-documentation of coral collections in the UPMSI, UP Institute of Biology and Silliman University museums
have also been completed and photos prepared for posting on the web-based `virtual museum'. Manuscripts for
the molecular identification of many species including the new Philippine record of Euphylliaparaglabrescens,
coral community structure of the Bolinao Reef System and a framework for the survey of coral communities using
digital phototransects is currently in preparation.
Project B (Coral Disease) continued outdoor
tank experiments for Porites ulcerative white
spot (PUWS) infection. Studies were modified
to al ow for a greater number of replications
using the same space to reduce the risk of
airborne particles. Lower temperatures during
the trial period dictated delayed responses to
the spread of disease compared to that of
higher temperature results. Unfortunately, due
to the devastation caused by typhoon Emong
in May 2009 the microbiological monitoring of
coral reef and fish farming sites at Bolinao had
to be abandoned.
Under Project C (Connectivity) experiment
results indicated that the patterns of genetic
structure of phylogeographic analysis carried
out may be attributed to historical barriers to Milkfish farm, Bolinao reef flats. Photo: Gabrielle Sheehan
27
dispersal as the spatial genetic structure of S.
Fuscescensis driven by the distribution of two
distinct mtDNA lineages (clades) estimated
to have diverged during the Pleistocene.
Nonetheless, significant structure detected
based on microsatel ite data suggest limited
demographic connectivity of S. fuscescens
across western Luzon.
Analysis of 144 individuals representing four
western Philippine sites, and three out-group
sites reveals that the western Luzon samples
are not genetical y structured indicating high
gene flow in the region. This is in contrast to
the observed limited genetic connectivity
of S. fuscescens populations from the same
geographical area. The contrasting patterns
of genetic connectivity of the two species are
attributed to their differing dispersal potential
as a function of life history traits.
Lastly, the Local Government Initiative (LGI)
Project conducted a workshop on "Reducing
Environmental Impacts of Marine Fish Cage/
Pen Culture" on 30 January 2009 in Bolinao,
Pangasinan. The workshop trained selected
stakeholders including operators, caretakers
and core LGU personnel on sustainable
mariculture
practices
and
encouraged
cooperation among the stakeholders with
respect to sustainable mariculture management
in their respective localities.
Coral gardening experimental transplants, Bolinao.
Outreach activities have also been a
prominent role for the CoE and in 2009 the
CoE supported three community-based
transplantation training sessions conducted
in Bolinao and, as part of the Information,
Education and Communication (IEC) initiative,
CRTR information packages were distributed
at the general assembly of the League of
Municipalities of the Philippines (LMP) held
in Manila.
Coral nursery, Bolinao. Photo: Dexter dela Cruz
28
2009 Annual Report
3
Linking Scientific Knowledge
to Management and Policy
3Component29
Linking Scientific Knowledge to
Management and Policy
Under Component Three: Linking scientific knowledge to management and policy, the final year of the CRTR
Program's first phase has been a period of consolidation and distribution of research outputs to target audiences.
The year has seen the consolidation of research under the `Common Sampling' project with monitoring sites
established at all four Centres of Excellence, as well as the dissemination of research and results to International
Waters projects and GEF personnel at the 5th GEF International Waters Conference in Cairns.
`Common Sampling' Project
Population dynamics of coral populations under environmental change
The `Common Sampling' project, under the guidance of Professor Robert van Woesik has been examining the
population dynamics of coral populations at all four Centres of Excellence. The primary task was to assess the
dynamics of coral populations and associated coral-reef organisms by defining the key ecological processes that
regulate the populations. Understanding these processes, assessing their spatial variation and their relationship
with state variables, including size-frequency distributions, leads to predictive models of population trajectories,
relative population size distributions, and community change under different climate change scenarios.
The project team predicted that size-frequency distributions coupled with partial mortality information could
provide a reliable indicator of coral stress and provide insight into the future of coral reefs.
Specifically the team examined:
· Spatial patterns in coral population size-frequency distributions and temporal changes of the populations at
three CoEs;
· Scale dependence of key process variables, including rates of recruitment, partial mortality, and mortality;
· Relationships between processes and state variables and whether size-frequency distributions reflected
population performance; and
· Effect of macro-processes, including herbivory (i.e., density and composition of urchins and fishes), on coral
population vital rates and diseases.
Outcomes included corrections developed to eliminate biases that occur because of boundary effects when
measuring the size of benthic organisms, as well as a series of relationships between 2-dimensional and
3-dimensional estimates of coral growth. Several important ecological phenomena were also identified, including
two modes of partial mortality-affected coral species in the Caribbean; with some species rapidly losing colony
integration while others maintained integration and sacrificed
marginal tissue.
Research within this group also identified the critical
observation that mild thermal stress events showed different
responses than extreme events. During extreme events, small
colonies do better than larger colonies, while during mild
events, colony size did not influence bleaching. In both cases
massive corals were found to be more sensitive than branching
corals. The research within this project also identified the
important influence of substrate reflection, for example from
sand, increasing available light and exacerbating the risk of
coral bleaching. Indeed, corals growing on and near sand
showed more intense bleaching than those growing on or
near substrate with lower reflectivity. The group also made
some interesting long-term observations, such as sea urchin
densities on the western reefs of Zanzibar increased 6-10 fold
since 1996; with fish on the same reefs increasing considerably
in the last three years.
More detailed information on this project can be viewed in
the `Bleaching and Related Ecological Factors: CRTR Working
Group Findings 2004-2009' report available on the CRTR
Program website at www.gefcoral.org.
30
2009 Annual Report
GEF International Waters Conference
The 5th Biennial GEF International Waters Conference, hosted by the Government of Australia in Cairns, North
Queensland took place from the 26-29 October 2009. The Conference was designed around a number of
participative learning opportunities. A key objective of the GEF International Waters portfolio learning event
is to promote sustainable development in basin and coastal communities sharing natural resource systems, to
achieve Millenium Development Goals through the benefits of transboundary cooperation in ecosystem-based
management. With an eye to integrated-ecosystem based management and mainstreaming climate variability
and change, this meeting builds on 2009's key freshwater and marine meetings with an eye to preparing the GEF
IW portfolio for the future.
The CRTR Program was an active participant, with representation at the pre-conference technical workshops,
plenary sessions and conference technical workshops. The pre-conference technical workshops (24-25 October)
featured leading Australian and international experts in complex basin and marine systems, dealing with resolving
conflicting demands among diverse stakeholders, and coping with water scarcity and the technical as well as
societal impacts of climate change. The CRTR Program was well represented at the marine workshop with many of
the Synthesis Panel either presenting or contributing as Panel members during the discussion periods.
Synthesis Panel members presented at
the conference and technical workshops,
with Professor Paul Greenfield and
Professor
Roberto
Iglesias-Prieto
addressing a plenary session, and chairs
Dr Alasdair Edwards (RRWG), Prof Ed
Gomez (RRWG) and Dr Roger Bradbury
(MDSWG)
presenting
during
the
technical workshops. Deb Cleland and
Jess Melbourne-Thomas, two scholars
from the MDSWG, also presented during
the modelling workshop.
The CRTR Program showcased its
many and varied research outputs at
the exhibition booth. Social media
techniques, including Twitter and web-
based news and video updates, used to
promote the Program's participation in
IWC to CRTR and external stakeholders.
CRTR Masters Scholar Deborah Cleland addresses an IWC workshop.
2009 Annual Synthesis Panel Meeting
The CRTR Program's international Synthesis Panel met from the 21-23 October 2009, in Brisbane, Australia, prior
to the 5th GEF International Waters Conference. The focus of the meeting including final discussions concerning
ongoing projects (due to be completed in early 2010); the completion of Phase One and continuation plans; and
Phase Two planning discussions.
31
Publications
Over the past five years, the CRTR Working Group and Centres of Excellence have been responsible for over
600 publications. This includes publications which have been either fully supported, or partially supported by
the Program, or publications which have been influenced by work from the CRTR Program, or which has in turn
influenced the CRTR Program's Working Groups.
Events
The CRTR Working Groups and Centres
of Excel ence have been responsible
for over 230 events since the Program
commenced in late 2004. These
events include participation at, and
contributions to, annual meetings,
workshops,
conferences,
science
meetings and media events.
A fisher from Zambales, the Philippines tries his luck in the open ocean during a
ReefGame session at a multi-sectoral workshop in November 2009 run by the Southeast
Asian CoE. Photo: K Balajadia
32
2009 Annual Report
Program Management
4 4
Component
33
Program Management
The Program Management component of the CRTR Program has progressed satisfactorily throughout the five
years of the phase, and is now in the final months of finalising the administrative components of the Program.
The management and communication components of the Program have been strong elements throughout the
Phase, and the final months will see the final suite of products produced, showcasing the work undertaken by the
Working Groups and Centres of Excellence.
Disbursements
Disbursements for 2009 have continued at a steady rate, with approximately 95% of the overall funds now disbursed.
Despite a slight delay in some sub-grant disbursements due to institutions not meeting their obligations under
the contractual arrangements, these are now completed and all sub-grants will have been fully disbursed by the
30 November 2009. The remaining GEF funding relates to the production of communication outputs from the
research, and it is expected that these funds will be fully disbursed by the end of February 2010.
Disbursements for the GEF and UQ funds for the five-year period, up until 31 October 2009 are as follows:
· GEF funds approved for the period 1 December 2008 to 30 November 2009 is USD$1,759,370.
· UQ funds approved for project administration for the period 1 January 2009 to 31 December 2009 is
AUD$739,957.
GEF Funding
The GEF funding allocations are on-target to be fully disbursed by the 31 December 2009. As mentioned, there
has been some delay in some sub-grant disbursements due to contractual obligations and reporting not being
met, however these are expected to be fully disbursed by 30 November 2009. The remaining GEF funds relate to
Synthesis Panel meeting expenditure, communication expenditure and peer review processes, and the expectation
is that these funds will be expended by 31 December 2009.
34
Panda clownfish and three-spot damselfish juveniles sheltering in an anemone, Schuman Island, Papua New Guinea. Photo: S Planes.
2009 Annual Report
Procurement
No procurement took place during the reporting period.
Sub-grants
There were no new sub-grants contracted during the reporting period.
Communication
The year has seen a marked increase in the number of research outputs developed and packaged for key
management, policy and research audiences. The Communications Team of Mark Paterson and Gabrielle Sheehan,
have worked with the Project Executing Agency to implement a range of activities, in order to (i) encourage
the application of CRTR research outcomes by reef managers and policy makers; and (ii) develop and enhance
networks between program members and with external stakeholders.
In the final year of Phase One, communications activity focused on producing a suite of products aimed at sharing
knowledge generated by the program, including:
· The Science of No-Take Fishery Reserves: A Guide for Managers. This booklet developed by the CWG
examines the science underlying use of no-take fishery reserves as a management tool for coastal fisheries.
CoE Chair, Professor Ed Gomez, talks with local government representatives and others at the Coastal Resources Management Forum,
Bolinao 2008 as part of the CRTR Local Government Initiative, profiled in a case study and online.
· Advisory Paper: Conserve coastal habitat today, preserve income for tomorrow. This paper from the CWG
provides advice for planners and policy makers on long-term approaches to coast development and actions
that can be taken today to preserve coastal habitats.
· Bleaching and Related Ecological Factors: CRTR Working Group Findings 2004-2009. This report details
the findings of the Bleaching Working Group, including major contributions to understanding the impact of
climate change on coral reefs.
· Research update: New frontiers of remote sensing for reef management. This update informs resource
managers about valuable remote sensing tools that can be used at all stages of coral reef conservation.
· Standard Operating Procedures for repeated measures of process and state variables of coral reef
environments. The CRTR Program has developed a set of procedures with which to collect state and process
variables, allowing data comparison and combination across regions.
35
Case studies were developed to
demonstrate the CoEs `in action',
working with local governments and
communities. These include:
· Community-based restoration
- the Bolinao experience. CRTR
researchers at the Southeast Asian
CoE are training local communities
to restore live coral cover to the reefs
of Bolinao, Pangasinan Province by
sharing low-cost reef restoration
techniques.
· Taboos, customs hold key to
managing Tanzania's reefs. The East
African CoE has investigated how
indigenous knowledge contributes
University of Queensland's Geoff Dews worked with the community of Makira
to costal management in local
Province, Solomon Islands, on conserving their marine resources.
communities. Customs, taboos
and beliefs, used in conjunction
with scientifical y-developed and
improved technology, promise to
help protect and sustain fish stocks
and coastal habitat.
· Managing marine resources at
the local level Makira Province,
Solomon Islands. Under the CRTR
Local Government Initiative, the
Australasian CoE worked with
communities in the Makira Province,
Solomon Islands to determine coastal
impacts and prioritise an action list on
how the community can work towards
reducing them.
· Local governments critical to effective management and protection of coral reefs Lingayen Gulf, the
Philippines. This case study reviews the Southeast Asian CoE's work under the CRTR Local Government
Initiative with coastal municipalities surrounding the Lingayen Gulf to improve management and protection
of reefs.
In the completing Phase One, several communications activities are planned over the next three to four months.
A five-year `synthesis' report, summarising key research findings from the CRTR Program is anticipated early in
2010. This report will focus on the baseline of what was known in the key CRTR research-targeted areas at the
commencement of the Program to what is now known after five years of targeted research.
In addition to this synthesis report, products under development include tools for management such as a remote
sensing guide; a reef restoration manual; a connectivity handbook, and various advisory or update papers. An
anthology of papers and articles from CRTR scholars is also being compiled, showcasing the science capacity built
through the Program.
To maintain the strong connections that have been built across the CRTR network, communications activity will
continue through the interim phase, including continued distribution of CRTR e-news and updating the website
with relevant developments and material.
36
2009 Annual Report
Information Dissemination
In addition to the production and dissemination of research outputs,
the CRTR Program has also focused on targeting media efforts, and
in utilising the website as the key portal for information dissemination
from the Program.
Throughout the year, the CRTR website, www.gefcoral.org, was
updated with various products, announcements and stories. At the
International Waters Conference, the site was updated with articles on
CRTR presentations, and supporting materials including video footage.
Sections of the website were also enhanced to highlight results from
projects, and other activities.
The estimated number of visits to the site from November 2008 to
October 2009 was 22,353; with an estimated 15,500 unique visitors;
859,782 hits; 288,455 pages accessed; and 23.91 gigabytes of data
downloaded. The highest number of visits in any one month was
recorded in October (2684 visits) coinciding with the International
Waters Conference.
Members of the CRTR Program have been very active in ensuring various
audiences are in receipt of critical information on the importance of
marine habitats, including coral reefs, and the impacts of environmental CRTR E-news, the program's online newsletter.
and human impacts on these ecosystems. In terms of Program media,
the Program has been targeted in its messages and responses to issues arising throughout the year. With coral
reefs worth an estimated $170 billion worldwide, the CRTR Synthesis Panel made a public call via the media for
the world's oceans to be high on the agenda at the Copenhagen meeting of the United Nations Framework
Convention for Climate Change (UNFCCC) in the lead up to the December meeting.
Another media announcement focused on the launch of the "Reefs for People" tool developed by the MDSWG.
The model will allow coastal communities and policy makers around the world to predict the impact of coastal
developments and climate change on their coral reefs and coastal environments.
Both of these media announcements were distributed using traditional methods and supported by promotion
through social media channels.
Lastly, given its broad global focus and membership, the CRTR Program has continued to communicate
with its network through two electronic newsletters. Three editions of CRTR e-News were distributed to
stakeholders, highlighting progress and achievements with contributions from program members. Two editions
of the Communications Team's bulletin Coralert! advised program members of communications activities and
opportunities, and invited their ideas and participation.
Artisanal fishing , Yucatan Peninsula. Photo: Ken Drouillard
37
Abbreviations
ACEP - African Coelacanth Ecosystem Programme
AIMS - Australian Institute of Marine Science
BWG - Bleaching Working Group
CoE - Centre of Excellence
CRTR - Coral Reef Targeted Research & Capacity Building for Management Program
DWG - Disease Working Group
EBM - Ecosystem-based Management
ECONAR Project - Ecological Connections Among Reefs Project
ESA - European Space Agency
GCI - Global Change Institute, The University of Queensland
GEF - Global Environment Facility
GBRMPA - Great Barrier Reef Marine Park Authority
HIRS - Heron Island Research Station
ICRS - International Coral Reef Symposium
IWC - International Waters Conference
KA - Kahua Association, Solomon Islands
LGI - Local Government Initiative
LGU - Local Government Unit
MACEMP - Marine & Coastal Environment Management Project
MPA - Marine Protected Area
MDSWG - Modelling & Decision Support Working Group
NGO - Non-government Organisation
NOAA - National Oceanic & Atmospheric Administration
PEA - Project Executing Agency
PEDs - Parrotfish exclusion devices
REEFRES -
RRWG - Restoration & Remediation Working Group
RSWG - Remote Sensing Working Group
SMs - Standardised Modules
TNC - The Nature Conservancy
UNAM - Universidad Nacional Autonoma de Mexico
UNU-INWEH - United Nations University International Network on Water, Environment and Health
UPMSI - University of the Philippines, Marine Science Institute
UQ - The University of Queensland
WIOMSA - West Indian Ocean Marine Science Association
38
The Coral Reef Targeted Research & Capacity Building for Management (CRTR) Program is a leading international coral reef
research initiative that provides a coordinated approach to credible, factual and scientifically-proven knowledge for improved coral
reef management. The CRTR Program is a partnership between the Global Environment Facility, the World Bank, The University of
Queensland (Australia), the United States National Oceanic and Atmospheric Administration (NOAA) and approximately 50 research
institutes and other third-parties around the world.