Oliver et al (2004) Monitoring bleaching

Draft
A Global Protocol for Assessment and Monitoring of
Coral Bleaching
Jamie Oliver
WorldFish Center
Paul Marshal
GBRMPA
Naneng Setiasih
WWF
Lara Hansen
WWF

A GLOBAL PROTOCOL FOR ASSESSMENT AND MONITORING OF CORAL
BLEACHING ..........................................................................................................................................................1
INTRODUCTION..................................................................................................................................................3
WHY IS A PROTOCOL NEEDED? ................................................................................................................4
WHO WILL USE THE PROTOCOL?.........................................................................................................................4
HOW SHOULD THE PROTOCOL BE USED?............................................................................................................5
QUICK GUIDE – START HERE......................................................................................................................5
HOW DO I IDENTIFY CORAL BLEACHING?..........................................................................................................5
HOW DO I MEASURE OR QUANTIFY CORAL BLEACHING?.................................................................................6
THE NOAA/REEFBASE BLEACHING QUESTIONNAIRE....................................................................................7
WHAT DO I DO IF I SEE BLEACHING? ..................................................................................................................7
DESIGNING A PROGRAM FOR YOUR NEEDS .......................................................................................8
TYPICAL QUESTIONS/OBJECTIVES......................................................................................................................8
MONITORING FOR DIFFERENT SCENARIOS......................................................................................................11
OUTLINE OF A TYPICAL MONITORING PLAN....................................................................................................11
SAMPLING DESIGN CONSIDERATIONS..............................................................................................................12
MONITORING PROCEDURES...............................................................................................................................15
DATA MANAGEMENT ................................................................................................................................... 23
LITERATURE ..................................................................................................................................................... 23
APPENDICES ...................................................................................................................................................... 25
APPENDIX 1. DATA FORMS................................................................................................................................25
APPENDIX 2. MONITORING VARIABLES...........................................................................................................28
APPENDIX 3. VARIABLE CODES.........................................................................................................................31
APPENDIX 4..........................................................................................................................................................36
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Introduction
Coral bleaching occurs when corals lose the single celled algae (zooxanthellae) which live within their
tissues. These golden brown coloured algae (Figure 1) occur in varying densities in reef corals (and
other reef invertebrates), and give them a light tan to deep chocolate brown colour. Where additional
pigments exist within the animal cells, this brown colour can be overlain by different additional hues
such as blue, green, purple or yellow (Figure 2). When corals lose their zooxanthellae, the white
skeleton can be seen through the transparent animal tissue, making the corals looked bleached white. In
cases where the corals possess additional animal pigments, bleached corals take on vivid fluorescent
hues, with no trace of the normal brown background colour (Figure 3).
Corals which have bleached are not dead. On close inspection it is possible to see the transparent
polyps and tentacles of bleached colonies. However corals cannot remain bleached indefinitely. If the
stress is not too severe or prolonged, stressed colonies can slowly regain their zooxanthellae and
survive. But in severe bleaching events many corals subsequently die, casing major changes to the
structure and function of the reef ecosystem, and possible cascading impacts on other organisms.
Although bleaching in individual corals was first observed early in this century, massive events
affecting reefs spanning tens to hundreds of kilometres have only been documented in the last two
decades . In the laboratory, or on a small scale in the field, bleaching has been attributed to a number of
factors which cause stress, including extremes (both high and low) of temperature and light, low
salinity, low oxygen, high concentration of toxic chemicals which affect respiration and
photosynthesis. In the case of “mass coral bleaching” involving a range of coral species over large
areas, elevated temperatures are the primary stress factor (Coles & Brown, 2003; Hoegh-Guldberg
1999). Elevated sea temperatures may be driven by regional phenomena (such as El Niño events), but
local conditions, such as periods of calm weather and clear skies, also play a major role in determining
sea temperatures in reefal regions. Decreased salinity from excessive rainfall and flood plumes can
increase the amount of bleaching, and may be a primary cause in some situations (mostly over limited
spatial scales). During the worst global bleaching event in 1998, more than 680 records of coral
bleaching were reported from over 55 different reef regions. Many of the affected reefs suffered
massive mortality from which they are still recovering (Wilkinson 2002). This event was also the most
intensively studied, and satellite data showing thermal anomalies or “hot spots” clearly showed that
large patterns of abnormally and consistently high temperature were very well correlated with
bleaching patterns, and in some cases appeared to be able to predict the events (Toscano et al. 2000,
Wilkinson et al 1999).
Coral bleaching is now considered to be one of the most significant and widespread threats to coral
reefs Hughes et al., 2003). When predicted temperature increases due to global warming over the next
100 years have been compared to the known temperature bleaching limits of corals, the depressing
conclusion is that by 2020 coral reefs in many parts of the world may suffer bleaching and mortality
every year Hoegh-Guldberg, 1999). Unless corals are able to adapt to raising temperatures, reefs may
suffer progressive deterioration and species loss, resulting in major ecological impacts and consequent
social and economic impacts on the human communities in many countries that depend on reefs for
their livelihoods. Global warming and greenhouse gas emission thus represent a relatively new and
severe threat to the sustainability and productivity of coral reefs and the services that that provide to
humans (Hughes et al., 2003; Wellington et al., 2001; Cesar et al., 2003).
There is an urgent need to obtain better information on bleaching events around the world. This
information is crucial to scientific understanding of the fate of coral reefs and to the feasibility and
practicality of developing management strategies to increase the resistance and resilience of reefs to
bleaching and associated mortality events. This protocol aims to provide a simple yet consistent set of
procedures to:
1. Document the spatial dis tribution, timing and severity of large scale bleaching events and how
they compare with maps of global temperature anomalies and other meteorological and
oceanographic factors. This will help in the developing and testing of predictive models of
bleaching which can focus attention on susceptible reefs which might benefit from better
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management of additional human impacts, and identify reefs which need to be protected since
they are most likely to survive further warming and bleaching events.
2. Determine the factors that, in addition to increased sea temperature, play a major role in
increasing (and decreasing) susceptibility to bleaching and subsequent mortality.
3. Develop a better understanding of which existing and new management practices can help
reefs deal with the additional stresses of a warming ocean.
4. Raise awareness of the extent and urgency of coral bleaching as a possible threat to the future
health and existence of coral reefs
Why is a Protocol needed?
Accurate and precise estimates of the severity, timing and spatial patterns of coral bleaching and
subsequent mortality are essential if we are to gauge the level and immediacy of the threat, and to
develop appropriate management actions to alleviate the ecological and social impacts. Unfortunately,
lack of standardised protocols has led to a proliferation of survey methods, surveyed variables and
variable definitions in different regions. Most reports are anecdotal and many are provided by people
with limited training in quantitative ecological assessments. This makes comparison between areas
exceedingly difficult. In addition there is considerable variability in the effectiveness of the various
monitoring procedures which have been used. Consequently some surveys have not made effective use
of personnel and time, and in some cases have collected data that are of limited use due to problems
observational bias and lack of standardization between observers.
There is a large number of global and regional monitoring programs aimed at assessing reef condition.
However few of these have formal assessment and monitoring protocols, for bleaching as a key
variable. Frequently, if it is mentioned bleaching is an added variable to be recorded in a comments
section or as a simple statement of percentage affected.
Those studies acquiring quantitative information use a wide variety of techniques that makes regional
comparisons very difficult and any global synopsis unreliable. A standard protocol for assessment and
monitoring would promote a higher quality of data, and a higher level of consistency between different
reports thus enabling more reliable comparisons between studies. A standard protocol would also
facilitate the ongoing development of a global database on coral bleaching events .
Currently there is no easily accessible and practically oriented document advising people what they can
and should do in order to better document and understand coral bleaching events. A flexible protocol
that takes into account the varying levels of resources and expertise of different groups, and the
different objectives is needed. This protocol aims to enable the further development and enhancement
of the current global repository of standardised bleaching observations and data (ReefBase).
Who will use the Protocol?
It is assumed that this guide will be used by people wishing to record basic features of a bleaching
event and to document overall impacts and possible relationships to causal factors. Two primary
purposes, are to document global patterns, and to understand smaller-scale patterns and variations that
may have local management implications. Thus this protocol is designed to produce more quantitative
data on the global distribution, severity, and frequency of bleaching events so that more rigorous
analysis of the relationship between coral reef status and climate change/global warming can be carried
out. At the same time it is recognized that many managers also wish to investigate bleaching in order to
determine what local management actions can be taken in order to lessen the impacts and increase the
resistance and resilience of their reefs to large scale bleaching events. More detailed investigations into
sub-lethal physiological impacts, subtle population ecosystem impacts etc are not covered here and
constitute major dedicated research programs for which it is assumed specialized scientific personnel
and specific research techniques will be involved
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This protocol is designed to assist individuals and groups with an interest in the occurrence and impacts
of coral bleaching on coral reefs. It offers advice to a range of people with varying backgrounds, skills,
resources and interests. In general the protocol divides potential users in to the following groups.
1. Volunteer groups and recreational divers with an interest in reef conservation and threats
2. Scientists with formal training in marine science who are able to record information during
field trips but whose primary focus is not coral bleaching
3. Members of dedicated volunteer organisations with an interest in monitoring coral reef status
and threats (e.g ReefCheck)
4. NGO and Management agencies wishing to assess and monitor the impacts of coral bleaching
and examine possible relationships between bleaching, and possible factors which could either
increase or decrease the impacts to reefs
5. Scientist wishing to conduct formal assessments of coral bleaching who wish to ensure that
their data will be comparable with other studies and who wish to contribute their summary
data to a global database
How should the protocol be used?
We anticipate that this protocol will serve as:
• a quick guide on what to do if bleaching is observed;
• a guide on how to use time and resources most effectively to observe and record bleaching;.
• an introductory resource on what bleaching is and how to recognise it;
• an aid in making immediate reports on coral bleaching when seen in the field;
• a guide for the development of structured and detailed assessments of bleaching as well as its
causes and consequences .
This protocol is a sourcebook for selecting an appropriate procedure from a range of possible
procedures. Details on many of the procedures can be found in other documents and this protocol
should be used in conjunction with GCRMN Methods Manual and other monitoring manuals.
Where possible, formal design and planning of monitoring program should be conducted in
consultation with scientists, managers, users and other relevant experts/stakeholders. The resulting
data should be lodged in a properly maintained and backed up database, with summary data being
provided to ReefBase. Data should be analysed and written up as a report as soon as possible and
submitted it to GCRMN regional or national node coordinator, or ReefBase (GCRMN coordinators are
listed at www.gcrmn.org).
Quick Guide – Start Here
This section should be used if you want some quick guidance on what to do if you have seen (or think
you have seen) coral bleaching, and you want to know what to do and what your options are. In
addition to providing an introduction on how to tell bleaching from other phenomena which result in
white coral, this section takes you through the steps needed to decide what type of measurements and
monitoring activities would be most appropriate for your circumstances.
A basic assumption of this protocol is that, regardless of the specific reasons for studying bleaching, all
readers will want to document the general extent and severity of bleaching as a first step. This section
will first provide quick advice and pointers for documenting the basic features of a bleaching event.
These steps should be conducted in all cases. It then proceeds to recommend various actions which
could be followed depending on the additional questions and issues that are of interest, and the
resources that available.
How do I identify coral bleaching?
Recently dead corals are also white, and can sometimes be confused with bleached corals. Bleached
corals can be distinguished from dead corals by careful examination of the coral surface. Completely
bleached corals look extremely clean and almost glow when seen underwater. (Figure 4). If the surface
is sediment free, and if you can see minute transparent tentacles when you view the colony from the
side, the coral is not dead. Dead, or dying colonies are unable to actively remove the sediment that
rains down on all but the clearest reef environments, and so any accumulation of even small amounts of
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sediment is a sign of mortality. Algae rapidly colonise dead coral surfaces, so if there is a thin film or
haze of green, brown or yellow this is also a sure sign that the coral is dead rather than bleached Figure
5. For some fleshy corals you can detect the presence of live tissue by gently touching the coral surface.
Bear in mind that bleached corals may ultimately die, and so dead colonies may be a final stage in the
bleaching process. However dead colonies can also result from disease, sudden weather events
(especially flooding), pollutants, and predation, so if your first observation is only of large numbers of
recently dead corals, you may have to look for other evidence to determine if this has been caused by
bleaching. Two common causes of non-bleaching related, recently dead corals can are crown-of-thorns
starfish (COTS) and disease. The visually diagnostic features of areas affected by COTS and disease
(Figure 6) are set out below.
Mortality due to COTS
• In low to moderate levels of infestation, COTS and other predators such as the snail Drupella,
leave discrete patches of dead white skeleton (feeding scars) which can look like bleaching.
Major outbreaks can leave quite large contiguous areas of dead white coral.
• Often there is a combination of recent scars (completely white) and progressively older “dirty”
scars with a coating of sediment or algae.
• If you see any COTS in the area (look among and under corals), you should immediately
suspect them as the cause of any apparent coral bleaching, especially if the white or dead coral
is patchily distributed
• COTS scars can also be distinguished from bleaching damage by the strong transition from
dead to live tissue within an affected colony
Mortality due to Disease
• Disease usually starts at one point and slowly spreads across a colony leaving dead and
progressively older “dirty” skeleton behind it. It can form circular patches or curved bands
across a colony
• The disease front is often a distinct band with a specific colour (black, red, white)
• Spotty white patches can be found in diseased corals but this is not a feature of bleached
corals
Appearance of corals in a bleaching event
• Colonies turn pale and bleach evenly over the whole colony or on the upper surfaces. Totally
bleached colonies appear exceptionally clean and almost gleam underwater (Figure 7). When
bleaching is moderate to severe and the water is fairly clear, whole reef surfaces appear white
from above the surface and even from the air (Figure 8)
• Partly bleached colonies appear very pale and there is usually a gradual change between the
paler and the darker parts of the colony. The upper surfaces are often the first, and sometimes
the only parts to bleach (Figure 9).
• On very close inspection you can often see the transparent tentacles of living polyps when the
colony is viewed from the side
• There is never a distinct line between bleach and unbleached parts of a colony
• In the early weeks and months of bleaching, colonies will remain bleached, or get even whiter
over periods of days and weeks. On the other hand, colonies killed by COTS or disease will
become covered in sediment and algae in just a few days
• Healthy, fast growing corals (especially Acropora species) will often have pale or white
growing margins or branch tips. This is a sign of active growth and should not be confused
with bleaching. While bleaching can also affect the upper surfaces of a colony only, the loss of
zooxanthellae will extend further down the branches beyond the growing tips.
How do I measure or quantify coral bleaching?
The most common way to quantify the level bleaching is first to determine the percentage of the reef
surface which is covered by corals and soft corals, and then to record the percentage of this cover
which is bleached. This can be accomplished by visually estimating the two measurements, or by using
one of several techniques to accurately measure bottom cover (line or point measurements, direct area
calculations from images). In areas where bleaching is well developed, and coral surfaces tend to be
either normal (“unbleached”) or completely white (“bleached”), this method can yield results quickly
6

and easily, even if only part of some colonies is bleached. However in cases where bleaching is mild,
or is just beginning to occur, many colonies may be paler than normal, rather than completely white. In
these cases a second category of “pale” can be added to the previous “bleached” and “un-bleached”
categories. Some care and experience is needed with this category, since healthy corals in some clear,
well lit environments can normally be very pale, even though this same colouration would be indicative
of significant stress in areas where corals are normally darker brown in colour. Even experts have been
known to mistake healthy corals for bleached ones in areas they have not previously visited. If in doubt
just use the bleached and unbleached categories.
The most basic form of bleaching data consists of a visual estimate of the percentage of total living
coral cover (hard and soft corals) which is bleached. This can be base on rapid surveys or casual
observations during visits to a reef. More accurate and precise methods, and a more structured way to
carry out surveys are discussed below, but at a minimum the percentage of bleaching should be
categorized into one of 5 levels to form a bleaching index which can be compared consistently between
locations anywhere in the world, and between different years (see Appendix 3, Table 8).
The NOAA/ReefBase Bleaching Questionnaire
ReefBase and NOAA have jointly developed an online and hard copy form which allows users to
record their observations of coral bleaching, and to store them within the ReefBase database
(www.reefbase.org/input/bleachingreport/index.asp). The bleaching questionnaire fulfils two
important functions. First it provides basic information on the basic aspects of the bleaching event in a
standard format which is stored on a global database so that the information can be shared with other
research worldwide and used to investigate global bleaching patterns. Second it can be distributed to
other people in your area to gain additional information of the distribution, severity and basic
characteristics of the bleaching event without having to dedicates special resources to additional survey
trips. The questionnaire in its basic form can be downloaded form the ReefBase website as an Word
Document (rtf format) and either emailed or distributed in hard copy form to other reef users in the
area. Further details can also be included on the web-based bleaching forms. It is important to follow
up and collect questionnaires from users, rather than having them send their results to ReefBase. That
way you can first examine the information in raw format and immediately follow up on any interesting
results. It also enables you to check the questionnaires for any errors. The completed forms should then
be sent to ReefBase. If you are in Australia, the Great Barrier Reef Marine Park Authority also has an
online questionnaire that can be used. The summary ReefBase questionnaire is included in Appendix 4.
What do I do if I see bleaching?
The box below sets out a series of steps to follow if you sea bleaching.
1. Record your observation and fill out a NOAA/ReefBase Questionnaire
(www.reefbase.org/input/bleachingreport/index.asp).
2. If bleaching is widespread or severe, send out a message on coral-list to advise others
3. If you cannot fill out most of the basic information in the questionnaire, consider returning to
the site as soon as possible for a reconnaissance visit to get additional general information. Ask
around and get other people who regularly visit the reef to indicate if they have seen bleaching
and where. Get them to fill out a ReefBase/NOAA Questionnaire – or make a note of these
observations yourself and send to them ReefBase
4. Ask yourself why you are interested in this event.
If you are not interested in formally answering the above questions (or any others you can think
of) then continue to record the basic information on the Questionnaire and send it to ReefBase.
5. If you want to formally answer questions similar to those in step 4, then you will need to design
a monitoring program (see below).
6. If you decide to implement a monitoring program, choose the methods and sampling protocol
that best suits the questions you wish to answer, and the resources you have available to you; or
pick a scenario that come closest to your situation and either follow the protocol suggested
there, or modify it to suit your situation
7. Take photographs to illustrate conditions that you see, and any unusually features. If using
digital camera, try to use at least 3 megapixel.
8. Store your data in a safe place and then share it with others by publishing it yourself or
sending summary data to ReefBase
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Designing a Program for your needs
In the previous sections we have had a quick look at what bleaching is, and what basic actions should
be taken if you see bleaching. Before describing the detailed procedures for taking the various
measurements recommended, it is important to take a bit of time to consider how to decide exactly
what questions you wish to address, what measurements are most appropriate and where and how
often they should be taken. While a set protocol in which everyone records the same measurements
might seem to be the best approach, this is not likely to work in practice. The unique circumstances and
sets of questions faced by different organizations and teams will require different monitoring programs.
In many people have particular methods or procedures that they prefer because of their skill or
experience. In many instances, alternat methods can provide similar data that can still be compared
across programs. Thus the most effective approach is to carefully identify the objectives of the
monitoring initiative and to then design a program from a list of commonly used and comparable
procedures to best suit the specific questions, and local environment, resources and logistics.
The design of a monitoring and assessment program for coral bleaching should be approached in the
same way as any monitoring program. A logical top-down approach should be used, beginning with the
identification of the specific objectives (often phrased in the form of a question) and the area over
which the question is addressed (global, national, a reef, a dive spot). This should be followed by the
selection of variables to measure, methods for measurement and sampling site and frequency. Only
after all these issues have been resolved should any field work be commenced. This is especially
important when a substantial investment in time and resources is to be made in monitoring a bleaching
event or events. However some careful thought about objectives and spatial scales will also result in
more relevant and reliable information even when assessment is limited to casual observations and
questionnaires. The following steps should always be followed in the development of any protocol.
The design of a monitoring and assessment program for coral bleaching should be approach in the same
way as any monitoring program. A logical top down approach should be used, beginning with the
identification of the specific objectives and (often phrased in the form of a question) and the area over
which the question is addressed (global, national, a reef, a dive spot). This should be followed by the
selection of variables to measure, methods for measurement and sampling site and frequency. Only
after all these issues have been resolved should any field work be commenced. This is especially
important when a substantial investment in time and resources is to be made in monitoring bleaching
events. However some careful thought about objectives and spatial scales will also result in more
relevant and reliable information even when assessment is limited to causal observations and
questionnaires. The following ten steps should always be followed in the development of any protocol
1. Identify question
2. Clarify spatial and temporal scope
3. Choose the best method from the options available
4. Choose the right variables to suit the question and scope
5. Select a sampling strategy to suit the methods, questions and scope
6. Carry out the field work
7. Enter the data
8. Check the data
9. Analyse the data or submit it for analysis by others
10. Store the data securely, or lodge it with a another database
Typical Questions/Objectives
In theory, there is an unlimited number of questions which could be posed in relation to coral
bleaching. The more specific the question which is being asked, the more specific the design of the
monitoring program can be. This will more likely will result in data which can unambiguously answer
to the questions. Vague questions like “Is bleaching affecting the health of the reef” can provide
frustratingly vague answers such as: “This depends on the measure you use for reef health” or “Yes in
some places and depths for some species, but not for others” Often, if some thought is given to the
general questions being posed, it turns out that they can, and should be separated out in to several more
specific questions, each of which need to be addressed separately in determining the optimum
monitoring protocol. It is possible to design a monitoring program that can efficiently address more
than one question, but there is a great risk that vague questions will result in a monitoring program
8

which has very poor power to answer any of the questions. Some typical questions relating to coral
bleaching are listed below.
A. What is the extent and severity of bleaching?
B. What environmental factors may be causing the bleaching and what is the relationship
of bleaching to global climate change?
C. What is the duration and frequency of bleaching?
D. What are the ecological impacts of bleaching? (How does bleaching affect the
biodiversity and overall “health” of the reef?)
o Does bleaching result in changes to species diversity?
o Does bleaching result in changes to relative abundances and dominance of different
species?
o Does bleaching result in changes to reef structure and habitat complexity?
o Does bleaching result in changes to reef productivity?
o Does bleaching result in changes to the ability of reefs to resist other impacts?
o Does bleaching result in changes to the ability of reefs to recover after an impact?
E. Do other anthropogenic stresses affect the severity of bleaching and can marine
protected areas help reefs faced with coral bleaching?
F. Can corals and reefs adapt to increased frequency and severity of bleaching conditions?
G. What are the social and economic impacts of bleaching?
o Do bleached reefs become less productive of commercially valuable species?
o Are there changes in reef aesthetics of value to tourism?
Picking a monitoring program to suit your situation
Although it is not possible to fully specify what monitoring activities should be carried out under every
possible situation, Table 1 provides a guide to the types and frequency of monitoring which should be
considered for different resource scenarios and for different questions. It is important to invest time in
considering how to tailor monitoring to your specific situation, and to use the points in Table 1 only as
a guide.
Table 1 Monitoring activities for various scenarios
Question
A.
What is the general
extent and severity
of the current
bleaching event?
B.
Is the bleaching
associated with
specific
environmental
factors such as
temperature, solar
radiation, water
circulation?
Resource Scenarios (see definitions below)
1. Low 2. Medium 3. High
A1
• Record variables from
questionnaire when visiting
any sites (affected and nonaffected
• Circulate questionnaires
amongst local divers and
other reef users
• Submit information to
ReefBase
B1
• Measure temperature using
hand held thermometer
whenever visiting sites
• Make a daily note of
weather conditions, and
record past observations of
any periods of calm
cloudless days
• Ask other reef users to
A2
• Carry out tasks in A1, plus
synoptic surveys of
representative areas
throughout the area you are
interested in (timed swims or
manta tow)
• Identify major species affected
(take photos or specimens)
B2
• Carry out tasks in A1,A2, &
B1
• install a maximum-minimum
thermometer at the main
bleaching site or take daily
temperature readings
• Get weather readings from
local ship’s logs (big tourist
boats, ferries etc)
A3
• Carry out tasks in scenario
A1 & A2, plus conduct
detailed surveys of
representative sites using
transects and some precise
measure of percentage of
coral affected (line transect,
photo-transect)
• Use aerial surveys (if water
clarity and tides permit) or
dedicated ship time to obtain
synoptic estimates over
wider geographic area
B3
• Carry out tasks in A1, A2
A3, B1, B2
• install recording temperature
loggers at main bleaching
site(s)
• install a remote weather
station at the site to record
temperatures, wind and solar
radiation
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C.
How long will it last
and is it a recurring
event?
D.
What are the
ecological impacts
on the reef system?
E.
Are adjacent human
impacts causing or
exacerbating the
bleaching?
collect similar data
C1
• Carry out repeated
observations (monthly) at
selected key sites until
bleaching disappears
• Revisit these same sites if
bleaching occurs in
subsequent years
• Ask local reef users for
details of any previous
bleaching events and record
these on ReefBase
Bleaching Questionnaires
D1
• Carry out tasks in A1
• Conduct before (if
possible) and after
bleaching observations
including
mortality/recovery
• General estimates of coral
cover over time
E1
• Carry out tasks in A1
• Note location, timing
(onset, duration, cessation)
and severity of local human
impacts.
• Carry out visual
assessments of the severity
of bleaching at 3 or more
sites with and without such
impacts
• Ask other reef users to give
you similar information
• Get local weather data from
Meteorological office on air
temperature, sun hours, wind
• consult with oceanographers
regarding the circulation
patterns, water exchange and
any upwelling features in the
area
• compare bleaching records
with published hotspots and
degree heating weeks on
NOAA’s website
C2
• Carry out tasks in A1, A2 &
C1
• Carry out the synoptic
observations in A2 at monthly
intervals till bleaching stops
• Repeat these same
observations for any
subsequent bleaching events
D2
• Carry out tasks in A1, A2 &
D1
• monitor tagged corals – track
mortality/recovery through
visual estimates
• measured estimates of benthic
cover through time
(transects/quadrats)
E2
• Carry out tasks in A1, A2 &
E1
• Detailed surveys at control
and impact sites
• Collate existing data on
human impacts such as water
quality, chronic disturbance
from destructive fishing
• Collect information on key
environmental variables at
impacts sites (turbidity,
sedimentation, gross pollution
indicators)
• measure currents and tidal
flow at key sites
• acquire and analyse NOAA
Local Area Coverage data to
correlate bleaching records
with thermal anomalies and
degree heating weeks
C3
• Carry out tasks in A1, A2,
C1 & C2
• Repeat detailed observations
in A3 at monthly intervals
till bleaching stops
• Repeat same observations for
any subsequent bleaching
events
D3
• Carry out tasks in A1, A2,
D1 & D2
• monitor tagged corals and
quadrats – measure mortality
and recovery using video or
photographic records
• measured estimates of
benthic cover through time at
higher taxonomic resolution
(transects/quadrats)
• transects of other macroinvertebrates
• fish abundance and diversity
surveys
E3
• Carry out tasks in A1, A2,
E1 & E2
• Detailed surveys at control
and impact sites
• Collate existing data on
human impacts such as water
quality, chronic disturbance
from destructive fishing
• Collect detailed data on all
relevant environmental
variables at impacts sites
(turbidity, sedimentation,
pollutants, nutrients, heavy
metals etc)
10

Monitoring for different scenarios
Since the level and extent of monitoring that can be conducted will depend largely on the time and
resources available, and the objectives for the monitoring program, we have made recommendations
based on 3 different resource scenarios, and 5 common questions/objectives related to bleaching. This
provides a quick guide for developing a monitoring program. More details on how to design a program
specifically tailored to your situation are given later in this protocol.
Resource Scenarios
Resources, in terms of funding, staffing and expertise, are all important constraints on the capacity of
an organization or team to respond to a coral bleaching event. Recognising these constraints and
working within them to maximise the quality and relevance of data is essential to a successful
monitoring program. Three generalised resource scenarios are described below to guide you in
selecting a suite of monitoring tools that are most suitable to your circumstances.
Low Resources
• No dedicated funds
• No or limited numbers trained staff
• Active volunteers available (with diving qualifications)
• Concern over plight of local reefs and global
Moderate resources
• Some levels of dedicated funding available for bleaching work
• Formal bleaching program exists or will be established
• Trained staff available (or funding exists to train new staff)
• Moderate level of logistic support (boats, computers, labs, scientifically qualified staff, good
communications)
High Resources
• Substantial funding available
• Dedicated bleaching program exists
• Highly qualified scientific team
• High level logistic support
• Strong community and government commitment to program
Outline of a typical monitoring plan
The following example outlines how one might develop a program to address Questions A (Severity
and Extent of Bleaching) & D (Ecological Impacts) with moderate resource levels.
Prior to any bleaching being observed
If your concern regarding the impacts of bleaching on a particular area has developed before any
bleaching occurs, then it is important to carry out some surveys prior to bleaching, so that specific
before and after comparisons can be used to gauge ecological impacts.
• If visibility and local conditions permit, carry out manta tows of the overall area of interest to
determine the distribution of habitats and the general characteristics of each habitat and zone.
• Choose replicate sites which are representative of the area (if more than one habitat or reef
zone is being investigated, choose replicate sites in each of these). Sites can be selected using
the results of the manta tow or local charts or aerial photographs
• Using timed swims (15 minutes around an area of about 50m x 20m) or manta tows (5 3
minute tows), estimate HCC, bleaching, anchor/blast damage at each area
• Carry out line replicate LIT surveys at each site to measure % cover of principal benthos
• Tag at least 20 corals at each site and record species, bleaching & mortality (presumably none
at this stage)
11

After onset of bleaching is observed (during peak of bleaching)
• Carry out extensive manta tow and/or timed swims to determine the extent/severity/variability
of bleaching.
• Determine if exiting sites adequately represent the areas bleached. If not add additional sites to
cover a range of levels of bleaching intensity
• Carry out belt transects (or LIT if the bleaching is very frequent) to get accurate estimates of
% of corals bleached at different levels of intensity
• Record condition of all tagged corals. If there is not a reasonable number of bleached corals at
each site (at least 10) then additional bleached corals should be tagged ant their condition
recorded. There is a great deal of additional work that could be done on these tagged colonies
(zooxanthellae counts and genetics, PAM fluorometry, reproductive studies). These might be
carried out by interested researchers at major Universities without much additional cost other
than collection time.
Further monitoring during and after bleaching
• Repeat synoptic surveys (manta tow or timed swims) at regular intervals. Suggested optimal
regime would be at , 2 months, 6 months, 12 months and 24 months after initial bleaching.
Full post-bleaching LIT surveys should be repeated once bleaching is not longer present and
all corals have either died or recovered. If resources permit, further recovery LIT surveys
using should be conducted annually or every two years.
Sampling Design Considerations
Deciding on the Spatial and Time Scale
For simple logistical reasons it is important to decide on the total area over which you wish to monitor
bleaching, and the overall time frame during which you will be monitoring. Given a fixed budget and
resources, larger spatial and time scales will usually mean less frequent, and fewer (less closely spaced)
samples. If you want to monitor a large area you will probably not be able to detect small scale
differences in bleaching pattern, and if you want to monitor for an entire year or for 5 years, then you
will probably be restricted to sampling at periods of 1-2 months and may not be able to detect the exact
timing of bleaching onset, recovery or mortality. These trade-offs needs to be carefully considered, and
choices should based on the specific issues which are important to you (as discussed in Step 1).
Before selecting a specific survey method, sampling sites and sampling frequency, it is important to
decide on the area over which you wish the program to be able to draw conclusions. Is the program
supposed to describe bleaching impacts globally, for a particular country, a single reef, or a single site
within a reef?
Deciding on the number, location and frequency of surveys (samples) is one of the most important and
difficult steps in a monitoring program. A clear understanding of the questions and the time a spatial
scales in which they will be addressed is crucial to the design of an effective sampling strategy. Some
general guidelines are provided below, however it is recommended that professional assistance is
sought in designing and sampling program and associated statistical analysis, especially if substantial
resources are to be invested in the monitoring.
Site and Sample Selection
A basic question which most monitoring programs will address is: what it the ext ent and severity of the
bleaching? In most cases the area over which this question is being asked is very large (10’s to 100’s of
kilometers or more), and thus sampling will need to cover as much of this area as possible, yet still
obtain sufficient quantitative information on specific variables to examine differences in intensity and
ecological impacts between sites. In such cases a nesting of sample locations and survey methods is
recommended. For instance, manta tow surveys could be used to obtain estimates of bleaching over the
entire area, while more detailed replicate line transects could be carried out at specific sites, nested
within locations around the entire area.
12

Sites within
a Location
Locations
within an area
Replicate Transects
within a Site
In choosing sampling sites, all available information on where bleaching is likely to occur or is known
to occur should be used, together with information on known distribution of reefs and coral community
types. Thus a variety of sources should be used to identify areas of important coral reef development,
and areas with differing physical influences on community structure such as sediments, exposure to
waves, currents and urban pollution. The following sources should be used in developing background
information on reefs, and physical influences prior to selecting any sites.
o
o
o
o
o
Satellite mapping
Aerial photos
Nautical charts
Local knowledge
Manta tow surveys
The primary purpose of site selection is to ensure that samples adequately represent the general area of
interest as outlined in the discussion of spatial scale (see above). This allows any conclusions based on
these samples to be applied to the whole area.
If you cannot adequately sample the whole area of interest, consider restricting the study to a smaller
area, bearing in mind that you will not be able to draw conclusions regarding bleaching in any excluded
areas.
Because coral bleaching can occur over a wide geographic area and because it is known to vary from
one place to another, it is important to record from as many different sites as possible. Sample sites
should be selected within areas known to have well developed coral communities and should be more
numerous in areas known to be highly variable (and thus less numerous in areas known to be very
similar in both community type and physical environment).
One way to allocate surveys would be to decide, on the basis of time, staff resources, logistics and
funding, how many surveys it is feasible to conduct and then to allocate these evenly along the entire
area to be sampled. This scheme should then be adjusted to cover areas known to be highly variable
with a few extra samples, taken from those areas which are highly uniform. Another way would be to
choose an inter-sample distance which is likely to capture the spatial variation in coral communities
and bleaching, and to then apply this interval to the whole area. If this results in a program which is too
expensive or time consuming, the number can be adjusted accordingly. Both of these methods assume
that there is some prior knowledge of the area, which could come from existing surveys and an analysis
13

of satellite images, aerial photos and nautical charts. Further details can be found in English et al.
(1997) and Devantier et al. (1998).
Sample size
Never take just one sample from any area which you hope to draw conclusions about, or which you
wish to compare with another area. If you have no idea of how variable the area is (how different one
sample is likely to be from another in the same area), then 3 samples should be the absolute
minimum, and 5 is likely to yield much more useful results. Areas which exhibit substantial
differences between sampling sites, in the measured parameter, require larger numbers of samples. In
general, more samples will yield a more precise result and a less ambiguous resutls . The optimal
sampling size will depend both on how variable the area is, and on what magnitude of difference
between areas you are hoping to detect (or how precise you wish your description of a single area to
be). If your questions involve detecting differences at different spatial scales, or if you believe that the
variability changes at different scales, then you should consider nested sampling, where replicate
measurement are taken at replicate sites within replicate broader locations. A more comprehensive
review of this topic can be found in Underwood (1997) and Andrew & Mapstone (1987).
Fixed vs Random vs Haphazard sampling
In order to ensure that the samples you monitor are representative, they should be randomly placed
within the area of interest. Truly random sampling requires the use of random number tables (or a
calculator which produces random numbers). Because this can be time consuming researchers often
resort to “haphazard” or “arbitrary” sampling. Haphazard sampling means that the researcher places
(or selects) samples without regard to any features on the reef, and without favouring any area or coral
types. Haphazard sampling is not truly random, and can result in significant biases if an inexperienced
person is involved in sampling corals for a conspicuous phenomenon such as bleaching. There is a
strong temptation to over-sample bleached colonies in most situations. Efforts to reduce this type of
bias should be used, either by using random number tables and allocation schemes, or by choosing a
method whereby the researcher cannot see what the area which is to be selected looks like until after is
has been selected. For instance, choosing sites from a boat without looking down at the reef is
advisable. In placing quadrats or laying out lines, the diver should keep his eyes closed. Monitoring
sites can also be established prior to a bleaching event to limit some sampling bias.
If a series of measurement of the same area are to be made in order to track changes over time
(increasing bleaching, increasing mortality, recovery) then consideration should be given to the use of
fixed units (quadrats or transects) which are re-measured each time. These units are initially placed
randomly but are then fixed for all other sampling times. Monitoring sites which are established prior
to a bleaching event to limit some sampling bias. The alternative is to measure from a new set of
randomly selected transects each time. There is some debate amongst experts regarding the use of fixed
vs random samples for long-term monitoring. Here is a quick outline of the advantages and
disadvantages of both.
Table 2 Comparison of Fixed vs Random Transects
Advantages
Disadvantages
Fixed
• Can detect changes over time more
precisely and thus
• Requires fewer replicates to detect a
specific level of change
• Takes longer to set up each one with
permanent markers
• Takes time to relocated markers
(especially in low visibility areas)
• Markers need to be maintained and
replaced (requires time and money)
• Permanent markers may not be
acceptable in MPAs or tourist sites
Random
• Much faster to set up and thus
• Can achieve larger sample size for
the same time in the water
• No maintenance costs
• No time needed to relocate markers
• No unsightly markers left underwater
• Much less precise estimates of
changes over time
14

• The initially random selection of units
can become less representative over
time
In general, if one of your principle objectives is to detect reasonably small changes over time then fixed
samples are a good choice. However if the time required to relocated and resurvey fixed transects is
more than 2-3 times greater than the time it takes to do survey a random site, then the advantage may
lay with random transects (especially if the area is not highly variable). A good compromise might be
to select a minimum number of fixed transects and then to supplement this with additional random
transects. Fixed quadrats can be particularly useful if a primary objective requires the tracking of
individual coral colonies over time.
Pilot Studies
An invaluable step in the development of a well resourced and rigorous monitoring program is to
conduct a pilot study, where a small number of samples (at each spatial level if it is a nested design) is
collected and used to calculate the variability of the area (variance) for each major variable to be
monitored. This is then used to calculate with much more accuracy the number of samples needed to
draw specific conclusions with a specified level of certainty. This last procedure, called Power
Analysis, requires advanced statistical skills. Pilot studies may not be feasible if the decision to monitor
is made after the onset of a bleaching event, or if it is likely be so short-lived that full sampling is
needed immediately. However some estimate of variance can usually be used, either from previous
bleaching events in the same area or other from other studies in other areas.
Monitoring Procedures
In theory, if we wish to know the percentage of living coral cover that is bleached in an area, then we
should measure levels of bleaching and the total living surface area for every single coral colony within
the area of general interest. Because this is not possible, a subset of these colonies (a sample) must
instead be measured, with the intent that this subset is representative of the whole set of all corals, and
thus that any conclusions drawn regarding this subset an accurate estimate of the whole set. Choosing a
sample which adequately represents the total population for which you wish to draw conclusions about
is a crucial step in the design of any monitoring program. It can be a complicated and sometimes highly
technical process. If the monitoring program in question involves substantial investments of time and
resources and/or if the conclusions which will be drawn form the program have important implications
for reef management or socio-economic status of communities dependent on the reef, then it is worth
seeking the assistance of someone with biostatistical training to help design the program. Poor
allocation of samples can lead to ambiguous or erroneous results. We present here some general rules
that can help to avoid the worst problems. However if at all possible, getting the final monitoring
design reviewed by a third party with some formal training in sampling and monitoring design will be
highly beneficial.
In general it is recommended that any monitoring program include a hierarchy of special scales starting
with broad regional assessments (questionnaires), then synoptic surveys and detailed rapid site
assessments (manta tows, timed swims), followed by fine scale monitoring within specific areas
(transects, quadrats) within these sites.
Table 3 Attributes of various monitoring procedures.
Procedure Advantages Disadvantages
Questionnaires Inexpensive; can be widely circulate
Can include retrospective assessments
Can include a wide range of variables
Data are usually based on subjective assessments, and subject to
recollection error
Reliability of information providers can be highly variable
Considerable follow up needed to obtained completed forms
Aerial Survey Covers huge areas in a short time Expensive; planes may not be available
Requires low tides, fairly clear water and moderate to high bleaching
Only overall bleaching data can be recorded and with fairly low
precision; cannot reliably distinguish between some areas of dead
coral and live coral, and high coral cover from low cover
Manta Tow
Covers large areas in short time
Provides more reliable estimates of bleaching severity
Best suited to reef edge and upper slope zones
Can be dangerous in rough weather
15

Timed Swim
Belt Transect
LIT (video or
manual recording)
Permanent
Quadrats (photo)
Tagged colonies
Can reliably distinguish between unbleached corals a and
dead corals, and low coral cover from high cover
Allows large numbers of site to be visited in a short time
Provide relatively precise estimates of bleaching and major
benthic categories
Allows accurate counts per unit area of uncommon entities
(useful if accurate measurements of bleaching needed when
only a few colonies are affected)
Enables size estimates of coral colonies to be made rapidly
Provides accurate measurements of all benthic categories
Close range of observat ions provides the highest taxonomic
resolution
Allows individual colonies to be repeatedly assessed.
Provides accurate measurements of colony size and area
Repeated measurements of bleaching and mortality can be
made on the same colony
Recurrence of bleaching in individual colonies (and hence
resilience development) can be tracked between bleaching
events
Samples for physiological, genetic and biochemical analysis
can be taken from colonies with a known bleaching history
Less precise than timed swims due to speed of travel and distance to
coral
Less precise than measured values from LIT or photo-quadrats
Less effective than aerial surveys or manta tow of covering large
areas (can miss small areas of bleaching since only a limited number
of sites can be surveyed)
Not useful for obtaining accurate measurements of benthic cover
Covers a small area – many replicates needed to sample a large area
Transects take longer to measure (manual) or longer to analyse
(video)
Quadrats take long time to analyse from photos.
Small spatial coverage per sample
Relocating colonies can be difficult and time-consuming
Large numbers of colonies for several species are required to obtain
useful population level estimates of bleaching and mortality
Questionnaires
The utility of questionnaires as a first step in documenting a bleaching event has already been
discussed. Questionnaires can be considered to be a special form of broad-scale survey. They are
useful if
• A large area needs to be covered
• The event has already occurred
• Many people visit the area that you are interested in
• You only need data on distribution, severity and gross taxonomic susceptibilities for bleaching
• You do not have the resources to carryout dedicated survey trips
• You do not need the data to be very precise (i.e. it will not be used to detect small difference
in bleaching severity between sites or years)
The ReefBase summary questionnaire is provided in appendix xx
Broad-scale Synoptic surveys
Since most bleaching studies involve at least some interest in the question of how extensive coral
bleaching is, broad-scale surveys are an excellent way of getting an overview of where bleaching is and
isn’t occurring over scales which are relevant to managers. It is strongly recommended that all
programs should have a broad-scale component. Fine scale or colony level monitoring can then be
nested with in these areas using the results of the broader survey to ensure that the local sites are not
anomalous compared with the larger area. For details on each of these procedures see the references.
Aerial Surveys
Aerial surveys are particularly useful for covering very large areas (>100km) in cases where bleaching
is severe over at least some areas and the water is clear. If carried out during low tide, with less than 1
meter covering the reef flat then it can be useful even in re latively turbid waters. Aerial surveys
provides data of lower precision and accuracy compared to other broad-scale methods, and should be
calibrated with timed swim data or LIT data. This method involve the use of a high-winged aircraft
which is flown at about 500ft along the perimeter of a reef with one or two observers recording
estimated percentage of coral bleaching. A similar approach could also be used to repeatedly monitor a
specific area by making regular observations from a fixed point on a hill overlooking a fringing reef.
Bleaching should be recorded using the categories in Appendix 3, Table 8. Further details can be
found in Berkelmans and Oliver (2000).
16

Recommended
Manta Tows
The manta tow technique is best used where the variables being measured (coral cover and % bleaching
in this case) are easily detectable at a distance, vary considerably and unpredictably over short
distances, and where the frequency of occurrence of the measured phenomenon is very low. In areas
with low visibility the method is not appropriate, and timed swims should be used. This method is well
described in English et al. 1997, and involves an observer on snorkel or SCUBA being towed behind a
small boat at a fixed speed. The observer uses a flat board at the end of a tow rope to manoeuvre in
such a way as to ensure a clear view of the reef surface. At fixed intervals the tow is stopped so that the
observer can communicate to a recording person on the boat the levels of key variables observed during
the tow. The major points to be considered are:
• Choose the tow path to cover as much of the area under investigation as possible
• Use standard AIMS method (2 minute tows)
• Record standard AIMS variables (especially total coral cover: Appendix 3; Table 7)
• Record coral bleaching characteristics including:
o % of all live coral bleached (use scale in Appendix 3; Table 8)
o top 5 coral families or genera bleached in rank order
A sample datasheet is provided in Appendix 1, and data tables are available in Microsoft Excel and
Access formats from ReefBase. Further details can be found in English et al. (1997).
Timed Swims
Times swims provide greater accuracy since the observer can spend more time in a particular area and
get closer to the substrate to ensure optimal visual resolution . However preliminary manta tow
surveys of an area which has not previously been visited, and about which nothing is known can be
useful in developing an understanding of where coral is best developed and how community type varies
over the entire study area. Since the timed swim method has not received as much attention in survey
manuals for coral reefs, we present here a basic description of the method.
At each site a diver should enter the water using scuba or snorkelling gear and then swim slowly along
the reef for a period of two minutes, keeping with in the prescribed depth zone. In general, a distance of
no more than 30m should be covered. Height above the substrate should be about 2m, but this may be
varied depending on the visibility (high in clear water; lower in murky water). Closer distances should
be used to verify identifications and coral condition where needed. Where possible 2 depth zones
should be recorded: shallow and deep. The shallow site should include the reef crest and upper slope (if
the sample is on the reef edge) from about 1m to 4m in depth. The deep site should include the mid to
lower reef slope from 5-10m. Actual depths will need to be varied according to the coral community. In
turbid environments, or areas with poor reef development, these depths may be shallower, while in very
clear conditions they may be deeper. In areas with very restricted reef development, only the shallow
depth zone may be present.
In general snorkelling gear can be used to asses the shallow station. However if necessary due to the
depths involved, or poor visibility, scuba gear should be used. Deep sites should be assessed on
SCUBA. A team of at least three people should be used. One person should act as a boatman and
record station details. Another person can use snorkel to assess the shallow zone, while the third person
prepares scuba gear. Two divers should then enter the water to conduct survey the deep site, with one
diver acting as the primary observer. The person snorkelling in the shallow zone should also be the
primary SCUBA observer in order to minimize variability in the observations caused by different
observers. The issue of inter-observer differences is addressed in more detail below.
The same primary observer should record all the variables in the data sheet at the end of each 2 minute
period. There are three sets of information to be recorded: Station information; general coral and
bleaching observations; and detailed information for selected coral groups. These are listed in Tables 2,
and 3. These tables should form the basis of a database on bleaching observations. An Access database
has been created to accompany this protocol, and can be downloaded from
www.reefbase.org/bleachingdatabase.
17

Table 4. Station Information (for all Synoptic and fine scale survey sites) This information only needs to
be entered once for any station. Whenever a station is revisited for repeated surveys, only the station ID code
needs to be recorded on the survey data sheet
Station ID: Use a logical method to give each station a unique code. This should include an indication
of the depth zone. E.g “BB001D” might be used to indicate Bali Barat, Station 1, deep
zone.
Country: Name of country
Region: Name of Region (e.g. Bali Barat) Use local administrative names such as province or
municipality where no other name is appropriate.
Location/Reef Enter the local name used for this site or reef. This should be a unique name. If none exists,
Name:
Latitude:
then used a modifier (e.g. a number)
Latitude (in decimal degrees if possible) of starting point of the sample where observer
enters the water. Use a GPS to get a fix if possible. If no GPS is available then mark the
station on an aerial photograph or nautical chart and calculate the actual latitude later.
Longitude: Longitude (as above)
Zone: Enter the reef zone using the standard list in Table 1 of Appendix 3.
Exposure: Enter the level of exposure to wind and waves for this station using the standard list in
Table 2 of Appendix 3: L=Low; M=Medium; H= High
Depth zone: Enter depth zone using the standard list in Table 3 of Appendix 3 (shallow/deep)
Depth zone Brief description of depth range of zone and any major features
notes:
Station notes: Brief description of the community character, existing stresses, etc.
Protection: Enter protection status of the station using the standard list in Table 4 of Appendix 3 (0 if
unprotected, -1 if protected but IUCN status unknown; 1-6 for protected status if IUCN
category known).
Table 5 Manta Tow & Timed Swim - General data:
Record ID:
Station ID:
Date:
Time:
Observer:
Buddy:
Vessel:
SCUBA:
Depth:
Temperature:
%HC:
%SC:
%MA:
%OT:
Bleaching:
Bleaching
notes:
Disease:
Enter a unique code for this observation
Enter the station ID code (as selected in the Station Details Table)
Enter the date of the observation
Enter the time of the observation
Enter the name of the observer
Enter the name of the dive buddy (where appropriate)
Enter the name of the main boat used for the survey (if available)
Enter “YES” if using SCUBA; otherwise enter “NO”
Enter depth where most of the observations were made (or enter depth range if
observations taken from several depths)
Enter the temperature (if available) of the water at the depth recorded in Depth
Enter % hard coral cover using cover categories (0-5) described in Table 7 of Appendix
3
Enter % soft coral cover using cover categories (0-5) described in Table 7 of Appendix
3
Enter % fleshy algal cover using cover categories (0-5) described in Table 7 of
Appendix 3
Enter % cover of other benthos using cover categories (0-5) described in Table 7 of
Appendix 3
Enter % of living benthos which is bleached using bleaching categories (0-4) described
in Table 8 of Appendix 3. NOTE: use the percentage of living cover which is bleached,
NOT the percentage of the total bottom area.
Enter any relevant observation on the severity, extent, variability or bleaching
Record the frequency of occurrence of all diseases using categories (0-3) described in
Table 6 of Appendix 3
COTS: Record the frequency of occurrence of crown-of-thorns starfish using categories (0-3)
Cyanide
fishing:
Blast fishing:
described in Table 6 of Appendix 3
Record the frequency of occurrence of evidence of cyanide fishing using categories (0-
3) described in Table 6 of Appendix 3
Record the frequency of occurrence of blast fishing using categories (0-3) described in
18

Anchor
damage:
Pictures:
Comments:
Table 6 of Appendix 3
Record the frequency of occurrence of anchor damage using categories (0-3) described
in Table 6 of Appendix 3
Note whether any pictures were taken and indicated ID codes (if any)
Add any additional comments or observations, including a note on any additional data
that has been collected for this site and time.
Table 6 Additional Bleaching details (recommended - for timed swims only)
Acropora % cover Enter % of total coral cover that is Acropora using cover categories (0-5)
described in Table 7 of Appendix 3
Acropora % bleaching: Enter % of all bleaching corals that is Acropora using bleaching categories
(0-4) described in Table 8 of Appendix 3
Pocilloporid % cover: Enter % of total coral cover that is Pocilloporidae using cover categories (0-
5) described in Table 7 of Appendix 3
Pocilloporid %
Enter % of all bleaching corals that is Pocilloporidae using bleaching
bleaching:
categories (0-4) described in Table 8 of Appendix 3
Faviid % cover: Enter % of total coral cover that is Faviidae using cover categories (0-5)
described in Table 7 of Appendix 3
Faviid % bleaching: Enter % of all bleaching corals that is Faviidae using bleaching categories (0-
4) described in Table 8 of Appendix 3
Fine-scale monitoring
Fine-scale monitoring provide the greatest level of detailed quantitative data. It should be used when
there is a need to reliably detect or demonstrate small to moderate bleaching effects. Because these
methods take more time and cover smaller areas, they should, where possible, be combined with
broader scale surveys which provide information on the overall effects at a larger scale.
For detailed surveys of coral cover and beaching for major coral groups, the line intercept transect
method is the most frequently used. Alternative methods include area assessment within belt transects,
quadrats, or other shapes covering a small discrete area or point-based assessments. The LIT is
recommended as a suitable method for most purposes. Since it is the most commonly used monitoring
method it is more readily compared with data from other programs The LIT provides a measured value
for cover and bleaching which is not possible from area assessments, where the cover is estimated
rather than directly measured. Point-based methods can provide good measures of cover, but may
require a very large number of points in order to match the precision obtained from line intercept
measurements. In addition point methods are also not able to provide estimates of colony abundance
and size frequency. Finally detailed, repeated analysis of tagged corals provides the ability to monitor
colony level effects of bleaching over time, and to examine inter-colony differences in bleaching
responses.
Belt Transects (English et al)
Belt transects are ideal if a larger are needs to be surveyed in order to pick up rare species or events. If
bleaching is only occurring in scattered colonies, but an accurate estimate of area or frequency of
occurrence is needed, then a belt transect is more efficient that the large number of quadrats or line
transects that would be required to record a useful number of occurrences. If other large scattered
organisms such as COTS, giant clams are being counted belt transects are again the most appropriate
method. The size of the transect should be determined based on a preliminary assessment of the
frequency of bleaching using manta tow/swim results, but generally about 20-30m x 1-2m is effective.
Use larger transects if bleaching is not very common. The width of the transect is often estimated from
a central tape, however bordering tapes can be laid for greater accuracy, or a measuring stick used of
the transect width is not more than 1-2m. For rapid assessments, bleaching severity should be recorded
using the categories in Appendix 3, Table 8, but if time permits separate estimates of level of
bleaching, and percentage of the colony which is dead should be recorded. Corals and other benthos
should be recorded to level 3 in Appendix 3, Table 10 if possible. For any site at least 3 transects
should be surveyed, and this should be repeated in shallow and deep sites if the depth range permits
and if depth variation in bleaching is evident or important to the question being addressed.
19

• record size, bleaching severity, and species/genus/family (use highest taxonomic resolution
possible given expertise of survey team)
• replicate transects (at least 3 – better 5) per site
Recommended
LIT (English et al.)
Line intercept transect (LIT) stations should be used to obtained more precise information about the
percentage of coral bleaching and mortality for an area, and the types of corals which have been
affected. This method should be used if quantitative comparisons are to be made between stations or
between times. It will also enable differences in coral community structure which may occur as a result
of bleaching and mortality to be detected, and will provide information on whether certain community
types are more susceptible to bleaching than others .
The standard AIMS method is recommended for the LIT surveys (English et al. 1997). At each station,
a minimum of three 25m transects should be laid haphazardly within the selected depth zone. Two
depth zones which match those used for the timed swims, should be sampled at each station where
possible. Video transect methods are also described in English et al., 1997).
Stations for LIT monitoring should be selected based on an analysis of the synoptic surveys. Because
of the time taken to survey a station (6 transects), far fewer stations can surveyed by LIT compared
with the synoptic surveys. It is recommended that LIT stations be chosen from the established synoptic
survey stations, and that a subset of these stations is chosen which is able to represent the full range of
community types and bleaching/mortality patterns observed in the timed swims. In areas where the
primary variables do not change greatly from station to station only one to a few LIT stations should be
established. Where there is a great deal of variability between timed swim stations, a higher proportion
of these stations should be surveyed by LIT.
For most projects random allocation of transects within each depth zone is recommended. This allows
for rapid establishment and surveying of transects, avoids leaving unsightly stakes and markers on the
reef, and avoids certain statistical problems when repeated surveys are conducted over a long time
period.
The use of video to record the benthos along transects is not recommended unless resources are
sufficient to ensure that both lab and field equipment can be purchased and maintained, and qualified
personnel are available to analyse the data. Video tape analysis takes a significant amount of time from
a person with good taxonomic skills, and if resources are not allocated for this stage, a backlog of
unanalysed tapes can cause delays in interpreting and disseminating the results. On the other hand if
there are no people with the ability to reliably identify benthic organisms at the required taxonomic
resolution, video transects are an ideal method of recording conditions using divers with limited
training, and then arranging for the tapes to be analysed by an expert at a later date. In general the data
which can be obtained from manual recording along a transect provide are similar to data from video
in their ability to detect change and document status. Manually recorded LIT data can be analysed
immediately after the survey with a standard computer and software and with comparatively little
effort. Table 8 summarizes the advantages and disadvantages of manual vs image recording for both
line transects and quadrats.
The variables which should be recorded for each transect are shown in Table 7. Further details on the
LIT method can be found in English et al. (1997).
Table 7 Data to be collected for LIT method
Variable
Record ID:
Station ID:
Date:
Time:
Observer:
Description
Enter a unique code for this observation
Enter the station ID code (from the Station Details Table)
Enter the date of the observation
Enter the time of the observation
Enter the name of the observer
20

Buddy:
Vessel:
Depth:
Replicate:
Benthic code:
Transition:
Occurrence:
Bleaching:
Bleaching notes:
Disease:
Dis ease notes:
COTS:
Physical damage:
Enter the name of the dive buddy (where appropriate)
Enter the name of the main boat used for the survey (if available)
Enter depth of the transect start
Enter the replicate number for this transect
Enter the code for the type of benthos for this transition
Enter the value in cm for the end point of the transition
Enter a number to indicate if this a part of a previously recorded colony
Enter the degree of bleaching for this colony section (if applicable) using
standard bleaching code (0-4) described in Table 8 of Appendix 3
Enter any other observations on the appearance of the bleached colony section
Is the colony section diseased? (yes/no)
Enter observations on the type, appearance and severity of the disease
Is the colony section part of a COTS feeding scar? (yes/no)
Has the colony section been physically damaged? (yes/no)
For benthic codes refer to Table 10 of appendix 3. Use 18 categories (level 4 in Table 10), with
additional detail to 30 categories (level 5) where possible.
Quadrats or other shapes of defined areas
Quadrats are useful for mapping all colonies in small defined area. If the quadrats are permanent, then
individual colonies can be easily relocated and tracked over time. Photo transects, in which the entire
quadrat is photographed (in one or a sequence of images) are recommended since the images can be
analysed to calculate percentage cover for all colonies. However direct field recording is advantages in
some circumstances (see Table 8). Photo quadrats are usually about 1m x 1m or 2m x 2m. In each
quadrat percentage cover for all relevant cover classes and % of this that is bleached in should be
calculated. The size and bleaching index of each colony greater that 3cm should be recorded. Details on
recording images for photo quadrats can be found in ?ref?.
Table 8 Image Analysis vs Field Measurements
Field recording
(slate and pencil)
Image recording
(camera, video)
Advantages
• highest resolution (eyes)
• lowest overall time from
observation to database
• data entry is rapid and does not
require an expert
• shorter time required in water
• Less expertise needed in field
• Can resurvey the images for
additional variables later
Disadvantages
• need higher level of expertise in the
field
• field component takes longer
• Cannot go back and resurvey for
additional variables
• lower resolution results in less reliable
identifications
• analysis of images takes time and high
level of expertise
• longer total time from observation to
database
Minimizing observer variation
In both the synoptic surveys (manta tows, timed swims) and the detailed LIT surveys, there are
variables which are subjectively estimated rather than being measured using a tape or other instrument.
This includes all cover estimates for the timed swims, and also bleaching, disease and damage
estimates for the LIT. As a result, differences between observers can result in apparent differences in
the observed variable. In order to minimise inter-observer variation, it is recommended that the same
person or small group of people are used to recorded all data. At the beginning of any sampling
program, and again at the end, all observers should survey the same 2-3 areas or transects at the same
time in order to document the extent of inter-observer variability. Where there is a large difference
between observers, additional training and discussion should be held to identify and minimise the
source of this variation. If a consistent difference between observers remains throughout the program,
careful consideration could be given to applying a correction factor for one or more observers.
21

Colony level monitoring
The following techniques should be used if you are asking a question which requires the fate of
individual colonies to be tracked. Video recording along line transects or still images along a belt
transect can also provide the relevant data for subsequent provided the imagery captures the same area
of bottom on each visit. Tagged colonies have the advantage that they can be located in the field
quickly without having to refer to the previous image. This allows tissue samples to be taken to track
actual abundances of zooxanthellae (by clade if needed) or concentrations of Chlorophyll.
Hybrid technique
Currently WWF is employing a hybrid of LIT and Quadrat technique for some of its field
projects. This method involves establishing a permanent 20m transect (marked at one end with a
temperature data logger) and taking digital photographs of a 0.5 x 0.75m quadrat set along the transect
every 0.5 m, alternating sides of the transect. This results in 40 photos. Additionally the quadrat is
arbitrary tossed on the benthos in the area that would consist of the arc of the circle created by the
transect line. Fifteen of these arbitrary tosses are made and a digital photo is taken of each. Digital
photo resolution is maintained at 2272 x 1704 pixels using a 4 megapixel camera. Photos are then
analysed by counting all of the colonies and assessing how many bleaching and to what degree.
Tagged Corals
The use of tagged colonies permits accurate assessment and ongoing monitoring of the health of
specific colonies. In particular, the tracking of a population of corals from the onset of bleaching until
mortality or full recovery has occurred, will provide the best measure of mortality that can be
unambiguously related to bleaching. In other methods, mortality can only be inferred from a decrease
in coral cover between sampling events. Tagged colonies are also particularly appropriate for
investigating the relationship between the severity of coral bleaching and subsequent
mortality/recovery, or the susceptibility of coral which have previously bleached and recovered to
bleach in subsequent years (adaptation). Tagged coral are also essential for time series studies of
physiological aspects of bleaching such as zooxanthellae density, changes in concentrations of UV
protective compounds and responses and population shifts in zooxanthellae strains.
If the above questions are of importance to the program at a particular location then one or more
representatives sites should be chosen in which to tag several colonies for a range of species. It is
recommended that a minimum of 20 (up to 50) colonies should be tagged for each species. If the
objective of the study is to obtain detailed information on mortality and bleaching susceptibility of the
coral community then species from several families should be chosen. In general, species from the
most abundant families should be selected: Pocilloporidae, Acroporidae, Faviidae, Poritidae, but in
areas where species from other families predominate, then these should also be tagged. Ultimately the
number of species and fami lies tagged will depend on time and resources. It is better to sample
adequately (~30) from a few species than to obtain inadequate sample sizes from a large number of
species.
During the initial survey (and at yearly intervals) the colony should be measured (length x height x
width) and for all surveys its condition should be scored in terms of bleaching, and optionally disease
and physical damage. A 4-point score should be used (Table 9 in Appendix 3) for bleaching, and a 3
point score for other types of stress.
Where possible colonies should be tagged in a well defined area which can be easily resurveyed
without having to swim over large distances. Colonies should be selected haphazardly and cover a
range of sizes. If repeated samples are to be taken from the colony for laboratory analysis then larger
colonies are essential. In order to facility relocation of tagged colonies, a rough map of the area should
be drawn whilst underwater, showing major landmarks (e.g. large or unusually shaped colonies; sand
patches; general reef features such as ridges, depressions, indentations and protrusion of the reef edge)
in relation to each tagged colony. Alternatively, if visibility is usually low at the site, a nylon line can
be strung from one colony to another to create a trail. This should be avoided in areas where other
divers and tourists are likely to visit as it is both unsightly and likely to be removed.
22

Colonies can be tagged using large plastic tags. Cattle ear tags or pot plant labels are both suitable.
Holes can be made in plastic tags using a small soldering iron or a skewer heated in a flame. The tags
should be attached to the colonies using plastic coated wire or zip ties for branching colonies and
galvanised roofing nails for massive colonies. For fragile plate species it may be necessary to attach the
tag to the adjacent substrate, making careful note of it position in relation to the colony.
Data management
Once the data have been recorded in the field, it is critical that the information is transferred from the
data sheets into the appropriate computer files as soon as possible (preferably the same or the next day).
If there is a delay in transcribing the information to computer it is possible that ambiguous or missing
information on the data s heet will be impossible to retrieve or remember. Data should preferably be
entered directly into the MS Access database provided with this protocol. However MS Excel
spreadsheets using the equivalent structure are also provided for users who are unfamiliar with MS
Access software. MS Excel and dedicated statistical and graphics packages are best used to analyse the
data. However, it is strongly recommended that the data is accumulated first into a single Access
database covering all sites and times. Subsets of the data for particular sites or times can then be
extracted for analysis by more specialised software. Data which are accumulated into a growing series
of spreadsheet files becomes increasingly difficult to keep organised as the number of sites and samples
grows.
Once entered, the data should be printed out and checked for errors within a few days of recording the
data (if longer you may forget important aspects which can help to resolve ambiguous entries). This
should be done by having another person read out the data from the print-out while the original
observer checks it with the entries on the datasheet. In addition it is worthwhile carrying out
preliminary analyses to see if the summary data of % cover are within expected ranges. Cover values of
more that 100% can then be checked for errors.
Once the data are checked, the files should be backed up onto a separate disk clearly labelled and
stored in a separate room or building. Summary data should be sent to collaborators and to ReefBase
for general dissemination and inclusion in the global bleaching database.
Literature
Andrew, N.L. and B.D. Mapstone, (1987). Sampling and the description of spatial pattern in marine
ecology. Oceanogr. Mar. Biol. Annu. Rev. 25 : 39-90
Berkelmans, R and J.K. Oliver (1999). Large-scale bleaching of corals on the Great Barrier Reef. Coral
Reefs vol. 18, no. 1, pp. 55-60.
Berkelmans, R., T. Done and V. Harriott (2002). Coral bleaching and global climate change :Current
state of knowledge. CRC Reef Research Centre, Townsville, Australia. P6.
Cesar, H., L. Burke and L. Pet-Soede (2003). The economics of worldwide coral reef degradation.
Cesar Environmental Economics Consulting (CEEC), 6828GH Arnhem, The Netherlands.
Coles, S.L. and B. E. Brown (2003). Coral bleaching-capacity for acclimatization and adaptation. Adv
Mar Biol. 46:183-223.
English S, C. Wilkinson, V. Baker (eds) (1997). Survey manual for Tropical Marine Resources ( 2nd
Edition) Australian Institute of Marine Science. ASEAN-Australia Marine Science Project. 390
pp.
Glynn, P.W. (1996). Coral reef bleaching: facts, hypothesis and implications. Global Change Biology
2:495-509.
Hoegh-Guldberg, O. (1999). Climate change, coral bleaching and the future of the world’s coral reefs.
Marine and Freshwater Research 50:839-866.
Hughes,T.P., A. H. Baird, D. R. Bellwood, M. Card, S. R. Connolly, C. Folke, R. Grosberg, O. Hoegh-
Guldberg, J. B. C. Jackson, J. Kleypas, J. M. Lough, P. Marshall, M. Nyström, S. R. Palumbi, J.
M. Pandolfi, B. Rosen and J. Roughgarden (2003). Climate Change, Human Impacts, and the
Resilience of Coral Reefs. Science 301: 929-933
Marshall, P.A and A.H. Baird. (2000). Bleaching of corals on the Great Barrier Reef: differential
susceptibilities among taxa. Coral reefs, vol. 19, no. 2, pp. 155-163, 2000
23

Toscano, M.A., Liu, G., Guch, I.C., Casey, K.S., Strong, A.E., and J.E. Meyer (2000). Improved
prediction of coral bleaching using high-resolution HotSpot anomaly mapping. In Moosa, M.K.,
S. Soemodihardjo, A. Soegiarto, K. Romimohtarto, A. Nontji, Soekarno and Suharsono (ed.).
Proceedings of the Ninth International Coral Reef Symposium, Bali. 23-27 Oct. 2000. Vol
2:1143-1148
Underwood, A.J. (1997). Experiments in Ecology: Their Logical Design & Interpretation Using
Analysis of Variance. Cambridge University Press.
Wilkinson, C. (2002). Coral Bleaching and Mortality – the 1998 Event 4 Years Later and Bleaching to
2002. In: C.R. Wilkinson (ed.), Status of coral reefs of the world:2002. GCRMN Report,
Australian Institute of Marine Science, Townsville. Chapter 1, pp 33-44
Wilkinson C, O. Linden, H. Cesar, G. Hodgson, J. Rubens, A.E. Strong (1999). Ecological and
socioeconomic impacts of 1998 coral mortality in the Indian Ocean: An ENSO impact and a warning
for future change? Ambio 28:188-196
24

Appendices
Appendix 1. Data Forms
Station Description
WWF Bleaching
Monitoring
Program
Timed Swim Data Sheet
Station ID:
Region:
Latitude:
Reef Zone:
Protection:
Country:
Locaton/Reef Name:
Longitude:
Exposure:
Depth Zone:
Depth Zone Notes:
Station Notes:
25

WWF Bleaching Monitoring Program
Line Transect Data Sheet
Station: Transect: Observer: Buddy:
Date: Time: Vessel: Depth:
Benthos Code
Transition
Occurence
Bleaching Code
Bleaching Notes
Disease (Y/N)
Disease Notes
COTS (Y/N)
Damage (Y/N)
Damage notes
26

WWF Bleaching Monitoring Program
Timed Swim Data Sheet
Station: Transect/Replicate: Observer: Buddy:
Date: Time: Vessel: Depth:
MC
SC
MA
OT
Bleaching
Bl Notes
Diseases
COTS
Blast Fishing
Anchor damage
Acropora Cover
Acropora Bl
Pocillopora Cover
Pocillopora Bl
Faviied Cover
Faviid Bl
27

Appendix 2. Monitoring Variables
Bleaching
Clearly the most important variable to be recorded in all programs is the amount of bleaching and
mortality that has occurred. Bleaching is not an “all or nothing” phenomenon. During bleaching, coral
colonies lose their algae over a period of days to weeks and can exhibit a continuous range of
colouration from a slight paling, to complete loss of colour resulting in a totally bleached white
appearance. Furthermore, colonies do not lose colour uniformly over their entire surface. Upper
surfaces bleach more rapidly and intensely than lower surfaces in some corals, while apparently
random patterns of bleaching intensity can often be seen in other corals. Finally some coral can
become pale as part of a normal seasonal response to changes in light intensity and water quality. Such
corals can appear to be bleached even to experienced experts if they are not familiar with the area the
normal colour variation of its corals. These features make it very difficult to quantify the intensity of
bleaching both within coral colonies and over an entire reef. Consequently, for synoptic surveys we
suggest that no attempt be made to grade the level of colony bleaching, and that only extremely pale or
totally bleached colonies are recorded to be “bleached”. Bleaching severity for a reef area should be
based on the proportion of the total living coral cover that is bleached. While this conservative
approach may tend to miss early stages of a bleaching event it will avoid over reporting of “bleaching”
caused by over-emphasizing the significance of slightly pale colonies which are either naturally pale, or
only slightly stressed. An index of overall bleaching, based on the percentage of total coral cover that
has bleached is presented in Appendix 3, Table 8 and should be used a minimum measurement for all
studies.
In addition to this, where time and resources permit, it is recommended:
1. Actual percentage of total coral cover be recorded directly and assigned to a category later
during summary analysis
2. Bleaching percentage be broken into contributions from major taxonomic groups. Table 10 in
appendix 2 shows different taxonomic levels which should be used depending on the skills
and resources available.
3. Bleaching percentage should be measured using point, transect or direct area measurements if
different measurements will be compared and differences of more than about 25% need to be
detected
4. The size of bleached colonies be recorded (as length, width and height, or as size categories) if
the ecological impact of bleaching is an important question.
Colony Indices
When fine scale monitoring is being conducted which permits measurements for individual colonies
(using tagged colonies, quadrats or belt transects), more detail on the bleaching status can be recorded.
The intensity of bleaching (whiteness) is difficult to measure precisely without resorting to
sophisticated analyses of zooxanthellae density or spectrophotometer measurements. Calibrated colour
cards could, in theory, be used to obtain semi-quantitative data on the degree of bleaching, but this
method (see www.coralwatch.org) requires additional field testing and calibration in a variety of
locations before it can be effectively used as a globally consistent index. Table 9 in Appendix 3 sets
out a recommended bleaching index for individual colonies base on visual assessment. If time permits
then individual assessments of level of bleaching and percentage mortality would be useful. These can
be converted into the appropriate category if needed for comparison purposes later during data analysis.
In addition the maximum length, width and height should be recorded using a transparent ruler in the
field.
Coral Mortality
The ultimate level impact of coral bleaching on coral reefs will depend on whether corals recover from
bleaching or die. If they recover, the impacts are likely to be minor, although there is some evidence to
suggest that bleached corals can suffer from reduced reproductive output in following years, and
growth rates are likely to be suppressed. However if most of the bleached corals die, this can have a
28

major effect not only on coral cover but on a range organisms (including humans) who depend on
living corals for their habitat or food.
Once a coral has died, it becomes rapidly overgrown by a succession of organisms. Recently dead
corals can be identified by a thin coating of algae with the underlying white skeleton still clearly
visible. Corals with this appearance are likely to have died within one or at most two months. Corals
which have been dead for longer periods can have a variety of appearances depending on the types of
organisms which have grown over the skeleton and the level of grazing that has. Unless they have been
monitored regularly during and after the bleaching event, it is extremely difficult to determine how
long such corals have been dead, and thus whether they died as a consequence of recent bleaching or
some other cause at an earlier date. Thus the percentage cover of dead coral should only be used as and
indictor of the impacts of bleaching for corals which are recently dead, and have died following an
observed bleaching of corals in the area. If individual tagged colonies are monitored repeatedly during
he bleaching event, however, changes in the percentage of its surface which are dead provide a good
measure of the impacts of bleaching.
Benthic Cover
In cases where more details on the types of corals and other organisms which are bleached is desired,
and where the longer term impacts on the distribution and abundance of major reef organisms is
needed, the percentage cover of all major benthic organisms should be recorded. While it is possible to
estimate some of the key cover categories, it is better to measure these objectively using standard
benthic monitoring techniques. The Line Intercept Transect (LIT) is the most commonly used
technique, however belt transects, quadrats and point intercept methods also yield satisfactory results.
Since each method has it own set of errors and biases, it is important that only one method be used
within a monitoring program so that comparisons between sites can be made with the greatest
confidence. If you have no strong preference, selection of the LIT method will make your data directly
comparable with a greater number of other programs. Benthic cover monitoring methods are well
covered in Hodgson et al (2003), English et al (1998 and Rogers et al. (1994).
Image recording – digital photography
In the last few years digital cameras have become reasonably priced, offer high resolutions and a wide
range of models. Many models have dedicated underwater housings and flash units. Increasingly,
digital photography offers a range of advantages over conventional film photography, and very few
disadvantages. A comparison of film vs digital cameras for coral reef monitoring is presented below.
Table 1. Film vs Digital Photographs
Advantages
Disadvantages
Film
• Film offers the highest resolution
• cameras and film are cheap and
available everywhere
• need to send film away for
processing
• cannot check exposure/focus until
film is developed
• maximum of 36 exposures per dive
• film is heat and age sensitive
resulting in altered colour balance
for old or improperly stored film
Digital
• can take 50-100 photos in one session (or
more - dependent only on size of memory
card)
• produces more consistent colour since its
not dependent on variations in the dyes used
in negatives and prints
• can be quickly viewed and computer
analysed without the extra step of
developing and scanning prints or negatives
• resolution is lower than film (but at 6-8
mega pixels, the difference becomes
negligible)
• digital cameras heat up when in use and can
cause fogging on the inside of the housing
lens port – this is a significant problem with
some models
• digital cameras and memory cards are
29

• film purchase and development
costs eventually exceed cost of a
digital camera
initially much more expensive than film
cameras (but cheaper in the long term since
there is no film purchase and processing
cost)
Measurement of environmental variables
Temperature
Since elevated water temperatures are believed to be the primary cause of almost all mass bleaching
events, water temperature measurements are a key variable in confirming this relationship. Global
water temperature anomaly data, at 50km 2 resolution, are calculated by NOAA and made available on
their website as Hotspots and degree heating weeks (http://orbitnet.nesdis.noaa.gov/orad/coral_bleaching_index..html
). These data, which can also be obtained from
ReefBase together with bleaching records for the same period, can provide a quick indication if the
current bleaching event is associated with a regional or global temp erature event. Higher resolution
data (10km 2 ) are available to institution with a satellite receiving and processing station, and can
provide much finer scale comparisons, especially near continental margins.
Wherever possible, direct measurements of water temperature should also be taken since this provide a
direct indication of the physiological conditions that the coral are experiencing. At a minimum take a
single measurement of temperature using a dive computer or handheld thermometer at the depth of
maximum coral bleaching, every time you visit a site with bleaching. Maximum-minimum
thermometers can be used, if available and left on the reef between trips.
The best way of determining the temperature regime that is being experienced by corals is to install an
electronic temperature logger set to record temperatures every hour. These can be left in place for 6-12
months and provide accurate reading which can be downloaded and immediately analysed on a
computer.
Inexpensive data loggers can be purchased from the USA (Hobo Stowaway Tidbit or Water Temp Pro
http://www.onsetcomp.com/Products/3654_temp.html#Anchor-35882 ) for about US$120 each and a
further US$100-300 for software and downloading equipment. Loggers, whilst reliable, have a
tendency to fail or get lost, so it is recommended that 2 loggers be installed at each location so that a
backup is always available. Loggers should be installed at more than one location if the distance is
more than about 50km, or if the oceanographic features of the site are know to be very different (e.g.
shallow bays compared to steep shelf edge slopes with upwelling). Loggers should be wired firmly to
a metal stake hammered at least 1m into the reef. It is a good idea to put the logger in an inconspicuous
place where other divers are not likely to come across it and collect it as a souvenir. By wrapping the
logger in a dark plastic bag you can keep it free from fouling organisms and also disguise it somewhat
from curious divers.
Because corals are sensitive to small deviation above normal summer maximum temperatures, it is
important to use a thermometer or logger with a precision of at least 0.5ºC.
Salinity
Freshwater runoff, and (if intense) direct rainfall can lower the salinity of water in shallow reef
environments enough to cause bleaching, or to greatly increase thermally induced bleaching. While
rainfall records will often provide a good indicator of the likelihood of lower salinity (if there has not
been any substantial rainfall in the weeks preceding or during bleaching, you can rule salinity out as a
major factor). If salinity is a possible factor for consideration a simple refractive salinometer can be
used to take readings on each visit. If available, a portable conductive salinometer is very useful, and
can be used to take a profile for both temperature and salinity at different depths and location. This is
probably not necessary unless you are interested in determining the exact relationship between salinity
and bleaching threshold. In this case repeated measurements will be needed leading up to and during
30

the event. Electronic salinity loggers can also be used, but these should be regularly calibrated, and can
only be used for short periods since fouling of the sensor can affect the readings.
Light, Rainfall, Wind
These are important additional variables which can significantly influence the risk and severity of
bleaching. The most appropriate way of obtaining data on these variables is to get it from the nearest
meteorological station, if one exist within about 50km from the bleaching site. If the weather station is
more than 5km away then these data should be treated with caution since all these variables can vary
significantly over short distances. Another source of meteorological information is from large tourists
boats visiting the reef being surveyed (or an adjacent reef). Large boats usually have wind gauges and
often record this in their logs. They may also record qualitative comments on rainfall and cloud cover,
or may be prepared to do so on request. If a major monitoring program is being developed then
portable weather stations which log all of the above variable as well as temperature can be bought for
about US$1000-2000.
Appendix 3. Variable codes
Table 1. Reef Zone
Category Description
1 Crest
2 Flat
3 Upper slope
4 Lower slope
5 Broken reef shallow
6 Broken reef deep
Table 2. Exposure zone
Category Description
Low Sheltered; rarely experiences
large waves
Medium Moderately sheltered;
sometimes experiences large
waves; may frequently
experience small waves
High Exposed to swell and waves;
frequently experiences large
waves; almost always
experiences small waves
Table 3. Depth zone
Category Desciption
Shallow Upper reef slope and crest; 1-5 m deep.
Deep Mid-lower reef slope; 5-10 m.
Notes In shallow reef environments (where reef does not
extend below 10 m), divide reef slope into shallow
and deep either side of mid-depth. (eg. If reef extends
only to 7 m, shallow zone is 1 - 3.5 m; deep zone =
3.5 - 7 m).
31

Table 4. Protection level table
Category Description
-1 Protected but unspecified level
0 Not protected
1 IUCN Category 1a *
2 IUCN Category 1b *
3 IUCN Category 2 *
4 IUCN Category 3 *
5 IUCN Category 4 *
6 IUCN Category 5 *
7 IUCN Category 6 *
* Note: see IUCN Categories (Table 5)
Table 5. IUCN Categories of Protected Area Table
Protected Areas by IUCN (World Conservation Union) Categories (I-V). IUCN has defined a series of
protected area management categories based on management objective. Definitions of these
categories, and examples of each, are provided in Guidelines for Protected Area Management
Categories (IUCN, 1994).
CATEGORY Ia
Strict Nature Reserve:
protected area managed
mainly for science
CATEGORY Ib
Wilderness Area: protected
area managed mainly for
wilderness protection
Area of land and/or sea possessing some outstanding or
representative ecosystems, geological or physiological features
and/or species, available primarily for scientific research and/or
environmental monitoring.
Large area of unmodified or slightly modified land, and/or sea,
retaining its natural character and influence, without permanent
or significant habitation, which is protected and managed so as
to preserve its natural condition.
CATEGORY II
National Park: protected
area managed mainly for
ecosystem protection and
recreation
CATEGORY III
Natural Monument:
protected area managed
mainly for conservation of
specific natural features
CATEGORY IV
Habitat/Species
Management Area:
protected area managed
mainly for conservation
through management
intervention
CATEGORY V :
Protected
Landscape/Seascape:
protected area managed
Natural area of land and/or sea, designated to (a) protect the
ecological integrity of one or more ecosystems for present and
future generations, (b) exclude exploitation or occupation
inimical to the purposes of designation of the area and (c)
provide a foundation for spiritual, scientific, educational,
recreational and visitor opportunities, all of which must be
environmentally and culturally compatible.
Area containing one, or more, specific natural or
natural/cultural feature which is of outstanding or unique value
because of its inherent rarity, representative or aesthetic
qualities or cultural significance.
Area of land and/or sea subject to active intervention for
management purposes so as to ensure the maintenance of
habitats and/or to meet the requirements of specific species.
Area of land, with coast and sea as appropriate, where the
interaction of people and nature over time has produced an area
of distinct character with significant aesthetic, ecological and/or
cultural value, and often with high biological diversity.
32

mainly for
landscape/seascape
conservation and recreation
CATEGORY VI :
Managed Resource
Protected Area: protected
area managed mainly for
the sustainable use of
natural ecosystems
Safeguarding the integrity of this traditional interaction is vital
to the protection, maintenance and evolution of such an area.
Area containing predominantly unmodified natural systems,
managed to ensure long term protection and maintenance of
biological diversity, while providing at the same time a
sustainable flow of natural products and services to meet
community needs.
Table 6. Stressors table
Category Description
1 Absent
2 Present or limited extent/severity
3 Common or extensive/severe
Table 7. Benthos abundance table
Category Description
0 0%
1 1-10%
2 11-30%
3 31-50%
4 51-75%
5 76-100%
* Note: see AIMS % cover table and figure
(Note addition of Category 0)
Figure 1. AIMS Benthos Cover Categories
Table 8. Site bleaching category table
Index % Description Visual Assessment
0 < 1 No Bleaching No bleaching observed, or only very occasional,
scattered bleached colonies (one or two per dive)
1 1-10 Low or Mild
Bleaching
Bleached colonies seen occasionally and are
conspicuous, but vast majority of colonies not
bleached
2 10-50 Moderate
bleaching
Bleached colonies frequent but less than half of
all colonies
3 50-90 High Bleaching Bleaching very frequent and conspicuous, most
corals bleached
4 >90 Extreme Bleaching Bleaching dominates the landscape, unbleached
colonies not common. The whole reef looks white
33

Table 9. Colony bleaching table (for use in LIT surveys)
Category Description
0 No bleaching evident
1 Partially bleached (surface/tips);
or pale but not white
2 White
3 Bleached + partly dead
4 Recently dead
34

Table 10. Benthic codes
Level 1 Level 2 Level 3 Level 4 Level 5
Hard
corals
HC
Soft
Corals SC
Fleshy
Macro MA
algae
Acropora ACR Acropora ACR Acropora ACR
Nonacropora
Soft
Corals
Fleshy
Macro
algae
NAC
Pocilloporid POC Pocilloporid POC
Table
Bush
Arborescent
Other Acropora
Pocilliopora
Seriatopora
Styolophora
ACT
ACR
ACA
ACO
PCL
SER
STY
Faviid FAV Faviid FAV Faviid FAV
Fungiid FNG Fungiid FNG
Other Hard
Corals
HCO
Lobophyllia LOB
Mussid MUS
Other Mussids MSO
Galaxea GAL Galaxea GAL
Merulina MER Merulina MER
Porites
Goniopora/
Alveopora
Agariciid
POR
GON
AGR
Porites massive PMS
Porites branching PBR
Goniopora/Alveopo
GON
ra
Pachyseris PAC
Pavona
PAV
Other Agaricids AGO
Turbinaria TUR Turbinaria TUR
Euphylliid EUP Euphylliid EUP
Pectinia PEC Pectinia PEC
Montipora MNT Montipora MNT
Misc. hard
corals
OHC Misc hard corals OHC
SC Soft Corals SC Soft Corals SC Soft Corals SC
MA
Other OT Other OT
Fleshy
Macro
Algae
MA
Fleshy Macro
Algae
MA
Fleshy Macro Algae MA
Crustose coraline
Algae
Sponges
Zoanthids
CCA
SPG
ZOA
Other
OT Other Benthos OT
Benthos
Gorgonians GOR
Misc. Benthic
OTB
Invertabrates
4 5 7 18 29
35

Appendix 4
ReefBase Coral Bleaching Form
Coral bleaching is a major threat to the health of coral reef, which occur during period of hot calm weather. Bleached
coral appear white or extremely pale compared to their natural brownish color. If you have recently seen any coral
bleaching, please provide detail of your observation below, or submit on line report at
www.reefbase.org/input/bleachingreport. Your contribution will be made available on the ReefBase website for
managers and researchers interested in managing the impact of bleaching on coral reef.
Name
Contact/email
Country
Place Name
Latitude and
longitude (if available)
Date of observation
Have you observed significant coral bleaching (more than 2-3 white coral) during your visit?
No Yes – If yes, please complete the rest of the form, if No, please send the form
with site
the site detail above.
Depth of Area
bleached
Percentage of live
coral cover in the
area
Type/species of
coral affected
(List top 5 species or
common name)
Percentage of dead
coral
Reef zone
(slope/reef flat/ etc)
Percentage of live
coral that is bleached
Water temperature
(if possible)
Types of dead coral
coral (if known)
Other observations
Approximate area
surveyed
Type of survey
When bleaching start
(if available)
Please mail or fax this report to:
Dr Jamie Oliver
ReefBase Project Leader
ICLARM - The World Fish Center
Jalan Batu Maung, Batu Maung,
11960 Bayan Lepas, Penang, Malaysia.
Telephone no: (604) 626 1606 Fax no: (604) 626 5530
email : y.yusuf@cgiar.org or j.oliver@cgiar.org
ReefBase is a project of The International Coral Reef Action Network
www.icran.org