GIYANTO, MUHAMMAD ABRAR, ANNA EW MANUPUTTY,

RIKOH M SIRINGORINGO, YOSEPHINE TUTI, DEWIRINA ZULFIANITA

SECOND
EDITION

Coral Reef
Health Monitoring
Manual Book
Oceanographic Research Center,
Indonesia Institute of Sciences

COREMAP-CTI
Indonesia Institute of Sciences
2017
Center of Oceanography Research -LIPI Jl. Pasir Putih No. 1, Ancol Timur, Jakarta 14430 Telp.
: 021-64712287, 6452425, 64713850 Fax. : 021-64711948, 64712287 E-mail :
humas@oseanografi.lipi.go.id Url. www.oseanografi.lipi.go.id
www.coremap.or.id
Giyanto, Muhammad Abrar, Anna EW Manuputty, Rikoh M Siringoringo, Yosephine Tuti, Dewirina Zulfianita

Coral Reef Health Monitoring

Manual Book
Second Edition
COREMAP-CTI Indonesia Institute of Sciences 2017
Coral Reef Health Monitoring
Manual Book
Second Edition
Oceanographic Research Center, Indonesia Institute of Sciences
CORAL REEF HEALTH MONITORING MANUAL BOOK (SECOND EDITION) © 2017 CRITC
COREMAP CTI LIPI
Authors: Giyanto, Muhammad Abrar, Anna EW Manuputty, Rikoh M Siringoringo,
Yosephine Tuti, Dewirina Zulfianita
Cover Design and Layout: Dewirina Zulfianita
Coral Reef Information and Training Center (CRITC) Coral Reef Rehabilitation and Management
Program (COREMAP)
Oceanographic Research Center, Indonesia Institute of Sciences
Jl. Pasir Putih No. 1, Ancol Timur, Jakarta 14430 Telp. : 021-64712287, 6452425, 64713850 Fax. : 021-
64711948, 64712287 E-mail : humas@oseanografi.lipi.go.id Url. www.oseanografi.lipi.go.id
www.coremap.or.id
Manual of Coral Reef Health Monitoring (Second Edition) /Giyanto, Anna EW Manuputty, Muhammad
Abrar, Rikoh M Siringoringo, Yosephine Tuti, Dewirina Zulfianita –-Jakarta : COREMAP CTI LIPI
2017
v + 48 hlm.; 5.83” x 8.27” ISBN.
Table of Content
Table of Content .................................................................................................................................................................................................................................. i
List of Figure ........................................................................................................................................................................................................................................... ii
List of Appendix ................................................................................................................................................................................................................................. iii
PREFACE ................................................................................................................................................................................................................................................... 1
1. Purpose ............................................................................................................................................................................................................................................. 1
2. Objective ........................................................................................................................................................................................................................................ 1
MONITORING PREPARATION ................................................................................................................................................................................ 2
1. Monitoring Team Formation ................................................................................................................................................................................ 2
2. Administration Preparation .................................................................................................................................................................................... 2
3. Materials and Equipment Preparation ...................................................................................................................................................... 2
4. Determining Locations and Stations .......................................................................................................................................................... 3
DATA COLLECTION ............................................................................................................................................................................................................... 4
DATA PROCESSING .............................................................................................................................................................................................................. 7
DATA PHOTO ANALYSIS .............................................................................................................................................................................................. 9
1. Level of Data Analyzer ............................................................................................................................................................................................... 9
2. Data Entry of Photo Analysis Result ........................................................................................................................................................ 10
3. Displaying the Result of Photo Analysis ............................................................................................................................................. 12
REPORTING ......................................................................................................................................................................................................................................... 13
Bibliography ........................................................................................................................................................................................................................................... 16
Appendix 1 ................................................................................................................................................................................................................................................ 17
Appendix 2 ................................................................................................................................................................................................................................................ 18
Appendix 3 ................................................................................................................................................................................................................................................ 20

CORAL REEF HEALTH MONITORING MANUAL i

List of Figures
Figure 1. Tools and Materials: (a) Diving Apparatus SCUBA, (b) GPS, (c) Protected and
Unprotected Digital Camera, (d) Measuring Tape (roll meter), (e) 58x44 cm
Rectangular Frames, (f) Waterproof paper mounted on writing board, (g) External
Harddisc, (h) Laptop, (i) CPCe Software ..................................................................................................................... 5
Figure 2. Taking picture of station name as an initial of the station concerned ....................................... 10
Figure 3. Initial pole at zero meter spot ....................................................................................................................................................... 10
Figure 4. Sausage-tipe buoy that indicates initial transec spot ..................................................................................... 11
Figure 5. Land photos at research station taken without zoom (left) and zoom ...................................... 11
Figure 6. 50 meters transec line ............................................................................................................................................................................. 11
Figure 7. Transec line withdrawal direction ........................................................................................................................................... 12
Figure 8. Profiles around transec line ............................................................................................................................................................. 12
Figure 9. Contrasted color painted frame .................................................................................................................................................. 12
Figure 10. Pictures taken in the field applying UPT method: (a). Scaled-tape position at odd
numbered frames, (b). Scaled-tape position at even numbered frames .................................. 13
Figure 11. Illustration of sample withdrawal utilizing Underwater Photo Transec (UPT) ............ 13
Figure 12. Pictures of the frame without zoom (left) and zoom (right) as an auxilliary photo
for photo analysis ......................................................................................................................................................................................... 13
Figure 13. Selection of random spot samples .......................................................................................................................................... 19
Figure 14. Initial appearance of CPCe V4.1 program ................................................................................................................... 21
Figure 15. OX menu to provide area boundary to be analyzed ......................................................................................... 22 B
Figure 16. Button to accept/cancel the measurement and boundary position .................................................. 22
Figure 17. Menu to determine data spot distribution ....................................................................................................................... 23
Figure 18. Menu of analyzed data information ....................................................................................................................................... 23
Figure 19. Display screen for data input .......................................................................................................................................................... 24
Figure 20. The table which is part of Figure19, containing menu to move forward to next
photo ............................................................................................................................................................................................................................. 24
Figure 21. Display to reserve analyzed files .............................................................................................................................................. 24
Figure 22. Display to convert cpc files into Excel .............................................................................................................................. 25
Figure 23. Example of output in Excel ............................................................................................................................................................. 25

ii CORAL REEF HEALTH MONITORING MANUAL

List of Appendix
Appendix 1. File content: coral_code_basic.txt ............................................................................................................................. 33
Appendix 2. File content: coral_code.txt ............................................................................................................................................... 34
Appendix 3. Identification of Benthic category and basic substrate of coral reef ............................. 41

CORAL REEF HEALTH MONITORING MANUAL iii

Preface
Covered by around 18% of the world coral reef, Indonesia is situated exactly on the center of “Coral
Triangle”, which is a region of the most diverse biodiversity of the world. The Indonesia coral reef covers
39.583 km2 or around 45,7%, consisting of around 590 species of corals and 2.200 species of reef fish.
Unfortunately, almost 45% of the coral reefs are significantly under high to very high devastating threats
(Huffard et al., 2012). Efforts to protect and manage the coral reefs have become priority in order to preserve
the coastal ecosystem which is closely linked to food security.
Reef health monitoring is defined as both data and information collection on bio-ecology of reefs and social
economic change of the coastal community. Proper monitoring relies on regular and timely based practice
conducted at the same representative areas. Change in spatial and temporal scale on the data will provide
critical information whether the management system applied is working properly or not.
In order to determine the state of reefs for monitoring, measuring the percent cover of benthic communities
as well as the associated reef fishes is the common practice applied globally. However, the techniques used
are always developing to improve the accuracy and precision while still user friendly. Therefore, it is
necessary to prepare a manual on coral reef monitoring as a standard reference.

PURPOSE
The purpose of this manual book is to provide a standard reference of coral reef monitoring, especially on
benthic communities.

OBJECTIVE
The objective of this manual is to give standard practice of preparation, data collection, data analysis and
interpretation, and reporting.

1
Monitoring Preparation
MONITORING TEAM FORMATION
The monitoring team is basically all well-trained personnel involved in field survey undertaking coral reef
health monitoring. The team is at least consist of 1-2 boat operators, 1 GIS Mapping, 2 data collectors, 2
SCUBA technicians and 1 person for data input and processing. These persons should be under supervision
of an expert/scientist.

ADMINISTRATION PREPARATION
According to applied regulation, it is necessary to acquire a working licence in order to work. It is
compulsory to notify local government agencies where the survey will take place to prevent any
contingency stuff regarding emergency situation during the survey. The letter of notification needs to be
acknowledged and signed by the authority of the team’s office.

MATERIAL AND EQUIPMENT REPARATION

The preparation is initiated by identification of materials and equipment, especially about the tipe,
specification, number and current condition.
Table of reef health monitoring materials.
No. EQUIPMENT/MATERIAL TYPE SPECIFICATION NUMBER REMARK
I Equipment
1
2
II Materials
1
2
SPESIFIKASI CHECK LIST KETERANGAN

Picture
Figure 1. Kind of materials: (a) Diving Apparatus SCUBA, (b) GPS, (c) Underwater housing and digital
camera, (d) Measuring Tape (roll meter), (e) Rectangular Frame of 58x44 cm, (f) Water proof paper
amounted on writing board. (g) External Harddisc, (h) Laptop, (i) CPCe Software
Kind of materials required during sample collecting to reef health monitoring using Underwater Transec
Photo method (UPT) (Giyanto et al., 2010; Giyanto, 2012a; Giyanto, 2012b) is as following:
1. Diving Apparatus SCUBA (Figure 1a).
2. GPS (Figure 1b) is to determine the coordinate position of research site.
3. The underwater camera (Figure 1c)
4. Measuring Tape (roll meter) (Figure 1d) with 50 meters long
5. Photo frame (made from metal or PVC pipe), 58 x 44 cm in size
2
6. Underwater paper (Figure 1f) .
7. External hard disc (Figure 1g), to save underwater photos.
8. Laptop is used to analyze photos. (Figure 1h)
9. CPCe Software (Kohler & Gill, 2006) (Figure 1i) which can be downloaded from
www.nova.edu/ocean/cpce/

DETERMINING LOCATIONS AND STATIONS

Determining the monitoring locations and the sites is udertaken together with mapping team who will
provide a basic map. The criteria of monitoring site as a permanent transect need to consider the following
factors, i.e.:
a. Representativeness. The determination of a transect station should be selected under the
representativeness, at least 3 transects represent one location, depending on the reef area coverage.
Such representativeness is based upon proportional selection of the distribution of the coral reefs, tipe
of area usage both on land and water, the status of the area (conservation/non-conservation) and the
local community social-cultural aspect.
b. Security. Locations and sites for permanent transect should consider possible human intervention,
therefore it should be away from the harbor, shipping lanes, tourism area or other human activity
locations.
c. Safety. It is better to avoid locations or sites which are potentially hazardous such as high waves, strong
current area, etc.
Preliminary estimation of monitoring sites can be observed on reef map distibution created from satellite
imagery map, navigation map, or thematic map of coral reef distribution. After determining certain sites
for monitoring, then we can estimate the coordinates to be saved on the GPS Tracker. Then we need to
check the field whether the position is pointing a reef or not. If it is pointing a reef, so we can start
establishing a monitoring station. If it does not, so we need move around to seek a nearest reef. The position
should be recorded using GPS therefore we can monitor again at the same point.

3
Data Collection
Coral reef monitoring has numbers of sample collecting methods applied (Loya, 1978; Moll, 1983; Mundy,
1990; English et al., 1997; DeVantier et al.,1998; Long et al., 2004; Oliver et al., 2004; Hill & Wilkinson,
2004; Lam et al., 2006, Alquezar & Boyd, 2007; Leujak & Ormond, 2007; Burt et al., 2008; Burt et al.,
2009a; Burt et al., 2009b; Giyanto et al., 2010; Giyanto, 2012a; Giyanto, 2012b). Various methods used to
monitor the condition of coral reefs have weaknesses, so that a better method is certainly needed. One of
the method is Underwater Photo Transect (UPT) (Giyanto et al., 2010; Giyanto, 2012a; Giyanto, 2012b).
The UPT method utilizes advanced technology, both the development of digital camera technology and
computer software technology. The underwater photos collected are analyzed using computer software to
obtain quantitative data.
Advantage in using the UPT method among other is to shorten diving time. Besides, the photos can be used
as documentation archieve which can be reviewed anytime (Giyanto et al., 2010; Giyanto, 2012b).
However, there are some weaknesses out of the method, including dependency on the camera and longer
time for photo analysis, especially when using technique of area calculation.
Data collecting from the field is done by diving using SCUBA diving apparatus. The process is using UPT
(Underwater Photo Transect) method utilizing underwater camera or specifically water protected digital
camera (housing) to hold sea water seeping.
There are procedures to collect the data using UPT method as following:
1. If it is a new location, put a name on the site and note the coordinate position using GPS. However, if
it is the existing location (same of monitoring location), make sure that the transec position is the same
as the previously noted coordination position (latitude and longitude are based on GPS).
2. Once the position of the permanent transect site of which the data will be collected is secured, before
diving write down on the slate the name of the site (Figure 2). This will provide accurate information
during photo processing, as it provides initial boundary of the photos sequence in the memory of the
camera.
Insert photo
Figure 2. Photo shooting on the name of the station as a photo starting mark of the concerned station.
3. Further, the diver who responsibe to pull the transec line, starts to dive and search the transec starting
points marked by two metal stakes and a buoy attached on those stakes or two nearby substrats (applied
to permanent transec data position which was taken a year before) (Figure 3). If it is a barely new
location, set the initial transec points and provide them with two metal stakes and two buoys.
Insert photo
Figure 3. Initial stake mark at zero meter.
4. After the initial points are found or determined, the diver has to hook up sausage-typed buoys and to
ensure the buoys arise on the surface that person on the boat may note the transec starting points (Figure
4). (insert photo)

4
5. Once the buoys on the water surface are spotted, the person on the boat take the picture of the land
from the transec site by both zooming and without zooming (Figure 5). Non-zoomed photos will
provide illustration on how far the transec position from the land, while zoomed photos depict general
description on coastal/land areas including the surrounding coastal vegetations.
Insert photo
Figure 5. Land pictures at the monitoring site taken without zoom (left) and using zoom (right)
Insert photo
Figure 6. Line transect along 50 meters.
6. The diver who responsible to pull the transec line starts to put the transec line using 50 meters
measuring tape (roll meter) in 5 m depth and align with coastal line, commencing from the starting
point of 0 meter. The illustration of transec line drawing is shown on Figure 6. To ensure the
uniformity of transec line withdrawal, the island position should be on the left of the transec line
(Figure 7). (insert photo)
7. Soon after the transec line installed, use the same camera to record the habitat condition of around the
transec line to get a general picture or basic description of the seabed around the transec line (Figure
8).(insert photo)
8. The following measure is data collecting by underwater picture takings, where the angle of the shooting
should be perpendicular to the base of substrat shooting field. The minimum shooting area is 2552 cm2
or (58 x 44) cm2 (Giyanto et al., 2010; Giyanto, 2012a; Giyanto, 2012b). If CANON G15 type of
camera is used, in order to obtain 2552 cm2 shooting area, the shooting should be undertaken 60 cm
away from the base of the substrat. It is possible to use other type of camera as long as the minimum
shooting field is 2552 cm2.
For practicallity, to ensure the shooting field to be analyzed has desired wide area, a metal frame of
58 x 44 cm can be used. The assessor should only shoot the substrate within the frame. The frame is
preferably painted with bright striking color (contrasting color against the substrate), whereas the four
tips of the frame apply different striking color against the frame rods (Figure 9). (insert photo)
9. The shooting starts from the first meter on the left of the transec line (closer part to the land) as ”Frame
1” (Figure 10a), followed by photo taking on the second meter of the right side of the transec line
(further part to the land) as ”Frame 2” (Figure 10b), and so on until the end of the transec. As to the
frame with odd number (1, 3, 5,...) the pictures are taken from the left of the transec line (Figure 10a),
while the frame with even number (2, 4, 6,...) the pictures are taken from the right of the transec line
(Figure 10b). Figure 11 is an illustration of sample withdrawal utilizing Underwater Photo Transec
method. Number within the frame on Figure 11 shows the frame number, and at the same time shows
the umpteenth meter the photos taken on the transec line.
10. For the smaller hard coral or abit hidden that supposedly difficult to be identified by photos, the
shooting can be done closer to the object as an auxilliary photograph to identify the name of the type
(Figure 12).
Insert photo

5
 Figure 10. Photo taking at the field utilizing UPT method; (a). Position of the scaled tape on the odd
numbered frame, (b). Position of the scaled tape on the even numbered frame.
Figure 11. Illustration of sample withdrawal utilizing Underwater Photo Transec (UPT) method.
Hard corals identification can also be done by writing down the name and the frame number on
underwater paper to facilitate photo analysis. If it is deemed difficult to do, the sample can be taken to
be identified in the lab.
11. Soon after the photo taking session is over, write down name of the station that previously recorded in
photo on the slate and complete it with “done”. This will make easy when photo processing is taking
place.
12. Hereafter, the saved photos in the camera memory card are ready to be neatly arranged before analysis
is done.
Figure 12. Photo frame taken without zoom (left) and with zoom (right) as auxilliary to photo analysis.

6
Data Processing
The photo collection of the reef utilizing UPT method consist of underwater photo data along 50 meter
transect line with 1 meter interval. The number of photo data are abundant and require higher capacity of
databank to preserve. If such data are not very well managed, the photos may unintentionally be exchanged
between different research stations. On this acccount, they should be properly handled by way of
transferring the preserved files in the memory card into separate databank (external harddisc). It is important
to secure out data since the camera might be broken at any time during underwater operation and may cause
damage on the camera memory card.
Measures taken during data processing in terms of underwater photos are as following:
1. After returning from the operation, clean the camera accroding to default procedure by the
manufacurer.
2. Prepare two external harddiscs. The first one is used for data backup (named: Harddisk ORI) and the
second one for data analysis process (named: Harddisk ANA).
To make file management easier, create folders on both external harddiscs with the names according
to the following format:
a. LLLMMMyyyyORI on external harddisc for data backup (Harddisc ORI),
b. LLLMMMyyyyANA on external harddisc data analysis process (Harddisk ANA)
3. Use the ORI Harddisc. Activate the LLLMMMyyyyORI folder that had been prepared, and make
subfolders containing station code /ID sample with LLLCnn format, where:
LLLL is an abbreviation code made of 4 letters which is refering to the location.
The abbreviation code is free but has to be logic and related to the location’s name and unambiguous
from the name of other locations.
Particularlly for COREMAP location, the name should be referring to the name of the station where
the COREMAP data collecting was accomplished in previous phase (since there is similarity on
longitude and latitude) that the LLL code is associated with the previously established code, which
are:
LLL, the first 3 letters show the location (abbreviated with 3 letters), for example BIA (for Biak),
MMR (for Maumere), TPT (for Central Tapanuli), and so on.
L at the 4th letter is written as C, show that the station is a station for coral.
nn shows the station code, for example 01, 02, ..., 12, and so forth.
Example: BIAC02 indicates the data is collected from Station 2 of Biak District.
Hence on the Harddisc ORI (for instance as drive F), the folder becomes:
F:\BIAJUN2014ORI\BIAC02\
4. Reactivate the Harddisc ORI of sub folder LLLLnn located in the LLLMMMyyyyORI folder. Copy
all photo files from the memory card of the camera taken from the station of code LLLLnn.

7
 For instance, LLLLnn code is BIAC02, then all photos taken at BIAC02 site is copied into BIAC02
subfolder. If the files are arranged base on the time the photos were taken, the copied photos are marked
with initial file containing photo slate with”BIAC02” inscription up to the last file containing photo
slate with”BIAC02 completed” inscription.
In such stage, do not change the name of the file inside the memory card of the camera. Leave them
as they are according to the names set by the camera.
5. Undertake step 3 and 4 above for every other LLLLnn codes. So if data collecting can be done in a
day at two different sites, provide 2 subfolders inside the LLLMMMyyyyORI folder.
For example, during the first day the survey was done in the District of Biak has managed to collect
data from two different stations which are BIAC02 and BIAC07stations, there are 2 groups of files
such as following:
o F:\BIAJUN2014ORI\BIAC02\ (containing all photo files taken at BIAC02 station)
o F:\BIAJUN2014ORI\BIAC07\ (containing all photo files taken at BIAC07 station).
6. Copy all subfolders containing station codes aling with files inside in Herddisc ORI into folder of
Harddisc ANA (e.g. Harddisc ANA is located in drive G), that the files will be as following:
o G:\BIAJUN2014ANA\BIAC02\ (containing all photo files take at BIAC02 station),
o G:\BIAJUN2014ANA\BIAC07\ (containing all photo files take ata BIAC07 station).
7. Keep the Harddisc ORI as an archieve as well as databackup. Do not change the file’s name, leave as
it is, as automatically given by the camera. For work and data analysis, use Harddisk ANA.
8. Activate Harddisc ANA. Select the photos to be used for analysis on each station, while those which
are unselected should be deleted from the station folder. Such selection is based on consideration of
accuracy of data retrieval (frame coverage in the photo) and photo sharpness.
Of each station, there are 50 photos containing the whole frame (full frame)(Figure 3 and Figure 5 left)
taken from the 1st meter up to 50th meter along the transec line. Zoomed photos from certain frame (as
auxilliary photos to enable data analysis) are also selected (are not deleted).
9. The selected file names (Phase 8) are based on automatic naming from the applied camera. In order to
enable the analysis, change all file names containing photos of the whole frames (full frame) with new
names by following LLLLnn_xx.jpg format where:
LLLLnn = in accordance with the rule of the above Phase 3.
_ = leave this mark”_” as separator mark.
xx = showing the frame number or photo to the umpteenth meters on the transec line. Value xx is
covering between 01 to 50.
.jpg = shows photo format.
For instance, a photo that is taken at 5th meter on the transec line so the file name is BIAC02_05.jpg
Zoomed photos from particular frames and serve as auxilliary photos (Figure 5 right) follow the same file
naming as above but underlines the word ”zoomed” at the end. Example file: BIAC02_05zoomed.jpg
reveals the auxilliary photo taken at the frame of 5th meter of BIAC02 station.

8
Data Photo Analysis
The data photos are analyzed to retrieve quantitative data such as percent cover of each benthic categories
or substrates. Such data photos can be analyzed using a number of softwares, which are Sigma Scan Pro,
Image J or CPCe.
In order to obtain quantitative data based on underwater photos resulted from the UPT method, the analysis
can be undertaken against each frame by way of selecting number of random point to be used to analyze
the photos. The number of random point used is 30 for each frame, and this is adequatly representative to
estimate the percentage of benthic categories and substrates closing (Giyanto et al., 2010).
Insert photo
Figure 13. Selection of random dot sample.
Based on photo analysis from each frame, the percent cover from benthic categories and substrates can be
calculated by the following formulation:

Number of dots for every category

Percent cover X 100%
a total of dots

LEVEL OF DATA ANALYZER

The category of reef benthos and substrate noted for coral reef data retrieval depends on the purpose and
capacity level of data analyzer. There are three levels of data analyzer:
a. Basic Level
At this level the purpose of research is designated only to find the percentage of the hard corals cover
and non hard corals cover. Thus, the photo data analyzer who maintains only ability to distinguish
between categories of hard corals and non-hard corals is included in this group, despite some experts
have also been practicing the job as long as the purpose of the research is to find out the percentage of
hard corals cover and non-hard corals cover.
b. Intermediate Level
At this level, the purpose of research is to find out all percentage of reef benthos cover and substrate
cover based on category of English et al., (1997). Therefore, the data analyzer is expected to be able to
distinguish all reef benthos and substrate categories dwelling in coral reef ecosystem.
c. Advanced Level
At the advanced level the purpose of the research beside to ensure the percentage of reef benthos cover
and substrates, it is also to find out biodiversity of hard corals. On this account, the data analyzer not
only able to distinguish all category of biota and substrates of the coral reef ecosystem, but also has the
capacity to identify type of hard corals.

9
The illustration of each reef benthos and substrate categories based on English et al. (1997), while the
naming of hard corals genus and species refers to Veron (2000a, 2000b, 2000c).

DATA ENTRY OF PHOTO ANALYSIS RESULT

After the data from the camera is managed in Harddisk ANA (see Data Management Part), thus data entry
of the photo analysis result are as following:
1. Prepare file containing category and substrate codes which are adjusted to the level of data analyzer.
The file has *.txt extension. To accelerate the step, the file should have been restored in file:
coral_code_basic. txt (for basic level analyzer) and file coral_code.txt (for intermediata and advance
level analyzer). The content of coral_code_ basic.txt file and coral_code.txt file can be viewed on
Appendix 1 and Appendix 2.
Figure 14. Initial display of CPCe V4.1 program.

2. Copy the file containing category and substrate codes (coral_code_basic.txt atau coral_code. txt) into
the desired folder. It is recommended to place it in folder C:\ Program Files\CPCe4.1

3. Open CPCe program and display will appear as seen on Figure 14. The reference of this book is based
on CPCe V4.1. program.

4. When the menu pops out, click”Options” menu, select ”Specify file code”, and at the available column
”File name” type on it, or move to folder directory where you save your files on biota and substrate
category. Then press ”Open” button.
By performing this step you have executed CPCe program to read files of reef benthos and subtrate
categories according to the desired file.

5. Open the file you want to make data input. Since there are 50 files to be input for each station, in order
to be more efficient, you do not do it one by one but retrieve all the file at once. Therefore, if you have
completed inputing the first data, then it will automatically save the first file, and the second is open
and ready for input. To perform this, the step is as following:
File →Multiple images/files processing →Process multiple images
Insert photo
Figure 15. Menu Box to create boundary of the desired area analyzed.

6. Select the drive including the folder of the file you want to make an input. Choosing the file can be
done by way of clicking the left button of your mouse on the name of the first file, then hold it and
move it down until the last name of the file you want to make an input. Foe example, the one that you
mark/select is file BIAC02_01 until BIAC02_50 that is located in folder
F:\BIAJUN2014ANA\BIAC02\.

7. Click”Start processing” button and a menu will pop out as seen in Figure15.

8. If the above menu does not show up automatically, then you should provide boundary to the photo
area to be analyzed since the object to analyze are only the reef benthos and the substrate within the

10
 frame. You just click: Mark border →Mark/remark region border.
If the area border or dot selection are have been previously determined, then a warning box will appear
saying if it is applied it will erase the boundary mark and dots that have been previously determined.
Select ”Yes” button by way of clicking it until a menu as seen in Figure 15 appear (see Step 7).

9. Put a check mark on ”Manually size and position the border” selection box, then click ”OK”.
Figure 16. Button to accept/abort the measurement and position of the boundary.
10. Click the left button of the mouse on the left part of the photo frame, hold it and move it down to the
right part of the photo frame until a rectangular line limiting the photo area to be analyzed appears,
and release the left button. Click ”Accept border size and position” button which means you have
accomplished bordering the photo area that you want to analyze (Figure 16).

11. Further you should determine 30 random sampling dots by clicking the Point Overlay menu
→Specify/apply overlay point until the following menu (as seen on Figure 17) appears.
12. Select ”Simple random” and type number ”30” in ”Number of random points” column, then
press”Overlay point” button.
Figure 17. Menu to determine distribution of dots data.
13. Menu ”Point count header information” will appear as seen in Figure 18. Type in information
according to data you want to analyze. When you are done, click ”Save header data” button and click
”Close” button.

14. Step to data input for each photo frame is begun. For each dot pointed out in the photo, type the data
in ”Point Data (30)” Table which is located at the right side according to selected category (Category
Code Table is right below the figure). You can just click the category code Table or you can directly
type in ID column. The display for data input can be seen in Figure 19.
In order to analyze basic level or intermediate level data, simply fill in the ID column according to
category Table that correspond to respective level (basic/intermediate level), while for data analysis of
advance level, beside filling out the ID column, you should also fill in the NOTES column (Figure 19
and Figure 20).
Insert photo
Figure 18. Fill out menu on analyzed data information.
Insert photo
Figure 19. Display for data input.
Insert photo
Figure 20. A table, as part of Figure 19, containing menu to move to next photo.
Table: “Point Data (30): In ID column, type the data according to their category while in NOTES
column put the type (only if hard corals) according to the Table below the picture.
Table : “Category Code and Type of Hard Corals ”. The Category Code of reef benthos and substrate
are all code located in first row (left of TWS code marked by red box), while the code for type of hard
corals located on the next row (righ of TWS code).
11
 Figure 21. Display for saving the analyzed file.

15. After completing filling in all points, press the button as seen on Figure 20 to move to the next photo
file.

16. Once the analysis on the entire photos until the last photo is accomplished, press the button as seen in
Figure 20, and a display will pop up as in Figure 21. Save the file in *.cpc.file format. It is better to
save file *.cpc in the same directory as the photo files.

DISPLAYING THE RESULT OF PHOTO ANALYSIS

When all transect photos are completely analyzed and saved in file with *.cpc format, then the next step is
to display the result of analyzed photos based on reef benthos and substrate categories, and the output will
be displayed in file with *.xls or *.xlsx formats. The steps are as following:
(1). Click the File → Save → Save .cpc file(s) to Excel.
(2). Put in all files (50 files) by way of highlighting all files of where *.cpc files are saved and show the
analysis result (Figure 22). Put the mark on ”New Excel workbook” selection and provide name in ”Transect
name” column. Further, click”Process files” button.
(3). Next, select Excel file format to be produced, whether in the form of ..xlsx or.xls formats. Click OK,
and the process starts. When the process is completed, save the files resulted form the photo analysis and
ready to be opened in Excel format (Figure 23).
Insert photo
Figure 22. Display of cpc file process to Excel.
Insert photo
Figure 23. Example of output in Excel.

12
Reporting
Format of report writing on coral reef monitoring is various and depend on type and format of the report
prepared by the implementor or institution who conducts the monitoring. In general, the sequence of the
format of report writing is as following:

1. Opening Pages
The pages are preliminary pages of a report that are viewed by the readers, which consist of outer and inner
covers, foreword, executive summary, table of content and list of table/picture.

2. Foreword
The foreword of a writing is the most important aspect since it reflects the basic idea on why and how a
research is conducted to address the issues. In such case the foreword is as if a “Window of Information”
from the main idea of why, how and for what a research is aiming to. The foreword consists of (1)
background that bears the reason why such research is undertaken; (2) Issues as the “gap” that causes the
research to be performed; (3) Basic consideration containing specific interest on why such issue has to be
solved and the benefit for scientific development; (4) The purpose contains actions to be taken in order to
discover “something”, where the “something” itself is the most critical issue to solve problems or gaps
existed. As to internal activity report, such as project report, commonly in the foreword the sub title “target”
is inserted which contain Terms of Reference (ToR) aspects that should be fulfilled in order to ensure the
expected final output can be obtain.

3. Methodology
The important parts of the methdology are time, area/location, monitoring sites and the map of monitoring
location along with table of coordinate points of monitoring sites. The methodology also contains data
retrieval method and data analysis, where the narration is a sequence on how to retrieve and process the
related data and information that closely related to the process of achieving goals (as has been establsished
in the foreword) from a research activity (monitoring).

4. Result and Discussion

Display of sub chapter result has to be separated from its sub chapter discussion. The sub chapter result of
a monitoring report provides all obtained data and information according to data processing principle as
mentioned earlier, without analysis. It is simply presenting tables containing result of data processing
according to the analysis and the station locations. The output of data processing can be in the form of
graphic illustrated information.
Presentation of discussion is an interpretation of research output. The meaning of data from the output is
mentioned in the discussion. It can be said as an implication of fulfillment on the purpose of a research that
from the discussion the conclusion can be drawn upon.
13
5. Conclusion and Recommendation
It is important to keep in mind that (1) conclusion is not a series of processed data to be re-presented; (2)
issues that are not the part of research discussion should not be added in the conclusion. The conclusion is
a single and concise paragraph that presenting answer to the purpose of a research.
Recommendation contains important issues related to the fulfillment of solution coming out of established
research output or unsolved issues in the research. It is important to ensure the issues or interests beyond
the context are not inserted as recommendation despite they are deemed important to the author.

6. Biliography
The bibliography is the alphabetical sequence from the references adopted in a monitoring report writing.
Selection upon the most recent year of the reference is important. Scientific journals are best used to support
scientific writing, as they conveys numerous advanced information in the journals instead of textbook. The
preparation of bibliography applies general principle.

7. Apppendix
It is crucial to bear in mind that the primary data does not have to be put in appendix, unless for internal
activity report. Such primary data can be processed into a ‘well-done” information in order to be a part of
the script and do not put the processed data from the primary source in the appendix. As to the unprocessed
primary data but consume larger space on paper, they can be put as appendix to the internal activity report.
Supporting material which are not directly related to the output of the research, such as secondary data and
illustrations, photos and so on which occupy large space of the paper can be attached as appendix.

14
Format of Report Writing
In brief, the format of report writing on coral reef monitoring described as following:
 TITLE (both on outer and inner cover)
 Sheet of Catalog and DOI
 FOREWORD
 SUMMARY
 TABLE OF CONTENT
 LIST OF TABLE
 LIST OF PICTURE
 PREFACE
 METHODOLOGY
 RESULT AND DISCUSSION
 CONCLUSION AND RECOMMENDATION
 BIBLIOGRAPHY
 APPENDIX

15
Bibliography
Brower JE, Zar JH, von Ende CN (1998) Field and laboratory methods for general ecology. WCB
McGraw-Hill, Boston
Burt J, Bartholomew A, Usseglio P. 2008. Recovery of corals a decade after a bleaching event
in Dubai, United Arab Emirates. Mar Biol 154:27-36.
DeVantier, LM; G. De’ath; T.J. Done & E. Turak. 1998. Ecological assessment of a complex natural system: A case study from
the Great Barrier Reef. EcolApplications 8(2): 480–496. English, S; C. Wilkinson& V. Baker. 1997. Survey Manual for Tropical
Marine Resources. Ed ke-2. Townsville: AIMS. 390p.
Giyanto. 2012a. Kajian tentang panjang transek dan jarak antar pemotretan pada penggunaan
metode transek foto bawah air. Oseanologi dan Limnologi di Indonesia 38 (1): 1-18.
Giyanto. 2012b. Penilaian Kondisi Terumbu Karang Dengan Metode Transek Foto Bawah Air.
Oseanologi dan Limnologi di Indonesia 38 (3): 377-390.
Giyanto; B.H. Iskandar; D. Soedharma & Suharsono. 2010. Effisiensi dan akurasi pada proses analisis foto bawah air untuk menilai
kondisi terumbu karang. Oseanologi dan Limnologi di Indonesia 36 (1): 111-130.
Hill, J. &C. Wilkinson. 2004. Methods for Ecological Monitoring of Coral Reefs. Versi ke-1, A Resources
for Managers. Townsville: AIMS. 117 hlm.
Kohler, K.E;M. Gill. 2006. Coral Point Count with Excel extensions (CPCe): avisual basic program for the determination of coral
and substratae coverage using random point count methodology. Comput Geosci 32(9):1259-1269.
Loya Y (1978) Plotless and transect methods. In: Stoddart DR, Johannes RE (eds) Coral reefs:
research methods. UNESCO, Paris, pp 197-217
Lam, K; P.K.S. Shin; R. Bradbeer; D. Randall; K.K.K. Ku; P. Hodgson& S.G. Cheung. 2006. A comparison of video and point
intercept transect methods for monitoring subtropical coral communities. J Exp MarBiol Ecol 333(1): 115-128.
Long, B.G.; G. Andrew; Y.G. Wang& Suharsono. 2004. Sampling accuracy of reef resource
inventory technique. Coral Reefs 23:378-385.
Loya, Y. 1978. Plotless and transect methods. Di dalam: Stoddart DR, Johannes RE, editor. Coral
Reefs: Research Methods.Paris: UNESCO.p.197-217.
Moll, H. 1983. Zonation and diversity of Scleractinia on reefs off S.W. Sulawesi, Indonesia.
Alblasserdam:Drukkery Kanters B.V. 107p.
Mundy, C.N. 1990. Field and Laboratory investigations of the Line Intercept Transect technique for monitoring
the effects of the Crown-of-thorns starfish, Acanthaster planci. Townsville: AIMS. 42p.
Obura, D.O. and Grimsdith, G. (2009). Resilience Assessment of coral reefs – Assessment protocol for coral reefs, focusing on
coral bleaching and thermal stress.IUCN working group on Climate Change and Coral Reefs. IUCN, Gland, Switzerland.70 pp.
Oliver, J; P. Marshall; N. Setiasih&L. Hansen. 2004. A global protocol for assessment and monitoring
of coral bleaching.[Penang]: WorldFish Center and WWF Indonesia. 35p.
Sukmara, A; A.J. Siahainenia& C. Rotinsulu. 2001. Panduan Pemantauan Terumbu Karang Berbasis-Masyarakat Dengan Metoda
Manta Tow. Jakarta: Proyek Pesisir-CRMP Indonesia.

16
Appendix 1
File content: coral_code_basic.txt
DFDFDF AFAFAF 3
“HC”,”Coral”,DFDFDF “NC”,”Non Coral”,DFDFDF “TWS”,”Tape, wand, shadow”,FF0000 “HC”,”Hard Coral”,”HC”
“NC”,”Non Coral”,”NC” “TWS”,”Tape, Wand, Shadow”,”TWS” NOTES,NOTES,NOTES

17
Appendix 2
File content: coral_code.txt
DFDFDF AFAFAF 12
“HC”,”Coral”,DFDFDF “DC”,”Recent Dead Coral”,DFDFDF “DCA”,”Dead Coral with Algae”,DFDFDF “SC”,”Soft
Coral”,DFDFDF “SP”,”Sponge”,DFDFDF “FS”,”Fleshy Seaweed”,DFDFDF “OT”,”Other Biota”,DFDFDF
“R”,”Rubble”,DFDFDF “S”,”Sand”,DFDFDF “SI”,”Silt”,DFDFDF “RK”,”Rock”,DFDFDF “TWS”,”Tape, wand,
shadow”,FF0000 “ACB”,”Acropora Branching”,”HC” “ACE”,”Acropora Encrusting”,”HC” “ACS”,”Acropora
Submassive”,”HC” “ACD”,”Acropora Digitate”,”HC” “ACT”,”Acropora Tabulate”,”HC” “CB”,”Coral Branching”,”HC”
“CE”,”Coral Encrusting”,”HC” “CF”,”Coral Foliose”,”HC” “CM”,”Coral Massive”,”HC” “CS”,”Coral Submassive”,”HC”
“CMR”,”Coral Mushroom”,”HC” “CHL”,”Coral Heliopora”,”HC” “CME”,”Coral Millepora”,”HC” “CTU”,”Coral
Tubipora”,”HC” “DC”,”Recently Dead Coral”,”DC” “DCA”,”Dead Coral with algae”,”DCA” “SC”,”Soft Coral”,”SC”
“SP”,”Sponge”,”SP” “ZO”,”Zoanthid”,”OT” “OT”,”Other(Fauna)”,”OT” “AA”,”Algal assemblage”,”FS” “CA”,”Coralline
algae”,”OT” “HA”,”Halimeda”,”OT” “MA”,”Makro Algae”,”FS” “TA”,”Turf Algae”,”DCA” “S”,”Sand”,”S” “R”,”Rubble”,”R”
“SI”,”Silt”,”SI” “RK”,”Rock”,”RK” “TWS”,”Tape, Wand, Shadow”,”TWS” NOTES,NOTES,NOTES “ACASP”,”Acropora
aspera”,”NA” “ACBRU”,”Acropora brueggemanni”,”NA” “ACCAR”,”Acropora carduus”,”NA” “ACCER”,”Acropora
cerealis”,”NA” “ACCLA”,”Acropora clathrata”,”NA” “ACCYT”,”Acropora cytherea”,””NA” “ACDIG”,”Acropora
digitifera”,”NA” “ACDIV”,”Acropora divaricata”,”NA” “ACECH”,”Acropora echinata”,”NA” “ACFLO”,”Acropora
florida”,”NA” “ACFOR”,”Acropora formosa”,”NA” “ACGEM”,”Acropora gemmifera”,”NA” “ACHUM”,”Acropora
humilis”,”NA” “ACHYA”,”Acropora hyacinthus”,”NA” “ACLAT”,”Acropora latistella”,”NA” “ACLON”,”Acropora
longicyathus”,”NA” “ACLOR”,”Acropora loripes”,”NA” “ACMIC”,”Acropora microphthalma”,”NA” “ACMIL”,”Acropora
millepora”,”NA” “ACMON”,”Acropora monticulosa”,”NA” “ACNAS”,”Acropora nasuta”,”NA” “ACPAL”,”Acropora
palifera”,”NA” “ACPRO”,”Acropora prostrata”,”NA” “ACPUL”,”Acropora pulchra”,”NA” “ACSAM”,”Acropora
samoensis”,”NA” “ACSAR”,”Acropora sarmentosa”,”NA” “ACSEC”,”Acropora secale”,”NA” “ACSUB”,”Acropora
subglabra”,”NA” “ACTEN”,”Acropora tenuis”,”NA” “ACVAL”,”Acropora valida”,”NA” “ACVER”,”Acropora verweyi”,”NA”
“ACYON”,”Acropora yongei”,”NA” “ACSP.”,”Acropora sp.”,”NA” “ALCAT”,”Alveopora catalai”,”NA” “ALSP.”,”Alveopora
sp.”,”NA” “ANPUE”,”Anacropora puertogalerae”,”NA” “ANSP.”,”Anacropora sp.”,”NA” “ASGRA”,”Astreopora
gracilis”,”NA” “ASMYR”,”Astreopora myriophthalma”,”NA” “ASSP.”,”Astreopora sp.”,”NA” “BAAMI”,”Barabattoia
amicorum”,”NA” “BASP.”,”Barabattoia sp.”,”NA” “CAFUR”,”Caulastrea furcata”,”NA” “CASP.”,”Caulastrea sp.”,”NA”
“COMAY”,”Coeloseris mayeri”,”NA” “COSP.”,”Coeloseris sp.”,”NA” “CTECH”,”Ctenactis echinata”,”NA”
“CTSP.”,”Ctenactis sp.”,”NA” “CYAGA”,”Cyphastrea agassizi”,”NA” “CYCHA”,”Cyphastrea chalcidicum”,”NA”
“CYMIC”,”Cyphastrea microphthalma”,”NA” “CYSER”,”Cyphastrea serailia”,”NA” “CYSP.”,”Cyphastrea sp.”,”NA”
“DIHEL”,”Diploastrea heliopora”,”NA” “DISP.”,”Diploastrea sp.”,”NA” “ECGEM”,”Echinopora gemmacea”,”NA”
“ECHOR”,”Echinopora horrida”,”NA” “ECLAM”,”Echinopora lamellosa”,”NA” “ECSP.”,”Echinopora sp.”,”NA”
“EUANC”,”Euphyllia ancora”,”NA” “EUGLA”,”Euphyllia glabrescens”,”NA” “EUSP.”,”Euphyllia sp.”,”NA”
“FAFAV”,”Favia favus”,”NA” “FAMAR”,”Favia maritima”,”NA” “FAMAT”,”Favia matthaii”,”NA” “FAPAL”,”Favia
pallida”,”NA” “FARTM”,”Favia rotumana”,”NA” “FARTN”,”Favia rotundata”,”NA” “FASPE”,”Favia speciosa”,”NA”
“FAVER”,”Favia veroni”,”NA” “FASP.”,”Favia sp.”,”NA” “FTABD”,”Favites abdita”,”NA” “FTCHI”,”Favites
chinensis”,”NA” “FTCOM”,”Favites complanata”,”NA” “FTFLE”,”Favites flexuosa”,”NA” “FTHAL”,”Favites halicora”,”NA”
“FTPAR”,”Favites paraflexuosa”,”NA” “FTPEN”,”Favites pentagona”,”NA” “FTRUS”,”Favites russelli”,”NA”
“FTSP.”,”Favites sp.”,”NA” “FUCON”,”Fungia concinna”,”NA” “FUDAN”,”Fungia danai”,”NA” “FUFUN”,”Fungia
fungites”,”NA” “FUGRA”,”Fungia granulosa”,”NA” “FUPAU”,”Fungia paumotensis”,”NA” “FUREP”,”Fungia repanda”,”NA”
“FUSP.”,”Fungia sp.”,”NA” “GLAST”,”Galaxea astreata”,”NA” “GLFAS”,”Galaxea fascicularis”,”NA” “GLSP.”,”Galaxea
sp.”,”NA” “GSEDW”,”Goniastrea edwardsi”,”NA” “GSFAV”,”Goniastrea favulus”,”NA” “GSPAL”,”Goniastrea
palauensis”,”NA” “GSPEC”,”Goniastrea pectinata”,”NA” “GSRAM”,”Goniastrea ramosa”,”NA” “GSRET”,”Goniastrea
retiformis”,”NA” “GSSP.”,”Goniastrea sp.”,”NA” “GOCOL”,”Goniopora columna”,”NA” “GOLOB”,”Goniopora lobata”,”NA”
“GOMIN”,”Goniopora minor”,”NA” “GOSTO”,”Goniopora stokesi”,”NA” “GOTNL”,”Goniopora tenella”,”NA”
“GOTND”,”Goniopora tenuidens”,”NA” “GOSP.”,”Goniopora sp.”,”NA” “HECOE”,”Heliopora coerulea”,”NA”
“HESP.”,”Heliopora sp.”,”NA” “HRLIM”,”Herpolitha limax”,”NA” “HRWEB”,”Herpolitha weberi”,”NA”
“HRSP.”,”Herpolitha sp.”,”NA” “HYEXE”,”Hydnophora exesa”,”NA” “HYMIC”,”Hydnophora microconos”,”NA”
“HYPIL”,”Hydnophora pilosa”,”NA” “HYRIG”,”Hydnophora rigida”,”NA” “HYSP.”,”Hydnophora sp.”,”NA”

18
“LAPRU”,”Leptastrea pruinosa”,”NA” “LAPUR”,”Leptastrea purpurea”,”NA” “LATRA”,”Leptastrea transversa”,”NA”
“LASP.”,”Leptastrea sp.”,”NA” “LEIRR”,”Leptoria irregularis”,”NA” “LEPHR”,”Leptoria phrygia”,”NA” “LESP”,”Leptoria
sp.”,”NA” “LIUND”,”Lithophyllon undulatum”,”NA” “LISP.”,”Lithophyllon sp.”,”NA” “LOHAT”,”Lobophyllia hataii”,”NA”
“LOHEM”,”Lobophyllia hemprichii”,”NA” “LOSP.”,”Lobophyllia sp.”,”NA” “MEAMP”,”Merulina ampliata”,”NA”
“MESCA”,”Merulina scabricula”,”NA” “MESP.”,”Merulina sp.”,”NA” “MIDIC”,”Millepora dichotoma”,”NA”
“MIEXE”,”Millepora exesa”,”NA” “MIPLA”,”Millepora platyphylla”,”NA” “MITEN”,”Millepora tenella”,”NA”
“MISP.”,”Millepora sp.”,”NA” “MOCUR”,”Montastrea curta”,”NA” “MOVAL”,”Montastrea valenciennesi”,”NA”
“MOSP.”,”Montastrea sp.”,”NA” “MPAEQ”,”Montipora aequituberculata”,”NA” “MPCAL”,”Montipora caliculata”,”NA”
“MPCAP”,”Montipora capricornis”,”NA” “MPCON”,”Montipora confusa”,”NA” “MPCRA”,”Montipora
crassituberculata”,”NA” “MPDEL”,”Montipora delicatula”,”NA” “MPDIG”,”Montipora digitata”,”NA” “MPFOL”,”Montipora
foliosa”,”NA” “MPHIS”,”Montipora hispida”,”NA” “MPINF”,”Montipora informis”,”NA” “MPMIL”,”Montipora
millepora”,”NA” “MPMON”,”Montipora monasteriata”,”NA” “MPNOD”,”Montipora nodosa”,”NA” “MPORI”,”Montipora
orientalis”,”NA” “MPPEL”,”Montipora peltiformis”,”NA” “MPTUR”,”Montipora turgescens”,”NA” “MPUND”,”Montipora
undata”,”NA” “MPVEN”,”Montipora venosa”,”NA” “MPSP.”,”Montipora sp.”,”NA” “MYELE”,”Mycedium
elephantotus”,”NA” “MYSP.”,”Mycedium sp.”,”NA” “OXLAC”,”Oxypora lacera”,”NA” “OXSP.”,”Oxypora sp.”,”NA”
“PARUG”,”Pachyseris rugosa”,”NA” “PASPE”,”Pachyseris speciosa”,”NA” “PASP.”,”Pachyseris sp.”,”NA”
“PVCAC”,”Pavona cactus”,”NA” “PVCLA”,”Pavona clavus”,”NA” “PVDEC”,”Pavona decussata”,”NA” “PVFRO”,”Pavona
frondifera”,”NA” “PVVEN”,”Pavona venosa”,”NA” “PVSP.”,”Pavona sp.”,”NA” “PEALC”,”Pectinia alcicornis”,”NA”
“PELAC”,”Pectinia lactuca”,”NA” “PESP.”,”Pectinia sp.”,”NA” “PLDAE”,”Platygyra daedalea”,”NA” “PLLAM”,”Platygyra
lamellina”,”NA” “PLPIN”,”Platygyra pini”,”NA” “PLSIN”,”Platygyra sinensis”,”NA” “PLSP.”,”Platygyra sp.”,”NA”
“PCDAM”,”Pocillopora damicornis”,”NA” “PCEYD”,”Pocillopora eydouxi”,”NA” “PCVER”,”Pocillopora verrucosa”,”NA”
“PCSP.”,”Pocillopora speciosa”,”NA” “PRANN”,”Porites annae”,”NA” “PRCYL”,”Porites cylindrica”,”NA”
“PRHOR”,”Porites horizontalata”,”NA” “PRLAT”,”Porites latistella”,”NA” “PRLIC”,”Porites lichen”,”NA” “PRLOB”,”Porites
lobata”,”NA” “PRLUT”,”Porites lutea”,”NA” “PRNEG”,”Porites negrosensis”,”NA” “PRNIG”,”Porites nigrescens”,”NA”
“PRRUG”,”Porites rugosa”,”NA” “PRRUS”,”Porites rus”,”NA” “PRSOL”,”Porites solida”,”NA” “PRSP.”,”Porites sp.”,”NA”
“PSCON”,”Psammocora contigua”,”NA” “PSDIG”,”Psammocora digitata”,”NA” “PSSP.”,”Psammocora sp.”,”NA”
“SAROB”,”Sandalolitha robusta”,”NA” “SASP.”,”Sandalolitha sp.”,”NA” “SCAUS”,”Scolymia australis”,”NA”
“SCSP.”,”Scolymia sp.”,”NA” “SECAL”,”Seriatopora caliendrum”,”NA” “SEHYS”,”Seriatopora hystrix”,”NA”
“SESP.”,”Seriatopora sp.”,”NA” “STARM”,”Stylocoeniella armata”,”NA” “STPIS”,”Stylophora pistillata”,”NA”
“STSP.”,”Stylophora sp.”,”NA” “SYAGR”,”Symphyllia agaricia”,”NA” “SYRAD”,”Symphyllia radians”,”NA”
“SYREC”,”Symphyllia recta”,”NA” “SYVAL”,”Symphyllia valenciennesii”,”NA” “SYSP.”,”Symphyllia sp.”,”NA”
“CAUL”,”Caulerpa sp.”,”NA” “PADI”,”Padina sp.”,”NA” “SARG”,”Sargassum sp.”,”NA” “TURAL”,”Turbinaria
sp.(algae)”,”NA” “LOBP”,”Lobophytum sp.”,”NA” “SARC”,”Sarcophyton sp.”,”NA” “SINU”,”Sinularia sp.”,”NA”
“XENI”,”Xenia sp.”,”NA” “ASCI”,”Ascidian”,”NA” “CRIN”,”Crinoid”,”NA” “ECHI”,”Echinoid”,”NA”
“GORG”,”Gorgonian”,”NA” “ANEM”,”Sea anemone”,”NA” “TRID”,”Tridacna sp.”,”NA”

19
Appendix 3
Description of reef benthic categories and substrate
Acropora (AC)

Acropora Branching (ACB) Acropora Tabulate (ACT) Acropora Digitata (ACD)

Acropora corals in the form of branched Acropora corals in the form of a table Acropora corals like finger colonies
colonies colonies

Acropora Submassive Acropora Encrusting

(ACS) (ACE)
Acropora corals in the form of sub- Acropora corals in the form of
massive colonies encrusting colonies

Non Acropora (NA)

Coral Branching ( CB) Coral Massive (CM) Coral Submassive (CS)

Non Acropora Corals with branched Non Acropora Corals with massive Non Acropora Coral with submassive
colonies colonies colonies

Coral Encrusting (CE) Coral Foliosa (CF) Coral Mushroom (CMR)

Non Acropora Corals with encrusting Non Acropora coral in the form of Non Acropora form like mushrooms,
colonies flate colonies or like leaves, the edge colonies do not stick to the base
of the colony is not attached to the substrate
substrate.

20
Photo Abrar 2008
Coral Millepora (CME) Coral Heliopora (CHL) Coral Tubifora (CTU)
Includes a calcareous soft coral group, Includes a calcareous soft coral group, Includes a group of soft corals with a
with branching life form, flate, and flate colonies, if the part of the colony frame such as a multilevel red pipe.
encrusting, and they are also called as a is broken it will see the blue part in it,
fire coral. so it is also known as the blue coral.

Soft Coral (SC)

Soft coral group from the Octocoralia Subclassic, Anthoza Class, soft colonies with spicular skeletons, diverse colony shapes

Source www.whittenfamily.com Source www.accessnoaa.noaa.gov Source: www.roatan.ws

Sponge (SP)
All groups of marine sponges, from the Phylum Porifera, form a multi-colored colony, from soft, hard or rough, consisting
of a spicule frame

21
Coraline Algae (CA) Algae Hallimeda (HA) Zooanthid (ZO)
Included calcareous algae, The calcareous algae group with thalus Benthos reef group from Anthozoa
encrusting, brick red color, is green, the plate form is vertically Philum Cnidaria, a sub class of
brown color arranged, sometimes it is found Hexacoralia, the order of Zoantharia,
abundantly and forms Halimeda generally colonizes many individual
limesand, polyps. The soft body has no frame,
the stolon is the part of the network
that connects each polyp in the colony.
The main characteristic of the
zooanthid is that all the tentacles are
exactly at the edge of the mouth plate
(coenosarc).

Photo: Abrar 2007 Source www.biology.unm.edu

Macro Algae (MA)
All groups of thalus algae from the Clorophyta family, Rhodophyta and

Photo: Abrar 2017 Photo Abrar 2017 Photo Abrar 2017

Turf Algae (TA)
A group of algae with thalus such as a filamentous form of thalus like fine threads, moss or hair.

22
Death Coral (DC)
Dead coral, characterized by white colonies of chalk, without tissue coral polyps (Source: www.aims.org)

Sourcer: www.aims.org
Death Coral With Algae (DCA)
Dead coral, characterized by white colonies of chalk, without tissue coral polyps.

Photo Abrar 2008

Photo Abrar 2016 Photo Abrar 2016 Photo Abrar 2016

Others (OT)
Other benthic biota groups associated with coral reefs include mollusks, echinoderms, crustaceans, tunicates,
bryozoans and anemones.
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 Silt (SI) Sand (S)
The muddy bottom, the grain is smoother The sandy bottom, grain is coarser, if touched it
and softer, if touched the water will be will quickly settle back and usually does not
cloudy and long clear again. make the water cloudy.

Ruble (R)
Dead coral fragments are 10-15 cm in size, separated from each other, algae and coraline algae are not grown.

Source: www.mariculturetechnology.com
Rock (RCK)
Hard bottom come from volcanic stone and others hard material, which they were indicated by rocky beach.

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