CORAL COMMUNITY STRUCTURE IN TIOMAN ISLAND MARINE PARK, MALAYSIA:

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CORAL COMMUNITY STRUCTURE IN TIOMAN ISLAND MARINE PARK, MALAYSIA:

FURTHER EMPHASIS ON HARD CORAL DISEASE AND PATHOGENIC Vibrio spp.

BY

MOHD FIKRI AKMAL BIN MOHD KHODZORI

A thesis submitted in fulfilment of the requirement for the degree of Doctor of Philosophy (Biosciences)

Kulliyyah of Science

International Islamic University Malaysia

FEBRUARY 2021

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ABSTRACT

Tioman Island has a remarkably high coral diversity. Hence, evaluating the coral health status in this Marine Park is important for sustainable reef ecosystem management. This study aims to determine the reef condition, coral distribution and disease prevalence using Coral Video Transect (CVT) method at twenty reef sites and two different depths around the east coast, west coast and the isolated zones of Tioman Island Marine Park (TIMP). Coral Point Count with Excel extension (CPCe) software was used to measure the coral coverage and disease prevalence. The present results indicated that Tioman reefs were in ‘fair’ average condition with the live corals cover 48.0% ± 0.7. Besides, 254 species from 61 genera and 15 families of the scleractinian hard corals were identified at all reef sites. Following the scleractinian taxonomic classification, coral surveys and past studies revealed 355 species from 67 genera and 15 families with an additional 30 new species records for TIMP and 15 species for the east coast of Peninsular Malaysia. Current data at this island also presented 29 rare, 86 vulnerable, 3 endangered scleractinian species. Moreover, visual photographic analysis using the CPCe software was recorded 77 genera from 24 families of hard and soft corals with mixed morphologies of branching Acropora, foliose Montipora and massive Porites corals predominantly found in reef assemblages. Extensive coastal development and widespread of tourism activities may have influenced on the variations of reef condition and coral distribution in the study area. In addition to coral disease prevalence, the findings showed lower severity of diseased (5.8% ± 0.8) and compromised (28.8% ± 2.5) compared to healthy (65.4% ± 2.6) coral colonies in TIMP. Reef sites with the highest concentration of tourism exhibited a high prevalence of coral diseases and signs of compromised health. Among the six identified coral diseases, yellow band disease/

YBD (1.70% ± 0.8) had the highest prevalence followed by ulcerative white spots/

UWS (1.14% ± 0.2) and white syndrome/ WS (1.08% ± 0.3). Meanwhile, algal and sponge overgrowth/ ASO (11.86% ± 2.3), sediment necrosis/ SN (7.05% ± 0.9), predation scars/ PS (5.60% ± 0.8) and physical damage/ PD (2.06% ± 0.8) were the most prevalence among eight identified states of coral compromised health. Altogether, 33 scleractinian genera were affected, with Fungia predominantly affected by YBD (>

30% colonies), while Porites and Acropora were affected by UWS and WS (11 - 20%

colonies), respectively. In continuation, the pathogenic Vibrio spp. isolated from WS infected corals (Acropora and Montipora) were identified using biochemical and molecular techniques. The infected coral tissues were confirmed based on the histological examination. A total of one hundred representative Vibrio isolates were characterized and most of them (n = 50) were identified as V. vulnificus, V. alginolyticus and Photobacterium damselae following the API 20NE kit. The 16S rRNA gene sequencing revealed six Vibrio spp. (V. coralliilyticus, V. hepatarius, V. brasiliensis, V.

tubiashi, V. campbellii and V. ishigakensis) and one P. rosenbergii. V. coralliilyticus, isolated from the infected corals also had the highest mean prevalence (45.4% ± 6.7) at three selected reef sites in TIMP. Such elevated of water temperatures and nutrient parameters may increase the Vibrio bacterial prevalence. As a conclusion, the data presented in this study constitutes the baseline information on coral health and disease prevalence, including the possible causal agents associated with WS disease sign for comprehensive coral conservation in the marine protected area of Tioman Island.

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ثحبلا ةصلاخ

ABSTRACT IN ARABIC

ةقيدلحا هذه في ةيناجرلما باعشلل ةيحصلا ةلالحا مييقت نإف ،ثم نمو. ظوحلم لكشب عفترم نياجرم عونت اهيدل نامويت ةريزج اهعيزوتو ةيناجرلما باعشلا ةلاح ديدتح لىإ ةساردلا هذه فدته. ةيناجرلما باعشلل يئيبلا ماظنلل ةمادتسلما ةرادلإل مهم ةيرحبلا ةقيرط مادختسبا ضارملأا راشتناو Coral Video Transect (CVT) ينقمعو ةيناجرلما باعشلل اًعقوم نيرشع في يرحبلا نامويت ةريزج هزتنم في ةلوزعلما قطانلماو بيرغلا لحاسلاو يقرشلا لحاسلا لوح ينفلتمخ (TIMP). جمنارب مادختسا تم Coral Point Count (CPCe) جمنارب عم (Excel) تراشأ. ضارملأا راشتناو ةيناجرلما باعشلا ةيطغت سايقل 0.7± ٪48.0 ةيلحا ةيناجرلما باعشلا يطغت ثيح" ةلدتعم" ةطسوتم ةلاح في تناك نامويت باعش نأ لىإ ةيلالحا جئاتنلا.

ةيناجرلما باعشلا عقاوم عيجم في ةبلصلا ةيناجرلما باعشلا نم ةلئاع 15 و اًسنج 61 نم اًعون 254 ديدتح تم ، كلذ بناج لىإ.

ةلئاع 15 و اًسنج 67 نم اًعون 355 نع ةقباسلا تاساردلاو ةيناجرلما تاحوسلما تفشك ، بلصتلما يفينصتلا فينصتلا دعب تلاجس نم اًديدج اًعون 30 عم TIMP هذه في ةيلالحا تناايبلا تمدق. يازيلام ةريزج هبشل يقرشلا لحاسلل اًعون 15 و ليلتح ليجست تم ،كلذ ىلع ةولاع. ضارقنلابا ةددهلما بلصتلما عونلا نم اًعاونأ 3 و اًفيعض 86 و اًردنااًعون 29 اًضيأ ةري زلجا جمنارب مادختسبا يئرم فيارغوتوف CPCe لاكشلأا عم ةمعانلاو ةبلصلا ةيناجرلما باعشلا نم ةلئاع 24 نم اًسنج 77 ـل نم ةطلتخلما Acropora ، و Montipora و Porites دق. ةيناجرلما باعشلا تاعمتج في بلاغلا في ةدوجولما ةمخضلا ةقطنم في اهعيزوتو ةيناجرلما باعشلا ةلاح في تايرغتلا في رثأ ةيحايسلا ةطشنلأل عساولا راشتنلااو ةعساولا ةيلحاسلا ةيمنتلل نوكي 28.8رطخلل ضرعلماو 0.8± ٪5.8 ضرلما ةدش في ا ًضافنخا جئاتنلا ترهظأ ،ناجرلما ضارمأ راشتنا لىإ ةفاضلإبا. ةساردلا٪

± 2.5 في 2.6± 65.4ةيحصلا ةيناجرلما باعشلا تارمعتسبم ةنراقم TIMP. ىلعأ تاذ ةيناجرلما باعشلا عقاوم ترهظأ اهديدتح تم تيلا ةتسلا ةيناجرلما باعشلا ضارمأ ينب نم. ةحصلا ىلع لدت تاملاعو ةيناجرلما ضارملأل اًيربكاًراشتنا ةحايسلل زيكرت

، رفصلأا طيرشلا ضرلم ناك / YBD (1.70٪ ± 0.8) ةيحرقتلا ءاضيبلا عقبلا هيلي راشتنا لدعم ىلعأ / UWS (1.14٪

± 0.2) ءاضيبلا ةمزلاتلماو / WS (1.08٪ ± 0.3). جنفسلإاو بلاحطلا ونم ناك ،هسفن تقولا فيو / ASO (11.86٪

± 2.3) ، بساورلا رنخ / SN (7.05٪ 0.9) ، ساترفلاا بودن / PS (5.60٪ ± 0.8) ةيدالما رارضلأاو /PD (2.06٪

± 0.8) بلصتلما عونلا نم ًاسنج 33 رثتأ ، ًلااجمإ. ةحصلا رطخلل ناجرلما نم ةددمح تلااح نياثم ينب راشتنا رثكلأا يه ، ـب يساسأ لكشب تيارطفلا ترثتأ ثيح YBD (> 30٪) تارمعتسم ترثتأ امنيب ،تارمعتسم Porites و Acropora ـب UWS و WS (11-20٪) ضرملما لماعلا نإف ، كلذل اًرارمتسا. لياوتلا ىلع Vibrio spp باعشلا نم هلزع تم ـب ةباصلما ةيناجرلما WS (Acropora و Montipora) ةباصإ ديكتأ تم. ةيئيزلجاو ةيويلحا ءايميكلا تاينقت مادختسبا نم ةيليثتم ةلزع ةئام هعوممج ام زييتم تم. يجيسنلا صحفلا ىلع ًءانب ةيناجرلما ةجسنلأا Vibrio اهمظعم ديدتح تمو (n = 50) انهأ ىلع V. vulnificus و V. alginolyticus و Photobacterium damselae ةعوممج دعب API 20NE. 16 نييلجا لسلستلا فشكS rRNA ةتس نع Vibrio spp. (V. coralliilyticus و V.

hepatarius و V. brasiliensis و V. tubiashi و V. campbellii و V. ishigakensis) و P.

rosenbergii. تلجس امك V. coralliilyticus 45.4 راشتنا لدعم ىلعأ ةباصلما ةيناجرلما باعشلا نم ةلوزعلما٪ ± 6.7) في ةراتمخ ةيناجرم عقاوم ةثلاث في TIMP. راشتنا ةدياز لىإ ةيئاذغلا تاملعلماو ءالما ةرارح تاجرد عافترا يدؤي دق ضارملأا راشتناو ةيناجرلما باعشلا ةحص نع ةيساسأ تامولعم ةساردلا هذه في ةمدقلما تناايبلا لكشت ، ماتلخا في. يايرتكبلا ، ضرم ةملاعب ةطبترلما ةلمتلمحا ةببسلما لماوعلا كلذ في ابم WS ةيرحبلا ةقطنلما في ةيناجرلما باعشلل لماشلا ظافلحا لجأ نم نامويت ةريزلج ةيملمحا

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APPROVAL PAGE

The thesis of Mohd Fikri Akmal has been approved by the following:

_____________________________

Shahbudin Saad Supervisor

_____________________________

Nur Nazifah Mansor Co-Supervisor

_____________________________

Normawaty Mohamad Noor Internal Examiner

_____________________________

Zaidi Che Cob External Examiner

_____________________________

Zaidnudin Bachok External Examiner

_____________________________

Norlelawati A. Talib Chairman

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DECLARATION

I hereby declare that this thesis is the result of my own investigations, except where otherwise stated. I also declare that it has not been previously or concurrently submitted as a whole for any other degrees at IIUM or other institutions.

Mohd Fikri Akmal Bin Mohd Khodzori

Signature ... Date ...

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vi COPYR

IG

INTERNATIONAL ISLAMIC UNIVERSITY MALAYSIA

DECLARATION OF COPYRIGHT AND AFFIRMATION OF FAIR USE OF UNPUBLISHED RESEARCH

CORAL COMMUNITY STRUCTURE IN TIOMAN ISLAND MARINE PARK, MALAYSIA:

FURTHER EMPHASIS ON HARD CORAL DISEASE AND PATHOGENIC Vibrio spp.

I declare that the copyright holders of this thesis are jointly owned by the student and IIUM.

No part of this unpublished research may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise without prior written permission of the copyright holder except as provided below

1. Any material contained in or derived from this unpublished research may be used by others in their writing with due acknowledgement.

2. IIUM or its library will have the right to make and transmit copies (print or electronic) for institutional and academic purposes.

3. The IIUM library will have the right to make, store in a retrieved system and supply copies of this unpublished research if requested by other universities and research libraries.

By signing this form, I acknowledged that I have read and understand the IIUM Intellectual Property Right and Commercialization policy.

Affirmed by Mohd Fikri Akmal Bin Mohd Khodzori

……..……….. ………..

Signature Date

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This thesis is dedicated to those who are sharing my passion for conserving coral reef ecosystems

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ACKNOWLEDGEMENTS

Alhamdulillah, all praise to Allah S. W. T. for giving me the strength throughout my PhD journey and guidance in overcoming challenges while completing this thesis. First and foremost, my deepest appreciation to my supervisor, Prof. Dr. Shahbudin Saad and co-supervisor, Asst. Prof. Dr. Nur Nazifah Mansor for supervision, guidance and encouragement throughout the completion of this PhD research. I have immense pleasure in expressing my sincere gratitude to both of you who have generously shared the suggestions and constructive criticisms at various stages from the beginning of the research proposal until this successfully completed thesis. In fact, this thesis would not have been possible to complete without your timely help and support. I am extremely grateful and your guidance will never be forgotten.

In particular, millions of thanks to all staff members from the Department of Biotechnology, Department of Marine Science, INOCEM Research Station, and the Central Research and Animal Facility, Kulliyyah of Science for giving me permission to use equipments, instruments and transports to conduct all the research works. Special thanks are also extended to Br. Khairul, Br. Azizul, Br. Muzammil, Br. Azwan, Br.

Masrul, Br. Saiful, Br. Taufik, Sr. Noorshamriza, Sr. Adah, Sr. Azlin and Sr. Liza for their assistance during the research progress of this study. I am also would like convey my sincere appreciation to Dr. Normawaty, Dr. Zaini, Dr. Zuhairi, Dr. Aimi. Dr. Wafi and Dr. Latif for giving me some encouraging words. Many thanks are also given to my colleagues from Fish Disease Lab, Sr. Amalin, Sr. Nadiah and Sr. Syakira for providing me assistance and consultation regarding biochemical and molecular works and also SeaQuest diving team, Br. Hamizan and Br. Faiz, for helping me to conduct samplings.

For my beloved wife, Nurfadhilah Mohamad Nizam as well as my beloved parents, Khodzori Sanusi and Rosmaidah Zuhdi, thank you very much for giving me moral support and motivation in completing my research works. Last but not least, I remain indebted to all my friends, Br. Fikri, Br. Addin, Br. Shanil, Br. Mutaqin, Sr.

Nani and those who are directly or indirectly involved in providing me the relief for the past three years of research activities. This project was fully funded by the E-Science Grant (SF16-002-0071) from Ministry of Energy, Science, Technology, Environment and Climate Change (MESTECC), Malaysia and partially supported by the Young Environmental Research Grant under Malaysian Nature Society (MNS). Jazakallahu Khairan Kathira. May Allah bless our efforts to disseminate the scientific knowledge for the ummah.

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LIST OF TABLES

Table No. Page No.

2.1 List of Previous Studies on the Taxonomic Revision of Scleractinian Corals Based on Morphological and Molecular Perspectives 19 2.2 Previous Records of Scleractinian Coral Species in Tioman Island

Marine Park 25

3.1 Locality Data of Survey Reef Sites and Transect Depths for Shallow

and Deep-Water Areas in Tioman Island Marine Park 53

4.1 List of Corals Used for Image Analysis in the CPCe Software 60 4.2 List of Benthic Communities Used for Image Analysis in the CPCe

Software 61

4.3 Three Coral Morphology Categories (Ruderal: r, Competitors: K and

Stress-tolerators: S) 65

4.4 ANOVA Test Analysis for Six Benthic Categories among Reef Sites

in Tioman Island 68

4.5 Mean Percentage Cover (% ± SE) of Six Benthic Categories at 20 Reef

Sites in Tioman Island 69

4.6 ANOVA Test Analysis for Six Benthic Categories among Depths in

Tioman Island 71

4.7 ANOVA Test Analysis for Three Benthic Categories among Reef

Sites and Zones in Tioman Island 72

4.8 Mean Percentage Cover (% ± SE) of Three Major Benthic Categories and Coral Condition at 20 Reef Sites in Tioman Island 73 4.9 List of Scleractinian Hard Coral Species at 20 Reef Sites in Tioman

Island 75

4.10 Checklist of Scleractinian Hard Coral Species in Tioman Island 87 4.11 Mean Percentage Cover of Coral Family and Genera at 20 Reef Sites

in Tioman Island 99

4.12 Diversity and Abundance Patterns of Coral Genera at 20 Reef Sites in

Tioman Island 103

4.13 Mean Percentage Cover, Diversity and Abundance Patterns of Coral

Genera at Two Depths in Tioman Island 108

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4.14 ANOVA Test Analysis for Mean Values of Simpson (D), Shannon- Weiner (H’) and Evenness (J’) Indexes among Reef Sites, Zones and

Depths in Tioman Island 111

4.15 Total Genera and Mean Values of Simpson (D), Shannon-Weiner (H’)

and Pielou (J’) Indexes at 20 Reef Sites in Tioman Island 112 4.16 Total Genera and Mean Values of Simpson (D), Shannon-Weiner (H’)

and Evenness (J’) Indexes at Two Depths in Tioman Island 112 4.17 Summary of r-K-S Percentage Cover and Coral Morphology Class

Score (CCs) at 20 Reef Sites in Tioman Island 113

5.1 Total Number of Diseased, Compromised and Healthy Coral Colonies in Tioman Island. Mean and Standard Errors Calculated Based on

Coral Colonies Counted at 20 Reef Sites 147

5.2 ANOVA Test Analysis for Diseased, Compromised and Healthy

Coral Colonies among Reef Sites and Zones in Tioman Island 148 5.3 Mean Prevalence (% ± SE) of Diseased, Compromised and Healthy

Coral Colonies at 20 Reef Sites and 3 Zones in Tioman Island 149 5.4 Mean Prevalence (% ± SE) of Coral Diseases at 20 Reef Sites and 3

Zones in Tioman Island 151

5.5 Mean Prevalence (% ± SE) of Signs of Compromised Health at 20

Reef Sites and 3 Zones in Tioman Island 152

5.6 ANOVA Test Analysis for Six Coral Diseases among Reef Sites and

Zones in Tioman Island 153

5.7 ANOVA Test Analysis for Eight Signs of Compromised Health

among Reef Sites and Zones in Tioman Island 153

5.8 ANOVA Test Analysis for Coral Diseases and Signs of Compromised

Health among Depths in Tioman Island 155

5.9 Mean Prevalence (% ± SE) and Disease Abundance among

Scleractinian Hard Coral Genera in Tioman Island 157

6.1 Sample ID, Location, Isolation Source and Accession No. of Sample

Sequences 180

6.1 Phenotypic Characterization of Bacteria Isolates Using API 20NE

Kit.. 186

6.3 Bacterial Species Identified Following Genbank and Eztaxon

Databases 187

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6.4 Pairwise Distance Matrix Calculated between 33 Nucleotide

Sequences Based on 16S rRNA Gene 190

6.5 Mean Prevalence of Seven Identified Bacterial Species (% ± SE) at

Three Reef Sites in Tioman Island 193

6.6 ANOVA Test Analysis for Seven Identified Bacterial Species among

Reef Sites in Tioman Island 193

6.7 Variations of Physicochemical Readings (Mean ± SE) between Three

Different Months 195

6.8 ANOVA Test Analysis for Physicochemical Readings among Three

Different Months 195

6.9 Variations of Physicochemical Readings (Mean ± SE) between Reef

6.10 ANOVA Test Analysis for Physicochemical Readings among Reef

6.11 Factor Loadings of 10 Measured Physicochemical Parameters in Sanggit, Salang and Bakau Bays Derived from Principal Component

Analysis (PCA) 198

7.1 Summary of Changes in Coral Community Structure in Response to Exposure with Low, Moderate and High Impacts of Human

Activities.. 211

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LIST OF FIGURES

Figure No. Page No.

2.1 Total Number of Tourists to Malaysian Marine Parks from 2000 to

2017 12

2.2 Corallite Morphologies of Corals 16

2.3 Colony Morphologies of Corals 16

2.4 Total Number of Tourist Visiting Tioman Island Marine Park from

2000 to 2017 23

2.5 Coral Disease Triad 31

3.1 General Methodology of this Study 48

3.2 Outline of General Methodology and Data Analyses of this Study 49 3.3 Location of Study Area in Tioman Island Marine Park 52

4.1 Procedure Steps of the CVT Method 58

4.2 Image Analysis Used in the Cpce Software with 50 Uniform Points

(Points A - x) per Image 59

4.3 r-K-S Ternary Diagram and Coral Morphology Class Scores (CC1 –

CC4) 66

4.4 Mean Percentage Cover (% ± SE) of Six Benthic Categories in

Tioman Island 67

4.5 Mean Percentage Cover (% ± SE) of Six Benthic Categories at Two

Depths in Tioman Island 70

4.6 15 New Scleractinian Species Records for the East Coast of Peninsular

Malaysia 96

4.7 Coral Morphology Class Scores (CCs) for 20 Reef Sites were Plotted

within the Ternary Diagram Based on the r-K-S Percentage Cover 114 4.8 Dendrogram (a) and nMDS Plot (b) were Clustered All Reef Sites

within Six Groups (G1 – G6) Based on 85% Similarity. All Groups

were Separated Based on Mean Percentage Cover of Coral Genera 116 4.9 Six Groups Derived from Cluster and nMDS Plot. Each Group

Consists of Five Different Dominant Coral Genera Derived From

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SIMPER Analysis and Values are Indicated Based on their Mean

Percentage Cover (% ± SE) 117

5.1 White Syndrome (WS) 137

5.2 Skeletal Eroding Band (SEB) 138

5.3 Yellow Band Disease (YBD) 138

5.4 Unexplained Growth Anomalies (UGA) 139

5.5 Ulcerative White Spots (UWS) 140

5.6 Atramentous Necrosis (AtN) 140

5.7 Focal Bleaching (FB) 141

5.8 Pigmentation Response (PR) 142

5.9 Algal and Sponge Overgrowth (ASO) 142

5.10 Predation Scars (PS) 143

5.11 Sediment Necrosis (SN) 145

5.12 Physical Damage (PD) 145

5.13 Explained Growth Anomalies (EGA) 146

5.14 Trematodiasis (T) 146

5.15 Mean Prevalence (% ± SE) of Diseased, Compromised and Healthy

Coral Colonies in Tioman Island 147

5.16 Mean Prevalence (% ± SE) of Coral Diseases and Signs of

Compromised Health at Two Depths in Tioman Island 154 5.17 Dendrogram (a) and nMDS Plot (b) were Clustered All Reef Sites

within Four Groups (G1 – G4) Based on 45% Similarity. All Groups were Separated Based on Mean Prevalence of Coral Diseases and

Signs of Compromised Health 160

5.18 Four Groups Derived from Cluster and nMDS Plot. Each Group Consists of Five Different Dominant Coral Diseases and Signs of Compromised Health Derived from SIMPER Analysis and Values are

Indicated Based on their Mean Prevalence (% ± SE) 161 6.1 Reef Sites for Sample Collection and Measurement of Physical

Parameters at 1 km (Location A), 3 km (Location B) and 5 km

(Location C) from the Shoreline 174

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6.2 Diffuse Pattern of Tissue Loss for (a) Acropora cytherea and (b) Montipora aequituberculata, Leaving White Colour in Active Lesion Fronts and Yellow to Brown Colours as Fouling Developed over the

Exposed Skeleton 184

6.3 Green (a) and Yellow (b) Colonies of Vibrio Isolates on TCBS (Left)

and TSA (Right) Media 184

6.4 Morphology of Gram-negative Bacilli with Curve and Rod Shapes for Vibrio Isolates after Gram Staining under Light Microscope with 40x

Objective 185

6.5 Amplification of PCR Products Using Universal Primer 187 6.6 Evolutionary Distance ML Phylogenetic Tree Based on 16S rRNA

Gene Sequences of Isolates Obtained in this Study 189 6.7 Prevalence (%) of Seven Identified Bacterial Species at Three Reef

Sites during Four Times Samplings on July 2018, October 2018,

March 2019 and June 2019 192

6.8 CCA Biplots Diagram Showing the Effect of Physicochemical

Parameters on the Prevalence of Bacterial Species in Sanggit Bay 200 6.9 CCA Biplots Diagram Showing the Effect of Physicochemical

Parameters on the Prevalence of Bacteria Species in Salang Bay. 200 6.10 CCA Biplots Diagram Showing the Effect of Physicochemical

Parameters on the Prevalence of Bacterial Species at Bakau Bay 201

6.11 Histological Structures of WS Coral Tissue 202

6.12 Histological Structures of Healthy Coral Tissue 203

7.2 Locations of Survey Reef Sites with Low, High and Moderate Exposure to Coastal Development and Tourism Impacts in Tioman Island. Individual Pie Charts Represent the Mean Percentage of 3

Classified Benthic Categories 212

7.2 Locations of Survey Reef Sites with Low, High and Moderate Exposure to Coastal Development and Tourism Impacts in Tioman Island. Individual Pie Charts Represent the Mean Prevalence of Coral

Colonies Classified within 3 Health Status Categories 213

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LIST OF SYMBOLS

km² Square kilometer

m² Square meter

cm² Square centimeter

km Kilometer

m Meter

cm Centimeter

% Percent

< Less than

> More than

± Plus minus

- Negative

+ Positive

mg Miligram

µl Microliter

µM Micromoles

nm Nautical miles

g Gram

ml Milliliter

L Liter

mg/l Milligrams per liter

mS/cm Millisiemens per centimeter µg/l Microgram per liter

psi Pound per square inch ppt Parts per thousand rpm Revolutions per minute

kb Kilobase

bp Basepairs

V Volt

°C Degree celsius

CaCO³ Calcium carbonate

NaCl Sodium chloride

NH3 Ammonia

NO3- Nitrate

NO2- Nitrite PO43- Phosphate

H2O2 Hydrogen peroxide

Zn Zinc

EtOH Ethanol

HCl Hydrochloric Acid

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β Beta

° Degree

D Simpson index

H’ Shannon-Weiner index

J’ Pielou index

SE Standard error

df Degrees of freedom

F Critical value

p rho-value

n Number of individual

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LIST OF ABBREVIATIONS

WS White Syndrome

WP White Plague

WB White Band

WPL I White Plague Type I WPL II While Plague Type II WPL III White plague type III WBD I White Band Disease Type I WBD II White Band Disease Type II SCTLD Stony Coral Tissue Loss Disease

BBD Black Band Disease

BrBD Brown Band Disease

RBD Red Band Disease

SEB Skeletal Eroding Band

CYBD Caribbean Yellow Band Disease

YBL Yellow Blotch

YBD Yellow Band Disease

GAs Growth Anomalies

UGA Unexplained Growth Anomalies EGA Explained Growth Anomalies UWS Ulcerative White Spot

PUWS Porites Ulcerative White Spot

FB Focal Bleaching

PR Pigmentation Response

PS Predation Scar

ASO Algal and Sponge Overgrowth

SN Sediment Necrosis

PD Physical Damage

DSD Dark Spot Disease

AtN Atramentous Necrosis

T Trematodiasis

PLS Pink-line Syndrome

VCB Vibrio coralliilyticus-induced Bleaching SCSDVs Single-stranded DNA Viruses

TIMP Tioman Island Marine Park GBR Great Barrier Reefs

USA United States of America

US United States

CT Coral Triangle

(23)

xxiii

MESTECC Ministry of Energy, Science, Technology, Environment and Climate Change

DOF Department of Fisheries

DMPM Department of Marine Park Malaysia

RCM Reef Check Malaysia

MNS Malaysian Nature Society MPAs Marine Protected Areas

WoRMS World Register of Marine Species COTW Corals of the World

NOAA National Oceanic and Atmospheric Administration IUCN International Union for Conservation of Nature AIMS Australian Institute of Marine Science

NCBI National Center for Biotechnology Information CVT Coral Video Transect

LIT Line Intercept Transect PIT Point Intercept Transect PLIT Photo Line Intercept Transect UVC Underwater Visual Census

CPCe Coral Point Count with Excel extension Software PAST Paleontological Statistical Software

nMDS Non-metric Multidimensional Scale SIMPER Similarity Percentage

PCA Principal Component Analysis CCA Canonical Correspondence Analysis

DNA Deoxyribonucleic Acid

rRNA Ribosomal Ribonucleic Acid

TCBS Thiosulfate Citrate Bile Salt-sucrose

TSA Tryptic Soy Agar

MEGA Molecular Evolutionary Genetics Analysis BLAST Basic Local Alignment Search Tool ANOVA Analysis of Variance

HSD Honest Significant Difference

HD High Definition

CCs Coral Classes

RA Relative Abundance

UV Ultraviolet

TRP Indole production

ADH Arginine dihydrolase

ESC Aesculin

GEL Gelatin

PNPG β-galactosidase

GLU Glucose

MNE Mannose

(24)

xxiv

MLT Malate

NE Non-enteric

MYR Malaysian Ringgit

COT Crown of thorn

NS Not significant

NJ Neighbor Joining

ML Maximum Likelihood

GTR General Time Reversible

N North

E East

r Ruderal

K Competitor

S Stress-tolerator

G Group

e.g. For example,

ver. Version

spp. Species

CORAL COMMUNITY STRUCTURE IN TIOMAN ISLAND MARINE PARK, MALAYSIA:

CORAL COMMUNITY STRUCTURE IN TIOMAN ISLAND MARINE PARK, MALAYSIA:

FURTHER EMPHASIS ON HARD CORAL DISEASE AND PATHOGENIC Vibrio spp.

BY

MOHD FIKRI AKMAL BIN MOHD KHODZORI

A thesis submitted in fulfilment of the requirement for the degree of Doctor of Philosophy (Biosciences)

Kulliyyah of Science

International Islamic University Malaysia

FEBRUARY 2021

ABSTRACT

ثحبلا ةصلاخ

ABSTRACT IN ARABIC

APPROVAL PAGE

DECLARATION

INTERNATIONAL ISLAMIC UNIVERSITY MALAYSIA

DECLARATION OF COPYRIGHT AND AFFIRMATION OF FAIR USE OF UNPUBLISHED RESEARCH

CORAL COMMUNITY STRUCTURE IN TIOMAN ISLAND MARINE PARK, MALAYSIA:

FURTHER EMPHASIS ON HARD CORAL DISEASE AND PATHOGENIC Vibrio spp.

ACKNOWLEDGEMENTS

TABLE OF CONTENTS

LIST OF TABLES

LIST OF FIGURES

LIST OF SYMBOLS

LIST OF ABBREVIATIONS