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Marine Microbial Diversity of Off-Terengganu Coastal Sediment in South China Sea

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Marine Microbial Diversity of Off-Terengganu Coastal Sediment in South China Sea PSZ 19:16 (Pind. 1/07) UNIVERSITI TEKNOLOGI MALAYSIA DECLARATION OF THESIS / UNDERGRADUATE PROJECT REPORT AND COPYRIGHT Author’s full name : MARZIAH BINTI ZAHAR Date of Birth : 11 MAY 1984 Title : MARINE MICROBIAL DIVERSITY OF OFF-TERENGGANU COASTAL SEDIMENT IN SOUTH CHINA SEA Academic Session : 2016/2017 (2) I declare that this thesis is classified as: CONFIDENTIAL (Contains confidential information under the Official Secret Act 1972)* RESTRICTED (Contains restricted information as specified by the organization where research was done)* OPEN ACCESS I agree that my thesis to be published as online open access ✓ (full text) I acknowledged that Universiti Teknologi Malaysia reserves the right as follows: 1. The thesis is the property of Universiti Teknologi Malaysia 2. The Library of Universiti Teknologi Malaysia has the right to make copies for the purpose of research only. 3. The Library has the right to make copies of the thesis for academic exchange. Certified by: SIGNATURE SIGNATURE OF SUPERVISOR AKBARIAH MOHD MAHDZIR 840511-12-5000 (NEW IC NO/PASSPORT) NAME OF SUPERVISOR Date: MARCH 2017 Date: MARCH 2017 NOTES: * If the thesis is CONFIDENTIAL or RESTRICTED, please attach with the letter from the organization with period and reasons for confidentiality or restriction. ii “I hereby declare that I have read this thesis and in my opinion this thesis is sufficient in terms of scope and quality for the award of the degree of Doctor of Philosophy” Signature : …………………………......... Name of Supervisor : Dr. Akbariah Mohd Mahdzir Date : 08 MARCH 2017 iii BAHAGIAN A – Pengesahan Kerjasama* Adalah disahkan bahawa projek penyelidikan tesis ini telah dilaksanakan melalui kerjasama antara _______________________ dengan _______________________ Disahkan oleh: Tandatangan : ……………………………….. Tarikh : ……………………. Nama : ………………………………………. Jawatan : …………………………………….. (Cop rasmi) * Jika penyediaan tesis/projek melibatkan kerjasama. BAHAGIAN B – Untuk Kegunaan Pejabat Sekolah Pengajian Siswazah Tesis ini telah diperiksa dan diakui oleh: Nama dan Alamat Pemeriksa Luar : Assoc. Prof. Dr. Nobuyuki Kawasaki Universiti Selangor (Bestari Jaya Campus), Jalan Timur Tambahan, 45600 Bestari Jaya, Selangor Nama dan Alamat Pemeriksa Dalam 1: Prof. Dr. Masafumi Goto Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia Jalan Sultan Yahya Petra 54100 Kuala Lumpur Disahkan oleh Timbalan Pendaftar di Sekolah Pengajian Siswazah: Tandatangan : ………………………………….. Tarikh : ………………… Nama : ASRAM BIN SULAIMAN @ SAIM iv MARINE MICROBIAL DIVERSITY OF OFF-TERENGGANU COASTAL SEDIMENT IN SOUTH CHINA SEA MARZIAH BINTI ZAHAR A thesis submitted in fulfilment of the requirements for the award of the degree of Doctor of Philosophy Malaysia-Japan International Institute of Technology Universiti Teknologi Malaysia MARCH 2017 ii I declare that this thesis entitled “Marine Microbial Community Distribution in Malaysia Seawater Off-Terengganu Coast of South China Sea” is the result of my own research except as cited in the references. The thesis has not been accepted for any degree and is not concurrently submitted in candidature of any other degree. Signature : .................................................... Name : MARZIAH BINTI ZAHAR Date : 08 MARCH 2017 iii "Blessed is He in Whose Hand is the dominion, and He is able to do all things, Who has created death and life, that He may test you which of you is best in deed, and He is the All-Mighty, the Oft-Forgiving." [Al-Mulk 67:1-2] This thesis is especially dedicated to my beloved family: Hj. Zahar, Hjh. Marisah, Zairi and Marzarina. iv ACKNOWLEDGEMENT This thesis would not have the spirit that has without the invaluable academic, educational, psychological, human support and, confidence in me as a writer and researcher. I wish to express a big gratitude to my main thesis supervisor Dr. Akbariah Mahdzir and my co-supervisor Assoc. Prof. Dr. Hirofumi Hara for their tact, diplomacy, and sincerity. Your patience and laboriously skills corrected my stylistic mistakes and awkwardness. Despite my passing perplexities and some unforeseen consequences issues, you encouraged me to continue my journey to manifest the wonderful world of Ph.D. Next, I am eternally grateful for having Prof. Dr. Md. Nor Musa and Prof. Dato’ A Bakar Jaafar for their endless guidance, wisdom and, being great father figures to me. I am also indebted to Malaysia-Japan International Institute of Technology for the scholarship. Ministry of Higher Education and Integrated Envirotech Sdn. Bhd (IESB) also deserves special thanks for their valuable research grant award. I would like to extend my appreciation to all UTM lecturers and staffs especially in Bio-iST MJIIT and, UTM-OTEC for their wonderful support at various occasions. To all my faithful postgraduate friends: - Noor Fazreen, Nurul Syazwani, Shamsul Faisal, Norzarini, Natasha, Shafiq, and many more. I thank you all for every delightful memory and endless support. Unfortunately, it is not possible to list every one of you in this limited space. v ABSTRACT Marine bacteria play a vital role in regulating global biochemical cycle for billions of years, and their function has been widely explored for the past fifty years. Marine bacteria exploration is considered as difficult and precarious, but every finding is fruitful in providing information to generate a better understanding of its purpose in the seawater. Marine bacteria exploration in Malaysia coastline is considered as new with no impactful data to represent the bacteria distribution in Malaysia’s coastline, specifically heading towards the South China Sea. The purpose of this study is to assess bacteria diversity off-Terengganu coast as the foremost marine bacteria abundance screening in these areas. In this study, surface sea sediment that contains a variety of bacteria cells is collected in three random locations with three different depths. The DNA obtained from the cell extraction was identified with Next Generation Sequence method, which specifically targeted 16SrDNA V3-V4 properties to obtain the overall bacterial metagenomic profile. Results showed that off- Terengganu coast, bacteria diversity consisted of 25518 amplicons of 3301 unique OTUs, which signify 27 phyla. The OTU abundance decreased gradually with depth of sediment in the sea. The metagenomic profile revealed two sulphur-degrading bacteria were dominant in the surveyed area. Sulfurovum genus dominate overall bacteria community in two locations situated in the northeast area of sampling stations. Conversely, Pseudoalteromonas dominated the overall bacterial community in the southeast coastline. The Physical-geochemical analysis revealed that all surveyed areas contained sulphur, oil, grease, gasoline, diesel, and mineral oil, which perhaps are influencing sulphur-degraded bacteria community growth in the surveyed area. There is no concrete evidence to link Sulfurovum and Pseudoalteromonas as pathogenic bacteria that causes illness to the human. However, there are possibility that the surveyed areas are anthropogenically polluted and further physical- geochemical analysis is required. In conclusion, the research findings suggested the necessity to conduct a broader bacteria diversity research, such as bacterial dispersion scale, and community variation in order to measure an inordinate extent of environmental pollution in the surveyed areas. vi ABSTRAK Bakteria marin memainkan peranan penting dalam mengawal selia kitaran biokimia global sejak berbilion-billion tahun dan fungsi ini telah diterokai secara meluas lima puluh tahun yang lepas. Penerokaan bakteria marin dianggap sukar dan merbahaya, tetapi hasil kajian amat berhasil dalam menyediakan maklumat bagi menjana pemahaman yang lebih baik terhadap fungsi bakteria marin di dalam air laut. Penerokaan bakteria marin di persisiran pantai Malaysia dianggap sebagai baru dan tanpa data yang berkesan untuk menerangkan taburan bakteria di perairan Malaysia, khususnya yang menghala ke Laut China Selatan. Tujuan kajian ini adalah untuk menilai kepelbagaian bakteria di perairan luar Terengganu bagi menjana maklumat awal mengenai kepelbagaian bakteria marin di persisiran pantai. Dalam kajian ini, sedimen di permukaan laut yang mengandungi sel bakteria telah diambil dari tiga lokasi rawak dengan mengambil kira kedalaman paras air yang berbeza. DNA yang diperoleh melalui proses pengekstrakan sel bakteria dikenalpasti melalui kaedah Next Generation Sequence, dengan mensasarkan sifat 16SrDNA V3-V4 khususnya untuk menjana keseluruhan profil metagenomik bakteria. Hasil kajian menunjukkan kepelbagaian bakteria di perairan luar Terengganu terdiri daripada 25518 amplikon daripada 3301 OTU yang unik, yang menandakan 27 filum. Kekuatan OTU semakin berkurangan dengan kedalaman sedimen di dalam laut. Profil metagenomik menunjukkan dua genus bakteria pendegradasi sulfur adalah dominan di kawasan kajian. Genus Sulfurovum mendominasi keseluruhan komuniti bakteria di dua lokasi yang terletak di kawasan timur laut dari stesen pensampelan. Sebaliknya, genus Pseudoalteromonas mendominasi komuniti bakteria di kawasan tenggara persisiran pantai. Analisis fisio-geokimia mendedahkan bahawa semua kawasan kajian mengandungi sulfur, minyak dan gris, gasolin, diesel dan minyak mineral, yang mungkin mempengaruhi pertumbuhan komuniti bakteria pendegradasi sulfur di kawasan kajian. Tidak ada bukti kukuh untuk mengaitkan Sulfurovum dan Pseudoalteromonas sebagai bakteria penyebab penyakit kepada manusia. Akan tetapi, ada kemungkinan kawasan-kawasan yang
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