discovery of novel rare actinobacteria isolated from mangrove environments in the east coast of ...

209 Pages·2016·13.89 MB·English

DISCOVERY OF NOVEL RARE ACTINOBACTERIA ISOLATED FROM
MANGROVE ENVIRONMENTS IN THE EAST COAST OF PENINSULAR
MALAYSIA

ADZZIE SHAZLEEN BINTI AZMAN
Honours Degree of Bachelor of Science (Biotechnology)

A thesis submitted for the degree of Doctor of Philosophy at
Monash University in 2016
Jeffrey Cheah School of Medicine and Health Sciences
SUPERVISORS

Main supervisor: Dr. Lee Learn Han
School of Pharmacy,
Monash University Malaysia,
Jalan Lagoon Selatan,
47500 Bandar Sunway,
Selangor Darul Ehsan, Malaysia.

Co-supervisors: Professor Dr. Iekhsan Othman
Jeffrey Cheah School of Medicine and Health Sciences,
Monash University Malaysia,
Jalan Lagoon Selatan,
47500 Bandar Sunway,
Selangor Darul Ehsan, Malaysia.

Associate Professor Dr. Fang Chee Mun
School of Pharmacy,
Faculty of Science,
The University of Nottingham Malaysia Campus,
Jalan Broga,
43500 Semenyih,
Selangor Darul Ehsan, Malaysia.

Associate Professor Dr. Chan Kok Gan
Institute of Biological Sciences,
Faculty of Science,
University of Malaya,
50603 Kuala Lumpur, Malaysia.

i
COPYRIGHT

©The author (2016).

I certify that I have made all reasonable efforts to secure copyright permissions for third-party
content included in this thesis and have not knowingly added copyright content to my work
without the owner's permission.

ii
DECLARATION

This thesis contains no material which has been accepted for the award of any other degree or
diploma at any university or equivalent institution and that, to the best of my knowledge and
belief, this thesis contains no material previously published or written by another person, except
where due reference is made in the text of the thesis.

Signature:
Print Name: Adzzie Shazleen Binti Azman
Date: 13th May 2016

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THESIS INCLUDING PUBLISHED WORKS DECLARATION

I hereby declare that this thesis contains no material which has been accepted for the award of
any other degree or diploma at any university or equivalent institution and that, to the best of my
knowledge and belief, this thesis contains no material previously published or written by another
person, except where due reference is made in the text of the thesis.

This thesis includes three original papers published in peer reviewed journals and one
manuscript (under review). The core theme of the thesis is discovery of novel bacteria from
mangrove sediment of Tanjung Lumpur, Pahang, Malaysia and the antibacterial, neuroprotective
and cytotoxic activity of the discovered rare actinobacteria extracts. The ideas, development and
writing up of all the papers in the thesis were the principal responsibility of myself, the
candidate, working within the Jeffrey Cheah School of Medicine and Health Sciences under the
supervision of Dr. Lee Learn Han.

The inclusion of co-authors reflects the fact that the work came from active collaboration
between researchers and acknowledges input into team-based research.

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In the case of Chapters 3-6, my contribution to the work involved the following:

Thesis Nature and extent of
Publication title Status
chapter candidate’s contribution
Microbacterium mangrovi Published in International 55%.
sp. nov., an amylolytic Journal of Systematic and Experimental conduct,
3 actinobacterium isolated Evolutionary laboratory analysis, data
from mangrove forest soil Microbiology collection

Sinomonas humi sp. nov., Published in International 55%.
an amylolytic Journal of Systematic and Experimental conduct,
4 actinobacterium isolated Evolutionary laboratory analysis, data
from mangrove forest soil Microbiology collection

Monashia flava gen. nov., Published in International 55%.
sp. nov., a novel Journal of Systematic and Experimental conduct,
5 actinobacterium of the Evolutionary laboratory analysis, data
family Microbiology collection
Intrasporangiaceae
Antibacterial, anticancer Indian Journal of 75%.
and neuroprotective Microbiology Experimental conduct,
activities of rare (Under review) laboratory analysis, data
6
actinobacteria from (INJM-D-16-00327) collection and preparation
mangrove forest soils of manuscript

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I have / have not renumbered sections of submitted or published papers in order to generate a
consistent presentation within the thesis.

Signature:
Date: 13th May 2016

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ACKNOWLEDGEMENT

~In the Name of Allah, the Most Gracious, the Most Merciful~

I would like to express my sincere gratitude to my main supervisor, Dr. Lee Learn Han
for the continuous support along my PhD study and research, for his patience, motivation,
enthusiasm, and immense knowledge. His guidance helped me during my time of research and
thesis writing. Besides my advisor, I would like to thank to my co-supervisors; Professor Dr.
Iekhsan Othman, Associate Professor Dr. Fang Chee Mun, and Associate Professor Dr. Chan
Kok Gan for their encouragement, insightful comments and support.

My sincere thanks also to all the academics and researchers including Associate Professor
Dr. Sharifah Syed Hassan, Associate Professor Uma Devi, Associate Professor Dr. Rakesh Naidu
and Dr. Goh Bey Hing for being part of my work, assessment and thesis. I also appreciate the
helps from all the technical officer and staffs in the research and administration offices in Jeffrey
Cheah School of Medicine and Health Sciences. Special thanks to my former Honours degree
supervisor, Dr. Tam Sheh May for her continuous support, guidance and advices.

I thank my fellow labmates in the Microbiology group; Nurullhudda Zainal, Eng Shu
Kee, Vengadesh Letchumanan, Ser Hooi Leng, Loh Teng Hern and Jodi Woan Fei Law for their
help and support. Also, to my friends; Jasmine Khairat, Nur Izyani, Athirah Bakhtiar, Shafiq
Asnawi, B Saatheeyavaane, Siti Aisyah, Chew Miaw Fang and Christina Injan, thanks for your
support and all the fun we had in the past four years.
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I would like to express my appreciation to Jeffrey Cheah School of Medicine and Health
Sciences, Monash University Malaysia for giving me a PhD scholarship and financial support.

Last but not least, I would like to express my deepest appreciation to all my beloved
family members; my husband, Mohd. Faiz Aziim, my daughter, Iman Kamilia, my parents,
Azman Haron and Zulaina Rasul, and my siblings, Adzzif Shazreel and Adzziq Shazmeer. Thank
you for your presence in our blessed family. I would not have been able to complete this thesis
without your continuous love and encouragement.

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TABLE OF CONTENTS
Supervisors i
Copyright ii
Declaration iii
Thesis including published works declaration vi
Acknowledgement vii
List of figures xii
List of tables xiii
Abbreviations xiv
Abstract xv
Chapter 1: Introduction and general objectives 1
1.1 Introduction 2
1.2 General objectives of the study 6
1.3 References 7
Chapter 2: Literature review 10
2.1 Mangrove in Malaysia 11
2.2 Diversity of bacteria in mangrove 12
2.2.1 Actinobacteria 15
2.2.2 Rare actinobacteria 17
2.3 Polyphasic approach: a consensus approach to bacterial systematic 22
2.3.1 Genotypic characterization 25
2.3.1.1 16S rRNA gene sequence 25
2.3.1.2 DNA-DNA hydridization (DDH) 26
2.3.1.3 DNA G+C content 27
2.3.1.4 DNA-based typing methods: Repetitive PCR 28
2.3.2 Chemotaxonomic characterization 29
2.3.2.1 Cell wall analysis 30
2.3.2.2 Whole cell sugar analysis 31
2.3.2.3 Phospholipids 32
2.3.2.4 Peptidoglycan 34
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