KULLIYYAH OF SCIENCE

INTERNATIONAL ISLAMIC UNIVERSITY

MALAYSIA
FINAL YEAR PROJECT PROPOSAL

NAME : AHMAD RIDZWAN BIN RAMLAN

MATRIC NUMBER : 1410635
SEMESTER : 1, 2017/2018
DEPARTMENT : BIOTECHNOLOGY
CONCENTRATION : ENVIRONMENT
TITLE : HALOGENASE GENE DIVERSITY OF SPONGE-ASSOCIATED
BACTERIA AND FUNGI FROM LANG TENGAH ISLAND

SUPERVISOR : ASST. PROF. DR. AZRUL NAIM BIN MOHAMAD

Co-SUPERVISOR : -

Students Signature : Date :

INTRODUCTION

In the past few decades, the interest in the research of marine organisms had increased in the
field of biotechnology, pharmaceuticals and genomics as the result of vast technology advancement
and massive innovation that occurs worldwide. This great interest is mainly due to the study of
complex symbioses model of sponge-microbe interaction, as well as the pharmaceutical benefits of
sponges from their derived natural products (Taylor, 2007). It is now clearly recognizable to the
world of researh that the marine environment is a home to a very large diversity of bacteria
population (Giovannoni & Stingl, 2005; Zinger et al., 2011), as well as other organisms such as
archaea, eukarya (Susana et al., 2015) and fungi. Marine organisms such as sponges are reported to
host a huge number of microbes that responsible to the production of many novel pharmaceutical
products and drugs which are widely used in the market today. Sponges are sessile, multicellular
marine invertebrate organisms which filter-feeding (Taylor, 2007) by pumping seawater (Michel et
al., 2014) which circulated into series of canals of the sponge body. It is reported that sponge and
their symbiotic microbes are accountable for more than 5,300 number of product varieties and to
the greater extend, hundreds of new substances uncovered from the organisms each year (Faulkner,
2000; Faulkner, 2001; Faulkner, 2002). Although there are much discoveries and novel findings in
this research area, there are still some gaps which can be investigate, for example the genomic and
metagenomic studies of the microbial communities which associated with the sponges. Many
studies had proven the ability of most sponge-associated microbial communities that can produce a
wealth of novel secondary metabolites which contributed greatly in the pharmaceutical industry.
However, some challenge had to be faced such as sustainable supply of sponge metabolites
(Amanda et al., 2014) in order to continuously supply the novel metabolites for the production of
pharmaceutical products. Hence, the main aim of this project is to identify the microbial
communities; bacteria and fungi, which associated with the sponges by laboratory cultivation;
culture-dependent and culture-independent method. In addition to that, this project also propose to
screen for halogenase gene from those microbial species communities.

Objectives

1. To study the bacterial and fungal species associated with the sponges (species) using
culture-dependent and culture-independent methods.
2. To identify the species of bacteria and fungi associated with the sponges (species) using
Next Generation Sequencing technique.
3. To screen for the halogenase gene of the bacterial and fungal species associated with
sponges (species).

Problem Statement

The symbiotic sponge-associated microorganisms which are not yet identified and characterized,
believed to have the halogenase gene.

Hypothesis

1. The sponge-associated bacteria and fungi are achieve by cultivation in the PDA media
culture as well as in the culture independent method.
2. The sponge-associated bacteria and fungi are identified by sequencing using Next
Generation Sequencer.
3. Halogenase gene in sponge-associated bacteria and fungi is screened using .
LITERATURE REVIEW

Sponges are sessile, old metazoan, a multicellular species (Bergquist, 1978; Simpson, 1984;
Leys & Meech, 2006) from Porifera phylum (Hopper & Van Soest, 2002; Tresa, Devanand &
Ponnapakkam, 2010; Ute et al., 2012; Naomi et al., 2014) which feeding on the microorganisms
and minute organic particles by pump-filtering enormous volume of surrounding seawater (Lee,
Lee & Lee, 2001; Michel et al., 2014) both in pelagic and benthic zone (Bell, 2008; Southwell et
al., 2008; Maldonado, Ribes & Van Duyl, 2012; Zhang et al., 2015).

In 1950s, the discovery of secondary metabolites from Cryptotethya crypta species of marine
sponge; the nucleoside spongothymidine and spongouridine (Bergmann & Feeney, 1950;
Bergmann & Feeney, 1951) had started the interest in the research of this organism. Both
nucleoside

1. Sponges, Species, Characteristic, Habitat, Diet, Function in ecosystem,

2. Past and current studies on sponges
3. Halogenase genes, function and importance, application
4. Study on halogenase genes
5. Study on halogenase genes in sponges
6. Study on halogenase genes in microbial community associated in sponges

METHODS

EXPECTED RESULTS

The bacterial and fungal associated with sponges (species) will be identified by sequencing using
the Next Generation Sequensor, and the halogenase gene will be detected by screening using

REFERENCES
GANTT CHART

2017 2018
Activity
S O N D J F M A M J J
Literature Review

Writing, Submission and

Presentation of Proposal

Preparation of sample (Subculture)

Extraction of DNA
(Next Generation Sequencing
Quality Genomic DNA Extraction)

Amplifying process of DNA

(Polymerase Chain Reaction)

Gel Electrophoresis of PCR result

Sequencing of DNA
(Next Generation Sequencing)

Construction of Phylogenetic Tree

Data analysis

Writing and Submission of Thesis

Milestones:

1. Proposal submitted (November, 2017)

2. Sample succesfully culture (November, 2017)
3. DNA succesfully extracted (December, 2017)
4. DNA succesfully amplified (December, 2017)
5. Successful viewing of gel electrophoresis (January, 2018)
6. DNA succesfully sequenced (February, 2018)
7. Phylogenetic tree successfully constructed (March, 2018)
8. Data analysis completed (May, 2018)
9. Thesis submitted (July, 2018)

________________ ___________________

Signature & Stamp (Supervisor) Date