PhD Opportunity in Environmental Biotechnology

My lab, in collaboration with the Advanced Membrane Technology Research Centre – AMTEC UTM, has an opening for a PhD position on biomethane production performance from palm oil mill effluent (POME). The project will investigate the effects of physicochemical parameters on methane production in a lab-scale bioreactor, and the association with the microbial community dynamics. The candidate will be exposed to bioprocess technology, wastewater treatment, environmental biochemistry, and molecular microbiology.

Monthly allowance will be provided to the successful candidate. Kindly drop me an email at if you are interested.

Candidates from chemistry, biochemistry, biosciences, chemical engineering, bioprocess engineering, and related fields are welcomed to apply. Only open to Malaysians due to the nature of the grant.

Position open until filled.

Microbial community dynamics and functional potentials in the conversion of oil palm wastes into biomethane

Our latest review article on the microbial community involved in the conversion of oil palm wastes into biomethane is now published in 3 Biotech! Read the article here.

Oil palm processing generates substantial waste materials rich in organic content, posing various environmental challenges. Anaerobic digestion (AD), particularly for palm oil mill effluent (POME), offers a sustainable solution, by converting waste into valuable biomethane for thermal energy or electricity generation. The synergistic activities of the AD microbiota directly affect the biomethane production, and the microbial community involved in biomethane production in POME anaerobic digestion has been reported. The composition of bacterial and archaeal communities varies under different substrate and physicochemical conditions. This review discusses the characteristics of POME, explores the microbial members engaged in each stage of AD, and elucidates the impacts of substrate and physicochemical conditions on the microbial community dynamics, with a specific focus on POME. Finally, the review outlines current research needs and provides future perspectives on optimizing the microbial communities for enhanced biomethane production from oil palm wastes.

Temporal Variation of Methanogenic Microbial Community in Palm Oil Mill Effluent (POME) Anaerobic Digester

Our recent preliminary results on the investigation of the POME anaerobic digester microbiomes are now published in the South Asian Journal of Research in Microbiology (Open Access). Check out the full paper here.

Palm Oil Mill Effluents (POME) serve as suitable substrates for methane gas production through anaerobic digestion. This process relies on a complex microbial community that plays a critical role in ensuring stable anaerobic digester operation and efficient biogas production. Among these microorganisms, methanogenic archaea are pivotal in methane generation by utilizing diverse substrates under anoxic conditions. However, the knowledge of the microbial communities, particularly those involved in methane production in POME anaerobic sludge at different time intervals, remains limited. This study aims to uncover temporal variations in microbial communities, including diversity, composition, and structure, within POME anaerobic sludge, specifically focusing on the methanogenic archaea community. The temporal dynamics of microbial communities in the eighteen POME anaerobic sludge samples collected from a palm oil mill were investigated through 16S rRNA amplicon sequencing. The results reveal consistent microbial community diversity in POME anaerobic sludge over the study periods. Then, the sequencing also showed that Bacillota (26.9 ± 3.3%), Bacteroidota (20.2 ± 5.3%), and Chloroflexota (15.0% ± 6.3%) were the dominant bacterial phyla in POME anaerobic sludge across different time frames. Concurrently, Halobacteriota (5.9 ± 2.8%), Methanobacteriota (2.5 ± 0.6%), and Nanoarchaeota (2.3 ± 1.2%) were the primary archaeal phyla identified in anaerobic sludge at various time intervals. Furthermore, amplicon sequencing revealed the presence of two methanogenic archaea genera, Methanothrix and Methanobacterium, associated with acetoclastic and hydrogenotrophic methanogenesis, respectively. These findings suggest that acetoclastic and hydrogenotrophic methanogenesis pathways are the primary contributors to methane production in the POME anaerobic digestion process.

Our article in UTMNexus magazine (April 2023) “Microorganisms in Climate Change and Energy Security”

An article by the lab members has been published in the UTMNexus magazine (April 2023 issue). UTMNexus is a publication coordinated by UTM DVCRI office, targeted at the general public, showcasing the state-of-the-art research conducted by the university researchers. Our article describes the role of microorganisms in climate change and energy security, in line with the theme of this issue. We introduced the readers to the characteristics and biotechnological potentials of archaea, which is among the least understood groups of microbes, in carbon capture and conversion. The article was also co-authored by our collaborators from PETRONAS Research Sdn. Bhd. 

Read the article here:
Find out more about UTMNexus:

Eka submitted her MPhil hardbound thesis

Eka Latiffah Nadia Dzulkarnain recently submitted her final hardbound Master of Philosophy (MPhil) thesis. Eka’s research project was on the effects of different heat pretreatment temperatures on biohydrogen production using inoculum from anaerobic sludge. She also investigated the changes caused by the pretreatment to the microbial community dynamics and functional potentials using metagenomics. We wish her all the best in all her future endeavours!

Julia won the Biosciences 3MP Competition!

Julia Ameera Johari bagged the first prize in the Biosciences 3-Minute Presentation (3MP) Competition held at the Faculty of Science recently. Julia is working on her Final Year Undergraduate Project in the lab, investigating the isotopic methane production from methanogenic microbial community in anaerobic sludge. Congratulations Julia!

Lab coffee session

A coffee session with the lab members was held on 14 December 2022, to commemorate Eka’s successful defence of her MPhil thesis on 13 December 2022. It was good to talk science and life over coffee and cakes!

From left: Roy (FYUP), Mustafa (PhD), Aliyu (PhD), Aliyu’s colleague, myself, Hui Jing (MPhil), Eka (MPhil), Judith (PhD), Jannah (FYUP)

Taking on Diplomacy Role as a Scientist: A Personal Reflection and What Next?

I was grateful to be given the opportunity to contribute to the Science Diplomacy magazine, which is a publication by the National Institute of Science Communication and Information Resources, India. I took the opportunity to write about my personal journey to science diplomacy, starting with my interest in international affairs and relations, to my participation in the TWAS-AAAS Course on Science Diplomacy in Trieste, Italy.
Read about it here (open-access). Click here for the Science Diplomacy magazine page.

Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook

We recently published a review on the microbiomes of biohydrogen production from dark fermentation of industrial wastes, with a special focus on palm oil mill effluent. Read the review at this link (open-access).


Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Under‐ standing of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome‐based technologies and knowl‐ edge can be used effectively in biohydrogen production systems, in order to maximise the production output.

Reference: Dzulkarnain et al. 2022. Microbiomes of Biohydrogen Production from Dark Fermentation of Industrial Wastes: Current Trends, Advanced Tools and Future Outlook. Bioresources and Bioprocessing. 9(16). 1-25. DOI: 10.1186/s40643-022-00504-8

Vacancy: Graduate Research Assistant (Masters by Research) “Insights into Microbial Methane Metabolisms in POME Anaerobic Sludge via Shotgun Metagenomics Sequencing”

Update: The position has been filled. Thank you for all the interests.

One (1) MPhil by research position is available in my lab. The project involves sampling trips at palm oil mill, sample DNA extraction, metagenomics sequencing, and computational biology analysis of the sequencing data.

Requirements: Malaysian citizen with BSc degree in Industrial Biology, Biology, Biotechnology, Biochemistry, Chemistry and similar, with minimum CPA 3.00.

Monthly allowance will be provided to the successful candidate, up to 18 months.

Kindly email me with your CV at Position is open until filled.