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: https://indd.adobe.com/view/c3f850ba-3dcf-4368-b682-ab813e43932d
Find out more about UTMNexus: https://research.utm.my/magazine/

First results presentation of our methanogenesis project

The findings of our collaborative project with PETRONAS Research Sdn. Bhd. (PRSB) on the methanogenic conversion of carbon dioxide into methane was recently presented at the International Petroleum Technology Conference in Bangkok, Thailand. The conference was held from 1-3 March 2023 and was attended by more than 3,500 energy professionals, representing more than 1,000 organizations from at least 50 countries. The paper entitled “Accelerated Methanogenesis for the Conversion of Biomethane from Carbon Dioxide and Biohydrogen at Hyperthermophilic Condition” was presented by our PRSB collaborator Dr. Ivy Chai Ching Hsia. Read the full paper here (open access).

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 firdausw@utm.my. Position is open until filled.

Optimization of the operational parameters for mesophilic biohydrogen production from palm oil mill effluent (POME) using enriched mixed culture

Our article on biohydrogen production from POME at mesophilic temperature is now published in Biomass Conversion and Biorefinery (Springer). We reported in the article the acclimatization of the sludge inoculum to increasing POME concentration, accompanied by analysis of microbial community changes during the acclimatization process. The physicochemical parameters for biohydrogen production using the acclimatized sludge as inoculum and POME as substrate was later optimized using response surface methodology (RSM)-based design of experiment.

Reference: Audu, J.O., Ibrahim, N., Ibrahim, Z. et al. Optimization of the operational parameters for mesophilic biohydrogen production from palm oil mill effluent using enriched mixed culture. Biomass Conv. Bioref. (2021). https://doi.org/10.1007/s13399-021-01488-9