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

Report of hypoxic-anoxic dead zone in Johor Straits

Harmful algal bloom (HAB) leading to fish kills is no longer a rare occurrence in Malaysian waters, particularly the strategically and economically important Johor Straits. It is a national border between Malaysia and Singapore, and the coastal areas of both sides are dotted with aquaculture, industrial and residential activities.

In our recent paper published in July 2020, in collaboration with the Institute of Ocean and Earth Sciences (IOES), University of Malaya, we discovered the presence a hypoxic-anoxic “dead zone” (low dissolved oxygen) in the inner Johor Straits, spanning an area of more than 10 km square. We also observed seasonal blooms of diatoms Skeletonema, Chaetoceros, Rhizosolenia and Thalassiosira. Diatoms are important for the marine ecosystems. However high nutrient concentration (particularly from human activities) in the water may lead to excessive proliferation of diatoms, inducing the hypoxic-anoxic conditions. Read more here.

This project was funded by the Transdisciplinary Research Grant Scheme (TRGS), Ministry of Education Malaysia.

Reference: Mohd-Din et al. 2020. Prolonged high biomass diatom blooms induced formation of hypoxic-anoxic zones in the inner part of Johor Strait. Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-020-10184-6

Image credit: Terence Ong / CC BY-SA (http://creativecommons.org/licenses/by-sa/3.0/)

Vacancy: Postdoctoral Researcher “Conversion of CO2 to CH4 by Methanogenic Microbes for Use in Valued-added Geologic Carbon Capture and Sequestration”

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

Conversion of CO2 to CH4 by Methanogenic Microbes for Use in Valued-added Geologic Carbon Capture and Sequestration

We are currently looking for one (1) postdoctoral researcher to work on this project, in collaboration with Petronas Research Sdn. Bhd. (PRSB). It is a multi-disciplinary project, with researchers coming from several UTM faculties and CoE (Department of Biosciences and Department of Physics, Faculty of Science; School of Chemical Engineering and School of Mechanical Engineering, Faculty of Engineering; and Advanced Membrane Technology Research Centre) together with reservoir geology and geochemistry researchers at PRSB.

Project summary:

Carbon capture and storage (or sequestration) (CCS), is the process of capturing CO2 from large-scale emitters such as fossil fuel refineries, power plants and product manufacturing industries, and transporting it to a storage site. This prevents the CO2 re-entry into the atmosphere. There are several routes available for CCS, which can be divided into physicochemical, biological, and geological route. CO2 sequestration in deep subsurface formations, such as oil and gas reservoirs provides several advantages, such as enhanced oil recovery, and the capability to store up to two thirds of the CO2 in underground systems. The injected CO2 can also be transformed into CH4 by microbes for energy recovery as value-added options, in the presence of suitable electron donors, for example formate and H2.

This exploratory project will involve cultivation of methanogens under laboratory conditions and evaluation of the CO2 to CH4 conversion capacity. It will also involve lab scale reactor optimisations for the production of H2. Self-designed reservoir-mimic reactor will be used for larger scale methanogenesis reactions with CO2 and H2 as feedstocks. Depending on sample availability, microbial community analysis and methanogenesis characterisations will also be done on environmental samples.

Candidate requirements:

Open to both Malaysian and international candidates.

PhD (in biochemistry, biotechnology, chemical engineering, bioprocess engineering, or any related fields) from local or foreign universities.

Experience in any of these skills are an advantage: archaea handling, anaerobic reactor systems, reservoir biology, microbial ecology.

The position is on contract-basis (renewable up to 24 months), based on the candidate and project performance.

A monthly salary of MYR5,000 will be provided.

How to apply:

Kindly e-mail your CV and cover letter to the project leader, Dr. Mohd Firdaus Abdul Wahab at firdausw@utm.my.

Only selected candidates will be contacted for interview.

Position is open until filled.

Research Book Publication “Current Techniques in Protein Science”

Our first research book has now been published by UTM Publisher. The book has 12 chapters altogether, compiling research on proteins carried out by UTM researchers and their collaborators. It is now available for purchase at:

eBook: https://www.e-sentral.com/book/info/316417/current-technique-in-protein-science

Hard copy: https://shopee.com.my/Current-Techniques-in-Protein-Sciences-i.86546040.4943749675


Book Preface

“Proteins are the basic building blocks of life. They are defined as large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a variety of functions in the cell, including catalysing metabolic and biochemical reactions, assisting DNA replication, responding to external and internal stimuli, and transporting molecules from one location to another intra-cellularly or extra-cellularly. The study of proteins is important in the fields of biomedicine, environmental sciences, and for industrial applications. The understanding on how protein works at the molecular level assists in the development of new disease therapy, discovery and improvement of the activity of industrially- important enzymes, and discovery of beneficial secondary metabolites in medicinal plants, among many other interesting applications.

Investigation of proteins at the molecular level requires specialised instruments and precise techniques. Other than the commonly used sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and Western blotting (also known as protein immunoblotting), there are many other advanced techniques currently used which include surface plasmon resonance (SPR) spectroscopy, mass spectrometry (MS), X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, cryo-electron microscopy (cryo-EM), and circular dichroism (CD) spectroscopy. Computational methods are also indispensable in supporting wet lab experiments, and to provide precious information not currently observable with wet lab experiments.

This edited book is aimed at showcasing various research on proteins previously or currently being carried out at UTM and at affiliated laboratories. With the acquisition of increasingly sophisticated instruments, software, and the development of many new techniques, research on protein science is currently on the rise. This book demonstrates the research capability of our young and established researchers, and hopefully will serve as a networking guide for researchers interested in the field.”

Understanding the Microbiomes of Green Leafy Vegetables using Multi-omics Approaches

Food security is a very important issue nowadays. It is an already complex issue made worse by climate change, and the growing scarcity of arable land due to rapid urbanisation. The UN has reported that “815 million people are hungry today, and the additional 2 billion people expected to be undernourished by 2050”. Goal 2 (Zero Hunger) of the UN Sustainable Development Goals (SDG) calls for an increased investment in agricultural research to increase the agricultural productive capacity, particularly in developing countries.

Genetic engineering of food crops has the potential to provide the promising solutions, by providing the technology to develop higher yield, drought resistance, and nutritionally-enhanced food crops. However, the public perception of genetically-modified organisms (GMO) and transgenic plants has hampered the acceptance of many GM products.

Advancements in microbiology and microbial ecology has shed light on the importance of plant-associated microorganisms, particularly the community around the root region (rhizosphere). It is now known that there is a complex network of interactions between plants and their root microbes, increasing the plant nutrient uptake, and provide resistance to biotic and abiotic stresses. The rhizosphere is populated by a diverse range of microorganisms, and rhizobacteria are the bacteria colonizing this habitat with the ones that promote plant growth are called plant growth-promoting rhizobacteria (PGPR) (Beneduzi et al., 2012). These PGPR can be used to enhance agricultural productivity without using plant genetic modifications, or synthetic fertilisers. But understanding these PGPR and how they interact with their plant hosts requires the latest technologies in microbial ecology, molecular biology, plant sciences and chemical analysis.

I joined the Swarup Lab at the National University of Singapore (NUS) in January 2019, as part of my post-doctoral training, to learn more about these latest technologies. My work here involves the use of multi-omics analysis (metagenomics, metatranscriptomics and metabolomics) to study plant-microbial interactions, particularly how the PGPR at the root region affect the growth of green leafy vegetables. Multi-omics analysis uses information obtained from DNA, RNA and small chemical molecules (known as metabolites) found in the plant rhizosphere. I will also use advanced culturing tools to culture and characterise the complex bacterial communities in the rhizosphere. Bacteria found to have beneficial plant improvements traits can be applied to enhance the yield of agricultural products, in this case the leafy vegetables commonly used in urban farming. This microbial-assisted plant growth enhancement technology can lead to a more sustainable agriculture, lowering the use of chemical fertilisers, pesticides and herbicides.



UN Sustainable Development Goals (https://www.un.org/sustainabledevelopment/sustainable-development-goals/)

Beneduzi et al., 2012. Plant growth-promoting rhizobacteria (PGPR): Their potential as antagonists and biocontrol agents. Genet Mol Biol. 35(4 Suppl): 1044-1051.

Call for Abstract: Taiwan-Malaysia Workshop on Clean Water and Sustainable Energy 2019

The Taiwan-Malaysia Innovation Centre for Clean Water and Sustainable Energy (WISE Centre) will organize the inaugural Taiwan-Malaysia Workshop on Clean Water and Sustainable Energy, to be held at Universiti Teknologi Malaysia, Johor Bahru, on 5-6 August 2019. This workshop is co-organized by the Centre for Environmental Sustainability and Water Security (IPASA), Faculty of Science, Research Institute for Sustainable Environment (RISE), Resource Sustainability Research Alliance (RSRA), UTM; the School of Chemical Sciences, Universiti Sains Malaysia (USM) and the Centre for Biomass Utilization, Universiti Malaysia Perlis (UniMAP); together with National Tsing Hua University (NTHU), Taiwan. It is also supported by the Ministry of Science and Technology, Taiwan (MOST).

The general theme of the workshop is “Clean Water and Sustainable Energy”, and abstract submission are now invited from academic staff, researchers and postgraduate students on all aspects related to the Workshop theme. Several prominent professors from NTHU will participate as keynote and invited speakers in the Workshop. Participants will have the opportunity to network with professors and researchers from Taiwan, Malaysia, and other South East Asian countries.

A nominal fee of MYR300 (academic staff and researchers) or MYR150 (students) will be charged on all participants to cover meals during the workshop.

Abstract can be submitted at this link: https://forms.gle/E3yxmbkNCPAvE5W79 

Submission will close on 20 July 2019, or until all places are filled as they are limited.

Any enquiries regarding the Workshop can be directed to the Secretariat, Dr. Mohd Firdaus Abdul Wahab at firdausw@utm.my.

For more information, visit: http://www.utm.my/ipasa/2019/06/24/taiwan-malaysia-workshop-on-clean-water-and-sustainable-energy/