Mohammed Ali, Ph.D.

Alumni

Now at Trinity College Dublin (Professor)

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Biography

Dr. Muhammad Ali is an environmental engineer specializing in wastewater treatment, microbial electrochemical technologies, and resource recovery. He earned his Ph.D. in Environmental Engineering from Hokkaido University, Japan, and his M.S. from the National University of Science and Technology (NUST), Pakistan.

In 2015, he joined Professor Pascal Saikaly’s group at KAUST as a Postdoctoral Fellow, focusing on advanced wastewater treatment technologies. He worked on pilot-scale bioreactors, including Aerobic Granular Sludge (AGS), Microbial Electrolysis Cell (MEC), and Anaerobic Fluidized Membrane Bioreactor (AFMBR), contributing to their design, fabrication, and automation. He later continued his work in the group as a Research Scientist, where he played a key role in commercializing KAUST-invented water reuse technologies and advancing decentralized wastewater treatment solutions.

In addition to his research, Dr. Ali co-founded NuRain with Professor Saikaly, a start-up focused on sustainable water solutions. His work at KAUST played a key role in bridging research and real-world applications in water treatment and resource recovery.

Dr. Ali is now an Assistant Professor in Environmental Microbiology at Trinity College Dublin, where he continues his research on sustainable water treatment and microbial resource recovery.

Research Interests

Dr. Ali's research focuses on optimizing and developing sustainable environmental biotechnologies to fully harness the biochemical potential and metabolism of microbial communities for resource recovery (reclaimed water, energy, biochemicals) from waste streams. He works at the interface of microbiology, microbial ecology, and bioprocess engineering, with a primary focus on studying water-related engineered ecosystems. To achieve this, he employs advanced omics tools (metagenomics and metatranscriptomics, third-generation sequencing), stable isotope analysis, molecular techniques, and mathematical modeling. A better understanding of these bioprocesses is used to optimize bioprocess to convert waste to resources (reclaimed water, energy, biochemicals) with minimum energy inputs, resources, and carbon footprint.

Selected Publications

  • Ali, M., Ruiz Haddad, L., Haroon, M. F., & Saikaly, P. E. (2024). Genomics Tools to Study Membrane-Based Systems. In S. G. Salinas-Rodríguez & L. O. Villacorte (Eds.), Experimental Methods for Membrane Applications in Desalination and Water Treatment. London, UK.
  • Saadatinavaz, F., Alomari, M. A., Ali, M., & Saikaly, P. E. (2024). Striking a Balance: Decentralized and Centralized Wastewater Treatment Systems for Advancing Sustainable Development Goal 6. Advanced Energy and Sustainability Research, p2400097.
  • Ruiz-Haddad, L., Ali, M., Pronk, M., van Loosdrecht, M. C. M., & Saikaly, P. E. (2024). Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection. Environmental Science and Ecotechnology.
  • Zhang, W., Liang, W., Jin, J., Meng, S., He, Z., Ali, M., & Saikaly, P. E. (2024). Filtration performance of biofilm membrane bioreactor: Fouling control by threshold flux operation. Chemosphere, 362, p142458.
  • Ali, M., Singh, Y., Fortunato, L., Rehman, Z. U., Manjunath, S. V., Vrouwenvelder, J. S., Pronk, M., van Loosdrecht, M. C. M., & Saikaly, P. E. (2023). Performance Evaluation of a Pilot-Scale Aerobic Granular Sludge Integrated with Gravity-Driven Membrane System Treating Domestic Wastewater. ACS ES&T Water, 3(8), 2681-2690.
  • Ali, M., Hong, P. Y., Mishra, H., Vrouwenvelder, J., & Saikaly, P. E. (2022). Adopting the circular model: Opportunities and challenges of transforming wastewater treatment plants into resource recovery facilities in Saudi Arabia. Journal of Water Reuse and Desalination.
  • Saikaly, P. E., Xu, J., Bian, B., & Ali, M. (2021). Fluidized Chain Elongation Membrane Bioreactor for Production and Recovery of Carboxylates from Organic Biomass. United States Patent and Trademark Office, WO/2022/053983.
  • Alqahtani, M. F., Bajracharya, S., Katuri, K. P., Ali, M., Xu, J., Alarawi, M. S., & Saikaly, P. E. (2021). Enrichment of salt-tolerant CO₂-fixing communities in microbial electrosynthesis systems using porous ceramic hollow tube wrapped with carbon cloth as cathode and for CO₂ supply. Science of the Total Environment, 766.
  • Matar, G. K., Ali, M., Bagchi, S., Nunes, S., Liu, W. T., & Saikaly, P. E. (2021). Relative Importance of Stochastic Assembly Process of Membrane Biofilm Increased as Biofilm Aged. Frontiers in Microbiology, 12.
  • Sapireddy, V., Katuri, K. P., Ali, M., & Saikaly, P. E. (2021). Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell. npj Biofilms and Microbiomes, 7.
  • Ali, M., Katuri, K. P., & Saikaly, P. E. (2019). The role of microbial electrolysis cell in urban wastewater treatment: Integration options, challenges, and prospects. Current Opinion in Biotechnology, 57, 101-110.
  • Ali, M., Shaw, D. R., Albertsen, M., & Saikaly, P. E. (2020). Comparative Genome-Centric Analysis of Freshwater and Marine Anammox Cultures Suggests Functional Redundancy in Nitrogen Removal Processes. Frontiers in Microbiology, 11, 1637.
  • Shaw, D. R., Ali, M., Katuri, K. P., Gralnick, J. A., Reimann, J., Mesman, R., van Niftrik, L., Jetten, M. S. M., & Saikaly, P. E. (2020). Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria. Nature Communications, 11, 2058.
  • Ali, M., Wang, Z., Salam, K. W., Hari, A. R., Pronk, M., van Loosdrecht, M. C. M., & Saikaly, P. E. (2019). Importance of species sorting and immigration on the bacterial assembly of different-sized aggregates in a full-scale aerobic granular sludge plant. Environmental Science and Technology, 53, 8291-8301.

Education

  • Ph.D., Environmental Engineering, Hokkaido University, Japan, 2015
  • M.S., Environmental Engineering, National University of Sciences and Technology (NUST), Pakistan, 2009
  • B.S., City/Urban, Community and Regional Planning, University of Engineering and Technology, Lahore, Pakistan, 2007

Scientific and Professional Membership

Members of Engineers Ireland, 2022 – 2025

International Water Association (IWA), 2025

Pakistan Council for Architects and Town Planners, 2025

Awards

"40 Under 40" honorees for 2024 by American Academy of Environmental Engineers and Scientists (AAEES), 2024