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Dr. Muhammad Ali

Assistant Professor (Civil Struct & Env. Eng.)
CIVIL ENGINEERING BUILDING (NEW)
      
Profile Photo

Dr. Muhammad Ali

Assistant Professor (Civil Struct & Env. Eng.)
CIVIL ENGINEERING BUILDING (NEW)

 MUHAMMAD.ALI@tcd.ie

 3531896 1743


Dr Ali joined Trinity College Dublin in Jan 2022 as an Assistant Professor. He, an environmental engineer by profession, holds an MS degree in Environmental Engineering from National University of Science and Technology (NUST), Pakistan. Furthermore, he earned a PhD in Environmental Engineering from Hokkaido University, Japan. With experience in both industry and academia, Dr Ali has made significant contributions to his field. In addition to his academic pursuits, he also co-founded a start-up company based at King Abdullah University of Science and Technology (KAUST), Saudi Arabia. His research primarily revolves around understanding microbial interactions within natural and engineered ecosystems. His aim is to deepen our understanding of these interactions and explore their broader implications. Moreover, his expertise lies in developing innovative environmental biotechnologies that effectively tackle and mitigate environmental pollution. Through his academic accomplishments, practical experience, and passion for environmental engineering, Dr Ali remains devoted to creating sustainable solutions that address the pressing environmental challenges of our time.
  Environmental engineering   Fresh water pollution   On-Site Wastewater Treatment   Waste water treatment   WASTEWATER TREATMENT   Water & Sanitation   Water Resources Engineering   WATER SUPPLY   Water Treatment
Project Title
 Conversion of ammonium (NH4+) to green hydrogen using electroactive anammox bacteria
From
01-Feb-2023
To
31-Jan-2026
Summary
Funding Agency
SEAI
Programme
National Energy Research Development and Demonstration (RD&D)
Project Title
 Efficient and effective biofiltration of methane generated from on site waste water treatment system
From
To
Summary
Funding Agency
SFI
Programme
SFI National Challenge Fund
Project Title
 Investigating microbial community composition in cores of gas fields in Ireland
From
2023
To
2023
Summary
Funding Agency
dCarbonX Ireland Limited
Project Title
 Consultancy on a KAUST project - scaling up a wastewater treatment technology
From
1st April 2022
To
31st December 2022
Summary
Funding Agency
King Abdullah University of Science and Technology (KAUST) Saudi Arabi
Project Type
Consultancy

Details Date
Editor, Water Research (Elsevier) " promoted from Associate Editor; one of the most prestigious journals in water science and technology Associate Editor 2025; Editor Aug 2026
Serving on the editorial board as Associate Editor in Frontier Microbiology for Microbiotechnology section (speciality section of Frontiers in Microbiology, Frontiers in Bioengineering and Biotechnology and Frontiers in Environmental Science)
External Examination Committee Member for Doctoral Dissertation for Julian Tobon at KAUST, Saudi Arabia. July, 2025
Serving as reviewer for Water Research, Frontier Microbiology, Environmental Science and Technology (ES&T), Environmental Science and Technology Water (ES&T Water) etc.
External expert on an interview panel for the hiring of Director of Civil Engineering Apprenticeship for Atlantic Technological University, Sligo, Ireland. 2024
Co-Founder NuRain September 2024
Guest Associate Editor for Frontiers in Membrane Science and Technology "Innovative Membrane Technology for Resource Recovery from Wastewater." May 2024
Lead Topic Editor for Frontiers in Microbiology "Microbial Biotechnologies for Efficient Wastewater Treatment and Resource Recovery" May 2024
Details Date From Date To
Members of Engineers Ireland 2022 2025
International Water Association (IWA) 2025
Pakistan Council for Architects and Town Planners 2025
Monleon Alejandro Javier Criad, Hardgrave Katherin, Ali Muhamma, Gill Laurence Willia, The significance of pre-treatment on microbial communities within soil treatment units for on-site wastewater systems, Scientific Reports, 2026, Journal Article, PUBLISHED  DOI  URL
Ruiz-Haddad, Lucia and Shaw, Dario Rangel and Ali, Muhammad and Pronk, Mario and van Loosdrecht, Mark C.M. and Samonina, Olena and Saikaly, Pascal E., Genome-ResolvedMetagenomics Revealed the FunctionalPotential of Core Novel and Known Genera Key to Processes in Full-ScaleAerobic Granular Sludge Plants, Environmental Science & Technology, 2026, Journal Article, PUBLISHED  DOI
Mohamed A.Y.A, Gill Laurenc, Monleon Alejandr, Pronk Mari, van Loosdrecht Mar, Saikaly Pascal E, Ali Muhamma, Genome-resolved metatranscriptomics unveils distinct microbial functionalities across aggregate sizes in aerobic granular sludge, Environmental Science and Ecotechnology, 25, 2025, p100560-, Journal Article, PUBLISHED  DOI  URL
Mohamed, A.Y.A., Monleon A., Pronk, M., Van Loosdrecht M., Gill, L.W., Saikaly, P., Ali M., Genome-resolved metatranscriptomics provide insights on immigration influence in structuring microbial community assembly of a full-scale Aerobic Granular Sludge plant, Environmental Science & Technology, 59, 2025, p6126 - 6141, Journal Article, PUBLISHED  DOI
Ruiz-Haddad Luci, Shaw Dario Range, Ali Muhamma, Pronk Mari, van Loosdrecht Mark C.M, Saikaly Pascal E, Characterization of the core microbial community across different aggregate sizes in full-scale aerobic granular sludge plants and their relevance to wastewater treatment performance, Water Research, 274, 2025, p123036-, Journal Article, PUBLISHED  DOI  URL
Zulkarnaini, Zulkarnaini and Komala, Puti Sri and Putra, Randi Permana and Ali, Muhammad and Matsuura, Norihisa and Koike, Kazuyoshi and Wang, Jinsong and Mawarda, Panji Cahya and Yamamoto-Ikemoto, Ryoko, Cultivation of anammox bacteria from a tropical lake in Indonesia using a novel filter bioreactor to enhance nitrogen removal efficiency, Water Science and Technology, 91, (7), 2025, p811-826 , Journal Article, PUBLISHED  DOI
Cormac O'Maolduin and Alexander Compeer and Jappe {De Best, The circular value of polyhydroxyalkanoate (PHA) bioplastic production from sludge at a large-scale wastewater treatment plant, Bioresource Technology Reports, 2025, p102272 , Journal Article, PUBLISHED  DOI
Genomics Tools to Study Membrane-Based Systems in, editor(s)Sergio G. Salinas-Rodríguez; Loreen O. Villacorte , Experimental Methods for Membrane Applications in Desalination and Water Treatment, London UK, 2024, [Muhammad Ali, Lucia Ruiz Haddad, Mohamed Fauzi Haroon, Pascal E. Saikaly], Book Chapter, PUBLISHED  TARA - Full Text  DOI  URL
Lucia Ruiz-Haddad, Muhammad Ali, Mario Pronk, Mark C.M. van Loosdrecht, Pascal E. Saikaly, Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection, Environmental Science and Ecotechnology, 2024, Journal Article, PUBLISHED
Rehman, Zahid Ur and Ghaani, Masoud and Mohamed, Ahmed Y. A. and Gallagher, John and Saikaly, Pascal E. and Ali, Muhammad, Alginate-like exopolysaccharides extracted from different waste sludges exhibit varying physicochemical and material properties, Frontiers in Microbiology, 15, 2024, Journal Article, PUBLISHED  DOI
  

Page 1 of 6
Muhammad Ali, Haley Noteboom, Sean Dillon, Pascal Saikaly, 'A Water Treatment System', Tomkins, EP26186535, 2026, 21 August 2026, Trinity College Dublin, Patent, SUBMITTED
Muhammad ALI, Krishna Prasad KATURI, Pascal Elias SAIKALY, 'WASTE WATER TREATMENT SYSTEM USING AEROBIC GRANULAR SLUDGE GRAVITY-DRIVEN MEMBRANE SYSTEM', United States Patent and Trademark Office, WO2020/104944, 2020, 15 August 2025, KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY, Patent, GRANTED
Muhammad Ali, Sher Jamal Khan, Muhammad Ukasha , Simulation of the impacts of land-use change on surface runoff: Lai Nullah Basin in Islamabad, Pakistan, 1, Saarbrücken, Germany, VDM Verlag Dr. Müller, 2011, Book, PUBLISHED

  


Award Date
Trinity Innovation Award 2024 2024
"40 Under 40" honorees for 2024 by American Academy of Environmental Engineers and Scientists (AAEES) 2024
Research Ally Prize 2024 award 2024
Nominated for Award for Excellence in Research Student Supervision 2024/25 2025
My research sits at the interface of environmental biotechnology, microbial ecology and bioprocess engineering, with the goal of developing sustainable environmental biotechnologies for treating water and wastewater, mitigating pollution and recovering valuable resources from waste streams. A central theme is understanding how microbial communities form, interact and function in natural and engineered ecosystems, and using this knowledge to build more efficient, resilient environmental biotechnologies. My programme focuses on aerobic granular sludge, anammox-based nitrogen removal, biological methane mitigation, and the microbial ecology of wastewater and soil treatment systems. I study the mechanisms governing these biosystems and apply this understanding to improve nutrient removal, mitigate greenhouse gas emissions, and recover resources such as water, energy and biochemicals, while reducing energy and chemical use and footprint. This work combines genome-resolved metagenomics and metatranscriptomics, isotope tracing and mathematical modelling to link microbial activity with real-world treatment performance, and is moving increasingly toward predicting and engineering microbial function. Since joining Trinity in 2022, I have built this into an independent, well-funded programme, securing over €2 million in competitive research funding as PI from Research Ireland (previously Science Foundation Ireland or Irish Research Council), EPA, SEAI, Teagasc and industry partners. This funding supports a growing group of PhD students, postdoctoral fellows and research assistants under my primary supervision. The translational strength of the programme is reflected in two patent applications (2025, 2026) and continuing publications in leading journals including Environmental Science & Technology and Water Research, alongside active international collaborations across various continents. As Founding Director of the Trinity Water Centre (2024"present), I have extended this direction into an institutional platform for water research, recognised through the Trinity Innovation Award, the American Academy of Environmental Engineers and Scientists "40 Under 40" honour and the Research Ally Prize.