Dr. Muhammad Ali

Dr. Muhammad Ali

Assistant Professor, Civil Struct & Env. Eng.

3531896 1743

Biography

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.

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.

Publications and Further Research Outputs

  • Ali, Muhammad, Oshiki, Mamoru, Awata, Takanori, Isobe, Kazuo, Kimura, Zenichiro, Yoshikawa, Hiroaki, Hira, Daisuke, Kindaichi, Tomonori, Satoh, Hisashi, Fujii, Takao, Okabe, Satoshi, Physiological characterization of anaerobic ammonium oxidizing bacterium `Candidatus"Jettenia caeni", Environmental Microbiology, 2015, pn/aJournal Article, 2015, DOI
  • Ali, Muhammad, Oshiki, Mamoru, Rathnayake, Lashitha, Ishii, Satoshi, Satoh, Hisashi, Okabe, Satoshi, Rapid and successful start-up of anammox process by immobilizing the minimal quantity of biomass in PVA-SA gel beads, Water Research, 79, 2015, p147-157Journal Article, 2015
  • Ali, M., Oshiki, M., Rathnayake, L., Ishii, S., Satoh, H., Okabe, S., Rapid and successful start-up of anammox process by immobilizing the minimal quantity of biomass in PVA-SA gel beads, Water Research, 79, 2015, p147-157Journal Article, 2015, DOI
  • Ali, Muhammad, Oshiki, Mamoru, Okabe, Satoshi, Simple, rapid and effective preservation and reactivation of anaerobic ammonium oxidizing bacterium "Candidatus Brocadia sinica", Water Research, 57, 2014, p215-222Journal Article, 2014, DOI
  • Ali, Muhammad, Khan, Sher Jamal, Aslam, Irfan, Khan, Zahiruddin, Simulation of the impacts of land-use change on surface runoff of Lai Nullah Basin in Islamabad, Pakistan, Landscape and Urban Planning, 102, (4), 2011, p271-279Journal Article, 2011, DOI
  • Ali, M., Shaw, D.R., Zhang, L., Haroon, M.F., Narita, Y., Emwas, A.-H., Saikaly, P.E., Okabe, S., Aggregation ability of three phylogenetically distant anammox bacterial species, Water Research, 143, 2018, p10-18Journal Article, 2018, DOI
  • MuhammadAli; Rathnayake M.L.D.Rathnayake; Lei Zhang; Satoshi Ishii; Tomonori Kindaichi; Hisashi Satoh; Sakae Toyoda; Naohiro Yoshida; Satoshi Okabe, Source identification of nitrous oxide emission pathways from a single-stage nitritation-anammox granular reactor , Water Research , 2016Journal Article, 2016
  • Ali, Muhammad, Okabe, Satoshi, Anammox-based technologies for nitrogen removal: Advances in process start-up and remaining issues, Chemosphere, 141, 2015, p144-153Journal Article, 2015, DOI
  • Ahmad Hafiz Adee, Ni Shou-qin, Ahmad Shakee, Zhang Jia, Ali Muhamma, Hao Hu, Guo Wensha, Tan Zuwa, Wang Q, Gel immobilization : A strategy to improve the performance of anaerobic ammonium oxidation ( anammox ) bacteria for nitrogen-rich wastewater treatment, Bioresource Technology, (June), 2020, p123642 - 123642Journal Article, 2020, DOI , URL
  • Manal F. Alqahtani and Suman Bajracharya and Krishna P. Katuri and Muhammad Ali and Ala†a Ragab and Grégoire Michoud and Daniele Daffonchio and Pascal E. Saikaly, Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool, Frontiers in Microbiology, 10, 2019Journal Article, 2019, DOI
  • Manal F. Alqahtani and Suman Bajracharya and Krishna P. Katuri and Muhammad Ali and Jiajie Xu and Mohammed S. Alarawi and Pascal E. Saikaly, Enrichment of salt-tolerant CO2â€"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, 2021Journal Article, 2021, DOI
  • Veerraghavulu Sapireddy and Krishna P. Katuri and Ali Muhammad and Pascal E. Saikaly, Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell, npj Biofilms and Microbiomes, 7, 2021Journal Article, 2021, DOI
  • Krishna P. Katuri and Sirisha Kamireddy and Paul Kavanagh and Ali Muhammad and Peter Conghaile and Amit Kumar and Pascal E. Saikaly and Dónal Leech, Electroactive biofilms on surface functionalized anodes: The anode respiring behavior of a novel electroactive bacterium, Desulfuromonas acetexigens, Water Research, 185, 2020Journal Article, 2020, DOI
  • Gerald K. Matar and Muhammad Ali and Samik Bagchi and Suzana Nunes and Wen-Tso Liu and Pascal E. Saikaly, Relative Importance of Stochastic Assembly Process of Membrane Biofilm Increased as Biofilm Aged, Frontiers in Microbiology, 12, 2021Journal Article, 2021, DOI , URL
  • Muhammad Ali and Zhongwei Wang and Khaled W Salam and Ananda Rao Hari and Mario Pronk and Mark C M Van Loosdrecht and Pascal E Saikaly, Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Scale Aerobic Granular Sludge Plant, Environ Sci Technol, 53, 2019, p8291â^'8301Journal Article, 2019, DOI
  • Muhammad Ali and Dario Rangel Shaw and Pascal E. Saikaly, Draft Genome Sequence of a novel Marine Anaerobic Ammonium-Oxidizing Bacterium †Candidatus Scalindua sp.†, Microbiology Resource Announcements, 8, 2019, pe00297-19Journal Article, 2019
  • Krishna P Katuri and Muhammad Ali and Pascal E Saikaly, The role of microbial electrolysis cell in urban wastewater treatment: integration options, challenges, and prospects, Current Opinion in Biotechnology, 57, 2019, p101-110Journal Article, 2019, DOI , URL
  • Muhammad Ali and Dario Rangel Shaw and Pascal E Saikaly, Application of an enrichment culture of the marine anammox bacterium †Ca . Scalindua sp . AMX11 †for nitrogen removal under moderate salinity and in the presence of organic carbon, Water Research, 170, 2020, p115345Journal Article, 2020, DOI , URL
  • Muhammad Ali and Dario Rangel Shaw and Mads Albertsen and Pascal E Saikaly, Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nitrogen Removal Processes, Frontiers in Microbiology, 11, 2020, p1637Journal Article, 2020, DOI
  • Dario R Shaw and Muhammad Ali and Krishna P Katuri and Jeffrey A Gralnick and Joachim Reimann and Rob Mesman and Laura van Niftrik and Mike S M Jetten and Pascal E Saikaly, Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria, Nature Communications, 11, 2020, p2058Journal Article, 2020, DOI , URL
  • Ala†a Ragab and Krishna P. Katuri and Muhammad Ali and Pascal E. Saikaly, Evidence of Spatial Homogeneity in an Electromethanogenic Cathodic Microbial Community, Frontiers in Microbiology, 10, 2019, p1747Journal Article, 2019, DOI , URL
  • N Garcias-Bonet and M Fusi and M Ali and D R Shaw and P E Saikaly and D Daffonchio and C M Duarte, High denitrification and anaerobic ammonium oxidation contributes to net nitrogen loss in a seagrass ecosystem in the central Red Sea, Biogeosciences Discussions, 2018, 2018, p1-36Journal Article, 2018, DOI , URL
  • Zahid Ur Rehman and Muhammad Ali and Hina Iftikhar and TOrove Leiknes, Genome-resolved metagenomic analysis reveals roles of microbial community members in full-scale seawater reverse osmosis plant, Water Research, 149, 2018, p263-271Journal Article, 2018, DOI , URL
  • Qian Wang and Giin-Yu Amy Tan and Mohammad Azari and Xiaowu Huang and Martin Denecke and Yujie Men and Jin-Young Jung and Satoshi Okabe and Muhammad Ali and Yu-Tzu Huang and Zhuoying Wu and Wai-hung Lo and Ji-Dong Gu and Jih-Gaw Lin and Po-Heng Lee, Insights into the roles of anammox bacteria in post-treatment of anaerobically-treated sewage, Critical Reviews in Environmental Science and Technology, 48, 2018, p655-684Journal Article, 2018, DOI , URL
  • Yuko Narita and Lei Zhang and Zen ichiro Kimura and Muhammad Ali and Takao Fujii and Satoshi Okabe, Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium 'Candidatus Brocadia sapporoensis', Systematic and Applied Microbiology, 40, 2017, p448-457Journal Article, 2017, DOI , URL
  • Lei Zhang and Yuko Narita and Lin Gao and Muhammad Ali and Mamoru Oshiki and Satoshi Ishii and Satoshi Okabe, Microbial competition among anammox bacteria in nitrite-limited bioreactors, Water Research, 125, 2017, p249-258Journal Article, 2017, DOI , URL
  • Lei Zhang and Yuko Narita and Lin Gao and Muhammad Ali and Mamoru Oshiki and Satoshi Okabe, Maximum specific growth rate of anammox bacteria revisited, Water Res, 116, 2017, p296-303Journal Article, 2017, DOI , URL
  • Muhammad Ahmad and Sitong Liu and Nasir Mahmood and Asif Mahmood and Muhammad Ali and Maosheng Zheng and Jinren Ni, Synergic Adsorption-Biodegradation by Advance Carrier for Enhanced Removal of High-strength Nitrogen and Refractory Organics, ACS Applied Materials & Interfaces, 9, 2017, p13188â^'13200Journal Article, 2017, DOI , URL
  • Muhammad Ahmad and Sitong Liu and Nasir Mahmood and Asif Mahmood and Muhammad Ali and Maosheng Zheng and Jinren Ni, Effects of porous carrier size on biofilm development, microbial distribution and nitrogen removal in microaerobic bioreactors, Bioresource Technol, 234, 2017, p360-369Journal Article, 2017, DOI , URL
  • Muhammad Ali and Mohamed Fauzi Haroon and Yuko Narita and Lei Zhang and Dario Rangel Shaw and Satoshi Okabe and Pascal E. Saikaly, Draft Genome Sequence of Anaerobic Ammonium-Oxidizing Bacterium †Candidatus Brocadia sp. 40†, Genome Announcement, 4, 2016, pe01377-16Journal Article, 2016, DOI
  • Mamoru Oshiki and Muhammad Ali and Kaori Shinyako-hata and Hisashi Satoh and Satoshi Okabe, Hydroxylamine-dependent Anaerobic Ammonium Oxidation (Anammox) by †Candidatus Brocadia sinica ", Environ Microbiol, 18, 2016, p3133-3143Journal Article, 2016, DOI
  • Alejandro Javier Criado Monleon, Jan Knappe, Celia Somlai, Carolina Ospina Betancourth, Muhammad Ali, Thomas P. Curtis, Laurence William Gill, Spatial Variation of the Microbial Community Structure of On-Site Soil Treatment Units in a Temperate Climate, and the Role of Pre-treatment of Domestic Effluent in the Development of the Biomat Community, Front. Microbiol., 13, (915856), 2022Journal Article, 2022
  • Muhammad Ali; Pei-Ying Hong; Himanshu Mishra; Johannes Vrouwenvelder; Pascal Saikaly, 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, 2022Journal Article, 2022, DOI , TARA - Full Text
  • 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, KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGYPatent, 2020, URL
  • Pascal SAIKALY, Jiajie XU, Bin BIAN, Muhammad ALI, 'FLUIDIZED CHAIN ELONGATION MEMBRANE BIOREACTOR FOR PRODUCTION AND RECOVERY OF CARBOXYLATES FROM ORGANIC BIOMASS', United States Patent and Trademark Office, WO/2022/053983, 2021, KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGYPatent, 2021, URL
  • Ali, Muhammad Singh, Yogesh Fortunato, Luca Rehman, Zahid Ur Manjunath, Sarvajith Vrouwenvelder, Johannes S. Pronk, Mario van Loosdrecht, Mark C. M. Saikaly, Pascal E., Performance Evaluation of a Pilot-Scale Aerobic Granular Sludge Integrated with Gravity-Driven Membrane System Treating Domestic Wastewater, ACS ES&T Water, 3, (8), 2023, p2681 - 2690Journal Article, 2023, DOI
  • Alshahri Abdullah H, Obaid M, Dehwah Abdullah H.A, Missimer Thomas M, Ali Muhamma, Ghaffour Noreddin, Combination of advanced coagulation Fe(VI) and UF membrane to effectively remove organic compounds and mitigate biofouling during harmful algal blooms, Desalination, 565, 2023, p116882-Journal Article, 2023, DOI , URL
  • Ali, M.A., Siddiki, S.M.A.H., Kon, K., Shimizu, K.-I., A Heterogeneous Niobium(V) Oxide Catalyst for the Direct Amidation of Esters, ChemCatChem, 7, (17), 2015, p2705-2710Journal Article, 2015, DOI
  • Moromi, S.K., Touchy, A.S., Hakim Siddiki, S.M.A., Ali, M.A., Shimizu, K.-I., Synthesis of indoles via dehydrogenative N-heterocyclization by supported platinum catalysts, RSC Advances, 5, (2), 2015, p1059-1062Journal Article, 2015, DOI
  • Alqahtani, M.F., Bajracharya, S., Katuri, K.P., Ali, M., Xu, J., Alarawi, M.S., Saikaly, P.E., 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, 2021Journal Article, 2021, 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, 2024, URL , TARA - Full Text
  • 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, 2024Journal Article, 2024
  • 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, 2011Book

Research Expertise

My 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. Environmental biotechnology and microbial ecology are naturally tied together. Understanding the microbial ecology of microbial communities is essential to harness their power for resource recovery fully. I work at the interface of microbiology, microbial ecology, and bioprocess engineering. My primary focus is to understand these water-related engineered ecosystems using advanced omics tools (metagenomics and metatranscriptomics, third-generation (long-read) 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.

  • Title
    Refined estimates of atmospheric emissions associated with wastewater treatment processes for Ireland
    Summary
    Funding Agency
    EPA
  • Title
    Investigating microbial community composition in cores of gas fields in Ireland
    Summary
    Funding Agency
    dCarbonX Ireland Limited
    Date From
    2023
    Date To
    2023
  • Title
    Consultancy on a KAUST project - scaling up a wastewater treatment technology
    Summary
    Funding Agency
    King Abdullah University of Science and Technology (KAUST) Saudi Arabi
    Date From
    1st April 2022
    Date To
    31st December 2022
  • Title
    Conversion of ammonium (NH4+) to green hydrogen using electroactive anammox bacteria
    Summary
    Funding Agency
    SEAI
    Date From
    01-Feb-2023
    Date To
    31-Jan-2026
  • Title
    Efficient and effective biofiltration of methane generated from on site waste water treatment system
    Summary
    Funding Agency
    SFI

Ecology and Marine Biology, Waste, Resource, Management & Chemicals, Waste to energy, Microbiology, Environmental Sciences including Marine, Water Quality and the Aquatic Environment, Population Health, Public & Environment Health, Industrial Biotechnology & Bioprocessing, Mathematical and Computational Biology including Bioinformatics and Systems Biology,

Recognition

  • Members of Engineers Ireland 2023
  • International Water Association (IWA)
  • Pakistan Council for Architects and Town Planners
  • Serving as reviewer for Water Research, Frontier Microbiology, Environmental Science and Technology (ES&T), Environmental Science and Technology Water (ES&T Water) etc.
  • 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)