Muhammad Ali, Ph.D.

Research Scientists

Research Scientist

Research Interest

Muhammad's research investigates various ecological and microbial aspects of advanced biological wastewater treatment processes, including aerobic granular sludge (AGS) system and biological nitrogen removal processes, particularly anaerobic ammonium oxidation (anammox) process. His primary focus is to understand these engineered ecosystems by metagenomics and metatranscriptomics profiling using high-throughput sequencing, which includes next-generation "short-read" and third-generation "long-read" sequencing methods. Further understanding of these bioprocesses' application would optimize wastewater reuse technologies to provide fit-for-purpose reuse water quality with minimum energy inputs, resources, and carbon footprint.

Selected Publications

  • Comparative Genome-Centric Analysis of Freshwater and Marine ANAMMOX Cultures Suggests Functional Redundancy in Nit... 
    M. Ali, D.R. Shaw, M. Albertsen, P.E. Saikaly
    Frontiers in Microbiology, Vol. 11, p. 1637, (2020)
  • Application of an enrichment culture of the marine anammox bacterium “Ca. Scalindua sp. AMX11” for nitrogen removal... 
    M. Ali, D.R. Shaw, P.E. Saikaly
    Water Research, Vol. 170, p. 115345, (2020)
  • Importance of Species Sorting and Immigration on the Bacterial Assembly of Different-Sized Aggregates in a Full-Sca... 
    M. Ali, Z. Wang, K.W. Salam, A.R. Hari, M. Pronk, M.C.M. van Loosdrecht, P.E. Saikaly
    Environmental Science & Technology, (2019)
  • Draft Genome Sequence of a Novel Marine Anaerobic Ammonium-Oxidizing Bacterium,“Candidatus Scalindua sp.” 
    M. Ali, D.R. Shaw, P.E. Saikaly
    Microbiology Resource Announcements, volume 8, Issue 20, p. e00297-19, (2019)
  • Aggregation ability of three phylogenetically distant anammox bacterial species 
    M. Ali, D.R. Shaw, L. Zhang, M.F. Haroon, Y. Narita, A.-H. Emwas, P.E. Saikaly, S. Okabe
    Water Research, volume 143, pp. 10-18, (2018)
  • Anammox-based technologies for nitrogen removal: Advances in process start-up and remaining issues 
    ​M. Ali, S. Okabe
    Chemosphere, 141, 144-153, (2015)
  • Rapid and successful start-up of anammox process by immobilizing the minimal quantity of biomass in PVA-SA gel bead... 
    M. Ali, M. Oshiki, L. Rathnayake, S. Ishii, H. Satoh, S. Okabe
    Water Research, 79, 147-157, (2015)
  • Physiological Characterization of Anaerobic Ammonium Oxidizing Bacterium “Candidatus Jettenia caeni” 
    M. Ali, M. Oshiki, T. Awata, K. Isobe, Z. Kimura, H. Yoshikawa, D. Hira, T. Kindaichi, H. ...
    Environmental Microbiology, 17. 21722189, (2015)
  • Simple, rapid and effective preservation and reactivation of an anaerobic ammonium oxidizing bacterium “Candidatus ... 
    M. Ali, M. Oshiki, S. Okabe
    Water Research, 57, 215-222, (2014)
  • Simulation of the impacts of land-use change on surface runoff of Lai Nullah basin in Islamabad, Pakistan 
    M. Ali, S.J. Khan, I.Aslam, Z. Khan
    Landscape and Urban Planning, 102, 271-279, (2011)


  • ​Ph.D., Environmental Engineering, Division of Environmental Engineering, Hokkaido University, Sapporo, Japan, 2015
  • M.S., Environmental Engineering, National University of Sciences and Technology, Islamabad, Pakistan, 2009

Professional Profile

  • ​2019-Present: Research Scientist, KAUST, Saudi Arabia
  • 2016-Present: Postdoctoral Fellow, KAUST, Saudi Arabia
  • 2015-2016:  Research Fellow, Laboratory of Water Quality Control Engineering, Hokkaido University, Sapporo, Japan
  • 2010-2012:  Lecturer, IESE (SCEE), National University of Sciences and Technology, Islamabad, Pakistan

KAUST Affiliations

  • ​​Water Desalination and Reuse Center (WDRC)
  • Biological and Environmental Sciences & Engineering Division (BESE)

Research Interests Keywords

​Biological wastewater treatment Biological nitrogen transformation Anaerobic ammonium oxidation​