Publications

Peer-reviewed articles, reviews, book chapters, and patents.

For a complete list of publications, please visit Professor Muhammad Ali’s Google Scholar page .
Jump to: 2025 2024 2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2011

2025

Graphical abstract
Genome-Resolved Metatranscriptomics Unveils Distinct Microbial Functionalities Across Aggregate Sizes in Aerobic Granular Sludge
Journal article Year: 2025
DOI: https://doi.org/10.1016/j.ese.2025.100560
Authors:
Mohamed, AYA; Gill, Laurence; Monleon, Alejandro; Pronk, Mario; van Loosdrecht, Mark; Saikaly, Pascal E; Ali, Muhammad
Journal: Environmental Science and Ecotechnology · Pages: 100560 · Publisher: Elsevier
Graphical abstract
Genome-Resolved Metatranscriptomics Provide Insights on Immigration Influence in Structuring Microbial Community Assembly of a Full-Scale Aerobic Granular Sludge Plant
Journal article Year: 2025
DOI: https://doi.org/10.1021/acs.est.4c14471
Authors:
Mohamed, A. Y. A.; Gill, Laurence; Monleon, Alejandro; Pronk, Mario; van Loosdrecht, Mark; Saikaly, Pascal E.; Muhammad Ali
Journal: Environmental Science & Technology
Graphical abstract
Cultivation of anammox bacteria from a tropical lake in Indonesia using a novel filter bioreactor to enhance nitrogen removal efficiency
Journal article Year: 2025
DOI: https://doi.org/10.2166/wst.2025.050
Authors:
Zulkarnaini; Komala, Puti Sri; Putra, Randi Permana; Ali, Muhammad; Matsuura, Norihisa; Koike, Kazuyoshi; Wang, Jinsong; Mawarda, Panji Cahya; Yamamoto-Ikemoto, Ryoko
Journal: Water Science & Technology · Volume: 91 · Issue: 7 · Pages: 811–826 · Publisher: IWA Publishing
Graphical abstract
The circular value of polyhydroxyalkanoate (PHA) bioplastic production from sludge at a large-scale wastewater treatment plant
Journal article Year: 2025
DOI: https://doi.org/10.1016/j.biteb.2025.102272
Authors:
Cormac O'Maolduin; Alexander Compeer; Jappe De Best; Laurence Gill; Muhammad Ali; John Gallagher
Journal: Bioresource Technology Reports

2024

Graphical abstract
Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection
Review Year: 2024
DOI: https://doi.org/10.1016/j.ese.2024.100387
Authors:
Lucia Ruiz-Haddad; Muhammad Ali; Mario Pronk; Mark C.M. van Loosdrecht; Pascal E. Saikaly
Journal: Environmental Science and Ecotechnology
Graphical abstract
Striking a Balance: Decentralized and Centralized Wastewater Treatment Systems for Advancing Sustainable Development Goal 6
Journal article Year: 2024
DOI: https://doi.org/10.1002/aesr.202400097
Authors:
Saadatinavaz, Fateme; Alomari, Mohammed A.; Ali, Muhammad; Saikaly, Pascal E.
Journal: Adv. Energy Sustainability Res · Pages: 2400097
Graphical abstract
Filtration Performance of Biofilm Membrane Bioreactor: Fouling Control by Threshold Flux Operation
Journal article Year: 2024
DOI: https://doi.org/10.1002/aesr.202400097
Authors:
Zhang, Wenxiang; Liang, Wenzhong; Jin, Jiarou; Meng, Shujuan; He, Ziqiang; Ali, Muhammad; Saikaly, Pascal E.
Journal: Chemosphere · Pages: 142458
Graphical abstract
Alginate-like exopolysaccharides extracted from different waste sludges exhibit varying physicochemical and material properties
Journal article Year: 2024
DOI: https://doi.org/10.3389/fmicb.2024.1493782
Authors:
Rehman, Zahid Ur; Ghaani, Masoud; Mohamed, Ahmed YA; Gallagher, John; Saikaly, Pascal E; Ali, Muhammad
Journal: Frontiers in Microbiology · Volume: 15 · Pages: 1493782 · Publisher: Frontiers Media SA
Graphical abstract
Characterization of the core microbial community across different aggregate sizes in full-scale aerobic granular sludge plants and their relevance to wastewater treatment performance
Journal article Year: 2024
DOI: https://doi.org/10.3389/fmicb.2024.1493782
Authors:
Ruiz-Haddad, Lucia; Shaw, Dario Rangel; Ali, Muhammad; Pronk, Mario; van Loosdrecht, Mark CM; Saikaly, Pascal E
Journal: Water Research · Pages: 123036 · Publisher: Elsevier
Graphical abstract
Genomics Tools to Study Membrane-Based Systems
Book chapter Year: 2024
DOI: https://doi.org/10.2166/9781789062977_0315
Authors:
Ali, Muhammad; Haddad, Lucia Ruiz; Haroon, Mohamed Fauzi; Saikaly, Pascal E.
Book: Experimental Methods for Membrane Applications in Desalination and Water Treatment · Publisher: IWA Publishing

2023

Graphical abstract
Performance Evaluation of a Pilot-Scale Aerobic Granular Sludge Integrated with Gravity-Driven Membrane System Treating Domestic Wastewater
Journal article Year: 2023
DOI: https://doi.org/10.1021/acsestwater.3c00178
Authors:
Ali, Muhammad; Singh, Yogesh; Fortunato, Luca; Rehman, Zahid Ur; Manjunath, Sarvajith; Vrouwenvelder, Johannes; Pronk, Mario; van Loosdrecht; andPascal Saikaly, Mark C. M.
Journal: ACS EST Water · Publisher: ACS
Graphical abstract
Combination of advanced coagulation Fe(VI) and UF membrane to effectively remove organic compounds and mitigate biofouling during harmful algal bloom
Journal article Year: 2023
DOI: https://doi.org/10.1016/j.desal.2023.116882
Authors:
Abdullah H. Alshahri; M. Obaidb; Abdullah H.A. Dehwah; Thomas M. Missimer; Muhammad Ali; Noreddine Ghaffour
Journal: Desalination
Graphical abstract
Successful characterisation of on-site wastewater treatment system biomats using the Microbes of Activated Sludge and Anaerobic Digesters (MiDAS) taxonomic database
Conference abstract Year: 2023
DOI: https://doi.org/10.5194/egusphere-egu23-16018
Authors:
Criado Monleon, Alejandro Javier; Knappe, Jan; Somlai, Celia; Ospina Betancourth, Carolina; Ali, Muhammad; Curtis, Thomas P; Gill, Laurence William
Conference: EGU General Assembly Conference Abstracts · Pages: EGU–16018
Graphical abstract
Fluidized chain elongation membrane bioreactor for production and recovery of carboxylates from organic biomass
Patent Year: 2023
DOI: https://patentimages.storage.googleapis.com/f9/20/a2/09ce3002aab67a/US20230332083A1.pdf
Authors:
Saikaly, Pascal; Xu, Jiajie; Bin, BIAN; Ali, Muhammad
Note: US Patent App. 18/044,522

2022

Graphical abstract
Spatial variation of microbial community structure of on-site soil treatment units in a temperate climate and the role of effluent pretreatment in the development of the biomat community
Journal article Year: 2022
DOI: https://doi.org/10.3389/fmicb.2022.915856
Authors:
Criado Monleon, Alejandro Javier; Knappe, Jan; Somlai, Celia; Betancourth, Carolina Ospina; Ali, Muhammad; Curtis, Thomas; Gill, Laurence
Journal: Frontiers in Microbiology · Volume: 13 · Pages: 915856 · Publisher: Frontiers
Graphical abstract
Adopting the circular model: opportunities and challenges of transforming wastewater treatment plants into resource recovery facilities in Saudi Arabia
Journal article Year: 2022
DOI: https://doi.org/10.2166/wrd.2022.038
Authors:
Ali, Muhammad; Hong, Pei-Ying; Mishra, Himanshu; Vrouwenvelder, Johannes; Saikaly, Pascal
Journal: Journal of Water Reuse and Desalination
Graphical abstract
Waste water treatment system using aerobic granular sludge gravity-driven membrane system
Patent Year: 2022
DOI: https://patents.google.com/patent/US12378142B2/en
Authors:
Ali, Muhammad; Katuri, Krishna Prasad; Saikaly, Pascal Elias
Note: US Patent App. 17/295,625

2021

Graphical abstract
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
Journal article Year: 2021
DOI: https://doi.org/10.1016/j.scitotenv.2020.142668
Authors:
Alqahtani, Manal F; Bajracharya, Suman; Katuri, Krishna P; Ali, Muhammad; Xu, Jiajie; Alarawi, Mohammed S; Saikaly, Pascal E
Journal: Science of the Total Environment · Volume: 766 · Pages: 142668 · Publisher: Elsevier
Graphical abstract
Competition of two highly specialized and efficient acetoclastic electroactive bacteria for acetate in biofilm anode of microbial electrolysis cell
Journal article Year: 2021
DOI: https://doi.org/10.1038/s41522-021-00218-3
Authors:
Sapireddy, Veerraghavulu; Katuri, Krishna P; Ali, Muhammad; Saikaly, Pascal E
Journal: npj Biofilms and Microbiomes volume · Volume: 7 · Issue: 47 · Pages: 2021
Graphical abstract
Relative Importance of Stochastic Assembly Process of Membrane Biofilm Increased as Biofilm Aged
Journal article Year: 2021
DOI: https://doi.org/10.3389/fmicb.2021.708531
Authors:
Matar, Gerald K.; Ali, Muhammad; Bagchi, Samik; Nunes, Suzana; Liu, Wen-Tso; Saikaly, Pascal E.
Journal: Frontiers in Microbiology · Volume: 12 · Pages: 708531

2020

Graphical abstract
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
Journal article Year: 2020
DOI: https://doi.org/10.1016/j.watres.2019.115345
Authors:
Ali, Muhammad; Shaw, Dario Rangel; Saikaly, Pascal E
Journal: Water Research · Volume: 170 · Pages: 115345 · Publisher: Pergamon
Graphical abstract
Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria
Journal article Year: 2020
DOI: https://doi.org/10.1038/s41467-020-16016-y
Authors:
Shaw, Dario R; Ali, Muhammad; Katuri, Krishna P; Gralnick, Jeffrey A; Reimann, Joachim; Mesman, Rob; van Niftrik, Laura; Jetten, Mike S M; Saikaly, Pascal E
Journal: Nature Communications · Volume: 11 · Pages: 2058
Graphical abstract
Gel immobilization: A strategy to improve the performance of anaerobic ammonium oxidation (anammox) bacteria for nitrogen-rich wastewater treatment
Journal article Year: 2020
DOI: https://doi.org/10.1016/j.biortech.2020.123642
Authors:
Ahmad, Hafiz Adeel; Ni, Shou-qing; Ahmad, Shakeel; Zhang, Jian; Ali, Muhammad; Hao, Huu; Guo, Wenshan; Tan, Zuwan; Wang, Qi
Journal: Bioresource Technology
Graphical abstract
Comparative genome-centric analysis of freshwater and marine ANAMMOX cultures suggests functional redundancy in nitrogen removal processes
Journal article Year: 2020
DOI: https://doi.org/10.3389/fmicb.2020.01637
Authors:
Ali, Muhammad; Shaw, Dario Rangel; Albertsen, Mads; Saikaly, Pascal E
Journal: Frontiers in Microbiology · Volume: 11 · Pages: 556715 · Publisher: Frontiers
Graphical abstract
Electroactive biofilms on surface functionalized anodes: the anode respiring behavior of a novel electroactive bacterium, Desulfuromonas acetexigens
Journal article Year: 2020
DOI: https://doi.org/10.1016/j.watres.2020.116284
Authors:
Katuri, Krishna P; Kamireddy, Sirisha; Kavanagh, Paul; Ali, Muhammad; Conghaile, Peter Ó; Kumar, Amit; Saikaly, Pascal E; Leach, Donal
Journal: Water Research

2019

Graphical abstract
The role of microbial electrolysis cell in urban wastewater treatment: integration options, challenges and prospects
Review Year: 2019
DOI: https://doi.org/10.1016/j.copbio.2019.03.007
Authors:
Katuri, Krishna; Ali, Muhammad; Saikaly, Pascal
Journal: Current Opinion in Biotechnology · Volume: 57 · Pages: 101–110
Graphical abstract
Draft Genome Sequence of a novel Marine Anaerobic Ammonium-Oxidizing Bacterium “Candidatus Scalindua sp.”
Journal article Year: 2019
DOI: https://doi.org/10.1128/mra.00297-19
Authors:
Ali, Muhammad; Shaw, Dario; Saikaly, Pascal
Journal: Microbiology Resource Announcements · Volume: 8 · Issue: 999 · Pages: e00297–19
Graphical abstract
Evidence of spatial homogeneity in an electromethanogenic cathodic microbial community
Journal article Year: 2019
DOI: https://doi.org/10.3389/fmicb.2019.01747
Authors:
Ragab, Ala'a; Katuri, Krishna; Ali, Muhammad; Saikaly, Pascal E.
Journal: Frontiers in Microbiology
Graphical abstract
Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated with Red Sea Brine Pool
Journal article Year: 2019
DOI: https://doi.org/10.3389/fmicb.2019.02563
Authors:
Alqahtani, Manal; Bajracharya, Suman; Katuri, Krishna Prasad; Ali, Muhammad; Ragab, Alaa; Michoud, Grégoire; Daffonchio, Daniele; Saikaly, Pascal E.
Journal: Frontiers in Microbiology
Graphical abstract
Importance of species sorting and immigration on the bacterial assembly of different-sized aggregates in a full-scale aerobic granular sludge plant
Journal article Year: 2019
DOI: https://doi.org/10.1021/acs.est.8b07303
Authors:
Ali, Muhammad; Wang, Zhongwei; Salam, Khaled W; Hari, Ananda Rao; Pronk, Mario; van Loosdrecht, Mark CM; Saikaly, Pascal E
Journal: Environmental Science & Technology · Volume: 53 · Issue: 14 · Pages: 8291–8301 · Publisher: ACS Publications

2018

Graphical abstract
Aggregation ability of three phylogenetically distant anammox bacterial species
Journal article Year: 2018
DOI: https://doi.org/10.1016/j.watres.2018.06.007
Authors:
Ali, Muhammad; Shaw, Dario Rangel; Zhang, Lei; Haroon, Mohamed Fauzi; Narita, Yuko; Emwas, Abdul-Hamid; Saikaly, Pascal E.; Okabe, Satoshi
Journal: Water Research
Graphical abstract
Insights into the roles of anammox bacteria in post-treatment of anaerobically-treated sewage
Review Year: 2018
DOI: https://doi.org/10.1080/10643389.2018.1474679
Authors:
Qian Wang; Giin-Yu Amy Tan; Mohammad Azari; Xiaowu Huang; Martin Denecke; Yujie Men; Jin-Young Jung; Satoshi Okabe; Muhammad Ali; Yu-Tzu Huang; Zhuoying Wu; Wai-hung Lo; Ji-Dong Gu; Jih-Gaw Lin; Po-Heng Lee
Journal: Critical Reviews in Environmental Science and Technology · Volume: 48 · Issue: 6 · Pages: 655–684
Graphical abstract
Genome-resolved metagenomic analysis reveals roles of microbial community members in full-scale seawater reverse osmosis plant
Journal article Year: 2018
DOI: https://doi.org/10.1016/j.watres.2018.11.012
Authors:
Rehman, Zahid Ur; Ali, Muhammad; Iftikhar, Hina; Leiknes, TOrove
Journal: Water Research
Graphical abstract
High denitrification and anaerobic ammonium oxidation contributes to net nitrogen loss in a seagrass ecosystem in the central Red Sea
Journal article Year: 2018
DOI: https://doi.org/10.5194/bg-15-7333-2018
Authors:
Garcias-Bonet, N; Fusi, M; Ali, M; Shaw, D R; Saikaly, P E; Daffonchio, D; Duarte, C M
Journal: Biogeosciences · Volume: 15 · Pages: 7333–7346

2017

Graphical abstract
Maximum specific growth rate of anammox bacteria revisited
Journal article Year: 2017
DOI: https://doi.org/10.1016/j.watres.2017.03.027
Authors:
Zhang, Lei; Narita, Yuko; Gao, Lin; Ali, Muhammad; Oshiki, Mamoru; Okabe, Satoshi
Journal: Water Research
Graphical abstract
Effects of porous carrier size on biofilm development, microbial distribution and nitrogen removal in microaerobic bioreactors
Journal article Year: 2017
DOI: https://doi.org/10.1016/j.biortech.2017.03.076
Authors:
Ahmad, Muhammad; Liu, Sitong; Mahmood, Nasir; Mahmood, Asif; Ali, Muhammad; Zheng, Maosheng; Ni, Jinren
Journal: Bioresource Technology · Volume: 234 · Pages: 360–369
Graphical abstract
Synergic Adsorption-Biodegradation by Advance Carrier for Enhanced Removal of High-strength Nitrogen and Refractory Organics
Journal article Year: 2017
DOI: https://doi.org/10.1021/acsami.7b01251
Authors:
Ahmad, Muhammad; Liu, Sitong; Mahmood, Nasir; Mahmood, Asif; Ali, Muhammad; Zheng, Maosheng; Ni, Jinren
Journal: ACS Applied Materials & Interfaces
Graphical abstract
Enrichment and physiological characterization of an anaerobic ammonium-oxidizing bacterium 'Candidatus Brocadia sapporoensis'
Journal article Year: 2017
DOI: https://doi.org/10.1016/j.syapm.2017.07.004
Authors:
Narita, Y.; Zhang, L.; Kimura, Z.; Ali, M.; Fujii, T.; Okabe, S.
Journal: Systematic and Applied Microbiology
Graphical abstract
Microbial competition among anammox bacteria in nitrite-limited bioreactors
Journal article Year: 2017
DOI: https://doi.org/10.1016/j.watres.2017.08.052
Authors:
Zhang, Lei; Narita, Yuko; Gao, Lin; Ali, Muhammad; Oshiki, Mamoru; Ishii, Satoshi; Okabe, Satoshi
Journal: Water Research

2016

Graphical abstract
Hydroxylamine-dependent Anaerobic Ammonium Oxidation (Anammox) by “Candidatus Brocadia sinica”
Journal article Year: 2016
DOI: https://doi.org/10.1111/1462-2920.13355
Authors:
Oshiki, Mamoru; Ali, Muhammad; Ali, Shinyako-Hata, Kaori; Satoh, Hisashi; Okabe, Satoshi
Journal: Environmental Microbiology · Volume: 18 · Issue: 9 · Pages: 3133–3143
Graphical abstract
Source identification of nitrous oxide emission pathways from a single-stage nitritation-anammox granular reactor
Journal article Year: 2016
DOI: https://doi.org/10.1016/j.watres.2016.06.034
Authors:
Ali, Muhammad; Rathnayake, Rathnayake M; Zhang, Lei; Ishii, Satoshi; Kindaichi, Tomonori; Satoh, Hisashi; Toyoda, Sakae; Yoshida, Naohiro; Okabe, Satoshi
Journal: Water Research
Graphical abstract
Draft Genome Sequence of Anaerobic Ammonium-Oxidizing Bacterium “Candidatus Brocadia sp. 40”
Journal article Year: 2016
DOI: https://doi.org/10.1128/genomea.01377-16
Authors:
Ali, Muhammad; Haroon, Mohamed Fauzi; Narita, Yuko; Zhang, Lei; Shaw, Dario Rangel; Okabe, Satoshi; Saikaly, Pascal E.
Journal: Genome Announcement · Volume: 4 · Issue: 6 · Pages: e01377–16

2015

Graphical abstract
Physiological characterization of anaerobic ammonium oxidizing bacterium ‘Candidatus Jettenia caeni’
Journal article Year: 2015
DOI: https://doi.org/10.1111/1462-2920.12674
Authors:
Ali, Muhammad; Oshiki, Mamoru; Awata, Takanori; Isobe, Kazuo; Kimura, Zenichiro; Yoshikawa, Hiroaki; Hira, Daisuke; Kindaichi, Tomonori; Satoh, Hisashi; Fujii, Takao; et al.
Journal: Environmental Microbiology · Volume: 17 · Issue: 6 · Pages: 2172–2189 · Publisher: Wiley
Graphical abstract
Rapid and successful start-up of anammox process by immobilizing the minimal quantity of biomass in PVA-SA gel beads
Journal article Year: 2015
DOI: https://doi.org/10.1016/j.watres.2015.04.024
Authors:
Ali, Muhammad; Oshiki, Mamoru; Rathnayake, Lashitha; Ishii, Satoshi; Satoh, Hisashi; Okabe, Satoshi
Journal: Water Research · Volume: 79 · Pages: 147–157 · Publisher: Elsevier
Graphical abstract
Anammox-based technologies for nitrogen removal: Advances in process start-up and remaining issues
Review Year: 2015
DOI: https://doi.org/10.1016/j.chemosphere.2015.06.094
Authors:
Ali, Muhammad; Okabe, Satoshi
Journal: Chemosphere · Volume: 141 · Pages: 144–153

2014

Graphical abstract
Simple, rapid and effective preservation and reactivation of anaerobic ammonium oxidizing bacterium “Candidatus Brocadia sinica”
Journal article Year: 2014
DOI: https://doi.org/10.1016/j.watres.2014.03.036
Authors:
Ali, Muhammad; Oshiki, Mamoru; Okabe, Satoshi
Journal: Water Research · Volume: 57 · Pages: 215–222 · Publisher: Pergamon

2011

Graphical abstract
Simulation of the impacts of land-use change on surface runoff of Lai Nullah Basin in Islamabad, Pakistan
Journal article Year: 2011
DOI: https://doi.org/10.1016/j.landurbplan.2011.05.006
Authors:
Ali, Muhammad; Khan, Sher Jamal; Aslam, Irfan; Khan, Zahiruddin
Journal: Landscape and Urban Planning · Volume: 102 · Issue: 4 · Pages: 271–279 · Publisher: Elsevier