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Dr. Muhammad Ali
Assistant Professor, Civil Struct & Env. Eng.

Publications and Further Research Outputs

Peer-Reviewed Publications

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), 2022 Journal 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, 2022 Journal Article, 2022 TARA - Full Text 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, 2021 Journal 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, 2021 Journal Article, 2021 DOI

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 TECHNOLOGY Patent, 2021 URL

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, 2021 Journal Article, 2021 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 - 123642 Journal Article, 2020 URL 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, 2020 Journal 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, p2058 Journal Article, 2020 DOI

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 TECHNOLOGY Patent, 2020 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, p115345 Journal Article, 2020 DOI

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, p1637 Journal Article, 2020 DOI

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, 2019 Journal Article, 2019 DOI

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^'8301 Journal 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, pe00297-19 Journal Article, 2019

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, p1747 Journal Article, 2019 DOI

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, p101-110 Journal Article, 2019 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, p10-18 Journal Article, 2018 DOI

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, p263-271 Journal Article, 2018 DOI

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, p655-684 Journal Article, 2018 DOI

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, p1-36 Journal Article, 2018 DOI

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, p360-369 Journal Article, 2017 DOI

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^'13200 Journal Article, 2017 DOI

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, p448-457 Journal Article, 2017 DOI

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, p296-303 Journal Article, 2017 DOI

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, p249-258 Journal Article, 2017 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, p3133-3143 Journal Article, 2016 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 , 2016 Journal Article, 2016

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, pe01377-16 Journal Article, 2016 DOI

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/a Journal Article, 2015 DOI

Ali, Muhammad, Okabe, Satoshi, Anammox-based technologies for nitrogen removal: Advances in process start-up and remaining issues, Chemosphere, 141, 2015, p144-153 Journal Article, 2015 DOI

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, p147-157 Journal 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, p147-157 Journal Article, 2015

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, p215-222 Journal 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, p271-279 Journal Article, 2011 DOI

Non-Peer-Reviewed Publications

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, 2011

Research Expertise

Description

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.

Projects

  • Title
    • Consultancy on a KAUST project - scaling up a wastewater treatment technology
  • Funding Agency
    • King Abdullah University of Science and Technology (KAUST) Saudi Arabi
  • Date From
    • 1st April 2022
  • Date To
    • 31st December 2022

Recognition

Representations

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)

Serving as reviewer for Water Research, Frontier Microbiology, Environmental Science and Technology (ES&T), Environmental Science and Technology Water (ES&T Water) etc.

Memberships

International Water Association (IWA)

Pakistan Council for Architects and Town Planners