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Online course

2. Microbiology and Metabolism

Microorganisms are central to biological wastewater treatment. This contemporary course covers basic topics of wastewater microbiology by questioning: “what are microorganisms and how do they grow?”. It progresses from descriptions of microbial cells and physiology, metabolic diversity and trophic groups, and niche establishment along environmental gradients, to formulations of stoichiometry, thermodynamics, and kinetics of microbial growth useful for modelling. It further addresses microbial ecology and ecophysiology methods to track microorganisms and functionalities in sludge. The course scope and coverage are expanded with examples and exercises that will enrich your experience in this exciting field. Several videos deal with experimental aspects of modern microbiology and molecular methods applied in wastewater treatment, and with simple mathematical models of microbial interactions in communities. By the end of the course, you will be able to approach microbial processes involved in nutrient removal with confidence. 

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Welcome by Prof. David Weissbrodt

Course information

  • Learning objectives

    After completion of the course you should be able to approach microbial processes involved in nutrient removal with confidence, by addressing these questions: what are microorganisms, how do they grow, how can we select for them, how can we model microbial processes, how can we monitor them?

  • Syllabus

    This course covers the following topics:

    • Basics of wastewater microbiology
    • Microbial cells and physiology
    • Metabolic diversity and trophic groups
    • Microbial niches along gradients
    • Stoichiometry, thermodynamics, and kinetics of microbial growth
    • Illustrations with simple mathematical models
    • Microbial ecology and ecophysiology methods
    • Integration of microbial knowledge in engineering practice
  • Organization

    This course consists of video lectures, presentation slides, reading materials, exercises, and assignments with solutions. In principle, each video presentation has its complementary presentation slides. All videos are available for viewing in the section “Video-recorded presentations”. The materials are packaged in three (.zip) files, namely, the “Videos”, the “Presentations”, and the “Documents”. All the files can be downloaded from the section “Download course materials”. Some files may be of considerable size, so you need to ensure that your computer has sufficient bandwidth and capacity for downloading.

  • Delivery method

    This course is currently designed for a SELF-STUDY mode. It is FREE, and does not include guidance, support, exams, assessment, and certification. It is possible that shortly, the series (or its parts) will be adopted by institutions that may deliver the guided version, including certification. As soon as this is the case, it will be advertised on this website.

  • Open Access

    The content is available for free unlimited access and use, consistent with Global Sanitation Graduate School’s commitment to ensuring open access to information and knowledge. Please note that the video materials fall under the Attribution 4.0 International (CC BY 4.0) license (, presentations under the Attribution 4.0 International (CC BY 4.0) license  (, readers (OA books of IWA Publishing) under the Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license (, and other readers under the license specified by the publisher. Although care has been taken to ensure the integrity and quality of these materials and information, no responsibility is assumed by the author(s), Global Sanitation Graduate School, or IHE Delft Institute for Water Education for any damage to property or persons as a result of the use of these materials and/or the information contained herein.

Video-recorded presentations

Here you can watch all video-recorded lectures in this course.

2.1 Introduction - Managing Microorganisms in Biological Wastewater Treatment

David Weissbrodt


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2.2 Microbial Cells - What are Microorganisms?

David Weissbrodt


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2.3 Microbial Growth - How do Microorganisms Grow?

David Weissbrodt


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2.4 Trophic Groups - What Shapes Microbial Diversity?

David Weissbrodt


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2.5 Elemental Cycles - How do Microbes Convert Nutrients?

David Weissbrodt


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2.6 Growth Systems - Sketching Microbial Metabolisms

David Weissbrodt


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2.7 Microbial Selection - Using Microbial Knowledge to Model and Analyze Selection

David Weissbrodt


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2.8 Stoichiometry - Redox Reactions

Michele Laureni

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2.9 Stoichiometry: Anabolism, Catabolism and Metabolism

Michele Laureni

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2.10 Thermodynamics: Fundamentals and Non-ideal Corrections

Michele Laureni

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2.11 Thermodynamics: Equilibrium and Non-equilibrium

Michele Laureni

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2.12 Kinetics: Activation Energy and Herbert-Pirt Equation

Michele Laureni

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2.13 Kinetics: Monod Equation and Parameters Generalization

Michele Laureni

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2.14 Simulating Microbial Interactions: Spreadsheet Implementations

Michele Laureni

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2.15 From Process to Microbial and Metabolic Scales - Where is the Microbial Information Contained?

David Weissbrodt


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2.16 Microbial Ecology Methods - Characterizing Mixed Cultures

David Weissbrodt


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2.17 Microbial Ecology Methods - Application to PAOs

David Weissbrodt


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2.18 Conceptual Ecosystem Models - Assembling Taxonomies and Functions

David Weissbrodt


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2.19 MiDAS Field Guide: Harmonizing Knowledge on Microbial Ecology and Physiology in Wastewater Treatment

Per Halkjær Nielsen

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2.20 Using Microbial Information in BNR Process Development and Innovation

Mark C.M. van Loosdrecht

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2. 21 Microbes in Process Optimization - From Physical to Chemical to Biological Insights

Yves Comeau


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2.22 Take Home - Microbial Knowledge for Biological Wastewater Treatment

David Weissbrodt


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Download course materials

In this section, you can download all presentations, and other documents that make up this course.

  • 2 │ Videos (.zip)
    David Weissbrodt ▪ Michele Laureni ▪ Per Halkjær Nielsen ▪ Yves Comeau ▪ Mark M.C. van Loosdrecht
    (0.0 MB)
  • 2 │ Presentations (.zip)
    David Weissbrodt ▪ Michele Laureni ▪ Per Halkjær Nielsen ▪ Yves Comeau ▪ Mark M.C. van Loosdrecht
    (0.0 MB)
  • 2 │ Documents (.zip)
    David Weissbrodt ▪ Michele Laureni ▪ Per Halkjær Nielsen ▪ Yves Comeau ▪ Mark M.C. van Loosdrecht
    (0.0 MB)


Prof. Damir Brdjanovic, PhD

Course resource person | IHE Delft Institute for Water Education