Skip to Navigation Skip to Content Skip to Footer

Microbiology Logo Microbiology & Immunology
Te Tari Moromoroiti me te Ārai Mate

MICR 222: Microbes in Action

Second Semester - 18 points

Course prescription

The ecology and functional diversity of microorganisms in natural ecosystems and the use of microorganisms in bioremediation, biocontrol, and industrial processes.

Course overview

Screen Shot 2020 05 28 at 1.20.26 PM

  • Microbes are ubiquitous and dominate the biosphere, but our understanding of the full contribution microbes and their communities make to life on Earth is hindered by our lack of ability (imagination) to culture microbes from the environment.
  • In MICR 222 you will study microbes in the environment and learn of new technologies used to study microbes at a community level. 
Screen Shot 2020 05 28 at 1.20.36 PM  
  • The course will focus on gaining an appreciation of the vast metabolic potential of bacteria and how this has been harnessed and put to work in biotechnology and agriculture.



Lecture course overview

MICR 222 is a 32-lecture course, lectures will cover the following areas:

Module 1: Microbial Evolution and Ecology

1. Molecules, origins of life and evolution

2. Microbial diversity: What drives it and how can we measure it

3. Bacterial species concept

4. Bacterial physiology and microbial ecology

5. Microbial community genetics, metabolic potential and how can we study them

Module 2: Microbial Interactions and Biogeochemical Cycles

6. Development of microbial communities

7. Microbial-Animal interactions

8. Oceans: marine microbes as mediators of global cycles

9. A living bioreacter - the symbiotic rumen microbiome

10. More than just dirt - how soils and microbes sustain the Earth's biosphere

Module 3: Water Microbiology and Public Health

11. The freshwater environment

12. The marine environment

13. Waterborne pathogens

14. Providing a safe drinking water supply

15. Measuring water quality

Module 4: Putting Microbes to Work in the Environment

16. Microbial life in biofilms

17. Microbes and biofouling

18. Microbes to clean the environment

19. Microbial design for bioremediation

Module 5: Putting microbes to Work in Biotechnology

20. Microbes as biocontrol and biological warfare

21. Microbes to produce recombinant proteins

22. Antibiotics produced by bacteria

23. Microbes in food and industrial microbiology

24. Probiotics

Module 6: Plant-Microbe Interactions

25. The plant-microbiome and its effects on plant growth - biological control in the rhizosphere

26. The plant-microbiome and its effects on plant growth - the phyllosphere and ice-nucleating bacteria

27. The rhizobium-legume symbiosis: Nodulation

28. The rhizobium-legume symbiosis: Nitrogen fixation

29. Mycorrhizae

30. Plant-pathogen interactions: innate immunity

31. Plant-pathogen interactions: gene-for-gene resistance

32. Agrobacterium - nature's genetic engineer

Lab course overview

The MICR 222 laboratory course has been designed to complement the lecture course. In the 7 labs you will:

  • Look at microbes as part of bacterial communities and the microbial interactions that can occur
  • See the impact of microbes in the nitrogen cycle, and the critical role they play in nitrogen recycling 
  • Look at how microbes cope with extreme environments including extreme heat, salinity, UV light and pH
  • Setup your own Winogradsky column and see what happens to the bacterial populations over the course of the labs
  • Explore the impact of microbes in the dairy industry – what microbes do you find associated with milk, how they affect quality of the milk you drink and how they can be harnessed to make different cheeses
  • Visit local industries to see microbes in action

Attendance at all 7 laboratory sessions is compulsory


  1. Lecture test (15%)
  2. Laboratory test (15%)
  3. A 3-hr final exam (70%)

Course prerequisites


CELS 191 & CHEM 191 & 72 further points

Recommended preparation:

MICR 221


Essential text:

Prescott's Microbiology by Willey, Sandman and Wood, 12th edition, 2023, McGraw-Hill Publishers.

This textbook is available in the library, both as a printed copy Close Reserve and as an eBook.

For more information

View the details of this paper on the University of Otago website

Students are encouraged to contact staff by email to make arrangements for a time to discuss course-related matters.