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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

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  • 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. 
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  • 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. Community genetics

5. Bacterial physiology and microbial ecology

Module 2: Microbial Interactions and Biogeochemical Cycles

6. Development of microbial communities

7. Bacteria, invertebrates, illumination, genetic engineering and fertility

8. Oceans: geochemical cycles

9. More than just dirt: how soils are formed and how microorganisms mediate soil processes

10. Soils: C and N cycling and the link to greenhouse gas emissions

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: Plant-Microbe Interactions

16. Biological control in the rhizosphere

17. The phyllosphere and ice-nucleating bacteria

18. Mycorrhizae

19. The Rhizobium-legume symbiosis: nodulation

20. The Rhizobium-legume symbiosis: nitrogen fixation

21. Plant-pathogen interactions: innate immunity

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

23. Agrobacterium: nature’s genetic engineer

Module 5: Putting microbes to work in the environment

24. Biofilms and biofouling

25. Bioremediation of sewage

26. Bioremediation of crude oil

27. Bioremediation of xenobiotics

28. Biological control of insect and animal pests

29. Industrial production of primary metabolites

30. Industrial production of secondary metabolites

31. Industrial production of recombinant proteins 

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 (10%)
  2. Laboratory test (10%)
  3. Laboratory assignment on nitrogen cycle (10%)
  4. 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, Sherwood and Woolverton, 10th edition, 2017, McGraw-Hill Publishers OR Prescott's Microbiology by Willey, Sandman and Wood, 11th edition, 2020, McGraw-Hill Publishers

Teaching staff

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.

For more information on this course, please contact Dr Judith Bateup.