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Te Tari Moromoroiti me te Ārai Mate

MICR 336: Microbial Ecology

Second Semester - 18 points

Course prescription

Ecology of microbial communities (human/environmental settings), what they do, and how we study them, focusing on microbial diversity, rare biosphere and microbial dark matter with their links to ecosystem functions.

"This paper taught me some awesome skills. I learnt to code, analyze data and make scientific figures: all really helpful skills for my future career. It's not the hardest MICR paper either, you guys did an amazing job :)" - MICR 336 student, 2019.

Course overview

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  • Microorganisms control the environmental processes that sustain the Earth's biosphere. From soils to the human gut, microbial communities are emerging as central drivers of the living world.

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  • This paper will introduce you to the many roles of microbes in everyday life and cover topics on microbial diversity, and how it can be studied, as well as how this diversity affects ecosystem functions. We will cover a broad range of ecosystems (from marine to human associated) and provide you with in-depth knowledge of the microbial makeup of the world.




Lecture course overview

There are 25 lectures, which address the following issues:

  • A framework for understanding microbial diversity
  • Understanding microbial functional potential
  • Spatial and temporal variance in microbial communities
  • Environmental stressor-resistance and resilience in microbial ecology

You will gain valuable skills required for working with BIG data; these include quality control, processing of amplicon data, data manipulation with PhylsoSeq and statistical analysis and metadata manipulation in R.

This course is for students interested in ecology of microorganisms in natural environments, and the tools used to study them.

Lab course overview

There are two lectures per week. All labs will be streamed. There are two laboratory sessions per week in week 5-8 of the second semester, with flexible times for students taking lectures on Wednesdays. Due to student numbers the lab days may be streamed and times could be altered.

The following concepts will be explored:

  • Week 1. Sampling, nucleic acid extraction, quality assessment and PCR amplification
  • Week 2. Handling and quality controlling amplicon data
  • Week 3. Basic data manipulation and visualization in PhyloSeq
  • Week 4. Statistical analysis, correlation, and metadata manipulation in R


  • Group oral presentation (formative assessment)
  • Project design-written report (formative assessment)
  • Project design critique (10%)
  • Final written report (25%)
  • Laboratory notebook/R markdown files (10%)
  • Final written exam (55%)

Course prerequisites

(MICR 221 or GENE 221 or BIOC 221) and MICR 222


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


There is no required text for this course but you will be directed to relevant scientific papers during lectures.

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.