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MICR336 Microbial Ecology

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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.Note: This paper includes additional non-streamed lab time that does not appear in the timetable. Please contact the department for further details.

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. 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.

Paper title Microbial Ecology
Paper code MICR336
Subject Microbiology
EFTS 0.15
Points 18 points
Teaching period Semester 2 (On campus)
Domestic Tuition Fees (NZD) $1,092.15
International Tuition Fees (NZD) $5,314.50

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

Note: In approved cases another paper from Science Schedule C may be substituted for one of the prerequisite papers.


Dr Sergio Morales

Teaching staff

Convenor: Dr Sergio Morales

Other Lecturers:

Paper Structure

25 lectures and 8 laboratory sessions
Lectures 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.

These concepts are further explored in laboratory exercises:

  • Week 1. Wet lab: Laboratory based experimental work will include sampling, nucleic acid extraction, quality assessment and PCR amplification. Computational analysis of experimental work will be covered in weeks 2 – 4 and will be held in the computer labs (CAL).
  • Week 2. Computer lab: Handling and quality controlling amplicon data
  • Week 3. Computer lab: Basic data manipulation and visualization in PhyloSeq
  • Week 4. Computer lab: Statistical analysis, correlation, and metadata manipulation in R


  • Group oral presentation (10%)
  • Final written report (25%)
  • Laboratory notebook/R markdown files (10%)
  • Final written exam (55%)
Teaching Arrangements
There are two lectures per week. There are two laboratory sessions per week in week 5-8 of the second semester, with flexible times for students taking lectures with overlap. Students may leave the lab for other commitments such as lectures and are able to plan their experiments to fit in with these commitments.

Textbooks are not required for this paper but you will be directed to relevant scientific papers during lectures.

Course outline

View the MICR 336 course outline

Graduate Attributes Emphasised
Scholarship, Communication, Critical thinking, Environmental literacy, Research, Teamwork.
View more information about Otago's graduate attributes.
Learning Outcomes

Students who successfully complete this paper will

  • Be able to demonstrate and utilise knowledge of the ecology of microorganisms in natural environments, and the tools used to study them
  • Display the ability to integrate basic scientific knowledge and link ecosystem processes with changes in microbial ecology and macro-ecology
  • Develop an enhanced ability to communicate ideas about microbiology to a lay and specialised audience

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Semester 2

Teaching method
This paper is taught On Campus
Learning management system


Stream Days Times Weeks
A1 Monday 13:00-13:50 28-34, 36-41
Wednesday 13:00-13:50 28-34, 36-41


Stream Days Times Weeks
A1 Tuesday 14:00-17:50 32-34, 36
Wednesday 09:00-11:50 32-34, 36
Wednesday 14:00-17:50 32-34, 36