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MICR336 Microbial Ecology

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.

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 Not offered in 2023 (On campus)
Domestic Tuition Fees (NZD) $1,141.35
International Tuition Fees Tuition Fees for international students are elsewhere on this website.

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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.


Teaching staff

Convenor: Dr Sergio Morales

Other Lecturers:

Paper Structure

Twenty-five lectures and eight 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. Computer lab: Learn how to do an R markdown. Handling and quality controlling amplicon data
  • Week 2. Computer lab: Basic data manipulation and visualization (alpha diversity) in PhyloSeq
  • Week 3. Computer lab: Basic data manipulation and visualization (beta diversity) in PhyloSeq
  • Week 4. Computer lab: Statistical analysis, metadata manipulation and written report


  • 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%)
Teaching Arrangements

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.


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

Course outline

Contact the course convenor for a 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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Not offered in 2023

Teaching method
This paper is taught On Campus
Learning management system