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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 0.1500
Points 18 points
Teaching period Second Semester
Domestic Tuition Fees (NZD) $1,038.45
International Tuition Fees (NZD) $4,680.00

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Prerequisite
(MICR 221 or GENE 221 or BIOC 221) and MICR 222
Schedule C
Science
Eligibility
MICR 221 or GENE 221, MICR 222
Note: in approved cases another paper from the Science schedule may be substituted for one of these papers.
Contact
sergio.morales@otago.ac.nz
Teaching staff
Teaching Staff: Dr Sergio Morales (Course Convenor), Dr Xochitl Morgan, Dr Jennifer Robson
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.
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
These concepts are further explored in laboratory exercises:
  • 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
Assessment:
  • Group oral presentation (10%)
  • Final written report (25%)
  • Laboratory notebook/R markdown files (10%)
  • Final written exam (55%)
Textbooks
There is no required text for this course but you will be directed to relevant scientific papers during lectures.
Course outline
View course outline for MICR 336
Graduate Attributes Emphasised
Scholarship, Communication, Critical thinking, Environmental literacy, Research, Teamwork.
View more information about Otago's graduate attributes.
Learning Outcomes
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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Timetable

Second Semester

Location
Dunedin
Teaching method
This paper is taught On Campus
Learning management system
Blackboard

Lecture

Stream Days Times Weeks
Attend
L1 Monday 13:00-13:50 28-34, 36-41
Wednesday 13:00-13:50 28-34, 36-41

Practical

Stream Days Times Weeks
Attend
P1 Tuesday 14:00-17:50 32-34, 36
Wednesday 09:00-12:50 32-34, 36
Wednesday 14:00-17:50 32-34, 36