Accessibility Skip to Global Navigation Skip to Local Navigation Skip to Content Skip to Search Skip to Site Map Menu

MICR336 Applied and Environmental Microbiology

Fundamental principles of environmental microbiology and microbial biotechnology for the generation of products and processes for industry and the environment including biofuels, bioremediation, recombinant proteins and the commercialisation of science.

Microorganisms provide the tools and engines that drive many important biotechnological and environmental processes. From discoveries of new technologies based on natural systems to the use of these tools at industrial scales, this paper will introduce you to the many roles of microbes in everyday life. Tackling the world's emerging environmental problems and developing new technologies for industrial processes will require in-depth knowledge of the microbial makeup of the world, the application of processes catalysed by microbes for human benefit and the ability to bio-prospect and bio-engineer new tools from natural systems.

Paper title Applied and Environmental Microbiology
Paper code MICR336
Subject Microbiology
EFTS 0.1500
Points 18 points
Teaching period Second Semester
Domestic Tuition Fees (NZD) $1,018.05
International Tuition Fees (NZD) $4,500.00

^ Top of page

Prerequisite
MICR 221
Recommended Preparation
MICR 222
Schedule C
Science
Eligibility
Appropriate for students studying Microbiology, Biochemistry and Genetics.
Contact
sergio.morales@otago.ac.nz
Teaching staff
Convenor: Dr Sergio Morales
Other lecturers: Professor Phil Bremer (Department of Food Science), Dr Robin Simmonds, Simon Jackson and Adam Heikal.
Paper Structure
Lectures address the following issues:
  • How to develop and launch your own commercialisable biotechnology idea
  • How to generate biotechnological products using recombinant bacteria and viruses
  • What technologies are available for bioremediation of contaminated sites
  • What technologies are available for large-scale industrial processes, including fermentation
  • What technologies are available for generation of biofuels
These concepts are further explored in laboratory exercises.

Assessment:
  • An individual commercialisation case study report 25% (mid-semester)
  • Lab assessment 10% (to be advised)
  • Final written exam 65%
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
Text books are not required for this paper, but you will be directed to relevant scientific papers during lectures, and you may like to read the following text which is held in the Science Library:

BR Glick and JJ Pasternak 2003 Molecular Biotechnology: Principles and applications of recombinant DNA. 3rd Edition, ASM Press
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 microbiological knowledge to solve real-world issues
  • Display the ability to integrate basic scientific knowledge into problem solving at a practical level
  • Develop an enhanced ability to communicate ideas about microbiology to a lay and specialised audience

^ Top of page

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

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 Tuition Fees for 2018 have not yet been set
International Tuition Fees Tuition Fees for international students are elsewhere on this website.

^ Top of page

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.

^ Top of page

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