2010BPS Systems Microbiology Semester 2 2009 - Griffith University


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Academic Organisation: School of Biomolecular and Physical Sciences
Faculty: Science, Environment, Engineering and Technology
Credit point value: 10
Student Contribution Band: Band 4A (Nat Priority Band)
Course level: Undergraduate
Campus/Location/Learning Mode: Nathan / On Campus / In Person
Convenor/s: Dr Tony Greene (Nathan)
Enrolment Restrictions: Nil
This document was last updated: 19 June 2009
This course covers emerging areas in microbiology. It integrates the latest knowledge in fundamental
microbial processes with genomics to understand the functioning of microbial cells and their interactions
with the surrounding environment. It looks at the critical roles played by microbes in the environment,
health, evolution and energy production.


The course aims to provide an understanding of the functioning of microbial cells with emphasis on their
structure, physiology, metabolism and genome. The systems microbiology approach forms a basis for
understanding applied microbiology including food microbiology, molecular microbiology and
biotechnology. The course examines the interactions of microorganisms with the environment, plants,
animals and humans, biogeochemical cycles and the impacts of microbes on the environment. It provides
in-depth studies of the molecular biology of prokaryotes as applied to genes, genome organisation,
evolution and physiology. The important and varied role of microorganisms in industrial and
biotechnological processes will also be studied. The course covers a number of emerging areas in
microbiology and examines survival mechanisms and the absolute limits of life in such habitats as
hydrothermal vents, saline lakes, deep sea trenches, and the possibility of extraterrestrial life.
The course follows on from the core General Microbiology course and prepares students for the option of
further postgraduate studies in Microbiology or Biotechnology and/or employment in a variety of industries.
It further emphases the importance of microorganisms in our understanding of life and will provide
information on current views and recent trends in microbial ecology, the role of microorganisms in
environmental and industrial processes and the origin of life. It also provides a background to the scientific
question- is there life on other planets and if yes, what would life be like (Astrobiology). After completion of
this course, students will have an understanding of the following:
1. The range of environments that microbes inhabit
2. The diversity and role of microorganisms in the environment
3. Characteristics, organisation and function of microbial genomes
4. Evolutionary changes in organisms, extremophiles and the prospect of life elsewhere
5. Growth, survival and evolution of microbes through interactions with their environment
6. How microbes are used in biotechnology processes and to improve the environment
7. How to critically analyse scientific literature and be able to present this information in the form of a
written assignment
This course will be presented as a series of lectures and workshops. Both the lectures and workshops can
be interactive and the students are encouraged to ask questions and contribute particularly during
workshops. Students are expected to attend all these classes.
Lectures will be presented as three-hour sessions once a week. Workshop classes are timetabled for one
hour at regular intervals through the semester. The workshops will be in the format of a set of prescribed
questions that will reinforce lecture material and encourage students to consult the texts and additional
Contact Summary

The lectures will be used to provide content, context and detailed explanation of the course material. There
will also be opportunity for students to ask questions and discussions. Students will be given a selection of
topics to prepare and submit a written assignment and deliver a seminar.


The lecture content will provide a guide for the students to then consult the prescribed texts and any extra
reading material suggested during the course to enhance learning. Microorganisms exist in all corners and
crevices of our planet and an understanding of their role and function in their natural habitat is critical to
our survival and quality of life. Course content will be presented in seven modules with each module
separated into numerous topics. Depending on the depth of material, the modules can run for one, two or
three weeks. The following table represents a summary of the course content and there maybe some slight
variations in the weeks in which modules are presented. A more detailed schedule will be provided in the
first class and on the learning@griffith course website.

Module 1. Microbial diversity
Microbial ecology
Aquatic, terrestrial & human habitats
Module 2. Genomics
Cell structure

Gene transfer
Molecular evolution
Module 3. Astrobiology
Extreme environments
Origins of life

Diversity of life
Extraterrestrial life
Module 4. Microbial Physiology
Microbial growth
Environmental effects
Module 5. Biogeochemical cycles
Major cycles
Metabolic processes

Environmental impacts: global warming,
biodegradation, acid release
Module 6. Microbial interactions
Microbial ecosystems
Microbe-microbe interactions

Microbe-plant interactions
Microbe-animal interactions
Module 7. Microbial biotechnology
Foods, supplements & beverages
Pharmaceutical chemicals

Commercial enzymes

Microbial-enhanced oil recovery (MEOR),
Wastewater treatment
Summary of Assessment

The following table summaries the assessment items for the course:

Due Day and
1. Assignment 1200-1500
15% 100 7 Friday Week 11,


2. Quiz 1 45 mins 15% 30 1-3 Friday Week 6
(in workshop)
3. Quiz 2 45 mins 15% 30 4-6 Friday Week 12
(in workshop)
4. Examination 2 hrs 55% 110 1-6
Assessment Details

Overall assessment in this course is designed to ensure students have understood and attained the four
learning outcomes listed above.
In order to pass this course a student must obtain a minimum overall grade of 50%.
The four assessment items for this course include:
Item 1; Assignment
The assignment will be used to assess the student’s ability to research and retrieve information from the
web, books and journals on a particular topic. It is expected to be written in a scientific form and is to be
primarily journal and web based, though you can use reference books as well. Journal articles, web sites
and books must be correctly referenced, preferably in the Harvard style. Students will receive the topics
within the first few weeks of semester. Failure to submit the assignment by the specified time will result in a
loss of 10% of marks per day unless there is documentary evidence of medical or other extenuating
circumstances preventing submission on time.
The assignment must be submitted by 5pm on Friday of Week 11:
Nathan: in person to the convenor at the lecture/workshop or at the Off Campus & Assignment Handling
Service (OCHAHS) office 0.02 Willet Centre (N53)
Items 2 and 3: Quizzes
The quizzes are a set of multiple choice questions that will cover the lecture material and readings from the
relevant modules. The questions are designed to assess the students’ ability to assimilate the lecture and
reading material that has been presented. They test the students understanding of the microbiological
concepts and fundamental aspects of microorganisms presented in the lectures.
Attendance at both quizzes is compulsory. Quizzes will be run in the workshop timeslot. Failure to
attend or complete each quiz at the specified time will result in a zero mark for that quiz unless
documentary evidence of medical or other extenuating circumstances is provided to the convenor within
one week
of the date of the quiz. Where satisfactory documentation is provided, an alternative sitting of
the quiz can be offered.
Item 4: End of semester examination
The final exam is aimed at testing the overall concepts and understanding of the course detail for all
modules. It will be a combination of multiple choice questions and short answer questions. It will be
undertaken during the end of semester exam period.
Return of Assessment Items

Results for the quizzes will be advised on the noticeboard on the
website within a week
after the quiz is held. Feedback can be provided when the results are given. Assignments will be available
for collection, with the venue and time to be advised on the


The course contributes to the development of graduate skills that students should acquire throughout their
program. These skills are listed below.

Graduate Skills

Effective communication (written)

Effective communication (oral)

Effective communication (interpersonal)

Information literacy

Problem solving

Critical evaluation

Work autonomously

Work in teams

Creativity and innovation

Ethical behaviour in social / professional / work environments

Responsible, effective citizenship

Course Convenor

Convenor Details
Campus Convenor Dr Tony Greene

Office Location N34 2.34
Phone 3735 4427
Fax 3735 7773
Consultation times Please make contact via email, phone or at lecture to arrange an
individual consultation if required.
Additional teaching team members

Details of any additional members to the teaching team will be provided in the lectures, via email or on the
noticeboard of the
The course convenor will communicate and make any announcements in the lectures and workshops.
Announcements and information will also be placed on the noticeboard of the Learning@griffith website
and students should consult it regularly in between scheduled classes. As students are expected to attend
the scheduled classes, explanations and clarification of any issues can be made then. Students can also
contact the convenor via email or phone or make an appointment at a suitable time for an individual
consultation. Students are advised to limit email communication to questions or issues that require a short
and definitive answer. If more complex issues or questions need to be discussed a consultation time
should be organised.


It is expected that students will take notes during lectures. Resources of the library and electronic
databases are the best source of additional information. Additional source material will be discussed in
lectures and may be posted to the learning at Griffith site appropriate to this course during semester.
There are no prescribed textbooks but the following textbook references will assist in learning.
• Atlas and Bartha, 1998. Microbial Ecology-Fundamentals & Applications. Benjamin Cummings
Press, 4
• Madigan, Martinko and Parker, 2009. Brock Biology of Microorganisms, Prentice Hall International,
12th edition
• Prescott, Harley and Klein, 2008. Microbiology. McGraw-Hill, 8

Enrolment in this course is granted on the basis that a grade of P (Pass) or better has been achieved in
any Pre-requisite or Prior Assumed requirement in this course as listed in this outline. Failure to meet this
requirement may result in you having difficulty with the course and not being able to complete it
successfully. Any additional support or special assistance cannot be expected nor requested if the
prerequisite and/or prior assumed requirements have not been met.
Students should refer to the Learning@Griffith website for further information about this course.
Students must conduct their studies at the University honestly, ethically and in accordance with accepted
standards of academic conduct. Any form of academic conduct that is contrary to these standards is
academic misconduct and is unacceptable.
Some students engage deliberately in academic misconduct, with intent to deceive. This conscious, pre-
mediated form of cheating is one of the worst forms of fraudulent academic behaviour, for which the
University has zero tolerance and for which penalties, including exclusion from the University, will be
However the University recognises many students commit academic misconduct without intent to deceive.
These students may be required to undertake additional educational activities to remediate their behaviour.
Specifically it is academic misconduct for a student to:
• Cheat in examinations and tests by communicating, or attempting to communicate, with a fellow
individual who is neither an invigilator or member of staff; by copying, or attempting to copy from a
fellow candidate; attempting to introduce or consult during the examination, any unauthorised
printed or written material, or electronic calculating or information storage device; or mobile
phones or other communication device, or impersonates another.

• Fabricate results by claiming to have carried out tests, experiments or observations that have not
taken place or by presenting results not supported by the evidence with the object of obtaining an
unfair advantage.

• Misrepresent themselves by presenting an untrue statement or not disclosing where there is a
duty to disclose in order to create a false appearance or identity.

• Plagiarise by representing the work of another as their own original work, without appropriate
acknowledgement of the author or the source. This category of cheating includes the following:


1. collusion, where a piece of work prepared by a group is represented as if it were the student's
2. acquiring or commissioning a piece of work, which is not his/her own and representing it as if it
were, by
 purchasing a paper from a commercial service, including internet sites, whether pre-written
or specially prepared for the student concerned
 submitting a paper written by another person, either by a fellow student or a person who is
not a member of the University;
3. duplication of the same or almost identical work for more than one assessment item;
4. copying ideas, concepts, research data, images, sounds or text;
5. paraphrasing a paper from a source text, whether in manuscript, printed or electronic form, without
appropriate acknowledgement;
6. cutting or pasting statements from multiple sources or piecing together work of others and
representing them as original work;
7. submitting, as one own work, all or part of another student's work, even with the student's
knowledge or consent.

A student who willingly assists another student to plagiarise (for example by willingly giving them their
own work to copy from) is also breaching academic integrity, and may be subject to disciplinary action.
Visit the following web sites for further details:
Institutional Framework for Promoting Academic Integrity among Students

Academic integrity for students

The University uses plagiarism detection software. Students should be aware that your Course Convenor
may use this software to check submitted assignments. If this is the case your Course Convenor will
provide more detailed information about how the detection software will be used for individual assessment
Griffith University is committed to providing a safe work and study environment, however all students, staff
and visitors have an obligation to ensure the safety of themselves and those whose safety may be affected
by their actions. Staff in control of learning activities will ensure as far as reasonably practical, that those
activities are safe and that all safety obligations are being met. Students are required to comply with all
safety instructions and are requested to report safety concerns to the University.
General health and safety information can be obtained from

Information about Laboratory safety can be obtained from

All University policy documents are accessible to students via the University’s Policy Library website at:
. Links to key policy documents are included below for easy reference:
Academic Calendar

Academic Standing, Progression and Exclusion Policy

Assessment Policy

Examinations Timetabling Policy and Procedures

Guideline on Student E-Mail

Health and Safety Policy

Institutional Framework for Promoting Academic Integrity Among Students

Policy on Student Grievances and Appeals

Student Administration Policy


Student Charter

The University provides many facilities and support services to assist students in their studies. Links to
information about University support resources available to students are included below for easy
Learning Centres
- the University provides access to common use computing facilities for educational
purposes. For details visit

- there is a dedicated website for this course via the Learning@Griffith student portal.
Student Services
facilitate student access to and success at their academic studies. Student Services
includes: Careers and Employment Service; Chaplaincy; Counselling Service; Health Service; Student
Equity Services (incorporating the Disabilities Service); and the Welfare Office.
Learning Services
within the Division of Information Services provides learning support in three skill areas:
computing skills; library skills; and academic skills. The study skills resources on the website include self-
help tasks focusing on critical thinking, exam skills, note taking, preparing presentations, referencing,
writing, proof reading, and time management.