Microbiology overview

Assoc Prof Kevin Pethe

[email protected]

Assoc Prof Scott Rice

[email protected]
SCELSE, SBS-B1n-27
 Learning Outcomes
o Evaluate the impact of microorganisms on the environment and
society in daily life
o List a number of important microorganisms and discoveries in
microbiology
o Describe and distinguish the main features of microorganisms
o Describe the needs and mechanisms important for microbial
growth and death
o Explain how different microorganisms interact with their
environment (disease, environmental biology)
 0830-1020
Week Lecture Lecturer
on-line
1 12-Aug Introduction to Microbiology A/P S Rice

2 19-Aug Prokaryote cell A/P K Pethe

3 26-Aug Food Microbiology A/P S Rice

4 2-Sep Energetics/ cellular biochemistry A/P K Pethe

5 9-Sep Microbial nutrition/cell division A/P K Pethe

6 16-Sep Microbial genetics/gene regulation A/P K Kline

7 23-Sep Photosynthesis O. Muller-Cajar

Term break
8 7-Oct Social interactions A/P S Rice

9 14-Oct Medical Microbiology A/P K Kline

10 21-Oct Control of Microorganisms & bacteriophage A/P R Case

11 28-Oct Evolution and taxonomy A/P R Case

12 4-Nov Biotechnology/Industrial microbiology A/P R Case

13 11-Nov Revision A/P Rice & Pethe

 Assessment
➢Three in-class quizzes, 10% each (30% total)
➢Final 2.5 hour examination (30%)
o short assays -1/4 page or less-

➢ Assessment for tutorials (40%)

o 40 points for a team-based project.
o 6 tutorial sessions
 Tutorial format
o Team-based project
Basic structure: find a topic of interest in popular science
magazines/news and :

a) Summarise the story

a) Identify 2 microbiology principles underlying the story

a) Make a plan for how to explain those concepts to a non-

science audience

a) Suggest if the article got the basic science correct or if key

details were missed out (or misrepresented something).
 Tutorial format
o 40% of the final grade

Exact breakdown released during the first tutorial,

components will include :

Quality of the Presentation, attendance, participation /

questions, etc.
 Tutorial Schedule
@ SBS-TR+5 and SBS-TR+6

Week 5 11-Sep Microbiology in action 1

Week 6 18-Sep Topic selection
Week 7 25-Sep Work on presentation and report
Week 10 23-Oct Work on presentation and report
Week 11 30-Oct Presentations
Week 12 6-Nov Presentations

o Order of the presentations chosen randomly: be ready to

present on Oct 30th.
 Why study
microbiology?
 Microbes
o Appeared on earth about 3.5 billion years ago
o Evolved to occupy every habitat on earth
o Most populous group of organisms
Importance of microorganisms

o Contribute to functioning of the biosphere; major role

in recycling essential elements
o Base of ecological food web - source of nutrient and
some are photosynthetic (fix carbon)
o Microbes contain 50% of biological carbon and 90% of
biological nitrogen on earth
Importance of microorganisms

o Benefit to society: production of food, beverages,

antibiotics and vitamins; cleaning waste-water and
remediating contaminated sites
o ..but can also cause disease in insects, plants and
animals
Members of the microbial world

o Cellular and acellular organisms - most of which are too

small to be seen (< 1 mm)
o Relatively simple and lack differentiated cells and tissues

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Members of the microbial world

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Types of microbial cells

o Prokaryotic cells lack a true membrane-

delimited nucleus (this is not absolute)
o Eukaryotic cells: membrane-bound nucleus,
more complex morphologically and usually
larger than prokaryotic cells
 Classification
o Three domains based on ribosomal RNA sequences
• Bacteria
• Archaea
• Eukarya
 Bacteria
o Usually single-celled with cell-wall containing
peptidoglycan
o Lack a membrane-bound nucleus
o Some live in extreme environments
o Some produce oxygen through photosynthesis
(e.g. Cyanobacteria)
 Archaea
o Unique rRNA sequences that differ from Bacteria
o Lack peptidoglycan in cell wall, unique membrane
lipids
o Some have unusual metabolic characteristics
(methanogens)
o Some live in extreme environments (thermophile,
halophiles, acidophiles)

http://www.learner.org/resources/series121.html?pop=yes&pid=1363
 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Acellular infectious agents

oViruses
• smallest of all microbes
• requires host cell to replicate
• cause range of diseases, some cancers
o Viroids – infectious encapsulated RNA
(only infect plants)
oPrions – infectious proteins

http://science.howstuffworks.com/life/cellular-microscopic/light-virus.htm
 Traits of living organisms
o Cell membrane and organisation
o Response to environmental changes
o Growth and development
o Biological evolution
o Energy use and metabolism (fight entropy)
o Regulation and homeostasis
o Reproduction
 Origins of life

o Oldest fossilised microbe

estimated to be 3.5 billion
years old
 THE key questions

o How did life begin and evolve ?

o What was the origin of life ?
o What is life ?
 RNA may have been the
earliest molecule
Prebiotic
soup
o Original molecule must have fulfilled
information and catalytic functions
liposome R

o Ribozymes RNA
• RNA that can form peptide bonds
• Possess information and catalytic
Probiont: RNA only
functions
o Earliest cells: possibly autoreplicative
RNA surrounded by liposomes Probiont: RNA and
proteins

Cellular life: RNA, DNA, proteins

“Central Dogma of Biology” =
flow of information
Key discoveries in Microbiology

o The discovery of micro-organisms

o Life-comes from life
o Infections are caused by living
microorganisms
o Chemoautotrophy and elemental cycling by
microorganisms
 Discovery of microorganisms
Antony van Leeuwenhoek
(1632-1723) - first to observe and
describe microorganisms:
microscopy
 The conflict over spontaneous
generation

o Spontaneous generation - idea that living organisms

develop from non-living matter
o Francesco Redi (1626-1697) - discredited
spontaneous generation theory - showed that
maggots on decaying meat came from fly eggs
What about microorganisms?
Louis Pasteur (1822-1895)
 Louis Pasteur: Swan-neck flask experiment
o placed nutrient solution in flask
o boiled solution
o left flasks exposed to air
➢No growth

➢Microbes comes from the

outside, not “created”
 Final blow to theory of
spontaneous generation

o John Tyndall (1820-1893)

➢ dust carries ‘germs’
➢ If dust was absent, nutrient broth remained
clear even if exposed to air
photo credit: The Royal Society

➢ proved existence of heat resistant

microorganisms
 Role of microorganisms in
disease

o Was NOT immediately obvious

o Infectious disease believed to be due to
supernatural forces or imbalances of 4 bodily
fluids ‘humors’.
o At the time, tools were lacking to link
bacteria/viruses/fungi to diseases
 Evidence for relationship between
microorganisms and disease
❖ First in insects and plants
o Agostini Bassi (1773-1856)
➢ Silkworm disease was caused by a fungus

o Miles J. Berkeley (1803-1889)

➢ The great Potato Blight of Ireland was caused by
a water mold

o Heinrich de Bary (1832-1888)

o Cereal crop diseases caused by Smut and rust
fungi
 Louis Pasteur

o Microorganisms carry out fermentations, helped

French wine industry
o Developed pasteurization to avoid wine/milk
spoilage by microbes
o Showed that the pébrine disease of silkworms was
caused by a protozoan
 Joseph Lister

o Indirect evidence that microorganisms are causal agents of

disease
➢ Treating instruments and surgical dressings with carbolic acid
(phenol) reduced post-operatives infections.
Link between phenolic-treatment and killing of microorganisms
was not understood
 Final proof...
o Robert Koch (1843-1910)

➢ Established relationship between

Bacillus anthracis and anthrax

➢ used criteria developed by his teacher Jacob Henle

o Criteria became known as Koch’s postulates: formal link
between a microorganisms and a disease
 The Koch postulates
❖Demonstration that bacteria X is pathogenic
1. Isolation of a bacteria from a diseased
patient

2. Pure culture

3. Inoculation to a healthy host

➢ Signs of disease

4. Re-isolation of the same bacteria from

the sick host/animal
 Limitations of Koch’s
postulates

o Some organisms cannot be grown in pure

culture
o Virulence may not be absolute but contextual
(e.g. opportunistic pathogens)
 Koch postulates: things are not always so
simple…

GOOD guys BAD guys:

: commensal pathogens

PATHOBIONTS OPPORTUNISTIC
PATHOGENS
Present in most
“healthy” microbiota Environmental/microbiota bacteria

Sometimes cause Cause diseases only in certain

Diseases populations.

e.g. Clostridium difficile e.g. Pseudomonas aeruginosa

Koch postulates do not always apply

 Things are not always so simple…

Salmonella typhy ?
Causes severe diarrhea /gastroenteritis

Commensal Pathobiont Opportunistic Pathogen

 Things are not always so simple…

Staphylococcus aureus ?

Commensal Pathobiont Opportunistic Pathogen

15-30% are healthy Infect immuno-deficient Infect wounds

carriers / Hospitalized patients and burns

Lung and soft-tissue

infections
 Koch contribution: techniques
for studying microbial pathogens

o Koch’s work led to discovery of

➢ petri dishes
➢ nutrient broth and nutrient agar
➢ methods for isolating microorganisms
 Most (>99.9%) bacteria do not
cause diseases
o Primordial to study: shape our environment;
economical interest

Sergei Winogradsky (1856-1953)

o Microbiologist, ecologist, soil scientist

o Key discoveries: bacterial fixation of CO2; methods to study

bacterial population and diversity (in soil); bacteria as key
component of large biogeochemical cycles

http://www.hhmi.org/biointeractive/poster-winogradsky-column-microbial-evolution-bottle
Recent microbiology developments: Molecular and
genomic methods

o Second golden age of microbiology (rapid expansion

of knowledge)
o Major discoveries
➢ restriction endonucleases (Arber and Smith)
➢ Synthesis of recombinant molecule (Jackson, Symons,
Berg): production of insulin at Genetech
➢ DNA sequencing methods (Woese, Sanger)
➢ bioinformatics and large-scale genomic sequencing and
analysis
Approaches to observe and
study microbes
 Culture-dependent
The 5 I’s
o Inoculation
o Incubation
o Isolation
o Inspection
o Identification
 Culture independent technics:
Labelling & microscopy

(Sulfate-Reducing Bacteria)
 Culture independent:
large-scale population sequencing
o e.g. DNA sequencing of all bacteria from a soil sanple:
 Natural mixed
community systems
o Acid mine drainage
o pH < 0
o limited number of
species
o large, macroscopic
biofilms
 [email protected]
[email protected]