Microbiology and Molecular Biology

Module Leader: Dr Joy Watts

joy.watts@port.ac.uk Room 4.03 KH
email to schedule a suitable time for a meeting
Emergency -Biology Office - (0)23 9284 2222
School Office Student Information- Moodle

After Christmas Break- Dr Darren Mernagh

darren.mernagh@port.ac.uk

Lectures – Attendance will be monitored

Laboratory MANDATORY- each lab is assessed
Assessment
Coursework 40%
Individual laboratory assessments - 20%
Assessment of practical skills- 20%

Examination 60%
1 hour unseen, end of unit MCQ and two drawings
examination.

Formative assessments throughout

Moodle page: Check this area frequently. I will post any important information
relevant to the entire class here. Use of forum.

Books CD ROM and Website: Textbooks are often packaged with a subscription
to the author’s commercial web page, which are specifically tailored to your
textbook. This resource contains many self help tutorials and independent
exercises that can help with certain difficult concepts.

BROCK Biology of Microorganisms. Madigan, Martinko, Dunlap & Clark.

Pearson-Benjamin Cummings.

Useful websites: Posted on moodle (http://moodle.port.ac.uk/)

How to be successful
• Turn up!!!!!!!
• Be engaged
• Re-write your notes
• Do extra reading
• Attempt all coursework

• Questions

• Recording lectures
Lectures can be considered to be broadcasts and are therefore subject to
copyright law, as described above. Students may audio record lectures for
private study purposes only and, out of courtesy, should request permission to
do so. Written permission from the lecturer must be obtained if students would
like to record a lecture for any other purpose.
Student Conduct
"Every student has the right to learn, as well as the
responsibility not to deprive others of their right to learn." To
ensure that we observe this philosophy, I will ask you to
respect the following policies:

Mobile Phone Policy

Mobile phones or similar communications devices must be
turned to silent. Students are not to place or receive calls or
messages during class time. Should your phone ring or even be
visible during the class period, you will be asked to leave the
classroom immediately.
If a student legitimately needs to respond to a telephone call
in class, prior notice and approval of the instructor is
required.
Syllabus Outline till Christmas
Week Date /Time Event Reading
9 26/9 Lecture 1 Unit Introduction/History of Chapter 1
Microbiology
10 3/10 Lecture 2 Microscopes and Microbial Cell Chapter 1 and 2
Structure
11 10/10 Lecture 3 Cell structure and function Chapter 2

All dates 12 14/10 Lecture 4 Microbial nutrition Chapter 3 (15

and times further reading)
12 17/10 (9-10, 11-12, Laboratory introduction and training Online Lab
are 2-3, 4-5) Manual
13 24/10 (9-11, 12-2, Laboratory 1 Lab Manual
subject to 3-5, 6-8)
25/10 Chapter 5
13 Lecture 5 Microbial Growth and Control
change-
15 7/11 (9-11, 12-2, 3- Laboratory 2 Lab Manual
please 5, 6-8)

check your 16 14/11 (9-11, 12-2,

3-5, 6-8)
Laboratory 3 Lab Manual

portal! 18 28/11 (9-11, 12-2,

3-5, 6-8)
LAB EXAM Lab Manual

20 9/12 Lecture 6 Viruses Chapter 8

Formative MCQ assessment online
Aims of the microbe section of the unit
•Describe microorganisms in the context of their habitats

•Summarise the classification of microbes

•Competence in safe and effective handling and

investigation of microorganisms in the laboratory

•Foundation for future courses in microbiology or

Biotechnology- maybe even a job in this area!
 The Microbiology Society

• Contact details:
• www.microbiologysociety.org
• Telephone +44 (0)20 7685 2691

Undergraduate Student rates start from £10/year

WHAT ARE THE BENEFITS?
• Online quarterly issues of the members’ magazine, Microbiologist, featuring scientific articles, news,
events and a section for Student members.
• 25% Off the list price of all Wiley Blackwell books.
• Networking opportunities
• by being a member of a Society with members in over 80 countries
• online through the members-only area of the SfAM website.
• Discounted rates to attend Society scientific meetings.
• Monthly e bulletin featuring latest news and information on current Society activities.
 Why study
microbiology?
• Decompose organic waste
• Producers in the ecosystem
• Produce industrial chemicals
• And a new country!
• Produce fermented foods
• Produce products used in manufacturing
• A FEW are pathogenic, disease-causing
http://time.com/3328813/pictures-of-the-week-23/
http://www.who.int/emergencies/mers-cov/en/
https://www.theguardian.com/environment/2019/sep/17/south-korea-confirms-african-
swine-fever-outbreak
Biggest recent pandemic?
http://www.ted.com/talks/bill_gates_the_next_disaster_we_re_not_ready?language=en
https://www.bbc.co.uk/programmes/b0blmn5l
The 2019-2020 trivalent influenza vaccine is made from the
following three viruses: A/Brisbane/02/2018 (H1N1)
A/Kansas/14/2017 (H3N2)
B/Colorado/06/2017-like (Victoria lineage)
Quadrivalent (four-component)
B/Phuket/3073/2013-like (Yamagata lineage)

http://www.cdc.gov/flu/protect/keyfacts.htm
The Impact of Microorganisms on Humans
• Beneficial and harmful to humans
• Emphasis is on harmful microorganisms (pathogens)
• Many more microorganisms are beneficial than are
harmful
 Human Contaminants

3,000,000,000,000,000,000 10,000,000,000,000,000,000
3 trillion cells 10 trillion cells
How old are
microbes?
Earth is 4.6 billion years old
First cells appeared
between 3.8 and 4.3 bya
Atmosphere was anoxic
until ~2.6 bya
Anaerobic until evolution
of oxygen-producing
phototrophs
Life was exclusively
microbial until ~1 billion
years ago
• Ancestors of bacteria were the first life on Earth.
• Stromatolites / BIFs

Recent stromatolites
at Hamelin Pool,
Australia
3 Domain Tree of Life You are here!

BACTERIA ARCHAEA EUKARYA

Macroorganisms
Animals
Entamoebae Slime
Green nonsulfur molds
bacteria Euryarchaeota
Fungi
Methanosarcina
Mitochondrion Methano- Plants
Extreme
Gram- Crenarchaeota bacterium
halophiles
Proteobacteria positive Thermoproteus Ciliates
bacteria
Chloroplast Pyrodictium Thermoplasma

Cyanobacteria Thermococcus
Flagellates
Nitrosopumilus Pyrolobus
Green sulfur Methanopyrus
Trichomonads
bacteria

Thermotoga

Thermodesulfobacterium Microsporidia

Aquifex Diplomonads

LUCA
https://astrobiology.nasa.gov/news/looking-for-luca-the-last-universal-common-ancestor/
What is life?
1. Compartmentalization and metabolism
Cells take up nutrients from the environment, transform them,
and release wastes into the environment. The cell is thus
an open system.

Cell

Environment
2. Reproduction (growth)
Chemicals from the environment are turned into new cells under
the genetic direction of preexisting cells.

3. Differentiation
Some cells can form new cell structures such as a spore, usually
as part of a cellular life cycle.
Spore

4. Communication
Cells communicate or interact by means of chemicals that are
released or taken up.

5. Movement
Some cells are capable of self-propulsion.

6. Evolution
Cells contain genes and evolve to display new biological
properties. Phylogenetic trees show the evolutionary
relationships between cells.
Distinct
Ancestral species
cell

Distinct
species
 Bacteria
• Prokaryotes - Microbial
• Peptidoglycan cell walls
• No nucleus or other
membrane-bound
organelles (really?)
• Binary fission - haploid
• Metabolically diverse
• For energy, use organic
chemicals, inorganic
chemicals, or
photosynthesis
Naming and Classifying Microorganisms
• Each organism has two names: the genus and
specific epithet.
• Italicized or underlined. The genus is capitalized and the
specific epithet is lower case.
• Are “Latinized” and used worldwide.
• Bacillus anthracis
• Escherichia coli - E. coli
The cell is the fundamental unit of life
 Archaea
• Microbial
• Lack peptidoglycan
• May live in extreme environments
– Methanogens
– Extreme halophiles
– Extreme thermophiles
Fungi
• Eukaryotes
• Chitin cell walls
• Organic chemicals for
energy.
• Molds and mushrooms are
multicellular -mycelia, which
are composed of filaments -
hyphae.
• Yeasts are unicellular.
Protozoa
• Eukaryotes
• Morphologically diverse
• Metabolically limited
• Absorb or ingest
organic chemicals
• May be motile via
pseudopods, cilia,
or flagella
 Algae
• Eukaryotes
• Cellulose cell walls
• Photosynthesis
• Produce molecular oxygen
and organic compounds
• Symbiosis - Lichens
• Coral reefs, sponges
Viruses
• Acellular
• Consist of DNA or RNA core
surrounded by a protein coat.
• Coat may be enclosed in a lipid
envelope.
• Require host for replication.
• Classified by the hosts they
infect
History of Microbiology

http://www.bbc.co.uk/programmes/b007753d
http://www.bbc.co.uk/programmes/p01f51s5
 The First Observations
• 1665, Robert Hooke
• Cell theory: All living things are
composed of cells and come
from preexisting cells.
• Anton van Leeuwenhoek
• The first microbes were
observed in 1684 ‘wee
animalcules’.
The Golden Age of Microbiology
• 1857-1914
• Beginning with Pasteur’s work,
• Discoveries included the relationship between microbes
and disease, immunity, and antimicrobial drugs

Pasteur Koch Ehrlich Lister Fleming

• Louis Pasteur (1822–1895)
• Discovered that living organisms
discriminate between optical isomers
• Alcoholic fermentation was a biological
process
• Disproved theory of spontaneous
generation
• development of aseptic technique
• Vaccines for anthrax, fowl cholera,
and rabies
 The Theory of Biogenesis supported
• Pasteur’s S-shaped flask kept microbes out but let
air in.
 Dust and microorganisms
trapped in bend Open end
Steam forced
out open end
Long time

Liquid cooled slowly Liquid remains

sterile indefinitely

Nonsterile Neck of flask Liquid Short time

liquid drawn out in sterilized
poured into flame by extensive
flask heating Flask tipped such that Liquid
microorganism-laden dust putrefies
contacts sterile liquid
Fermentation and Pasteurization
• Pasteur - microbes are responsible for fermentation.
• Fermentation =sugar to alcohol.
• Microbial growth food spoilage
• Bacteria that use alcohol and produce acetic acid spoil
wine by turning it to vinegar (acetic acid).
• Spoilage bacteria- killed by heat that was not hot
enough to evaporate the alcohol in wine.
• Pasteurization
The Germ Theory of Disease
• 1835: Agostino Bassi -silkworm disease - fungus.
• 1865: Pasteur another silkworm disease -
protozoan.
• 1840s: Ignaz Semmelwise hand washing to
prevent transmission of puerperal fever from one
OB patient to another.
• 1860s: Joseph Lister used phenol on wounds
• 1876: Robert Koch - anthrax -Koch’s postulates,
to prove that a specific microbe causes a specific
disease. (Nobel prize in 1905)
Fig. 1-29
 Martinus Beijerink
• Early 1900s
• Delft School
• Enrichment methods
• Isolation of methanogens,
methylotrophs, SRB
• Symbiotic and non-symbiotic N2
fixation
• Microbes as transformers of the
global environment
 Sergei Winogradsky
• Founder of soil microbiology
• Metabolic significance of
microbes
• Nitrification
• N2 fixation
• Oxidation of H2S, S, Fe(II)
• Proposed chemolithotrophy
Knowledge of Microorganisms
• Allows humans to
– Prevent food spoilage
– Prevent disease occurrence
• Led to aseptic techniques