Lecture One

ES 212: Environmental Microbiology

Course instructor: Amina Lwasa

Day, Time & Venue Monday: 7:30 am - 10:30 am

(COESE_LR 2)
Monday : 11:00 pm - 12:00 pm
(COESE_LR 5)
Nov, 2023

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 Learning outcomes
At the end of the course students are expected to:
• Appreciate the presence, diversity and role of micro-organisms in
nature
• Describe evaluate the biochemical basis of important physiological
characteristics of micro-organisms including: pathogenecity, motility,
and unique forms of energy production
• Explain how micro organisms can be used in biodegradation
processes Use some micro-organisms to ascertain to tell the level of
contamination.
• Know the kind of micro-organisms responsible for contamination of
water and their impact on public health and design means of
controlling them.
• Handle laboratory equipment and techniques including isolating,
culturing and identification of micro-organisms
• Use practical techniques to culture, identify, and study micro-
organisms 2
 Course content
• Types and distribution of micro-organisms in terrestrial and aquatic
environments, micro-organisms in soil environments, biochemical
processes important in natural and disturbed eco-systems, nutrient
cycling, transformation of inorganic and organic contaminants;
• Microbial contamination of potable water resources and impact on
public health inhibition and the killing of micro-organisms sources and
types of micro-organisms associated with waterborne diseases and
their residence times in the environment; indicator organisms of
microbial contamination of water; atmospheric dispersion of
(pathogenic) micro- organisms;
• Bioremediation: Overview of biodegradation processes at the
microbial level, investigating specific scenarios, range of biological
remediation technologies applicable to contaminated land.
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 Assessment
Assessment

1. University Examination = 60%

2. Coursework = 40%
[2 Tests = 30%, 2 Home works = 6% and 4 quizzes
= 4%]

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Key References:

1. Bitton, G. (2010) Waste Water Microbiology, 4th edition. John
Wiley & Sons, New York

2. Dale, J. (2013). Understanding Microbes: An Introduction to a

Small World. John Wiley & Sons, New York

3. Mitchell, R.(ed)(2009) Environmental Microbiology, 2nd

edition. John Wiley & Sons, New York

4. Prescott, L.M., Harley, J.P. and Klein, D.A. (2007).

Microbiology. McGraw Hill Inc., USA
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Basic Microbiology
• Microbiology is the study of microorganisms.
• Microorganisms, are all single-celled microscopic organisms
and include the viruses, which are microscopic but not cellular.
• Microbial cells differ from plants and animals cells in that they
are independent entities that carry out their life processes
independently of other cells.
• While plant and animal cells are unable to live alone.

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 Basic Microbiology
• So, Microbiology is about microbial cells and how they
work, especially the bacteria, a very large group of very
small cells.
• Aim at:
1) understanding the living world of
microscopic organisms, and
• 2) applying our understanding of microbial life
processes for the benefit of human kind.
• Microbial cells can be grown to extremely high
densities in small-scale laboratory cultures making
them readily amenable to rapid biochemical and
genetic study (as we will see later).
Microbial Cell
Different types of microbes exist, However, can be divided into
two types based on the cell structure:
• Prokaryotic – Simples, Without nucleus
• Eukaryotic – complex, with nucleus
Prokaryotic and Eukaryotic cells
 Brief survey of the

Diversity of Microoganisms
All organisms divided into two types:
Prokaryotic Microorganism
Archaea
Bacteria
Eukaryotic Microorganisms
Protozoa
Fungi
Algae
Virus – Genetic element
The phylogenetic tree of life -Three Domains
Survey of MO’s – Prokaryotic Microbes

Archaea
• Consist of three kingdoms
• 1) Crenarchaeta – e.g. Thermoproteus, Sulfolobus
• 2) Euryarchaeota – Methanogens, Halobacteria,
Themococcus
• 3) Korarchaeota – Only from molecular (no pure culture)
• A common feature of Archaea is adaptation to extreme
environment
- High salts 3-8% NaCl
- High temperature – optimum above 80 oC
- extremely low temperature – below 4 oC
- Anaerobic conditions- Inside other organisms, sediments
- Non pathogenic
 Bacteria
• Bacteria are unicellular prokaryotes, ranging from
diameter of 0.2 – 2 µm.
• Bacteria consist of 14 Kingdoms; ~1600 species
• Identification based on characteristics such as:
• Morphology (size, shape, arrangement
• Staining (gram-negative or gram-positive, acid fast)
• Nutritional requirements
• Growth characteristics
• Physical chemical requirement (temp. pH, salinity optima)
• Biochemistry, genetic, spore forming ability, type of
movement, pathogenicity etc
 Bacteria morphology
• Although thousands of species of bacteria exists, the
cell of most of bacteria have 1 of 3 fundamental
shapes:
• 1) Spherical or ellipsoidal – Cocci (Coccus); Diplococcal
cells divide to form pairs, Streptococcal cells remain
attached after dividing and form chains, Staphylococci
divide three dimensionally to form irregular clusters of
cocci, resembling bunches of grapes,
• 2) Cylindrical or rodlike – are called bacilli (bucillus);
Mainly as single but can also be found in pairs
(Diplobacillus) or chain (Streptobacillus). Some are
referred as Cocco-bacillus. There are many variation in
thickness and length of the cells
 • 3) Spiral or helically coiled – are called
spirilla (spirillum); Usually occur as
individual cells. Many variation in length
and frequency and amplitude of spirals (so
referred as spirochete, spirillum and Vibrio).
• Some bacteria have external structures –
• glycocalyx, for attachment – Consists of capsule and/or
slime layer
• Flagella – for movement
• Pili – a tiny hollow projection smaller than flagella. For
exchange genetic material or attachment to surfaces
Primary bacteria shapes
 Important Bacteria Species
• Out of more than 1600 known species, only few are
pathogenic,
• Examples of important bacteria:
• important to medicine industry and environment
• Bacteria of genusPseudomonas , Rhizobium , Acetobactor ,
Agrobacterium, Spirillum &Azospirillum spp. are important
to medicine industry and the environment.
• Some species produce antibiotic e.g. Actinomycetes which
includeStreptomyces Frankia
, andMicromonospora spp.
• Primary producers - photosynthesize
Many bacteria are the primary
producers in environments.
• Important pathogens, include Escherichia ,
Salmonella Shigella
, Klebsiella
, Yersinia
, ,
Enterobacter, Bacillus, Vibrio etc
• Anthrax – caused by Bacillus anthracis
• Tuberculosis – caused by Mycobacterium
tuberculosis
• Typhoid fever – caused by Salmonella spp.
• Cholera – Caused by Vibrio cholerae
• Members of genera Coxiella and Rickettsia and Chlamydia
are important pathogen of anthropods and animals.
• Mycoplasmas spp. Lack cell wall, parasite to animals plants
and insects
 Eukaryotic Microbes
Under Eukaryotic Microorganisms, three
main groups:
Protozoa
Fungi
Algae
will cover:
- Characteristics of the group
- Economic importance
- Examples of some common/important species
Protozoa
Characteristics of Protozoa (phylum)
• Are unicellular eukayotes, Lacking cell wall,
Microscopic, most are motile and heterotrophic
• Have no cell wall, tissue or organs but have
organelles – Advanced,
• Their organelles do show a great deal of functional
differentiation for purpose of;
–locomotion,
–food procurement,
–sensory reception and response,
–protection and
–water regulation
 Protozoa characteristics
• Classification is based on mode of locomotion:
• Using whiplike flagella are called Mastigophora or
Flagellates
• Using hair-like cilia are the Ciliates
• Moving via pseudopodia (amoeboid movement) are the
Sarcodina
• Lacking a means of locomotion are the Sporozoa (all
sporozoa are obligate parasites)
• Most are heterotrophic while few have chlorophyll and
are autotrophic – e.g.Euglena
 Protozoa
• Mechanism for the acquisition of nutrition is variable;
– some are holozoic, ingesting solid foods and other
organisms like bacteria
– saprozoic i.e. they absorb dissolved nutrients directly
– holophytic i.e. food by photosynthesis or
– mixotrophic i.e. use both saprozoic and holophytic
methods
• Found in various habitats including;
– aquatic environments,
– soil,
– aerial habitants and
– bodies of other organisms
 Protozoa characteristics
• Protozoans live either singly or in colonies
• Large number are parasitic in other organisms
• Reproduce by asexual;
– budding,
– binary fission or multiple fission or sporulation
– plasmotomy splitting into two or more multinucleated cells
• They also reproduce sexually:
– Conjugation – transfer of DNA between cells via a
temporary connection
– autogamy - is a modification of conjugation do not involve
2 cells (production of gametes by the division of a single
parent cell)
– Syngamy is the fusion of different types of sex cells
 Economic importance of Protozoa
• Several species in soil improve structure and fertility
• Disease in man , plant and animals; for example:
• Malaria caused by Plasmodium spp
• Sleeping sickness caused byTrypanosoma spp.
• Stomach Amoeba byEntoamoeba giardia
• Genitourinary byTrichomonas
• Coccidiosis in poultry byEimeria sp.
• Babesiosis in cattle byBabesia sp.
 ALGAE
• The term Algae refer to Both unicellular and
multicellular photosynthetic aquatic organisms.
• Varied greatly in size and shape; Most species are
microscopic (microbes) while some are macroscopic,
can be 30 m long.
• They are like plants but no roots, vascular stem, flower
or seeds
• Algae are the primary energy producer in aquatic
environments.
• Reproduction may be either sexual or asexual
(Fragmentation, binary fission, and unicellular spores)
 Classification of algae
• Classification of algae has been mainly based of
pigments; four major division for unicellular:
• Chlorophyta - green algae – form pond scum
• Bacillariophyta – diatoms – have complex cell wall
composed of two halves that overlap like petri dish
containing pectin and silica. Usually golden brown or yellow
brown
• Euglenophyta – Euglenoids are unicellular, flagellated
organism and usually green
• Chrysophyta: biflagellate cells, chiefly found in fresh water,
also the marine silicoflagellates.
Algae
• Pyrrophyta – dinoflagellates are free floating whose cell
wall contain silica and cellulose. Usually brown. Many
species produce toxin e.g.
• Gonyaulax is a dinoflagellate, which produce
neurotoxin which cause paralytic shellfish
poisoning. The toxin is very effective to other
organism that eat them including man who eat
invertebrates.
• Others which are Multicellular algae include;
• Phaeophyta (brown algae) and
• Rhodophyta (Red algae)
 Economic importance of algae
• Primary producer- Carbon fixation and oxygen
production (80% of the worlds oxygen is produced by
plankton)
• Recycling of important minerals improving fertility
• Oil droplets in diatom contain vit. A & D. Deposits of
dead diatom form diatomaceous earth, which is used
in detergents, and paint removers etc
• Some species used as animal feed e.g.Chlorella spp.
• Few species cause disease to plant e.g. Red rust
disease of tea caused byCephaleura parasitica
• Toxic production in aquatic ecosystems; to
vertebrates,
 Fungi
• The fungi are non-motile, non-photosynthetic
eukaryotes. Major group are:
• Molds – Filamentous Fungi
• Yeasts – Unicellular Fungi
• Mushrooms – form large fruiting bodies
• A few species are parasitic, but most are saprophytic,
absorbing nutrient from dead organic matter.
• Fungi Contain cell wall and produce spores
• The cell wall generally contain chitin, although yeast
cell wall contain complex polysaccharides glucan and
mannan.
 Fungi
• They reproduce either sexually or
asexually.
• Classification based on type of their
reproduction
• Habitat are quite diverse –terrestrial in
soil and dead plants, but also aquatic.
• Large group are parasitic to plants and
animals including human
 Economic important of Fungi
• Fungi are both beneficial and detrimental to humans
• They are along with bacteria, the decomposers of
the world. Play big role in mineralization of O.M
• Fungi are used routinely for food production. E.g.
• Yeast for liquor (alcohol) & bread manufacturing
• Penicillium spp. are used for cheese production
• About 200 species of mushroom are Edible e.g.Agaricus
spp.
 Economic important of Fungi
• Fungi exploited industrially
– To manufacture drugs and antibiotics – e.g. penicillin from
Penicillium notatum .
• Fungi are very significant as can cause disease in
Plant and animals
• ~8,000 species cause diseases in plants; 100,000 live
in dead O.M
• Examples
– Members of the Oomycetes (water molds) cause plant
seedling diseases, downy mildew of grapes and potato
blight.
– Basidiomycetes cause agricultural damage – smuts
(damage corns) and rusts (damage sereal crops)
 Fungi economic importance
• Fungi are also important b’se of diseases they cause
in human and livestock example:
–Candida albicans – causes a throat and mouth disease
(thrust), also infects the mucous membrane of lungs and
genital organ.
–Aspergillus furnigatus – cause disease to young animals
– Fungi attaching Fish e.g.Saprolegria parasitica
• Food spoilage e.g.Rhizopus stolonifer , black bread
mold
• Toxin production – several species can produce toxin
and are poisonous when consumed.
Microorganisms control/ Techniques
• Mo’s are (almost) everywhere
• Mo’s generally grow very fast
• This rapid increase in cells numbers is
• positive in the case of useful microorganisms,
• problem in the case of harmful organisms
• Need to control microorganism using various
techniques
 Brief History of Microbiology
• The existence of creatures too small to be seen with the eye had
long been suspected,
• Discovery of MO’s were not know until invention of microscopes
by Dutch amateur microscope builder, Antoni van Leeuwenhoek,
1677
• Microbiology as a science did not develop until the latter part of
the nineteenth century (1800’s). Due to
• The origin of mo’s became a puzzle to scientists of that time
and a theory of “spontaneous generation” developed
• The idea of spontaneous generation – putrefies food found to
be teeming with bacteria. Some people said bacteria come from
seeds or germs; others said arose from nonliving materials.
• From 1799-1857, investigation of two questions led to the development of
various techniques (sterilization, association with disease), :
• Does spontaneous generation occur?; What is the nature of contagious
disease?
 Louis Pasteur
• 1857-1876 -Louis Pasteur - settled the controversy
surrounding the theory of spontaneous generation trough
various expts:
• Mo’s in air same as putrefying food – cotton wool
• If correct, sterilized food should not putrefy (decay) –
done
• The proponent criticized - fresh air was necessary
• Pasteur settled this objection simply and brilliantly by
constructing a swan-necked flask, now called Pasteur
flask (Drawing).
• Pasteur made other extensive study on:
• fermentation processes - all fermentation is by MO’s
• in absence of oxygen microbial growth occurs
• Pasteur also developed vaccines for the disease anthrax,
fowl cholera, and rabies during productive period from
1880-1890
The defeat of spontaneous generation
 1876-1884 – Robert Koch
• In 16th century – it was believed something could be transmitted from diseased
person to induce disease to healthy person.
• After discovery of Mo’s, it was believed were Mo’s but proof was lacking.
• Robert Koch, a physician, studied anthrax, a disease of cattle which sometimes
also occur in humans. Caused by a bacterium now calledBacillus anthracis .
• He established that the bacteria were always present in blooded of sick animal.
• Transfer of the blood from one animal to another - cause the disease
• He cultivated the bacteria in nutrient fluid outside the animal body and even after
many transfers in pure culture the bacteria could still cause the disease.
• On the basis of these experiments Koch formulated the following criteria, Koch’s
Postulates, for proving that a specific type of Mo’s causes a specific disease:
• The Mo’s should be present in sick animals and absent in healthy one.
• The organism must be cultivated in a pure culture away from the animal
body
• Such a culture, when inoculated into susceptible animals, should initiate the
characteristic disease symptoms.
• The organism should be re-isolated from experimental animals and re-
cultured, after which it should still be the same as the original organism.
Koch’s Postulates
Early days of Microbiology
 Self study
• Read:
1) Why can it be said that microbial cells differ
fundamentally from the cells of higher organisms?
2) Explain the importance of bacteria/Fungi/Algae in
environment
3) Explain the principle behind the use of the Pasteur
flask in studies on spontaneous generation
4) Why was knowledge of how to obtain a pure culture
important for development of the science of
microbiology