UNIT TWO

MICROORGANISM

2. What is Microorganism?
 Organisms too small to be seen clearly by the unaided eyes.
 Are only seen by the use of microscope
 Are studied by a science called microbiology
 Are all single- celled microscopic organisms that include viruses which
 It includes: Bacteria, Viruses (acellular), Protozoa (Amoeba, Paramecium, Fluke), Helminthes
(Parasitic Worm) some Fungi, Some algae

Where do microorganisms live?

 Microorganisms are ubiquitous (we can get them everywhere)
 They live in water, soil, and in the air.
 They occur in all situations except in pits of volcanoes, deep strata or rock and rainwater, distilled
water, in deep wells, blood of normal animals.
 They constitute the major part of the soil microflora and intestine of animals. Viz. E. coli in the
Intestine of human beings
 Some species have been found in extreme hot spring as well as extreme cold condition, these are
referred to as thermophilic (survive > 40 oC) and psychrophilic (on-190°C) respectively.
 They can tolerate and remain alive at a pH lower than 1 at one end and 13 at another end.
 Generally, 1 gm. soil contains about 1000 -10 million bacteria.
 A bacterium also occurs in a variety of foods and food products such as fruit, vegetables, milk, butter,
and cheese and milk beverages.

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Why is it important to study microbiology?
 Microorganisms matter because they affect every aspect of our lives.
 They are in us, on us, and around us.
 Microorganisms are most famous for causing disease, however, microorganisms are
also vital to agriculture, industry and ecology.
Based on evolutionary lines, Organisms are grouped into three domains: Bacteria, Archaea and Eukarya

2.1. Eubacteria
2.1.1. What characteristics are common to all bacteria?
The following are the general characteristics of bacteria.
 they are omnipresent i.e., present in soil, air and water.
 They are unicellular, prokaryotic microorganism.
 The cell bears a thick rigid cell wall outside the plasma membrane (because of this characteristic, they
are kept in plant kingdom).
 They have great variation in the mode of nutrition i.e. may be autotrophic and heterotrophic. In
heterotrophic mode of nutrition, they may be parasite saprophyte or symbiotic in nature.
 With the exception of few photosynthetic bacteria that have a special type of chlorophyll called
bacterio-chlorophyll, they lack true chlorophyll.
 they lack true nucleus (lacking nuclear membrane and nucleolus), genetic material is in the form of
composite structure known as genophore/nucleoid/ Unlike the cell wall of plants, which is made up
of cellulose, the cell wall of bacteria is made up of mucopeptide
 They lack mitochondria, Golgi apparatus, plastid and endoplasmic reticulum.
 They lack basic protein histone in their DNA
 Ribosomes are of 70s type.
 At some places, the plasma membrane invigilates in folds to form mesosomes
 All the enzymes required for respiration are found in the cell membrane.
 Both DNA and RNA are available in the bacterial cell. DNA is in the form of single circular
chromosome (therefore the ce.il is haploid)
 Vegetative reproduction generally takes place by binary fission, cyst, budding and gonidia.
 Asexual reproduction occurs through conidia, motile spores and endospore
True sexual reproduction is absent in bacteria but there are examples of genetic recombination which
may be of following types. conjugation, transduction and transformation

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 Figure 1. Internal structure cell surface appendages of bacterial cells

Pili: are short, hair-like structures on the cell surface of

 Are short, thick straight hair like surface appendages

 They can have a role in movement, but are more often involved in adherence to surfaces, which
facilitates infection, and is a key virulence characteristic structure of a bacterial cell.

Flagella:

 Flagella are long, thin surface appendages that extend up to 20μm and which are important for
motility and chemotaxis.
 Flagella actually extend from the interior of the cell body.
 Flagella and fimbriae are important for the attachment of pathogens to fresh production.

The general Flow chart of cellular organization of a prokaryotic cell

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 2.1.2. What is the difference between eukaryotes and prokaryotes?
 Both prokaryotes and eukaryotes contain nucleic acids, proteins, lipids and carbohydrates.
 They use the same kinds of chemical reactions to metabolize food, build proteins, and store energy.
The structure of cell walls and membranes, and the absence of organelles (specialized cellular structures
that have specific functions) primarily distinguish prokaryotes from eukaryotes

The chief distinguishing characteristics of prokaryotes as follows:

I. Typically, their DNA is not enclosed within a membrane and is usually a singular, circularly arranged
chromosome. Gemma obscuringlobus has a double membrane around its nucleus.
(Some bacteria, such as Vibrio cholerae have two chromosomes, and some bacteria have linearly
arranged chromosome.)
II. Their DNA is not associated with histones other proteins are associated with the DNA.
III. They generally lack organelles, other membrane enclosed organelles such as nuclei, mitochondria, and
chloroplasts.
IV. Their cell walls almost always contain the complex polysaccharide peptidoglycan.
V. They usually divide by binary fission, where DNA is copied, and the cell splits into two cells.

Figure 2. Main feature of prokaryotic cell, Bacteria

Eukaryotes have the following distinguishing characteristics:

I. Their DNA is found in the cell’s nucleus, which is separated from the cytoplasm by a nuclear
membrane, and the DNA is found in multiple chromosomes
II. Their DNA is consistently associated with chromosomal proteins called histones and with non-histones.
III. They have a number of membrane-enclosed organelles including mitochondria, endoplasmic reticulum,
Golgi complex, lysosomes, and sometimes chloroplasts.
IV. Their cell walls (if there is any) are chemically simple.
V. Cell division usually involves mitosis, in which chromosomes replicate

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 Figure 3. main structure of eukaryotic Cell

2.1.3. Classification of bacteria based on their Shapes

 Morphologically bacteria are classified based on numerous features like shape, arrangement, Cell
wall composition
Based on the their shapes, bacterial cells can be grouped into the following main shapes:
A. Cocci (singular, coccus) – spherical bacteria
B. Bacilli (singular, bacillus) – rod-shaped bacteria
C. Spirochaetes – spiral or corkscrew-shaped bacteria
D. Comma -shaped – Vibrio cholerae

What is the shape of Lactobacillus and streptococcus bacteria?

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 Lactobacillus

 any of the group of rod-shaped, aerotolerant anaerobes or microaerophilic, gram-positive, non-spore-

forming bacteria of the family Lactobacillaceae.
 Lactobacillus are characterized by their ability to produce lactic acid
 The organisms are widely distributed in animal feeds, silage, manure, and milk and milk products.
Various species of Lactobacillus are used commercially for the production of sour milks, cheeses, and
yogurt, and they have an important role in the manufacture of fermented vegetables (pickles and
sauerkraut), beverages (wine and juices), sourdough breads, and some sausages.
Streptococci
 are Gram-positive, nonmotile, non-spore forming, catalase-negative cocci that occur in pairs or
chains. Older cultures may lose their Gram-positive character.
 Most streptococci are facultative anaerobes, and some are obligate (strict) anaerobes.
 Most require enriched media (blood agar).
 Group A streptococci have a hyaluronic acid capsule.

2.1.4. Classification of bacteria based on Cell wall composition

Key points
Gram’s staining: a test for distinguishing bacteria (named after Hans Christian Gram,
who developed the technique in 1884)
Differential staining: is a staining procedure that distinguishes organisms based on their
staining properties

What is the purpose of gram staining? It is the laboratory test technique used to diagnosis the presence of
the bacterial infection quickly as gram negative or gram positive
A. Gram-positive bacteria
 Gram-positive bacteria have a distinctive purple appearance when observed under a light microscope
following Gram staining.
 They retain the purple crystal violet stain in the thick peptidoglycan layer of the cell wall.
 Their cell wall contain:
 Peptidoglycan
 Teichoic acid
 Lipoteichoic acid
 They lack outer membrane
 They have narrow periplasmic space
 Lipid and Lipoprotein content is low
 They produce exotoxin
 Their resistant to physical disruption is high
 Cell wall disruption by Lysosome is high
 Susceptibility to penicillin and Sulfonamide is high
 Susceptibility to streptomycin, and Tetracycline is low
 Examples of Gram-positive bacteria include all staphylococci, all streptococci and some listeria
species.

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B. Gram-negative Bacteria
 lose the crystal violet stain (and take the color of the red counterstain) in Gram's method of staining.
 They have a cell wall composed of a thin layer of peptidoglycan.
 Have two membranes spatially separated (periplasm and peptidoglycan separate the membrane from
the outer membrane from the inner membrane = have two layers
 They have outer membrane
 Chemical composition of cell wall are:
 Lipopolysaccharide
 Lipoprotein
 Peptidoglycan
 They have extensive periplasmic space
 They produce endotoxin
 Their resistant to physical disruption is low
 Cell wall disruption by Lysosome is low
 Susceptibility to penicillin and Sulfonamide is low
 Susceptibility to streptomycin, and Tetracycline is high

Examples of Gram-negative bacteria are:

E.coli, Pseudomonas, Klebsiella, Salmonella,
Steps in gram staining

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 Q1. What is the role of bacteria cell wall protecting against lysis?
 The bacterial cell wall is made of thick, rigid peptidoglycan that maintains the shape of the cell,
protects the cell interior, and prevents the cell from bursting during osmosis.
 In most prokaryotic cells, the cell wall provides support and helps cells resist mechanical pressures,
but they are not solid so that materials can pass through rather easily.
 Cells that have a cell wall are better able to withstand subtle changes in osmotic pressure and maintain
their shape.
 In hypertonic environments, cells can become dehydrated, causing crenation or shriveling of the cell.
 In contrast, cells that possess a cell wall undergo plasmolysis rather than crenation.
 In plasmolysis, the plasma membrane contracts and detaches from the cell wall. There is a decrease in
interior volume, thus allowing the cell to maintain some shape and integrity for a while.
 Cells that lack a cell wall are more prone to lysis in hypotonic environments
 Penicillin can be used to break down the peptidoglycan wall as it inhibits the construction of the
bacterial cell wall making the bacteria more prone to bursting.

Q2. Describe the following: periplasmic space, envelope, teichoic acid, adhesion site, lipopolysaccharide,
and porin protein.

 The periplasmic space is a concentrated gel-like matrix in the space between the inner cytoplasmic
membrane and the bacterial outer membrane called the periplasmic space in gram-negative bacteria.
 The bacteria cell envelope is a complex multilayered structure that serves to protect these organisms
from their unpredictable and often hostile environment.
 Teichoic acids (TA) are anionic polymers found in Gram-positive bacteria CW and are made of
polyglycerol phosphate units (approximately 20–30 repeats). They are involved, among others, in the
regulation of cell morphology as well as in cell division. They can represent up to 50% of the dry-weight
of the CW.
 Adhesion site-bacterial attachment structures (e.g. Pili)
 Lipopolysaccharides are large molecules consisting of a lipid and a polysaccharide composed of O-
antigen, outer core and inner core joined by a covalent bond. They are found in the outer membrane of
Gram-negative bacteria. Are extremely variable surface polysaccharide of Gram-negative bacteria. It
offered selective advantage in the niche occupied by that clone
 Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which
molecules can diffuse.
 Unlike other membrane transport proteins, porins are large enough to allow passive diffusion, i.e., they
act as channels that are specific to different types of molecules
2.1.5. Classification of bacteria based on their mode of nutrition
Bacteria have evolved different mode of nutrition: needed for growth and developments
Photoautotrophs: organism that obtain energy from sunlight
 Obtain their carbon from inorganic carbon dioxide
Example: Cyanobacteria
I. Photolithoautotrophs: an organism that uses light energy and an inorganic electron donor (H2O, H2,
H2S and CO2 as its carbon source
Purple and Green sulfur bacteria – utilizes sulfide and hydrogen as an electron donor

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II. photoheterotrophic: organism that uses light for energy, but cannot use carbon dioxide as their sole
source of carbon.
 Example: Purple sulfur bacteria
 Green sulfur bacteria
 Helicobacteria
III. Photo organoheterotrophs: organism that use light energy, and uses organic compound from the
environment to satisfy their carbon requirement
 They are inhabitant of polluted lake Their electron and carbon source is organic CPD.
 E.g., Green and Purple non-sulfur bacteria – utilizes organic cpd as an electron donor
Heterotrophic: organism that obtain at least some of their carbon from organic molecules like glucose.
 Obtain energy from the oxidation of organic compounds
 they can be: Parasitic, Saprophytic and Symbiotic
IV. Chemolithoautotrophy: organism that harvest energy from inorganic chemicals. They use carbon
from carbon dioxide and inorganic electron donor
 They oxidize reduced inorganic compounds such as iron, nitrogen, or sulfur to derive
both energy and electron for biosynthesis
 Bacteria utilize the oxidation and reduction of chemical compound as primary energy
e.g. Nitrosomonas: Oxidize ammonia to nitrite
Chemoheterotrphs: Organism that harvest energy from organic molecules
 Example: Methanotroph uses methane as carbon source to derive energy
Chemoheterotrophs can be:
V. Chemolithoheterotrophs: Bacteria/organism that utilize inorganic electron sources such as sulfur,
Hydrogen gas, Sulfide, Nitrite, Ammonia…..
 They use reduced inorganic substance as electron source
 They donate electron directly to electron transport chain to make ATP
 They derive their cellular carbon from carbon dioxide
 They can grow without organic compound and light
 example: Sulfur oxidizing bacteria (Beggiata, H2S --- S and H2)
 thiobacillus thioxidans uses thiosulfate and sulfide as source of energy to produce sulfuric acid:
 Hydrogen Oxidizing bacteria;
VI. Chemo organoheterotrophs: organism that utilize organic electron and carbon sources such as
carbohydrate, lipid and proteins
 They use reduced organic compounds as source of energy (they extract electron from it )
 They regenerate NADH from oxidation of reduced NADH which are then used to donate electron to
electron transport system
 e.g. Most non-photosynthetic microbes including most pathogen, E.coli, fungi and protista,
Decomposers: obtain carbon and electron from dead matters

2.1.6. Reproduction In Bacteria

A. Asexual reproduction
Bacteria and archaea reproduce asexually by splitting one cell into two equal halves in a process called
binary fission.

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Bacteria reproduce by Vegetative, Sexual and Asexual methods
Vegetative method includes: Budding, Fragmentation and Binary fission
Budding: the bud develops from the end of the cell, enlarge and become daughter cell and gets separated.
Fragmentation: the process by which the organisms split into two or more fragments to become new
individual. e.g. Cyanobacteria, Neisseria G=gonorrhoeae and Staphylococcus aureus
Binary fission: the most common method of reproduction in Archaea, bacteria and fungi.
 When an organism splits into two identical individual without sex taking place
 During this process chromosome (DNA) replicate
 Bacteria lack Mitotic spindle fiber and Cell fission make septum which separate mother cell into
two which are genetically identical
The process of binary fission.
1. The parent cell contains a large circular chromosome and a smaller plasmid.
2. The Cell elongated, chromosome and plasmid are replicated
3. A copy of the chromosome and plasmid move to each end (pole) of the cell.
4. The cell wall and cell membrane begins to grow inwards(invaginate) at the middle point (septation)
5. The growing cell walls meet in the middle to form a septum/Cross wall forms two distinct cells
6. The cells separate into two identical daughter cells (cytokinesis)

Figure 4 The stages of binary fission in prokaryotic cell replication

Sexual reproduction in bacteria
 Prokaryotes do not undergo sexual reproduction, but they are able to exchange genetic information
through other processes
 There is a process that is comparable to sexual reproduction (primitive form of sexual reproduction)
 This Exchange of genetic material is called Conjugations.
 Conjugation is a form of sexual reproduction in bacteria
 In Transformation: Bacterium takes up extracellular Donor DNA.
 In transduction: Donor DNA packaged in a bacteriophage infects the recipients bacterium
 In Conjugation: the donor bacterium transfers DNA to the recipient by mating.
 During conjugation, DNA is directly transferred from one prokaryote to another by means of a
conjugation pilus, which brings the organisms into contact with one another. In E. coli, the genes
encoding the ability to conjugate are located on bacterial plasmid called the F plasmid, also known
as the fertility factor, and the conjugation pilus is called the F pilus. The F-plasmid genes encode
both the proteins composing the F pilus and those involved in rolling circle replication of the

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 plasmid. Cells containing the F plasmid, capable of forming an F pilus, are called F+ cells or donor
cells, and those lacking an F plasmid are called F− cells or recipient cells
 F-Cell: Plamid lacking fertility plasmid
 Do not possess any form of a plasmid
 During conjugation, the F factor is transmitted from F+ cell into Recipient cell
+
 F Cells: donor of fertility plasmid
 It Produces sex pilus
 Sex pilus develop into Conjugation bridge
 Posses’ fertility plasmid which is separated from bacterial chromosome
 The F factor which consists of about 20 genes, can be in the form of a plasmid or part of the
DNA in the bacterial chromosome
 The genes encode enzymes essential for transferring DNA
 Certain F genes encode sex pili, long, hair like extension that project from the cell surface
 Sex pilus recognizes and binds to the surface of an F-cell, forming a cytoplasmic
Conjugation bridge between two cells
 The F plasmids replicate itself, and DNA is transferred from Donor to recipient bacterium
through conjugation bridge
 F plasmid may also have other gene like resistance to antibiotics

Figure 5. Bacterial reproduction by Conjugation

2.1.7. Common Bacterial Disease

1. Pertussis (Whooping cough)
 A very contagious respiratory illness caused by bacteria called Bordetella pertussis
 The disease is only found in human that affects upper respiratory tract

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  Transmitted through air
2. Meningitis : caused by Neisseria meningtidis and S.pneumoniae
 leads inflammation of membrane of brain and spinal cord, upper respiratory tract infection
and invade meninges
 spread/ vector is air . Bacteria Neisseria species are Gm (-) diplococcus and S.pneumoniae
are Gm(+) diplococcus
3. Tuberculosis : Caused by Mycobacterium tuberculosis
 Most often affect lungs, bones
 Transmitted through air and causes symptoms like persistent cough, weight loss, fatigue,
and night sweat
 Tested/Differentiated by using Acid-Fast staining that indicates presence of Mycobacterium
in sputum or blood sample
4. Syphilis: Caused by Treponema pallidum
 Are spirochete and Brain, Skin, hearts and blood vessels, Bones are affected
 Transmitted through sexual contact
5. Tetanus: Caused by Clostridium tetani
 Are Gm + spore forming anaerobic rod bacteria
 Affects Nerves at synapses. Transmitted from soil that contain spores
6. Leprosy: also called Hansen’s disease Caused by Mycobacterium Leprae
 Affects skin, bone, peripheral nerves and lining of nose
Transmitted through contacts
7. Diphtheria: caused by caused by Corynebacterium diphtheriae
 Spread through droplet infection and affects respiratory systems
 Prevented through vaccination
8. Chancroid: Caused by Haemophilus ducreyi
 Characterized by painful genital ulcers and swollen lymph nodes in the groin area
 Transmitted through sexual contact
9. Gonorrhea: Caused by Neisseria gonorrhoeae
 causes painful urination, abnormal discharge and pelvic pain in women
10. Anthracis: serious infectious disease Caused by bacillus anthracis.
 Primarily affect animal and transmitted to human
11. Shigellosis: caused by a group of bacteria called Shigella.
 Affect intestine and spread through fecal-oral route(contaminated food and water
12. Pneumonia – caused by bacteria like Streptococcus pneumoniae
 Leads to inflammation of the lung, with symptoms like; cough, chest pain, fever, and
difficulty in breathing

2.2. Archaea
2.2.1. Characteristic of archaea
Like bacteria, Archaean’s are
 They are unicellular
 They are microscopic
 They lack membrane bounded organelles

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 Unique feature of Archaea
 They lack peptidoglycan in their cell wall
 Their cell membrane lipids have branched hydrocarbon chains
 The initial amino acid in their polypeptide chain is coded by the AUG start codon (Methionine as in
eukaryotes)
 Many are found in extreme environment (abundant in hostile environment
Eg. Methanogen. Thermophile, Halophile
Where are archaea bacteria found?
 Archaean’s are inhabitants of some of the most extreme environments on the planet. Some live near
hydrothermal (rift vents) in the deep sea at temperatures well over 100 oc
 Those archaea that live in extreme habitats such as hot springs and deep-sea vents are called
extremophiles.
 Others live in hot springs, in extremely alkaline or acid waters
 Archaea are unique because of their ability to live in extremely hot or chemically aggressive
environments.
Why are archaea-bacterial and other bacterial groups placed together?
 Because both are prokaryotic organisms
2.2.2. Importance of archaea
Because of their tolerance to high temperatures, they have been exploited for a wide variety of
commercial uses.
a. source of enzymes that are usually added to detergents in order to help it maintain its activity even
at higher temperature and H.
b. Some enzymes from archaea also used to convert cornstarch into the fiber dextrin.
c. Some Archaea also bear the potential for bioremediation or help in cleaning contaminated sites.
d. The thermophilic Archaea, Thermus aquaticus, is an essential part of the development of molecular
biology as a science. As a result, Archean has become the source of the enzyme harnessed as the
basis for the amplification of the DNA in a technique called Polymerase Chain Reaction (PCR)
2.2.3. Physical factors that affecting microbial growths
 The environment in which some microbes grow would kill most other microbes
 Major physical factors are:
o Solutes and water activity, Pressure, Temperature
o PH, Radiation Oxygen level
I. Temperature: includes three groups
 Cold temperature → Bacteria that reproduce at optimum temp 15 degree are called Psychrophiles:
and Psychrotrophs uses 25 degrees
 Warm temperature: Bacteria that need Optimum temp near 37 oc is called thermophiles.
 Hot temperature- bacteria that uses temperature with optimum of 60 oc and 95 oc are called
thermophiles and Hyperthermophiles respectively.
II. Oxygen requirement:
 Microbes not using oxygen (Anaerobes)
 Aerotolerant → microbes tolerating oxygen
 Obligate anaerobes → Microbes sensitive to Oxygen are

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  Microbes using oxygen(aerobic) can be:
 Obligate aerobes →microbes requiring oxygen
 Microaerotrophiles →Microbes requiring reduced oxygen
 Facultative aerobes → microbes growing with without oxygen
III. PH: Microbes growing below PH of 6 are termed as: acidophiles
IV. Osmotic conditions
 Halotolerant →Microbes tolerating NaCl
 Non-halophiles → microbes not tolerating NaCl
 Halophiles → microbes requiring about 15% Nacl
 Extreme halophiles → microbes requiring NaCl at 15-30%

KEY TERMS
A. Thermophiles live at high temperatures
B. Hyperthermophiles live at really high temperatures (present record is 121°C!)
C. Psychrophiles (also called cryophiles) live at cold (one in the Antarctic grows
2.2.4. Difference
best at 4°C) between Archaea and Eubacteria
D. Halophiles live in very saline environments (like the Dead Sea)
E. Acidophiles live at low pH (as low as pH 1 and who die at pH 7!)
F. Alkaliphiles thrive at a high pH.

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What are the major differences among bacteria, archaea, and Eukaryia?

2.3. Fungi
 Microbiologist describe fungi as Saprophytic and parasitic spore-bearing organism eukaryotic organism.
 Biologist who studies about fungi are called Mycologists
 The scientific discipline devoted to fungi is called Mycology
 The study of fungal toxin and their effect is called myco-toxicology
 The disease caused by fungi in animals are known as mycoses or mycosis

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2.3.1. What are the general Characteristics of Fungi?
 All are eukaryotic
 Possess membrane-bound nuclei and organelles
 Most are filamentous. Are composed of individual microscopic filaments called hyphae, which exhibit
apical growth and which branch to form a network of hyphae called a mycelium.
 Some fungi have septate hyphae while some have nonseptate hyphae(Coenocytic hyphae):Septate
hyphae have distinct cellular compartments separated by the walls called septae. Coenolytic hyphae
lack septa and content of the hyphae move freely.
 Some are unicellular e.g. yeasts. And many are multicellular
 Protoplasm of a hypha or cell is surrounded by a rigid wall
 Are composed primarily of chitin and glucans, although the walls of some species contain cellulose.
 Many reproduce both sexually and asexually by producing spore
 Their nuclei are typically haploid and hyphal compartments are often multinucleate
 However, the Oomycota and some yeasts possess diploid nuclei.
 All are achlorophyllous
 They lack chlorophyll pigments and are incapable of photosynthesis.
 All are chemoheterotrophic (chemo-organotrophic)
 They utilize pre-existing organic sources of carbon in their environment and the energy from chemical
reactions to synthesize the organic compounds they require for growth and energy.
 Possess characteristic range of storage compounds e.g. trehalose, glycogen, sugar alcohols and lipids.
 May be free-living or may form intimate relationships with other living organisms

2.3.2. Economic Importance of Fungi

 They exist as saprobes and are agents of biodegradation and biodeterioration
 They recycle nutrients in ecosystem
 responsible for the majority of plant diseases and several diseases of animals (including humans)
 used in industrial fermentation processes e.g Protein, Alcohol, Fat and Glucose solution from fungi like
Fusarium and Molds
 used in the commercial production of many biochemical
E.g. Antibiotic-Penicillium, Immunosuppressive drug like Cyclosporin) From Aspergillus –
Production of Citric, Oxalic and Gluconic acid)
 Cultured commercially to provide us with a direct source of food e.g. Basidiomycetes
 Beneficial in agriculture, horticulture and forestry.
 Fungi are useful tools for studying complex eukaryotic events, such as cancer and aging within a simple
cell

2.3.3. Ecology of Fungi

 Fungi are found in cool, dark and moist places with a supply of decaying matter
 Fungi are agents of biodegradation and biodeterioration:
 SAPROTROPHIC fungi utilize dead organic materials as sources of nutrients and are responsible
for the biodegradation of organic materials in our environment, such types of fungi play a vital role
in recycling essential elements, particularly carbon.
 Fungi are saprobes and decompose organic matter

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  Many are mutualistic. They establish complex mycorrhizal associations with the roots of plant
 Lichens are a symbiotic relationship between a fungus and a photosynthetic organism
2.3.4. Classification of Fungi
The current classification of Kingdom fungi into five phyla based on their mode of reproduction and
molecular Data: these are: -
A. Chytridiomycota: (Chytrids) is the simplest and most primitive true fungi.
 The only class in this phylum is Chytridiomycetes
 Most of them are unicellular while few are Multicellular
 They have rhizoids with no true mycelium
 Live in aquatic habitat, some in gut land animals
 Asexually produce zoospore which is motile
 Sexually produces Flagellated diploid or haploid gametes in
sporangium in male and female. eg. Allomyces and water molds
B. Glomeromycota – E.g. Mycorrhizal fungi called fruit bodies
 Monophyletic group of soil-borne fungi
 They are the most important microorganism on the earth
 They form intimate obligate symbionts and form mycorrhizal associations with nearly 80% land
plants
 They are believed to have been crucial in the initial colonization of the terrestrial
 They are the oldest multicellular and reproduce asexually through glomerospores and Blastospore
C. Zygomycota: are called conjugated fungi and Sporangial fungi
 Reproduce asexually by producing Sporangiospore
 (Non-motile spore or asexual spore)
 Asexual spore develops in sporangium on tip of hyphae
 Are Terrestrial and most are saprobes
 They also reproduce sexually when environmental condition become Unfavorable by creating
Zygospore - sexual spore and share genetic content through conjugate. This is why they are
termed as conjugated fungi
 Sexual spore called Zygospores can remain dormant in adverse environment
 Are mainly multicellular, Mycelia of continuous hyphae with many haploid nuclei
 Include familiar bread molds. sporangial fungi.
 E.g. Rhizopus and mucor, Stolonifer, Black bread molds
D. Ascomycota: are also called Sac fungi
 Ascospore producing fungi: non motile spore
 Unicellular and multicellular with septate mycelia
 Asexual reproduction, is common by budding (Conidiospores)
 Sexual reproduction involves the formation of an ascus(sac) on
specialized hyphae
 They inhabit terrestrial, on fruit other organic material
 E.g. Saccharomyces cerevisiae, Aspergillus and penicillium
E. Basidomycota: are called club fungi. Basidia producing fungi.
 Are multicellular, uninucleate mycelia,

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  Asexual reproduction is absent
 Sexually produces basidiospore that are borne on club
shaped structures at the tips of the hyphae
 E.g. Rust and smuts are important plant pathogenic fungi and Mushroom
2.3.4. Reproduction in Fungi
2.3.4.1. Asexual reproduction
 Sporulation: the process of spore formation in fungi
 Fungi reproduce asexually by (Producing spore, Budding, Fragmentation)
 Many asexual spore develop within sacs (vessel) called Sporangia(Sporangium)
 Spores are called Sporangiospores
 Some fungi produce spore asexually on supportive structure called Conidiophores (special spore
producing hyphae)
 Conidiophores can be arranged singly on hyphae or grouped in special asexual fruiting bodies
 They are unprotected dust like spores called conidia(Conidium=dust)
 They are extremely light and blown by winds easily
 In others spore may form by fragmentation of the hyphae yielding arthrospores (Arthro = joint).
Egg. Athlete’s foot Multiply in this manner
 Many yeast reproduce asexually by budding, Cell become swollen and new cell called Blastospore
develop. (Blasto = bud)
 Blastospore is an asexual fungal spore produced by budding
2.3.4.2. Sexual reproduction fungi
 Many fungi produce spores by sexual reproduction
 The process of sexual reproduction in fungi is unique. Ex. Nuclear membrane remain intact, diploid
chromosome are pulled apart by spindle fiber with in intact nucleus
 It involves three sequential stages: Plasmogamy, Karyogamy and meiosis
 Plasmogamy: fusion of two protoplast = two haploid nuclei in the same cell
 Karyogamy: Fusion of two haploid nuclei and forming diploid nuclei containing two sets of
chromosomes from each parent and zygote is formed.
 Fusion cell represents heterokaryon (different nucleus)
 Meiosis: Restores haploid number of chromosomes which produces gametes

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 Figure 6. Reproductive cycle of Basidiomycetes

2.3.5. Harmful aspect of fungi

I. Fungi are the major cause of plant diseases. Over 5000 species attack
economically valuable crops,
It also causes disease in animal and human
II. Molds can causes deterioration of fabrics, leather, electrical insulation and other
manufactured goods
III. Cause mycotoxicosis ingestion of toxin:
A. Aflatoxin: Is mycotoxin produced by Aspergillus flavus and A. parasiticus. It
contaminate grains, Cereals,Peanuts, sweet potatoes, corns, Rice and animal
feed. They can be carcinogenic
B. Ergotism: caused by Claviceps purpurea an ascomycete producing powerful
toxins. Found on grain products like rye bread
C. Mushroom poisoning (mycetism): Mycotoxin that affect human body
IV. Superficial Fungal infections: Affects outer most areas of the human body (Hair,
fingernails, Toenails, epidermis). The type of fungi that affect these are ;
Trichophyton, Epidermophyton, Microsporum
Major forms of dermatophytosis are:
 Tinea Corporis or Ringworm: caused by Microsporum canis and
Trichophyton mentagrophyes: affect hairless skin
 Tinea pedis(Athlete’s foot) : T. rubrum.. affects lower legs
 Tinea Capitis: T.tonsurans. Affects scalp, eyebrows and eyelashes

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  Tinea Barbae: T.rubrum and T.mentagrophytes: Beard ringworm
 Tinea unguium (Onychomycosis): Affect nails
Candidiasis caused by Candida albicans:
 Sign and symptom are itching, burning pains, Cheesy discharge
 Transmitted sexually
Aspergillosis: by A.fumigatus
 Symptoms are Bloody cough, chest pain, Wheezing, shortness of breath
 Transmitted through air borne
Thrush: Caused Candida albicans
 White flecks on mucous membrane is the main sign of thrush
 It is prevented by practicing good oral hygiene and limiting sugar intake
Which are common in food spoilage?
 Yeast, Rhizopus stolonifer (Black bread molds) Penicillium, and aspergillus
What does a fungal disease mean?
 A fungus that invades the tissue of plant and animals that can cause a disease.
Examples of diseases caused by fungi
 Candidiasis Coccidioidomycosis (Valley Fever)
 Cryptococcosis Histoplasmosis
 Aspergillosis Blastomycosis.
 Pneumocystis pneumonia Ringworm
What are the main human diseases caused by fungi?
 Black Piedra of hair, Ringworm, Aspergillosis Coccidioidomycosis
 Histoplasmosis, Blastomycosis, Pneumocystis pneumonia
What is the difference between fungi with prokaryotes?

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2.4. Protozoa
 The term Protozoa (Greek, protos-first zoon - animal)
 Are eukaryotic, unicellular and Heterotrophic protist
 The study of protozoan is called Protozoology

2.4.1. Characteristics of Protozoa

 Fungi are unicellular microorganism that lack cell wall
 They are eukaryotic, most are Microscopic
 They are either free living, parasitic
 Most are beneficial and few are harmful
 They are generally heterotrophic
 They divide asexually by binary fission or budding and Cyst formation and sexually by
Conjugation or Syngamy (Union of gametes to form Zygotes)
 They are motile with cilia, Flagella, Pseudopodia
 Have nutrition of all types; autotrophic, heterotrophic, Saprozoic(using nutrirnts dissolved in the
surrounding medium
 Inhabit Terrestrial or aquatic
2.4.2. Classification of Protozoa
Fungi are divided into four groups Based on the structure and part involved in locomotion
A. Mastigophora or Flagellated Protozoans
 They are parasitic or free living
 Their body is covered by Pellicle or a cuticle
 They have flagella for locomotion
 Reproduce asexually by Budding / binary fission and sexual reproduction is absent
E.g. Giardia, Leishmania, Trypanosoma, Chlamydomonas, Trichomonas
B. Amoeboid or Sarcodina: E.g., Amoeba,
 They lack definite shape
 They live in fresh water or moist soil
 Use pseudopodia for movement and pellicle is absent
 Reproduce by asexually by binary fission and Cyst formation
 Sexually when present by flagellated sex cell
 Have contractile vacuole
 E.g., Amoebas are single-celled organisms that reproduce asexually. Reproduction occurs when an
amoeba doubles its genetic material, creates two nuclei, and starts to change in shape, forming a
narrow "waist" in its middle.

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Figure 7. Structure of Amoeba

 C. Sporozoans:
 They are endoparasites, Reproduction is by sporozoites formation.
 They are generally non motile except for certain sex cell
 Reproduce sexually by conjugation and involve flagellated sex cell
 Reproduce Asexually- Transverse fission /Multiple fission
 Lack specialized organ for locomotion
Example: Plasmodium, Toxoplasma gondi, Cryptosporidium
D. Ciliophoran (Ciliated Protozoa):
 They are aquatic and move actively with thousands of cilia
 They have fixed shape covered by Pellicle
 Reproduce asexually by Transverse fission and sexually by conjugation
 E.g. Paramecium reproduction is asexual, by binary fission, which has been characterized as "the sole mode of
reproduction in ciliates" (conjugation being a sexual phenomenon, not directly resulting in increase of numbers).
During fission, the macronucleus splits by a type of amitosis, and the micronuclei undergo mitosis.
 e.g. Euglena reproduce asexually by means of longitudinal cell division, in which they divide down their length,
and several species produce dormant cysts that can withstand drying

2.4.3. Reproduction In Protozoa

Asexual reproduction: Most protozoa are asexual and reproduce in one of the three ways
A. Fission: occur when a cell divides evenly to form new cells
B. Budding: occur when a cell divides unevenly
C. Multiple fission (Schizogony) : occur when the nucleus or cell divide multiple times before the rest
of the cell divides.

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Figure 8. Asexual reproduction Protozoa
Sexual Reproduction: occur during the life cycle of most protozoa
 Syngamy or sexual fusion is a permanent form of sexual reproduction whereby two
protozoan cells fuse together to create a fertilized cell, also known as zygote.
 Genetic variation results from conjugation

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 2.4.4. Nutrition in Protozoa
Protists obtain food in one of three ways’
A. Absorption: food is absorbed through plasma membrane of protist
B. Ingestion: Cilia create mouth like opening called Cytostome e.g., paramecium
C. Ingulf: By using Pseudopodia, pull in to cell by phagocytosis e.g., Amoeba
 Food is digested in the vacuole w=and waste products are excreted using exocytosis
2.4.5. Common disease caused by protozoans
 Many protozoans are beneficial and few are harmful (causes disease).
Table 1. Major Protozoal parasites of human and other organism
Disease Causative Organ, it Transmissions Clinical Feature
agent/Etiologic affects
al Agents
1. Malaria Plasmodium Liver and Anopheles Mosquito Fever, shivering, cough, respiratory
falciparum, RBC distress, pain in the joints, headache,
P. vivax watery diarrhea, vomiting, convulsions,
severe anemia
2. African Trypanosoma Brain Tsetse Fly/Sand fly Initial haemolytic phase (fever, joint pains
trypanosomiasis brucei and followed by neurological disorder,
Blood somnolence)
3. Chagas Trypanosoma Spread by insect fecal Acute phase (fever and splenomegaly)
disease cruzi contamination of its Chronic phase (irreversible damage to
own bite heart, esophagus and colon)
4.Leishmaniasis Leishmania WBC, Phlebotomine sand Skin ulcers, mucocutaneous complications
/kala-azar donovani, Skin, flies and visceral diseases
L. major, intestine (hepatosplenomegaly)
L.mexicana,
L. braziliensis
5.Toxoplasmosis Toxoplasma Blood, Domestic cat, Blindness and mental retardation can result
gondii Eye Food in congenitally infected children.
Immunosuppressed patients can present
more severe symptoms: splenomegaly,
polymyositis, dermatomyositis,
chorioretinitis, myocarditis, pneumonitis,
hepatitis, encephalitis, and multisystem
organ failure.
6.Trichomoniasis Trichomonas Urogenit Sexual contact Vaginal discharge, odor and edema or
vaginalis al erythema
7. Giardiasis Giardia Intestine Fecal-oral Ingested cysts survive stomach passage,
lamblia Contaminated water trophozoites emerge from the cysts in the small
intestine, impair mucosal function
8. Amoebiasis Entamoeba Intestine, Ingestion of fecal, Multiplication of organism causes tissue
histolytica Liver Contaminated food destruction, result in amebic abscesses. It
and water causes muscle cramp and diarrhea. Due to
Associated with intestinal ulceration, the fluid is bloody, and the
poverty, Homosexual condition is called amebic dysentery
men, Migrant workers

What are Babesia and Theileria?

 Babesia also called Nuttallia is an apicomplexan parasite that infects red blood cells and is
transmitted by ticks. Originally discovered by the Romanian bacteriologist Victor Babeș, over 100
species of Babesia have since been identified.

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  Theileria is a genus of parasites that belongs to the phylum Apicomplexa, and is closely related to
Plasmodium. Two Theileria species, T. annulata and T. parva, are important cattle parasites.
T. annulata causes tropical theileriosis and T. parva causes East Coast fever.
 Theileria species are transmitted by ticks.
State the common species of plasmodium found in Ethiopia.
Among the five Plasmodium species known to infect human beings, Plasmodium falciparum and
Plasmodium vivax malaria are by far the most predominant and widely distributed in Ethiopia.
What is Trypanosomiasis and explain the causative agent and vector of Nagana (Gandii)/(Gendi).
Trypanosomiasis is the name of several diseases in vertebrates caused by parasitic protozoan
trypanosomes of the genus Trypanosoma. In humans this includes African trypanosomiasis (Africa
sleeping sickness) and Chagas disease. In livestock, cattle Trypanosomiasis-Nagana (in Afaan
Oromo - Gandii), (Amaharic - Gendi).
The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing sleeping sickness
in humans and nagana in animals. Due to some of its unique properties, it has emerged as a popular
model organism in systems biology.
tsetse flies are the vector for Nagana diseases
Describe the vector and life cycle of leishmania spp.
 The vector for leishmania is sandfly
 Leishmaniasis is a parasitic disease that is found in parts of the tropics, subtropics, and southern
Europe.
 It is classified as a neglected tropical disease (NTD).
 Leishmaniasis is caused by infection with Leishmania parasites, which are spread by the bite of
phlebotomine sand flies. Three types are common
A. Cutanious leshimaniasis – (In Afaan oromoo-Sinbira halkanii = lamxii), Amharic- Kunchir)
B. Mucocutanious leshimaniasis ,
C. Visceral leshimaniasis are some

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2.5. Viruses
2.5.1. Characteristics of Viruse
 A virus is a very small, non-cellular parasite of cell
 Are obligate intracellular particles seen only with electron microscope
 Genome is either DNA or RNA covered by capsid, which is single stranded or double stranded but
not both
 They infect host cell and replicate; they lack chemical machinery for generating energy and
synthesizing large molecules
 Have an inner core of nucleic acid covered by protein coat called envelope
 They cannot be grown on artificial cell free media
 Most viruses range in sizes from 20 – 250 nm. Viruse varies in size when compared with others e.g.
Eukaryotic cell: 2000nm, Bacterium: 2000nm, Small pox: 250nm,Tobacco mosaic : 240nm,
Influenza:100nm, Rabies: 150nm, Bacteriophage: 95nm, Common cold: 70nm, Polio: 28nm,
Parvoviruses: 20nm
 Viruses are inert (nucleoprotein) outside their host cell.
 Viruses are obligate intracellular parasites and filterable agents
 Viruse do not have cellular organization, are acellular
 They occupy a space in between living and non-living, because they are crystallizable and non-living
outside the body of host
 They lack an enzyme for protein and nucleic acid synthesis independent of replication of host cells

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  They are unaffected by antibiotics
 They do not fulfil the characteristic of life
 They are responsible for a number of dreadful diseases in human and plants
 Viruses infect all cellular life forms (Eukaryotes and Prokaryotes-bacteriophage)

2.5.2. Basic structure of viruses

The basic structural component of a viruses are:

 Core – the genome material (DNA/RNA) Single stranded or double stranded

 Capsid – a protective coat of protein surrounding the core
 Nucleocapsid – the combined structure formed by the core and capsid
 Envelope – a few viruses such as the HIV and influenza, have an additional lipoprotein layer
around the capsid derived from the cell surface membrane of the host cell
 Capsomeres – Capsids are often built up of identical repeating subunits called capsomeres
 Some Viruse contain enzymes like Lysozyme which makes small hole in bacterial cell that allows
viral nucleic acid to get in. e.g. Bacteriophage
 Some virus contains their own nucleic acid polymerase which transcribe the viral genome into
mRNA during replication process

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  E.g. Retroviruses are RNA that replicate inside host cell as DNA intermediate. These viruses
possess an RNA dependent DNA polymerase called reverse transcriptase
 The particle of a virus is called a virion. All virions contain at least two components Capsid and
DNA/RNA

 2.5.3. Classification of viruses

Primary criteria for delineating the main viral taxa are:
I. Symmetry of the viral capsid (helical, icosahedral or spherical, complex)
II. The type and character of the viral genome (DNA, RNA, and Retrovirus)
III. The strategy of viral replication (Lytic, lysogenic)
IV. The type of organism they infect (Human, animal, plant, Bacteria

2.5.3.1. Classification of virus based on Viral Symmetry

Structure of capsid give the symmetry to the virus. Virus particle may be either helical, icosahedral or
spherical, complex in symmetry
I. Helical symmetry
 Helical structure provides flexibility of the filaments
e.g. Tobacco mosaic virus

II. Icosahedral Symmetry (spherical)

 A type of polyhedron with 20 equilateral triangular faces and 12 vertices
 The rigid structure provides protection to the genome
E.g. Papovavirus, picornavirus, adenovirus, Toga virus, etc

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III. Complex Symmetry
 Consists complex structural components which made it different from the
others two groups. E.g. Bacteriophages: a virus that uses a bacterium to replicate
its genetic information

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2.5.3.2. Classification of virus based on their genetic material
 Retroviruses that can converts its genetic information from RNA into DNA after it has infected a
host E. g. HIV (Human Immunodeficiency Virus): Virus that attacks the body’s immune system
 DNA Virus: store genetic information in the form of DNA
 RNA Viruse: Store genetic information in the form of RNA
Difference between DNA and RNA Viruses

2.5.4. Viral Replication

 Viruses hijacks the host cell metabolism and produces copies of itself
 They often destroy the host cell when new virions assembled and released
 To produce new virions, Viruses go through the following five steps of replication cycle
e.g. Replication of bacteriophage
 Bacteriophages are Bacterial viruses and also called phages
 Are viruses that infect bacteria
 They are obligate intracellular parasites that multiply inside bacteria
Adsorption → Penetration → Synthesis → Maturation → Release
I. Adsorption: attachment of viruses to host cell
II. Penetration: the entry of virions (genomes) into the host cell
III. Synthesis: the synthesis of new nucleic acid, capsid, proteins, enzymes using host cell machine
IV. Maturation: the assembly of newly synthesized viral components into complete virions
V. Release: the departure of new virions from host cells by killing (lysis), lysogenic (released
continually without killing host cell)
Replication of HIV
HIV is type of retrovirus that inserts a copy of its RNA genome into the DNA of a host cell where it
invades and changes the genome of that cell.
the major steps in the HIV replication cycle are;
binding and fusion→ reverse transcription → integration → transcription → assembly
→budding

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HIV Spike is made from
glycoproteins spikes on virus
surfaces bind receptors on
host cells to propagate
infection.

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 Structure of Bacteriophage contain the following components
Genome: carries the genetic material necessary for replication of new phages particles
Tail sheath: retracts so the genome can move from the head into the host cell’s cytoplasm
Plate and tail fiber: attach to specific receptor sites on the cell wall of a susceptible host bacterium

Phages exhibit two different types of life cycle

a. Lytic cycle
 Also known as virulent cycle/phage
 Cycle result in the lysis of host bacteria, releasing of progeny virions
 Enzyme called lysozyme breaks down cell wall allowing viruses to escape.
 The phage like T4 is virulent and lyse and destroy bacteria they infect
Cycle involves: Attachments →Penetration→ Replication →Assembly→ Release

b. Lysogenic cycle:
 Infection with every phage does not result in lysis of the host cells

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  Some phages like temperate integrates into the genome of bacterial chromosomes without causing
any lysis of the bacteria.
 The integrated phage nucleic acid is also called prophage.
 Prophage behaves like a segment of host the host chromosomes and multiplies synchronously with
it. This is called lysogeny
 The bacterium that carries a prophage within its genome is called lysogenic or temperate phage

What is the difference between Lytic and lysogenic cycle?

Lytic cycle Lysogenic cycle
The DNA of the virus does not integrate into the host DNA The DNA of the virus integrate into host cell DNA
Host DNA hydrolyzed Host DNA not Hydrolyzed
There is no prophage stage There is prophage stage
Replication of virus takes place independently from Replication of viral DNA along with host DNA
the host DNA replication replication
Occur with in short period of time Takes long time
Symptoms of viral replication are evident Symptoms of viral replication are not evident
Genetic recombination in the host bacterium not allowed Genetic recombination in the host bacterium allowed
The cellular mechanism of the host cell is totally The cellular mechanism of the host cell is
undertaken by the viral genome somewhat disturbed by the viral genome

Importance of viruses for human beings

Phage typing of bacteria, Anti-tumor agent
Pesticides, Gene vectors for protein production 33 | P a g e
Gene vectors for treatment of genetic diseases
What feature of viruses could be used to characterize them as life forms?
They show multiplication (only inside the host cell).
They have genetic material i.e. DNA/RNA.
They can direct protein synthesis (though they use host machinery for it).
They show mutation.
They can be transmitted from the diseased host to the healthy ones or possess the ability to infect.
They react to heat, chemicals, radiation, and shows irritability, a character of only living organisms.
They possess genetic continuity and have definite races/strains.
Similarity between nucleoproteins of viruses with the protein and nucleic acid of living organisms.
What make viruses more similar to lifeless molecules?
They can be crystallized
They behave as inert chemicals outside the host cell.
A cell wall or cell membrane of any type is absent in viruses
They lack any energy producing enzyme system.
They do not show functional autonomy.
 They do not move
 they do not grow
 They do not respire or excrete or they do not show any sign of metabolism except
reproduction.

2.5.6. Common viral disease in Ethiopia

Viruses are responsible for causing many diseases, including:
AIDS, Common cold, Ebola, Genital herpes, Influenza, Coronavirus disease (COVID-19)
Table 2. Common viral disease
Disease Causative Sign and symptoms Transmission Prevention and
agent control
Mumps Mumps virus Swollen and painful protid Person to person in Vaccine
glands pain on chewing and infected saliva
swallowing
Meales(rubeola) Measles virus Caugh, nasal discharge, eye Droplet contact Vaccine
redness, and high fever
Rabies Rabies virus Tingling, burning, Coldness at Bite from rabid Avoiding rabid
bite site, fever, headache. animal animal
Increased muscle tension, Pre -vaccination
paralysis and hydrophobia
Polio Polio virus Often no sign and symptom Fecal-oral- route Polio vaccine
Good personal
hygiene
Common cold Rhinoviruses Sneezing, sore throat, runny Respiratory droplet Practicing good
(rhinitis) Adenoviruses and stuffy nose, hacking cough hygiene
Chicken pox Varicella Fever, headache, malaise, with Droplet contact Chickenpox
(Varicella) Zoster virus red, itchy rash on face, scalp, vaccine
chest and back

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 2.6. Normal Microbiota/ Flora
Is the population of microbe routinely found growing on the body of healthy individuals
They can be resident biota – extended period or Transient microbiota – temporary occupants

Knowing about microbiota

 Knowing where they located allows us to insight into the possible infections that might result from
injury to these body sites.
 Helps the physician investigator understand the causes and consequences of colonization and growth by
microorganisms normally absent at a specific body site
 Increases awareness of the role that microbiota plays in stimulating the host immune response can be
gained. Immune system protects pathogens
Importance of microbiota
Norma microbiotas are soldiers of the body, they compute for the space and food with the pathogenic
microorganisms and they produce different metabolites that the pathogenic microorganisms could not
tolerate
The most significant importance of normal flora is protection against pathogen! They exclude
pathogens by:
I. Covering binding sites/attachment site: Provides first line of defense against microbial pathogen
II. Consuming available nutrients that pathogens use
III. Producing toxic to other bacteria.
IV. Play role in toxin degradation
V. Assist in digestion, they also produce small quantities of Vitamin K used in blood clotting, bone
health, protect certain forms of cancer and heart disease
VI. Stimulate adaptive immune system: contribute to maturation of immunity
VII. Maintenance of structural integrity of the gut mucosal barrier
When they are suppressed, pathogen can colonize and causes disease
e.g., Oral antibiotics can inhibit normal intestinal microbiota and allowing the over growth of toxin
producing strains of Clostridium difficile that causes antibiotic-associated diarrhea and colitis.

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2.7. The Germ Theory of Disease and Koch’s Postulates
 Koch used an experment that proved diseases are caused by microorganism
 He used mice as an experimental animal
 E.g. he discovered that the anthrax bacteria could be grown in nutrient fluids outside the host
 He also identified the causative agent of tuberculosis
He formulated a set of regorious Criteria known as Koch’s postulates for definitively linking a
specific microorgansim to a specific disease.
Koch’s postulates state the following
I. The disease-causing organism must always be present in animals suffering from the disease but
not in healthy animals.
II. The organism must be cultivated in a pure culture away from the animal body.
III. The isolated organism must cause the disease when inoculated into healthy susceptible animals.
IV. The organism must be isolated from the newly infected animals and cultured again in the
laboratory where it should then be seen to be the same as the original organism

Q. Which are the common Pathogenic microorganisms?

e.g. Salmonella typhae, Shigella dysentery, Mycobacterium tuberculosis

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2.7. Modes of Disease transmission
There are four main routes for the transmission of pathogens:
Disease Transmitted by Contact
Direct contacts: Many skin infections, such as athlete’s foot, ring worms…
Sexual contact: Candidiasis, Syphilis, Gonorrhea, Chancroid, AIDS
Disease Transmitted by Droplet
many are respiratory diseases affecting the airways of the lungs
transmitted by droplet when infected person cough, sneeze, talk
e.g. Common cold, Flu, Pneumonia, TB…
Disease Transmitted by drinking contaminated water (Water-borne)
They often infect regions of the gut
E.g. Cholera, Typhoid fever, Legionnaire’s disease, Amoeba, Giardia …
Disease Transmitted by eating contaminated food(Food-borne)
Most Food posisoning bacteria.they initially inect a region of gut
E.g. Salmonellosis, Shigellosis, Botulinism, Listerosis, Typhoid fever…
Disease Transmitted by vectors
Spread through insect, animals
E.g. Malaria – Anopheles mosquito
Sleeping sichness- Tsetse fly

2.8. Uses of Microorganism

 Microbiology has made great advances in understanding the role of microorganism in health, food,
agriculture, medicine, energy, clean up the environment.
 Microbes involve in recycling of essential element in the ecosystem
2.8.1. The role of Microorganism in Agriculture
The role of microbes in agricullture is indispensable. E.g.
 Microbes helps in decomposition( ammonification, humus formation, Composting)
 Nitrogen fixation
 Phosphate solubilization
 Potassium Mobilization
 Antagonism towards pests
Elements like C, N, O, S, P are essential and abundnat, but not necessarly in the forms organism can use. Microbes
are primarly responsible in converting essential elements of life in the form they need. E.g. Nitrogen in the form of
nitrate. Bacteria andd fungi convert carbon in organic matter to CO2 that is used by plants and algae.
Microbes are used in producing Bt Crops, GR crops by serving as vector
2.8.2. The role of Microorganism in Sewage Treatment
Anaerobic microbes reduces the volume of sludge and produce methane gas which is used alternative
energy source
They reduces energy consumed to treat waste water
Microbes also removes Phosphorus from waste water
2.8.3. The role of bacteria in Bioremediation
Bioremediation: is a natural process that relies on microbes or their products to degrade
contaminants
Microbes involves in biodegeradation and biotransformation (Solubilization of insoluble nutrients)
and Toxic to less toxic

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 Microbes suppress soil born pathogens
Recycle and increase availability of plant nutrients,
Degradation of toxicants including pesticide and heavy metals
2.8.4. The role of bacteria in food production and Processing
The tart taste of Yoghurt, Pickles, sharp cheese, and Some Sausage is due to the production of
lactic acid by lactobacillus bacteria like Lactococcus, Streptococcus, Leuconostoc, Pediococcus
are Obligate fermenter

The role of microbes in making Medicine

Antibiotics were extracted from microbes such bacteria and fungi
Insulin --- harvested from bacteria
Penicillins—produced from genus Penicillium,
Cephalosporin--Derivatives of fermentation products of Cephalosporium
Carbapenems—produced by Streptomyces spp.
Aminocyclitol ---Produced by Streptomyces spectabilis,
Aminoglycosides--Naturally occurring antibiotics from Micromonospora spp.
Ansamycin---Semisynthetic antibiotic derived from compounds produced by Streptomyces
mediterranei etc
2.8.5. The role of Microbes in regulating Health
 Microbes serve as soldiers, some aid digestion,
 some protect against pathogens that causes infection
 Some secrete vitamins like biotin, Vitamin K and Folic acid
2.8.6. The role of Bacteria in Recycling minerals through ecosystems
2.8.6.1. Carbon cycle
 Fundamental aspect of carbon cycle is carbon fixation,the defining characteristic of primary producers
 Oxygen supply in the ecosystem influence carbon cycle
 Many organsim uses sugar,amino acids and Protein as energy source. Amount of Oxygen used
determine type of degradable organic matter and type of carbon containing gases formed.
 When organic matter is degraded aerobically, a great deal of CO2 is produced
 In anaerobic enviroments, CO2 is used by methanogens. These archaea obtain energy by oxidizing
hydrogen gas, using CO2 as terminal electron acceptor, generating methaneCH4.
 Methane in atomesphere is oxidized by ultraviolet light and chemical ions, forming carbon monoxide
and carbon dioxide
 Methylotrophs can use methane as an energy source, oxidizing it to produce CO2.

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 2.8.6.2. The Nitrogen Cycle
 Root nodules are found on the roots of plants, primarily legumes, which form a symbiosis with nitrogen-
fixing bacteria (Rhizobia).
 Under Nitrogen limiting conditions, capable plants form a symbiotic relation with a host-specific strain of
bacteria known as rhizobia.
 Nitrogen fixation in the nodule is very oxygen sensitive
Table 1. Key processes and Prokaryotes in the Nitrogen Cycle
Processes Example of Organisms
Nitrification (NH4+ → NO3−)
(NH4+ → NO2−) Nitrosomonas
(NO2− → NO3−) Nitrobacter
Denitrification (NO3− → N2 Pseudomonas, Bacillus, Paracoccus
Free living, aerobic Azotobacter, Cyanobacteria
Anaerobic Clostridium, Purple, and Green phototrophic bacteria,
Methanobacterium (Archaea)
Symbiotic Rhizobium, Brady rhizobium, Frankia
Ammonification (Organic -N → NH4+) Many organisms can do this, Decomposers
Anammox (NO2− + NH3 → 2N2) Brocadia

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 2.8.6.3. The sulfur cycles
 Sulfur is found in fewer types of organic molecules than nitrogen.
Table 2. Key processes and Prokaryotes in sulfur cycle
Processes Example of Organisms
2-
1. Sulfide/Sulfur Oxidation (H2S → S → SO4 )
O

Aerobic Sulfur chemolithotrophs (Thiobacillus, Beggiata)

Anaerobic Purple and green phototrophic bacteria and chemolithotrophs
2. Sulfate reduction (Anaerobic) SO42- → H2S Desulfovibrio, Desulfobacter, Archaen
o
3. Sulfur reduction (Anaerobic) S → H2S Desulfuromonas, Many Hyperthermophilic Archaea
4. Sulfur disproportionation (S2O3 → H2S + SO42- by Desulfovibrio
5. Organic sulfur cpd oxidation or reduction CH3SH → CO2 + H2S By many organism
6. Desulfurylation(Organic – S → H2S Many organism can do this

2.8.6.4. The Phosphorus Cycle

 Phosphorus occur in soil as both organic and inorganic forms.
 The relative amounts of each form of Phosphorus vary greatly among soils
e.g. P in a clayey textured soil being up to ten times greater in a sandy soil.
 Organic P in soils is high and held very tightly which is not available for plant uptake until,
decomposed by mineralization process carried out by microbes.
 The rate of P release is affected by factors such as:
 Soil moisture
 Composition of organic material’
 Oxygen concentration and PH
 Inorganic P in soils. the concentration of inorganic P or orthophosphates in the soil solution at any
given time is very small. It exist mostly as aluminum, Iron or Calcium compound.

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 2.9. Controlling Microorganisms
I. Sterilization is the process by which surface or medium is freed of all living organism either in the
vegetative or spore state. This material is said to be sterile!
 An object cannot be slightly sterile or almost sterile: it is either sterile or not sterile.
 Sterilization is by physical agents like Heat a few chemicals called sterilant
 Chemical agents that kill pathogenic microorganisms are termed as a germicide
 Germicide can be used on inanimate or nonliving material or on living tissues
 Germicide may not ordinarily kill resistant microbial cells (Spore)
 Any physical or chemical agents that kills ‘’Germs’’ is said to have germicidal properties
Sterilization can be by
a. Phyical method b. Chemical method
• Boiling: • Disinfectant
• Autoclaving: • Antiseptics
• Pasteurization:
• Ultra-High temperature:
• Dry heat sterilization
• Incineration:
a. Disinfectants are agents that destroys vegetative pathogens and their products like toxin that
causes infection but not bacterial endospores
 Disinfectants are only applied only on inanimate objects, because they can be toxic to human or
other tissues when used in higher concentration.
 Disinfection removes harmful microorganism and their toxin from material
Example of Disinfectants are:

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 a. Applying a solution of 5% bleach to examining table
b. Boiling food utensils used by a sick person
c. Immersing thermometers in an isopropyl alcohol solution between uses
b. Antiseptics: are Chemical agents applied directly to the exposed body surface e.g. Skin, Wound,
and surgical incision
Examples of Antiseptics includes
a. Preparing the skin before surgical incisions with iodine compound
b. Swabbing an open root canal with hydrogen peroxide
c. Ordinary hand washing with a germicidal soap.
II. Sanitization: is any cleansing technique that mechanically removes microbes to reduces the level of
contaminants (along with food debris).
 Performed by Soap or detergents. This may not completely free of microbes. but considered
safe for normal use
 Air sanitization with ultraviolet Lamps reduces airborne microbes in hospital rooms,laboratory
installation..
III. Preservation: a general term for measures taken to prevent microbe caused spoilage of susceptible
products like pharmaceuticals and foods
IV. Decontamination: removal or count reduction of microorganisms contaminating an object.
 The objective of antiseptic measures and technique is to prevent microbial contamination of
material or wounds
 In antiseptic measures, chemical agents are used to fight pathogens in or on living tissues
2.9.1. Physical method of Sterilization and Disinfectants
 Heat is a simple, cheap and effective
 Application of heat var according to specific pathogens like as follows:
I. Pasteurization: antimicrobial treatment used for food in liquid forms like milk.
 Low temperature pasteurization at 65 Oc for 30 Minutes or at 71 OC for 15 seconds
 High temperature pasteurization: brief seconds of exposure to 80-85 OC in continuous operation
 Uperization: heating to 150 OC for 2.5 seconds in a pressurized container using steam injection
Disinfection
 Application of temp. below what would be required for sterilization.
 Boiling medical instruments, needles, syringes does not constitute sterilization! Because many spores are
not killed
II. Dry heat sterilization includes sterilization by:
a. Flamming: sterilization of inoculating loop, forceps on Bunsen burner flame
b. Incineration: an excellent method for safely destroying infective materials by burning them to ashes.
Used in hospital, research labs used for complete destruction of infective material like syringes,
needles, culture and pathology samples. Fast and effective for most hospital waste, except metal and
heat resistant glass.
c. Hot air oven: Sterilization by hot-air oven requires exposure to 160-180 oC for 2hrs and 30 minutes
which ensure destruction of spore through heating of objects
 Dry heat sterilization is used to sterilize scientific equipment which are less sensitive to high temp.e.g.
Glass ware, Gause, dressing etc…by using temp of 171 oC for an hour or 160 oC for two hours.
III. Moist heat sterilization
Autoclaves charged with saturated, pressurized steam are used for this purpose:

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  121 0C, 15 minutes, one of atmosphere of pressure (a total = 202kPa)
 134 0C, 3 minutes, two atmospheres of pressure (total = 303 kPa)
IV. Intermittent Sterilization
 Heat-labile substance like serum, sugar, egg cannot withstand the high temp of the autoclave can be
sterilized by a process of intermittent sterilization or tyndallization
 Tyndallization is carried out over a period of 3 days and requires a chamber to hold the materials
and a reservoir for boiling water 1000C for 20 minutes for each of three consecutive days.

2.10. Bacterial Isolation techniques

 Microbes can be isolated from food, soil, air, water.
 It can be separated on artificial media by serial dilution method.
 Each of the isolates are purified on new media and experimented for morphological characteristic
like shape, Gm nature motility and arrangement of cells
 Enzymatic activities were tested to characterize
 Finally, molecular techniques are used for further identification: like figure below(Fig2.41)

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