Micro Biology

Unit 2 microorganism
Overview
- Microorganisms are organisms too small to be seen by unaided
eyes.
- Microorganisms must be viewed with a microscope.
- They include fungi, bacteria, algae, protozoa and viruses.
- Some microorganisms , like the eukaryotic microorganisms are
visible without magnification.
- Microbiology is the study of microorganisms.
- Based on evolutionary lines, organisms are grouped into three
domains: these are bacteria, archaea and eukarya
2.1. Eubacteria
Eubacteria means “true bacteria,”. Bacteria are simple in structure.
They are prokaryotic unicellular organisms with no nuclear
membrane, mitochondria, Golgi bodies, or endoplasmic reticulum
that reproduce asexually.
General characteristics
They are omnipresent i.e. present in soil, air and water.
They are unicellular, prokaryotic microorganism.
The cell bears a thick rigid cell wall (Peptidoglycan) outside the
plasma membrane.
- 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.
- They lack true chlorophyll but few photosynthetic bacteria have
bacteriochlorophyll.
- Lack true nucleus (lacking nuclear membrane and nucleolus).
- They lack mitochondria, Golgi apparatus, plastid and endoplasmic
reticulum.
- Both DNA and RNA are present in the bacterial cell.
- Although the prokaryotic cell does not have a membrane enclosed
nucleus, it does have a nuclear area( nucleoid) which contains DNA.
From Solomon
- Some bacteria have hairlike appendages known as pili. These

protein structures help bacteria adhere to one another or attach to
certain surfaces, such as the cells they infect.
- Some elongated pili, called sex pili, are important in transmitting
DNA between bacteria.
Solomon
-In addition to their bacterial chromosome, bacteria also have
plasmids, small, circular DNA molecules that are replicated
separately.
-A plasmid has only a small number of genes; these genes may be
useful when the bacterium is in a particular environment but may not
be required for survival or reproduction. Campbell
- An important character that distinguishes the archaea from
the bacteria is the absence of the compound peptidoglycan in
the cell walls of the archaea .
- Gene sequencing indicates that the archaea have a combination of
bacteria-like and eukaryote like genes.
Eldra Solomon page 486
Audesirk page 354

Prokaryotic Movement
-Many prokaryotes have long flagella to move toward food sources
or away from danger.
-Prokaryotes can have a single whiplike flagellum or many flagella.
Some bacteria do not have flagella.
Modern biology.
Capsules and Pili
- Many bacteria have an outer covering of polysaccharides called a
capsule.
- These sugars bind to the cell wall and protect the cell
against drying or harsh chemicals. The capsule also helps protect
a pathogenic bacterium from the host’s WBC.
- A capsule made up of a sticky sugars is called a glycocalyx. This
structure allows bacteria to connect to the surface of host cells and
tissues.
- Pili are short, hairlike protein on the surface of some bacteria. Pili
help bacteria connect to each other and to surfaces of a host cell.
-Some species of bacteria produce a capsule or slime layer that
surrounds the cell wall.
The capsule may provide the bacteria with added protection against
phagocytosis.
The ability of Streptococcus pneumoniae to cause bacterial
pneumonia depends on its capsule.
- A strain of S. pneumoniae that lacks a capsule does not cause the
disease.
- Bacteria also use their capsules to attach to surfaces such as rocks,
plant roots, or human teeth (where they cause dental plaque).
Eldra solomon
Structure of Bacterial Cell
bacterial cells are studied under electron microscope in which it
reveals various structures. Some of these are external to the cell wall
while other are internal to the cell wall.
The walls of many bacteria are coated with an external layer of
polysaccharides called the glycocalyx.
The glycocalyx protects cells from physical damage and desiccation, and
to the effects of some antibiotics, and may enable a cell to attach to a
surface.
The capsule prevents bacterial viruses, enzymes, antibiotics, and
antibodies from reaching the cell surface.
- Various organelles are suspended within the fluid component of the
cytoplasm, which is called the cytosol.
- The term cytoplasm includes both the cytosol and all the organelles
other than the nucleus.(Eldra S)
Cytoplasm :- the part of the cell outside the nucleus

Nucleoplasm:- the part of the cell within the nucleus
- Certain bacteria develop resistant cells called endospores when they
lack an essential nutrient.
- The original cell produces a copy of its chromosome and surrounds that
copy with a tough multilayered structure, forming the endospore.
- Water is removed from the endospore, and its metabolism halts. The
original cell then lyses,releasing the endospore.
Most endospores are so durable that they can survive in boiling water.
- In less hostile environments, endospores can remain dormant but
አስቸጋሪ
viable for centuries, able to rehydrate and resume metabolism when

መኖር
their environment improves. Campbell

lyses,(destruction)
- Eukaryotes are diverse group, including species with a wide range of
life cycles, morphological specializations, and nutritional needs.
- Although more diseases are caused by viruses and bacteria than by
microscopic eukaryotes, these eukaryotes are responsible for some
diseases.
- Eukaryotic cells that have a variety of membranous organelles in the
cytoplasmic matrix and the majority of their genetic material within
membrane-delimited nuclei.
- A cytoskeleton composed of microtubules, microfilaments, and
intermediate filaments helps give eukaryotic cells shape.
- The cytoskeleton is also involved in cell movements, intracellular
transport, and reproduction.
- When eucaryotes reproduce, genetic material is distributed between
cells by mitosis and meiosis.
2.1.1. Bacterial Shapes
Morphologically bacteria are classified based on numerous features.
For example, cell shape , nature of multi cell aggregates, motility,
formation of spores, and reaction to the gram stain.
Bacterial cells can be grouped into the following three main shapes:
1. Spherical –cocci
2. Rod –bacilli
3. Spiral or corkscrew , Comma – vibrio cholera
Bacteria can be classified based on their cell wall composition. One of
these ways is whether they are retaining dyes during Gram’s stain.
1. Gram positive:- bacteria have purple appearance when observed
under a light microscope. This is due to retention of the purple crystal
violet stain in the thick peptidoglycan layer of the cell wall.
Examples:- all staphylococci, all streptococci and some listeria.
2. Gram negative:- Gram negative bacteria lose the crystal violet stain
and take the color of the red counterstain. This is the characteristic of
bacteria that have a cell wall composed of thin layer peptidoglycan.
For example:- Neisseria gonorrhoeae, spirochetes.
Comparison of Gram-Positive and Gram-
Negative Cell Walls
Characteristics Gram-positive Gram-negative
No of major layers 1 2
Chemical composition Peptidoglycan Lipopolysaccharide
Teichoic acid Lipoprotein
Lipoteichoic acid Peptidoglycan
Overall thickness Thicker (20-80 nm) Thinner (8-11 nm)
Outer membrane No yes
Periplasmic space Narrow Extensive
Porin protein No Yes
Permeability to molecules More penetrable Less penetrable
The Gram staining process
1. Heat fix/ attach the bacteria to the side,
2. Covered with crystal violet for 1 minute and then rinsed with water
to remove the excess dye.
3. Flooded with Gram’s iodine solution for 1 min, to precipitate the
dye. The smear then is rinsed with water to remove the excess iodine.
4. Rinsed with a decolorizer, such as 95% alcohol or an alcohol–
acetone mixture for about 5 seconds. The alcohol will not wash
away the dye–iodine complex from some bacterial cells because
the iodine attaches the crystal violet dye to those cells. The cells
remain blue-purple in color. The alcohol will wash away the dye–
iodine complex from other bacterial cells.
The Gram staining process
These cells are now colorless, and they would be difficult to contrast
in the microscope. Therefore, after rinse off the decolorizer, these
cells need to be counterstained.
5. Flooded with safranin (a red, basic dye) for 30 to 60 sec, which
gives the colorless cells red color.
Excess safranin is rinsed away, the slide is gently blotted dry, and the
specimen is observed with bright-field microscopy using the oil-
immersion (100×) lens.
2.1.2. Nutritional types of bacteria
Bacteria have evolved many mechanisms to acquire energy and
nutrients they need for growth and reproduction. Many are
autotrophs, organisms that obtain their carbon from CO2.
Autotrophs that obtain their energy from sunlight are called
photoautotrophs, while those that harvest energy from inorganic
chemicals are called chemoautotrophs.
2.1.2. Nutritional types of
bacteria
1. Photoautotrophs: are photosynthetic organisms that use light as
their energy source and CO2 as their carbon source.
for example, the cyanobacteria, the green sulfur bacteria, and the
purple sulfur bacteria, plants and protists.
The cyanobacteria use water as their source of electrons for reducing
CO2, while the two types of sulfur bacteria use sulfur.
bacteria
2. Chemoautotrophs: obtain energy by oxidizing inorganic
substances such as hydrogen, iron, sulfur, ammonia, nitrites, and
nitrates.
-Use CO2 as their carbon source. They use the electrons they remove
in the oxidations to make organic molecules by reducing CO2 or to
provide the energy for ATP synthesis (using an electron transfer
system embedded in the plasma membrane).
-Chemoautotrophy occurs widely among prokaryotes, but is not
found among eukaryotes.
bacteria
3. Photoheterotrophs: use light as their energy source but obtain
carbon in organic form rather than as CO2.
- Photoheterotrophs are limited to two groups of bacteria, the green
and purple non sulfur bacteria.
“Non sulfur” indicates they are unable to oxidize sulfur or other
inorganic substances as an ultimate source of electrons for
reductions; instead, they use a variety of substrates, including H2,
alcohols, or organic acids.
bacteria
4. Chemoheterotrophs: oxidize organic molecules as their energy
source and obtain carbon in organic form. They include most of the
bacteria that cause disease and many bacteria that are responsible
for decomposing matter. Russel
Phototrophs use light as their energy source,
Chemotrophs obtain energy from the oxidation of chemical
compounds (either organic or inorganic).
Lithotrophs ( "rock-eaters") use reduced inorganic substances as their
electron source.
Organotrophs extract electrons from reduced organic compounds.
bacteria
Photolithoautotrophs ( photoautotrophs) use light energy and CO2 as
their carbon source. Photosynthetic bacteria and cyanobacteria
employ water as the electron donor and release oxygen.
Other photolithoautotrophs, such as the purple and green sulfur
bacteria, cannot oxidize water but extract electrons from inorganic
donors such as hydrogen, H2S, and sulfur.
Chemoorganoheterotrophs (chemoheterotrophs or
chemoorganotrophs) use organic compounds as sources of energy,
hydrogen, electrons, and carbon.
bacteria
-Nearly all pathogenic microorganisms are chemoorganoheterotrophs.
-Some photosynthetic bacteria (purple and green bacteria) use organic
matter as their electron donor and carbon sources.
-These Photoorganoheterotrophs are common inhabitants of polluted
lakes and streams.
-Photolithoautotrophs:- use H2 as an electron donor.
Chemolithoautotrophs oxidize reduced inorganic compounds such as Fe,
N2, or S to derive both energy and electrons.
CO2 is the carbon source.
bacteria
Chemolithoheterotrophs:-
- Use reduced inorganic molecules as their energy and Electron
source
- Derive their carbon from organic sources.
Chemolithotrophs contribute greatly to the chemical transformations
of elements (e.g., the conversion of NH3 to NO3 or sulfur to sulfate).
2.1.3 Reproduction of bacteria
2.1.3.1 Asexual reproduction
- Most bacteria reproduce by an asexual process called binary fission.
- At this time, the chromosome (DNA) replicates and the two DNA
molecules separate.
Chromosome segregation is not well understood.
Unlike eukaryotic cells, bacterial cells lack a mitotic spindle to separate
replicated chromosomes.
segregation involves specialized chromosomal-associated proteins.
Cell fission at midcell involves the synthesis of a partition, or septum,
that separates the mother cell into two genetically identical daughter
cells.
2.1.3.2. reproduction in bacteria
-In conjugation, two cells of different mating types come together, and
genetic material is transferred from one to the other.
-In contrast to transformation and transduction, conjugation involves
contact between two cells.
Conjugation has been studied in E. coli. In the E. coli, there are donor
cells, or F+ cells, which have DNA that can be transmitted to recipient
cells, or F– cells. F+ cells have a DNA sequence known as the F factor that
is necessary for a bacterium to serve as a donor.
The F factor can be in the form of a plasmid, or it can be part of the DNA
in the chromosome.
-F genes encode enzymes essential for transferring DNA. Certain F
genes encode sex pili, long, hair-like extensions that project from the
cell surface. The sex pilus of an F+ cell recognizes and binds to the
surface of an F– cell, forming a cytoplasmic conjugation bridge
between the two cells.
- The F plasmid replicates itself, and DNA is transferred from donor to
recipient bacterium through the conjugation bridge.
- F plasmids may also have other types of genes, including those that
determine resistance to antibiotics.
During conjugation, horizontal gene transfer takes place resulting in
genetic recombination.
acid-fast :-Not decolorized by acid after staining, as bacteria that retain dye after an acid rinse. --ac“id-fast”ness n.-fast
Diphtheria is caused by a gram-positive bacillus (Corynebacterium
diphtheriae) that produces a toxin. The diphtheria toxin kills cells and
causes inflammation.
Transmitted by intimate respiratory and physical contact. Endemic in
developing countries. Not common in U.S. since vaccine became
available in 1920s.
Infects the heart muscle and respiratory passageways.
Pneumonia caused by Streptococcus pneumoniae
Transmitted from person to person. Strains of S. pneumoniae are resistant
to some antibiotics. Incidence has decreased since introduction of a
vaccine.
Anthrax is caused by the Gram positive rod Bacillus anthracis, anthracis is
often linked to its use as a biological weapon.
Anthrax Most commonly occurs in domestic animals. It Can be transmitted
to humans from infected animals or animal products. Endospores can live
in soil for many years. Infection can occur in three ways: cutaneous, by
inhalation, and gastrointestinal.
Shigellosis is caused by members of the genus Shigella, which
are gram-negative, nonmotile rods.
Humans are the primary host of Shigella, which is transmitted by the
fecal–oral route.
The pathogen also is transmitted by flies and contaminated water.
Foods, such as eggs, vegetables, shellfish, and dairy products can become
contaminated through unsanitary handling.
2.2. Archaea
Archaea:
- Similar to bacteria.
- live as producers or decomposers.
- They are prokaryotic.
- They are single celled organisms.
- They lack membrane bound nucleus and membrane bounded
organelles.
- Archaea lack true peptidoglycan in their cell walls.
- Their cell membrane lipids have branched hydrocarbon chains.
- Many are found in extreme environments.
2.2. Archaea
Phylogenetic tree of archaea. The tree, based on sequences of 16S rRNA genes, reveals
evolutionary split of Archaea into two phyla, the Crenarchaeota and the Euryarchaeota.
2.2. Archaea
Generally three major groups of archaea are recognized:
1. Methanogens (they generate methane),
2. Extreme halophiles, and
3. Extreme thermophiles
These groupings are based on physiology of the organisms and so
cannot be considered phylogenetic, or evolutionary, classifications.
1. The methanogens are strictly anaerobic organisms, having been
isolated from such divergent anaerobic environments as waterlogged
soils, lake sediments, marshes, marine sediments, and the
gastrointestinal tracts of animals.
2.2. Archaea
2. Extreme halophiles grow in highly saline environments such as the
Great Salt Lake, the Dead Sea, salt evaporation ponds, and the
surfaces of salt-preserved foods. extreme halophiles are obligate
aerobes.
3. Extreme Thermophiles: (hyperthermophiles) are found near
volcanic vents and fissures that release sulfurous gases and other hot
vapors. With optimum temperatures usually in excess of 80C, they
may be either obligate aerobes, facultative aerobes, or obligate
anaerobes.
4. Thermophilic Extreme Acidophiles: Members of two genera,
Thermoplasma and Picrophilus, are notable for growing in extremely
acidic, hot environments.
2.2. Archaea
Acidophiles:- live at low PH ( as low as PH 1 and who die at PH 7)
Hyperthermophiles :- live at high temperature (at 121C)
Psychrophiles:- Organisms living in extreme cold environments are
known as psychrophiles.
- Some of them are able to live from 4 °C up to -20 °C.
- In the Antarctic grows best at 4 °C
Scientists identified archaea as a distinct type of prokaryotes on the
basis of unique rRNA sequences.
Archaea multiply by binary fission, budding, fragmentation or other
mechanisms.
In budding , the cell becomes swollen at one edge, and a new cell, develops from the parent
cell ,A few species of bacteria (actinomycetes) divide by fragmentation. Walls develop within
the cell, which then separates into several new cells.
2.2. Archaea
2.2. Archaea
2.2. Archaea
Intron: a segment of DNA in a eukaryotic gene that does not code for
amino acids in a protein.
Formylmethionine
Methionine is a sulfur-containing amino acid with the side chain
─CH2CH2SCH3. Among the 20 protein amino acids, only methionine
and cysteine have sulfur.
2.2.1. Beneficial aspects of Archaea
Because of their tolerance to high temperatures and extreme
environments, some members of the domain have already been
exploited for commercial uses.
1) The source of enzymes that are usually added to detergents in
order to maintain its activity even at higher temperature and pH.
2) Proteases and lipases derived from alkaliphilic bacteria are being
used as detergent additives to increase their stain removal ability
3) Some Archaea also bear the potential for bioremediation.
2.2.1. Beneficial aspects of
Archaea
4) The thermophilic Archaea, Thermus aquaticus, is an essential part
of the development of molecular biology. 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).
PCR can create millions of copies of a single gene, or any specific
piece of DNA, in a test tube. This means that a single gene among all
the human genes can be amplified (copied) using PCR.
2.2.2. Physical factors that affecting microbial growths
The environments in which some microorganisms grow would kill
most other microorganisms, the major physical factors which affect
microbial growth are solutes and water activity, pH, temperature,
oxygen level, pressure and radiation.
2.3 Fungi
Fungi are :-
-Eucaryotic
-Spore-bearing,
-Have absorptive nutrition
-Lack chlorophyll
-Reproduce sexually and asexually.
-Scientists who study fungi are mycologists.
-The scientific discipline devoted to fungi is called mycology.
-The study of fungal toxins and their effects is called mycotoxicology.
-The diseases caused by fungi in animals are known as mycoses (s.,
mycosis).
2.3.1. General Characteristics of True Fungi
1. All are eukaryotic

Possess membrane-bound nuclei and membrane bound organelles.
2. Most are filamentous .
Composed of individual microscopic filaments called hyphae, which
exhibit apical growth and which branch to form a network of hyphae
called a mycelium.
some have septate hyphae, and the other have non-septate
(coenocytic hyphae)
3. Some are unicellular e.g. yeasts.
Fungi exist mainly in the form of slender filaments, visible to the

naked eye, which are called hyphae.
-Their hyphae are divided into cells by septa (si, septum).
These hyphae are made up of long chains of cells joined end-to-end.
-Septa have pores large enough to allow ribosomes, mitochondria,
and even nuclei to flow from cell to cell.
-Some fungi lack septa Known as coenocytic fungi which consist of a
continuous cytoplasmic mass having many nuclei.
2.3.1. General Characteristics of True
Fungi
4. a hypha or cell is surrounded by a rigid wall Composed primarily of
chitin and glucans, although the walls of some species contain
cellulose.
5. Many reproduce both sexually and asexually Both sexual and
asexual reproduction often result in the production of spores.
6. Their nuclei are typically haploid and hyphal compartments are
often multinucleate Although the Oomycota and some yeasts possess
diploid nuclei.
7. All are achlorophyllous
• They lack chlorophyll pigments and are incapable of photosynthesis.
2.3.1. General Characteristics of True
Fungi
8. All are chemoheterotrophic (chemoorganotrophic).
9. Possess characteristic range of storage compounds
e.g Trehalose ,glycogen ,sugar, Alcohols and lipids
10. Nutritionally categorized into three (saprophytic, parasitic, and
symbiotic).
Most fungi are saprophytic—that is, they live on organic compounds
that they absorb from dead organisms.
A symbiosis is a close, long-term relationship between two
organisms. Three examples of symbiotic relationships include:
Parasitism is a relationship in which one individual is harmed while
the other individual benefits.
Mutualism is a relationship in which both organisms derive some
benefit.
In commensalism, one organism benefits, but the other organism is
neither helped nor harmed.
2.3.2. Ecology of Fungi
Fungi have colonized nearly all environments, but are frequently
found in cool, dark, moist places with a supply of decaying material.
Many fungi establish complex mycorrhizal associations with the roots
of plants.
- Mycorrhizae Are Associations Between plant Roots and Fungi.
The association between plants and mycorrhizal fungi benefits both
the fungi and their plant.
- The mycorrhizal fungi receive sugar that are produced by plants.
- Mycorrhizal fungi absorb mineral nutrients and water from the soil,
passing some of them into the plant.
- Lichens are a symbiotic relationship between a fungus and a
photosynthetic organism, usually an alga or cyanobacterium.
- The photosynthetic organism provides energy and carbohydrates,
while the fungus supplies minerals and protection.
Lichen
- A variety of asexual spores are formed by different fungi. For
example, sporangiophores are specialized hyphae.
- On top of a sporangiophore is a sac called a sporangium.
- Inside each sporangium, sporangiospores are made.
- Rhizopus grows on bread, is a sporangiospore forming fungus.
- Rhizopus is the example of Zygomycota.
- Dikaryotic:- Hyphae that contain two nuclei per cell.
- These two nucleus are genetically distinct, sexually compatible.
- Monokaryotic:- Hyphae that contain only one nucleus per cell
2.3.3 classification of fungi
2.3.3 classification of fungi
Historically, fungi have been classified on the characteristics of their
sexual spores and fruiting bodies. More recently, comparative DNA
and RNA sequences, used for classification.
Currently, mycologists assign fungi to five main groups:
Chytridiomycota, Zygomycota, Glomeromycota, Ascomycota, and
Basidiomycota
1. Zygomycota:- There are 1,000 known species of zygomycetes.
Eg;- molds
molds responsible for causing foods to rot.
2. Ascomycota:-
- have septate hyphae
- form ascospores within saclike asci.
- Eg; Saccharomyces cervieiae
Asci :- saclike structure in which ascospores are formed.
3. Chytridiomycota :- They produce flagellated asexual spores,
called zoospores. eg; Allomyces and water mold
4. Basidiomycota includes mushrooms , rusts, smuts
Mushrooms have sexual reproductive structures called basidiocarps.
Basidiocarps produce basidia, on which basidiospores form.
5. Glomeromycota ; mycorrhizae with plant roots
2.3.4 Reproduction in fungi
Sporulation is the process of spore formation. spores are blown on air
or carried away by insects.
The reproductive structures producing spores are usually aerial. They
can be asexual and invisible to the naked eye or sexual structures,
called fruiting bodies, such as the macroscopic mushrooms.
A . Asexual Reproduction
- Asexual reproductive structures develop at the ends of specialized
hyphae. Here, mitotic divisions produce thousands of genetically
identical spores.
- Many asexual spores develop within sacs called sporangia. the
spores are called sporangiospores.
- Other fungi produce spores on conidiophores. These unprotected,
dust like spores are known as conidia.
- Asexual spores formed by fragmentation of the hyphae, yielding
arthrospores.
- The fungi that cause athlete’s foot multiply in this manner.
Asexual Reproduction
(A) Sporangia of the common bread mold Rhizopus
The conidiophores and conidia in Penicillium roqueforti
Some fungi produce arthrospores by simple fragmentation of the hyphae
Yeast ;Saccharomyces cerevisiae.
Many yeasts reproduce asexually by budding. In this process, the cell
becomes swollen at one edge, and a new cell, called a blastospore ,
develops (buds) from the parent cell.
B. Sexual Reproduction
- Many fungi produce spores through sexual reproduction. In this process,
hyphae of opposite mating types come together and fuse .
- Because the nuclei are genetically different in each mating type, the
fusion cell represents a heterokaryon.
- Heterokaryon:- a cell having two or more genetically different nuclei.
the nuclei fuse, and a diploid cell is formed.
- The chromosome number soon is halved by meiosis, returning the cell or
organism to a haploid condition.
Sexual reproduction occurs in the fruiting body, in which spores are
formed.
- The spores are ejected from the fruiting body and are carried away by air.
Sexual Reproduction
- A visible fruiting body often results during sexual reproduction and it is
the location of the haploid spores.
- Perhaps the most recognized fruiting body from which spores are
produced is the mushroom.
Sexual Reproduction
Sexual Reproduction
Basidium (plu, basidia):- A reproductive appendage that produces sexual
spores on the gills of mushrooms.
2.3.5. Economic importance of fungi
Beneficial aspects of fungi
1. Fungi exist either as saprobes or parasites. Their preeminent ability to
break down complex organic substrates is an important and essential
activity in the recycling of carbon and other elements.
2. Edible wild or domesticated varieties of mushrooms (Basidiomycotes)
are important as food sources.
3. Fungi (yeasts) are essential to industrial processes involving
fermentation. Examples:- making of bread, wine, and beer.
4. To prepare some cheeses, soy sauce, Enjera, Tela, Tej, bulla.
- Commercial production of organic acids (citric, gallic) and certain drugs
(ergometrine, cortisone).
5. Molds (Aspergillus species) are used in the production of citric, oxalic,
gluconic and itaconic acid.
Products of fermentation yield industrial alcohol, fats and proteins.
Fusarium can produce 12-15 grams of fat from a litre of 50% glucose
within 48 hours.
6. To manufacture of many antibiotics (penicillin, griseofulvin) and the
immunosuppressive drug cyclosporin.
adriamycin
Amphotericin B:- A drug derived from actinomycete and used in treating
fungal infections.
Bleomycin:-antibiotic used to treat cancers
7. Fungi are useful tools for studying cancer and aging.
Harmful aspects of Fungi
1. Fungi are the major cause of plant diseases. Plants are particularly
vulnerable to fungal diseases because fungi can invade leaves through
their stomates. Over 5,000 species of fungi attack plants.
Fungi also cause many diseases of animals.
2. Molds can cause deterioration of fabrics, leather, electrical
insulation etc.. Extensive losses may follow failure to protect material
from ravages of fungi .
3.Spoil agricultural product.
Destroy vegetables, fruits and cereals.
4. Mycotoxicoses (ingestion of fungal toxin ) and mycetismus
(mushroom poisoning through ingestion of fungal elements).
A. Aflatoxis: Two closely related fungi, Aspergillus flavus and A.
parasiticus, produce mycotoxins called aflatoxin.
The molds are found in warm, humid climates, where they
contaminate peanuts, grains, cereals, sweet potatoes, corn, rice,
animal feed, meat and dairy products
Aflatoxins are ingested by humans where they are thought to be
carcinogenic, especially in the liver.
B. Ergotism is caused by Claviceps purpurea.
producing a powerful toxin.
C. purpurea grows as hyphae on kernels of rye, wheat, and barley.
As hyphae penetrate the plant, the fungal cells consume the
substance of the grain, and the dense tissue hardens into a purple
body called sclerotium.
a group of peptide derivatives called alkaloids are produced by
sclerotium and deposited in the grain as a substance called ergot.
products such as bread made from rye grain may cause ergot rye
disease, or ergotism.
C. Mushroom poisoning, or mycetism, can occur from mushrooms
that produce mycotoxins that affect the human body.
5. Superficial Fungal infections
Superficial mycoses are fungal infections of the outermost areas of the
human body: hair, fingernails, toenails, and epidermis.
Various forms of dermatophytoses are referred to as tineas or
ringworm.
Clinically, the tineas are classified according to the anatomic site or
structure affected:
1. Tinea corporis (ringworm of the trunk, shown here on the shoulder):
Microsporum Canis and Trichophyton mentagrophytes. Affects hairless
skin. It is ringworm
of the smooth or non hairy skin of the body.
Dermatophytoses
Dermatophytoses are also known as tinea (ringworm) infections and
dermatomycoses.
Dermatomycoses are caused by various filamentous fungi (moulds),
collectively referred to as dermatophytes. Examples include species of
Microsporum,Epidermophyton, and Trichophyton.
2. Tinea pedis (athlete's foot): T. rubrum, T.mentagrophytes , and
Epidermophyton floccosum. Affects mainly the lower legs.
3. Tinea capitis: T. tonsurans and M Canis. the scalp, eyebrows, and
eyelashes
4. Tinea barbae (face and neck), T.rubrum and T.mentagrophytes.
beard ringworm It is involvement
of the bearded areas of the face and neck.
5. Tinea unguium (onychomycosis):- T. rubrum, T.mentagrophytes,
and E. floccosum. Affect the nails (fingernails and toenails)
Mode of transmission: Dermatomycoses are infections that are
transmitted directly by human contact, animal-human contact or
indirectly on inanimate objects
The localization of the primary foci corresponds to the contact site.
Thus feet, uncovered skin (hair, head, facial skin) are affected most
frequently.
Prevention:- Regular disinfection of showers and wardrobes can
contribute to prevention of athlete's foot.
2.4. Protozoa
Protozoa has referred to chemoorganotrophic protists.
Protozoology:- the study of protozoa.
Characteristics of protozoa :-
- Unicellular microorganisms that lacks cell wall.
- They are may be free living or parasitic.
- Aerobic.
- They have true nucleus.
- They are eukaryotic cells.
Mostly microscopic, although some are large enough to be seen with
the unaided eye .
2.4. Protozoa
Locomotion by pseudopodia, flagella, cilia, and direct cell
movements, some sessile.
Nutrition of all types:
autotrophic :-manufacturing their own nutrients by photosynthesis
heterotrophic:- depending on other plants or animals for food)
Saprozoic:- using nutrients dissolved in the surrounding medium
Aquatic or terrestrial habitat, free-living or symbiotic mode of life
Reproduction:- asexually by fission, budding, and cysts and
sexually by conjugation or by syngamy (union of male and female
gametes.
2.4. Protozoa
Reproduction in protozoa
Most protozoa are asexual and reproduce in one of three ways. These
are:
Fission: Fission occurs when a cell divides evenly to form two new
cells (Figure 2.20).
Budding: Budding occurs when a cell divides unevenly.
Multiple fission (schizogony):- Multiple fission is when the nucleus of
the cell divides multiple times before the rest of the cell divides.
Forms around each nucleus when the nucleus divides then each
nuclei separates into a daughter cell.
Most protozoa reproduce sexually. A distinctive feature of ciliates is
the presence of two types of nuclei: tiny micronuclei and large
macronuclei.
A cell has one or more nuclei of each type. Genetic variation results
from conjugation.
a sexual process in which two individuals exchange haploid
micronuclei but do not reproduce.
Ciliates reproduce asexually by binary fission, during which the
existing macronucleus disintegrates and a new one is formed from
the cell's micronuclei.
Each macronucleus contains multiple copies of the ciliate's genome.
Genes in the macronucleus control the functions of the cell, such as
feeding, waste removal, and maintaining water balance.
Nutrition in Protozoans
Protists receive nutrients by breaking down organic matter and can
grow in both aerobic and anaerobic environments, such as protists
that live in the intestine of animals.
Some protists, such as Euglena, receive nutrients from organic matter
and through photosynthesis because they contain chlorophyll. These
protists are considered both algae and protozoa.
Protists obtain food in one of three ways:
Absorption: Food is absorbed across the protist's plasma membrane.
Ingestion: Cilia outside the protist create a wave-like motion to move
food into a mouth like opening in the protist called a cytosome.
An example is the paramecium.
Nutrition in Protozoans
Engulf: Pseudopods (false feet) on the protist engulf food, then pull it
into the cell using a process called phagocytosis.
Example:- amoeba.
Food is digested in the vacuole after the food enters the cell. The
vacuole is a membrane-bound organelle.
Waste products are excreted using a process called exocytosis.
2.4.1.Common diseases caused by protozoa
Most protozoans are not harmful but there are a few disease-causing
protozoans.
Many types of protozoa are even beneficial in the environment
because they help make it more productive.
They improve the quality of water by eating bacteria and other
particles. Some of the human diseases caused by protozoans include
chagas disease,cryptosporidiosis.
1. Amebiasis
Causative agent :-Entamoeba histolytica
Organs affected:- Intestine, liver
Transmission:- Ingestion of fecally contaminated food or water; disease
associated with poverty, homosexual men, and migrant workers.
Clinical features:-Multiplication of the organisms and tissue destruction
in the intestine and in other body can result in amebic abscesses. The
irritating effect of the amoebas on the cells lining the intestine causes
intestinal cramps and diarrhea.
Due to intestinal ulceration, the diarrhea is often bloody, and the
condition is referred to as amebic dysentery
2. Giardiasis
Causative agent:-Giardia lamblia
Organs affected:- Intestine
Transmission:-Ingestion of fecally contaminated water,
Person to person, in day care centers
Clinical features:-Ingested cysts survive stomach passage,
trophozoites emerge from the cysts in the small intestine, where
some attach to epithelium and others move freely, mucosal function
is impaired by adherent protozoa and host immune response.
3. Trichomoniasis
Causative agent:-Trichomonas vaginalis
Organs affected:- Urogenital
Transmission:- sex with someone who is infected
Clinical features:- Vaginal discharge, odor and edema or erythema
In females, trichomoniasis is accompanied by intense itching and
discomfort during urination and sexual intercourse.
Usually, a yellow-green, frothy discharge with a strong odor also is
present.
4. African Trypanosomiasis (African Sleeping Sickness)
Causative agent:-Trypanosoma brucei
Organs affected:- blood , brain
Transmission:- Tsetse flies (Glossina)
Clinical features:-Initial haemolytic phase (fever, joint pains followed
by neurological disorder, somnolence)
a painful chancre at the site of a tsetse fly bite, fever, intense
headache, insomnia, lymphadenitis, anemia, local edema, and rash.
Later stages of the disease include body wasting, falling asleep, coma,
and death if untreated. The latter stages of the disease have given rise
to the name African sleeping sickness.
5. Visceral leishmaniasis (kala azar)
Causative agent:-Leishmania donovani
Organs affected:- WBC skin intestine
Transmission:- Sandfly bites
Clinical features:-Skin ulcers, mucocutaneous complications and
visceral diseases (hepatosplenomegaly)
6. Malaria
Causative agent:-caused by four species in the genus Plasmodium:
Plasmodium vivax , P. falciparum (the most deadly), Plasmodium
malariae, and Plasmodium ovale.
Organs affected:- Liver, RBC
Transmission:- Bite from an infected female Anopheles mosquito
Clinical features:-Fever, shivering, cough, respiratory distress, pain in
the joints, headache, watery diarrhea, vomiting, convulsions, severe
anemia
7. Toxoplasmosis
Causative agent:-Toxoplasma gondii
Organs affected:- blood, eye
Transmission:- domestic cat, food
Clinical features:-Blindness and mental retardation can result in
congenitally infected children.
Immunosuppressed patients can present more severe symptoms:
splenomegaly polymyositis, dermatomyositis chorioretinitis, and
myocarditis, pneumonitis, hepatitis, encephalitis and multisystem
organ failure.
2.5. Viruses
Viruses are obligate intracellular particles, that is, most can be seen
only with the electron microscope.
Viruses must infect and take over a host cell in order to replicate.
This is because they lack the chemical machinery for generating
energy and synthesizing large molecules.
2.5. Viruses
2.5. Viruses
- Viruses have an inner core of nucleic acid surrounded by protein
coat known as an envelope.
- They cannot be grown on artificial cell free media (However, grow in
animals, eggs or tissue culture).
- Viruses do not have cell wall or cell membrane.
- They do not have organelles.
- They do not occur free in nature but act as obligate intracellular
parasite.
- They lack the enzymes necessary for protein and nucleic acid
synthesis.
2.5. Viruses
- viruses are unaffected by antibiotics.
- Viruses are inert (nucleoprotein) filterable Agents
- Virus occupy a space in between living and non-living, because they
are crystallizable and non-living outside the body of host.
- Obligate intracellular parasites of bacteria, protozoa, fungi, algae,
plants, and animals.
- Ultramicroscopic size, ranging from 20 nm up to 450 nm.
- Do not independently fulfill the characteristics of life.
- Inactive outside the host cell and active only inside host cells.
- Basic structure consists of protein shell (capsid) surrounding nucleic
acid core.
2.5. Viruses
- Nucleic acid can be double-stranded DNA, single-stranded DNA,
single-stranded RNA, or double-stranded RNA.
- Molecules on virus surface impart high specificity for attachment to
host cell.
- Multiply by taking control of host cell's genetic material and
regulating the synthesis and assembly of new viruses
- Lack machinery for synthesizing proteins
Structure of viruses
- Central core of nucleic acid of a virus is called genome and the
protein coat surrounding is called as capsid.
- In some virus, an envelope made up of glycoprotein and
phospholipid bilayer is present outside the capsid.
The basic structural components of a virus are:
- Core:- the genomic material, either DNA or RNA.
- 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 viruses, have
an additional lipoprotein layer around the capsid derived from the cell
surface membrane of the host cell.
The coat is made up of regularly packed protein units called capsomeres each
containing many protein molecules. The protein coat is called a capsid.
from igcse biology
Capsids are built from protein subunits called capsomeres, but the number of
different kinds of proteins in a capsid is usually small.
Some virus contains enzymes to infect.
Some bacteriophage contains an enzyme lysozyme, which makes small hole in
bacteria that allows viral nucleic acid to get in.
Some virus contains their own nucleic acid polymerase which transcribe the viral
genome into mRNA during replication.
E.g., Retrovirus are RNA virus that replicates inside host cell as DNA intermediate.
Retrovirus possess an RNA dependent DNA polymerase called reverse transcriptase.
Retroviruses have a DNA polymerase called reverse transcriptase, which transcribes
the RNA genome into a DNA intermediate.
This DNA becomes integrated into the host DNA by an enzyme also carried by the
virus.
Copies of the viral RNA are synthesized as the incorporated DNA is transcribed by host
RNA polymerases.
The thesis of mRNA from a DNA template is called transcription.
The synthesis of protein from information in mRNA is called translation.
By analogy, transcription transfers information from one nucleic acid to another you
might transcribe handwritten sentences to typewritten sentences in the same
language.
Translation transfers information from the language of nucleic acids to
language of amino acids as you might translate English sentences into another
language.
Then, the discovery of enzymes for reverse transcription revealed a process whereby
RNA can make DNA. This DNA can then make more RNA. Such viruses are known as
retroviruses because of this reverse process.
The process of copying the information found in RNA into DNA is called reverse
transcription, and thus these viruses require an enzyme called reverse transcriptase.
Enzymes that catalyze the addition of deoxynucleotides are called DNA polymerases.
Transcription:- The synthesis of RNA from a DNA template

Transcription is the process by which the genetic instructions in a specific gene are
transcribed or “rewritten” into an RNA molecule.
Transcription takes place in the nucleus of eukaryotic cells and in the DNA-containing
region in the cytoplasm of prokaryotic cells.
∙ Obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals
∙ Ultramicroscopic size, ranging from 20 nm up to 450 nm (diameter)
∙ Not cellular in nature; structure is very compact and economical
∙ Do not independently fulfill the characteristics of life
∙ Inactive macromolecules outside the host cell and active only inside host cells
∙ Basic structure consists of protein shell (capsid) surrounding nucleic acid core
∙ Nucleic acid of the viral genome is either DNA or RNA but not both
∙ Nucleic acid can be double-stranded DNA, single-stranded DNA, single-stranded RNA, or
double-stranded RNA
∙ Molecules on virus surface impart high specificity for attachment to host cell
∙ Multiply by taking control of host cell’s genetic material and regulating the synthesis and
assembly of new viruses
∙ Lack enzymes for most metabolic processes
∙ Lack machinery for synthesizing proteins
From Kathleen P. Talaro, Barry Chess - Foundations in Microbiology 10th-McGraw Hill Education (2018)
The process of copying the information found in RNA into DNA is called reverse
transcription, and thus retroviruses employ the enzyme reverse transcriptase to
carry out this process.
Retroviruses synthesize DNA using their RNA genome as a template. They
accomplish this by means of a reverse transcriptase that comes packaged with
each virus.
HIV comes equipped with reverse transcriptase for synthesizing DNA from RNA.
Retroviruses contain an RNA genome that is replicated via a DNA intermediate.
Retroviruses transfer information from RNA to DNA.
Two infectious agents that are simpler than viruses are viroids and prions. Both
of these agents lack capsids.
Viroids are plant pathogens that consist solely of single-stranded, circular RNA
without capsids.
No viroids are known that infect animals or prokaryotes.
The prion particle contains neither DNA nor RNA.
Prions degenerate the nervous system in mammals. One of these diseases is
scrapie, a brain disease that causes sheep to rub against fences, rocks. From russel
Enzymes called DNA polymerases catalyze the synthesis of new DNA by adding
nucleotides to a preexisting chain.
Virion:- completely assembled virus outside its host cell. Campbell and Jeffrey
- Nearly all viruses form a protein sheath, or capsid, around their
nucleic acid core.
- The capsid is composed of one to a few different protein molecules
repeated many times. The repeating units are called capsomeres. Kenneth
2.5.2.Viral symmetry
Symmetry refers to the way in which the capsomeres are arranged in the virus
capsid.
Rod-shaped viruses have helical symmetry, and spherical viruses have
icosahedral symmetry. The structure of virus is determined by the structure of
the capsomeres of which it is constructed.
1. Helical symmetry
These viruses consist of identical protein subunits which assembled in a helical
structure.
This type of protein subunits , forms a rigid nucleocapsid.
Moreover, the helical structure provides flexibility.
Ex:- tobacco mosaic virus and Sendai virus.
tobacco mosaic virus (TMV)
2. Icosahedral symmetry:- is a polyhedron with 20 equilateral
triangular faces and 12 vertices.
The rigid structure provides protection to the genome.
Ex:- papovavirus, picornavirus, adenovirus, togavirus, poliovirus etc.
3. Complex Symmetry
Consist of complex structural components which made it different
from the other two groups.
Ex:- pox virus.
Difference between DNA & RNA Viruses
Viruses infect all cells.
Reverse transcriptase:- An enzyme encoded by retroviruses that uses RNA as
a template for DNA synthesis.
Retrovirus is an RNA virus that converts its genetic information from RNA
into DNA
DNA virus RNA virus
Contains DNA as genetic material contain RNA as their genetic material
Mostly double stranded Single stranded
Has low mutation rate Has high mutation rate
2.5.3 classification of viruses
Today, the primary criteria for delineating the main viral taxa are:
(1) the type and character of the viral genome,
(2) the strategy of viral replication, and
(3) the types of organisms they infect.
Viral Replication
A virus hijacks the metabolism of the cell to produce copies of itself,
and often destroys the host cell when new virions are released.
The replication of bacteriophages can follow one of two pathways
These viruses exhibit two strategies of infection:
1. Lytic (virulent) pathway
2. Lysogenic (temperate) pathway.
1. The lytic Pathway
One of the best-studied processes of replication is that carried out by
bacteriophages of the T-even group (T for “type”). Bacteriophages T2, T4, and
T6 are in this group.
They are large, complex, DNA virions with head and tail structure. They contain
tail fibers, which, like the spikes on animal viruses, function to attach the phage
to a bacteria.
The T-even phages are virulent viruses, meaning they lyse the host cell while
carrying out a lytic pathway of replication.
We use phage T4 replication in E.coli as a model for the lytic pathway.
Viral replication
General Characteristics of replication
Viruses go through the following five steps in their replication cycles to produce
virions:
1. Adsorption, the attachment of viruses to host cells.
2. Penetration, the entry of virions (or their genome) into host cells.
3. Synthesis, the synthesis of new nucleic acid molecules, capsid proteins, and
other viral components within host cells while using the metabolic machinery of
those cells.
4. Maturation, the assembly of newly synthesized viral components into
complete virions.
5. Release, the departure of new virions from host cells.
Viruses can reproduce only when they enter cells. When viruses are outside of a
cell, viral particles are called virions and are metabolically inert.
Bacteriophage
The functions of Bacteriophage structural Components
Component Function
Genome Genome Carries the genetic information necessary
for replication of new phage particles
Tail sheath Retracts so that the genome can move from the
head into the host cell’s cytoplasm
Plate and tail Attach phage to specific receptor sites on the cell
fibers wall of bacterium
Bacteriophages (phages) are viruses that infect bacteria. They are obligate
intracellular parasites that multiply inside bacteria by making use of some or
all of the host biosynthesis machinery.
Uses a bacterium to replicate its genetic information.
Two types of viral reproductive cycles are lytic and lysogenic cycles.
1. Lytic Cycle (Virulent Cycle)
Lytic cycle:- A type of phage reproductive cycle in which the release of
phages from the bacterial cell results in rapid cell lysis (destruction).
Resulting in the release of progeny virions.
In a lytic cycle, the virus lyses (destroys) the host cell. When the virus
infects a host cell, it forces the host to use its metabolic machinery to
replicate viral particles.
Viruses that have only a lytic cycle are described as virulent (cause death).
The enzyme lysozyme, which is coded by a phage gene, breaks down
the cell wall, allowing viruses to escape. In the process the bacterial
host cell is lysed.
Phages such as T4 are called virulent (lytic) phages because they lyse
and destroy the bacteria.
The released phages can now infect more bacteria, starting the
infection process again.
Bacteriophage
2. Lysogenic Cycle (Temperate Cycle)
Temperate phages integrate into the genome of the bacterial
chromosome without causing any lysis of the bacteria.
The integrated phage nucleic acid is known as the prophage. The
prophage behaves like a segment of the host chromosome and
multiplies synchronously with it.
This phenomenon is known as lysogeny.
The bacterium that carries a prophage within its genome is called
lysogenic bacterium, and such phages are called lysogenic or
temperate phages.
Properties of Lysogeny (Temperate phages)
- The phage nucleic acid becomes incorporated into the host nucleic
acid. Such participating bacteria are called lysogenic cells.
E.g:- lambda (λ) phage of E.coli.
- Lambda phages insert their linear DNA into the bacterial cytoplasm.
- in the cytoplasm, the phage DNA circularizes and then integrates
into the circular bacterial chromosome.
- This viral DNA within the bacterial chromosome is called a prophage.
- The combination of a bacterium and a temperate phage is called a
lysogen.
jacqulin
- Lysogenic phages inject their DNA into the bacteria, the phage DNA
integrates into the bacterial chromosome
- The nucleic acid of the phages integrated into the DNA of its
bacterial host. The phage is then called a prophage.
- The bacterial cell containing the prophage is referred to as a
lysogenic bacterium.
- a lysogenic bacterium undergoes binary fission, the phage DNA is
replicated with the bacterial DNA and is passed on to the daughter
cells.
Thus, the daughter cells are also lysogenic bacterium
- Although the prophage does not usually cause the lytic cycle to
occur, certain events (e.g., exposure of the bacterium to ultraviolet
light) can trigger it to do so.
- While the prophage is integrated into the bacteria, the bacterial cell
can produce gene products that are coded by the prophage genes.
The bacterium will show new properties—a phenomenon known as
lysogenic conversion.
- i.e., the bacterium has been converted as a result of lysogeny and is
now able to produce one or more gene products that it previously
was unable to produce.
From Paul G
Bacteriophage
Bacteriophage
Bacteriophage
Lytic Cycle Lysogenic Cycle
The DNA of the virus doesn't integrate into The DNA of the virus integrates into the host
the host DNA DNA
Host DNA hydrolyzed Host DNA not hydrolyzed
Absence of prophage stage Presence of prophage stage
DNA replication of virus takes place DNA replication of the virus takes place along
independently from the host DNA replication with the host DNA replication
Occurs within a short period of time Takes time
Symptoms of viral replication are evident Symptoms of viral replication not evident
Genetic recombination in the host bacterium Genetic recombination in the host bacterium
not allowed allowed
The cellular mechanism of the host cell is The cellular mechanism of the host cell is
totally undertaken by the viral genome somewhat disturbed by the viral genome
Common viral diseases in Ethiopia
Disease Causative Sign and symptoms Transmission Prevention and control
agent
Mumps Mumps virus Swollen and painful parotid glands Person to person vaccine
Pain on chewing and swallowing in infected saliva
Measles Measles virus Cough, nasal discharge, eye redness, Droplet contact vaccine
(rubeola) and high fever; Koplik spots
Rabies Rabies virus Tingling, burning, coldness at bite Bite from rabid -Avoiding rabid animals
site,Fever, headache, increased muscle animal -washing the bitten area
Tension Paralysis, hydrophobia -vaccination
Polio Poliovirus Asymptomatic, Abortive Nonparalytic, Fecal–oral Vaccine, good
Paralytic route personal hygiene
Common Rhinoviruses Sneezing, sore throat, runny and stuffy Respiratory Practicing good
colds Adenoviruses nose, hacking cough droplets hygiene
(rhinitis) Other viruses
Chickenpox Varicella- Fever, headache, malaise with red, Droplet contact Chickenpox vaccine
(varicella) zoster itchy rash on face, scalp, chest, and
virus (VZV) back
2.6 Normal microbiota
The normal microbiota is the population of microorganisms routinely
found on the body of healthy individuals.
Resident microbiota:- Microbes that inhabit body sites for extended
periods.
Transient microbiota:- temporary occupants
Why we study human microbiota:
1. Understanding of different microorganisms at particular locations
provides greater insight into the possible infections that might result from
injury to these body sites.
2. Helps the physician understand the causes and consequences of
colonization and growth by microorganisms normally absent at a specific
body site.
3. An increased awareness of the role these normal microbiota play in
stimulating the host immune response can be gained.
Considering how important this population is to human health, little is
known about its members.
The normal human microbiota have protective role from diseases
causing microorganism.
One of the most significant contributions of the normal microbiota to
health is protection against pathogens. The normal microbiota
excludes pathogens by:
1. Covering binding sites that might otherwise be used forattachment.
2. Consuming available nutrients,
3. Producing compounds toxic to other bacteria,
4. To stimulate the adaptive immune system.
When members of the normal microbiota are killed, as can happen
during antibiotic treatment, pathogens may colonize and cause
disease.
Oral antibiotics can inhibit the normal intestinal microbiota, allowing
overgrowth of toxin producing strains of Clostridium difficile that
cause diarrhea and colitis.
The Germ Theory of Disease and Koch’s
Postulates
-Koch studied anthrax, a disease of cattle and occasionally of humans. -
Anthrax is caused by an endospore-forming bacterium called Bacillus
anthracis.
Koch demonstrated that when a small amount of blood from a diseased
mouse was injected into a healthy mouse, the latter quickly developed
anthrax.
He took blood from this second animal, injected it into another, and again
observed disease symptoms.
He discovered that the anthrax bacteria could be grown in nutrient fluids
outside the host and that even after many transfers in culture, the bacteria
still caused the disease when inoculated into a healthy animal.
The germ theory of disease and Koch’s
postulates
A German physician,
Robert Koch
(1843–1910)
postulates
Koch announced his discovery of the cause of tuberculosis in 1882.
For his contributions on tuberculosis, Robert Koch was awarded the
1905 Nobel Prize.
Koch discovers the causative agent of cholera(Vibrio cholerae)
postulates
Koch formulated a set of criteria, known as Koch’s postulates, for linking a
specific microorganism to a specific disease.
Koch’s postulates:
1. The disease-causing organism must always be present in animals
suffering from the disease but not in healthy animals.
2. The organism must be cultivated in a pure culture away from the animal.
3. The isolated organism must cause the disease when inoculated into
healthy animals.
4. The organism must be isolated from the newly infected animals and cultured
again, after which it should be seen to be the same as the original organism.
postulates
2.7. Modes of disease transmission and ways of prevention
Microorganisms are transmitted by four main routes:
1. Contact
2. Droplet
3. Airborne
4. Common vehicle
Method of How the transmission route works Examples of diseases
transmission
Droplet Many of these diseases are respiratory Common cold, 'flu,
infection diseases - diseases affecting the lungs. The pneumonia
organisms are carried in tiny droplets
through the air when an infected person
coughs or sneezes. They are inhaled by other
people.
transmission
Drinking The micro-organisms transmitted in this way Cholera, typhoid
contaminated often infect regions of the gut. When fever
water unclean water containing the organisms is
drunk, they colonize a suitable area of the
gut and reproduce. They are passed out with
faeces and find their way back into the
water.
Eating Most food poisoning is bacterial, but some Salmonellosis, typhoid fever,
contaminated viruses are transmitted this way. listeriosis, botulism
food The organisms initially infect a region of the
gut.
transmission
Direct Many skin infections, such as athlete's foot, Athlete's foot, ringworm
Contact are spread by direct contact with an infected
person or contact with a surface carrying the
organism.
Sexual organisms infecting the sex organs can be Candidiasis, syphilis, AIDS
intercourse passed from one sexual partner to another gonorrhea
during intercourse.
Some are transmitted by direct body contact,
such as the fungus that causes candidiasis
(thrush). others are transmitted in semen or
vaginal secretions, such as the AIDS virus.
Some can be transmitted in saliva, such as
syphilis.
transmission
Blood-to- Many of the sexually transmitted diseases can AIDS, hepatitis B
blood contact also be transmitted by blood-to-blood contact.
Drug users sharing an infected needle can
transmit AIDS.
Animal Many diseases are spread through the bites of Malaria, sleeping
vectors insects. Mosquitoes spread malaria and tsetse sickness
flies spread sleeping sickness. in both cases, the
disease-causing organism is transmitted when
the insect bites humans in order to suck blood.
Flies can carry microorganisms from faeces onto
food.
Airborne Transmission. High-speed video imaging of a sneeze.

2.8 Uses of microorganisms
Agriculture
Microorganisms :-
-play an important role in agriculture.
-help in organic matter decomposition, humus formation.
-play important role in N2 fixation, PSO4 solubilization, K mobilization,
antagonism towards pathogens, pests.
-converting these elements into forms that plants and animals can use.
return CO2 to the atmosphere when they decompose organic wastes and
dead organisms.
-Algae, cyanobacteria, and plants use CO2 during photosynthesis.
-Only bacteria can convert N2 to nitrate (NO3−).
Swage treatment
Anaerobic bacteria are used in wastewater treatment.
The main role of bacteria in sewage treatment is:
- to reduce the volume of sludge
- produce gas from it.
The gas can be used as energy source.
Phosphorus removal from wastewater is another benefit of anaerobic
microbes used in sewage treatment.
Bioremediation
Bioremediation is a natural process that relies on microorganisms and
plants and/or their derivatives (enzymes or biomass) to degrade
contaminants.
pollutants in the different environment always come into contact
with microorganisms.
Microbes break down pollutants via their metabolic processes with
or without slight pathway modifications to allow the pollutant to be
channeled into the normal microbial metabolism for degradation and
biotransformation.
Bioremediation focus on tapping the naturally occurring microbial
catabolic capabilities to degrade, transform or accumulate most of the
synthetic compounds such as hydrocarbons (e.g., oil), polychlorinated
biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), radionuclides and
metals.
The existence of a large diversity of microbial species expands the
variety of chemical pollutants that are degraded.
Microbes increase in numbers when the contaminant is present.
The residues are harmless products including H2O, CO2 & cell biomass.
Food production and processing
The tart taste of yogurt, pickles, sharp cheeses, and some sausages is
due to the production of lactic acid by one or more members of a
group of bacteria known as the lactic acid bacteria.
These bacteria - including species of Lactobacillus, Lactococcus,
Streptococcus, Leuconostoc , and pediococcus are obligate
fermenters that produce lactic acid.
Some produce flavorful and aromatic compounds that contribute to
the overall quality of fermented foods.
Medicine
-It is very difficult to decode the human genome if any disorders
occur in it as humans are eukaryotic.
-It means their body consists of various types of cells and all of them
differentiated into different tissues and organs.
-Microorganisms have made it to make medicines when enter the
body, target the defected genes and make healthy changes in them
and they become functional again.
-Now it is possible to synthesize the insulin in microorganisms.
-Microorganisms are inserted in the body in the form of vectors and cure the
defected genes.
-scientists have made use of microorganisms for making medicines and also
used them for drug delivery.
Health
-Our body contains ten times more microorganisms than the body cells.
-E.coli releases components which help in digestion.
however microorganisms also take nutrients from the body.
One purpose of bacteria in the body is to fight against those harmful bacteria.
-a bacterium in the gut helps in synthesizing vitamins like biotin, vitamin K and
folic acid.
Biotechnology
Biotechnology is one field which has made use of microorganisms
most.
By using biotechnology, scientists have succeeded in developing
insulin, growth hormones and other useful components.
- use microorganisms for the drug delivery in the form of vectors and
plasmids.
-Microorganisms are responsible for increasing the fertility of the
soil. Due to this:
- the production of the plants increases.
- economy becomes strong.
MOS have a big role in:
- suppression of soil-borne pathogens,
-recycling and increased availability of plant nutrients,
-degradation of toxicants including pesticides,
-Production of bioactive compounds,
-Production of simple organic molecules for plant uptake.
-alleviating complexation of heavy metals to limit plant uptake
-solubilization of insoluble nutrient sources, and
Production of polysaccharides to improve soil aggregation
There are ten bacterial cells inside you for every one of your own
cells. Most of these are found in the alimentary canal.
The role of bacteria in recycling minerals
- Many bacteria are decomposers. When organisms die, these
bacteria break down the complex molecules that are found in the
bodies of the dead organisms into much simpler molecules.
- The bacteria use some of these for their own metabolism, but in
the process, they release some minerals, in various forms, into the
environment.
- 90% of living organisms are made up of C, O, N and H and these
substance are limited in their availability.
-Thus in order for life to continue the substances should be recycled.
This is done by decomposers.
The carbon cycle
All organisms are composed of proteins, lipids, and carbohydrates.
The carbon travels through the food chain. Decomposers then use
the remains of primary producers and consumers.
Carbon Fixation
A fundamental aspect of carbon cycle is carbon fixation, the defining
characteristic of primary producers.
When heterotrophs consume organic material, they break it down
using respiration and/or fermentation to release the energy, which is
captured to make ATP
the processes usually make CO2. The type of organic material helps
dictate which species degrade it. A wide variety of organisms use
sugars, amino acids, and proteins as energy sources, but rapidly
multiplying bacteria often the O2 supply has a strong influence on the
carbon cycle. Not only does O2 allow degradation of certain
compounds such as lignin, it also helps types of carbon- containing
gases produced. When organic matter is degraded aerobically, a
great deal of CO2 is produced. When the O2 level is low, however, as
is the case in marshes, swamps, and manure piles, the degradation is
incomplete, generating some CO2 and a variety of other products.
Methanogenesis and Methane Oxidation
In anaerobic environments, CO2 is used by methanogens. These
archaea obtain energy by oxidizing H2, using CO2 as a terminal
electron acceptor, generating methane (CH4).
Methane is oxidized by ultraviolet light and chemical ions, forming
CO and CO2.
Methylotrophs can use methane as an energy source, oxidizing it to
produce CO2.
The Nitrogen cycle
Root nodules are found on the roots of legumes, which form a
symbiosis with nitrogen-fixing bacteria.
Under nitrogen-limiting conditions, capable plants form a
symbiotic relationship with a host-specific bacteria known as
rhizobia.
Nitrogen fixation in the nodule is very oxygen sensitive.
1. Nitrogen fixation:- convert N2 to ammonia (NH3). This process fixes nitrogen into a
form that organisms can use. Combustion, volcanic action, lightning discharges, and
industrial processes also fix nitrogen as nitrate (NO3−). Certain archaea and nitrogen-
fixing bacteria, including cyanobacteria carry on biological nitrogen fixation in soil and
aquatic environments.
These nitrogen-fixing prokaryotes employ an enzyme called nitrogenase to break up
molecular nitrogen and combine the resulting nitrogen atoms with hydrogen. Solomon
nitrogen-fixing bacteria convert N2 to NH3, which then picks up H+ in the soil , forming
NH4+. Campbell
2. Nitrification:- the conversion of ammonia (NH3) or ammonium (NH4+) to nitrate (NO3−).
Soil bacteria are responsible for the two-phase process of nitrification, which furnishes these
bacteria, called nitrifying bacteria, with energy. Solomon
In addition to NH4+, plants can also acquire nitrogen in the form of nitrate (NO3−). Soil NO3−
is largely formed by a two-step process called nitrification, which consists of the
oxidation of ammonia (NH3) to nitrite (NO2−), followed by oxidation of NO2− to NO3−.
Campbell
3. assimilation:- roots absorb ammonia (NH3), ammonium (NH4+), or nitrate (NO3−) and
incorporate the nitrogen into proteins, nucleic acids, and chlorophyll. When animals
consume plant tissues, they assimilate nitrogen by taking in plant nitrogen compounds and
converting them to animal nitrogen compounds.
4. ammonification:- is the conversion of organic nitrogen compounds into ammonia (NH3)
and ammonium ions (NH4+). Ammonification begins when organisms produce nitrogen-
containing wastes such as urea in urine and uric acid in the wastes of birds (see Fig. 48-1). As
these substances, along with the nitrogen compounds in dead organisms, decompose,
nitrogen is released into the abiotic environment as ammonia (NH3). The bacteria that
perform ammonification in both the soil and aquatic environments are called ammonifying
bacteria. Most available nitrogen in the soil derives from the recycling of organic nitrogen by
ammonification. solo
When a plant or animal dies, or an animal expels waste, the initial form of nitrogen is
organic. Decomposers convert the organic nitrogen within the remains back into ammonium
(NH4+), a process called ammonification. Campbell
The bodies of dead organisms contain nitrogen, mainly in proteins and nucleic acids. Urine
and dung also contain nitrogen. Decomposers break down these materials and release the
nitrogen they contain as ammonia, NH3, which in soil becomes ammonium,NH4+. This
process is known as ammonification. Modern
5. denitrification:- the reduction of nitrate (NO3−) to gaseous nitrogen (N2). Denitrifying
prokaryotes are anaerobic.
Sulfur Cycle
Sulfur is found in fewer types of organic molecules than nitrogen, but it is found in many
proteins.
Sulfur is a key constituent of amino acids. bacterial and fungal species decompose the
proteins and break down the sulfur-containing amino acids to yield various compounds,
including hydrogen sulfide (H2S).
Sulfur also can be released in the form of sulfate molecules (SO4–2) commonly found in
organic matter.
Desulfovibrio convert SO4–2 to H2S anaerobically.
Thiobacillus, Beggiatoa, release sulfur from H2S during their metabolism and convert it into
SO4–2.
The SO4–2 now is available to plants and microbes, where it is assimilated into the sulfur-
containing amino acids. Further assimilation by animals completes the cycle.
Other bacteria cycle sulfur compounds, oxidizing toxic sulfur species such as hydrogen
sulfide (H2S) into sulfate (SO42-),which is an essential plant nutrient. Michael
Sulfate reduction is the reduction of sulfate (SO42−) to hydrogen sulfide (H2S) by bacteria
Sulfhydryl (—SH) groups in proteins of dead organisms are converted to hydrogen sulfide
(H2S) by a variety of microorganisms.
Sulfur reduction is the reduction of sulfate to hydrogen sulfide. Like sulfate-reducing
bacteria, sulfur-reducing bacteria are anaerobes.
Sulfur oxidation is the oxidation of various forms of sulfur to sulfate. Thiobacillus and
similar bacteria oxidize hydrogen sulfide, ferrous sulfide, or elemental sulfur to sulfuric
acid (H2SO4).
DMS, dimethyl sulfide; DMSO, dimethyl sulfoxide.

The phosphorus cycle
Phosphorus (P) occurs in soils as both organic and inorganic forms (Figure 2.40).
Phosphorus can be found dissolved in the soil solution in very low amounts or
associated with soil minerals or organic materials.
The relative amounts of each form of phosphorus vary greatly among soils, with the total
amount of P in a clayey-textured soil being up to ten times greater than in a sandy soil.
Organic P in soils:- A large number of compounds make up the organic phosphorus in
soils, with the majority being of microbial origin.
Organic phosphorus is held very tightly and is generally not available for plant uptake
until the organic materials are decomposed and the phosphorus released via the
mineralization process. Mineralization is carried out by microbes, and as with nitrogen,
the rate of P release is affected by factors such as soil moisture, composition of
the organic material, oxygen concentration and pH.
Inorganic P in soils:- The concentration of inorganic P (orthophosphates) in the soil
solution at any given time is very small, amounting to less than l lb. IA. Phosphorus
in the inorganic form occurs mostly as aluminum, iron or calcium compounds.
The phosphorus cycle (Figure 25.9) involves the movement of phosphorus among
inorganic and organic forms.
Soil microorganisms are active in the phosphorus cycle in at least two important ways:
(1) They break down organic phosphates from decomposing organisms to inorganic
phosphates, and (2) they convert inorganic phosphates to orthophosphate (PO43−), a
water-soluble nutrient used by both plants and microorganisms. These functions are
particularly important because phosphorus is often the limiting nutrient in many
environments. Freeman
2.9 Controlling microorganisms
Sterilization is defined as a process by which an article, surface, or medium is freed of all
living microorganisms either in the vegetative or in the spore state. Any material that has
been subjected to this process is said to be sterile.
An object cannot be slightly sterile or almost sterile, it is either sterile or not sterile.
Although most sterilization is performed with a physical agent, such as heat, a few
chemicals called sterilants can destroy spores.
A germicide (a microbicide) is any chemical agent that kills pathogens. A germicide can
be used on inanimate (nonliving) materials or on living tissue, but it ordinarily cannot kill
resistant microbial cells. Any physical or chemical agent that kills "germs" is said to have
germicidal properties.
Disinfection refers to the use of a chemical agent that destroys all pathogens.
Disinfection destroys vegetative pathogens but not endospores.
disinfectants are used only on inanimate objects because they can be toxic to animal
tissue, when used in higher concentrations.
Disinfection remove the harmful products of microorganisms (toxins) from materials.
Examples of disinfection:-
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.
antiseptics are applied directly to the exposed body surfaces e.g., skin and mucous
membranes), wounds, and surgical incisions to destroy vegetative pathogens.
Examples of antisepsis:
a. Preparing the skin before surgical incisions with iodine compounds,
b. Swabbing an open root canal with hydrogen peroxide
c. Ordinary hand washing with a germicidal soap.
Sanitization:- mechanically removes microorganisms (along with food debris) to reduce
the level of contaminants. A sanitizer is a compound (e.g., soap ) that is used to perform
this task. Cooking utensils, dishes, bottles, cans, and used clothing that have been
washed and dried may not be completely free of microbes, but they are considered safe
for normal use.
Air sanitization with ultraviolet lamps reduces airborne microbes in hospital, clinics and
laboratory.
Preservation is a general term for measures taken to prevent microbe caused spoilage of
products (pharmaceuticals, foods).
Refrigeration/freezing
Decontamination is the removal or count reduction of microorganisms contaminating
an object.
Asepsis, disinfection, sanitization, degermation, sterilization
Asepsis :-Techniques that prevent the entry of microorganisms into sterile tissues
Cleansing the skin with iodine prior to surgery, using sterile needles
The objective of aseptic measures and techniques is to prevent microbial contamination
of materials or wounds. In antiseptic measures, chemical agents are used to might
pathogens in or on living tissue, for example in a wound.
Physical methods of sterilization and disinfection
Heat
The application of heat is a simple, cheap and effective method of killing pathogens.
Methods of heat application vary according to the specific application.
Pasteurization. This is the antimicrobial treatment used for foods in liquid form
Low-temperature pasteurization: 61.5 ℃ ,30 minutes; 71 ℃, 15 seconds.

(milk):
High-temperature pasteurization: brief (seconds) of exposure to 80-85 ℃ in
Uperization: heating to 150 ℃ for 2.5 seconds in a pressurized container using

continuous operation.
steam injection.
Disinfection. Application of temperatures below what would be required for sterilization.
Important: boiling medical instruments, needles, syringes, etc. does not constitute
sterilization! Many bacterial spores are not killed by this method.
Dry heat sterilization:- Sterilization by dry heat includes
A. Flaming : Sterilization of inoculating loop or wire, the tip of forceps, searing spatulas,
etc., is carried out by holding them in the flame of the Bunsen burner till they become
red hot.
B. Incineration: Incineration is an excellent method for safely destroying infective
materials by burning them to ashes. It has many uses:
 Incinerators are used to carry out this process and are regularly employed in hospitals
and research labs to destroy hospital and laboratory wastes.
 The method is used for complete destruction and disposal of infectious material, such
as syringes, needles, culture material, dressings, bandages, bedding, animal carcasses
and pathology samples.
C. Hot air oven: Sterilization by hot-air oven requires exposure to 160-180°C for 2
hours and 30 minutes, which ensures thorough heating of the objects and destruction of
spores.
Moist heat sterilization. Autoclaves charged with saturated, pressurized steam are used
for this purpose:
Autoclaves contain a sterilizing chamber into which the objects to be sterilized are
placed. As steam flows into the chamber, it forces out the air, increases the pressure to
15 pounds per square inch (psi), and raises the temperature to 121°C. The time for
destruction of the most resistant bacterial species is about 15 minutes (see Figure 9.5).
For denser objects or large volumes of liquids, more than 30 minutes of exposure might
be required. Jeffrey.
Sterilization with Steam Under Pressure At sea level, normal atmospheric pressure is 15
pounds per square inch (psi), or 1 atmosphere. At this pressure, water will boil (change
from a liquid to a gas) at 100°C, and the resultant steam will not go above 100 °C. But
boiling temperature is not hot enough to kill all microbes. The only way to raise the
temperature of steam is to expose it to increased pressure. At higher pressures the
temperature at which water boils and the temperature of steam both rise. For example,
at a pressure of 20 psi (5 psi above normal), the temperature of steam is 109°C. As the
temperature is increased to 10 psi above normal, the steam’s temperature rises to 115°C,
and at 15 psi above normal (a total of 2 atmospheres), it will be 121°C. It is not the
pressure by itself that is killing microbes but the increased temperature it produces.
Such pressure-temperature combinations can be achieved only with a special device that
can subject pure steam to pressures greater than 1 atmosphere.
the most efficient pressure-temperature combination for achieving sterilization is 15 psi,
which yields 121°C
It is possible to use higher pressure to reach higher temperatures (for instance,
increasing the pressure to 30 psi raises the temperature to 132°C), but doing so will not
significantly reduce the exposure time and can harm the items being sterilized.
The duration of the process is adjusted according to the bulkiness of the items in the
load (thick bundles of material or large flasks of liquid) and how full the chamber is. The
range of holding times varies from 10 minutes for light loads to 40 minutes for heavy
or bulky ones; the average time is 20 minutes.
Kathleen P. Talaro, Barry Chess - Foundations in Microbiology
intermittent sterilization.
Certain heat-labile substances (e.g., serum, sugar, egg, etc.) that cannot withstand the
high temperature of the autoclave can be sterilized by a process of intermittent
sterilization, known as tyndallization.
This technique requires a chamber to hold the materials and a reservoir for boiling
water. Items in the chamber are exposed to free-flowing steam for 30 to 60 minutes. This
temperature is not sufficient to reliably kill spores, so a single exposure will not suffice.
On the assumption that surviving spores will germinate into less resistant vegetative
cells, the items are incubated at appropriate temperatures for 23 to 24 hours, and then
again subjected to steam treatment. This cycle is repeated for 3 days in a row. Because
the temperature never gets above 100°C, highly resistant spores that do not germinate
could survive even after 3 days of this treatment.
2.10. Bacterial Isolation techniques
Microorganisms can be isolated from food, soil, water or from other materials. For
bacterial/fungal isolation, the soil (food) samples are collected from the desired sites.
Microorganism are separated on artificial media by serial dilution method. Each of the
isolates are purified on new media and experimented for the morphological
characteristic like shape, gram nature and arrangement of cells, motility etc. Enzymatic
activities were tested by biochemical characterization. Finally, molecular techniques are
used for further identifications.
2.10. Bacterial Isolation techniques

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Unit 2 microorganism

- Some bacteria have hairlike appendages known as pili. These

Audesirk page 354

Cytoplasm :- the part of the cell outside the nucleus

viable for centuries, able to rehydrate and resume metabolism when

their environment improves. Campbell

1. All are eukaryotic

Fungi exist mainly in the form of slender filaments, visible to the

Transcription:- The synthesis of RNA from a DNA template

Airborne Transmission. High-speed video imaging of a sneeze.

DMS, dimethyl sulﬁde; DMSO, dimethyl sulfoxide.

Low-temperature pasteurization: 61.5 ℃ ,30 minutes; 71 ℃, 15 seconds.

High-temperature pasteurization: brief (seconds) of exposure to 80-85 ℃ in

Uperization: heating to 150 ℃ for 2.5 seconds in a pressurized container using

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