Hidase Lideta Secondary School

Biology Handout for Grade 12

Unit 2: Microorganisms

Prepared by: Shoma Abdissa and Amanu Negash

Department: Biology

Academic Year: October, 2017 E.C

Unit 2: Microorganisms

 Microorganisms are organisms too small to be seen clearly by the unaided eyes.

 Microbiology can be defined as the study of microbes.

 Microbes can be observed only with the use of various types of microscopes.

 Microorganisms include:

 Fungi (some)

 Algae (some)

 Bacteria

 Protozoa

 Viruses

 Helminthes (parasitic worms).

Microbial community structure

 Prokaryotes

 Bacteria

 Eukaryotes

 Fungi

 Algae

 Amoeba

 Paramecium

 Fluke

 Tapeworm

 Flagellates

 Acellular (viruses)
The 3 domains of organisms based on evolutionary lines

 Eukarya

 Archaea

 Bacteria

Eubacteria

 Eubacteria (biology definition): Literally means “true bacteria”.

 Bacteria are relatively simple in structure.

 They are prokaryotic unicellular organisms with no nuclear membrane, mitochondria,

Golgi bodies, or endoplasmic reticulum.

 They reproduce by asexual division.

General characteristics of bacteria

 Bacteria are omnipresent.

 Present in soil, air and water.

 They are unicellular, prokaryotic microorganisms.

 The cell bears a thick rigid cell wall (peptidoglycan) outside the plasma membrane.

 They have great variation in the mode of nutrition.

 May be autotrophic and heterotrophic (parasitic, saprophyte/symbiotic in nature).

 They lack true chlorophyll but few photosynthetic bacteria have a special type of
chlorophyll called bacteriochlorophyll.

 Lack true nucleus (lacking nuclear membrane and nucleolus).

 Lack mitochondria, Golgi apparatus, plastid and endoplasmic reticulum.

 Have both DNA and RNA.

The general structural plan of a prokaryotic cell represented by flow chart

1. Prokaryotic cell (Domains bacteria and archaea)

1.1. External

 Appendages (flagella, pili, and fimbriae)

 Glycocalyx (capsule, slime layer)

1.2. Cell envelope

 Cell wall

 Cell membrane

1.3. Internal

 Cytoplasmic matrix

 Ribosomes

 Inclusions

 Nucleoid/chromosome

 Actin cytoskeleton

 Endospore

Eukaryotic microbes

 Are an extraordinarily diverse group.

 Have species with a wide range of life cycles, morphological specializations, and
nutritional needs.

 Responsible for diseases of great public health importance, although more diseases are
caused by viruses and bacteria than microscopic eukaryotes.

 Have eukaryotic cells.

 A cytoskeleton composed of microtubules, microfilaments, and intermediate filaments

helps eukaryotic cells give shape.

 Cytoskeleton is also involved in cell movements, intracellular transport, and

reproduction.
2.1.1. Bacterial shapes

Morphologically bacteria are classified based on:

 Cell shape (Figure 2.5)

 Nature of multi cell aggregates

 Motility

 Formation of spores

 Reaction to the gram stain.

The 4 groups of bacterial cell based on shapes

 Cocci: Spherical bacteria

 Coccus

 Diplococcus

 Tetrad

 Sarcina

 Streptococci

 Staphylococci

 Bacilli : Rod shaped bacteria

 Coccobacillus

 Bacillus

 Diplobacilli

 Streptobacilli

 Palisades

 Spirochaetes : Spiral or corkscrew shaped bacteria

 Spirilla

 Spirochete

 Comma : Vibrio cholera

  Vibrios

Classifications of bacteria based on cell wall composition and retaining dyes during Grams
stain

i. Gram positive

 Stained purple by gram stain.

 Retains the purple crystal violet stain in the thick peptidoglycan layer of the cell wall
(Figure 2.5).

 Examples: - all staphylococci, all streptococci and some listeria species.

ii. Gram negative

 Stained pink by gram stain

 Loses the crystal violet stain due to the cell wall composed of a thin layer of a particular
substance called peptidoglycan.

Comparison of Gram-positive and Gram-negative cell walls

Characteristic Gram-positive Gram-negative

Number of major layers 1 2

Chemical composition  Peptidoglycan  Lipopolysaccharide

 Teichoic acid  Lipoprotein

 Lipoteichoic acid  Peptidoglycan

Overall thickness Thicker (20-80nm) Thinner (8-11nm)

Outer membrane No Yes

Periplasmic space Narrow Extensive

Porin proteins No Yes

Permeability to molecules More penetrable Less penetrable

The five basic steps of the Gram staining process

 1. Heat fix/attach the bacteria to the slide

2. Applying a primary stain (crystal violet)

3. Adding a mordant (Grams iodine)

4. Rapid decolorization with ethanol, acetone or a mixture of both

5. Counterstaining with safranin.

In short, Fixation, crystal violet, iodine treatment, decolorization, and counter stain safranin.

Gram staining technique

 Includes simple staining (using single dye) or differentiated staining (use different dyes)
(Figure 2.6)

Key words

 Gram's staining: A test for distinguishing bacteria.

 Named after Hans Christian Gram, who developed the technique in 1884.

 Differential staining: A staining procedure that distinguishes organisms based on their

staining properties.

 Peptidoglycan: The rigid layer of the cell walls of bacteria.

 Endotoxin: The lipopolysaccharide portion of the cell envelope of certain gram negative
bacteria, which is toxin to human when solubilized.

2.1.2. Nutritional types of Bacteria

 Bacteria have evolved many mechanisms to acquire the energy and nutrients they need
for growth and reproduction.

 Many are autotrophs (organisms that obtain their carbon from inorganic CO2).

 Photoautotrophs: Autotrophs that obtain their energy from sunlight.

 Chemoautotrophs: Autotrophs that harvest energy from inorganic chemicals.

 Other bacteria are heterotrophs (organisms that obtain at least some of their carbon from
organic molecules like glucose).

 Photo heterotrophs: Obtain their energy from sunlight.

 Chemo heterotrophs: Harvest energy from organic molecules.

Sources of energy

i. Light energy

ii. The energy derived from oxidizing organic or inorganic molecules.

 Phototrophs: Use light as their energy source.

 Chemotrophs: Obtain energy from oxidation of chemical compounds

(organic/inorganic).

 Bacteria also have only two sources for electrons: Lithotrophs and organotrophs.

 Lithotrophs (Rock-eaters): Use reduced inorganic substances as their electron source.

 Organotrophs: Extract electrons from reduced organic compounds.

 Despite the great metabolic diversity seen in bacteria, most may be placed in one of the
five nutritional classes based on their primary sources of carbon, energy, and electrons.

 The majority of bacteria are either photolithoautotrophs (photoautotrophs) or

chemoorganoheterotrophic (chemo heterotrophs).

 Photoautotrophs: Use light energy and have CO2 as their carbon source.

 Chemo heterotrophs: Use organic compounds as a source of energy, hydrogen, electrons,

and carbon.

 Nearly all pathogenic microorganisms are chemoorganoheterotrphs.

 Some photosynthetic bacteria (purple and green bacteria) use organic matter as their
electron donor and carbon source.

 Some of these bacteria can also grow as photolithoautotrophs with molecular hydrogen as
an electron donor.

 Chemolithoautotrophs: Oxidize reduced inorganic compounds such as iron, nitrogen, or

sulfur molecules to derive both energy and electrons for biosynthesis. Carbon dioxide is
the carbon source.

 Chemolithoheterotrophs: Use reduced inorganic molecules as their energy and electron

source but derive their carbon from organic sources.

 Chemolithotrophs contribute greatly to the chemical transformations of elements.

Example, the conversion of ammonia to nitrate or sulfur to sulfate that continually occurs
in ecosystems.
Table 2.2 of students’ text book, page 53

2.1.3. Reproduction of bacteria

2.1.3.1. Asexual reproduction

 Most bacteria reproduce by asexual process called binary fission.

 Unlike eukaryotic cells, bacterial cells lack a mitotic spindle to separate replicated
chromosomes.

 The segregation process does not involve specialized chromosomal associated proteins.

 No clear picture describing how most of these proteins work to ensure accurate
chromosome segregation.

 In any event, cell fission at midcell involves the synthesis of a partition, or septum, which
separates the mother cell into two genetically identical daughter cells.

2.1.3.2. Sexual reproduction in bacteria

 Involve transformation, transduction, and conjugation.

 Conjugation: The two cells of different mating types come together, and genetic material
is transferred from one to the other.

 Transformation: The transfer of DNA of capsulated bacteria to non capsulated.

 Transduction: DNA of bacterial cell (donor) to occur.

 In contrast to transformation and transduction, conjugation involves contact between two

cells.

 Example: E. coli

 In the E. coli population, there are donor cells or F cells that can be transmitted to
recipient cells or F cells.

 F cells have a DNA sequence known as the F factor (F stands for fertility) that is
necessary for a bacterium to serve as a donor during conjugation.

 F factor consists of about 20 genes.

 It can be in the form of a plasmid or

 It can be part of the DNA in the bacterial chromosome.

 Gene code enzymes essential for transferring DNA.

  F genes encode sex pili, long, hair like extensions that project from the cell surface.

 The sex pilus recognizes and binds to the surface of 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.

2.2. Archaea

 Archaea are unicellular microscopic organism that lives as producers or decomposers.

Characteristics of archaea

 Archaea are prokaryotic.

 They are single celled organisms.

 They lack membrane bound nucleus and membrane bounded organelles.

 Lack true peptidoglycan in their cell walls.

 Their cell membrane lipids have branched hydrocarbon chains.

 Many are found in extreme environments.

Table 2.3. Common bacterial diseases

The three major groups of archaea based on physiological characteristics

 Methanogens

 Generate methane.

 They are strictly anaerobic organisms that have been isolated from such divergent
anaerobic environments: water logged soil, lake sediments, marshes, marine sediments,
and the gastrointestinal tracts of animals including humans.

 They degrade organic molecules to methane.

 Extreme halophiles

 They grow in highly saline environments such as the great salt lake, the dead sea, salt
evaporation ponds, and the surfaces of salt preserved foods.

 Unlike the methanogens, they are generally obligate aerobes.

  Extreme thermophiles (hyper thermophiles)

 Found near volcanic vents and fissures that release sulfurous gases and other hot vapors.

 They may be obligate aerobes, facultative aerobes, or obligate anaerobes (with optimum
temperatures usually in excess of 80 degree centigrade).

 Thermophilic extreme Acidophiles

 Thermoplasma and Picrophilus are notable for growing in extremely acidic, and hot
environments.

 Live at low PH (as low as PH 1 and who die at PH 7).

 Psychrophiles (cryophiles)

 Like cold (One in Antarctic grows best at 4d.c).

 Draw Figure 2.9.

Figure 2.9. Phylogenetic tree of archaea

 The tree, based on sequences of 16S ribosomal RNA genes, reveals a major evolutionary
split of Archaea into two phyla, the Crenarchaeota and the Euryarchaeota.

 Scientists originally identified archaea as a distinct type of prokaryotes on the basis of

unique rRNA sequences.

 Archaea also share other common features that distinguish them from bacteria:

 Archaea lack true peptidoglycan in their cell walls.

 Their cell membrane lipids have branched hydrocarbon chains.

 The initial amino acid in their polypeptide chains, coded by the AUG start codon, is
methionine (as in eukaryote and in contrast to the N-formylmethionine used by bacteria).

 Archaea multiply by binary fission, budding, fragmentation or other mechanisms.

 Nutritionally, they are either aerobic, facultative anaerobic or strictly anaerobic,

Chemolithoautotrophs to organotrophs.

2.2.1. Beneficial aspects of Archaea

Archaea, a unique domain of life distinct from bacteria and eukaryotes, offer several beneficial
aspects:
  Biogeochemical Cycles: Archaea play crucial roles in biogeochemical cycles, particularly
in carbon and nitrogen cycling. Methanogenic archaea are essential in producing methane
in anaerobic environments, contributing to the global carbon cycle.

 Extreme Environments: Many archaea thrive in extreme conditions (high temperatures,

salinity, acidity), which can provide insights into early life on Earth and the potential for
life on other planets.

 Biotechnology Applications: Enzymes from extremophilic archaea are used in various

industrial processes, including biofuels, food production, and pharmaceuticals, due to
their stability and efficiency under extreme conditions.

 Environmental Remediation: Some archaea can degrade pollutants, making them

valuable for bioremediation efforts in contaminated environments.

 Symbiotic Relationships: Archaea form symbiotic relationships with other organisms,

contributing to the health of ecosystems, such as in the human gut microbiome, where
they aid in digestion and nutrient absorption.

 Research Insights: Studying archaea enhances our understanding of evolutionary

biology and the origins of life, as they share characteristics with both bacteria and
eukaryotes.

 The source of enzymes:

 Those are added to detergents to maintain its activity even at higher temperature and PH.

 Those are used as detergent additives to increase their stain removal ability (e.g.
Proteases and lipases derived from alkaliphilic bacteria).

 Cleaning contaminated sites (bioremediation).

 The Thermophilic archaea, Thermus aquaticus, is an essential part of the development of

molecular biology as a science.

 They are the sources of the enzyme harnessed as the basis for the amplification of the
DNA in a technique called Polymerase Chain Reaction (PCR).

2.2.2. Physical factors that affect microbial growths

The major physical factors which affect the microbial growth are:

 Solutes and water activity

 PH
  Temperature

 Oxygen level

 Pressure

 Radiation

2.3. Fungi

 Fungi are eukaryotic organisms that:

 Bear spore

 Have absorptive nutrition

 Lack chlorophyll

 Reproduce sexually and asexually.

 Mycologists: Scientists who study fungi.

 Mycology: The scientific discipline devoted to fungi.

 Mycotoxicology: The study of fungal toxins and their effects.

 Mycoses (mycosis): The diseases caused by fungi in animals.

2.3.1. General characteristics of true fungi

 All are eukaryotic.

 Most are filamentous.

 Composed of individual microscopic filaments called hyphae.

 Special branches of hyphae called mycelium.

 Some have septate hyphae, and others have nonseptate (coenocytic hyphae).

 Some are unicellular. E.g. yeasts

 Protoplasm of a hypha or cell is surrounded by a rigid wall.

 The wall is composed of chitin and glucans.

 Many reproduce both sexually and asexually.

 Often result in the production of spores.

  Their nuclei are typically haploid and hyphal compartments are often multinucleate.

 Oomycota and some yeasts possess diploid nuclei.

 All are achlorophyllous.

 They lack chlorophyll pigments and are incapable of photosynthesis.

 All are chemoheterotrophic (chemoorganotrophic).

 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.

 Nutritionally, categorized into three (Saprophytic, parasitic, and symbiotic).

2.3.2. Ecology of Fungi

 Fungi colonize nearly all environments on earth.

 Frequently found in cool, dark, moist places with a supply of decaying material.

 They are saprobes that decompose organic matter.

 Many are mutualistic relationships.

 Many establish complex mycorrhizal associations with the roots of plants.

 Lichens are a symbiotic relationship between a fungus and a photosynthetic organism.

E.g. algaor cyanobacterium.

 The photosynthetic organism provides energy derived from light and carbohydrates,
while the fungus supplies minerals and protection.

 Zygomycota: Sporangial fungi. E.g. rhizopus and mucor.

 Ascomycota: Ascospore producing fungi. E.g. Saccharomyces cerviciae.

 Basidomycota: Basidia producing fungi. E.g. rusts and smuts.

2.3.3. Classification of fungi

  Many mycologists currently recognize five major groups of fungi, although recent
genomic evidence indicates that the chytrids and zygomycetes are paraphyletic.

 The current classifications of fungi includes:

 Chytridomycota: Zoospore producing fungi. E.g. allomyces and water molds.

 Glomeromycota: Fruiting bodies which represent the part of a fungus in which spores are
formed and from which they are released.

 These structures may be asexual and invisible to the naked eye, or sexual structures, such
as the macroscopic mushrooms.

 E.g. mycorrhizal fungi.

2.3.4. Reproduction in fungi

 Sporulation: The process of spore formation.

Asexual reproduction

 Asexual reproductive structures develop at the ends of specialized hyphae.

 Many asexual spores develop within sacs/vessels called sporangia.

 The spores are called sporangiospores.

 Other fungi produce spores on supportive structures called conidiophores.

 Conidia (conidio=dust): Unprotected, dust-like spores.

 Fungal spores are extremely light and are blown about in huge numbers by wind currents.

 In yet other fungi, spores may form simply by fragmentation of the hyphae yielding
arthrospores (arthro= joint). E.g. Sporangia of the common bread mold Rhizopus and the
conidiophores and conidia.

 Many yeasts reproduce asexually by budding.

 The cell becomes swollen at one edge, and a new cell called a blastospore (blasto= bud)
develops (buds) from the parent cell.

Sexual reproduction
  Many fungi also produce spores by sexual reproduction.

 Opposite mating types come together and fuse.

 The nuclei are genetically different in each mating.

 The fusion cell represents a heterokaryon (hetero= different); (karyo= nucleus).

 The nuclei fuse and diploid cell formed.

2.3.5. Economic importance of fungi

 Fungi are among the economic important microorganisms.

 Are agents of biodegradation and biotierioration

 Responsible for the majority of plant and animal diseases.

 Used in industrial fermentation process.

 Used in the commercial production of many biochemicals.

 Used in bioremediation.

 Beneficial in agriculture, horticulture and forestry.

Beneficial aspects of fungi

 Fungi exist either as saprobes or parasites.

 Are edible wild or domesticated varieties of mushrooms (Basidiomycetes).

 Essential to many industrial processes including making of bread, wine, and beer. e.g.
yeast.

 Play major roles in the preparation of some cheeses, soy sauce, and sufu, injera, Tela
(farsoo), Tej (Dadhii), bulla,etc and in the commercial production of many organic acids
(citric, Gallic) and certain drugs (ergometrine, cortisone).

 Are used in the production of citric, oxalic, gluconic and itaconic acid from molds
(Aspergillus species).

 Fusarium (mold) can produce within 48 hours 12-15 grams of fat from a litre of 50%
glucose solution.

 Fungi play a major role in the manufacture of many antibiotics (penicillin, griseofulvin)
and the immunosuppressive cyclosporin.
  Actinomycetes and fungi are important sources of antibiotics such as penicillin,
amphotericin B, adriamycin and bleomycin,etc.

 Fungi are useful tools for studying complex eukaryotic events, such as cancer and aging
within a simple cell.

Harmful aspects of fungi

 Fungi are the major cause of plant diseases.

 Over 5,000 species of fungi attack economically valuable crops, garden plants, and many
wild plants.

 Fungi also cause many diseases of animals and humans.

 Molds can cause deterioration of fabrics, leather, electrical insulation and other
manufactured goods.

 Fungi spoil the agricultural products.

 They also destroy vegetables, fruits and cereals.

 Mycotoxicoses (ingestion of toxins of fungal origin) and mycetismus (mushroom

poisoning through ingestion of fungal elements).

 Aflatoxis

 Two closely related fungi, Aspergillus flavus and A. parasiticus, produce mycotoxins
called aflatoxins.

 They contaminate agricultural products such as peanuts, grains, cereals, sweet potatoes,
corn, rice, and animal feed.

 They are deposited in these foods and ingested by humans where they are thought to be
carcinogenic, especially in the liver.

 Contaminated meat and dairy products are also sources of the toxins.

 Ergotism

 Caused by Claviceps purpurea (an ascomycete fungus producing a powerful toxin).

 C. purpurea grows as hyphae on kernels of rye, wheat, and barley.

 The dense tissue hardens the grain into a purple body called a sclerotium.

 Alkaloids are produced by the 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.

 Mushroom poisoning, or mycetism

 Occurs from mushrooms that produce mycotoxins that affect the human body.

 Superficial fungal infections

 Superficial mycoses are fungal infections of the outer most areas of the human body:
hair, fingernails, toenails, and the dead, outermost layers of the skin (the epidermis).

 Caused by any of several species of taxonomically related flamentous fungi in the genera
Trichophyton, Epidermophyton, and Micosporum.

 The various forms of dermatophytosis are referred to as tineas or ringworm.

 Clinically, the tineas are classified according to the anatomic site or structure affected:

1. Tinea corporis (ringworm): Micosporum canis and Trichophyton mentagrophytes.

 Affects hairless skin.

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.

 Affects the scalp, eyebrows, and eyelashes.

4. Tienea barbae: T. rubrum and T. mentagrophytes.

 Beard ringworm.

5. Tinea unguium (also known as onychomycosis): T. rubrum, T. mentagrophytes, and E.

floccosum.

 Affects the nails.

Mode of transmission
  Superficial mycoses (Dermatomycoses) are infections that are transmitted directly by
human contact, animal-human contact or indirectly on inanimate objects (clothes, carpets,
moisture, and dust in showers, swimming pools, wardrobes, gyms).

Prevention

 Regular disinfection of showers and wardrobes can contribute to prevention of athletes

foot.

Table 2.4. Summary of some fungal diseases

2.4. Protozoa

 The term protozoa: protos (first), and zoon (animal).

 Traditionally referred to as chemoorganotrophic protists.

 Protozoology: The study of protozoa.

Characteristics of protozoa

 Protozoa are unicellular microorganisms that lack cell wall.

 May be free- living or parasitic.

 Aerobic.

 Have true nucleus.

 Are eukaryotic cells.

 Mostly microscopic.

 Locomotion by pseudopodia, flagella, cilia, and direct cell movements; some are 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 to form a zygote.

Table 2.5. Classification of protozoa

Reproduction in protozoa

 Most protozoa are asexual and reproduce in one of the three ways.

 Fission: Occurs when a cell divides evenly to form two new cells.

 Budding: Occurs when a cell divides unevenly.

 Multiple fission (schizogony): Occurs when the nucleus of the cell divides multiple times
before the rest of the cell divides.

 Sexual reproduction: Also occurs during the life cycle of most protozoa.

 A distinctive feature of ciliates is the presence of two types of nuclei: tiny micronuclei
(controls reproduction), and large macronuclei (control everyday functions of the cell,
such as feeding, waste removal, and maintaining water balance).

Nutrition in protozoa

 Protozoa are heterotrophic.

 Grow in both aerobic and anaerobic environment. E.g. Live in the intestine of animals.

 Euglena: Autotrophic and heterotrophic.

 Protists obtain food in one of the three ways: Absorption, ingestion, and engulf.

 Absorption: Food is absorbed across the protists plasma membrane.

 Ingestion: Cilia outside the protist create a wave-like motion to move food into mouth-
like opening in the protist called a cystosome. E.g. paramecium.

 Engulf: Engulf food by using pseudopodia, and then pull it into the cell using a process
called phagocytosis. E.g. Amoeba.

 Digestion: Done in the vacuole.

 Exocytosis: The process of excreting waste products.

2.4.1. Common diseases caused by protozoa

 Most protozoa are not harmful.

 Many are beneficial in the environment because they help make it more productive.

 They improve the quality of water by eating bacteria and other particles.

 Few protozoans are diseases causing.

  Some of the human diseases caused by protozoans include:

 Malaria

 African trypanosomiasis

 Amoebiasis

 Giardiasis

 Chagas disease

 Leishmaniosis

 Toxoplasmosis

 Cryptosporidiosis

Table 2.6. Major protozoal parasites of human and other organisms

2.5. Viruses

 Viruses are small, obligate, intracellular particles.

 Most can be seen only with the electron microscope.

 They must infect and take over a host cell in order to replicate.

 They lack the chemical machinery for generating energy and synthesizing large
molecules.

2.5.1. Characteristics of virus

 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.

 Grow in animals, eggs or tissue culture.

 They do not have a cellular organization.

 They do not have cell wall or cell membrane or cellular organelles including ribosomes.

 They do not occur free in nature but act as obligate intracellular parasite.

 They lack the enzymes necessary for protein and nucleic acid synthesis .

 They depend on the synthetic machinery of host cells for replication.

  They are unaffected by antibacterial antibiotics.

 They are inert (nucleoprotein) filterable agents.

 Occupy a space in between living and non-living, because they are crystallizable and
non-living outside the body of host.

 They are obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and
animals.

 They are ultramicroscopic size, ranging from 20nm up to 450nm (diameter).

 They do not independently fulfill the characteristics of life.

 Inactive macromolecules outside the host cell and active only inside host cells.

 Have 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:

 Ds DNA

 Ss DNA

 Ss RNA

 dsRNA

 Molecules on virus surface impart high specificity for attachment to host cell.

 Multiply by taking control of host cells genetic material and regulating the synthesis and
assembly of new viruses.

 Lack machinery for synthesizing proteins.

 The basic structure of virus is nucleic acid core (either DNA or RNA but not both)
surrounded by protein coat.

 The central core of nucleic acid of a virus is called genome.

 The protein coat surrounding is called 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

  Core: The genomic material, either DNA or RNA.

 DNA or RNA may be 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: An additional lipoprotein layer around the capsid derived from the cell surface
membrane of the host cell. E.g. HIV and influenza viruses.

 Capsomeres: The identical repeating subunits forming capsids.

 Lysozyme: Plays central role during infection process. E.g. Bacteriophage.

 Polymerase: Transcribes the viral genome into m RNA during replication process. E.g.
Retrovirus.

2.5.2. Viral symmetry

1. Helican symmetry

 Several viruses are found with a helical morphology.

 Consists of identical protein subunits or protomers which assembled in a helical structure

around the genome.

 Forms a rigid Nucleocapsid.

 Provides flexibility to the filaments.

 Example: Tobacco mosaic virus and Sendai virus.

Icosahedral Symmetry

 An icosahedron structure refers to a type of polyhedron with 20 equilateral triangular

faces and 12 vertices.

 Provides protection to the genome.

 E.g. Papovavirus, picornavirus, adenovirus, togavirus, etc.

Complex Symmetry

 Consist of complex structural components which made it different from the other two
groups. E.g. pox virus

Viruses occur in three main shapes

 1. Spherical/ polyhedral: Naked capsids (e.g. poliovirus, Adenovirus, papilloma virus), and
Enveloped capsids (e.g. Herpes simplex virus).

2. Cylindrical/helical: Naked capsids (e.g. Bacteriophage M13, TMV), and Enveloped

capsids (e.g. Influenza virus).

3. Complex: No clearly identifiable capsid. E.g. vaccinia virus capsids to which other
structures are attached. E.g. Some bacteriophage

Differences between DNA and RNA viruses

DNA viruses RNA viruses

Contain DNA as their genetic material. Contain RNA as their genetic material.

Mostly double- stranded. Single-stranded.

Mutation rate is less than RNA mutation rate. Mutation rate higher than DNA mutation rate.

Replicate in the nucleus. Take place in the cytoplasm.

Key words

 DNA virus: Contains genetic information stored in the form of DNA.

 RNA virus: Contains genetic information stored in the form of RNA.

 Retrovirus: An RNA virus that converts its genetic information from RNA into DNA
after it has infected a host.

 Bacteriophage: A virus the uses a bacterium to replicate its genetic information.

2.5.3. Classification of viruses

The primary criteria for delineating (describing) the main viral taxa are:

 The type and character of the genome.

 The strategy of viral replication.

 The types of organisms they infect.

Viral replication
  One of the best studied processes of replication is that carried out by bacteriophages of
the T-even group (T for “type”).

 In general, viruses go through the following 5 steps in their replication cycles.

The 5 steps of viral replication cycles

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. Release generally, but not always, kills
(lyses) host cells.

Bacteriophages

 Are bacterial viruses.

 Infect bacteria.

 Obligate intracellular parasites that multiply inside bacteria by making use of some or all
of the host biosynthesis machinery.

 Also called phages.

Component and function of bacteriophages

Component Function

Genome Carries the genetic information necessary for replication of new phage particles.

Tail sheath Reacts so that the genome can move from the head into the host cells cytoplasm.

Plate and tail Attach phage to specific receptor sites on the cell wall of a susceptible host bacterium.
fibers

Phages exhibit two different types of life cycle

1. Lytic cycle of bacteriophage

  Also known as virulent cycle.

 Intracellular multiplication of phage results in the lysis of host bacteria, resulting in

release of progeny virions(See figure 2.28: The lytic cycle of phage T4)

 Replication of a virulent bacteriophage.

 Undergoes a lytic cycle to produce new phage particles within a bacterium cell.

 Cell lysis releases new phage particles that can infect more bacteria.

2. Lysogenic cycle

 Infection with every phage does not result in lysis of the host cells (See figure 2.29 of
lysogenic bacteriophage cycle)

 Replication of a temperate bacteriophage.

 Prophage: The integrated phage nucleic acid. It behaves like a segment of the host
chromosome and multiplies synchronously with it. This phenomenon is known as
lysogeny.

 Lysogenic bacterium: The bacterium that carries a Prophage within its genome. Such
phages are called lysogenic or temperate phages.

The differences between lytic and lysogenic cycle

Criteria Lytic cycle Lysogenic cycle

The DNA of the virus Does not integrate into the Integrates into the host DNA.
host DNA.

Host DNA Hydrolyzed Not hydrolyzed

Prophage stage Absent Present

DNA replication of virus Takes place independently Takes place along with the host DNA replication
from the host DNA
replication

Occurs Within a short period of Takes time

time
Symptoms of viral replication Evident Not evident

Genetic recombination in the Not allowed Allowed

host bacterium
Totally undertaken by the Somewhat disturbed by the viral genome
The cellular mechanism of the viral genome
host cell

Common viral diseases in Ethiopia

 Viral disease: Any condition that is caused by a virus.

Table 2.7. Viral diseases

2.6. Normal microbiota

 Normal microbiota: The population of microorganisms routinely found growing on the

body of healthy individuals.

 Resident microbiota: Microbes that typically inhabit body sites for extended periods.

 Transient microbiota: Temporary occupants.

Reasons to acquire knowledge of the normal human microbiota

1. An understanding of the different microorganisms at particular locations provides greater

insight into the possible infections that might result from injury to these body sites.

2. A knowledge of the normal microbiota helps the physician investigator 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 that these normal microbiota play in stimulating the host
immune response can be gained.

The normal human microbiota

 Have protective role from diseases causing microorganisms.

  One of the 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 for attachment.

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 or their growth suppressed, as can
happen during antibiotic treatment, pathogens may colonize and cause disease.

 Example:

 Oral antibiotics can also inhibit members of the normal intestinal microbiota.

 Oral antibiotics allow the overgrowth of toxin-producing strains of Clostridium difficile

that cause antibiotic-associated diarrhea and colitis. (See figure 2.30: Normal microbiota
of the human body).

The Germ Theory of Disease and Koch's Postulates

 In order to prove whether or not diseases are caused by microorganisms, Koch used mice
as experimental animals.

 Koch discovered anthrax bacteria.

Koch's postulates state the following

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 body.

3. The isolated organism must cause the disease when inoculated into healthy susceptible
animals.

4. The organism must be isolated from the newly infected animals and cultured again in the
laboratory, after which it should be seen to be the same as the original organism.

2.7. Modes of disease transmission and ways of prevention

 Microorganisms are transmitted in health care settings by four main routes:

  Contact

 Droplet

 Airborne

 Common vehicle

 Copy table 2.8: Modes of disease transmission, from pages 95-96.

2.8. Uses of microorganisms

 Microorganisms play an important role in food and agriculture.

 Microbiologists exploit microbial activities to produce valuable human products, generate

energy, and clean up the environment.

Uses of microorganisms in agriculture

 Microorganisms (bacteria, fungi, algae, protozoa, and viruses) play an important role in
agriculture.

 They help in organic matter decomposition, and humus formation.

 Nitrogen fixation.

 Phosphate solubilization.

 Potassium mobilization.

 Antagonism towards pathogens, and pests.

 Converting elements into the forms that plants and animals can use.

 To increase the fertility of the soil.

Uses of microorganisms in Sewage treatment

 Anaerobic bacteria are used in wastewater treatment on a normal basis.

 Reducing the volume of sludge and producing methane gas (an alternative energy
source) from it.

 Removing phosphorus from waste water.

Uses of microorganisms in bioremediation

 Bioremediation: A natural process that relies on microorganisms and plants and/or their
derivatives (enzymes or spent biomass) to degrade or alter environmental contaminants.
  To clean-up environmental contaminants.

 To break down/transform pollutants via their inherent metabolic modifications to allow

the pollutant to be channeled into the normal microbial metabolic pathway for
degradation/and biotransformation.

 To degrade, transform or accumulate most of the synthetic compounds such as

hydrocarbons (e.g. oil), polychlorinated biphenyl (PCBs), polyaromatic hydrocarbons
(PAHs), radionuclides and metals.

 To detoxify chemical pollutants.

Uses of microorganisms in food production and processing

 The tart (sharp) 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.

Uses of microorganisms in medicine

Microbial have made it possible to make medicine. E.g. Human insulin

Uses of microorganisms in health

 Microbial perform useful functions for the body. E.g. E. coli-Resides in the intestine and
release components in the digestion of food.

 Microbiota in gut fight against harmful bacteria which cause disease by synthesizing
vitamins like vitamin K and folic acid (drug taken during fetus).

Uses of microorganisms in biotechnology

 Biotechnology: One field which has made use of microorganisms for the drug delivery
in form of vectors and plasmids.

 Generally, microorganisms have a big role in:

 Suppression of soil-borne pathogens

 Recycling

 Increasing availability of plant nutrients

 Degradation of toxicants including pesticides

 Production of antibiotics and other 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.

 Decomposers bacteria are used in recycling substances.

 90% of all living organisms are made up of C, O, N and H.

 Life to continue these substances should be recycled by decomposers.

The carbon cycle

 Carbon travels through food chain.

 Primary producer primary consumer secondary consumer.

 Decomposers use the remains of primary producers and consumers.

Carbon fixation

 A fundamental aspect of carbon cycle.

 Respiration and fermentation involve in processes to release energy ATP and CO2.

 Methanogenesis and Methane Oxidation

 In anaerobic environments, CO2 is used by methanogens.

 Archaea obtain energy by oxidizing hydrogen gas using CO2 as a terminal electron
acceptor, generating methane (CH4).

 Methane is oxidized by ultraviolet light and chemical ions, forming Carbon monoxide
(CO) and CO2.

 Methylotrophs (a group of microorganisms): Use methane as an energy source, oxidizing

it to produce CO2.

 Draw figure 2.37: The carbon cycle, page 104.

The nitrogen cycle

 Root nodules are found on the roots of plants, primarily legumes, which form a symbiosis
with nitrogen-fixing bacteria.
  Draw figure 2.38: The nitrogen cycle, from page 105.

The sulfur cycle

 Sulfur is found in fewer types of organic molecules than nitrogen.

 Found in many proteins.

 Draw figure 2.39: The sulfur cycle, from page 105.

The phosphorus cycle

 Phosphorus (P) occurs in soils as both organic and inorganic forms (Figure 2.40).

 P is releases via mineralization process carried out by microbes.

 Organic P in soils: Not available for plant uptake until the organic materials are
decomposed and the phosphorus released via the mineralization process.

 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 1lb/A.

 It occurs mostly as Al, Fe or calcium compounds.

 Read figure 2.40: The phosphorus cycle, from page 106.

2.9. Controlling microorganisms

 Sterilization: A process by which an article, surface, or medium is freed of all living

microorganisms either in the vegetative or in the spore state.

 Sterile: Any material that has been subjected to sterilizing process.

 Most sterilization is performed with physical agents such as heat.

 A few chemicals called sterilants can be classified as sterilizing agents because of their
ability to destroy spores.

 Germicide/microbicide: Any chemical agent that kills pathogenic microorganisms.

 Used on inanimate (non-living) materials or on living tissue.

 Disinfection: The use of a chemical agent that destroys or removes all pathogenic
organisms or organisms capable of giving rise to infection.
  Destroys vegetative pathogens but not bacterial endospores.

 Used only on inanimate objects because they can be toxic to human and other animal
tissue, when used in higher concentrations.

 It also removes the harmful products of microorganisms (toxins) from materials.

Examples of disinfection

1. Applying a solution of 5% bleach to examining table.

2. Boiling food utensils used by a sick person

3. Immersing thermometers in an isopropyl alcohol solution between uses.

 Antiseptics: Are chemical agents applied directly to the exposed body surfaces.

 It destroys (inhibits) vegetative pathogens from wounds and surgical incisions.

Example of antiseptics

1. Preparing the skin before surgical incisions with iodine compounds

2. Swabbing an open root canal with hydrogen peroxide

3. Ordinary hand washing with a germicidal soap.

 Sanitization: Any cleansing technique that mechanically removes microorganisms

(along with food debris) to reduce the level of contaminants. E.g. soap or detergent.

 Air sanitization with ultraviolet lamps reduces airborne microbes in hospital rooms,
veterinary clinics, and laboratory installations.

 Preservation: A general term for measures taken to prevent microbe capsid spoilage of
susceptible products (pharmaceuticals, foods).

 Decontamination: The removal or count reduction of microorganisms containing an

object.

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: The antimicrobial treatment used for foods in liquid form (milk).

 Low temperature pasteurization: 61.5 °C, 30 minutes; 71d.c, 15 seconds.

 High temperature pasteurization: Brief (seconds) of exposure to 80-85 d.c in continuous

operation.

 Uperization: Heating to 150 °C for 2.5 seconds in a pressurized container using steam
injection.

 Disinfection: Application of temperatures below what would be required for sterilization.

Importance of disinfection

 Boiling medical instruments, needles, syringes, etc.

 Not constitute sterilization

 Many bacterial spores are not killed by this method.

 Dry heat sterilization

 Flaming: Carried out by holding them in the flame of the Bunsen burner till they become
red hot.

 E.g. Sterilization of inoculating loop or wire, the tip of forceps, searing spatulas, etc.

 Incineration: An excellent method for safely destroying infective materials by burning

them to ashes.

Uses of incineration

 To destroy hospital and lab wastes.

 For complete destruction and disposal of infectious materials, such as syringes, needles,
culture materials, dressings, bandages, bedding, animal carcasses, and pathology samples.

 Fast and effective for most hospital wastes, but not for metals and heat-resistant glass
materials.

 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 moist heat
sterilization.

 121 °C 15 minutes, one atmosphere of pressure (total: 202kpa).

 134 °C 3 minutes, two atmosphere of pressure (total: 303kpa).

 Intermittent sterilization (Tyndallization): A process of sterilizing certain heat-labile

substances (e.g. Serum, sugar, egg, etc) that cannot withstand the high temperature of the
autoclave.

 Carried out over a period of 3 days and requires a chamber to hold the materials and a
reservoir for boiling water.

 The items to be sterilized are kept in the chamber and are exposed to free-flowing steam
at 100 °C for 20 minutes, for each of the 3 consecutive days.

2.10. Bacterial Isolation Techniques

 Microorganisms (bacteria or fungi) 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 (See fig. 2.41).

 Microorganisms 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.

2.11. Renowned Microbiologists in Ethiopia

 Activity 2.10: Search for, study the works of a renowned microbiologist/ Parasitologist in
Ethiopia, and evaluate the contribution of his/her research to the world of science.