chapter 1science of microbiology

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CHAPTER 1

THE SCIENCE OF MICROBIOLOGY

Microbiology- the study of microorganisms.

* effects to living organisms

* characteristics of microbes-microorganisms

( pathogenic, non pathogenic)

-microscopes- microbiologists



Relevance of studying microbiology:

1. Microorganisms in the living body.

* indigenous microflora

Micrococcus of the SkinLactobacillus



2. Some Microorganisms colonize the host.

* opportunistic pathogens

Escherichia coli Streptoccus pneumoniaStaphylococcus aureus



3. Microorganisms are essential for somelife’s processes.

4. Microorganisms are involved in thedecomposition processes.

* saprophytes

Rhizobium bacteria for bean plants



5. Microorganisms in the industry

- bioremediation

Example:Bioremediation of Petroleum

Pollutants in Cold Environments

Process:a. Bioaugmentation

b. Biostimulation

- genetic engineering



Colonies of E. coli

Genetic

Engineering



6. Some microorganisms are useful in someof the environmental processes

- nitrogen cycle



Nitrogen fixing bacteria nodules Nitrogen fixing bacteria



7. Algae and bacteria serve as food for tinyanimals.

8. Many microorganisms are essential in foodand beverage industries.

9. Certain bacteria are used in drug

production (antibiotics)



10. Microbes are used in cell model.

11. Microbiology and the diseases.

- infectious diseases- microbial intoxication

Fungi: Aspergillus

Alternaria Penicillium

Chaetomium Rhizopu s

Bacteria: Clostridium botulinum Bacillus cereus

Vibrio cholera



Specializations of Microbiology:

1. Bacteriology- bacteriologists (bacteria)

2. Phycology- Phycologists (algae)3. Mycology- Mycologists (fungi)

4. Virology-Virologists (virus)

Disciplines of Microbiology:

1. Agriculutural Microbiology-beneficial andharmful roles of microbes

-soil formation and fertility

- Carbon, Nitrogen, Phosphorus and Sulfurcycles



-diseases of plants

- digestive processes of cows and other

ruminants- production of crops and foods

2.Biotechnology ( Industrial Microbiology)

- The exploitation of microbes for use inindustrial processes.

*Biopolymers

* Bioremediation

*Waste Biotreatment* fermentation



3. Medical microbiology-The study of thepathogenic microbes and the role of

microbes in human illness.* Epidemiology

* Transmission of diseases

* Treatment of infectious diseases* Disease prevention measures

* Aseptic techniques

* Immunology* Production of drugs



4. Microbial Physiology-The study of howthe microbial cell functions bio-chemically.

* Microbial growth* Microbial metabolism

* Microbial cell structure

5. Veterinary Microbiology- The role ofmicrobes in veterinary medicine or animaltaxonomy.

6. Paleomicrobiology- the study of ancientmicrobes.



7. Parasitology- study of microorganims thatlive on or in another living organisms.

Categories of parasites:* Parasitic protozoa

* Helminths (Parasitic worms)

* Arthropods ( Parasitic insects)8. Sanitary Microbiology- processing and

disposal of garbage and sewage wastes.

* inspects food processing installationsand eating establishments



History of Microbiology:

- Contributions to

*Microscopy1677: Anton von Leeuwenhoek

― Father of Microbiology

― Father of Bacteriology‖ -Observed "little animals―

1882: Paul Ehrlich-Developed acid-fast Stain

1884: Christian Gram-DevelopedGram Stain



*Culture Methods

1882: Robert Koch-Growth of Bacteria on solid

media

-First proof of Germ Theory ofDisease

1887: R. J. Petri-Invented Petri Dish



*Germ Theory of Disease1860: Louis Pasteur

– disproved the theory ofspontaneous generation.-designed method for foodpreservations ( pasteurization)

a.63- 65 degree centigrade for 30minutes

b. 73-75 degree centigrade for 15

seconds- states that specific

microorganisms cause specific diseases.



1867: Joseph Lister – madecontributions on antiseptic.

1876: Robert Koch- developed methods of

fixing, staining and photographing bacteria

- developed methods ofcultivating bacteria in solid media

- discovered Mycobacterium

tuberculosis- work in tuberculin( protein

from MT) used for skin testing

K h P t l t



Koch Postulates:

1.The microorganism must be found in abundancein all organisms suffering from the disease, but

should not be found in healthy animals.2.The microorganism must be isolated from a

diseased organism and grown in pure culture.

3.The cultured microorganism should causedisease when introduced into a healthy organism.

4.The microorganism must be re-isolated from theinoculated, diseased experimental host andidentified as being identical to the originalspecific causative agent



*Defense or Control of Microbes1796: Edward Jenner -First scientific

Small pox vaccination1850: Ignaz Semmelweis-Advocatedwashing hands to stop the spread ofdisease

1900 :Walter Reed-Proved mosquitoescarried the yellow fever agent

1910 :Paul Ehrlich- Discovered cure for

syphilis1928 :Alexander Fleming-Discovered

Penicillin



*Virology

1892:Dmitri Iosifovich Ivanovski

-Discovered viruses

1899:Martinus Beijerinck

-Recognized viral dependenceon cells for reproduction



CHAPTER II

MICROSCOPY

Microscopy- the study of microscopes

- the use of microscopes

Microscopes-A microscope is an instrumentthat enables one to observe objects toosmall to be seen clearly by the naked eye. T



Types of Microscopes:

1. The light microscope

a. Compound Microscopeb. Dark-Field Microscope

c. Phase-Contrast Microscope

2. The fluorescent microscope-usesultraviolet light as its light source

-When ultraviolet light hits an object, it

excites the electrons of the object, andthey give off light in various shades ofcolor.



Compound Microscope



3. Electron microscope- The energy sourceused in this instrument is a beam ofelectrons.

-Viruses and some large molecules can beseen with this instrument.*transmission electron microscope

- To use this instrument, one places ultrathin slices of microorganisms or viruses on awire grid and then stains them with gold or

palladium before viewing. The denselycoated parts of the specimen deflect theelectron beam, and both dark and lightareas show up on the image.



4. Scanning electron microscope (SEM)

- the more contemporary form electron

microscope.-Although this microscope gives lower

magnifications than the TEM, the SEM

permits three-dimensional views ofmicroorganisms and other objects.

-Whole objects are used, and gold or

palladium staining is employed.



ELECTRON MICROSCOPE

TEM SEM



Bacterial Flagella



Criteria Gram Positive Gram Negative1. Number ofbasal body rings

2 rings 4 rings

2. Type of basalbody rings

*P ring-peptidoglycan

* M ring-PlasmaMembrane

*P ring*L ring

*S ring

*M ring

Comparison of Bacterial Flagella

Cl ifi ti f b t i di t th



Classification of bacterium according to thenumber of flagellum‖

a. monotrichous bacterium

b. amphitrichous bacteriumc. lophotrichous bacteriumd. peritrichous bacterium

2 Th ll ll d ll b



2.The cell wall and cell membrane- With the exception of mycoplasmas, all

bacteria have a semirigid cell wall.-The chief component of the prokaryotic

cell wall is peptidoglycan, a large polymercomposed of N-acetylglucosamine and N-

acetylmuramic acid.-Gram-positive bacteria have more

peptidoglycan in their cell wall, which may

account for their ability to retain the stainin the Gram stain procedure.-Gram-negative bacteria have more lipids

in their cell wall.



Bacillus

Listeria

Staphylococcus

Streptococcus

Enterococcus

Clostridium

Escherichia coli

Salmonella

Shigella

Enterobacteriaceae

Pseudomonas

Moraxella

Helicobacter



Pseudomonas aeruginosa Bacillus anthracis



3.The cytoplasm

-contains ribosomes and various other

granules used by the organism. The DNA iscontained in the nuclear region (thenucleoid) and has no histone protein to

support it. Prokaryotic cells have in theircytoplasm a single, looped chromosome, aswell as numerous small loops of DNA calledplasmids. Genetic information in theplasmids is apparently not essential for thecontinued survival of the organism.



4. Pili

-are used for attachments to surfaces such

as tissues.- Many pathogens possess pili, which arecomposed of the protein pilin. Certain pili,

known as conjugation pili, unite prokaryoticcells to one another and permit the passageof DNA between the cells.

*Fimbriae-often used for the attachmentpili.



Schematic drawing of bacterial conjugation:

1- Donor cell produces pilus.2- Pilus attaches to recipient cell, brings the two cells together.

3-The mobile plasmid is nicked and a single strand of DNA is thentransferred to the recipient cell.

4- Both cells recircularize their plasmids, synthesize second strands,

and reproduce pili; both cells are now viable donors.



5. The glycocalyx

-composed of a thick, gummy material,

serves as a reservoir for nutrients andprotects the organism from changes in theenvironment.

- When the glycocalyx is a tightly boundstructure, it is known as a capsule. When itis a poorly bound structure that flows

easily, it is known as a slime layer.



Reproduction of Prokaryotic cell

-Bacteria and archaea reproduce through

asexual reproduction, usually by:a. Binary fission

-This process results in the reproduction

of a living prokaryotic cell by division intotwo parts which each have the potential togrow to the size of the original cell.

b. Budding-is the formation of a new organism by theprotrusion of part of another organism.



Binary Fission Budding

H P ER 1V



CHAPTER 1VDIVERSITY OF MICROORGANISMS

1. Bacteria (monera)- make up the largest group ofmicroorganisms.

-Bacterial cells are about one tenth the sizeof eukaryotic cells and are typically 0.5–5.0 micrometres in length.-Bacteria multiply by binary fission or celldivision. Bacteria double every 1/2 hour at90° F, 1hour at 70° F, 2 hours at 60° F, 6hours at 40° F, 20hours at 32° F, 60 hours at

28° F.



Classification of Bacteria according to:

A. Requirement of oxygen

• Some grow only in the presence of oxygen(aerobes)

• Others grow only in the absence of oxygen

(anaerobes).• Some are able to grow with or without

oxygen

• (facultative anaerobes).



B. Shape

Most bacterial species are either:

1.spherical, called cocci (sing . coccus, fromGreek kókkos , grain, seed)

2.rod-shaped, called bacilli (sing . bacillus,

from Latin baculus , stick).3.vibrio, are slightly curved or comma-shaped;

4.spiral-shaped, called spirilla5.tightly coiled, called spirochaetes.



Different shape and arrangement of Bacteria

P f



C. Pattern of arrangement

1.Many bacterial species exist simply as

single cells, others associate incharacteristic patterns:

2.Neisseria form diploids (pairs),

3.Strepto- form chains,4. Staphylo group together in "bunch of

grapes" clusters.

D N



D. Nutrition:

1.heterotrophic, living off other

organisms.a. Saprophytic

b. Parasitic

2. Autotrophica. photosynthetic bacteria -include

the green and purple bacteria and the

cyanobacteria.b.chemosynthetic autotrophs

-thermophilic archaebacteria

2 Vi s (f m th L tin i s m nin t xi



2. Virus-(from the Latin virus meaning toxinor poison )

-is a sub-microscopic infectious agentthat is unable to grow or reproduceoutside a host cell.

-Viruses infect all cellular life.-The first known virus, tobacco mosaic

virus, was discovered by Martinus

Beijerinck in 1898,and now more than5,000 types of virus have been described.



AH1N1 virus

Hemagglutinin (H) and Neuraminidase (N)

Viruses consist of two or three parts:



-Viruses consist of two or three parts:

a. genes made from either DNA orRNA, long molecules that carry geneticinformation;

b. all have a protein coat that protectsthese genes;

c. and some have an envelope of fatthat surrounds them when they are outside acell.

-Viruses vary in shape from simple helical andicosahedral shapes, to more complexstructures. They are about 100 times smallerthan bacteria



Bacteriophage Rotavirus Influenza virus

Origin of viruses:



Origin of viruses:1. Regressive theory:

- Viruses may have once been small cellsthat parasitized larger cells. Over time,genes not required by their parasitismwere lost. The bacteria rickettsia and

chlamydia are living cells that, like viruses,can reproduce only inside host cells. Theylend credence to this theory, as theirdependence on parasitism is likely to havecaused the loss of genes that enabledthem to survive outside a cell. This is alsocalled the degeneracy theory .

2 Cellular origin theory (sometimes called the



2. Cellular origin theory (sometimes called thevagrancy theory )

- Some viruses may have evolved from bits of

DNA or RNA that "escaped" from the genes of alarger organism. The escaped DNA could havecome from plasmids (pieces of naked DNA thatcan move between cells) or transposons

(molecules of DNA that replicate and movearound to different positions within the genes ofthe cell).

-Once called "jumping genes", transposons

are examples of mobile genetic elements andcould be the origin of some viruses. They werediscovered in maize by Barbara McClintock in1950

3. Coevolution theory:Vi h l d f l



-Viruses may have evolved from complexmolecules of protein and nucleic acid at the sametime as cells first appeared on earth and would

have been dependent on cellular life for manymillions of years.-Viroids are molecules of RNA that are not

classified as viruses because they lack a proteincoat. However, they have characteristics that arecommon to several viruses and are often calledsubviral agents. Viroids are important pathogensof plants. They do not code for proteins butinteract with the host cell and use the host

machinery for their replication. The hepatitisdelta virus of humans has an RNA genome similarto viroids but has protein coat derived fromhepatitis B virus and cannot produce one of itsown. It is therefore a defective virus and cannot

replicate without the help of hepatitis B virus.



Helical shaped virus

Icosahedral shaped virus

Replication of Viruses:



Replication of VirusesThe life cycle of viruses differs greatly betweenspecies but there are six basic stages in the life

cycle of viruses:1.Attachment-is a specific binding between viralcapsid proteins and specific receptors on thehost cellular surface. This specificitydetermines the host range of a virus.

-For example, HIV infects only human T cells,because its surface protein, gp120, can interactwith CD4 and receptors on the T cell's surface.This mechanism has evolved to favour those

viruses that only infect cells in which they arecapable of replication. Attachment to thereceptor can induce the viral-envelope protein toundergo changes that results in the fusion ofviral and cellular membranes.

2 Penetration -viruses enter the host cell



2. Penetration viruses enter the host cellthrough receptor mediated endocytosis ormembrane fusion. This is often called viral entry.

The infection of plant cells is different to thatof animal cells. Plants have a rigid cell wall madeof cellulose and viruses can only get inside thecells following trauma to the cell wall. Viruses

such as tobacco mosaic virus can also movedirectly in plants, from cell-to-cell, throughpores called plasmodesmata Bacteria, like plants,have strong cell walls that a virus must breachto infect the cell. Some viruses have evolvedmechanisms that inject their genome into thebacterial cell while the viral capsid remainsoutside

3.Uncoating -a process in which the viral capsid is



3.Uncoating a process in which the viral capsid isdegraded by viral enzymes or host enzymes thusreleasing the viral genomic nucleic acid.

4.Replication -involves synthesis of viral messengerRNA (mRNA) for viruses except positive senseRNA viruses (see above), viral protein synthesisand assembly of viral proteins and viral genomereplication.

5. Assembly of the virus particles, post-translationalmodification of the viral proteins often occurs. In

viruses such as HIV, this modification, (sometimescalled maturation), occurs after the virus has beenreleased from the host cell.

6 Viruses are released from the host cell by



6.Viruses are released from the host cell bylysis—a process that kills the cell bybursting its membrane. Enveloped viruses(e.g., HIV) typically are released from thehost cell by budding. During this process thevirus acquires its envelope, which is a

modified piece of the host's plasmamembrane



6.Other groups consist of single-celled



6.Other groups consist of single celledorganisms in which each cell has hundreds orthousands of nuclei.

7.Still others consist of multicellularorganisms that have one or two nuclei percell.

8.The bodies of multicellular fungi usuallyconsist of slender, cottony filaments calledhyphae. A mass of hyphae is called a

mycelium. The mycelium carries on all thelife-maintaining processes of the organism,including sexual reproduction.

Major Groups of Fungi:



j p g1.Conjugating Fungi

-There are about 600 species ofconjugating fungi. Most species are land-based and feed on organic matter, althoughthere are a few parasitic species. The

algaelike conjugating fungi have a continuousmycelium containing hundreds or thousandsof nuclei, with no divisions between them.Species of conjugating fungi cause potato

blight, downy mildew, black bread mold, andwater mold (which affects dead leaves andsticks in water).



Conjugating Fungi

Pilobolaceae Spinellus Piptocephalis

2. Sac Fungi



g-Sac fungi are so-named because many

species in this group reproduce sexually by

forming a spore-filled structure called anascus, which means literally "a sac." Thislarge group of fungi includes many species

that are beneficial to humans. For example, yeasts are a major group of sac fungi.Different yeasts are used by bakers,brewers, and vintners to make their bread,

beer, or wine. Truffles, regarded as a fooddelicacy, are underground sac fungi thatgrow in association with tree roots.



3. Club fungi



g

-species reproduce sexually by forming sporeson top of club-shaped structures called basidia.

The club fungi are believed to be closely relatedto the sac fungi. This large group includes speciesthat are known as mushrooms, toadstools,earthstars, stinkhorns, puffballs, jelly fungi, coralfungi, and many other interesting names. Somespecies, such as the rusts and smuts, causedisease in agricultural grains. Other species, such

as the fly agaric, produce chemical hallucinogens(chemicals that induce visions) and have been usedby numerous cultures in their religious ceremonies.



Club Fungi

Basidiocarp Basidiocarp

4. Imperfect Fungi



p g

-Mycologists have never observed the

sexual reproduction of fungi in theimperfect fungi group. Since this part oftheir life cycle is missing, they are referredto as imperfect fungi. These fungi may have

lost their sexual phase through the courseof evolution. Species in this group produceplant and animal diseases. Athlete's foot

and ringworm in humans are caused byimperfect fungi.



Imperfect Fungi

Aspergillus Deuteromycetes

4.Protozoa



Characteristics:

-usually range from 10–50 μm, but cangrow up to 1 mm.

-exist throughout aqueous environments

and soil, occupying a range of trophic levels.-absorb food via their cell membranes,some, e.g. amoebas, surround food and

engulf it, and yet others have openings or"mouth pores" into which they sweep food.-All protozoa digest their food in

stomach-likes compartments called vacuoles.

Sub-groups



g p

Protozoa have traditionally been divided on

the basis of their means of locomotion,although this character is no longer believedto represent genuine relationships:

1.Flagellates (e.g. Giardia lamblia )

2.Amoeboids (e.g. Entamoeba histolytica )

3.Sporozoans (e.g. Plasmodium knowlesi )

4. Ciliates (e.g. Balantidium coli )

5. Algae



g

-(Latin "seaweeds", singular Alga) are a

large and diverse group of simple, typicallyautotrophic organisms, ranging fromunicellular to multicellular forms.

-The largest and most complex marineforms are called seaweeds. They arephotosynthetic, like plants, and "simple"because they lack the many distinct organs

found in land plants.



1. Green algae



g-form the phylum Chlorophyta and are namedfor their green chloroplasts, which are similar

in composition to the chloroplasts found in landplants.

-Green algae range in shape from unicellular

plankton that grow in lakes and oceans tocolonial filaments of pond scum to leaflikeseaweeds that grow along rocky and sandyintertidal areas. Some green algae also live on

tree trunks and soil.-Several green algal species are symbiotic,forming lichens with fungi or living with corals.

2.Red algaef h h l h d h h l



-form the phylum Rhodophyta with approximately500 genera and 6000 species.

-Found in warm coastal waters and in water asdeep as 260 m (850 ft), red algae species adapt tovaried water depths by having differentproportions of pigments. Their red color is due to

a red pigment, phycoerythrin , which is well suitedto absorb the blue light that penetrates deeperinto water than the other colors of light.-Most red algae are multicellular .

-Unlike most other eukaryotic algae, red algaehave no flagella.-Red algae use diverse strategies to reproduce,including fragmentation and spore production.

3.Golden-brown algae, brown algae, and



g gdiatoms

-form the large and complex phylumHeterokontophyta ,

-with organisms ranging in size from afraction of a millimeter to more than 100 m(300 ft) long.

-Heterokontophyta have carotenoidsecondary pigments that tend to mask thegreen of the primary chlorophyll pigment,giving them a golden or golden-brownappearance.

4. Dinoflagellates



-from the phylum Dinoflagellata

- mostly unicellular organisms that may becovered with stiff cellulose plates thatresemble armored helmets.

-Many species have unusual ornamentation,such as horns, spines, or wings.

chapter 1science of microbiology

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