Introduction to Microbiology 1

CHAPTER 1

INTRODUCTION TO MICROBIOLOGY

Microbiology is simply means the study of microorganisms. The word microbiology derives from the
Greek micros meaning small and bios meaning life and logos meaning study, for it examines organisms
too small to be visible to the naked eye. Parasitology comes from the Greek words para, with, and site,
food and logos, that is, dealing with living beings inhabiting another living organism (host) from which
they obtain their food.

The History and Scope of Microbiology

Microbiology has had a long, rich history, initially centered in the causes of infectious diseases but now
including practical applications of the science. Many individuals have made significant contributions to
the development of microbiology.
➢ Discovery of microorganisms
• Robert Hooke – 1665, discovered the cell using a piece of cork; reputed to have
observed strands of fungi among the specimens of cells he viewed
• Anton Van Leeuwenhoek – 1673-1723, Dutch merchant discovered live microorganisms
(animacules); regarded as one of the first to provide accurate descriptions of protozoa,
fungi, and bacteria.
➢ Debate over spontaneous generation
Spontaneous generation- believed that some forms of life could arise spontaneously from non
living matter. The belief in the spontaneous generation of life from nonliving matter was introduced by
Aristotle, who lived around 350 BC. According to Aristotle, it was: “readily observable that aphids arise
from the dew which falls on plants, fleas from putrid matter, mice from dirty hay.” This belief remained
unchallenged for more than 2000 years.
• Francesco Redi – 1668, a strong opponent of spontaneous generation, Redi’s experiment were a
serious blow to the long-held belief that fly maggots do not arise from decaying meat (as others
believed) if the meat is covered it prevents the entry of flies.
• John Needham – 1745, agrees on the spontaneous generation of microorganisms, and observed
the formation of microorganisms after boiling meat.
• Lazzaro Spallanzani- microorganisms from the air might entered Needham’s experiment; by
showing that covered boiled broth would not give rise to microscopic forms of life.
• Laurent Lavoisier – showed the importance of oxygen, Lavoisier’s experiments demonstrated
when something burned, it actually absorbed something from the air, instead of releasing
anything. He later named the ‘something’ from the air as oxygen, when he found that it
combined with other chemicals to form acid.
• Rudolf Virchow – 1858, Theory of Biogenesis

➢ Other Discoveries
• Edward Jenner – 1798, introduced the vaccine – “vacca”, vaccine for small pox, using cow
pox
• Agostino Bassi preceded Louis Pasteur in the discovery that microorganisms can be the
cause of disease (the germ theory of disease). He discovered that the muscardine disease
of silkworms was caused by a living, very small, parasitic organism, a fungus that would be
named eventually Beauveria bassiana in his honor. In 1844, he stated the idea that not only
insect but also human diseases are caused by other living microorganisms; for
example, measles, syphilis, and the plague.
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➢ Golden age of microbiology

▪ Louis Pasteur – discovered that microorganisms called yeast convert sugars to alcohol in the
absence of air- fermentation
• Souring and spoilage of wine and dairy products : bacteria – pasteurization
• Establishment of microbiology as a science
• 1861, demonstrated that microorganisms are present in the air and can contaminate
sterile solutions, but air itself does not create microbes ; formed the basis of aseptic
techniques.
• disprove spontaneous generation to sustain his theory, and he therefore devised a
series of swan-necked flasks filled with broth. He left the flasks of broth open to the
air, but the flasks had a curve in the neck so that microorganisms would fall into the
neck, not the broth
• encouraged the belief that microorganisms were in the air and could cause disease.
Pasteur postulated the germ theory of disease, which states that microorganisms
are the cause of infectious disease.
▪ Robert Koch – isolated Bacillus anthracis, spore forming bacteria
• isolated the bacteria from cow, the causative agent of Anthrax.
• postulate – specific microorganisms cause specific diseases, provided the proof by
cultivating anthrax bacteria apart from any other type of organism. He then injected
pure cultures of the bacilli into mice and showed that the bacilli invariably caused
anthrax. The procedures used by Koch came to be known as Koch's postulates. They
provided a set of principles whereby other microorganisms could be related to other
diseases.
• “Germ theory of disease” – a particular disease is caused by specific bacteria or
microorganisms.
• Cultured tuberculosis bacteria
▪ Joseph Lister- discovered that phenol or carbolic acid can kill bacteria

➢ Birth of modern therapy

• After the relationship between microorganisms and disease was established, next
focused of study is search for substances that can destroy pathogenic organisms.
• Chemotherapy : Synthetic drugs : First synthetic drug was—Paul Ehrlich --“salvarsan”,
an arsenic derivatives effective against syphilis ; developed theories on immunity
• Quinine- malaria
• Sulfonamides
• Antibiotics : Alexander Fleming – penicillin – Penicillium notatum
• Rene Dubos – 1939, gramicidin and tyrocidine – Bacillus brevis

Modern Developments in Microbiology

▪ Development of branches of microbiology : bacteriology, mycology, parasitology,
immunology, and virology
▪ Heide Schulz – 1997, discovered large bacterium :Thiomargarita namibiensis
▪ Genomics
▪ Recombinant DNA Technology or genetic engineering – manufacture of human
hormones - Paul Berg
▪ microbial genetics/molecular biology
▪ Hans A. Kreb – 1953, developed chemical steps of the kreb cycle in carbohydrate
metabolism

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▪ James Watson and Francis Crick – identified the physical structure of DNA : helical DNA
and replication

In the 1940s, the electron microscope was developed and perfected. In that decade, cultivation
methods for viruses were also introduced, and the knowledge of viruses developed rapidly. With the
development of vaccines in the 1950s and 1960s, such viral diseases as polio, measles, mumps, and
rubella came under control.

Microorganism
Microorganisms are minute living things that have impacts in our daily life. They live on and in
us, they are ubiquitous meaning they are found everywhere. Microorganisms are a collection of
organisms that share the characteristic of being visible only with a microscope. They constitute the
subject matter of Microbiology. Members of the microbial world are very diverse and include the
bacteria, cyanobacteria, archaea, fungi, unicellular algae, protozoa, and viruses. Although very small
they play an important significant role in our life as well as the environment. They are necessary in many
industries, as source materials for drugs and food products. They are even used to clean up waste
(bioremediation) and for genetic engineering and gene therapy. The majority of microorganisms
contribute to the quality of human life by doing such things as maintaining the balance of chemical
elements in the natural environment, by breaking down the remains of all that dies, and by recycling
carbon, nitrogen, sulfur, phosphorus, and other elements.

Some species of microorganisms cause infectious diseases. They overwhelm body systems by
sheer force of numbers, or they produce powerful toxins that interfere with body physiology. Viruses
inflict damage by replicating within tissue cells, thereby causing tissue degeneration.

Types of microorganisms

Bacteria
▪ unicellular organisms whose genetic material is not enclosed in nuclear membrane (prokaryotic)
▪ cells appear in several shapes: rodlike (Bacillus), spherical or ovoid (Coccus), and spiral
(corkscrew or curved)
▪ may form pairs, chains, cluster or other grouping
▪ enclosed in cell walls that are largely composed of a substance called peptidoglycan
▪ reproduce by binary fission
▪ most bacteria use organic material both from dead or living organisms
▪ some can make their own food
▪ some can derived food from inorganic material
▪ flagella
▪ exist in most environments on earth. For instance, they live at temperatures ranging from 0° to
100°C and in conditions that are oxygen rich or oxygen free. A microscope is necessary to see
and study them.
Archaea
▪ often found in an extreme environment
▪ methanogens
▪ halophiles
▪ thermophiles
▪ prokaryotic cell but wall does not have peptidolgycan

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Fungi
▪ eukaryotic organisms : unicellular or multicellular
▪ true fungi have cell walls composed of chitin
▪ large multicellular fungi : mushroom
▪ unicellular fungi : yeasts are slightly larger than bacteria and are used in alcoholic fermentations
and bread making. Certain yeasts such as Candida albicans are pathogenic (disease causing).
▪ Molds are filamentous, branched fungi that use spores for reproduction.
▪ prefer acidic environments, and most live at room temperature under oxygen-rich conditions.
▪ most typical fungi : molds
▪ reproduce sexually or asexually
▪ obtain nourishment by absorbing organic material from their environment
Protozoa
▪ unicellular eukaryotic microbes
▪ move by pseudopods, flagella, or cilia
▪ have variety of shapes
▪ live as either free entities or as parasites
▪ reproduce sexually or asexually
▪ exist in an infinite variety of shapes because they have no cell walls. Many species cause such
human diseases as malaria, sleeping sickness, dysentery, and toxoplasmosis. Slime molds,
amoebas, flagellates, ciliates.
Algae
▪ photosynthetic eukaryotic ; a variety of plantlike organisms
▪ variety of shape
▪ reproduce sexually or asexually
▪ abundant in fresh and salt water, soil, and in association with plants
▪ many algae have cellulose/call wall
▪ Examples are the diatoms and dinoflagellates that inhabit the oceans and are found at the bases
of marine food chains
Viruses
▪ ultramicroscopic bits of genetic material (DNA or RNA) enclosed in a protein shell and,
sometimes, a membranous envelope that can be seen only by electron microscope
▪ have no metabolism; therefore, it is difficult to use drugs to interfere with their structures or
activities.
▪ multiply in living cells and use the chemical machinery of the cells for their own purpose. Often,
they destroy the cells in the process of replicating
▪ acellular
Multi-cellular animal parasites
▪ they are not strictly microorganisms but of medical importance
▪ helminthes
▪ some stages of their life they are microscopic

SIGNIFICANCE OF MICROORGANISMS
-Modern microbiology reaches into many fields of human endeavor:
Microbes and Human Welfare
• indigenous microflora
• opportunistic pathogens
• decomposers

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• development of pharmaceutical products, the use of quality-control methods in food and dairy
product production, including fermented dairy products (sour cream, yogurt, and buttermilk), as
well as other fermented foods such as pickles, sauerkraut, breads, and alcoholic beverages.
• the control of disease-causing microorganisms in consumable waters, and the industrial
applications of microorganisms.
▪ used to produce vitamins, amino acids, enzymes, and growth supplements.
▪ One of the major areas of applied microbiology is biotechnology. In this discipline,
microorganisms are used as living factories to produce pharmaceuticals product. These
substances include the human hormone insulin, the antiviral substance interferon, numerous
blood-clotting factors and clot dissolving enzymes, and a number of vaccines : Modern
Biotechnology and Genetic Engineering/Gene therapy
▪ Bacteria can be reengineered to increase plant resistance to insects : Insect pest control
▪ sewage treatment
▪ Bioremediations – some bacteria being utilize to clean the environment ;
▪ recycling vital elements: decomposition
o fix atmospheric nitrogen to be used by the plants (nitrogen cycle)
o involve in oxygen/carbon dioxide cycle through photosynthesis and
chemosynthesis
▪ Maintain the normal flora of the vaginal environment
▪ Helps in the digestion of food : E. coli

Microbes and Human Disease

▪ cause spoilage of food
▪ emerging infectious diseases: mad cow disease (1988); bloody diarrhea (E.coli O157:H7, 1982);
Ebola Hemorrhagic fever ; Streptococcus-IGAS ; SARS ; AIDS ; DENGUE fever

THE SPECTRUM OF MICROBIOLOGY

Taxonomy – science of classifying living organisms. Its objective is to establish the relationship
between one group of organisms and another and to differentiate between them. It provides a common
reference for identifying organisms and universal language of communication among scientist.
Taxonomy displays the unity and diversity among living things, including microorganisms.
Among the first taxonomists was Carolus Linnaeus. In the 1750s and 1760s, Linnaeus classified
all known plants and animals of that period and set down the rules for nomenclature. Organisms are
arranged into taxonomic categories (taxon) that is to show degrees of similarities among organisms.
Systematics of phylogeny is the study of the evolutionary history of a group of organisms

Classification Schemes
Species - For organisms such as animals and plants, a species is defined as a population of individuals
that breed among themselves. For microorganisms, a species is defined as a group of organisms that are
70 percent similar from a biochemical standpoint.
Genus - In the classification scheme, various species are grouped together to form genus
Among the bacteria, for example, the species Shigella boydii and Shigella flexneriare in the
genus Shigella because the organisms are at least 70 percent similar.
Family - Various genera are then grouped because of similarities as family
Order - various families are placed together in an order.
Class - a number of orders are grouped as a class,
Phylum or division - several classes are categorized in a single phylum or division.
Kingdom - various phyla or divisions are placed in the broadest classification entry, the kingdom.

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• Aristotle : plant and animals

• 1857 Carl von Nageli : proposed that bacteria and fungi be placed in plant
kingdom
• 1866 Ernst Haeckel : proposed Kingdom Protista : bacteria, protozoa, algae, and
fungi.
• 1959 Fungi were placed in their own kingdom
• 1937 Edward Chatton introduced the word prokaryote: cells having no nucleus
• 1961 Roger Stanier defined prokaryote as cells in which nuclear material is not
surrounded by nuclear membrane
• 1968 Robert Murray proposed the kingdom prokaryote
• 1969 Robert H. Whittaker founded the five kingdom system in which prokaryotes
were placed in the Kingdom Prokaryote or Monera

In writing the binomial name, the first letter of the genus name is capitalized, and the remainder
of the genus name and the complete species modifier are written in lowercase letters. The entire
binomial name is either italicized or underlined. It can be abbreviated by using the first letter of the
genus name and the full species modifier. An example of a microbial name is Escherichia coli, the
bacterial rod found in the human intestine. The name is abbreviated E. coli.
Numerous criteria are used in establishing a species and in placing species together in broader
classification categories. Morphology (form) and structure are considered, as well as cellular features,
biochemical properties, and genetic characteristics. In addition, the antibodies that an organism elicits in
the human body are a defining property. The nutritional format is considered, as are staining
characteristics.

WHITTAKERS CLASSIFICATION: Five Kingdom

The five kingdoms. The generally accepted classification of living things was devised by Robert
Whittaker of Cornell University in 1969. Whittaker suggested a five-kingdom classification.

Kingdom Plantae are mostly multicellular, autotrophic, and eukaryotic organism.

Kingdom Animalia are eukaryotic multicellular, heterotrophs with embryonic development organisms.
They do not have cell wall and plastids.
Kingdom Fungi are eukaryotic organism called Thallophytes, they are soft bodied and lacks chloroplast
and non photosynthetic. They are saprophytic or parasitic.
Kingdom Protista are eukaryotic organism which are mostly unicellular, though some are colonial. They
possess animal like and plant like characteristics.
Kingdom Monera are bacteria, they are unicellular organism and has a prokaryotic type of cell.

THE THREE DOMAINS

In 1978, Carl R. Woese proposed elevating the three cell types to a level above kingdom, called
domain. Bacteria, Archaea, and Eukarya.
Basis : ribosomes are not the same in all cells, comparing the nucleotides in ribosomal RNA
shows that there are three distinct different cell group. They also differ in membrane lipid structure,
transfer RNA molecules and sensitivity to antibiotics
The oldest known fossils are the remains of prokaryotes that lived more than 3.5 billions years
ago. Eukaryotic cells evolved more recently about 1.4 billions years ago. According to endosymbiotic
theory, eukaryotic cells evolved from prokaryotic cells living inside one another as endosymbionts.

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Evolution of eukaryotes - endosymbiotic theory

Prokaryotic cell Eukaryotic cell Mitochondria/chloroplast

Circular DNA Linear DNA Circular DNA
No histones w/ histones No histones
Ribosomes 70S 80S 70S

The Three Domains

Archaea Bacteria Eukarya
Cell type Prokaryotic prokaryotic Eukaryotic
Members Methanogens, extreme Pathogenic and non Plant, protista, fungi
halophiles, pathogenic bacteria and animalia
hyperthermophiles fond in soil and water
Cell wall Varies in composition; Contains peptidoglycan Varies in composition
no peptidoglycan contains
carbohydrates
Membrane lipid Composed of branched Composed of straight Composed of straight
carbon chains attached carbon chains attached carbon chains
to glycerol by ether to glycerol by ester attached to glycerol by
linkage linkage ester linkage
Start signal for Methionine formylmethionine methionine
protein synthesis
Antibiotic No Yes no
sensitivity
rRNA loop Lacking Present lacking
Methasarcina Escherichia coli Entamoeba coli

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Basic Apparatus and Equipment in Microbiology

1. Incubator (Microorganisms) – for the cultivation of microorganisms cultures such as bacteria,

and fungi, contained in test tube of a Petri dish under controlled conditions of temperature,
moisture, and gas content.
2. Oven – for drying and heating glassware, it is often used as a means of dry air sterilization.
3. Petri dish/ petri plates – used to culture microorganisms in solid media
4. Screw-capped test tube or test tube - used for containing liquid or aqueous media and used for
chemical reaction observation of biochemical tests.
5. Erlenmeyer flask – used to mix liquids together and to heat and for preparation of culture media
6. Hot plate – used for general heating and mixing of culture media, equipped with a magnetic
stirring function
7. Water steam bath – is used to heat liquids and solutions, especially for those solutions that
could burn easily such as alcohol or there is a need for slow heating. Also used for controlled
temperature experiments.
8. Autoclave – indispensable equipment for sterilization. Of all sterilization methods, high-pressure
steam is most widely used because of its efficiency, speed and reliability. This method is suitable
for a wide range of media, and waste products. It provides a safe, reliable high-pressure steam
sterilizing environment.
9. Laminar flow hood - is a close chamber device that reduces the risk of bacterial contamination
and assures that experiment are prepared in the most aseptic manner. The hood is designed to
prevent contamination to whatever one is handling or experimenting on. It prevents
contamination of cultures as microorganisms are being transferred
10. Digital weighing balance – electrical scale used for accurate weighing of solids and other
chemicals
11. Glass slide – a piece of glass where microscopic specimens are placed for observation; coverslip
12. Pipettes, pipettors, and pipette tips – used to transfer and measure liquids. They are especially
important for handling small amounts of liquids
13. Wash bottle – contains liquids that are to be added in quantities when the amount needed is
not important. It is especially used in microbiology to wash stains for glass slides.
14. Inoculating loops or needles are used for transferring microorganisms
15. Stirring rod – used for mixing liquids
16. Graduated cylinder - used for measurement of liquids and chemicals
17. Alcohol lamp – used to sterilize the inoculating loop and needle as well as the flaming of Petri
dishes and test tubes during the transfer of microorganisms. Also used in fixing and heating of
slide preparation of organisms
18. Microscope – used to observe minute objects
19. Caliper – used to measure a small distance

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