Microorganisms and Diversity of Bacteria

Abstract

Microbiology is the branch of science that investigates microscopic organisms known as microorganisms and their isolation by various methods Microorganisms can have single or multicellular eukaryotic cell structure as well as prokaryotic unicellular structure. When prokaryotic cells are examined, they are cells that do not have organelles surrounded by membranes and whose genetic material is dispersed in the cytoplasm. Until 30-35 years ago, Archaea, which were included in a different class, were defined as having a prokaryotic cell structure and considered bacteria. It has been observed that some archaea can cause diseases in humans, animals, and many plant species. It is possible to come across many areas in nature. Microbiology is also divided into different branches within itself. Virology, mycology, bacteriology, and parasitology are examined from four primary areas. This study provides basic information for understanding the diversity and characteristics of microorganisms and bacteria. In this way, it is tried to recognize the interest of humanity in the world of microorganisms and to explain basic information in this way. Currently, when scientists classify species based on microorganisms and consider that only about 5% of the microorganisms existing in the world have been identified, it will be easily understood how important a field of study microbiology is.

Full text

185
Chapter 12
Microorganisms and Diversity of Bacteria
Orhan Uluçay1
Abstract
Microbiology is the branch of science that investigates microscopic
organisms known as microorganisms and their isolation by various
methods Microorganisms can have single or multicellular eukaryotic cell
structure as well as prokaryotic unicellular structure. When prokaryotic
cells are examined, they are cells that do not have organelles surrounded by
membranes and whose genetic material is dispersed in the cytoplasm. Until
30-35 years ago, Archaea, which were included in a different class, were
defined as having a prokaryotic cell structure and considered bacteria. It
has been observed that some archaea can cause diseases in humans, animals,
and many plant species. It is possible to come across many areas in nature.
Microbiology is also divided into different branches within itself. Virology,
mycology, bacteriology, and parasitology are examined from four primary
areas. This study provides basic information for understanding the diversity
and characteristics of microorganisms and bacteria. In this way, it is tried
to recognize the interest of humanity in the world of microorganisms and
to explain basic information in this way. Currently, when scientists classify
species based on microorganisms and consider that only about 5% of the
microorganisms existing in the world have been identified, it will be easily
understood how important a field of study microbiology is.
Introduction
According to the Turkish Language Association Dictionary of Veterinary Medicine
Terms, microorganisms are living organisms including bacteria, fungi, protozoa
and microscopic algae. Although there have been various information about
some effects and usage areas of microorganisms for centuries, microorganisms
were first seen and started to be studied in 1675 with Leewenhoek’s discovery
of the microscope. In approximately 200 years, Louis Pasteur proved some
functions of microorganisms in the emergence of undesirable flavors in
1 Kafkas Üniversitesi, ORCID: 0000-0002-0820-5372, orhanulucay@gmail.com;
orhanulucay@kafkas.edu.tr
https://doi.org/10.58830/ozgur.pub81.c476

186 | Microorganisms and Diversity of Bacteria
winemaking in his studies on the fermentation stage and concluded that heat
treatment has an effect on the death of unwanted microorganisms. This practice,
called pasteurization, is still accepted today. At that time, Robert Koch’s work
also made essential contributions to microbiology, and his work in this field has
continued with rapid progress until today (Aran, 1993).
Microorganisms and General Properties
This chapter, it is tried to give general content about microorganisms by
taking into account the undergraduate programs and considering the basic
information that is felt to be lacking in the program. Microorganisms are
divided into biological groups such as microscopic algae, viruses, bacteria,
fungi (moulds and yeasts), and protozoa (Fung, 1987).
Protozoa
They are single-celled microscopic organisms and are found in both
terrestrial and aquatic environments. They have animal characteristics
such as movement, ingestion of food and the absence of a cell wall. Some
protozoa take their nutrients in dissolved form by absorption. Others feed
by swallowing bacteria and other protozoa in their environment. There are
free-living species in the sea, fresh water and soil, as well as species living
symbiotically or parasitically in or on living host cells or tissues. Protozoa
are divided into four branches as flagellates, pseudopods, spores and ciliates
according to their movement patterns (Clarholm et al., 2007).
Microscopic Algae
Most algae are considered plant-like protists because they carry
chloroplasts and have a cellulose cell wall. More than seven thousand
species of green algae have been described. Most of them are aquatic, living
in freshwater and seas (Jankovská & Komárek, 2000). Some species can
be found symbiotically on the surface of snow, moist soils, green parts on
the surface of tree stumps, and some species can be found symbiotically in
lichens and protozoa (Hurst, 2021).
Viruses
Since viruses are different from other microorganisms in terms of their
structural and general characteristics, they do not belong to any of the above
groups (Ulucay et al.). They are expressed as genetic elements located inside
and outside the cell containing DNA or RNA. They are not involved in any
metabolic activity when outside the cell, but can reproduce within the living
host cell (Brown & Bhella, 2016).

Orhan Uluçay | 187
Bacteria
They are organisms that can be found in almost every environment.
Some of them cause diseases such as typhoid, tuberculosis and cholera.
In addition to such harmful activities, they also have many benefits. For
example, they transform organic dead residues into reusable materials
(Ulucay et al., 2022b). This prevents the loss of essential nutrients. The
simplest distinguishing features are their shape and size. Their size varies
between 1 and 10 µ. Most bacteria are ready feeders (heterotrophs). They
analyse the surrounding organic food sources with their enzymes, convert
them into simple organic compounds and then absorb them (Ulucay et al.,
2022a). Some bacteria are autotrophs (autotrophs), which can produce
their own food by photosynthesis or chemosynthesis from simple inorganic
compounds with a special pigment. Bacteria reproduce towards their width.
Bacteria are one of the most effective groups of organisms in the life of
living organisms, both beneficial and harmful. Although their harms are
emphasized more, they also have many benefits (Oztas Gulmus & Gormez,
2020). In vaccine production, disease-causing bacteria are either killed or
rendered harmless. For example, typhoid and cholera vaccines are produced
from dead bacteria, while tuberculosis (= tuberculosis) vaccine is produced
from weakened live bacteria. In the production of some serums, weakened
disease bacteria are inoculated into some animals such as horses and cows,
and then the serum obtained from the liquid part of the blood taken is used
in the treatment of some diseases such as tetanus and diphtheria (Hifumi et
al., 2017). Most antibiotics are produced by bacteria. As in the production
of antibiotics, bacteria are also utilized in the production of some vitamins
(group B, K, etc.), hormones, and amino acids (Singh et al., 2017). It is
known that some food spoilage is the result of the harmful activities of
bacteria. However, these harmful activities can be controlled and converted
into useful ones. For example; yoghurt, cheese, butter, vinegar, pickles, and
brine are prepared by this method. Bacteria are also used in the production
of some alcohols, acids, and acetone. Is the presence of bacteria in our body
beneficial or harmful to us? Bacteria on our skin, which covers our whole
body, is actually a shield that protects us from disease factors. In this way, our
body is protected from many diseases. There are some bacteria not only on
our skin but also in our digestive tract (Probert & Gibson, 2002). Bacteria
in small nodules on the roots of plants such as chickpeas or broad beans
flick free nitrogen from the atmosphere. Thanks to the nitrogen formed by
these bacteria, plants continue their development. On the other hand, the
soil is enriched in terms of nitrogenous compounds (Reinikovaite et al.,
2023). For this reason, legumes are called green fertilizers. Bacteria are also

188 | Microorganisms and Diversity of Bacteria
utilized in the fight against insects that cause great damage to agricultural
and industrial plants. Chemical insecticides (insecticides) are known to cause
environmental pollution and even cancer. Therefore, biological control is
gaining importance. One of the ways of biological control is the control
of pests by using bacteria-containing some toxic substances. These bacteria
reproduced under special conditions are sprayed on the plants in the fields.
One of the most important activities of bacteria is the cycling of matter
(Ulucay et al., 2022a). With the processing of the residues accumulated
with the death of living organisms by bacteria, dead organic substances are
converted into CO2, H2O, and mineral salts that can be used in new nutrient
synthesis. Even the formation of oil deposits takes place as a result of the
activities of bacteria (Xu et al., 2023).
Fungi (Mould and Yeasts)
Fungi are characteristically filamentous (mycelial) organisms in
eukaryotic cell structure (Patel et al., 2023). They have a cell wall like plants
and most of them cannot move. Since they lack photosynthetic pigments,
they obtain their nutrients from organic substances mostly by absorption.
Today, there are more than one hundred thousand species of fungi. The
living conditions (habitat) of fungi have some differences. Some of them
are aquatic, but most of them live in soil and dead plant residues. Fungi,
which can be encountered almost everywhere, generally perform useful
activities for us, but some of them can cause various economic losses and
jeopardize our health. The useful activities of fungi can be summarised as
follows: a) Fungi, most of which live in the soil, together with other soil
microorganisms, play a major role in the mineralization of dead organic
residues that fall to the ground, thus eliminating garbage heaps. In the
meantime, the physical, chemical, and biological properties of the soil
improve, and its productivity increases. In addition, the CO2 they release
during these activities passes into the air and regulates the CO2 balance of
the air. b) Fungi are among the organisms we use as food. Some of them
are cultured (e.g. Agaricus bisporus); some are collected from nature [e.g.
Morchella esculenta (morel)] and consumed as vegetables. In recent years,
some fungi with high protein value have been produced by cell culture
method and used as human food or animal feed. (Amara & El-Baky, 2023).
Some fungi are used in the preparation of some special cheeses (Rokfort,
Gorgonzola, Kamembert, mouldy cheese produced in Anatolia). These
provide special flavour and odour to the cheese. Foods such as tempeh and
shoyu prepared in some Far Eastern countries are also matured with fungi.
c) As we all know, the CO2 released by the yeast used in bread making

Orhan Uluçay | 189
causes the dough to gain a sponge-like appearance and allows the bread to
bake inside. Yeast cells also enrich bread with protein and vitamins. Yeasts
are also used in the preparation of some beverages such as beer and wine
(Satora & Pater, 2023). The first known antibiotic penicillin was obtained
by Fleming in 1929 from a mould species (Penicillium notatum) (Houbraken
et al., 2011). Fungi are also utilized in the production of alcohols, organic
acids, vitamins, enzymes, and hormones. As for the harmful activities of
fungi; fungi that live as parasites in many living things, including humans,
cause their death known. Saprophytic fungi, on the other hand, cause
deterioration in various foodstuffs; leather, wood, etc. They cause goods,
structures, and clothing made of leather, wood, etc. to become useless by
rotting (Kukovinets et al., 2008).
Classification of Bacteria
The categorization of living things according to their characteristics,
living conditions, and/or kinship status is called classification, and the field
of biology that performs classification is called taxonomy (systematic). The
purpose of classification is to find an easy way to understand nature. Living
things are classified and named according to their common characteristics
and kinship status. The first classifications were made only according to
the external appearance of living things and the first classification of living
things was made by Aristotle by dividing them into plants and animals.
The main element of classifications based on science is species. Organisms
that have the same origin, have the same characteristics, have the same
number of chromosomes, and produce fertile offspring when mated with
each other are called organisms of the same species (Taylor & Ingvarsson,
2003).
Organisms are grouped into 3 super kingdoms according to the type of
ribonucleic acid in their cells. Viruses are excluded from this classification
because they are acellular (acellular, cell-free). The distinction between
eukaryotes and prokaryotes refers to a definition made according to the
nucleus. Eukaryotes are those with true nuclei, while prokaryotes are those
with primitive nuclei. The distinction between eukaryotes and prokaryotes
refers to a definition based on the nucleus (Sapp, 2005).
Prokaryote
It is the upper realm that covers microorganisms that do not have true
nuclear membranes and membrane-bound organelles, and whose DNA
molecule is free within the cell.

190 | Microorganisms and Diversity of Bacteria
Eukaryote
Their genetic material is contained in a membrane-enclosed nucleus.
There are various membrane-enclosed organelles. Studies on the taxonomy
and nomenclature (nomenclature) of bacteria were initiated in the early
20th century by Chester, Buchanan, and their teams (Winslow et al., 1917).
Bacteria are usually classified according to their shape, although different
classes are known. The two main groups of bacteria are cocci (spherical) and
bacilli (rod-shaped). These two groups are further subdivided into gram-
positive and gram-negative bacteria. Gram staining uses a mixture of purple
dye and iodine to stain the magnesium ribonucleate found in some bacteria
dark purple. The purple stain cannot be washed with alcohol. Bacteria that
stain purple are gram-positive. Those that stain pink are gram-negative.
Mycobacteria are not revealed by gram staining and are instead stained
by an acid-resistant method called the Ziehl-Nielsen method (Zinserling,
2022). A second subdivision of bacteria is between aerobic and anaerobic
organisms.
Characteristics of Bacteria
Morphological Properties
In this method, different colours are applied to different bacteria or
bacterial structures according to their staining properties (Gram staining).
The two most commonly used differential staining methods are Gram
staining and acid-based staining. Gram staining was designed as a method
by histologist Christina gram. Gram (+) bacteria are those bacteria that
are blue-black or purple in colour on microscopic analysis of Gram-stained
media. Gram (+) bacteria get this colour because of a mixture of ultraviolet
and iodine in their cell walls. Gram (+) bacteria with thicker cell walls
produce more vivid colour. The gram classification system of Gram (+)
bacteria is “empirical” and is based on differences in the structure of the “cell
wall”. They show themselves in purple colour under the microscope (Ulucay
et al., 2022b).
Characteristic Properties of Gram (+) Bacteria;
Cytoplasmic membrane (membrane or wall)
Thick cell Wall
Single-ring flagellar structure
Polysaccharide capsules
They contain teichoic or lipoteichoic acid

Orhan Uluçay | 191
For example: Streptococcus equi, Bacillus anthracis
Gram (-) bacteria are bacteria that do not take crystal violet stain in the
Gram staining stage. In the Gram staining stage; counter dye is added after
the crystal violet, so that Gram (-) bacteria have a red-pink colour. Most gram
(-) bacteria are pathogenic. Pathogenic gram (-) bacteria have high disease-
causing properties in humans. Pathogenicity is due to some properties of a
gram (-) bacteria in the cell wall, namely LPS (lipopolysaccharide). They are
seen in pink colour under the microscope.
Characteristic Properties of Gram (-) Bacteria;
Cell walls contain thinner peptidoglycan than gram (+) bacteria.
Outside the peptidoglycan layer there is a “Lipopolysaccharide”
membrane.
The outer membrane of the cell contains “Porins” that pass certain
molecules.
There is a “periplasmic space” between the peptidoglycan layer and
the outer membrane
The S layer is attached to the outer membrane
Flanella has 4 rings
Teichoic acid or lipoteichoic acid is absent
Cytoplasmic membrane
For example: Brucella abortus, Escherchia coli
Microscopic Morphology
Cocs: It is called round-shaped bacteria. In microbiology, such as Streptoco
and Staphylococ coccus, it is a spherical-shaped bacteria. Many bacterial
species have characteristic arrangements that are useful in identification.
(Bacilli (Basil/Bacillus): They are divided into 4 groups according to
their physiological characteristics.
Acid resistant
Gram (+) spore formers
Gram (+) non-spore forming
Gram (-) bacilli
The Bacillaceae family of endospore-forming rod-shaped bacteria has two
main subdivisions: anaerobic spore-forming bacteria of the genus Clostridium

192 | Microorganisms and Diversity of Bacteria
and aerobic or facultatively anaerobic spore-forming bacteria of the genus
Bacillus, often known as ASB (aerobic). The bacterial cells of Bacillus
cultures are Gram-positive when young, but in some species become Gram-
negative as they age (Turnbull, 1996). Most Bacillus species are saprophytes.
They have unusual physiological characteristics that enable them to survive
or thrive in harsh environments, from Arctic soils and freshwater to marine
sediments. The genus includes thermophilic, psychrophilic, acidophilic,
alkaliphilic, alkaliphilic, halotolerant, and halophilic representatives that can
grow at temperatures, pH values, and salt concentrations where few other
organisms can survive (Ulucay et al., 2022b)
Spirochetes
It is an element of the phylum bacteria. Spirochetes, which are
diderm (double-membraned) gram-negative bacteria, belong to the
long, helical (corkscrew-shaped or spiral-shaped) cells. Spirochetes are
chemoheterotrophic, characterized by lengths between 3 and 500 µm and
diameters from 0.09 to at least 3 µm in diameter. They are spiral-structured
bacteria. For example; Borrelia, Treponema, Leptospira.
Forms of involution (degeneration)
Under the influence of unfavorable conditions (food, pH, osmotic
pressure, oxygen depletion, change in surface tension, accumulation of
metabolites, etc.) microorganisms undergo many changes in their original
form, which are called involution forms. These changes are recognized
as abnormal forms such as elongated, oval, branching, swelling, delayed
division, etc. If optimal conditions are created in the cultures, the bacteria
reach their previous normal form.
Macroscopic Morphology of Bacteria (Colony Morphology)
If a bacterium is grown in a suitable solid medium and under favourable
conditions (temperature, time, humidity, oxygen, etc.), it forms a visible
cluster (colony) in a short time (Ulucay et al., 2021). Bacterial species form
colonies with their own specific colour, odour, size and shape. These types
provide genetic control of the cell. Depending on the size, there are millions
or billions of microorganisms in a colony. Some bacteria (E. coli, P. vulgaris,
B. subtilis, etc.) form very large and visible colonies after 24 hours under
favourable conditions, while some (Brucellas, corine bacteria, etc.) form
colonies that reach the visible stage in 3-5 days. Mycobacteria belonging
to human and mammalian animals, on the other hand, form colonies after
15-20 days. The size and shape of the colony is a characteristics of the

Orhan Uluçay | 193
species under favorable conditions (composition of the medium, oxygen,
temperature, etc.). These are;
Flamentöz Bacteria
Actinomyces
Nocardia
Streptomyces
According to Physiological Properties
There are distinctions according to the different physiological states of
bacteria. For example, the Bacillaceae family is divided into aerobes (those
that need oxygen to reproduce) and anaerobes (those that do not need
oxygen) according to their oxygen requirements.
According to Antigenic Structure
They are classified according to their antigenic properties. Serological
methods are used for this purpose. By detecting certain antigens formed by
bacteria with serological methods, the structure similarity between bacteria
is compared.
Numerical Classification
Many characters of bacteria such as morphological, cultural, and
biochemical properties are analyzed and the results are transferred to the
computer. The origins that are similar to these characteristics are classified. A
score of +1 for similarity and -1 for dissimilarity is given and the similarity
index is obtained at the end of the general sum of the similarity scores. As a
result, bacteria are classified in the range of 100% to 0%.
Genetic Classification
It is found according to the number of G+C in bacterial DNA. The ratio
of the sum of Guanine (G) + Cytosine (S) numbers to all DNA numbers is
constant for each species. In this case, bacteria with similar or very similar
G+C/DNA numbers are referred to as the same group. This ratio differs
between different genera.
Nomenclature of Microorganisms
The nomenclature is based on the BINOMINAL system described by
CARL von LINNE. Microbe names consist of two words:
For example: Bacillus anthracis, Brucella abortus, The genus name can be
abbreviated. For example: B. Anthracis

194 | Microorganisms and Diversity of Bacteria
Classification of Microorganism Groups
Domain / Prokaryote
A prokaryote is a microorganism without a distinct nucleus and other
organelles because it has no internal membranes. Bacteria are among the most
recognizable prokaryotic organisms. The absence of internal membranes in
prokaryotes distinguishes them from others. In eukaryotes, the prokaryotic
cell membrane is composed of phospholipids and forms the cell’s primary
osmotic barrier. The cytoplasm contains ribosomes, which carry out protein
synthesis, and a double-stranded deoxyribonucleic acid (DNA) chromosome,
which is usually circular. Many prokaryotes also contain additional circular
DNA molecules called plasmids.
Phylum / Gracilıcutes
It is a class in bacterial genesis. Traditionally, gram staining results are
most commonly used as a classification tool. Consequently, until the advent
of molecular genealogies, Kingdom Monera was divided into four phyla;
Gracilicutes
Firmacutes
Mollicutes
Mendosicutes
Order / Ricketsiales
The order Rickettsiales of Proteobacteria contains a large number of
medically important bacteria, including pathogens responsible for Rocky
Mountain spotted fever and typhus. Among them are emerging pathogens
that cause similar diseases and share many bacterial characteristics. All
organisms are small, Gram-negative coccobacilli or bacilli. Most are
transmitted to mammals by an arthropod vector. They multiply by binary
fission in eukaryotic cells, either in the cytoplasm or inside vesicles, and have
a circular genome of only 1 to 1.6 Mb.
Family / Ricketsiaceae
Rickettsia is a gram-negatively stained, small, obligate intracellular
parasites of the Ricketsiaceae family (Ogata et al., 2005). They reproduce
in the cytoplasm of endothelial cells and smooth muscle cells of capillaries,
arterioles, and small arterioles and cause necrotizing vasculitis. They are
transmitted to humans by arthropods such as fleas, lice, ticks, and mites
and cause typhus or spotted fever group diseases. They are characterized by

Orhan Uluçay | 195
sudden onset of fever lasting for one or several weeks, headache, weakness,
muscle pain, and in all cases a characteristic rash.
Species / Coxiella Burnetii
Coxiella burnetii is a gram negative, pleomorphic, necessary intracellular
microorganism. Although it was previously known as Rickettsiaceae family,
it was determined to be in the Coxiellaceae family with genetic applications
Morphology of Bacteria
Microscopic Morphology;
Depending on their shape, bacteria are divided into several types. Round-
shaped bacteria are cocci, rod-shaped bacteria are bacilli and spiral-shaped
bacteria are spirochetes. But if we make a general definition, we can make a
ranking as follows.
Cocci (from kokkos, meaning berry) are spherical or oval cells.
Basil (from bacillus, meaning rod) are rod-shaped cells.
Vibrios are comma-shaped curved rods and are named after their
structure. They are characterized by vibratory motility.
Spirilla are rigid spiral forms
Spirochetes (from speira, meaning fold, and chaite, meaning hair) are
flexible and helical forms.
Actinomycetes are branching filamentous bacteria; when seen in
tissue, they bear an imaginary resemblance to the radiating rays of the
sun (from actis meaning ray, and mykes meaning fungus).
Mycoplasmas have a cell wall-deficient and therefore stable morphology.
They have the shape of round or oval bodies and interlacing filaments.
Cocs, The term cocci is derived from the Greek word kokkos, meaning
fruit or seed. Cocci include archaeons or bacteria, usually round, oval,
or spherical in shape.
Cocci bacteria species Cocci can grow in chains, clusters, or pairs.
Depending on the arrangement of cocci cells, they can be further
subdivided.
Streptococcus - cocci arranged in chains. Streptococcus mutans
Diplococci - cocci arranged in pairs. Neisseria gonorrhoeae
Monocoque - single coke

196 | Microorganisms and Diversity of Bacteria
Staphylococci - clusters of cocci. Staphylococcus aureus
Tetrads - smells in groups of four. Pediococcus
Sarcina - cocci in groups of eight. Sarcina ventriculi
Streptococci and diplococci are mostly formed because the daughter cells
do not separate after cell division. In Sarcinae, cell division is organized in
cubic pockets alternating between three vertical planes.
Gram-positive coccus bacteria
Like any other gram-positive bacteria, they also become positive for Gram
staining (they retain the violet stain). Bacterial cell walls have thick layers of
peptidoglycan. Gram-positive cocci most commonly cause infections in the
intestine, vagina, nasopharynx, and in mouth.
Staphylococci - Gram-positive cocci organized in grape-like clusters.
They do not form spores, are immobile, and are about 1 µm in
diameter.
Micrococci - Gram-positive cocci that appear in irregular clusters.
They are tetrads and differ from staphylococci in their oxidative attack
on sugars.
Streptococci - Another group of gram-positive cocci that appear in
chains. They are usually part of the normal human flora. Some of
them are important human pathogens causing pyogenic infections.
Their growth in the cellular environment is enhanced by the addition
of glucose, serum, or blood.
Some Gram-positive cocci samples; Parvimonas, Peptonifilus
There are also some cocci with a thin layer of peptidoglycan (gram-
negative cocci). They do not retain the violet stain during Gram staining and
instead take up the counterstain such as safranin and appear red in colour.
Some gram-negative cocci samples: Anaeroglobüs, Asidaminokok, Veillonella,
Megasfera
Bacillus
Bacilli (genus Bacillus) are rod-shaped, gram-positive, aerobic, or (under
certain conditions) anaerobic bacteria, commonly found in soil and water.
The term bacillus has been generally applied to all cylindrical or rod-like
bacteria. The largest known Bacillus species, Bacillus megaterium, is about 1.5
µm (micrometer; 1 µm = 10-6 m) in diameter and 4 µm long. Bacillus often
occurs in chains. In 1877, the German botanist Ferdinand Cohn provided

Orhan Uluçay | 197
an authorized person with different forms of hay bacillus (Bacillus subtilis):
the heat-resistant forms, which can be killed by exposure to heat, are called
“spores”. It is known that these dormant forms can be converted into a
vegetative or actively growing state (Cavalier-Smith, 2002). It is now known
that all Bacillus species can form spores under unfavorable environmental
conditions. These endospores can remain viable for a long time. Endospores
are resistant to heat, chemicals, and sunlight and are widely distributed in
nature in the soil they invade.
Sporikets
Spirochete, (order Spirochaetales), also spelled spirochaete, are a group
of spiral-shaped bacteria, some of which are serious pathogens for humans
and cause diseases such as syphilis, yaws, Lyme disease, and relapsing fever.
Examples of spirochete genera include Spirochaeta, Treponema, Borrelia,
and Leptospira. Spirochetes are gram-negative, motile, spiral bacteria from
3 to 500 m (1 m = 0.001 mm) long. Spirochetes are unique in that they
have endocellular flagella (axial fibrils or axial filaments), of which there
are between 2 and more than 100 per organism, depending on the species.
Each axial fibril is attached to an opposite end and wrapped around the cell
body surrounded by an envelope. Spirochetes are characteristically found in
a liquid medium (e.g., mud and water, blood, and lymph).
Spirillum
Spirillum, a genus of spiral-shaped bacteria from the family Spirillaceae,
causes a type of rat bite fever in humans. The spirillum is microbiologically
characterized as a gram-negative, motile spiral cell with whip-like flagella at
each end. The spiral of the largest spirillums is 5 to 8 µm (micrometers; 1
µm = 10-6 meters) in diameter and 60 µm long.
Vibrio
Their bodies are rigid, with a single curved, comma-shaped body structure.
Vibrios harbour a wide variety of genomes as revealed by different genomic
techniques including amplified fragment length polymorphism, multilocus
sequence typing, repetitive extragenic palindrome PCR, ribotyping, and
whole genome sequencing. The 74 species of this group are distributed in
four different families such as Entero vibrionaceae, Photo bacteriaceae, Salini
vibrionaceae and Vibrionaceae. Comparative genome analyses, mutations,
chromosomal rearrangements, loss of genes through decay or deletion,
and gene gains through duplication or horizontal transfer, are probably
important drivers in the evolution and speciation of vibrios.

198 | Microorganisms and Diversity of Bacteria
Bacteria always reproduce in the same cell form under favorable conditions.
But sometimes they can be found in different shapes. If bacteria are produced in
the presence of substances that inhibit cell wall synthesis (penicillin, chemicals,
etc.), there are some differences in their shapes. These are;
L- Form
They are capable of normal reproduction but have no cell walls.
They are found in shapes such as oval, star, ring, and disc under a
microscope.
Bacteria are found in different shapes with many environmental effects
in the environment where they grow. pH change, oxygen reduction,
surface tension, and osmotic pressure changes, and reduction of food
in the environment. Bacteria in these environments have irregular
shapes (filament, branching, angular form).
Colony Morphology of Bacteria
Bacteria grow in colonies on solid media. A colony is defined as a visible
mass of microorganisms all originating from a single mother cell, so a colony
forms a genetically similar colony of bacteria. The culture medium plays an
important role in the demonstration of bacterial colony characters and the
actual morphology of the bacteria. Media consisting of simple components
and without any inhibitory substances are suitable for characterizing the
colony characters of a bacterium (nutrient agar). Bacterial colonies differ in
shape, size (measured in diameter), odour, colour (pigmented), texture and
degree of adhesion to the medium (pitting and crusting). Different bacteria
show different colony morphologies, such as rhombic (e.g. Pseudomonas
spp.), large mucoid colonies (e.g. Klebsiella spp.), colonies with wavy
edges (e.g. Bacillus anthracis), fusing colonies (e.g. Proteus)); colonies can
be mucoid (M colonies), smooth (S colonies) and dry (R colonies). An
M colony looks water-like, shimmering, and mingled together (individual
or separated colony). S colonies are recognizable by their moist structure
and are indicative of freshly isolated bacterial strains. R colonies are rough,
dry, granulated, and mutant bacterial strains lacking most surface proteins,
including capsules and lipopolysaccharides. R colonies are usually formed
by bacteria that are avirulent. The ability of bacteria to vary in both smooth-
to-rough (SR) shapes and rough-to-smooth (RS) colonies has also been
observed. Rough colonies that form on blood agar and reveal spore-forming
gram-positive bacilli (aerobic spore-bearing bacilli) on Gram stain are often
overlooked as laboratory contaminants.

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Colony Shape
It includes the shape, height, and boundary of the bacterial colony. The form
of the bacterial colony: Form refers to the shape of the colony. These four forms
represent the most common colony shapes you are likely to encounter. These are
circular, irregular, filamentous, and rhizoid. The height of the bacterial colony:
Gives information about how high the colony rises on the agar. This describes
the “side view” of a colony. The six most common elevations of bacterial colonies
and the prevalence theme of bacterial colonies are given (Figure 1)
Figure 1. Bacterial Colony Types
Size of the Bacterial Colony
The size of the colony is a useful feature for identification. The diameter
of a representative colony can be measured in millimeters or described in
relative terms such as pinpoint, small, medium, and large. Point and other
types of bacterial colonies are shown in Figure 2.
Figure 2. Schematic of Point Bacterial Colonies
Tiny colonies are also called pinpoints. Colonies larger than about 5 mm
are likely to be mobile organisms. Pinpoint colonies differ from circular
colonies by their very small size.
Colony Morphology

200 | Microorganisms and Diversity of Bacteria
When bacteria are grown in suitable solid nutrient media and under
suitable conditions, they come together and form visible clusters called
colonies. Bacterial species form colonies with their own colour, smell, size,
and structure. These characters are under the genetic control of the cell. The
formation time of colonies in solid nutrient media varies according to the
bacterial species. For example, E. coli can grow in 24 hours, Brucellae in 2-3
days, Mycobacteria in 15-20 days. The size of colonies also varies according
to bacterial species.
Colony Forms Observed in Bacteria
S (Smooth) Colony
It is a colony formed by bacteria newly isolated from disease cases. It has
a smooth, shiny and homogenous appearance.
R(Rough) Colony
Colonies formed by bacteria that are old or passaged many times. They
are granular with rough edges and top. Bacteria forming R-type colonies
lose their pathogenicity and are easily phagocytised. Their antigenic ability
weakens.
M (Mucoid) Colony
It is seen in bacteria forming capsules or mucoid secretions. When these
colonies are touched with a swab, they elongate like threads.
L-Colony
Bacteria can transform into various forms as part of their natural life
cycle. One of these stages is L-Colony. L-form bacteria, also known as cell
wall-deficient bacteria, are a stage of bacteria that are very small and lack
cell walls. Despite being the subject of numerous studies over the last 100
years and implicated in various diseases, L-forms continue to be largely
misunderstood by the medical research community. According to Marshall
Pathogenesis, L-forms are part of the metagenomic microbiota responsible
for chronic diseases (Proal et al., 2011). Their tops and sides are irregular. The
size of microorganisms is measured in micrometers (µm, 10-6) in eukaryotic
organisms and bacteria in the international metric system. In bacteria, some
phages, and viruses, the length of the double-stranded genomic DNA is
defined in base pairs (ba, base pair, bp) and in single-stranded genomic
phages and viruses in bases.

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