BACTERIA (PROKARYOTE)
3.1 Composition and Ecology
The monera are prokaryotic organisms having nuclei not surrounded by a membrane envelope. The
monera include three classes of organisms namely; cyanobacteria, eubacteria and archaebacteria.
Prokaryotes are among the earth's most abundant and diverse organisms, found in virtually every habitat
because of their metabolic diversity. This metabolic diversity has made the prokaryotes to be able of
survive some of nature's most hostile conditions, such as those found in hot springs, at temperatures close
to boiling point of water. Prokaryotes can also be found in desert soil, artic ice shelves, the depth of the
ocean, salt, mines, plant roots and the surface of larger organisms.
3.2 General Characteristics
Prokaryotic cells are typically smaller than eukaryotic cells, having dimension approximately like those
of mitochondria (2µmThe small sizes of prokaryotes enable them to have a higher rate of surface area to
cell volume than eukaryotic cells. This greater surface-to-volume ratio allows for efficient movement of
nutrients and waste between the environment and the interior of the cell, without the need for cytoplasmic
streaming or intricate internal membrane network or cytoplasmic organelles. Being small, allows
prokaryotic cells to be structurally simple and to increase their number rapidly.
3.3 Phylogenetic (molecular) Classification of Prokaryotes
Prokaryotes (monera) have no official classification scheme. However, the most stable taxonomic
classification scheme is one based on similarity in chromosomal DNA, the ultimate indicator of genetic
relatedness. Closely related bacteria descend from a common ancestor more recently, than does more
distantly related bacteria. This type of classification, which, help us to understand the evolutionary
relationship among organisms, is called phylogenetic classification.
In phylogenetic studies, modern systematists describe how species are related to one another on the basis
of fossil records and comparative anatomy. Phylogenetic trees commonly represent these relationships.
The tree branches at several points show where one species must have divided into two or more.
Individual branches of tree lines of evolution-often show a trend such as an increase in size or a change in
the manner of coiling. The study requires extensive information about the genetic composition of all
known bacteria. The genetic criterion for classifying prokaryotes into species relies on directly comparing
the nucleic acid of different bacteria.
3.3.1 DNA Base composition.
,A linear molecule of DNA is composed of nucleotides each of which contains one or four bases adenine,
cytosine, guanine or thymine. In base composition studies, the amount of two DNA components, guanine
(G) and cytosine (C) are measured, yielding a value, called the percent G + C. The sum of the guanine
and cytosine present in an organism's DNA is stable from generation to generation, and related organisms
have similar or identical G + C content. Thus, base composition can determine that two organisms are
different, but cannot be used to ensure that they are related.
3.3.2 DNA-DNA hybridisation (DNA homology)
DNA extracted from different species of an organism can be heated to break the hydrogen bonds and
separate the complementary strands completely. If single strands of different species are then mixed
together, the extent to which the DNA strand from one species will bind to the DNA from another species
will depend on the degree of similarity between their base sequences. Double stranded DNA reconstituted
from strands derived from a single species serves as a control, a perfect match against which hybrid DNA
can be compared. The extent of hydrogen bonding between strands of the hybrid DNA is measured by
gradually increasing temperature until the strands separate. The more closely related the DNA, the greater
the number of hydrogen bond, and the higher the temperature must be to separate the strands apart.
DNA-DNA hybridization measures the extent of hydrogen bonding between single stranded DNA
molecules obtained from two sources. The degree of similarity in the DNA strand will determine the
extent of the bonding together of two species DNA. Evolutionary trees constructed by this technique
generally agree with the phylogeny deduced by other methods, such as comparative morphology.
Although DNA-DNA hybridization can estimate the overall similarity of two genomes, it does not give
precise information about the match up in specific nucleotide sequences of DNA.
3.3.3 Ribosomal RNA analysis
The evolutionary history within the eukaryotes, cubacteria and archaebacteria is recorded in their rRNA.
Each of this cell type is characterised by unique 16S rRNA nucleotide sequence. called signature
sequence that defines that cell type. Based on this, some systematists have traced the entire eubacteria
back to eleven distinct evolutionary groups. These groups a proteobacteria, cyanobacteria, gram positive
bacteria, chlamydia, plantoyces, anaerobic bacteriodes and aerobic flavobacterium, green sulfur bacteria,
thermotoga and thermosipha. spirochete, deinococcus and green non sulfur bacteria.
Ribosomal RNA analysis helps in defining whether a prokaryote is a eubacterium or an archaebacterium
and the specific group to which it is most closely related. Organism that are about 20 to 60% related
according to DNA homology are usually considered members of a single genus. Organisms that are more
than 60 percent related are assigned to a single species. There is however, substantial natural variability
within a species, expressed as differences in immunological, structural and physiological characteristics.
For example, one organism may have the ability to produce a capsule, while another that does not, may be
able to use particular sugar as a nutrient. These differences are often used to further subdivide the
members of a species into sub groups called strains. Different strains within a species may differ from
,each other in biochemical properties, morphological characteristics. ability to infect different host, or
reactivity with different antibodies.
3.4 "Practical" Classifications
Generally very few details are known about the genetic make up of most known bacteria. This lock of
genetic data makes it currently impossible to assemble a classification scheme that is both phylogenetic in
its ability to reveal evolutionary relationship and practical in its usefulness as a tool for routine
identification of unknown bacteria. The identification of bacteria relies primarily on a combination of
requirements for growth, morphological and biochemical characteristic that are relatively easy to
determine.
3.4.1 Energy and carbon sources
Growth, movement, metabolism, protein synthesis and many other essential cell processes demand
energy. Based on energy sources, prokaryotes can either be phototrophs-derives energy on chemical
energy harvested the breaking of chemical bonds. Organisms that use organic compounds, such as sugars
and amino acids as energy source are called organotrophs, while bacteria that obtains energy from
inorganic compounds, especially those containing nitrogen, iron and sugar are called heterotrophs.
Carbon creates another pair of categories for characterising bacteria according to their nutritional needs.
Some bacteria uses inorganic carbon in the form of carbon dioxide as the sole source of carbon, and
assimilates it into complex organic compounds that constitute part of the cell. These bacteria are called
autotrophs. Other bacteria that require a supply of carbon in the form of organic molecules are called
heterotrophs. Based on the energy and carbon sources, prokaryotes can generally be characterised into
four groups namely: photoautotrophs, photoheterotrophs, chemoautotrophs and chemoheterotrophs
3.4.2 Temperature requirement
The minimum temperature below which bacterial growth is possible is usually 30 - 40 0C lower than the
minimum temperature that can support growth. Based on temperature requirement for optimum growth,
bacteria can be categories into thermophiles, mesophiles and psychrophiles.
a) Thermophiles are bacteria whose optimum temperature is above 40 0C Such bacteria dwell in hot
springs, tropical soils, compost piles, hot water heater and thermal vents in ocean floor.
b) Mesophiles prefer temperature between 20 and 40 0C Human pathogens are mesophiles, adapted to our
body temperature of 37*C
c) Psychrophiles grow best at temperatures below 20 0C They are capable of growing at 0*C and some
grow at - 7*C These organisms proliferate in deep ocean waters, in artic and Antarctic and in frozen food.
, 3.4.3 pH requirement
Bacteria have a minimum, optimum and maximum pH for growth. Based on pH optimum, bacteria are
classified into three categories. Most bacteria grow best at a pH between 6 and 8, and are called
neutrophiles. Many neutrophiles produce acidic and alkaline waste products of normal metabolism, that
can rapidly lower or elevate pH to intolerable levels. A few bacteria prefer acidic or alkaline conditions.
Bacteria that grow best at pH below 5.5 are called acidophiles e.g Thiobacilli. They are found in soil
acidified by volcanic run-off or by acidic drainage from mines. Bacteria that thrives at a pH greater than
9, are called alkalophiles. Alkałophiles are most commonly found in alkaline lakes and soils.
3.4.4 Molecular oxygen requirement
Bacteria can be classified as aerobic, requiring the presence of molecular oxygen. Facultative anaerobes
can proliferate in either the presence or absence of molecule oxygen. Bacteria that require some oxygen in
a way that too much or too little is detrimental to them are classified as microaerophilic. Bacteria that do
not use molecular oxygen, and may even be killed by it presence are called anaerobes.
Anaerobes that can survive in the presence of oxygen but cannot use it are called the aerotolerant, while
those that are killed by even the briefest exposure to oxygen are called obligate or strict anaerobes.
Anaerobes and microaerophiles make up part of the normal flora inhabiting the vagina, urethra, mouth,
intestinal tract, as well as seawater, sewage and food.
3.4.5 Osmotic pressure tolerance
Some bacteria grow only at high osmotic pressures and are called halophiles e.g. Vibrio
parahaemolyticus. Organisms such as Staphylococcus that normally resides on the salty of human skin
can grow in high salts concentration. They are called halotolerant. Organisms that grow in the presence of
high sugar concentration are called osmophiles. Microbes that require high pressure to live are
Barophiles, while those that prefer atmospheric pressure and are able to withstand significant increase in
pressure are barotolerant, bacteria that require increasing level of carbon dioxide are called capnophiles.
Adaptation in these organisms include lipid components that allow the plasma membrane to maintain
fluidity and amino acid sequence that fold into active protein at high pressures.
3.6 Class Eubacteria e.g. Salmonella typhi
3.6.1 Composition and habitat.
3.1 Composition and Ecology
The monera are prokaryotic organisms having nuclei not surrounded by a membrane envelope. The
monera include three classes of organisms namely; cyanobacteria, eubacteria and archaebacteria.
Prokaryotes are among the earth's most abundant and diverse organisms, found in virtually every habitat
because of their metabolic diversity. This metabolic diversity has made the prokaryotes to be able of
survive some of nature's most hostile conditions, such as those found in hot springs, at temperatures close
to boiling point of water. Prokaryotes can also be found in desert soil, artic ice shelves, the depth of the
ocean, salt, mines, plant roots and the surface of larger organisms.
3.2 General Characteristics
Prokaryotic cells are typically smaller than eukaryotic cells, having dimension approximately like those
of mitochondria (2µmThe small sizes of prokaryotes enable them to have a higher rate of surface area to
cell volume than eukaryotic cells. This greater surface-to-volume ratio allows for efficient movement of
nutrients and waste between the environment and the interior of the cell, without the need for cytoplasmic
streaming or intricate internal membrane network or cytoplasmic organelles. Being small, allows
prokaryotic cells to be structurally simple and to increase their number rapidly.
3.3 Phylogenetic (molecular) Classification of Prokaryotes
Prokaryotes (monera) have no official classification scheme. However, the most stable taxonomic
classification scheme is one based on similarity in chromosomal DNA, the ultimate indicator of genetic
relatedness. Closely related bacteria descend from a common ancestor more recently, than does more
distantly related bacteria. This type of classification, which, help us to understand the evolutionary
relationship among organisms, is called phylogenetic classification.
In phylogenetic studies, modern systematists describe how species are related to one another on the basis
of fossil records and comparative anatomy. Phylogenetic trees commonly represent these relationships.
The tree branches at several points show where one species must have divided into two or more.
Individual branches of tree lines of evolution-often show a trend such as an increase in size or a change in
the manner of coiling. The study requires extensive information about the genetic composition of all
known bacteria. The genetic criterion for classifying prokaryotes into species relies on directly comparing
the nucleic acid of different bacteria.
3.3.1 DNA Base composition.
,A linear molecule of DNA is composed of nucleotides each of which contains one or four bases adenine,
cytosine, guanine or thymine. In base composition studies, the amount of two DNA components, guanine
(G) and cytosine (C) are measured, yielding a value, called the percent G + C. The sum of the guanine
and cytosine present in an organism's DNA is stable from generation to generation, and related organisms
have similar or identical G + C content. Thus, base composition can determine that two organisms are
different, but cannot be used to ensure that they are related.
3.3.2 DNA-DNA hybridisation (DNA homology)
DNA extracted from different species of an organism can be heated to break the hydrogen bonds and
separate the complementary strands completely. If single strands of different species are then mixed
together, the extent to which the DNA strand from one species will bind to the DNA from another species
will depend on the degree of similarity between their base sequences. Double stranded DNA reconstituted
from strands derived from a single species serves as a control, a perfect match against which hybrid DNA
can be compared. The extent of hydrogen bonding between strands of the hybrid DNA is measured by
gradually increasing temperature until the strands separate. The more closely related the DNA, the greater
the number of hydrogen bond, and the higher the temperature must be to separate the strands apart.
DNA-DNA hybridization measures the extent of hydrogen bonding between single stranded DNA
molecules obtained from two sources. The degree of similarity in the DNA strand will determine the
extent of the bonding together of two species DNA. Evolutionary trees constructed by this technique
generally agree with the phylogeny deduced by other methods, such as comparative morphology.
Although DNA-DNA hybridization can estimate the overall similarity of two genomes, it does not give
precise information about the match up in specific nucleotide sequences of DNA.
3.3.3 Ribosomal RNA analysis
The evolutionary history within the eukaryotes, cubacteria and archaebacteria is recorded in their rRNA.
Each of this cell type is characterised by unique 16S rRNA nucleotide sequence. called signature
sequence that defines that cell type. Based on this, some systematists have traced the entire eubacteria
back to eleven distinct evolutionary groups. These groups a proteobacteria, cyanobacteria, gram positive
bacteria, chlamydia, plantoyces, anaerobic bacteriodes and aerobic flavobacterium, green sulfur bacteria,
thermotoga and thermosipha. spirochete, deinococcus and green non sulfur bacteria.
Ribosomal RNA analysis helps in defining whether a prokaryote is a eubacterium or an archaebacterium
and the specific group to which it is most closely related. Organism that are about 20 to 60% related
according to DNA homology are usually considered members of a single genus. Organisms that are more
than 60 percent related are assigned to a single species. There is however, substantial natural variability
within a species, expressed as differences in immunological, structural and physiological characteristics.
For example, one organism may have the ability to produce a capsule, while another that does not, may be
able to use particular sugar as a nutrient. These differences are often used to further subdivide the
members of a species into sub groups called strains. Different strains within a species may differ from
,each other in biochemical properties, morphological characteristics. ability to infect different host, or
reactivity with different antibodies.
3.4 "Practical" Classifications
Generally very few details are known about the genetic make up of most known bacteria. This lock of
genetic data makes it currently impossible to assemble a classification scheme that is both phylogenetic in
its ability to reveal evolutionary relationship and practical in its usefulness as a tool for routine
identification of unknown bacteria. The identification of bacteria relies primarily on a combination of
requirements for growth, morphological and biochemical characteristic that are relatively easy to
determine.
3.4.1 Energy and carbon sources
Growth, movement, metabolism, protein synthesis and many other essential cell processes demand
energy. Based on energy sources, prokaryotes can either be phototrophs-derives energy on chemical
energy harvested the breaking of chemical bonds. Organisms that use organic compounds, such as sugars
and amino acids as energy source are called organotrophs, while bacteria that obtains energy from
inorganic compounds, especially those containing nitrogen, iron and sugar are called heterotrophs.
Carbon creates another pair of categories for characterising bacteria according to their nutritional needs.
Some bacteria uses inorganic carbon in the form of carbon dioxide as the sole source of carbon, and
assimilates it into complex organic compounds that constitute part of the cell. These bacteria are called
autotrophs. Other bacteria that require a supply of carbon in the form of organic molecules are called
heterotrophs. Based on the energy and carbon sources, prokaryotes can generally be characterised into
four groups namely: photoautotrophs, photoheterotrophs, chemoautotrophs and chemoheterotrophs
3.4.2 Temperature requirement
The minimum temperature below which bacterial growth is possible is usually 30 - 40 0C lower than the
minimum temperature that can support growth. Based on temperature requirement for optimum growth,
bacteria can be categories into thermophiles, mesophiles and psychrophiles.
a) Thermophiles are bacteria whose optimum temperature is above 40 0C Such bacteria dwell in hot
springs, tropical soils, compost piles, hot water heater and thermal vents in ocean floor.
b) Mesophiles prefer temperature between 20 and 40 0C Human pathogens are mesophiles, adapted to our
body temperature of 37*C
c) Psychrophiles grow best at temperatures below 20 0C They are capable of growing at 0*C and some
grow at - 7*C These organisms proliferate in deep ocean waters, in artic and Antarctic and in frozen food.
, 3.4.3 pH requirement
Bacteria have a minimum, optimum and maximum pH for growth. Based on pH optimum, bacteria are
classified into three categories. Most bacteria grow best at a pH between 6 and 8, and are called
neutrophiles. Many neutrophiles produce acidic and alkaline waste products of normal metabolism, that
can rapidly lower or elevate pH to intolerable levels. A few bacteria prefer acidic or alkaline conditions.
Bacteria that grow best at pH below 5.5 are called acidophiles e.g Thiobacilli. They are found in soil
acidified by volcanic run-off or by acidic drainage from mines. Bacteria that thrives at a pH greater than
9, are called alkalophiles. Alkałophiles are most commonly found in alkaline lakes and soils.
3.4.4 Molecular oxygen requirement
Bacteria can be classified as aerobic, requiring the presence of molecular oxygen. Facultative anaerobes
can proliferate in either the presence or absence of molecule oxygen. Bacteria that require some oxygen in
a way that too much or too little is detrimental to them are classified as microaerophilic. Bacteria that do
not use molecular oxygen, and may even be killed by it presence are called anaerobes.
Anaerobes that can survive in the presence of oxygen but cannot use it are called the aerotolerant, while
those that are killed by even the briefest exposure to oxygen are called obligate or strict anaerobes.
Anaerobes and microaerophiles make up part of the normal flora inhabiting the vagina, urethra, mouth,
intestinal tract, as well as seawater, sewage and food.
3.4.5 Osmotic pressure tolerance
Some bacteria grow only at high osmotic pressures and are called halophiles e.g. Vibrio
parahaemolyticus. Organisms such as Staphylococcus that normally resides on the salty of human skin
can grow in high salts concentration. They are called halotolerant. Organisms that grow in the presence of
high sugar concentration are called osmophiles. Microbes that require high pressure to live are
Barophiles, while those that prefer atmospheric pressure and are able to withstand significant increase in
pressure are barotolerant, bacteria that require increasing level of carbon dioxide are called capnophiles.
Adaptation in these organisms include lipid components that allow the plasma membrane to maintain
fluidity and amino acid sequence that fold into active protein at high pressures.
3.6 Class Eubacteria e.g. Salmonella typhi
3.6.1 Composition and habitat.
