BIO 320/ Diploma Science

Introduction to Biological Diversity

CHAPTER 3 : MONERA
BACTERIA
Introduction.
Initially, organisms are divided into Eukaryote and Prokaryote. In the five-kingdom system,
organisms are further divided into five kingdoms: Monera, Protista, Plantae, Fungi and Animalia.
The taxonomic Kingdom Monera consists of the bacteria. Bacteria are prokaryotes, and their
cell structure is basically different from the cells of other living organisms. The other four
kingdom in five kingdom system are consists of eukaryotic organisms.
In 1977, Carl Woese proposed dividing prokaryotes into the Bacteria and Archaea because of
the major differences in the structure and genetics between the two groups of organisms. This
arrangement of Eukaryota (also called "Eukarya"), Bacteria, and Archaea is called the threedomain system. Bacteria consist of kingdom Eubacteria, Archaea consists of kingdom
Archaeabacteria and Eukarya consists of kingdom Protista, Fungi, Plantae and Animalia.

Figure 3.1 Classification of living things

Metabolic diversity
Metabolic diversity of bacteria can be divided into heterotrophic and autotrophic. Autotrophic
bacteria can be divided into photoautotrophic and chemoautrophic. Like plants,
photoautotrophic bacteria synthesize organic compound by photosynthesis and they are selffeeders.
Chemoautotrophs bacteria are also self feeders. Carbon dioxide is the normal carbon source.
Some species strip organic compounds for electron and hydrogens. Others use inorganic
substances, such as gaseous hydrogen, sulfur, nitrogen compounds, and a form of iron.
Heterotrophic bacteria can be divided into photoheterotrophic and chemoheterotrophic.
Photoheterotrophic bacteria are not self-feeders. They use energy from the sun for

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

photosynthesis, but their carbon sources are fatty acid, complex carbohydrates and other
compounds that other various organisms produce.
Chemoheterotrophic bacteria are parasites or free-living saprobes and they are not self-feeder.

Shape of bacteria
Bacteria come in many shapes and sizes. Bacteria typically have one of three shapes: rodsshaped, spherical or spiral.
1.

Spherical bacteria, referred to as cocci (sing., coccus), occur singly or in groups. Cells
may be grouped in two (diplococci), in long chains (streptococci) or in cluster that looks
like bunches of grapes (staphylococci).

2.

Rod-shaped bacteria, known as bacilli (sing., bacillus) can occur as single rods or as
long chain of rods.

3.

Bacteria that have a shape of short helix is known as vibrio. Bacteria with rigid shape of
long helix are known as spirillum (pl., spirilla) while with flexible long helical shape is
known as spirochete.

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Figure 3.2 Shapes and grouping forms of various bacteria.

Bacterial Structure
Bacteria lack a nuclear membrane and membrane-bound organelles. Biochemical processes
that normally occur in a chloroplast or mitochondrion of eukaryotes will take place in the
cytoplasm of prokaryotes. The following are the important structures that make up the bacteria.
1.

Capsule - Some species of bacteria have a third protective covering, a capsule made up
of polysaccharides (complex carbohydrates). Capsules play a number of roles, but the
most important are to keep the bacterium from drying out and to protect it from
phagocytosis (engulfing) by larger microorganisms. The capsule is a major virulence
factor in the major disease-causing bacteria, such as Escherichia coli and
Streptococcus pneumoniae. Nonencapsulated mutants of these organisms are
avirulent, where they donot cause disease.

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Figure 3.3 Diagram of bacteria cell

2.

Cell Wall - Each bacterium is enclosed by a rigid cell wall composed of peptidoglycan, a
complex polymer consists of two unusual type of sugar (long polysaccharides) linked
with short polypeptides to form a single macromolecules that surrounds the entire
plasma membrane.
The wall provides rigid framework in order to maintain its shape. It also helps to anchor
appendages like the pili and flagella, which originate in the cytoplasm membrane and
protrude through the wall to the outside. The wall surrounds the cytoplasmic membrane,
protecting it from the environment.The strength of the wall is responsible for keeping the
cell from bursting under hypotonic condition or under stress.
Cell wall composition varies widely amongst bacteria and is one of the most important
factors in bacterial species analysis and differentiation.
A technique devised by Danish physician Hans Christian Gram in 1884, uses a staining
and washing technique to differentiate between the two forms of bacteria, gram-positive
and gram-negative bacteria.
When exposed to a gram stain, gram-positive bacteria retain the purple color of the
stain because the structure of their cell walls traps the dye. In gram-negative bacteria,

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

the cell wall is thin and releases the dye readily when washed with an alcohol or acetone
solution.
The cell wall of gram positive bacteria is very thick and consists mainly of peptidoglycans
which held together by amino acids. The cell wall of gram negative bacteria consists of
two layers, a layer of peptidoglycans and another layer of thick outer membranes. The
outer membrane resembles plasma membrane but contains polysaccharide linked to
lipids.

Figure 3.3(a) Gram staining

3.

Cytoplasm - The cytoplasm, or protoplasm, of bacterial cells is where the functions for
cell growth, metabolism, and replication are carried out. It is a gel-like matrix composed
of water, enzymes, nutrients, wastes, and gases and contains cell structures such as
ribosomes, a chromosome, and plasmids.
The cell envelope encases the cytoplasm and all its components. Unlike the eukaryotic
(true) cells, bacteria do not have a membrane enclosed nucleus. The chromosome, a
single, continuous strand of DNA, is localized, but not contained, in a region of the cell
called the nucleoid. All the other cellular components are scattered throughout the
cytoplasm.

4.

Cytoplasmic Membrane Consists of a layer of phospholipids and proteins. It encloses

the interior of the bacterium, regulating the flow of materials in and out of the cell.
Membranes are highly organized and asymmetric, having two sides, where each side
with a different surface and different functions. Membranes are also dynamic, constantly
adapting to different conditions.

5.

Flagella - Flagella (singular, flagellum) are hair like structures that provide a means of
locomotion for those bacteria that have them. They can be found at either or both ends
of a bacterium or all over its surface. The flagella beat in a propeller-like motion to help
the bacterium move toward nutrients; away from toxic chemicals; or, in the case of the
photosynthetic cyanobacteria; toward the light.

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

6.

Introduction to Biological Diversity

Nucleoid - The nucleoid is a region of cytoplasm where the chromosomal DNA is

located. It is not a membrane bound nucleus, but simply an area of the cytoplasm where
the strands of DNA are found. DNA is found attached to the cell wall as a single circular
thread.
Most bacteria have a single, circular chromosome that is responsible for replication,
although a few species do have two or more. In addition to DNA , most bacteria have
small amount of genetic information in the form of smaller circular fragments of DNA
strands, called plasmids, are also found in the cytoplasm.

7.

Plasmids - Plasmids are small, extrachromosomal genetic structures carried by many

strains of bacteria. Like the chromosome, plasmids are made of a circular piece of DNA.
Unlike the chromosome, they are not involved in reproduction. Only the chromosome
has the genetic instructions for initiating and carrying out cell division, or binary fission,
the primary means of reproduction in bacteria.
Plasmids replicate independently of the chromosome or become integrated into it.
Plasmids are passed on to other bacteria through two means. For most plasmid types,
copies in the cytoplasm are passed on to daughter cells during binary fission. Other
types of plasmids, however, form a tubelike structure at the surface called a pilus that
passes copies of the plasmid to other bacteria during conjugation, a process by which
bacteria exchange genetic information.
Plasmids often have gene that codes for catabolic enzymes, for genetic exchange or for
resistance to antibiotic drug, resistance to heavy metals, and virulence factors necessary
for infection of animal or plant hosts. The ability to insert specific genes into plasmids
have made them extremely useful tools in the fields of molecular biology and genetics,
specifically in the area of genetic engineering.

Figure 3.4 Structure of a bacterium highlighting the bacterial plasmid

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

8.

Introduction to Biological Diversity

Pili - Many species of bacteria have pili (singular, pilus), small hair like projections
emerging from the outside cell surface. These outgrowths assist the bacteria in attaching
to other cells and surfaces, such as teeth, intestines, and rocks.
Without pili, many disease-causing bacteria lose their ability to infect because they're
unable to attach to host tissue. Specialized pili are used for conjugation, during which
two bacteria exchange fragments of plasmid DNA.

9.

Ribosome - Ribosome are microscopic "factories" found in all cells, including bacteria.
They translate the genetic code from the molecular language of nucleic acid to that of
amino acidsthe building blocks of proteins. Proteins are the molecules that perform all
the functions of cells and living organisms.
Bacterial ribosomes are similar to those of eukaryotes, but are smaller and have a
slightly different composition and molecular structure. Bacterial ribosomes are never
bound to other organelles as they sometimes are (bound to the endoplasmic reticulum)
in eukaryotes, but are free-standing structures distributed throughout the cytoplasm.

Bacterial Reproduction
The usual method of asexual reproduction of bacteria is through cell division known as binary
fission. The bacterial chromosome is a single DNA molecule that first replicates, then attaches
each copy to a different part of the cell membrane. When the cell begins to pull apart, the
replicate and original chromosomes are separated. Following cell splitting (cytokinesis), there
are then two cells of identical genetic composition.

Figure 3.5 Rod-Shaped Bacterium, E. coli, dividing by binary fission.

A less common form of asexual reproduction among bacteria is budding. In budding a cell
develops a swell, or bud, that become bigger, matures, and finally separates from the mother

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

cell. A few species of bacteria such as actinomycetes, divide by fragmentation. Walls form
within the cell, which separates into several new cells.
Genetic material exchanged also occurs in bacteria. This process takes place by three different
mechanisms: transduction, transformation, and conjugation.
1.

In transformation, fragments of DNA released by dead bacteia or secreted by live

bacteria cell are taken in by another bacterial cell. This later on causes an alteration of
the bacterial cells genotype by taking up of foreign DNA.

Figure 3.5 Donation of DNA. Note that the entire DNA is not usually transferred,
only a small piece. The recombination is the bacterial equivalent of
sexual reproduction in eukaryotes.
2.

In the DNA-transfer process known as transduction, bacteriophages or virus that infect

bacteria carry portion of bacterial DNA or genes from one bacterial host to another as a
result of abnormality in the phage reproductive cycle. Transduction can be divided into
generalized transduction and specialized transduction.
In both type of transduction, the transferred DNA may recombine with the genome of the
new host cell.
In generalized transduction, random pieces of host chromosome are package within a
phage capsid. The phages carry only bacterial genes, no phages genes.
In specialized transduction, it involves the transfer of only a few specific genes from ane
bacterial cell to another by means of a phage, the lambda phage, which infects E.coli.

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Figure 3.5 Generalized transduction.

3.

In conjugation, a bacterial cell with DNA called F (fertility) factor is able to replicate and
transfer a copy of it's DNA to another cell without F factor through a tube called a sex
pilus. F factor may exist as a plasmid or become integrated into the chromosome. If it is
integrated into the chromosome, it may also transfer part of the chromosome. The sex
pilus usually breaks before the entire DNA from the donor cell is transferred. The DNA
that is transferred is used to replace similar genes in the recipient cell. Enzymes destroy
the replaced genes.
The DNA transfer is one way, where one cell donates DNA, and the other receives the
DNA. The donor, which can also be referred to as male and the recipient, sometimes
called the female.

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Figure 3.6 Diagram of bacterial conjugation.

10

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Figure 3.7 Conjugation and recombination in E. coli

Some bacteria form a spore within their cell membrane and this is known as endospores.
Endospores are dormant, extremely durable cells. Endospores can survive in very dry, hot or
frozen environment, or when food is insufficient.
Endospores are a method of survival, not one of reproduction. Endospore allows bacteria to
wait for favorable environmental conditions. When the condition becomes favorable, the cell wall
of the original cell lyses, releasing the endospore. This endospore will germinates, forming an
active, growing bacterial cell.
Certain disease causing bacteria, such as the one that causes the disease Anthrax can be
virulent or capable of causing an infection 1300 years after forming their endospore!

11

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Figure 3.8 Electron micrographs illustrating formation of an endospore.

Note, the sequence illustrated above goes from left to right.

Grouping of Bacteria
There are two different ways of grouping bacteria. The can be grouped by how they obtain their
energy.
1.

Bacteria that have to consume and break down complex organic compounds are
heterotrophs. This includes species that are found in decaying material as well as those
that utilize fermentation or respiration.

2.

Bacteria that able to manufacture their own organic molecules from simple raw materials
are known as autotroph. Photosynthetic autotroph, or photoautotroph, obtain their
energy from light. Chemosynthetic autotroph or chemoautroph, get their energy by
oxidizing inorganic chemicals.

They can be divided into three types based on their response to gaseous oxygen.
1.

Whether they are heterotroph or autotroph, most bacteria cells are aerobic. Aerobic
bacteria require oxygen for their health and existence and will die without it.

2.

Obligate anerobic bacteria cannot tolerate gaseous oxygen at all and die when exposed
to it.

3.

Facultative anaerobes prefer oxygen, but can live without it.

Importance of Bacteria
Bacteria play important ecological function as decomposers and are important in recycling
nutrients. Many bacteria have symbiotic relationship with other organism and some are
important pathogens of plants and animals.
Bacteria also involve in fermentation of many food and beverages. Lactic acid bacteria are used
in the production of acidophilus milk, yogurt, pickles, olives, and cheeses. Bacteria also involve
in the production of antibiotics. They are also used in the production of industrial compounds
such as acetone.

12

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Some pathogenic bacteria produce exotoxins, strong poisons that either is secreted from the
cell or leak out when the bacterium is damaged. Exotoxin can cause specific symptoms
Other pathogenic bacteria produce endotoxins. Endotoxins are not secreted by the pathogenic
bacteria but are components of the cell walls of most gram-negative bacteria. These substances
affect the host only when they are released from dead bacteria. Endotoxins can cause systemic
symptoms such as fever and they are destroyed by heating.

ARCHAEA

Introduction
The scientific community was understandably shocked in the late 1970s by the discovery of an
entirely new group of organisms, the Archaea. Dr. Carl Woese and his colleagues at the
University of Illinois were studying relationships among the prokaryotes using DNA sequences,
and found that there were two distinctly different groups.
Those "bacteria" that lived at high temperatures or produced methane clustered together as a
group different from the usual bacteria and the eukaryotes. Because of this huge difference in
genetic makeup, Woese proposed that life be divided into three domains as in the fundamental
three-domain system of classification: Eukarya, Eubacteria or Bacteria, and Archaebacteria or
Archaea. Archaea are, similarly to bacteria, single-celled organisms lacking nuclei and are
therefore classified as prokaryotes, known as Monera in the five kingdom taxonomy.
Characteristics of Archaea
Like bacteria, archaeans have no internal membranes and their DNA exists as a single loop
called a plasmid. However, their tRNAs have a number of features that differ from all other
living things.
The tRNA or transfer RNA molecules are important in decoding the message of DNA and in
building proteins. Certain features of tRNA structure are the same in bacteria, plants, animals,
fungi, and all known living things except the Archaea.
There are even features of archaeal tRNA that are more like eukaryotic than bacteria, meaning
that Archaea share certain features in common with eukaryotic and not with bacteria.
The same is true of their ribosomes, the giant processing molecules that assemble proteins for
the cell. While bacterial ribosomes are sensitive to certain chemical inhibiting agents, archaeal
and eukaryotic ribosomes are not sensitive to those agents. This may suggest a close
relationship between Archaea and eukaryotes.
Several other characteristics also distinguish Archaea from Bacteria. Unlike most bacteria, in
Archaea there is no peptidoglycan in their cell wall. Further, both bacteria and eukaryotes have
membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes
composed of glycerol-ether lipids.

13

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

These differences may be an adaptation on the part of Archaea to be hyperthermophe.

Archaeans also have flagella that are particularly different in composition and development from
the superficially similar flagella of bacteria.

Table 1: A Comparison of the Three Domains of Life

14

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

Form
Individual archaeans range from 0.1 to over 15 m in diameter, and some form aggregates or
filaments up to 200 m in length. They occur in various shapes, such as spherical, rod-shaped,
spiral, lobed, or rectangular. They also exhibit a variety of different types of metabolism.
Habitats
Based on their physiology, the Archaea can be divided into three types: methanogens (archaea
that produce methane); extreme halophiles (archaea that live at very high concentrations of
salt (NaCl); and extreme (hyper) thermophiles (archaea that live at very high temperatures).

1.

Methanogens are obligate anaerobes that will not tolerate even brief exposure to
oxygen. Anaerobic environments are plentiful, and these include marine and fresh-water
sediments, bogs (swamps) and deep soils, intestinal tracts of animals, and sewage
treatment facilities. Methanogens are normal inhabitants of the rumen of cows and other
ruminant animals.
Methanogens have an incredible type of metabolism that can use H2 as an energy
source and CO2 as a carbon source for growth. In the process of making cell material
from H2 and CO2, the methanogens produce methane (CH4) in a unique energygenerating process. The end product (methane gas) accumulates in their environment.
Methanogen metabolism produced most the natural gas (fossil fuel) reserves that are
tapped as energy sources for domestic or industrial use. Methanogens represent a
microbial system that can be exploited to produce energy from waste materials. Large
amounts of methane are produced during industrial sewage treatment processes, but
the gas is usually wasted rather than trapped for recycling.

2.

Extreme halophiles live in natural environments such as the Dead Sea, the Great Salt
Lake, or evaporating ponds of seawater where the salt concentration is very high, which
is as high as 5 molar or 25 percent NaCl.
These prokaryotes require salt for growth and will not grow at low salt concentrations.
Their cell walls, ribosomes, and enzymes are stabilized by Na+.
Halobacterium halobium, the prevalent species in the Great Salt Lake, adapts to the
high-salt environment by the development of "purple membrane", actually patches of
light-harvesting pigment in the plasma membrane. The pigment is a type of rhodopsin
called bacteriorhodopsin. This bacteriorhodopsin protein is chemically very similar to
the light-detecting pigment rhodopsin, found in the vertebrate retina.
Bacteriorhodopsin captures and reacts with light in a way that forms a proton gradient on
the membrane allowing the synthesis of ATP. The process is different from
photosynthesis carried out by plants, algae, or cyanobacteria. This is the only example in
nature of non photosynthetic photophosphorylation.

15

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

3.

Introduction to Biological Diversity

The extreme thermophiles or hyperthermophiles require a very high temperature (45o

110o C) and sometimes acidic environment for growth. Their membranes and enzymes
are unusually stable at high temperatures.
Most of these Archaea require element sulfur for growth. Some are anaerobes that use
sulfur as electron acceptors for respiration in place of oxygen. Some are lithotrophs that
oxidize sulfur as an energy source. Lithotroph is an organism that depends on inorganic
compounds as electron donors for energy production.
Sulfur-oxidizers grow at low pH that is less than pH 2 because they acidify their own
environment by oxidizing S (sulfur) to SO4 (sulfuric acid). These hyperthermophiles are
inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as
hot springs and geysers in Yellowstone National Park at pH values 1 to 2 and at
temperature near 60o C.
Others live in volcanic areas under the sea. One species, found in and thermal deep-sea
vents ("smokers") and cracks in the ocean floor able to live at temperature from 80o to
110o C

Archaeans may be the only organisms that can live in extreme habitats such as thermal vents or
hypersaline water. They may be extremely abundant in environments that are hostile to all other
life forms. Nevertheless, archaeans are not restricted to extreme environments; new research is
showing that archaeans are also quite abundant in the plankton of the open sea.

16

Ainun Jariah Manaf/UiTM Pahang

BIO 320/ Diploma Science

Introduction to Biological Diversity

QUESTIONS
1.

Describe the important metabolic and structural features of bacteria. Make sketches of
the three basic shapes of bacterial cells

2.

What are the differences between the archaebacteria and the eubacteria.?

3.

Contrast the cell wall of a gram-positive bacterium with that of a gram-negative

bacterium.

4.

Compare between binary fission, transduction, transformation and conjugation

5.

By using labeled diagrams, describe conjugation processes of bacteria.

6.

Archaea can be divided into three types: methanogens, extreme halophiles and
extreme thermophiles. Briefly describe each of the types of archaea.

7.

Explain the metabolic diversity of bacteria of each of the group below

a.
b.
c.
d.
e.

8.

Obligate anaerobes
Facultaive anaerobes
Aerobes
Autotrophic bacteria
Heterotrophic bacteria

(10 marks)

Illustrate a prokaryote. Label the diagram accordingly

Compare between extreme halophiles and extreme thermophiles

17

(6 marks)
(4 marks)

Ainun Jariah Manaf/UiTM Pahang