2 Classification of Microorganisms

2.1 Taxonomy
The science of classification, especially the classification of living forms, is called
taxonomy (from the Greek for orderly arrangement). The objective of taxonomy is to
classify living organisms - that is, to establish the relationships between one group of
organisms and another and to differentiate them. There may be as many as 100
million different living organisms, but fewer than 10% have been discovered, much
less classified and identified. Taxonomy also provides a common reference for
identifying organisms already classified. For example, when a bacterium suspected of
causing a specific disease is isolated from a patient, characteristics of that isolate are
matched to lists of characteristics of previously classified bacteria to identify the
isolate. Finally, taxonomy is a basic and necessary tool for scientists, providing a
universal language of communication.

2.2 What is Classification?

Whenever we work with a large number and variety of things, we usually sort them
into groups. Each group contains those things that are similar to one another. We
may then separate each of those groups into smaller groups that are even more
alike. The grouping of similar things for a specific purpose is called classification.
Although it may be instinctive for human to classify things, there are also practical
reasons for doing this. For example, a supermarket manager classifies the foods in
his/her store by storing all the cereals together, all the meats together, all the
cookies together, and so on. Stamp collectors classify their stamps. They place all
the Canadian stamps in one page and all the American stamps in another. The words
in a dictionary are classified by alphabetical listings. Clearly, we classify things to
make it easier to keep track of what we have, and to find particular items.

2.2.1 Early Biological Classification: Aristotle’s Classification

System
Biologists have long recognized the need to classify living things. In fact, humans
have been classifying living things for thousands of years. The earliest humans
probably classified organisms as plants and animals. They may have further
classified plants as edible or poisonous, and the animals as harmful or harmless.
However, it was 300 BC before the first serious attempt was made to classify all the

1
organisms known. This attempt was made by the Greek philosopher and scientist,
Aristotle and his students.

Since only about 1,000 kinds of organisms were known at that time, a very simple
classification scheme could be used. Aristotle and his students first classified the
organisms as plant or animal. They then classified the animals according to where
they lived. This resulted in three groupings: Air Animals, Water Animals, and
Land Animals. They classified the plants according to the structure of stems. Those
with soft stems were called Herbs; those with a single woody stem were called
Trees; and those with many small woody stems were called Shrubs.

All Living Things

Plants Animals

Herbs Shrubs Trees Water Air Land

Animals Animals Animals

Aristotle’s classification system survived for almost two thousand years. However, by
the beginning of the 18th century, over 10,000 kinds of organisms were known and
Aristotle’s system was unable to classify them all. Many of newly discovered
organisms would not fit into any category of Aristotle’s simple system. A new system
was obviously needed.

2.2.2 Beginning of Modern Biological Classification:

The Contribution of Carolus Linnaeus
Carolus Linnaeus, a Swedish botanist, developed a simple classification system
that forms the basis of our modern method of classification. At the start of the 18th
century about 10,000 kinds of organisms were known. By the end of that century
over 70,000 kinds were known. Linnaeus tried to develop a classification system for
this large number of organisms. By 1753 his system was well developed and modern
taxonomy began.

2
2.2.2.1 The Basis for Linnaeus Classification
Biologists use the word diversity to mean differences, or the number of kinds of
living things. There seed to be so many kinds of living things and they seem to be so
different from one another. Yet, if we study them closely, we can see many
likenesses. For example, at first glance lions, horses, humans, and mice seem to
have little in common. A closer look however, shows that all have hair, a distinct
head, four limbs, two ears, and warm blood. That is, they have similar structural
features.

Linnaeus decided to use structural features as the basis for his classification system.
Therefore, he grouped organisms according to their structural similarities. These
organisms with very similar structural features were considered to be the same
species. Thus all modern-day humans belong to one species, all house cats belong to
one species, and all sugar maple trees belong to one species.

2.2.2.2 Binomial Nomenclature

Once Linnaeus had decided on a basis for classifying organisms, he then developed a
system for naming them. His system is quite simple. He gave each species a name
that consists of two words. This system is called binomial nomenclature. He used
Latin words for these names because all scientists wrote in Latin in time of Linnaeus.
Thus, the human is Homo sapiens, and the domestic (house) cat is Felis domesticus.
The first word of each name is called the genus and the second word is called the
species. The genus begins with a capital letter and the species does not. The genus
and species are either printed in italics or underlined.

2.2.2.3 Why Use Scientific Names?

One reason for using Latin scientific names instead of common names is that
common names can be confusing or misleading. For example Felis concolor is called
a cougar, mountain lion, puma, panther, painter, and many names. The common
name for a domestic cow is “la vache” in French, ‘die Kuh” in German, “la vaca” in
Spanish, and “garoo” in Bengali. However, in all languages the scientific name is the
same, and there is no confusion if we call the cow Bos taurus.

3
2.3 Naming and Classifying Microorganisms
2.3.1 Nomenclature
The system of nomenclature (naming) for organisms in use today was established in
1735 by Carolus Linnaeus. Scientific names are latinized because Latin was the
language traditionally used by scholars. Scientific nomenclature assigns each
organism two names-the genus (plural: genera) is the first name and is always
capitalized; the specific epithet (species name) follows and is not capitalized. The
organism is referred to by both the genus and the specific epithet, and both names
are underlined or italicized. By custom, after a scientific name has been mentioned
once, it can be abbreviated with the initial of the genus followed by the specific
epithet.

Scientific names can, among other things, (i) describe an organism, (ii) honor a
researcher, or (iii) identify the habitat of a species. For example, consider
Stapllylococcus aureus, a bacterium commonly found on human skin. Staphylo-
describes the clustered arrangement of the cells; coccus indicates that they are
shaped like spheres. The specific epithet, aureus, is Latin for golden, the color of
many colonies of this bacterium. Table 2.1 contains more examples. The genus of
the bacterium Escherichia coli is named for a scientist, Theodor Escherich, whereas
its specific epithet, coli, reminds us that E. coli live in the colon, or large intestine.

Table 2.1: Making scientific names familiar

___________________________________________________________________________
Organism Source of genus name Source of specific epithet
___________________________________________________________________________
Salmonella typhimurium Honors public health Causes stupor (typh-) in mice
(Bacterium) microbiologist (muri-)
Daniel Salmon
Streptococcus pyogenes Appearance of cells in chains Forms pus (pyo-)
(Bacterium) (strepto-)
Saccharomyces cerevisiae Fungus (-myces) that uses Makes beer (cerevisia)
(Yeast) sugar (saccharo-)
Penicillium chrysogenum Tuftlike or paintbrush Produces a yellow (chryso-)
(Fungus) (penicill-) appearance pigment
microscopically
Trypanosoma cruzi Corkscrew- (trypano-, borer; Honors epidemiologist
(Protozoan) soma-, body) Oswaldo Cruz
___________________________________________________________________________

Let's consider some more examples. Our own genus and specific epithet are Homo
sapiens. The noun, or genus, means man; the adjective, or specific epithet, means

4
wise. A mold that contaminates bread is called Rhizopus stolonifer. Rhizo- (root)
describes root-like structures on the fungus; stolo- (a shoot) describes the long
hyphae.

Binomials are used by scientists worldwide, regardless of their native language,

which enables them to share knowledge efficiently and accurately. Several scientific
entities are responsible for establishing rules governing the naming of organisms.

(1) Rules for assigning names for protozoa and parasitic worms are published in
the International Code of Zoological Nomenclature.
(2) Rules for assigning names for fungi and algae are published in the International
Code of Botanical Nomenclature.
(3) Rules for naming newly classified prokaryotes and for assigning prokaryotes to
taxa are established by the International Committee on Systematics of
Prokaryotes and are published in the Bacteriological Code.
(4) Descriptions of prokaryotes and evidence for their classifications are published
in the International Journal of Systematic and Evolutionary Microbiology before
being incorporated into a reference called Bergey's Manual.

According to the Bacteriological Code, scientific names are to be taken from Latin (a
genus name can be taken from Greek) or Latinized by the addition of the appropriate
suffix. Suffixes for order and family are -ales and -aceae, respectively.

As new laboratory techniques make more detailed characterizations of microbes

possible, two genera may be reclassified as a single genus, or a genus may be
divided into two or more genera. For example, the genera "Diplococcus" and
Streptococcus were combined in 1974; the only diplococcal species is now called
Streptococcus pneumoniae. In 1984, DNA hybridization studies indicated that
"Streptococcus faecalis" and "Streptococcus faecium" were only distantly related to
the other streptococcal species; consequently, a new genus called Enterococcus was
created, and these species were renamed E. faecalis and E. faecium.

In 2001, based on DNA-DNA hybridization and rRNA studies, some species of

Chlamydia were moved to a new genus, Chlamydophila, based on rRNA analysis.
Making the transition to a new name can be confusing, so the old name is often
written in parentheses. For example, a physician looking for information on the cause
of a patient's pneumonia-like symptoms (meliodosis) would find the bacterial name

5
Burkholderia (Pseudomonas) pseudomallei. Obtaining the name of the organism is
important in determining what treatment to use; antifungal drugs will not work
against bacteria, and antibacterial drugs will not work against viruses.

2.3.2 Classification of Prokaryotes

The taxonomic classification scheme for prokaryotes is found in Bergey's Manual of
Systematic Bacteriology, 2nd edition. The first two volumes have been published, with
the remaining three volumes to follow over the next few years. In Bergey's Manual,
prokaryotes are divided into two domains: Bacteria and Archaea. Each domain is
divided into phyla. Remember, the classification is based on similarities in nucleotide
sequences in rRNA. Classes are divided into orders; orders, into families; families,
into genera; and genera, into species.

A prokaryotic species is defined somewhat differently than a eukaryotic species,

which is a group of closely related organisms that can interbreed. Unlike
reproduction in eukaryotic organisms, cell division in bacteria is not directly tied to
sexual conjugation, which is infrequent and does not always need to be species-
specific. A prokaryotic species, therefore, is defined simply as a population of cells
with similar characteristics. The members of a bacterial species are essentially
indistinguishable from each other but are distinguishable from members of other
species, usually on the basis of several features. As you know, bacteria grown at a
given time in media are called a culture. A pure culture is often a clone, that is, a
population of cells derived from a single parent cell. All cells in the clone should be
identical. However, in some cases, pure cultures of the same species are not
identical in all ways. Each such group is called a strain. Strains are identified by
numbers, letters, or names that follow the specific epithet. Bergey's Manual provides
a reference for identifying bacteria in the laboratory, as well as a classification
scheme for bacteria.

2.3.3 Classification of Eukaryotes

In 1969, simple eukaryotic organisms, mostly unicellular, were grouped as the
Kingdom Protista, a catchall kingdom for a variety of organisms. Historically,
eukaryotic organisms that didn't fit into other kingdoms were placed in the Protista.
Approximately 200,000 species of protistans have been identified thus far, and these
organisms are nutritionally quite diverse-from photosynthetic to obligate intracellular

6
parasite. Ribosomal RNA sequencing is making it possible to divide protists into
groups based on their descent from common ancestors. Consequently, for the time
being, the organisms once classified as protists are being divided into clades, that
is, genetically related groups. For convenience, we will continue to use the term
protist to refer to unicellular eukaryotes and their close relatives.

Fungi, plants, and animals make up the three kingdoms of more complex eukaryotic
organisms, most of which are multicellular. The Kingdom Fungi includes the
unicellular yeasts, multicellular molds, and macroscopic species such as mushrooms.
To obtain raw materials for vital functions, a fungus absorbs dissolved organic matter
through its plasma membrane. The cells of a multicellular fungus are commonly
joined to form thin tubes called hyphae. The hyphae are usually divided into
multinucleated units by cross-walls that have holes, so that cytoplasm can flow
between the cell-like units. Fungi develop from spores or from fragments of hyphae.

The Kingdom Plantae (plants) includes some algae and all mosses, ferns, conifers,
and flowering plants. All members of this kingdom are multicellular. To obtain
energy, a plant uses photosynthesis, the process that converts carbon dioxide and
water into organic molecules used by the cell.

The kingdom of multicellular organisms called Animalia (animals) includes sponges,

various worms, insects, and animals with backbones (vertebrates). Animals obtain
nutrients and energy by ingesting organic matter through a mouth of some kind.

2.3.4 Classification of Viruses

Viruses are not classified as part of any of the three domains. Viruses are not
composed of cells, and they use the anabolic machinery within living host cells to
multiply. A viral genome can direct biosynthesis inside a host cell, and some viral
genomes can become incorporated into the host genome. The ecological niche of a
virus is its specific host cell, so viruses may be more closely related to their hosts
than to other viruses. The International Committee on Taxonomy of Viruses defines a
viral species as a population of viruses with similar characteristics (including
morphology, genes, and enzymes) that occupies a particular ecological niche.

Viruses are obligatory intracellular parasites, so they must have evolved after a
suitable host cell had evolved. There are two hypotheses on the origin of viruses: (I)
they arose from independently replicating strands of nucleic acids (such as

7
plasmids), and (2) they developed from degenerative cells that, through many
generations, gradually lost the ability to survive independently but could survive
when associated with another cell.

2.3.5 Methods of Classifying and Identifying Microorganisms

A classification scheme provides a list of characteristics and a means for comparison
to aid in the identification of an organism. Once an organism is identified, it can be
placed into a previously devised classification scheme. Microorganisms are identified
for practical purposes-for example, to determine an appropriate treatment for an
infection. They are not necessarily identified by the same techniques by which they
are classified. Most identification procedures are easily performed in a laboratory and
use as few procedures or tests as possible. Protozoa, parasitic worms, and fungi can
usually be identified microscopically. Most prokaryotic organisms do not have
distinguishing morphological features or even much variation in size and shape.
Consequently, microbiologists have developed a variety of methods to test metabolic
reactions and other characteristics to identify prokaryotes.

Bergey's Manual of Determinative Bacteriology has been a widely used reference

since the first edition was published in 1923. The American bacteriologist David
Bergey was chairman of the group who compiled information on the known bacteria
from articles published in scientific journals. Bergey's Manual of Determinative
Bacteriology (9th edition, 1994) does not classify bacteria according to evolutionary
relatedness but instead provides identification (determinative) schemes based on
such criteria as cell wall composition, morphology, differential staining, oxygen
requirements, and biochemical testing. The majority of Bacteria and Archaea have
not been cultured, and scientists estimate that only 1% of these microbes have been
discovered.

Medical microbiology (the branch of microbiology dealing with human pathogens) has
dominated the interest in microbes, and this interest is reflected in many
identification schemes. However, to put the pathogenic properties of bacteria in
perspective, of the more than 2,600 species listed in the Approved Lists of Bacterial
Names, fewer than 10% are human pathogens.

We next discuss several criteria and methods for the classification and routine
identification of microorganisms. In addition to properties of the organism itself, the

8
source and habitat of a bacterial isolate are considered as part of the identification
processes. In clinical microbiology, a physician will swab a patient's pus or tissue
surface. The swab is inserted into a tube of transport medium. Transport media are
usually not nutritive and are designed to prolong viability of fastidious pathogens.
The physician will note the type of specimen and testes) requested on a lab
requisition form. The information returned by the lab technician will help the
physician begin treatment.

2.4 The Genus and the Species Concepts

2.4.1 The Genus Concept
A genus (plural genera) groups species that are similar. For example, maple trees
belong to the genus Acer. Thus sugar maple (Acer saccharum), silver maple (Acer
saccharinum), and red maple (Acer rubrum) belong to the same genus Acer. Their
leaves are similar and other features are similar but not identical. Every genus has
characteristics that make it stand out clearly from other living things.

2.4.2 The Species Concept

Linnaeus grouped as a species those organisms that he felt were very similar in
structural features. In simple terms, a single species is a distinct kind of organism,
with a characteristic shape, size, behaviour, and habitat that remains constant from
year to year. Today a species (plural also species) is defined as a group of individuals
that are alike in many ways and interbreed under natural conditions to produce
fertile offspring (children). Potato (Solanum tuberosum) and the eggplant (Solanum
melongena) belong to the same genus because they are similar in many ways.
However, they belong to two different species because they are not identical and
they have reproductive barrier, that is, they cannot mate (cross or breed) with one
another to produce fertile offspring. The members within a species can mate or
cross. Thus all varieties of potatoes are in the species because they can interbreed to
produce fertile offspring.

9
2.5 The Main Classification Groups (Taxa)
There are seven main taxa (singular: taxon) or classification groups (Table 2.1).
This system of classification can be compared to a tree. Many leaves (Species) are
on a tiny twig (Genus). Several tiny twig is (genera) are on a larger twig (Family).
Several larger twigs (families) are on a little branch (Order). Some little branches
(orders) are on a larger branch (Class). Some larger branches (classes) are on a
main limb of the tree (Phylum). The few main limbs (phyla) make up the whole tree
(Kingdom).

1. Species: Species (plural also species) is a group of individuals that are alike in
many ways and interbreed under natural conditions to produce fertile offspring
(children).
2. Genus: Genus (plural genera) is a group of species that are closely similar in
structure and evolutionary origin.
3. Family: Family is a group of similar kinds of genera. That is, similar genera are
grouped to form a taxon called family.
4. Order: Similar families are grouped to form a taxon called order.
5. Class: Similar orders are grouped to form a taxon called class.
6. Phylum or Division: Similar classes are grouped to form a taxon called
phylum or division. Zoologists favour phylum and botanists favour division.
7. Kingdom: All the phyla or divisions that contain animals are grouped in the
kingdom Animalia, and all the phyla or divisions that contain plants are grouped
in the kingdom Plantae.
8. Domain: Related kingdoms are grouped into a domain.

Table 2.1: Classification of Human Being and Escherichia coli

___________________________________________________________________________
Taxon Human Gorilla Dog Cat Colon bacillus
___________________________________________________________________________
Domain Eukarya Eukarya Eukarya Eukarya Bacteria
Kingdom Animalia Animalia Animalia Animalia None assigned
Phylum/Division Chordata Chordata Chordata Chordata Proteobacteria
Class Mammalia Mammalia Mammalia Mammalia -Proteobacteria
Order Primates Primates Carnivora Carnivora Enterobacteriales
Family Homonidae Pongigae Canidae Felidae Enterobacteriaceae
Genus Homo Gorilla Canis Felis Escherichia
Species sapiens gorilla familiaris domesticus coli
___________________________________________________________________________

10
2.6 Selecting a Classification System
Some biologists feel that two kingdom, Plantae and Animalia, are enough to classify
all living things. Others prefer three kingdoms; still others use four, and some use
five kingdoms.

2.6.1 A Two-Kingdom System of Classification

Carolus Linnaeus introduced this system of classification in 1753. This is the oldest
and perhaps still the most widely used system of classification. It groups all
organisms into two Kingdoms, (1) Plantae, which includes bacteria, algae, fungi and
higher plants, and (2) Animalia, which includes protozoa and higher animals. That
is, all living things are assumed to be either plants or animals.

This system works well for most organisms. Problems arise, however, with some of
the one-celled organisms, particularly the flagellates. Because these organisms have
flagella and show locomotion (movement from one place to another) they seem to be
animals. However, they also contain chlorophyll and make their own food by
photosynthesis. In this respect they are like plants. For many years botanists have
claimed that the flagellates were plants and zoologists have claimed that they were
animals.

2.6.2 A Three-Kingdom System of Classification

Ernst H Haeckel introduced this system of classification in 1866. The problem of
the flagellates is handled by a 3-Kingdom System of classification. This system still
has the Kingdoms (1) Plantae and (2) Animalia, however, it has a third Kingdom,
(3) Protista. The kingdom Protista contains all microorganisms, including the
bacteria, blue-green algae, protozoa, unicellular algae (e.g., flagellales), and
microscopic fungi.

This system was recognized by many biologists during the first half of the 20 th
century and is still very popular. Yet it also has some problems. For example, the
bacteria are very different from the other protists like flagellates, protozoa and one-
celled algae. Their cells lack true nuclei (prokaryotic in nature) unlike all other
protists, which have true nuclei (eukaryotic in nature).

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2.6.3 A Four-Kingdom System of Classification
To solve the problem with prokaryotic and eukaryotic microorganisms in classification
some biologists proposed a fourth Kingdom, Monera, which contains only the
bacteria or prokaryotic microorganisms. Therefore, the four kingdoms are (1)
Plantae, (2) Animalia, (3) Protista which includes only the eukaryotic
microorganisms, and (4) Monera which includes prokaryotic microorganisms.

Still there have some major problems in 4-Kingdom System. Some biologists took a
close look at the fungi. They decided that the fungi were so different from the other
organisms in Kingdom Plantae that they should also be moved to a Kingdom of their
own. Fungi do not have chlorophyll and therefore cannot carry out photosynthesis;
therefore, they are very different from plants.

2.6.4 A Five-Kingdom System of Classification

Robert H Whittaker introduced this system of classification in 1969. In this system
fungi were separated from the Kingdom Plantae as they are quite different from the
usual plants. Therefore, the five Kingdoms are (1) Plantae, (2) Animalia, (3) Fungi
(4) Protista, and (5) Monera.

Even the 5-Kingdom System is not without problems. Organisms that have
traditionally been called algae are now spread over three Kingdoms. The blue-green
algae (cyanobacteria) are in Kingdom Monera, unicellular algae are in kingdom
Protista, and multicellular algae in Kingdom Plantae. Already some biologists think
that blue-green algae are not algae at all, but are simply bacteria. Remember, no
classification system is perfect. No classification system will remain unchanged.

2.6.5 Phylogenetic System of Classification

Carl R Woese introduced a completely new approach in classification of organisms
in 1978 that is based on evolutionary (phylogenetic) relationship among organisms.
While at the University of Illinois, Woese turned his attention toward determining the
origins of life on earth. He meticulously analysed ribosomal ribonucleic acid (rRNA),
genetic molecules that coordinate part of protein production. Because rRNA shows
only slight variation from one generation to the next, it is an excellent tool for
revealing the evolutionary, or family, relationships among organisms. Woese spent
nearly a decade analysing the rRNA of various types of bacteria and arranging them

12
into a microbial evolutionary tree. Use this concept all organisms are now classified
into three Domains. They are (1) Archaea, (2) Bacteria, and (3) Eukarya.

The summary of various classification systems is shown in Table 2.2.

Table 2.2: Summary of Various Classification Systems

______________________________________________________________________________________
Classification System Kingdom/Domain Organisms Included
______________________________________________________________________________________
2-Kingdom System (1) Plantae Bacteria, Cyanobacteria,
Carolus Linnaeus, 1753 Unicellular algae, Multicellular algae,
Fungi and Higher plants
(2) Animalia Protozoa and Higher animals
______________________________________________________________________________________
3-Kingdom System (1) Plantae Multicellular algae, Fungi and
Ernst H Haeckel, 1866 Higher plants
(2) Animalia Higher animals
(3) Protista All microorganisms: Bacteria,
Cyanobacteria, Unicellular algae and
Protozoa
______________________________________________________________________________________
4-Kingdom System (1) Plantae Multicellular algae, Fungi and
Higher plants
(2) Animalia Higher animals
(3) Protista Eukaryotic microorganisms:
Unicellular algae and Protozoa
(4) Monera Prokaryotic microorganisms: Bacteria,
Archaebacteria and Cyanobacteria
______________________________________________________________________________________
5-Kingdom System (1) Plantae Multicellular algae and Higher plants
Robert H Whittaker, 1959 (2) Animalia Higher animals
(3) Fungi All fungi: Yeasts and Molds
(4) Protista Eukaryotic microorganisms:
Unicellular algae and Protozoa
(5) Monera Prokaryotic microorganisms: Bacteria,
Archaebacteria and Cyanobacteria
______________________________________________________________________________________
Phylogenetic System (1) Archaea Archaebacteria
Carl R Woese, 1978 (2) Bacteria Bacteria
(3) Eukarya Eukaryotic organisms: Algae, Fungi,
Higher plants, Protozoa and
Higher animals
______________________________________________________________________________________

13
2.7 The Study of Phylogenetic Relationships
2.7.1 The Three Domains
The discovery of three cell types was based on the observations that ribosomes are
not the same in all cells. Ribosomes provide a method of comparing cells because
ribosomes are present in all cells. Comparing the sequences of nucleotides in
ribosomal RNA from different kinds of cells shows that there are three distinctly
different cell groups: the eukaryotes and two different types of prokaryotes - the
Bacteria and the Archaea.

In 1978, Carl R Woese proposed elevating the three cell types to a level above
kingdom, called Domain. Woese believed that the Archaea and the Bacteria,
although similar in appearance, should form their own separate Domains on the
evolutionary tree (Figure 2.1).

Figure 2.1: The Three-Domain System.

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Organisms are classified by cell type in the three domain systems. In addition to
differences in rRNA, the three domains differ in membrane lipid structure, transfer
RNA molecules, and sensitivity to antibiotics (Table 2.3).

Table 2.3: Some Characteristics of Archaea, Bacteria, and Eukarya

______________________________________________________________________________________
Characteristic Archaea Bacteria Eukarya
______________________________________________________________________________________
Cell type Prokaryotic Prokaryotic Eukaryotic

Cell wall Varies in Contains Varies in

composition; peptidoglycan composition;
contains no contains
peptidoglycan carbohydrates

Membrane lipids Composed of branched Composed of straight Composed of straight

carbon chain sattached carbon chains carbon chains
to glycerol by ether attached to glycerol attached to glycerol
linkage by ester linkage by ester linkage

First amino acid in Methionine Formylmethionine Methionine

protein synthesis

Antibiotic sensitivity No Yes No

rRNA loop Lacking Present Lacking

Common arm of Lacking Present Present

tRNA
______________________________________________________________________________________

In this widely accepted scheme, Animals, Plants, Fungi, and Protists are kingdoms in
the Domain Eukarya. The Domain Bacteria includes all of the pathogenic prokaryotes
as well as many of the non-pathogenic prokaryotes found in soil and water. The
photoautotrophic prokaryotes are also in this domain. The Domain Archaea includes
prokaryotes that do not have peptidoglycan in their cell walls. They often live in
extreme environments and carry out unusual metabolic processes.

Archaea include three major groups:

1. The methanogens, strict anaerobes that produce methane (CH4) from carbon
dioxide and hydrogen.
2. Extreme halophiles, which require high concentrations of salt for survival.
3. Hyperthermophiles, which normally grow in extremely hot environments.

The evolutionary relationship of the three domains is the subject of current research
by biologists. Originally, Archaea were thought to be the most primitive group,

15
whereas bacteria were assumed to be more closely related to eukaryotes. However,
studies of rRNA indicate that a universal ancestor split into three lineages. That split
led to the Archaea, the Bacteria, and what eventually became the nucleoplasm of the
eukaryotes. The oldest known fossils are the remains of prokaryotes that lived more
than 3.5 billion years ago. Eukaryotic cells evolved more recently, about 1.4 billion
years ago. According to the endosymbiotic theory, eukaryotic cells evolved from
prokaryotic cells living inside one another, as endosymbionls. In fact, the similarities
between prokaryotic cells and eukaryotic organelles provide striking evidence for this
endosymbiotic relationship (Table 2.4).

Table 2.4: Prokaryotic cells and eukaryotic organelles compared

______________________________________________________________________________________
Characteristic Prokaryotic cell Eukaryotic cell Eukaryotic organelles
(Mitochondria and
Chloroplasts)
______________________________________________________________________________________
DNA One circular; Linear Circular
some two circular;
some linear
Histones In Archaea Yes No
First amino acid Formylmethinine Methionine Formylmethinine
in protein (Bacteria)
synthesis Methionine
(Archaea)
Ribosomes 70S 80S 70S
Growth Binary fission Mitosis Binary fission
______________________________________________________________________________________

The original nucleoplasmic cell was prokaryotic. However, infoldings in its plasma
membrane may have surrounded the nuclear region to produce a true nucleus.
Recently, French researchers provided support for this hypothesis with their
observations of a true nucleus in Gemmata bacteria.

That nucleoplasmic cell provided the original host in which endosymbiotic bacteria
developed into organelles. An example of a modern prokaryote living in a eukaryotic
cell is shown in Figure 2.2. The cyanobacterium-like cell ( Cyanophora paradoxa)
and the eukaryotic host require each other for survival.

16
Figure 2.2: Cyanophora paradoxa. This organism. in which the eukaryotic host and the
bacterium require each other for survival, provides a modern example of how eukaryotic cells
might have evolved.

In sequencing the genome of a prokaryote called Thermotoga maritima,

microbiologist Karen Nelson has discovered that this species has genes similar to
members of both the Domain Bacteria and the Domain Archaea. Her findings suggest
that Thermotoga is one of the earliest cells. For this reason, Thermotoga is referred
to as one of the "deeply branching genera," that is, it is near the origin or "root" of
the evolutionary tree.

Taxonomy provides tools for clarifying the evolution of organisms, as well as their
interrelationships. New organisms are being discovered every day, and taxonomists
continue to search for a natural classification system that reflects phylogenetic
relationships.

2.7.2 A Phylogenetic Hierarchy

In a phylogenetic hierarchy, grouping organisms according to common properties
implies that a group of organisms evolved from a common ancestor; each species
retains some of the characteristics of the ancestor. Some of the information used to
classify and determine phylogenetic relationships in higher organisms comes from
fossils. Bones, shells, or sterns that contain mineral matter or have left imprints in
rock that was once mud are examples of fossils.

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The structures of most microorganisms are not readily fossilized. Some exceptions
are the following:
1. A marine protist whose fossilized colonies form the White Cliffs of Dover,
England.
2. Stromatolites, the fossilized remains of filamentous bacteria and sediments that
flourished between 0.5 and 2 billion years ago.
3. Cyanobacteria-like fossils found in rocks in Western Australia that are 3.0 to 3.5
billion years old. These are widely believed to be the oldest known fossils.

Because fossil evidence is not available for most prokaryotes, their phylogeny must
be based on other evidence. But in one notable exception, scientists may have
isolated living bacteria and yeast 25 to 40 million years old. In 1995, the American
microbiologist Raul Cano and his colleagues reported growing Bacilus sphaericus
and other as yet unidentified microorganisms that had survived embedded in amber
(fossilized plant resin) for millions of years. If confirmed, this discovery should
provide more information about the evolution of microorganisms.

Conclusions from rRNA sequencing and DNA hybridization studies of selected orders
and families of eukaryotes are in agreement with the fossil records. This has
encouraged workers to use DNA hybridization and rRNA sequencing to gain an
understanding of the evolutionary relationships among prokaryotic groups.

References

1. Microbiology: An Introduction, Tenth Edition. 2010. Gerard J Tortora, Berdell R Funke and
Christine L Case. 2010. Pearson Benjamin Cummings, San Francisco.
2. Foundations in Microbiology, Eighth Edition. 2011. Kathleen Park Talaro and Arthur Talaro. The
McGraw−Hill Companies, Inc., New York.

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