MODULE IN GENERAL MICROBIOLOGY

Unit 2
Microbial Taxonomy
Introduction
In the previous unit, you have been introduced to the different groups of microbes and have learned
that microbes remain to be the most diverse group among the biological diversity on Earth. The
microbes are composed of archaea, bacteria, fungi, protozoa and viruses which are very different
and taxonomically diverse groups. You have learned that they are present in all geographical
locations implying that they are capable of adapting and surviving under varied physico-chemical
conditions. You have also learned of their vast contribution in maintaining a balanced, sustainable
ecosystem and their contribution to the growth of the industry through the various biomolecules, i.e.
enzymes, antibiotics, biofuels, obtained from them. Microbes have unabashedly contributed much
to the quality of life. These significant microbial characteristics and their uncontestable
contributions despite their microscopic sizes warrant their proper documentation and cataloguing.

In addition, there remains to be untapped potential of the microbes and it is because either they have
not been discovered or they have not been fully characterized. To understand this vast microbial
diversity, some of the initial steps involve discovering, classifying and identifying them.

In this unit, you will learn the various systems of classification, criteria used for classification, and
tests that are used to identify microorganisms.

Learning Outcomes
At the end of this unit, you are expected to:

1. Discuss the need for a comprehensive classification system

2. List the different levels of the taxonomic classification system
3. Describe how systematics and taxonomy relate to phylogeny
4. Explain why the traditional definitions of species using reproductive isolation do not apply
to Bacteria and Archaea.
5. Explain what features of 16S rRNA make it useful to compare the evolutionary
relationship between organisms.
6. Determine the two most related and two least related organisms from a short list of 16S
rRNA sequences.
7. Draw inferences about evolutionary relatedness of organisms based on phylogenetic trees.

Lesson 1: Taxonomy and Phylogeny

Introduction
Taxonomy (from the Greek for orderly arrangement) is the science of classification of living forms.
It is a system of orderly classification of organisms into categories called taxons (taxa).It aims to
establish the relationships between one group of organisms and another and to differentiate them.
Moreover, taxonomy places organisms in meaningful, useful groups with precise names to provide
1
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022
MODULE IN GENERAL MICROBIOLOGY

a common reference for identifying organisms already classified. For example, when a bacterium
capable of hydrolyzing cellulose is isolated from termites, identifying the isolate is facilitated by
matching its characteristics to a list of characteristics of previously classified bacteria. This would
allow microbiologists to work with them and communicate with other scientists efficiently.

Taxonomy has evolved from the typological concept of classification into a very dynamic field
brought about by the development of new techniques in molecular biology and genetics. Modern
taxonomy, also known as biosystematics, identifies taxonomic affinity based on evolutionary,
genetic, and morphological characteristics. Systematics or phylogeny is the science of naming and
organizing organisms based on common ancestry, or evolutionary relatedness. Hence, taxonomy
can be considered as a branch of systematics.

In this lesson, you will learn about the development of the field of taxonomy and systematics, the
important contribution of pioneer taxonomists, and the goal of taxonomy and systematics.

Learning Objectives
At the end of this lesson, you will be able to:

 define taxonomy, taxon, systematics and phylogeny.

 discuss the limitations of a two-kingdom system.
 identify the contribution of Linnaeus, Whittaker and Woese.
 discuss the advantages of the three-domain system.
 differentiate a eukaryotic species and prokaryotic species.
 classify microbes into taxonomic ranks.

Activating Prior Learning

Before you proceed with this lesson, let us do some simple classification activity. Below are some
microbes which you encountered in the previous lessons. Think of a criterion or a basis for
classifying them and put the microbes under each category.
Saccharomyces Gonyaulax Penicillium Plasmodium
Rhizopus Escherichia Spirogyra Thiomargarita
Giardia Staphylococcus
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
_______________________________________________________________________________
What criterion did you use in grouping the microbes? ____________________________________
_______________________________________________________________________________

2
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022
MODULE IN GENERAL MICROBIOLOGY

CORE CONTENT
I. History of Taxonomy

Aristotle (384-322 BC), the Greek philosopher, first introduced two key concepts of classification
of organisms by type and binomial definition. He was the first to attempt to classify all the kinds
of living organisms by grouping them according to their similarities, such as animals with blood
and animals without blood. He further classified the animals with blood to live-bearing and egg-
bearing. Aristotle’s view of life was hierarchical. He assumed that creatures can be grouped from
lowest to highest with humans at the highest. Aristotle divided organisms into plants and animals.
He subdivided them by their habitat - land, sea, or air dwellers.
John Ray (1627–1705), a British naturalist, was the first to use Latin for naming plants but are
actually long descriptions about the plant. He was sometimes referred to as the father of English
natural history because of his published works on plants, animals, and natural theology which were
an important step towards modern taxonomy. He coined the term species.
In 1735, Carolus Linnaeus, a Swedish naturalist, considered as the “Father of Taxonomy”
introduced a hierarchical system of classification and the system of binomial nomenclature. He
classified based on structure and proposed dividing all living organisms into two kingdoms -
Plantae and Animalia. He divided each kingdom into classes and later grouped into phyla for
animals and divisions for plants. Binomial nomenclature is the system of giving two-word names,
for the genus and species. Though modern taxonomy is based on the Linnaean binomial system,
the original rationale behind this system is not used now.
In 1857, Carl von Nageli proposed for the inclusion of bacteria and fungi in Kingdom Plantae.
However, as studies continue to provide information, Ernst Haeckel, an eminent German biologist
and naturalist, proposed the Kingdom Protista in 1866 to include all single-celled organisms and
those multicellular forms not developing complex tissues. A diverse group of organisms including
protozoa, algae, fungi, sponges and slime molds were classified within this kingdom, though their
relatedness was minimal. Haeckel divided animals, plants, and microorganisms into 3 kingdoms
namely Animalia, Plantae and Protista.
However, it was with the advent of electron microscopy that physical differences between cells have
been elucidated further. In 1957, Roger Stainer and his associates used electron microscopy to
demonstrate significant differences between prokaryotic and eukaryotic cells, suggesting more than
three kingdoms were required. In 1968, Robert G.E. Murray proposed the Kingdom Prokaryotae, or
Monera to include the bacteria.
Robert Whittaker (1920-1980) recognized an additional kingdom for the fungi. The basis was
mainly on differences in nutrition. Kingom Plantae consists mostly of multicellular autotrophs;
Animalia with multicellular heterotrophs; and Fungi with multicellular saprotrophs. Kingdoms
Protista and Monera included unicellular and simple cellular colonies. In 1969, Whittaker devised
the five-kingdom system in which the prokaryotes were placed in the Kingdom Prokaryotae, or
Monera, and the eukaryotes comprised the other four kingdoms: Protista, Fungi, Plantae and
Animalia.
3
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022
MODULE IN GENERAL MICROBIOLOGY

Viruses are not included in the Five-Kingdom System of Classification because they are not living
cells; they are acellular. Because viruses are non-cellular entities, they are not included in any of the
taxonomic schemas described above. Viruses are often categorized according to the organisms they
infect, but new taxonomic schemes are being developed to better demonstrate the natural
relationships between viruses.
 Self-Assessment Questions
2.1.1. What are the 2 Kingdoms of organisms proposed by Carolus Linnaeus? _____________
_____________________________________________________________________
2.1.2. What were the criteria used by Linnaeus in dividing organisms into 2 kingdoms?
_____________________________________________________________________
2.1.3. What were the demerits of grouping organisms into the following classification systems?
a) 2-kingdom
_______________ ______________________________________________________
_____________________________________________________________________

b) 3-kingdom
_____________________________________________________________________
_____________________________________________________________________

c) 4-kingdom
_____________________________________________________________________
_____________________________________________________________________

II. Phylogeny and the Six-Kingdom Classification

The search for a natural classification system began as the field of biological sciences developed.
But this time the modern classification rationale is based on evolutionary relatedness. In modern
classification, organisms are placed into categories, or taxa, that reflect their evolutionary
relationships. The study that deals with the evolutionary history of organisms is known as
phylogeny. The hierarchy of taxa reflects evolutionary, or phylogenetic, relationships. Phylogeny
as a method of classification uses molecular biology to analyze a cell’s DNA or RNA specifically
the 16S rRNA. This technique will ultimately be more reliable and easier than taxonomy.
Subsequent discoveries brought about by the advent of new molecular biology techniques revealed
that there are actually two types of prokaryotic cells and one type of eukaryotic cell. These findings
have been derived from observations that there are differences in the nucleotide bases of their
ribosomal RNA (rRNA) indicating that there are three distinctly different cell groups: the
eukaryotes and two different types of prokaryotes - the bacteria and the archaea. Therefore, 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 (Fig. 2.1). In the three-domain system,
4
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022
MODULE IN GENERAL MICROBIOLOGY

organisms are classified by cell type. However, other differences include membrane lipid structure,
transfer RNA molecules, and sensitivity to antibiotics.

Under the Domain Eukarya are the kingdoms of plants, animals, fungi and protists. On the other
hand, the Domain Bacteria includes all the pathogenic prokaryotes as well as the many of the
nonpathogenic prokaryotes found in soil and water, including the photoautotrophic prokaryotes. 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) methanogens, 2) extreme halophiles, and 3) hyperthermophiles.
Carl Woese showed that the three domain system is a ‘six kingdom system’ that unites the
eukaryotic kingdoms into the Domain Eukarya based on their relative genetic similarity when
compared to the Domain Bacteria and the Domain Archaea. Hence, he proposed the six-kingdom
classification, namely, Kingdom Archaebacteria, Kingdom Eubacteria, Kingdom Protista,
Kingdom Fungi, Kingdom Plantae, and Kingdom Animalia. Woese found that the six kingdoms
naturally cluster into the three main categories based on the sequence of 16S ribosomal RNA
genes.

Taxonomic Hierarchy

Adding domains to the previously established taxonomic ranks generates a slightly modified
hierarchy as shown below:
Domain (plural = Domains, the largest or most encompassing)
Kingdom (plural = Kingdoms)
Phylum (plural = Phyla), sometimes called Divisions
Class (plural = Classes)
5
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022
MODULE IN GENERAL MICROBIOLOGY

Order (plural = Orders)

Family (plural = Families)
Genus (plural = Genera)
Species (the most specific category)

Each kingdom consists of divisions or phyla, which, in turn, are divided into classes, orders,
families, genera, and species.

The smallest unit for classification using taxonomy is species. A eukaryotic species is a group of
closely related organisms that are capable of interbreeding and is reproductively isolated. Groups of
similar species are called genera or genus (singular). Collections of genera with similar properties
are called families. A group of similar families constitutes an order, and a group makes up a
phylum.

All phyla or divisions that are related to each other make up a kingdom, and related kingdoms are
grouped into domains.

In the case of prokaryotes, species is defined somewhat differently than eukaryotic species. A
prokaryotic species is a collection of strains (i.e., populations) that share many stable properties
(i.e., have a high degree of overall similarity) and that differ considerably from populations or strains
in related groups.

Strains are subgroups that have some characteristic that is measurably different from other members
of the species, but not so different that they should be considered different species. A strain is a
population of cells that descended from a single cell, hence, clone.

 Self-Assessment Questions

2.1.4. What is the meant by a natural system of classification? _________________________

_____________________________________________________________________
_____________________________________________________________________

2.1.5. Compare the 5-kingdom classification proposed by Robert Whittaker and the 6-kingdom
classification proposed by Carl Woese.
a) What are the essential differences between the 2 systems? _______________________
____________________________________________________________________
____________________________________________________________________
b) What are the justifications for the 6-kingdom classification? ____________________
____________________________________________________________________
____________________________________________________________________

6
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022
MODULE IN GENERAL MICROBIOLOGY

III. Components of Taxonomy

The basic components of taxonomy are the following: 1) identification, 2) nomenclature and 3)
classification. On the other hand, the basic components of systematics are the following: 1)
identification, 2) nomenclature, 3) phylogeny and 4) classification.
Identification is the practical side of taxonomy. It is the process of determining that a particular
(organism) belongs to a recognized taxon. Identification places an individual into an already
existing classification scheme.
Nomenclature is the branch of taxonomy concerned with the assignment of names to taxonomic
groups in agreement with published rules. Carolus Linnaeus proposed the binomial
nomenclature system which formally gives two names to organisms. These names are the genus
name and specific epithet (species). The genus name is capitalized and the specific epithet is in
lower cases, and these are either italicized when in print or underlined when written by hand. Both
names are Latinized and include either a Latin or Greek roots providing descriptive information.
For example, in Escherichia coli, the genus is Escherichia and the species is coli. Note the correct
form used, genus name is underlined and capitalized, species name is not capitalized and is
underlined. Alternatively the two words can be italicized, such as Escherichia coli. The genus
name can be abbreviated like E. coli. More importantly, Linnaeus used latinized names to provide
“one” common language for systematists. E. coli is the species that is known as “coliforms” in a
nonscientific fashion. This bacterium which was discovered in the human colon was named in
honor of its discoverer, Theodor Escherich.

Several scientific entities are responsible for establishing rules governing the naming of organisms.
These are the following:

1. International Code for Zoological Nomenclature (for protozoa)

2. International Code for Botanical Nomenclature (for fungi and algae)
3. International Committee on Systematics of Prokaryotes published in the Bacteriological
Code
4. International Committee on the Taxonomy of Viruses

Classification is the arrangement of organisms into groups or taxa. It assembles groups into larger
groups. The taxonomic classification scheme for prokaryotes is found in Bergey’s Manual of
Systematic Bacteriology, the standard manual for identifying bacteria. Here, prokaryotes are divided
into two domains: Bacteria and Archaea. Each domain is divided into phyla. 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.

An earlier manual, Bergey’s Manual of Determinative Bacteriology provides identification schemes

for identifying bacteria and archaea based on morphology, differential staining and biochemical
tests.

Phylogeny is the study of the ancestral relationship and evolutionary history of a taxonomic group.
Modern taxonomy brings out phylogenetic classification or classification based on evolutionary
relationships or lineages.
7
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022
MODULE IN GENERAL MICROBIOLOGY

 Self-Assessment Questions

2.1.6. Distinguish traditional taxonomy and modern taxonomy. _________________________

______________________________________________________________________
______________________________________________________________________
______________________________________________________________________

2.1.7. Is goal of identification similar to nomenclature? Why or why not? ________________

______________________________________________________________________
______________________________________________________________________

Application I:
 Activity 2.1.1. Understanding Nomenclature and Classification
Write the taxonomic classification of the following microorganisms:
Bacillus anthracis Lactobacillus caseii Clostridium
botulinum
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
Background of its
name

Assessment
This shall be conducted in the LENS. Schedule shall be announced later.

8
College of Arts and Sciences, CAGAYAN STATE UNIVERSITY
First Semester, SY 2021-2022