Learning Module in

Module 1

MARK ANTHONY I. JOSE

Microbiology and Biotechnology Group
Department of Biological Sciences
College of Science and Mathematics
MSU-Iligan Institute of Technology
Outline for Module 1
I. Module Objectives
II. Definition of Taxonomy
III. Introduction to Microbial
Taxonomy
IV. Importance of Microbial Taxonomy
V. Brief History of the different
System of Classification
VI. Definition of Species in
Microbiology
 Module Objectives

:
Module 1
Introduction DEFINE TAXONOMY WHY TAXONOMY IS WHAT IS THE AIM OF

to Microbial IMPORTANT? TAXONOMY?

Taxonomy

DEFINE SYSTEMATICS DISCUSS THE HISTORICAL DISCUSS THE DEFINITION OF

BACKGROUND OF THE SPECIES IN THE FIELD OF
KINGDOM SYSTEM AND THE MICROBIOLOGY
DOMAIN SYSTEM
 • The word taxonomy derived the Greek
words Taxis (arrangement or order) and
Nomos (law) or Nemien (to distribute or
govern).
• Taxonomy is the branch of science that
deals with naming and grouping of
What is organisms based on the degree of
similarity and arranging them based on
Taxonomy? their evolutionary relationship. Thus,
taxonomy is related to the nomenclature,
classification, and phylogeny of the
organisms.
• For classification purposes, organisms are
organized into sub-species, species,
genera, families, orders, classes, etc.
 Essential for accurate identification of
organisms

Importance
Place organisms into useful groups
of with precise names which will help in
facilitating scientific communications.

Taxonomy
Allows the researchers and scientists
in organizing huge amounts of
knowledge important in making
hypotheses about the organisms.
 It deals with It also deals with the Relationships are Phylogenetic trees of Thus,
characterizing and study of the visualized as species and higher
arranging the organisms diversification of living evolutionary trees taxa are used to
systematics is
in an orderly manner. forms (past and
such as cladograms, study the used to
present) and the
relationship among phylogenetic trees, evolutionary traits understand the
living things through phylogenies etc. (molecular evolutionary
time. characteristics) and history of
the biogeographical
distribution of the organism’s life
organisms. on Earth.
AIMS OF TAXONOMY

To provide
To show the
Classification of universal
relationships
organisms identification of an
among organisms
organism
 CLASSIFICATION and
IDENTIFICATION
• Classification refers to the orderly arrangement of
organisms into groups.
• Identification is the practical use of classification
criteria to distinguish certain organisms from the
others.
• this is important in:
• Verifying the authenticity and utility of a
strain
• Isolation and identification of a disease-
causing organisms
Nomenclature and Taxonomic Hierarchy
• Carolus Linnaeus (1707-1778) a Swedish Botanist known as father of
taxonomy is credited for establishment of taxonomy as a separate
science. He was instrumental in framing the rules for naming the
organisms, which he applied uniformly while giving his classification. It
was he who popularized the binomial nomenclature that is the
modern scientific way of naming organisms.

• In binomial nomenclature name of every organism is composed of two

parts: first is called generic name representing the taxon – Genus to
which it belongs and second is called specific epithet- Species.
➢ The generic name always starts with capital letter and specific
name always with small letter. These scientific names are used
https://creation.com/carl-linnaeus uniformly regardless of regions/countries or languages, and two
Carolus Linnaeus different organisms cannot possess same scientific name.
(1707-1778) ➢ The names of different organisms used in binomial nomenclature
system must be derived from Latin or if names to be used are from
different languages they must be treated as Latin.
The nomenclature of organisms is governed by the set of rules by the International
Codes of Nomenclature.

International Code for Nomenclature for Bacteria (ICNB)

There are different codes of nomenclature International Code of Zoological Nomenclature (ICZN)

for the different groups of organisms: International Code of Botanical Nomenclature (ICBN)
International Code of Nomenclature for Algae, Fungi, and Plants (ICN)

The scientific name of an organisms is always mentioned in italics or underlined font

style, when cited in any text.

The name of the author who gave the first correct name is written (Roman style) in an
abbreviated form after the scientific name.
 • Another aspect of taxonomy is classification, the
grouping of different organisms based on shared
features into different categories called TAXA.
• Different taxa are then arranged in a hierarchical
manner starting from lower to higher ranks:

Taxonomical Species
Genus

Hierarchy Family
Order
Class
Phylum/Division
Kingdom
Domain
• The ordered arrangement of various
taxa is called TAXONOMIC
HIERARCHY.
• In this hierarchy, the organism is
assigned with a species name and
species of very similar organisms are
grouped into genus. The genera
having very similar characteristics
are grouped together into a family,
and similarly several families form an
order, several orders into a class,
similar group of classes into
phylum/division, and ultimately
similar phyla are grouped into a
Kingdom.
• Earlier taxonomists divided the living
organisms based on morphological
characters, and there was no
sophisticated tool available to study
the living world.
• The only information available were
only from visible macro-organisms
and were arranged into two groups
based on the easily observable
(phenotypic) characteristics. These
groups are known as PLANTS and
ANIMALS. This system of
classification is known as TWO-
KINGDOM CLASSIFICATION SYSTEM
and was followed for a very long
period of time in the history of
biological sciences.
• The invention of the microscope in the 16th
century made it possible to explore the living
word, which was impossible to do with the naked Euglena Gerd Guenther/Science Photo Library/Getty Images
eyes.
• This exploration revealed the new world of
microorganisms sharing features of both plants
and animals. A classic example for this is the
Euglena, an autotrophic, green-colored motile
organism with definite shape and size and
obtains food by ingestion process in the absence
of light. Similarly, a photoautotrophic organism
called Chlamydomonas exhibits an animal-like
features such as motility and definite size and
shape.
Chlamydomonas https://cbs.umn.edu/blogs/cbs-connect/convenient-chlorophyte
 https://microbenotes.com/haeckels-three-kingdom-system-of-classification/

• Fungi have plant-like features such as irregular shapes and

indefinite growth, immobile, and possess heterotrophic
mode of nutrition which is a common characteristics of
animals. However, this microorganisms could not have an
appropriate placement in two-kingdom.
• In order to classify these microorganisms, Ernst H. Haeckel
(1866) proposed a three-kingdom classification in which he
added a new kingdom called the PROTISTA. In this new
kingdom, he included all simple living microscopic organisms http://scihi.org/ernst-haeckel-phyletic-museum/

such as bacteria, protozoa, fungi, microalgae, and sponges. Ernst Haeckel (1837 – 1919)
 Five-Kingdom System
(Whittaker’s concept) • In 1969, Robert H. Whittaker
(American taxonomist),
proposed a five-kingdom
classification in which
Kingdom Protista was split
into Protista and Fungi.
• In this classification, cellular
organisms have been
divided into five kingdoms,
namely: Animalia, Plantae,
Protista, Fungi, and Monera.

https://link.springer.com/article/10.1007%2FBF00726879 http://www.biologychamps.com/Blog/54

R.H. Whittaker(1920 – 1980)

• Whittaker delimited the five kingdoms based on the three main criteria:
• Type of cell structure
• Degree of cellular organization
• Mode of nutrition
• Beside these major characteristics, he also gave importance to the
characters of ecological role-played and mode of reproduction.
• He also attempted to establish a phylogenetic relationship among
various groups of different kingdoms.
• According to him, the earliest living forms called Progenote,
produced prokaryotic organisms known as Monerans.
• Monera gave rise to protists probably through the association of several
types of primitive and advanced monerans.
• Protists in tern gave rise to plants, animals, and fungi.
Whittaker’s five-kingdom classification based on complexity of cell, cellular organization, mode of nutrition and ecological role played
 • Includes all multicellular
Kingdom Plantae photosynthetic eukaryotic
organisms commonly called as
PLANTS. The important
constituents are macroalgae,
bryophytes, pteridophytes,
gymnosperms, and
angiosperms.
• Plant body is either thalloid
(macroalgae and some
bryophytes) or differentiated
into roots, stem, leaves, and a
non-motile with cell wall that
is made of cellulose.
• Can undergo sexual and
asexual reproduction. It’s
mode of nutrition is through
photosynthesis (Autotrophic).
• Ecological role: PRODUCERS

https://www.biologyexams4u.com/2013/02/the-plant-kingdom-introduction.html#.YC5YWWEzbDc
Kingdom Animalia

• Vertebrate and invertebrate animals

• Group of macroscopic animals derived from zygote and
includes coelenterates, worms, arthropods, annelids,
mollusks, fishes, amphibians, birds, reptiles, and
mammals.
• Multicellular organisms with higher degree of body
organization where tissue differentiation usually leads to
specialized organ formation.
• Eukaryotic organisms without cell wall and chlorophyll
• Exhibits mobility, definite growth, and sensitive to
different stimuli.
• Mode of reproduction: sexual; embryo stage is usually
present.
• Ecological role: CONSUMERS
 Kingdom Fungi

• Generally composed of multicellular or multinucleate

achlorophyllous and spore-producing eukaryotic
organisms that includes molds, mildews, truffles,
truffles, morals, mushrooms, etc.
• Organism’s body is in mycelial form; cell wall is present
and made up of chitin or cellulose.
• Mode of nutrition is absorptive heterotrophy in which
an organism secretes digestive enzymes into the
substrate and then absorbs the digested food.
• Asexual reproduction is the primary mode of
reproduction. Some may exhibit sexual reproduction
that leads to the formation of specialized spores.
• They play the ecological role as DECOMPOSERS.
https://www.facebook.com/HiBesshy/photos/pcb.1874271289354379/1874270249354483/?type=3&theater
Kingdom Protista
• Group of organisms differing widely with
one another except that they are all simple
and minute eukaryotes such as microalgae,
protozoa, and slime molds.
• They are generally unicellular, but some may
be colonial in form.
• They contain true nuclei and membrane-
bound organelles; cell wall may be present
or absent.
• Mode of nutrition is either autotrophic (via
photosynthesis) or heterotrophic
(ingestion/absorption).
• They usually reproduced asexually, but when
sexual reproduction is present, embryo is https://discover.hubpages.com/education/Kingdom-Protista

not formed.
Kingdom Monera

• Generally composed of all the prokaryotic organisms such as

eubacteria, cyanobacteria (blue-green algae), and
archaebacteria.
• They are unicellular, mycelial, colonial, and filamentous in form. https://kingdomsmidtermproject.weebly.com/monera.html

• They lack true nuclei and other membrane bound organelles such
as mitochondrion, chloroplast, Golgi bodies, lysosomes, etc.
• They also lack DNA which is the genetic material and is called
nucleoid, is not found associated with histone proteins; cell wall
is often present but chemically made up of a material other than
the cellulose.
• Their mode of nutrition varies from autotrophy and
heterotrophy.
• Only asexual reproduction is present an may take place through
binary fission, fragmentation, budding, and sporulation.
https://www.askiitians.com/biology/biological-classification/kingdom-monera.html
Merits of the Five-Kingdom System
Separation of Prokaryotes as placed in Kingdom Monera is well appreciated as they differ from the
eukaryotes in terms of cellular, physiological, and reproductive organization.

There are intermediate and transitional forms of unicellular eukaryotes which had been included amongst
animals and plants were placed under Kingdom Protista that helps resolved conflict or anomaly.

Fungi have their own unique physiological, biochemical, and structural characteristics and have never been
related to plants. Their placement in a separate Kingdom was long overdue.

Creation of the five-kingdom was based on the level of organization and nutritional strategy. As a result, the
animal and plant kingdom appear to be more homogenous than they were in the two-kingdom system.

The five-kingdom system has tried to bring out phylogenic relationships even amongst the primitive forms
hence appear more natural.
The cons

• Although this system is advanced, it fails to distinguish archaebacteria

from eubacteria.
• The Kingdom Protista is highly heterogenous group of organisms which
seems to have polyphyletic evolution.
• placement of algae based on the degree of cellular organization into
different Kingdoms appears to be unrealistic.
• The placement of brown and red algae in the plant kingdom even if they
are unrelated to other members.
• Viruses are important form of life was not considered to be part of this
classification system.
 The Three Domain Classification

• This is known as the Three Domains of Life

• The most important sequence-based investigation was initiated in 1977
by Carl Woese and his collaborator George Fox. They compared the
small subunit ribosomal RNAs (SSU rRNAs) from a variety of organisms
to determine that all living organisms belong to one of three domains:
Archaea, Bacteria, and Eukarya, thereby separating the procaryotes or
“Monera” into two groups.
• This initial observation has been further refined and substantiated by
additional biochemical and genetic evidence. Recall from chapter 3 that
most bacteria have cell walls with peptidoglycan and membrane lipids
with ester-linked, straight-chained fatty acids that resemble eucaryotic
membrane lipids
The study of chemical structure and
Example: cytochrome protein, a component of the
sequences of macromolecules such as proteins electron transport chain occurring in the
and nucleic acids can give insights and mitochondria; rbcl gene, encoding the rubisco
enzyme present in the chloroplast; small subunit
understanding the functions and evolutionary ribosomal RNAs (SSUrRNAs)
relationship of different organisms.

Found uniformly distributed in all self-replicating

Among various probable contender cells as one of the basic components of the
ribosomes
macromolecules that can help in the Easy to isolate
determination of the relationship amongst the Structurally stable due to its very low mutation rate,
entire living world is the rRNA. This is because: therefore making it as an ideal molecule for the
detection of relatedness amongst distant species.
• Carl Woese and George Fox (1977) compared the 16s/18s rRNA present
in different species and concluded that rather than two different basic
cell types which is the eukaryotic and prokaryotic cells as suggested by
cytological data, molecularly, there actually three basic types of cells:
one is present in Eukarya, one in Archaebacteria, and another one in
Eubacteria.
• If organisms are grouped based on the three basic cells, the
molecular dissimilarity among different cell type-based groups
appear to be prominent. Thus, this group cannot be equivalent to
a Kingdom.
• In a proposal made in 1990, Woese et al. introduced a new taxon called
domain, which is above all the level of kingdom as the new system of
classification.
• Under this system, life has been divided into the three domains:
Domain Bacteria, Domain Archaea, and the Domain Eukarya.
 The Phylogeny of
Domain Eukarya
• The domain Eukarya is divided into four
kingdoms by most biologists:
➢ Kingdom Plantae: the multicellular
plants
➢ Kingdom Animalia: the multicellular
animals
➢ Kingdom Fungi: the fungi such as
molds, yeast, and fleshy fungi
➢ Kingdom Protista: the protozoans and
algae
This Photo by Unknown Author is licensed under CC BY-SA
The Phylogeny of
Domain Archaea
• This domain is divided into two phyla
based primarily on the rRNA sequence
data:
• Phylum Crenarchaeota
- originally containing
thermophilic and hyperthermophilic
sulfur-metabolizing
archaea.
• Phylum Euryarchaeota
- contains primarily
methanogenic archaea, halophilic
archaea, and thermophilic, sulfur-
reducing archaea.

This Photo by Unknown Author is licensed under CC BY-SA

The Phylogeny of Domain • The 2nd edition of Bergey’s Manual
of Systematic Bacteriology divides

Bacteria the Domain Bacteria into 23 phyla.

Nine of the more notable phyla are
described as follows:

• Phylum Aquiflexa
• The earliest “deepest”
branch of Bacteria
• Contains the genera
Aquiflex and
Hydrogenobcter that can
obtain their energy from
hydrogen via
chemolithotrophic
pathways.
• Phylum Cyanobacteria
• Oxygenic photosynthetic
bacteria

This Photo by Unknown Author is licensed under CC BY-SA This Photo by Unknown Author is licensed under CC BY-SA
• Phylum Chlorobi
• The “green sulfur bacteria”
• Anoxygenic photosynthesis
• Genus Chlorobium

• Phylum Proteobacteria
• The largest group of gram-negative bacteria
• Extremely complex group, with over 400 genera and 1300
This Photo by Unknown Author is licensed under CC BY-SA

named species
• All major nutritional types are represented: photoautotrophy,
heterotrophy, and several types of chemolithotrophy.
• Sometimes called the “purple bacteria” although very few are
purple. The term refers to a hypothetical purple photosynthetic
bacterium from which the group believed to have evolved.
• Divided into 5 classes: Alphaproteobacteria,
Betaproteobacteria, Gammaproteobacteria,
Deltaproteobacteria, Epsilonproteobacteria
This Photo by Unknown Author is licensed under CC BY
• Phylum Proteobacteria (continuation)
• Photosynthetic genera such as Rhodospirillum (purple non-
sulfur bacteria) and Chromatium (a purple sulfur bacteria)
• Sulfur chemolithotrophs with the genera Theobacilus and
Beggiatoa
• Nitrogen chemolithotrophs (nitrifying bacteria) with the
genera Nitobacter and Nitromonas.
• Other chemolithotrophs such as the genera Alcaligenes,
Methylobacillus, and Burkholderia.

• The family Enterobacteriaceae, the “gram-negative enteric

bacteria” which includes the genera Escherichia, Proteus,
Enterobacter, Klebsiella, Salmonella, Shigella, Serratia, and
others.
• The family Pseudomonaceae which includes the genus
Pseudomonas and other related genera.
• Other medically important Proteobacteria include the
genera Haemophilus, Vibrio, Camphylobacter, Helicobacter,
Rickessia, and Brucella.
This Photo by Unknown Author is licensed under CC BY
• Phylum Firmicutes
• The “Low G + C” gram-positive bacteria
• Divided into 3 classes:
• Class I – Clostiridia: includes the genera
Clostiridium and Desulfoto maculatum
and others.
• Class II – Mollicutes: the bacteria in this
class cannot make peptidoglycan and they This Photo by Unknown Author is licensed under CC BY
lack cell walls; includes genera
Mycoplasma, Ureaplasma, and others.
• Class III – Bacilli includes the genera
Bacillus, Lactobacillus, Streptococcus,
Lactococcus, Geobacillus, Enterococcus,
Listeria, Staphylococcus, and others.
• Phylum Actinobacteria
• The “High G + C” gram-positive bacteria
• This includes the genera Actinomyces,
Streptomyces, Corynebacterium, Micrococcus,
Mycobacterium, and Propionibacterium
• Phylum Chlamidiae This Photo by Unknown Author is licensed under CC BY-SA

• Small phylum containing the genus Chlamydia

 • Phylum Spirochaetes
• The spirochaetes characterized by flexible,
helical cells with a modified outer
membrane (outer sheath) and modified
flagella (axial filaments) located within the
outer sheath.
• Important pathogenic genera include
Treponema, Borrelia, and Leptospira
• Phylum Bacteriodetes
• Includes genera bacteriodes,
Flavobacterium, Flexibacter, and
Cytophyga
• Flexibacter and Cytophyga are
motile bacteria that moves by
“gliding motility”
This Photo by Unknown Author is licensed under CC BY-NC-ND
 Addressed various demerits of the five-
kingdom system of classification.

Merits of the
Provides natural classification and
Three
recognizes the independent lineages of
Domain archaebacteria and bacteria.
System

By introduction of the rank of domain, this

system has become natural up to the highest
level.
 Definition of Species in
Microbiology
• The term species in microbiology is defined as a collection
of strains having similar characteristics. It is the collection
of microbial strains that share many properties and differ
significantly from other group of strains.
• The original culture of bacterium based on which the
description is derived forms the type of strains and all other
strains that are sufficiently like the type of strain, together
form the species.
• Species are identified by comparison to a known type of
strain – a well characterized pure culture and a reference
for the identification of the unknown culture.
• The type of strain that is generally deposited in a bacterial
culture collection center.
This Photo by Unknown Author is licensed under CC BY-NC
What is a strain?
• In microbiology, a strain refers to
the basic unit of classification.
• A strain is defined as a cell
population, arising from a single
organism as a pure culture.
• Different strains represent genetic
variability within a species. A strain
is usually a genetic variant or
subtype of a microorganism.
• For non-culturable microorganisms,
a type can be served by a preserved
specimen, a photograph, or some
other appropriate device.
• Sometimes, the type are lost, and
new ones must be set up to replace
them and are called the neotypes.
 A species maybe divided into two or more subspecies based on minor but
consistent phenotypic variations within the species, or on genetically
determined clusters of strains within the species.

A genus is a collection of species, one of them being the type of species.

The type of species serves as a permanent example of a genus.

A group of similar genera forms a Family. Similar families form a Class.

A group of classes form a Phylum, and similar phyla into a Kingdom and
thus goes the taxonomic hierarchy.

This Photo by Unknown Author is licensed under CC BY-SA

 • Biovars – refer to the strains
that differ in biochemical or
physiological differences from
the other strains in a particular
species.

• Morphovars – refer to the

strains that vary in morphology.
https://www.researchgate.net/figure/Biovars-of-Gallibacterium-anatis-show-difference-in-hemolytic-properties-Colonies-of-G_fig1_278042853

• Serovars – refers to the strains

that vary in their antigenic
properties from the other
strains in a particular species.

https://www.microbiologyinpictures.com/bacteria%20photos/salmonella%20enterica%20photos/SAEN4.html