DEPARTMENT OF MICROBIOLOGY

Students Group : I B.Sc

Course Title :Microbial Diversity

Course Code: 23MBU04
Unit - 1

Lecture-2&3

SKASC 1
Taxonomic ranks, Phylogenetic tree

2
CONTENTS

• Taxonomic ranks
• Classification
• Phylogenetic tree

3
Taxonomy is the science dealing with the description, identification,
naming, and classification of organisms.

Classification is the ‘grouping’ of organisms based on

particular characters and is not arranged in hierarchical
order.
Taxonomy is the science dealing with the description,
identification, naming, and classification of organisms.

Taxonomy provides basic understanding about the

components of biodiversity which is necessary for effective
decision-making about conservation and sustainable use.
 Taxonomy's first father was the
philosopher Aristotle(384-322 BC), sometimes
called the “father of science ."
He first introduced the two key concepts of :
classification of organisms by type and
binomial definition.

Aristotle was the first to attempt to classify all the

kinds of by grouping the types of creatures
Sir according to their similarities: animals with blood
Aristotle and animals without blood. He further divided
the animals with blood into live-bearing and
egg- bearing.
Aristotle's view of life was hierarchical. He
assumed that creatures could be grouped in
order from lowest to highest, with the human
species being the highest.
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 *A Swedish naturalist named Carolus Linnaeus is
considered the 'Father of Taxonomy‘ since 1700s

*His two most important contributions to

taxonomy were:
•A hierarchical classification system
•The system of binomial nomenclature

*He proposed that there were three

broad groups, called kingdoms,
into which the whole of nature could
fit.
These kingdoms were
animals, plants, and
*Binomial
minerals. nomenclature meant
naming species in 2 words : genus ,
followed by species.
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Microbial Taxonomy

• Classification Systems
• Levels of Classification
• Definition of “Species”
• Nomenclature
• Useful Properties in Microbial Classification
• Microbial Phylogeny
Classification Systems

• Taxonomy:
• Classification of living organisms into groups
• Phylogenetic Classification System:
• Groups reflect genetic similarity and evolutionary relatedness
• Phenetic Classification System:
• Groups do not necessarily reflect genetic similarity or evolutionary relatedness.
Instead, groups are based on convenient, observable characteristics.
Levels of Classification

• Taxon:
• A group or “level” of classification
• Hierarchical; broad divisions are divided up into smaller divisions:
• Kingdom (Not used by most bacteriologists)
• Phylum (Called “Division” by botanists)
• Class
• Order
• Family
• Genus (plural: Genera)
• Species (Both singular & plural)
 Definition of “Species”

• The “basic unit” of taxonomy, representing a specific, recognized type

of organism
• For sexually reproducing organisms, a fundamental definition of
“species” has been reproductive compatibility
• This definition fails for many microbial species (including bacteria),
because they do not reproduce sexually
Definition of “Species”

• Definition of “species” in microbiology:

• Classic definition: A collection of microbial strains that share many properties
and differ significantly from other groups of strains
• Species are identified by comparison with known “type strains”: well-
characterized pure cultures; references for the identification of unknowns
• There are several collections of type strains, including the American Type
Culture Collection (ATCC)
 Definition of “Species”

• Definition of “species” in microbiology (cont.):

• Strain:
• A population of microbes descended from a single individual or pure culture
• Different strains represent genetic variability within a species
• Biovars: Strains that differ in biochemical or physiological differences
• Morphovars: Strains that vary in morphology
• Serovars: Stains that vary in their antigenic properties
Nomenclature

• Scientific name (Systematic Name)

Binomial System of Nomenclature
• Genus name + species name
• Italicized or underlined
• Genus name is capitalized and may be abbreviated
• Species name is never abbreviated
• A genus name may be used alone to indicate a genus group; a species name is never used
alone
• eg: Bacillus subtilis
B. subtilis
Nomenclature

• Common or descriptive names

(trivial names)
• Names for organisms that may be in common usage, but are not taxonomic
names
• eg: tubercle bacillus
(Mycobacterium tuberculosis)
• meningococcus
(Neiserria meningitidis)
• Group A streptococcus
(Streptococcus pyogenes)
Useful Properties in Classification

• Colony morphology
• Cell shape & arrangement
• Cell wall structure (Gram staining)
• Special cellular structures
• Biochemical characteristics
Useful Properties in Classification

• Serological Tests
• Use group specific antiserum isolated from the plasma of animals that have
been sensitized to the organism
• The antiserum contains antibody proteins that react with antigens on the unknown
organism.
• The reaction can be detected by examining agglutination or by using sera labeled with
colorimetric or fluorescent labels
Useful Properties in Classification

• Serological Tests (cont.)

• Advantages:
• Highly specific
• Does not usually require the organism to be isolated into pure culture
• Can be used to identify organisms that can’t be grown on medium
Useful Properties in Classification

• G + C content GC
Mol% (G  C)  100%
GCAT
• Estimated by determining the melting temperature of the DNA
• Higher G + C gives a higher melting temperature
Useful Properties in Classification

• Nucleic acid hybridization

• By mixing ssDNA from two different species and determining the percentage
of the DNA that can form dsDNA hybrids
• The greater the percent hybridization, the closer the species
Useful Properties in Classification

• Nucleic acid sequencing

• Genes for specific enzymes
• The nucleic acid sequence for the complete genome of several species is now
available
• 5S and 16S rRNA (ribosomal RNA) sequences; comparison of these sequences
has been extensively used to determine the phylogenetic relationships of
microbial groups
 Microbial taxonomy and phylogeny

Taxonomy - the science of biological classification

Phylogeny - the evolutionary development of a species

 Taxonomy

Consists of three parts:

Classification - arrangement of organisms into groups or taxa

Nomenclature - assignment of names to taxonomic groups

Identification - determining which group an organism belongs in

 Importance of taxonomy

Allows for the organization of a large amount of knowledge

Allows scientists to make predictions and form hypotheses about organisms

 Importance of taxonomy

Facilitates communication by placing organisms into groups with precise names

Essential for the accurate identification of organisms (e.g. clinical

laboratories)
 Taxonomic ranks

Organisms placed in a small homogenous group that is itself a member of a larger

group
Most commonly used levels (or ranks) are:
Species, Genus, Family, Order, Class, Phylum, Domain
Taxonomic ranks
 Species

Often defined as organisms that are capable of interbreeding

Prokaryotes reproduce asexually, therefore another definition is required

 Prokaryotic species

A group of strains that are share many stable properties and differ significantly from
other groups of strains

A group of strains that have similar G + C composition and ≥ 70% sequence

similarity

A collection of strains that share the same sequences in their core housekeeping genes
 Strains

A population of organisms that is distinguishable from other populations within a

taxon

Considered to have descended from a single organism or a pure culture isolate

Strains within a species may vary in different ways

 Strains

Biovars - differ biochemically or physiologically

Morphovars - differ morphologically

Serovars - differ antigenically

 Type strain

Usually one of the first strains of a species studied

Usually the most well characterized example of the species

Not necessarily representative of the species

 Binomial system of nomenclature

Devised by Carl von Linné (Carolus Linnaeus)

Italicized name consists of two parts

Genus name/generic name (capitalized)

Species name/specific epithet (uncapitalized)

Key words:

Taxonomy
Classification
Nomenclature
Species
Strain
father of science
 MCQ
The first organisms were
(a) chemoautotrophs
(b) chemoheterotrophs
(c) autotrophs
(d) eucaryotes

Evolutionary convergence is development of

(a) common set of characters in group of
different ancestry
(b) dissimilar characters in closely related
groups
(c) common set of characters in closely related
groups
Genetic drift is change of
(a) gene frequency in same generation
(b) appearance of recessive genes
(c) gene frequency from one generation to
next
(d) none of the above.
The homologous organs are those that show
similarity in
(a) appearance
(b) function
(c) origin
(d) size.

Which period is dubbed as the age of

prokaryotic microbes?
(a) precambrian
(b) phanerozoic
(c) archean
(d) proterozoic
Points to ponder
New aspects of evolution have come to light with the introduction
of advanced technologies that didn't exist during Darwin's era.

One of the most arresting statements in your book is that “we

humans probably came from creatures that, as recently as 40
years ago, were unknown to exist.” Introduce us to archaea.
SUMMARY:
Microbial taxonomy is a means by which microorganisms can be grouped
together. Organisms having similarities with respect to the criteria used
are in the same group, and are separated from the other groups of
microorganisms that have different characteristics
Next class:Classification systems- phenetic, numerical and phylogenetic
THANK YOU

SKASC