DM111-Fundamentals of Microbiology
Classification of Microbes
Contents: Microbial classification systems,
Numerical taxonomy, General properties and principles of microbial classification,
Whittaker’s five kingdom and Carl Woese’s three domain classification system
Systematics of bacteria and Bergey’s manual of systematic bacteriology, Phylogenetic tree.
Rashmi H M
Senior Scientist
Dairy Microbiology Div.
ICAR-National Dairy Research Insitute
Resource Materials
• 1. Presscot et al
• 2. Microbiology Principle and exploration By Black
• 3. Microbiology An Introduction By Tortora et al
• 4. Textbook of Microbiology By Surender Kumar
Microbial Taxonomy
• Taxonomy is the science of the classification of organisms, with the goal
of showing evolutionary relationships among organisms
• From ancient Greek words: Taxis meaning Arrangement and Nomia
meaning Method.
• 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
Microbial Taxonomy includes
a) Identification.
b) Nomenclature.
c) Classification.
Microbial Identification, Nomenclature and Classification
• Identification – is the process of studying and recording the identical
and distinguishing features
• Nomenclature – is the process of assigning names to the various
taxonomic ranking of each living organism.
• Classification – is the orderly arrangement of organisms into groups,
preferably in a format, that shows evolutionary relationships.
Phenetic and Phylogenetic system in microbial taxonomy
• Phenetic system groups organisms based on mutual similarity of
phenotypic characteristics. May or may not correctly match
evolutionary grouping, e.g. motile v/s non motile bacteria
• Phylogenetic system groups organisms based on shared evolutionary
genetic heritage.
Classical Classification System
• Two Kingdom Classification
• Three Kingdom Classification
• Five Kingdom Classification
• Six Kingdome Classification
Two Kingdom Classification
• Living organisms were once divided into only two kingdoms: plantae
and animaliae: bacteria, fungi, and algae were classified with plants;
• Protozoa were classified as animals.
Three Kingdom Classification
• Haeckel in 1865 proposed third kingdom Protista for unicellular
microorganisms such as bacteria, algae, fungi and protozoa.
Five Kingdom Classification
• Whitaker proposed that organisms should be broadly divided into kingdoms, based
on certain characters like the structure of the cell, mode of nutrition, the source of
nutrition, interrelationship, body organization, and reproduction.
The kingdoms include:
Bacteria and archaea are in the Kingdom Prokaryotae (or Monera)
Algae and protozoa are in the Kingdom Protista (organisms in this kingdom are
referred to as protists)
Fungi are in the Kingdom Fungi
Plants are in the Kingdom Plantae
Animals are in the Kingdom Animalia
Kingdom Monera
These organisms are prokaryotic and unicellular.
They do not have a well-defined nucleus and also lack
cell organelles.
Some organisms show the presence of cell wall while
there are others without a cell wall.
Consequently, some organisms are autotrophic and
others are heterotrophic.
Examples include Bacteria, Cyanobacteria, and
Mycoplasma.
Kingdom Protista
Organisms grouped under Kingdom Protista are all
unicellular, but eukaryotic organisms.
These are the simplest forms of eukaryotes that exhibit
either autotrophic or heterotrophic mode of nutrition.
Some organisms have appendages such as cilia or flagella
or pseudopodia to move around.
Some examples are Diatoms, Protozoans like Amoeba,
Paramecium
Kingdom Fungi
Heterotrophic, Multicellular and Eukaryotic organisms
are grouped under Kingdom Fungi.
Their mode of nutrition is saprophytic as they use decaying
organic matter as food.
They have cell walls, which are made up of a substance
called Chitin.
Fungi also form a symbiotic association with some blue-
green algae.
Yeast, Mushroom, Aspergillus are examples of Fungi.
Kingdom Plantae
These are Eukaryotic, Multicellular organisms with a cell wall
that is made up of cellulose.
They are autotrophs and synthesize their own food through the
process of photosynthesis. This kingdom includes all plants.
Based on the body differentiation and presence or absence of
specialized vascular tissue, Kingdom Plantae is divided into
different divisions, namely Thallophyta, Bryophyta, Pteridophyta,
Gymnosperms, and Angiosperms.
Examples are
Spirogyra, Ferns, Pines, and Mango Plant etc.
Kingdom Animalia
This Kingdom includes organisms that are Multicellular, Eukaryotic,
without the presence of cell wall.
They have a heterotrophic mode of nutrition.
They also exhibit great diversity. Some organisms are simple while others
have a complex body with specialized tissue differentiation and body
organs.
The Animal Kingdom is divided into many phyla and classes.
Some of the phyla
are Porifera, Coelenterata, Arthropoda, Echinodermata, Chordata etc.
Examples – Hydra, Starfish, Earthworms, Monkeys, Birds etc.
Limitations or Objections to the Five Kingdom System of Classification
Some scientists do not agree that algae and protozoa should be placed into the same kingdom.
In some classification schemes, protozoa are placed into a subkingdom of the Animal Kingdom.
A distinction between unicellular and multicellular organisms is not possible in case of algae in
this system of classification.
Each group has so many diversities that it is difficult to keep them together. For example,
monera and Protista contain both walled and wall-less organisms. Photosynthetic and non-
photosynthetic organisms, cellular or filamentous organism.
Virus has not been included in this kingdom.
Archaebacteria differ from other bacteria in structure, composition and physiology.
Mycoplasma are quite different form bacteria where they have been placed along with
prokaryotes.
Symbiotic associations are not considered in this classification system. For example, lichens are
organisms which are formed by the symbiotic association between fungi and algae.
Three-domain Classification system
The three-domain system is a biological
classification introduced by Carl Woese et al. in 1990 that
divides cellular life forms into archaea, bacteria,
and eukaryote domains.
The Three Domain System was proposed by Woese and
others,
It is an evolutionary model of phylogeny based on differences
in the sequences of nucleotides in the cell's ribosomal
RNAs (rRNA), as well as the cell's membrane lipid structure
and its sensitivity to antibiotics.
Why rRNA molecule ?
Because rRNA molecules throughout nature
carry out the same function, their structure
changes very little over time.
Therefore similarities and dissimilarities in rRNA
nucleotide sequences are a good indication of
how related or unrelated different cells and
organisms are.
last universal common ancestor (LUCA)