Classification of Microorganisms

Classification of Microorganisms


• System of classification

• Binomial system of classification

• Whittaker’s five kingdom classification

• Prokaryotes and eukaryotes

• Characteristics for bacterial classification

• Methods for bacterial classification

Intended Learning objectives

At the end of this lecture, student will be able to

• Identify the importance of classification

• Outline the developments in taxonomy

• Differentiate between prokaryotic and eukaryotic cells

• Describe the relationship between different kingdoms

• Classify organisms based on their characteristics


• The science of classification - the classification of living forms

• From the Greek word meaning ‘orderly arrangement’

Objective of classification:

• To establish the relationships between one group of organisms and another and to differentiate them

• Provides a common reference for identifying organisms

• To show degrees of similarities among organisms

History of taxonomy

• Aristotle, living organisms were categorized in just two ways, as either plants or animals. 

In 1735, the Swedish botanist Carolus Linnaeus introduced a Aristotle formal system of classification dividing living organisms into two kingdoms - Plantae and Animalia.

• 1857 - Carl von Nageli proposed that bacteria and fungi be placed in the plant kingdom

• 1866 - Ernst Haeckel proposed the Kingdom Protista, to include bacteria, protozoa, algae, and fungi

• Fungi were placed in their own kingdom in 1959


Advent of electron microscopy

German physicist Ernst Ruska and the electrical engineer Max Knoll constructed the prototype electron microscope in 1931 

• Ernst Ruska was awarded half of the Nobel Prize for Physics in 1986 for his invention.

• The physical differences between cells became apparent

• Introduction of the term prokaryote in 1937 by Edouard Chatton - to distinguish cells having no nucleus from the nucleated cells of plants and animals

• In 1961, Roger Stanier defined prokaryotes: cells in which the nuclear material (nucleoplasm) is not surrounded by a nuclear membrane

• In 1968, Robert G.E. Murray proposed the Kingdom Prokaryotae

Prokaryotic and Eukaryotic cell

• 1969, Robert H. Whittaker founded the five-kingdom system

• Prokaryotes were placed in the Kingdom Prokaryotae, or Monera

• Eukaryotes comprised the other four kingdoms

The five kingdom classification

Kingdom Monera

• All members are prokaryotes

• Includes organisms that are single-celled

• Considered as the most ancient living forms on earth

• Divided into two groups Archaebacteria and Eubacteria

Kingdom Protista

• Protists are eukaryotic organisms that cannot be classified as a plant, animal, or fungus

• Mostly unicellular, but some, like algae, are multicellular

• Kelp, or 'seaweed,' is a large multicellular protist that provides food, shelter, and oxygen for numerous underwater ecosystems

• Protists can be heterotrophic obtain energy by consuming other organisms or they can be autotrophic, which means they obtain energy from the environment through photosynthesis

• Protists primarily live in water, though some live in moist soil

• Protists are grouped by how they move and how they obtain nutrients

• ‘”Animal-like” – also called protozoans (Latin for “First animals”)

• “Plant-like” – Example: algae

• “Fungus-like” – Example: Slime mold

Kingdom fungi

• The kingdom Fungi includes a diverse group of organisms that are neither plant nor animal. 

• Unicellular or multicellular

• Absorb the nutrients

• Play an important role of ecological decomposers

Kingdom Plantae

• Includes every plant you could imagine from the moss growing on the forest floor to the mighty, towering fir trees. 

• Plants are autotrophs, meaning they can make their own food

• Multicellular

• Contain chlorophyll

Kingdom Animalia

• Animals are classified under the Kingdom Animalia

• Multicellular, Eukaryotes

• Heterotrophs, they depend on other organisms directly or indirectly for food

• Most of the animals ingest food and digest in the internal cavity

• Motile which means they can move independently and spontaneously

The Three Domains

Three distinctly different cell groups based on comparing the sequences of nucleotides in ribosomal RNA 

• The eukaryotes 

• 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

• Organisms are classified based on the similarity in ribosomal RNA in the three domain systems

Domain Eukarya

• Includes kingdoms animals, plants, fungi and protists

Domain Bacteria

• Includes prokaryotes 

Domain Archaea

• Includes prokaryotes that do not have peptidoglycan in their cell walls

• Often live in extreme environments and carry out unusual metabolic processes 

Archaea include three major groups

1. The methanogens, strict anaerobes that produce methane 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

Scientific nomenclature

• Every organism is assigned two names, or a binomial. 

• Genus name

• Specific epithet (species)

• Because this system gives two names to each organism, the system is called binomial nomenclature.

The Taxonomic HierarchyLinnaeus developed the taxonomical hierarchy for his classification of plants and animals

Species, Genus, Family, Order, Class, Phyllum, Kingdom, Domain

Classification of Prokaryotes

• A prokaryotic species. Therefore, is defined simply as a population of cells with similar characteristics

 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

• In some cultures, the same species may not be identical in all ways. Such group is called a strain

• Strains are identified by numbers, letters, or names that follow the specific epithet

Classification of Eukaryotes

Unicellular eukaryotes 

• Protists

• Eukaryotic organisms that didn't fit into other kingdoms were placed in the Protista

Multicellular eukaryotes 

• Fungi

• Plants

• Animals

Kingdom Fungi

• Unicellular yeasts

• Multicellular molds

• Macroscopic species such as mushrooms.

• Fungus absorbs dissolved organic matter through its plasma membrane

• Fungi develop from spores or from fragments of hyphae

Kingdom Plantae

• Includes some algae, Mosses, Ferns, Conifers and Flowering plants

• Multicellular

• To obtain energy, a plant uses photosynthesis

Kingdom Animalia

• Multicellular organisms

• Includes sponges, various worms, insects, and animals with backbones

• Obtain nutrients and energy by ingesting organic matter


• Not classified as part of any of the three domains

• Viruses are not composed of cells

• They use the anabolic machinery within living host cells to multiply

• A viral genome can direct biosynthesis inside a host cell

• Some viral genomes can become incorporated into the host genome

• Viruses are obligatory intracellular parasites

Characterization of microorganisms

In order to identify and classify microorganisms, we need to learn their characteristics. Major characteristics of microorganisms:

• Morphological

• Chemical composition

• Cultural

• Metabolic: the way in which cells obtain and use their energy

• Antigenic: chemical components / antigens that are characteristic of the cell

• Genetic: DNA base composition and Sequence of nucleotide bases in the DNA

• Pathogenicity: Ability to cause disease

• Ecological: Habitat and distribution of the organism in nature Metabolic

Characteristics of Microorganisms – Morphological

Cell Shape

Cell Size

Cell arrangement

Special structures

Flagellar arrangement

Staining reactions

Motility: Motile or Non-motile

Characteristics of Microorganisms - Chemical

Chemical constituents of the cell


• Presence of lipopolysaccharides in the cell wall of gram negative cells

• Presence of teichoic acid in gram positive cells

• Presence of DNA or RNA in virus

Characteristics of microorganisms - Cultural

Nutritional requirements

Organic compounds

Inorgainc compounds

Physical conditions required for growth

Optimum temperature for growth - 40⁰C or 20 ⁰C 

Manner in which the growth occurs


General methods of classifying bacteria

Three methods:

1. Intuitive method

2. Numerical taxonomy

3. Genetic relatedness

3. Genetic relatedness

      Based on the hereditary material, DNA

                                           Mol % G + C values

a. DNA homology experiments

b. Ribosomal RNA homology experiments and ribosomal RNA oligonucleotide cataloguing


• Classification give relationships between one group of organisms and another and differentiates them

• Aristotle – classified living things as plants or animals

• Carolus Linnaeus- introduced the formal system of classification

• Robert H. Whittaker introduced the five-kingdom system

• Prokaryotes – cells having no nucleus

• Eukaryotes – nucleated cells

• Major characteristics of microorganisms used for classification:

 Morphological

 Chemical composition

 Cultural

 Metabolic

 Antigenic

 Genetic

 Pathogenicity

 Ecological

• Methods used for bacterial classification

1. Intuitive method

2. Numerical taxonomy

3. Genetic relatedness

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