Taxonomy & Bacterial Classification

By: Dr. MohammedAzim Bagban Assistant Professor Why do we classify?

• Classification puts organisms into groups by looking at characteristics (traits) they share.

• Classifying living things into groups based on their body structures (anatomy), DNA or other traits.

Carolus Linneaus • Swedish botanist, lived 1707-1778 • Invented binomial nomenclature, the 2- word naming system we still use today to classify organisms • Called “the father of taxonomy.”

Binomial Nomenclature

• Gives a unique 2-word, Latin, scientific name to all living things • Genus is capitalized; species is not; both are italicized • Examples: Homo sapiens = human Felis domesticus = cat Panthera tigris = tiger Hierarchical arrangement:

1. Domain 2. Kingdom 3. Phylum 4. Class 5. Order 6. Family 7. Genus Binomial name or Scientific Name 8. Species 8 taxa of classification DOMAIN “Trick” to remember the 8 taxa of classification: • Dumb • King • Phillip • Came • Over • For • Grape • Soda History

Carl Carolus Ernst Edourd Herbert R. H. Cavalier- Woese et Linnaeus Haeckel Chatton Copeland Whittaker Smith al. 2015 1735 1866 1925 1938 1969 1998[ 1990

2 2 2 3 4 5 2 empires 3 domains empires, 6 empires, 7 kingdoms kingdoms kingdoms kingdoms kingdoms kingdoms

Prokaryot Bacteria Monera Monera Bacteria a Archaea Archaea (not Protista Protozoa Protozoa treated) Protoctist Protista a Chromist Chromist Eukaryot a a Eucarya Vegetabili a Plantae Plantae Plantae Plantae Plantae a Fungi Fungi Fungi Animalia Animalia Animalia Animalia Animalia Animalia Species • Species is the smallest, most specific group in classification • Organisms in the same species can reproduce together and their offspring are fertile. Species Identification

• Characterized by Phenotypic, genotypic, and phylogenetic criteria. • Species of bacteria are identified by rRNA sequencing rely on 16S RNA in which 95% resembles in same species. • Because of progressive increase in genomic data the definition needs revision: • “ A collection of organisms having same sequence in their core housekeeping genes”. Tool: Phylogeny a “family tree” that classifies organisms by their evolutionary history Tool: Cladogram • Shows older traits (bottom) • Shows newer or “derived” traits (top)

Tool: Dichotomous Key • Helps identify organisms • Questions with 2 answer choices lead you through the key until you find the correct organism

Strain

• In biology, a strain is a low-level taxonomic rank used at the intraspecific level (within a species). • When two clones of same species differ genetically and express different characters are called Strains. • Arises because of mutation. • Denoted by capital letters followed by some numbers. • E.g. thuringensis AB3 Strain

• Several types: 1. Biovers: Variant of strain with different biochemical and physiological character.

2. Morphover: Morphological varient

3. Serovar: Distinct antigenic properties.

4. Phagover: Differing in susceptibility & resistance towards bacteriophages.

ATCC: American Type Culture Collection Methods for classification of Bacteria

• Bacteria can be classified in many ways. The first classification scheme was published in 1773 and many more have appeared since.

• Science of microbiology has developed other kind of classification but medically important classification is as follows Based on several major properties • Morphological • Anatomical • Staining • Based on pathogenicity • Based on relationship of host and organism • Nutrition • Environmental factors Morphological characters

• Shape and size of the cell

• Based on Anatomical features:

Based on Staining

• (A) Gram stain: • 1) Gram positive: after the gram stain organism which occur violet in colour. • 2) Gram negative: Which appear pink or red

• (B)Acid fast stain: • 1) Acid fast organism: after the ziehl – neelsen stain it will show pink in colour • 2) Non acid fast organism: after this stain organism will appear blue in colour

Physiological & Metabolic characteristics I. Mode of Nutrition:

Mode of Nutrition

Autotrophic Heterotrophic Phototrophic Chemotrophic

II. Physiological Characteristics:

Physiological Characteristics

Oxygen Antibiotic Growth Temp. pH Requirement sensitivity Biochemical Characteristics

• Catalase test • Sugar Fermentation • Gelatin Liquefaction • Sugar Fermentation • Indole Production • Hydrogen sulfide production • Mixed acid fermentation • Nitrate reduction • Urease production • Utilization of specific nutrients Molecular characteristics

• 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

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 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

Bergey’s Manual of Systematic Bacteriology • In 1923, David Bergey & colleagues published Bergey’s Manual of Determinative Bacteriology, a manual that is used to classify bacteria based on their structural and functional attributes by arranging them into specific familial orders. • In 1984, a more detailed work entitled Bergey’s Manual of Systematic Bacteriology was published, still primarily phenetic in its classification.

Bergey’s Manual of Systematic Bacteriology

• The change in volume set to "Systematic Bacteriology" came in a new contract in 1980, whereupon the new style included "relationships between organisms" and had "expanded scope" overall. This new style was picked up for a four- volume set that first began publishing in 1984. The information in the volumes was separated as: Bergey’s Manual of Systematic Bacteriology First Edition

• Volume 1 included information on all types of Gram- negative bacteria that were considered to have "medical and industrial importance.“ • Volume 2 included information on all types of Gram- positive bacteria. • Volume 3 deals with all of the remaining, slightly different Gram-negative bacteria, along with the Archaea. • Volume 4 has information on filamentous actinomycetes and other, similar bacteria. Bergey’s Manual of Systematic Bacteriology Second Edition

• Volume 1 (2001): The Archaea and the deeply branching and phototrophic Bacteria • Volume 2 (2005): The Proteobacteria—divided into three books: • 2A: Introductory essays • 2B: The Gammaproteobacteria • 2C: Other classes of Proteobacteria • Volume 3 (2009): The • Volume 4 (2011): The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Aci dobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmat imonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes • Volume 5 (in two parts) (2012): The Actinobacteria

Bacterial cell size

• Bacteria are very minute in size ranging from 0.2-8.0 µm. • 1 µm = 10-3 mm = 10-6 cm • Some exceptional bacteria are found below and above this range also. • Some examples are shown below…. •

Shape of the Bacteria

• Three basic bacteria shapes are coccus (spherical), bacillus (rod- shaped), and spiral (twisted).

• Arrangement of cocci • Cocci may be oval, elongated, or flattened on one side. Cocci may remain attached after cell division. These group characteristics are often used to help identify certain cocci.

Bacilli • Bacillus is a shape (rod shaped) and only divide across their short axis there are fewer groupings.

Spiral bacteria • Spiral bacteria have one or more twists. Other shapes

Ultra structure of typical bacterial cell

Bacterial spores & Cysts

• Bacterial spores and cysts are the dormant (functionally Inactive) structures of prokaryotes. Endospore • An endospore is a dormant, tough, and non- reproductive structure produced by some bacteria in the phylum Firmicutes. • The name "endospore" is suggestive of a spore or seed-like form (endo means within), but it is not a true spore (i.e., not an offspring). • Endospore formation is usually triggered by a lack of nutrients, and usually occurs in gram- positive bacteria. • In endospore formation, the bacterium divides within its cell wall, and one side then engulfs the other. • Endospores enable bacteria to lie dormant for extended periods, even centuries. There are many reports of spores remaining viable over 10,000 years, and revival of spores millions of years old has been claimed. • When the environment becomes more favorable, the endospore can reactivate itself to the vegetative state. Most types of bacteria cannot change to the endospore form. Examples of bacterial genera that can form endospores include Bacillus and Clostridium. • The endospore consists of the bacterium's DNA, ribosomes and large amounts of dipicolinic acid. Dipicolinic acid is a spore-specific chemical that appears to help in the ability for endospores to maintain dormancy. This chemical accounts for up to 10% of the spore's dry weight. • A stained preparation of the Phase-bright endospores cell Bacillus subtilis showing of alvei imaged endospores as green and with phase-contrast the vegetative cell as red microscopy

Shapes of spores

• The shape & position of the cell is characteristic of the species. • Spherical, oval or elongated in shape • May be narrower or bulged than parent cell. Position of the spore  Terminal (located at one of the poles)  Sub terminal or sub central(between center & one of the poles) Equatorial (central) Structure of endospore

(Protoplast) . Exosporium • Thin delicate covering of spore arises from cell membrane.

. Spore coat • Thick layer consist of several layers of proteins. • Impermeable to toxic chemicals • Contains enzymes for sporulation

. Cortex • Structure more than half of spore volume. • Less cross linked peptidoglycans • High amount of calcium dipicolonate • 15% of the cellular dry weight

. Spore core (Protoplast) • Consist of core wall, cytoplasm, ribosome & nucleiod. • Water content is complex with protein.

Sporogenesis Germination

• Transformation of dormant spore into vegetative cells called germination. • Dormancy may be long but return to the vegetative stage is very rapid involves three stages: • 1. Activation • 2. Germination • 3. out growth Activation

• Condition of the spores when nutrition available • It can be achieved by: • Heat treatment (60°C- 70°C ) • Storage of suspension at room temperature

Germination

• Rapture of spore coat. • Loss of calcium dipicolonate and cortex components. • Increase in stainability. • Loss of resistance to heat • Release spore components • Increase metabolic activity

Out growth

• Outgrowth follows germination and involves the core of the endospore manufacturing new chemical components and exiting the old spore coat to develop into a fully functional vegetative bacterial cell, which can divide to produce more cells.