MKS-Microbial Taxonomy

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Microbial Taxonomy:

Microbial Taxonomy Phylogentic Tree Dr. M.K. SATEESH Molecular Diagnostics Laboratory, Department of Microbiology and Biotechnology Bangalore University Jnana Bharathi campus Bangalore-560 056

Approximate timing of major events in the history of life on Earth:

Approximate timing of major events in the history of life on Earth 2 Dr.M.K. SATEESH

Taxonomy:

Taxonomy The science of biological classification, by grouping organisms with similar characteristics. 3 Dr.M.K. SATEESH

Importance of Microbes:

Importance of Microbes Life is microbial ! (to the first approximation) Micro-organisms colonise every environment on earth >80% of life’s history was bacterial You have more bacterial cells than human cells Microbes play a key role in the biosphere Pathogenic microbes globally are the most important cause of human disease and death 4 Dr.M.K. SATEESH

Three Interrelated Parts of Taxonomy:

Three Interrelated Parts of Taxonomy Classification Arrangement into groups Nomenclature Assignment of Names Identification Determining Identity 5 Dr.M.K. SATEESH

Taxonomy / Systematics:

Taxonomy / Systematics Nomenclature Providing a formal name Genus & species Ford Crown Victoria Chevy Impala Toyota Camry Honda Civic Classification Organization into groups Car Truck Bus Van Identification Distinguishing features Engine size Mileage Number of passengers Type of transmission Consistent rules for all scientist Relevant Meaningful Make biological sense Evolutionary context Taxonomy is the field of biology that deals with identifying, naming, and classifying species. The rules for description, naming and formal grouping of organisms. Classification Nomenclature Identification 6 Dr.M.K. SATEESH

Taxonomy of Bacteria and Archaea:

Taxonomy of Bacteria and Archaea Modern taxonomy comprises the following features: Nomenclature: giving names of appropriate taxonomic rank to the classified organisms. Classification: the theory and process of ordering the organisms, on the basis of shared properties, into groups. Identification: obtaining data on the properties of the organism (characterization) and determination which species it belongs to. This is based on direct comparison to known taxonomic groups. 7 Dr.M.K. SATEESH

CLASSIFICATION:

CLASSIFICATION Classification: an orderly grouping of organisms The study of classifying organisms is called taxonomy Provides universal names for organisms Provides a reference for identifying organisms There are two approaches (systems) to classification Convenience Vs Phylogenetic Classification The classification schemes in place today are mainly based on the convenience method . ANY PHYLOGENY IS ASSUMED AND HAS TO BE PROVED SCIENTIFICALLY. 8 Dr.M.K. SATEESH

History of Kingdom:

History of Kingdom Haeckel’s three kingdom classification; Whittaker’s five kingdom classification - A CONVENIENCE METHOD. THE HISTORY OF KINGDOM CLASSIFICATION SCHEMES THE FIRST CLASSIFICATION SCHEME WAS DEVELOPED BY ARISTOTLE 2000 YEARS AGO . PLANTS AND ANIMALS . IN THE LATE 1866, A THIRD KINGDOM WAS ADDED: PROTISTA by Ernst Haeckel IN THE 1950’S, A FORTH KINGDOM WAS ADDED: MONERA PROCARYOTIC AND EUCARYOTIC CELL STRUCTURE 9 Dr.M.K. SATEESH

Kingdom Plantae:

Kingdom Plantae Absence of locomotion, unlimited growth, autotrophic nutrition or saprotrophic nutrition, distinct cell wall and vacuole filled with sap etc., CONVENIENCE METHOD OF CLASSIFICATION 10 Dr.M.K. SATEESH

Kingdom Animalia:

Kingdom Animalia Move from place to place, generally heterotrophic, have property of irritability, cells do not have a cell wall etc., 11 Dr.M.K. SATEESH

Carolus Linnaeus 1707-1778:

Father of modern taxonomy Swedish biologist Binomial nomenclature Image: Biodiversity Heritage Library Carolus Linnaeus 1707-1778 12 Dr.M.K. SATEESH

Linnaean hierarchy has seven taxa :

Linnaean hierarchy has seven taxa Biggest taxonomic rank is Kingdom The next higher rank within a kingdom is the Phylum or Division Species is generally the lowest taxonomic rank representing organisms that are very much closely related to one another. Taxonomic ranks 13 Dr.M.K. SATEESH

Slide 14:

Ernst Haeckel (1834-1919) THIRD KINGDOM CLASSIFICATION Haeckel, a Swiss naturalist placed all unicellular (microscopic) organisms in a new kingdom, “Protista” -bacteria, algae, fungi & protozoa on the level with the existing kingdoms for plants ( Plantae ) and animals ( Animalia ), which are multicellular (macroscopic) organisms. 14 Dr.M.K. SATEESH

Slide 15:

Three-kingdom classification 15 Dr.M.K. SATEESH

Slide 16:

Edouard Chatton (1883-1947) French biologist First person to distinguished between the eukaryotic and prokaryotic systems of cellular organisation (1937) He reported that members of Kingdom Protista containing both eukaryotic and prokaryotic type of organisms 16 Dr.M.K. SATEESH

Slide 17:

Herbert Copeland (1902-1968) American biologist He argued that prokaryotes were so different to eukaryotes that they should be moved out of Kingdom Protista altogether . He proposed a new Kingdom; Monera . Four Kingdoms 17 Dr.M.K. SATEESH

Slide 18:

Five Kingdom Classification 18 Dr.M.K. SATEESH

Slide 19:

Five-Kingdom System of Biological Classification Proposed in 1969 by Robert Whitaker : 1. Kingdom Procaryotae ( Monera ): Oldest known cells. Lived over 3.5 billion years ago. Lack a nucleus and membrane bound organelles. The other four kingdoms are eucaryotes . Have a true nucleus and membrane bound organelles. 2. Kingdom Protista : Mostly unicellular, lack tissue organization. Most have flagella during life. 3. Kingdom Fungi : May be unicellular (yeasts) or multicellular (molds). Many are saprotrophs . 4. Kingdom Plantae : Multicellular , photosynthetic. 5. Kingdom Animalia : Multicellular , heterotrophs that ingest food through a mouth or oral cavity. 19 Dr.M.K. SATEESH

Slide 20:

20 Five Kingdoms by Robert Whitaker in 1969 Bacteria Archaea Prokaryotic Unicellular Eukaryotic Unicellular Uni or multicellular Eukaryotic Protozoa Dr.M.K. SATEESH

The Basis of Five Kingdom:

The Basis of Five Kingdom WHITTAKER’S FIVE KIGNDOM CLASSIFICATION RELATED ALL ORGANISMS ON THE BASIS OF : 1. MODES OF NUTRITION 2. POSITION IN THE ECOLOGICAL FOOD CHAIN A. PRODUCER B. CONSUMER C. DECOMPOSER 3. CELLULAR ORGANIZATION A. SINGLE CELL B. MULTICELLULAR C. PROCARYOTIC/EUCARYOTIC 4. EVOLUTIONARY TREND WITHIN THE INDIVIDUAL KINGDOMS, ORGANISMS ARE FURTHER GROUPED INTO SMALLER GROUPS AS FOLLOWS: PHYLUM/DIVISION CLASS ORDER FAMILY GENUS SPECIES STRAIN/VARIANT/SUBSPESCIES 21 Dr.M.K. SATEESH

THE PHYLOGENETIC APPROACH:

THE PHYLOGENETIC APPROACH Organisms that are genetically related will have more characteristics in common than organisms that look a like. Carl woese and coworkers have been working since 1970 to put in place a phylogenetic classification scheme. Compare hereditary molecules of organisms. THEY SELECTED RIBOSOMAL RNA BECAUSE: all cells have it and plenty of it. its function is the same in all cells. its nitrogen base sequence is moderately conserved from generation to generation. 22 Dr.M.K. SATEESH

Slide 23:

Carl Woese 1978 The Universal phylogenic Tree of Life 23 Dr.M.K. SATEESH

:

Phylogeny: The Three Domain System Domain: In 1978 Carl Woese proposed this level of classification above kingdom . There are three domains based on the following distinguishing criteria: Cell wall composition Membrane lipids RNA sequence Protein synthesis Antibiotic sensitivity I. Domain Eubacteria : “True bacteria”. II. Domain Archaeabacteria: “Ancient bacteria” III. Domain Eucarya: All eucaryotes: Protista, Fungi, Plantae, and Animalia. 24 Dr.M.K. SATEESH

Slide 25:

The Three-Domain System Carl Woese 1978 25 Dr.M.K. SATEESH

Slide 26:

26 Dr.M.K. SATEESH

Position of microbes in the living world:

Position of microbes in the living world 27 Dr.M.K. SATEESH

Slide 28:

Domain Kingdoms Representative Microorganisms Procarya Eubacteria True bacteria, green and purple sulfur bacteria, actinomycetes , sporogenic bacilli, cyanobacteria Archaea Euryarcheota Extreme halophiles , methanogens Crenarcheota Extreme thermophiles , sulfur reducers Eucarya Protozoa Ciliates, zooflagellates , amoebae, slime molds Chromista Oomycetes , Algae Mycota Zygomycetes , the fungi Animalia Nematodes, mites, millipedes, centipedes, annelid worms, collembolans, winged insects Planta Higher Plants, Alage Table . Representative MICROBES organisms in the Universal Tree. 28 Dr.M.K. SATEESH

Microbial Taxonomy:

Microbial Taxonomy 1735 Plant and Animal Kingdoms 1857 Bacteria & fungi put in the Plant Kingdom 1866 Kingdom Protista proposed for bacteria, protozoa, algae, & fungi 1937 "Prokaryote" introduced for cells "without a nucleus" 1961 Prokaryote defined as cells in which nucleoplasm is not surrounded by a nuclear membrane 1959 Kingdom Fungi 1968 Kingdom Prokaryotae proposed 1978 Two types of prokaryotic cells found; three Domain classification-more natural, accepted 29 Dr.M.K. SATEESH

Slide 30:

Linnaeus 1735 2 kingdoms Haeckel 1866 3 kingdoms Chatton 1937 2 empires Copeland 1956 4 kingdoms Whittaker 1969 5 kingdoms Woese et al. 1977 6 kingdoms Woese et al. 1990 3 domains (not treated ) Protista Prokaryota Monera Monera Eubacteria Bacteria Archaebacteria Archaea Eukaryota Protista Protista Protista Eukarya Vegetabilia Plantae Plantae Fungi Fungi Plantae Plantae Plantae Animalia Animalia Animalia Animalia Animalia Classification systems for microorganisms 30 Dr.M.K. SATEESH

Phenetic Classification:

Phenetic Classification Phenetic Classification System: Microbes were classified on the basis of their phenotypic characterization (morphology, staining reactions, biochemistry, substrates/products, antigens etc). These classification systems were artificial . 31 Dr.M.K. SATEESH

Phylogenetic Classification:

Phylogenetic Classification Phylogenetic Classification System: Microbes were classified based on the information carried in the genes i.e. the genome. This type of classification Groups reflect genetic similarity and evolutionary relatedness. These classification systems were natural (phylogenetic) systems. 32 Dr.M.K. SATEESH

Levels of Classification:

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) 33 Dr.M.K. SATEESH

Definition of “Species”:

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. 34 Dr.M.K. SATEESH

Definition of “species” in microbiology:

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. American Type Culture Collection (ATCC)→ type strains collections centre 35 Dr.M.K. SATEESH

Definition of “Strain”:

Definition of “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 36 Dr.M.K. SATEESH

History of the Bacteriological Code:

History of the Bacteriological Code The International Committee on Systematics of Prokaryotes (ICSP) and the International Code of Nomenclature of Bacteria (ICNB) are responsible for the naming of prokaryotes, eubacteria and archaebacteria or archaea. Up to 1920s bacteriologists tried to follow the provisions of the Botanical Code of Nomenclature, because bacteria had traditionally been considered fungi, the Schizomycetes. Much emphasis had to be put on cultural characteristics, so that type cultures were of critical importance. Type cultures are not permitted under the Botanical Code; therefore, at the First International Congress of Microbiology in Paris in 1930, proposals were made for bacteriology to establish its own Code of Nomenclature. A committee under the able guidance of the American bacteriologist R.E. Buchanan began work on this and, at the Second Congress in London in 1936, a draft Code was presented and placed under the aegis of the Internl. Committee for Bacteriological Nomenclature [later, the International Committee on Systematic Bacteriology (ICSB), and now, the ICSP]. 37 Dr.M.K. SATEESH

All new names had to be published in the IJSB (now the IJSEM):

All new names had to be published in the IJSB (now the IJSEM) A journal for bacterial nomenclature was started, the International Bulletin of Bacterial Nomenclature and Taxonomy , later the International Journal of Systematic Bacteriology (IJSB) and now the International Journal of Systematic and Evolutionary Microbiology (IJSEM). At the same time, the Code was completely rewritten by the British bacteriologist S. P. Lapage to make it easier to follow and to put the Rules into a more logical order. Its main sections are Rules , which are obligatory, and Recommendations , which are guides to good practice. There are sections on how to describe, name and publish on a novel bacterium, and on how to request the Judicial Commission to look into nomenclatural problems. It also lists names that have been protected (conserved) and those that must be rejected, and advises on naming of infrasubspecific divisions. The statutes of the ICSB are included. 38 Dr.M.K. SATEESH

Slide 39:

original publication or validation list CONCEPT OF SPECIES VALIDATION 39 Dr.M.K. SATEESH

Binomial Nomenclature:

Binomial Nomenclature Approved Lists of Bacterial Names , 1980 V.B.D. Skerman Aus. It is the system of giving a scientific name to an living organisms, for avoiding the confusion of using common names Common or descriptive names of the 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 ) 40 Dr.M.K. SATEESH

Binomial Nomenclature:

Binomial Nomenclature International Council for Binomial Nomenclature ( ICBN ) introduced rules and regulations regarding Binomial Nomenclature. According to this system, any organism is given a scientific name consisting of two words . The first word refers to name of the genus, while the second word refers to the name of the species . The name of the genus should start with a capital letter and name of the species with a small letter . Genus comes first before species Both the genus and the species are must be Latinized . Both the names should be in italics or they should be underlined separately. E.g. Staphylococcus aureus ( Staphylococcus- genus & aureus - species; Staphylococcus aureus ) 41 Dr.M.K. SATEESH

Nomenclature of Bacteria and Archaea:

Nomenclature of Bacteria and Archaea The names can be derived from any language but they must be Latinized. Take for example Staphylococcus aureus . The genus name is capitalized and the species name is lower case . The name is italized to indicate that is Latinized. Staphyl is derived from the Greek staphyle meaning “a bunch of grapes” and coccus from the Greek meaning “a berry”. Aurous is from Latin and means “gold”. A yellow bunch of berries. 42 Dr.M.K. SATEESH

Binomial Nomenclature:

Binomial Nomenclature Genus name is capitalized and may be abbreviated and Species name is never abbreviated eg: Bacillus subtilis B. subtilis A genus name may be used alone to indicate a genus group; a species name is never used alone Bacillus → Yes subtilis → No 43 Dr.M.K. SATEESH

Binomial Nomenclature:

Binomial Nomenclature Genus name may be abbreviated but It must be used first with out abbreviation If abbreviated it must be used with the species name It must be abbreviated unambiguously If abbreviating as the first letter of the genus is unambiguous, than abbreviating as the first letter is what one dose (e.g. Escherichia abbreviated as E but only if no other genera considered also starts with E; such as Erwinia ) Genus abbreviation are only used in conjunction with the species name . 1990 Revision by S. P. Lapage & Peter H. Sneath The naming of bacteria is controlled by the International Code of Nomenclature of Bacteria (Lapage et al., 1992). The correct name of a bacterial taxon is based on: 1. Valid publication 2. Legitimacy 3. Priority of publication International Code of Nomenclature of Bacteria Bacteriological Code , 1990 44 Dr.M.K. SATEESH

Slide 45:

Domains can be Divided into Many Sub-classifications Domain: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Enterobacteriales Family: Enterobacteriaceae Genus: Escherichia Species: Escherichia coli Biological species concept does not apply to prokaryotes!!! Species – a collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly 45 Dr.M.K. SATEESH

How would you classify humans or a protist (protozoa) But this system doesn’t work for bacteria:

How would you classify humans or a protist (protozoa) But this system doesn’t work for bacteria

Slide 47:

Classification of Bacteria Scientific Nomenclature Bacterial species : Population of cells with similar characteristics. Bacterial strain : A subgroup of a bacterial species that has distinguishing characteristics. Identified by numbers, letters, or names that follow the scientific name. Escherichia coli O157:H7 : Strain that causes bloody diarrhea. Bergey’s Manual: Provides a reference for identifying and classifying bacteria. Classification initially based on cell morphology, staining, metabolism, biochemistry, serology, etc. More recently, DNA, RNA, and protein sequence analysis are being used to study evolutionary relationships. 47 Dr.M.K. SATEESH

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Bacteria 48 Dr.M.K. SATEESH

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49 Dr.M.K. SATEESH

Ribosomal Database project:

Ribosomal Database project The database contains over 78,000 bacterial 16S rDNA sequences Approximately 7000 Type strains (the bacteria are in pure culture) Approximately 70000 Environmental samples (bacteria and archaea samples have been collected from the environment and characterized by molecular methods.) http://rdp.cme.msu.edu/html/index.html 50 Dr.M.K. SATEESH

Slide 51:

Dr. M.K. SATEESH 51 Dr.M.K. SATEESH

Slide 52:

for feedback, doubts and query; mk.sateesh@gmail.com mk.sateesh 52 Dr.M.K. SATEESH

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