Taxonomy of Prokaryotes that include Bacteria and Archea, Brief description of taxonomy history types of classification numerical taxonomy different classification system basic characters used for classification International code of Nomenclature of Bacteria Bergey's manual pathovar concept

1. Taxonomy of phyto-
pathogenic prokaryotes

2. Overview
• Extraordinary diversity of microbes necessitates grouping of
organisms together in a non-overlapping hierarchical order.
• Taxonomy in Greek:
taxis -order/ arrangement
nomos – law/science
• Taxonomy encompasses other disciplines including Morphology,
Physiology, Biochemistry, Epidemiology, Molecular Biology and
Ecology

3. Introduction
 Taxonomy is a science that deals with naming, describing and
classification of all living organisms. Group of organisms classified as
a unit are called taxon.
 It consists of separate but interrelated parts:
Classification: grouping and characterizing organism into taxon on
the basis of particular characters.
Identification: practical side of taxonomy, process of determining if a
particular isolate belongs to recognised taxa or not.
Nomenclature: Branch of taxonomy concerned with assigning names
to taxonomic groups according to published rules.
 Sytematics: often used for taxonomy, defined as scientific study of an
organism with ultimate objective of characterizing and arranging them
in an orderly manner.

4. Why Taxonomy is important?
• Permits the organization of huge amounts of information about
microorganisms .
• Allows predictions and hypotheses to be made upon available
information.
• Places organisms in groups with precise names that permit effective
communication between investigators.
• Essential for the correct identification of organisms.

5. Taxonomic hierarchy

6. • Species - basic taxonomic group.
Prokaryotic species - collection of strains that share many stable
properties and differ significantly from other groups of strains
• Genus - defined group of one or more species
• Family- a collection of similar genera, suffix aceae
• Order:- a collection of similar families, suffix –ales
• Class:- a collection of similar orders, suffix -ia
• Phylum or division:- a collection of similar classes
• Kingdom:- a collection of similar phyla or divisions
• Domain:-collection of similar kingdom, new taxonomic category

7. Linnaeus
(1735)
Haeckal
(1866)
Chatton
(1925)
Copeland
(1938)
Whittaker
(1969)
Woese et
al. (1977)
Woese et al.
(1990)
Cavalier-
Smith
(1993)
Cavalier-
Smith
(1998)
Ruggiero et
al. (2015)
Not treated Not treated 2 empires
2 empires 2 empires 2 empires 3 empires 3 super
kingdoms
2 empires 2 super
kingdoms
2
kingdoms
3 kingdoms Not treated 4 kingdoms 5 kingdoms 6 kingdoms Not treated
8
kingdoms
6 kingdoms 7 kingdoms
Not treated
Protista
Prokaryota Monera
Monera
Eubacteria Bacteria Eubacteria
Bacteria
Bacteria
Archaebact
eria
Archaea
Archaebact
eria
Archaea
Eukaryota
Protista
Protista Protista
Eucarya
Archezoa Protozoa Protozoa
Protozoa
Chromista Chromista
Chromista
Vegetabilia
Plantae Plantae
Plantae Plantae Plantae Plantae Plantae
Fungi Fungi Fungi Fungi Fungi
Animalia
Animalia Animalia Animalia
Animalia Animalia
Animalia
Animalia
History of Classification

8. Six kingdom classification by Carl Woese et al.
(1977)
Prokaryota
Eukaryota

9. Classification Systems
• Three basic types of classification systems are used :
 Phenetic classification :
• Natural classification system that groups organisms together based
upon mutual similarity of their phenotypic characteristics.
• Phylogenetic (phyletic) classification :
• Based solely on evolutionary relationships.
• Has been difficult to use in the past for prokaryotes due to a lack of
a fossil record.
• Modern methods instead use gene sequences (e.g., RNA genes) or
their products (proteins) to estimate phylogenetic relationships.
Genetic classification :
• Based solely on genotypic relationships.

10. Numerical Taxonomy
• Concept introduced by Michel Adanson in 1763(18th Century), a
contemporary of Linnaeus
• Robert Sokal and Peter H.A Sneath defined numerical taxonomy as
“grouping by numerical methods of taxonomic units into taxa on
the basis of their character states’’.
• Association Coefficient: function that measures the agreement
between characters possessed by two organisms.
• Phenons, 80% phenon similarity = species
• Results are expressed in tree like diagram - dendrogram

11. Major Characteristics used in
Taxonomy
Classical Characters
• Morphological
• Physiological/Biochemical
• Serological
• Ecological
• Genetic
Molecular characters
• Comparison of proteins
• Nucleic acid base composition
• Nucleic acid Hybridization
• Nucleic acid sequencing

12. Morphological studies
• Cell shape
• Cell size
• Colony morphology
• Ultrastructure
• Staining behaviour
• Flagella and cilia
• Mechanism of motility
• Spore shape and location
• Cell inclusions
• Colour

13. Physiological/Biochemical studies
• Carbon and nitrogen source
• Cell wall constituents
• Energy source
• Fermentation products
• Nutritional type
• Optimum temperature
• Photosynthetic pigments
• Salt requirements and tolerance
• Luminescence
• Mechanism of energy conversion
• Osmotic tolerance
• Oxygen relationship
• Optimum PH
• Sensitivity to antibiotics/
inhibitors
• Storage inclusions

14. Ecological characters
• Life cycle patterns
• Nature of symbiotic relationships
• Ability to cause disease in a particular host
• Habitat preferences(temp, PH, O2, Osmotic conc.)
Genetic characters
• Procaryotic gene exchange analysis through;
• Transformation- Haemophilus,Micrococcus,&Rhizobium
• Conjugation- Gram negative enteric bacteria
• Plasmids

15. Molecular characters
Comparisons of proteins
• Sequence of cytochrome, heat shock protein, electron transport
protein, histones, transcription and translation proteins as well as
varieties of metabolic enzymes.
Nucleic acid base composition
• DNA base composition
• G+C content determination by melting temperature method
• % G+C= (G+C/A+C+G+T) x 100%
• Plants and animals have G+C content 40% (30-50%)
• Prokaryotes G+C content ranges 25-80%
Contd…

16. Nucleic acid Hybridization
• Genome similarity compared more directly by nucleic acid hybridization.
• DNA –RNA hybridization using radioactive ribosomal or transfer RNA is
better for detecting distantly related organisms.
• rRNA and tRNA are used because they represent only a small portion of
total DNA genome and have not evolved as rapidly as other gene.
Nucleic acid sequencing
• Sequencing of 5s and 16s rRNAs isolated from the 50s and 30s subunits
respectively.
rRNA are almost ideal for sequencing because;
• are essential to a critical organelle found in all organisms.
• structure changes very slowly with time.
• constant and variable sequences are useful for assessing close and
distant relationships.

17. Nomenclature code
• First separate code for bacteria i.e. International Bacteriological code
of Nomenclature published in 1948.
• Since 2000, it is called International Code of nomenclature of
Prokaryotes governed by International Committee on Systematics of
Prokaryotes.
• Bergey’s Manual of Determinative Bacteriology and Bergey’s Manual
of Systematic Bacteriology are most comprehensive and authorative
publications in field of bacterial taxonomy.

18. Bergey’s Manual
• David Hendricks Bergey(1860-1937), Professor of Bacteriology at
University of Pennsylvania.
• Studied at university of Pennsylvania, obtained doctor of medicine in
1884 Joined University’s Hygiene laboratory, taught Hygiene and
Bacteriology & lead from 1929-1932 .
• Was first person to isolate Actinomyces from a human being in 1907.
• David Hendricks Bergey and four colleagues at University of
Pennsylvania, published a classification scheme of bacteria that could
be used for identification of bacterial species, the Bergey’s Manual of
Determinative Bacteriology.
• Was the chairman of editorial board for the first edition of Bergey’s
manual of determinative Bacteriology.

19. Bergey’s Manual of Determinative Bacteriology
• First edition 1923,provided both a classification of Bacteria and a scheme to help
with their identification.
• Upto 7 editions: 1925, 1930,1934, 1939, 1948 and 1957
• 8th edition (1974): bacteria divided into 19 groups
• Bergey’s manual of Determinative Bacteriology 9th Edition(1994): bacteria have
been divided into 35 groups including 5 groups of Archaeobacteria.
• Second edition of Bergey’s Manual of Systematic Bacteriology is latest edition of
manual
• Domain Archea divided to 2 phyla and 9 classes and Bacteria into 24 phyla and 32
classes.
• Till now 40 genre of phyto pathogenic bacteria have been reported in which
37established species and 3 candidatus categories.

20. Domain Bacteria
• Divided into 24 phylum
Phylum BI. Aquificae
Phylum BII. Thermotogae
Phylum BIII. Thermodessulfobacteria
Phylum BIV. Deinococcus-Thermus
Phylum BV. Chrysiogeneles
Phylum BVI. Chloflexi
Phylum BVII. Thermomicrobia
Phylum BVIII. Nitrospira
Phylum BIX. Deferribacteres
Phylum BX. Cyanobacteria
Phylum BXI. Chlorobi
Phylum BXII. Proteobacteria
Phylum BXIII. Firmicutes
Phylum BXIV. Actinobacteria
Phylum BXV. Planctomycetes
Phylum BXVI. Chlamydiae
Phylum BXVII. Spirochates
Phylum BXVIII. Fibrobacteres
Phylum BXIX. Acidobacteria
Phylum BXX. Bacteriodetes
Phylum BXXI. Fusobacteria
Phylum BXXII. Vermicomicrobia
Phylum BXXIII. Dictyoglomi
Phylum BXXIV. Gemmatimonadetes

21. Phyla of phytopathogenic bacteria

24. Classification of phyto-pathogenic bacteria
• 1976 revised edition of International code of Nomenclature of Bacteria major effect on taxonomy of
bacterial plant pathogens.
• Pathovar concept:
• Executive committee of International society For plant Pathology set up Committee on Taxonomy of Plant
Pathogenic Bacteria to see consequences of 1976 revised code.
• Infrasubspecific taxon “pathovar” record most accurately the differences exihibited in terms of host range
and symptoms.
• Pathovar is defined as “a strain or a group of strains with the same or similar characteristics, differentiated at
the infrasubspecific level from other strains of same species or subspecies on the basis of distinctive
pathogencity to one or more plant hosts”.
• ISPP published International Standards for Naming Pathovars of Phytopathogenic Bacteria first time in
January 1, 1980.
• Now plant pathologists or bacteriologist have to follow two separate set of rules set forth in:
International code of Nomenclature of Prokaryotes: subspecies level
International Standards for Naming Pathovars of Plant Pathogenic Bacteria: Pathovar