Identification and Classification of Prokaryotes

Chapter 10

Taxonomy
The science of classification Provides an orderly basis for the naming of

organisms
Places organisms into a category or taxon

(plural: taxa)
Carolus Linnaeus: 18th century Swedish

botanist; the Father of Taxonomy

Carolus Linnaeus

(1707-1778)

Identification and Classification

Living organisms are divided into groups to better

understand relationships among species Taxonomy is the science that studies organisms to order and arrange them Taxonomy can be viewed in three areas

Identification Process of characterizing in order to group them Classification Arranging organisms into similar or related groups Nomenclature System of assigning names

Binomial Nomenclature
The system used to name all living things The first name designates the genus (plural: genera)

and its first letter is capitalized

The second name is the specific epithet, and it is not

capitalized
Together the genus and specific epithet identify the

species

The Meaning of the Names of Some Microorganisms

Escherichia coli: Named after Theodore

Escherich in 1888; found in the colon

Entamoeba histolytica: Ent, intestinal;

amoebae, shape/movement; histo, tissue; lytic, lysing or digesting tissue

Strain: A subgroup of a species with one or

more characteristics that distinguish it from other members of the same species

Principles of Taxonomy
Strategies Used to Identify Prokaryotes

Wide assortment of technologies used to identify organisms including

Microscopic examination Culture characteristics Biochemical test Nucleic acid analysis

Principles of Taxonomy
Strategies Used to Classify Prokaryotes

Understanding organisms phylogeny assists in classification

Allows for organized classification of newly recognized organisms

Development of molecular techniques for classification and identification make genetic relatedness possible

Principles of Taxonomy
Taxonomic hierarchies Classification categories arranged in hierarchical order Domain collection similar to kingdoms
Archaea, Prokaryotes, Eukaryotes

Kingdom collection of similar phyla

Monera, Protista, Fungi, Plantae, Animalia

Phylum collection of similar classes Class collection of similar orders Order collection of similar families Family collection of similar genera Genus group of related species Species group of related isolates or strains
Most basic unit

Classification of Human Dog Wolf and a Bacterium

Principles of Taxonomy
Classification system

No such thing as official classification system Scheme favored by most microbiologists is three domain system

Before three domain system five kingdom system was used

Principles of Taxonomy
Nomenclature

Names given according to International Code for the Nomenclature of Bacteria

Using Phenotype to Identify Prokaryotes

Phenotype can be used in the process

identification of bacteria Methods used include

Microscopic morphology

Gram -. Gram +, cocci, rod, vibro, spirillum, etc.

Anaerobic, aerobic, Produces SH, Lactose, etc

Metabolic capabilities

Serology- do specific antibodies attach

Using Phenotype to Identify Prokaryotes

Microscopic morphology Important initial step in identification Can be used to determine size, shape and staining characteristics Size and shape can readily be determined microscopically Gram stain differentiate Gram + from Gram Narrows possible identities of organism Special stains Identifies unique characteristics of organisms
Acid fast stain

Using Phenotype to Identify Prokaryotes

Metabolic capabilities

Identification relies heavily on analysis of metabolic capabilities Culture characteristics

Colony morphology can give clues to identity

Red pigment of Serratia marcescens

Biochemical tests

More conclusive identification

Most test rely on pH indicators

Commercial biochemical tests allow for series of test with single inoculation

Using Phenotype to Identify Prokaryotes

Serology

Technique relying on specific interaction between antibodies and antigens Serological tests are available for rapid detection of numerous organisms

Streptococcus pyogenes the causative agent of strep throat

Using Genotype to Identify Prokaryotes

Nucleic acid probes can locate unique

nucleotide sequence of a particular species Numerous technologies discussed previously are being used to identify organisms based on genotype Advantage

Identification of organism that cant be grown in culture

Using Genotype to Identify Prokaryotes

Using PCR

Used to amplify sequences that allow for detection of specific sequences for identification Sequencing ribosomal RNA genes There is little genetic variation in rRNA

Newer technologies are available to sequence rDNA

The DNA that encodes rRNA

Characterizing Stain Differences

Biochemical typing Biochemical tests can be used to identify species

They can also be used to identify strains by tracing specific biochemical characteristics called biovar or biotype

Serological typing Identification made based on differences in serological molecules Serological characteristics are termed serovar or serotype

Characterizing Stain Differences

Phage typing

Certain strains of given species susceptible to various bacteriophages

a.k.a phage
Virus that infect bacteria

Phage typing identifies organism by phage that infect them

Phage type has been largely replaced by molecular methods

Characterizing Stain Differences

Antibiograms Identifies organism based on antibiotic susceptibility Disc impregnated with antimicrobial placed on inoculated plate Clear are indicates microbial susceptibility Different strain will have different susceptibility patterns

Classifying Prokaryotes
Classification historically based on phenotype Size, shape, staining characteristics and metabolic capabilities New molecular techniques make identification more

accurate

Allows for accurate construction of phylogenetic tree Trees show divergence and relationships between organism Molecular techniques highlighted transfer mechanism of prokaryotic cells Horizontal or lateral transfer of DNA

Classifying Prokaryotes
Sequencing methods include

16s rDNA sequence analysis

Comparison of 16s rRNA and rDNA sequences revolutionized classification

Lack of mutation allows identification of distant relatedness DNA hybridization better tool for assessing relatedness on species level

Classifying Prokaryotes
DNA hybridization

Relatedness of organism can be determined by similarity of nucleotide sequences

Sequence homology is measured by DNA hybridization

Extent of hybridization reflects degree of similarity

If two strain show high percentage of DNA hybridization they are considered related
70% similarity is considered same species

Classifying Prokaryotes
DNA base ratio

Comparison of genomes to determine DNA base ratio

Looking at relative proportion of A:T and G:C bonding in DNA Base ratio is expressed in G:C content

If GC ratio deviate more than a little organism are not related

Similarity of base composition does not mean relatedness

Using a Taxonomic Key

Dichotomous Key: A commonly used

key to identify organisms.

Has paired statements describing

characteristics of organisms.

Dichotomous Key for Classifying U.S. Coins

Bacterial Identification Tree

David H. Bergey (1860-1937)