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. Metabolic capabilities Anaerobic, aerobic, Produces SH, Lactose, etc 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 can’t 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)