Taxonomy II: Applied systems

Modern Classification Systems Robert Whittaker (1969) Five Kingdom System –Monera –Protista –Fungi –Plantae –Animalia

Modern Classification Systems Carl Woese Three domain system »Archea »Eubacteria » Eukarya

Fig stromatolites

Fig. 14-9

Archaea may be closer to Eukarya than Eubacteria.

Phenotypes

Replica plating (lederberg) All colonies grow Mutants do not grow Press plate onto velveteen Velveteen with imprint of all colonies Complete medium Incubate All colonies grow Mutants do not grow Minimal medium Transfer imprint of colonies to fresh media Master plate; growth on complete medium Velveteen; sterilized Plastic hoop Wooden block Testing phenotypes

Complementation via recombination DNA from Trp + cells Agar lacking tryptophan Trp – cellsNo growthTrp – cellsRecombinants form colonies Agar lacking tryptophan “Trp auxotroph”

16s RNA map

Basic Local Alignment Search Tool BLAST Number of sequence of matches After alignment Before alignment Species 1 Species 2 Species 1 Species Nonidentities Gaps More distant = more differences

Making a phylogenetic tree

node 1 node 2 node 3 node 4

Hybridization analysiis Hybridization experiment: Same genus, but different species Organisms to be compared: Genomic DNA Heat to denature Mix DNA from two organisms—unlabeled DNA is added in excess: DNA preparation Genomic DNA Results and interpretation: Same species Different genera 100%< 25% Same strain (control) 1 and 2 are likely different genera Percent hybridization Unhybridized Organism 2 DNA Hybridized DNA Shear and label ( ) Hybridized DNA Shear DNA Organism 1 Organism 2

Fig Genomic DNA–DNA hybridization (%) 16S rRNA gene sequence similarity (%)

GC content Thermophiles have higher GC content, why?

B. Applied Taxonomic Systems

3. Bacterial taxonomy Bergey's Manual Criteria for identification and classification

3a. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Morphology –Cell Shape & Arrangement –Cell Size –Staining Reactions

3b. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Chemical –Chemical Composition »Teichoic acid »LPS

3c. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Cultural –Nutritional Requirements –Living Host Requirement –Physical Conditions »Temperature, Light, Gas

3d. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Metabolic –Energy Yielding Processes - Fermentation –Energy Utilizing Processes - Nutrient transport –Motility –Enzymes

3e. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Antigens –Stimulate the immune system -antigens Genetics –G-C ratio –Plasmids

3f. Bacterial taxonomy - Bergey's Manual Criteria for identification and classification Pathogenic –Cause disease –Host - plant, animal Ecological least reliable –Habitat

C. Nomenclature

1a. Nomenclature Sample First Words »Latin Root Bacillus - Small Rod »Greek Root Clostridium - small spindle Corynebacterium - club bacterium »Personal Names Erwinia

1b. Nomenclature Sample Second Words –Albus - White –Aureus - Gold –Lutea - Yellow –Meningitis - inflammation of meninges

2. Nomenclature Writing technical names –First word - always capitalized & in italics –Second word - never capitalized & in italics Bacillus subtilis B. subtilis