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Modern Classification Systems
Robert Whittaker (1969)• Five Kingdom System
– Monera
– Protista
– Fungi
– Plantae
– Animalia
Replica plating (lederberg)All colonies grow Mutants do not grow
Pressplate ontovelveteen
Velveteen withimprint of allcolonies
Completemedium
Incubate
All colonies grow Mutants do not grow
Minimalmedium
Transfer imprintof colonies tofresh media
Master plate;growth oncompletemedium
Velveteen;sterilized
Plastic hoop
Wooden block
Testing phenotypes
Complementation via recombination
DNA fromTrp+ cells
Agar lackingtryptophan
Trp– cells No growth Trp– cells Recombinantsform colonies
Agar lackingtryptophan
“Trp auxotroph”
Basic Local Alignment Search Tool BLAST
Number ofsequence ofmatches
Afteralignment
Beforealignment
Species 1
Species 2
Species 1
Species 2
9
15
Nonidentities
Gaps
More distant = more differences
Hybridization analysiis
Hybridizationexperiment:
Same genus,but differentspecies
Organisms tobe compared:
Genomic DNA
Heat todenature
Mix DNA from two organisms—unlabeledDNA is added in excess:
DNApreparation
Genomic DNA
Results andinterpretation:
Same species
Differentgenera 100% < 25%
100 75 50 25 0 Same strain(control)
1 and 2 are likelydifferent generaPercent hybridization
Unhybridized Organism 2 DNAHybridized DNA
Shear and label ( )
Hybridized DNA
Shear DNA
Organism 1 Organism 2
Fig. 14-21
Genomic DNA–DNA hybridization (%)16S
rR
NA
gen
e se
qu
ence
sim
ilari
ty (
%)
0 20 40 60 70 80 100
100
98
96
94
92
90
88
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
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