Classification of Classification of Microorganisms Microorganisms

TaxonomyTaxonomy

Organizing, classifying Organizing, classifying and naming living thingsand naming living things

Formal system originated Formal system originated by Carl von Linnby Carl von Linné (1701-é (1701-1778) 1778)

Identifying and classifying Identifying and classifying organisms according to organisms according to specificspecific criteria criteria

Each organism placed Each organism placed into a classification into a classification system system

TaxonomyTaxonomy

DomainDomain KKingdomingdom PPhylumhylum CClasslass OOrderrder FFamilyamily GGenusenus sspeciespecies

3 Domains3 Domains

EubacteriaEubacteria true bacteria, peptidoglycantrue bacteria, peptidoglycan

ArchaeaArchaea odd bacteria that live in extreme odd bacteria that live in extreme

environments, high salt, heat, etc. (usually environments, high salt, heat, etc. (usually called extremophiles)called extremophiles)

EukaryaEukarya have a nucleus & organelles (humans, have a nucleus & organelles (humans,

animals, plants)animals, plants)

TaxonomyTaxonomy

4 main kingdoms:4 main kingdoms: ProtistaProtista FungiFungi PlantaePlantae AnimaliaAnimalia AlgaeAlgae

Naming MicoorganismsNaming Micoorganisms

Binomial (scientific) nomenclature Binomial (scientific) nomenclature Gives each microbe 2 names:Gives each microbe 2 names:

GenusGenus - noun, always capitalized - noun, always capitalized speciesspecies - adjective, lowercase - adjective, lowercase

Both italicized or underlinedBoth italicized or underlined Staphylococcus aureus (S. aureus)Staphylococcus aureus (S. aureus) Bacillus subtilisBacillus subtilis (B. subtilis)(B. subtilis) Escherichia coliEscherichia coli (E. coli)(E. coli)

Evolution - living things Evolution - living things change gradually over millions change gradually over millions of yearsof years

Changes favoring survival are retained and less Changes favoring survival are retained and less beneficial changes are lostbeneficial changes are lost

All new species originate from preexisting All new species originate from preexisting speciesspecies

Closely related organism have similar features Closely related organism have similar features because they evolved from common ancestral because they evolved from common ancestral formsforms

Evolution usually progresses toward greater Evolution usually progresses toward greater complexitycomplexity

Insert figure 1.15Woese-Fox System

Classification Classification Systems in the Systems in the ProcaryotaeProcaryotae

Classification Systems in Classification Systems in the Procaryotaethe Procaryotae

1.1. Microscopic morphologyMicroscopic morphology

2.2. Macroscopic morphology – colony Macroscopic morphology – colony appearanceappearance

3.3. Physiological / biochemical characteristicsPhysiological / biochemical characteristics

4.4. Chemical analysisChemical analysis

5.5. Serological analysisSerological analysis

6.6. Genetic and molecular analysisGenetic and molecular analysis• G + C base compositionG + C base composition• DNA analysis using genetic probesDNA analysis using genetic probes• Nucleic acid sequencing and rRNA analysisNucleic acid sequencing and rRNA analysis

Bacterial Taxonomy Based Bacterial Taxonomy Based on on Bergey’s ManualBergey’s Manual

Bergey’s Manual of Determinative Bergey’s Manual of Determinative BacteriologyBacteriology – five volume resource – five volume resource covering all known procaryotescovering all known procaryotes classification based on genetic information –classification based on genetic information –

phylogeneticphylogenetic two domains: Archaea and Bacteriatwo domains: Archaea and Bacteria five major subgroups with 25 different phylafive major subgroups with 25 different phyla

Major Taxonomic Groups Major Taxonomic Groups of Bacteriaof Bacteria Vol 1A: Domain ArchaeaVol 1A: Domain Archaea

primitive, adapted to extreme habitats and primitive, adapted to extreme habitats and modes of nutritionmodes of nutrition

Vol 1B: Domain BacteriaVol 1B: Domain Bacteria Vol 2-5:Vol 2-5:

Phylum ProteobacteriaPhylum Proteobacteria – Gram-negative cell – Gram-negative cell wallswalls

Phylum FirmicutesPhylum Firmicutes – mainly Gram-positive – mainly Gram-positive with low G + C content with low G + C content

Phylum ActinobacteriaPhylum Actinobacteria – Gram-positive with – Gram-positive with high G + C contenthigh G + C content

Diagnostic Scheme for Diagnostic Scheme for Medical UseMedical Use

Uses phenotypic qualities in Uses phenotypic qualities in identificationidentification restricted to bacterial disease agentsrestricted to bacterial disease agents divides based on cell wall structure, shape, divides based on cell wall structure, shape,

arrangement, and physiological traitsarrangement, and physiological traits

Species and SubspeciesSpecies and Subspecies SpeciesSpecies

collection of bacterial cells which share an overall similar collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern pattern of traits in contrast to other bacteria whose pattern differs significantly differs significantly

StrainStrain or or varietyvariety culture derived from a single parent that differs in structure culture derived from a single parent that differs in structure

or metabolism from other cultures of that species (biovars, or metabolism from other cultures of that species (biovars, morphovars)morphovars)

TypeType subspecies that can show differences in antigenic makeup subspecies that can show differences in antigenic makeup

(serotype or serovar), susceptibility to bacterial viruses (serotype or serovar), susceptibility to bacterial viruses (phage type) and in pathogenicity (pathotype)(phage type) and in pathogenicity (pathotype)

Archaea: The Other Archaea: The Other ProcaryotesProcaryotes

Constitute third Domain ArchaeaConstitute third Domain Archaea Seem more closely related to Domain Eukarya than to Seem more closely related to Domain Eukarya than to

bacteriabacteria Contain unique genetic sequences in their rRNAContain unique genetic sequences in their rRNA Have unique membrane lipids and cell wall constructionHave unique membrane lipids and cell wall construction Live in the most extreme habitats in nature, Live in the most extreme habitats in nature,

extremophilesextremophiles Adapted to heat, salt, acid pH, pressure and Adapted to heat, salt, acid pH, pressure and

atmosphereatmosphere Includes: methane producers, hyperthermophiles, Includes: methane producers, hyperthermophiles,

extreme halophiles, and sulfur reducersextreme halophiles, and sulfur reducers

EukaryotesEukaryotes

EukaryotesEukaryotes

ProtistaProtista FungiFungi PlantaePlantae AnimaliaAnimalia AlgaeAlgae

Fungal ClassificationFungal Classification

Sexual reproduction Sexual reproduction Spores are formed following fusion of male and Spores are formed following fusion of male and

female strains and formation of sexual structurefemale strains and formation of sexual structure

Sexual spores and spore-forming structures Sexual spores and spore-forming structures are one basis for classificationare one basis for classification ZygosporesZygospores AscosporesAscospores BasidiosporesBasidiospores

Fungal ClassificationFungal Classification

Subkingdom Amastigomycota Subkingdom Amastigomycota Terrestrial inhabitants including those of Terrestrial inhabitants including those of

medical importance:medical importance:

1.1. ZygomycotaZygomycota – zygospores; sporangiospores and – zygospores; sporangiospores and some conidiasome conidia

2.2. AscomycotaAscomycota – ascospores; conidia – ascospores; conidia

3.3. BasidiomycotaBasidiomycota – basidiospores; conidia – basidiospores; conidia

4.4. DeuteromycotaDeuteromycota – majority are yeasts and molds; – majority are yeasts and molds; no sexual spores known; conidiano sexual spores known; conidia

Protozoan ClassificationProtozoan Classification Difficult because of diversityDifficult because of diversity Simple grouping is based on method of motility, Simple grouping is based on method of motility,

reproduction, and life cyclereproduction, and life cycle1.1. MastigophoraMastigophora – primarily flagellar motility, some – primarily flagellar motility, some

flagellar and amoeboid; sexual reproduction; cyst flagellar and amoeboid; sexual reproduction; cyst and trophozoiteand trophozoite

2.2. SarcodinaSarcodina – primarily ameba; asexual by fission; – primarily ameba; asexual by fission; most are free-livingmost are free-living

3.3. CiliophoraCiliophora – cilia; trophozoites and cysts; most are – cilia; trophozoites and cysts; most are free-living, harmless free-living, harmless

4.4. ApicomplexaApicomplexa – motility is absent except male – motility is absent except male gametes; sexual and asexual reproduction; complex gametes; sexual and asexual reproduction; complex life cycle – all parasiticlife cycle – all parasitic