3 classification of microorganisms
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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) Linneaus1778) Linneaus
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 KKingdom ingdom AnimaliaAnimalia PPhylumhylum CordataCordata CClasslass MammaliaMammalia OOrderrder perissodactylaperissodactyla FFamilyamily EquidaeEquidae GGenus equsenus equs SSpeciespecies ferusferus
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 5 main kingdoms:5 main kingdoms: EukaryoticEukaryotic
Fungi - heterotrophsFungi - heterotrophs Plantae - autotrophsPlantae - autotrophs Animalia - heterotrophsAnimalia - heterotrophs Protoctista – Some heterotrophs some Protoctista – Some heterotrophs some
autotrophs Eukaryoteautotrophs Eukaryote
ProkaryoticProkaryotic Prokaryotes / monera can be heterotrophic Prokaryotes / monera can be heterotrophic
or have chloroplasts so can be autotrophs or have chloroplasts so can be autotrophs too like rhodospirilium, or cholera too like rhodospirilium, or cholera https://www.youtube.com/watch?v=-_r2uhvYIyMhttps://www.youtube.com/watch?v=-_r2uhvYIyM
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 ProkaryotaeProkaryotae
Classification Systems in Classification Systems in the Prokaryotaethe Prokaryotae
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
ColonyColony
MorphologyMorphology
Flagella arrangementFlagella arrangement•Monotrichous bacteria have a single flagellum (e.g., Vibrio cholerae).
•Lophotrichous bacteria have multiple flagella located at the same spot on the bacteria's surfaces which act in concert to drive the bacteria in a single direction.
•Amphitrichous bacteria have a single flagellum on each of two opposite ends (only one flagellum operates at a time, allowing the bacteria to reverse course rapidly by switching which flagellum is active).
•Peritrichous bacteria have flagella projecting in all directions (e.g., E. coli).
Electron microscope picture of a Electron microscope picture of a Salmonella bacterium with several Salmonella bacterium with several flagellaflagella
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
Gram PositiveGram Positive
Diagnostic Scheme for Diagnostic Scheme for Medical UseMedical Use
Uses phenotypic qualities in identificationUses phenotypic qualities in identification 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
Physiological traits inc anaerobic, or aerobic Physiological traits inc anaerobic, or aerobic respirators, sulfur emitting, motility etcrespirators, sulfur emitting, motility etc
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
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 Classificationhttps://www.youtube.com/watch?v=dj9m7Oc36wMhttps://www.youtube.com/watch?v=dj9m7Oc36wM
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
https://www.youtube.com/watch?v=-zsdYOgTbOk
Classification of virusClassification of virus
Nature of the nucleic acid: RNA or DNA Symmetry of the capsid Presence or absence of an envelope Dimensions of the virion and capsid
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