Classification week2

KLASIFIKASI KLASIFIKASI MIKROORGANISME MIKROORGANISME

27/02/2012 1Masdiana Padaga

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 Identifying and classifying organisms classifying organisms according to 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

Insert figure 1.15Woese-Fox System

Bacterial PhylogenyBacterial Phylogeny

BACTERIABACTERIA

ARCHAEBACTERIAARCHAEBACTERIA• Introns in DNAIntrons in DNA• Lack peptidogycan Lack peptidogycan

in cell wallsin cell walls• Live in extreme Live in extreme

environmentsenvironments

EUBACTERIAEUBACTERIA• Includes most Includes most

bacteriabacteria• Most have one of Most have one of

three shapesthree shapes• May be divided May be divided

into up to 12 into up to 12 phylaphyla

• Classification is Classification is controversialcontroversial


TYPES OF TYPES OF ARCHAEBACTERIAARCHAEBACTERIA

Thermoacidophilies Living in hot springs

Methanogens living in

sewage

Extreme halophile

living in the Great Salt Lake27/02/2012 7Masdiana Padaga

Bacteria Morphological DiversityBacteria Morphological Diversity

From http://ag.arizona.edu/plp/courses/plp329/micdivintro.ppt27/02/2012 8Masdiana Padaga

BASIC SHAPES OF BASIC SHAPES OF EUBACTERIAEUBACTERIA

SPHERICAL

ROD-SHAPED

SPIRILLA


Most Species of Eubacteria Most Species of Eubacteria may be Grouped Based on may be Grouped Based on StainingStaining

Gram-NegativeGram-Negative

• Lack thicker layer Lack thicker layer of peptidoglycanof peptidoglycan

• Stain pinkStain pink

• EndotoxinsEndotoxins

Gram-PositiveGram-Positive• Thicker layer of Thicker layer of

peptidogycanpeptidogycan• Stain purpleStain purple• Exotoxins Exotoxins

(released when (released when bacteria die)bacteria die)

Gram- negative Gram-positive


ArchaebacteriaArchaebacteria


Bacterial Taxonomy Based on Bacterial Taxonomy Based 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 classification based on genetic

information –information –phylogeneticphylogenetic• two domains: Archaea and Bacteriatwo domains: Archaea and Bacteria• five major subgroups with 25 different five major subgroups with 25 different

phylaphyla

Major Taxonomic Groups of Major Taxonomic Groups of BacteriaBacteria

Vol 1A: Domain ArchaeaVol 1A: Domain Archaea• primitive, adapted to extreme habitats primitive, adapted to extreme habitats

and modes of nutritionand modes of nutrition Vol 1B: Domain BacteriaVol 1B: Domain Bacteria Vol 2-5:Vol 2-5:

• Phylum ProteobacteriaPhylum Proteobacteria – Gram- – Gram-negative cell wallsnegative cell walls

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

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

Naming and Classifying Naming and Classifying microorganismsmicroorganisms

• Linnaeus system for scientific Linnaeus system for scientific nomenclaturenomenclature

• Each organism has two names:Each organism has two names: 1) Genus1) Genus

2) Specific epithet2) Specific epithet


Scientific NamesScientific Names Italicized or underlined.Italicized or underlined.

The genus is capitalized, and the specific epithet is with The genus is capitalized, and the specific epithet is with lowercaselowercase

Could be as an honor for the scientistCould be as an honor for the scientist

A Latin originA Latin origin

e.g. e.g. Escherichia coli Escherichia coli ((E. coliE. coli))

- discoverer: Theodor Escherich- discoverer: Theodor Escherich

- describes the habitat (colon/intestine)- describes the habitat (colon/intestine)

e.g. e.g. Staphylococcus aureus Staphylococcus aureus ((S. aureusS. aureus))

- Clustered (staphylo), spherical (cocci)- Clustered (staphylo), spherical (cocci)

- Gold colored colonies (aureus)- Gold colored colonies (aureus)

In intestine

On skin27/02/2012 16Masdiana Padaga

Binomial Nomenclature Binomial Nomenclature Examples: Escherichia coli, E. coli, Escherichia spp., and “the genus Escherichia”

The genus name (Escherichia) is always capitalized

The species name (coli) is never capitalized

The species name is never used without the genus name (e.g., coli standing alone, by itself, is a mistake!)

The genus name may be used without the species name (e.g., Escherichia may stand alone, though when doing so it no longer actually describes a species)

When both genus and species names are present, the genus name always comes first (e.g., Escherichia coli, not coli Escherichia)27/02/2012 17Masdiana Padaga

Binomial Nomenclature Binomial Nomenclature Both the genus and species names are always italicized (or underlined)—always underline if writing binomials by hand

The first time a binomial is used in a work, it must be spelled out in its entirety (e.g., E. coli standing alone in a manuscript is not acceptable unless you have already written Escherichia coli in the manuscript)

The next time a biniomial is used it may be abbreviated (e.g., E. for Escherichia) though this is done typically only when used in combination with the species name (e.g., E. coli)

The species name is never abbreviated27/02/2012 18Masdiana Padaga

Binomial Nomenclature Binomial Nomenclature

It is a good idea to abbreviate unambiguously if there is any potential for confusion (e.g., Enterococcus vs. Escherichia)

These rules are to be followed when employing binomial nomenclature even in your speech. It is proper to refer to Escherichia coli as E. coli or even as Escherichia, but it is not proper to call it coli or E.C.!

When in doubt, write the whole thing out (and underline)!


Types of EukaryotesTypes of EukaryotesProtozoaProtozoa

Unicellular Unicellular eukaryoteeukaryote

Absorb or ingest Absorb or ingest organic chemicalsorganic chemicals

May move using May move using pseudopods, cilia or pseudopods, cilia or flagellaflagella

e.g. Amoebae.g. Amoeba

AlgaeAlgae

Unicellular/Unicellular/multicellular eukaryotemulticellular eukaryote

Has cellulose cell wallsHas cellulose cell walls Gain energy through Gain energy through

photosynthesisphotosynthesis Produce molecular and Produce molecular and

organic compoundsorganic compounds


Fungi (singular: Fungus)Fungi (singular: Fungus)

EukaryotesEukaryotes Chitin cell wallsChitin cell walls Use organic chemicals for Use organic chemicals for

energyenergy Molds and mushrooms Molds and mushrooms

are multicellular, consists are multicellular, consists of mycelia (composed of of mycelia (composed of filaments called hyphae)filaments called hyphae)

Yeasts are unicellularYeasts are unicellular27/02/2012 21Masdiana Padaga

Multicellular animal parasitesMulticellular animal parasites

Helminths: flatworms Helminths: flatworms and roundwormsand roundworms

MulticellularMulticellular


VirusesViruses

Too small to be observed with light Too small to be observed with light microscopemicroscope

Consists of DNA/RNA coreConsists of DNA/RNA core Core is surrounded by protein coatCore is surrounded by protein coat Coat may be enclosed in a lipid envelopeCoat may be enclosed in a lipid envelope Viruses are replicated only when they are in Viruses are replicated only when they are in

living host cellliving host cell Bacteriophage-viruses that infect bacteriaBacteriophage-viruses that infect bacteria Viroids-nucleic acid without protein coatingViroids-nucleic acid without protein coating Prions- Infectious protenacious particlesPrions- Infectious protenacious particles27/02/2012 23Masdiana Padaga

Classification week2

Technology

Transcript of Classification week2