Classification of Microorganisms - Las Positas Collegelpc1.clpccd.cc.ca.us/lpc/zingg/Micro/lecture...

Ch 10

Classification

of

Microorganisms

Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings

Student Learning Outcomes

Define taxonomy, taxon, and phylogeny.

List the characteristics of the Bacteria, Archaea, and Eukarya domains.

Differentiate among eukaryotic, prokaryotic, and viral species.

Explain the scientific naming

Differentiate between culture, clone, and strain.

Compare and contrast classification and identification.

Explain the purpose of Bergey’s Manual.

Describe how staining and biochemical tests are used to identify bacteria.

Explain how serological tests and phage typing can be used to identify an

unknown bacterium.

Describe how a newly discovered microbe can be classified by ribotyping,

DNA fingerprinting, and PCR.

Describe how microorganisms can be identified by nucleic acid

hybridization, DNA chips, and FISH.

Explain and apply a dichotomous key


Taxonomy and Phylogeny

Taxonmoy: Science of classifying organisms. Provides universal names for organisms.

Taxonomic categories: Taxon / Taxa

Phylogeny or Systematics: Evolutionary history of group of organisms.

Taxonomic hierarchy shows phylogenetic (evolutionary), relationships among organisms.

1969: Living organisms divided into five kingdoms.

1978: Two types of prokaryotic cells found. Prokaryotic relationships determined by rRNA sequencing.

All Species Inventory (2001–2025)


The Three-Domain SystemFoundation Fig 10.1


Level Above Kindom: The Three-Domain System

Carl

Woese

1978

Eubacteria (virtuosos)

Archaea (weirdoes)

Eukarya (predators and thieves)


Endosymbiotic Theory: Origin of Eukaryotes

Cyanophora paradoxa: modern example of

possible evolutionary process

Figs 10.2, 10.3


Scientific Nomenclature

Common names

Vary with languages

Vary with geography

Binomial Nomenclature (genus + specific epithet)

Used worldwide

Escherichia coli

Homo sapiens

Scientific Names

Scientific Binomial Source of Genus Name

Source of Specific Epithet

Klebsiella pneumoniae Honors Edwin Klebs The disease

Pfiesteria piscicida Honors Lois Pfiester Disease in fish

Salmonella typhimurium Honors Daniel Salmon Stupor (typh-) in

mice (muri-)

Streptococcus pyogenes

Chains of cells (strepto-) Forms pus (pyo-)

Penicilliumchrysogenum Tuftlike (penicill-) Produces a yellow

(chryso-) pigment

Trypanosoma cruziCorkscrew-like (trypano-, borer; soma-, body)

Honors OswaldoCruz


Classification: Species Definition

Eukaryotic species: A group of closely related organisms that breed among themselves

Prokaryotic species: A population of cells with similar

characteristics (Bergey’s Manual of Systematic

Bacteriology is standard reference on bacterial

classification).

Culture: Grown in laboratory media

Clone: Population of cells derived from a single cell

Strain: Genetically different cells within a clone

Viral species: Population of viruses with similar characteristics occupying a particular ecological niche. Viruses: not placed in kingdom nor domain – not composed of cells – cannot grow without a host cell.

Copyright © 2006 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 10.6

Phylogenetic Relationships of Prokaryotes


Domain Eukarya

Animalia: Multicellular; no cell walls;

chemoheterotrophic

Plantae: Multicellular; cellulose cell walls;

usually photoautotrophic

Fungi: Chemoheterotrophic;

unicellular or multicellular; cell walls of chitin;

develop from spores or hyphal fragments

Protista: A catchall kingdom for eukaryotic

organisms that do not fit other kingdoms

Grouped into clades based on rRNA


Classification: Placing organisms in

groups of related species. Lists of

characteristics of known organisms.

Identification: Matching characteristics

of an “unknown” to lists of known

organisms.

Fig 10.8

Classification and Identification


Applications,

p. 283

Identifying Bacteria


Bergey’s Manual:Classifying and Identifying Prokaryotes

Bergey’s Manual of Determinative BacteriologyProvides identificationschemes for identifying bacteria and archaea

Morphology, differential staining, biochemical tests

Bergey’s Manual of Systematic BacteriologyProvides phylogeneticinformation on bacteria and archaea

Based on rRNAsequencing


Clinical Lab Identification

Morphological

characteristics

Useful for identifying

eukaryotes

Differential staining

Gram staining, acid-

fast staining

Biochemical tests

Determines presence

of bacterial enzymes

Numerical Rapid Identification


Serology

Involves reactions of microorganisms with specific antibodies: Combine known anti-serum with unknown bacterium

Useful in determining the identity of strains and species, as well as relationships among organisms.

Fig 10.10: Slide Agglutination

Examples: Slide agglutination ELISA (see lab) Western blot (no details)


Phage TypingFig 10.13

Identification of

bacterial species

and strains by

determining their

susceptibility to

various phages.

More details on

bacteriophages

in Ch 13


Genetics

DNA fingerprinting:Number and sizes of DNA fragments (fingerprints) produced by RE digests are used to determine genetic similarities.

Ribotyping: rRNA sequencing

Polymerase chain reaction (PCR) can be used to amplify a small amount of microbial DNA in a sample. The presence or identification of an organism is indicated by amplified DNA. (see lab)

Fig 10.14: Electrophoresis of RE digest of plasmid DNA


Nucleic Acid Hybridization

Fig 10.15

Single strands of DNA or RNA, from related organisms

will hydrogen-bond to form a double-stranded molecule;

this bonding is called nucleic acid hybridization.

Examples of Applications:

• Southern blotting,

• DNA chips, and

• FISH

Nucleic Acid Hybridization: DNA Chip

Fig 10.17

Fluorescent In Situ Hybridization (FISH)

Fig 10.18a–b

Add DNA or RNA

probe attached to

fluorescent dye

for S. aureus

Dichotomous Key

ANIMATION Dichotomous Keys: Practice

ANIMATION Dichotomous Keys: Sample with

Flowchart

ANIMATION Dichotomous Keys: Overview

dichotomous_practice.html

dichotomous_sample.html

dichotomous.html

Classification of Microorganisms - Las Positas Collegelpc1.clpccd.cc.ca.us/lpc/zingg/Micro/lecture...

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