Chapter 19Microbial Taxonomy

12-17-2008

Taxonomyscience of biological classificationconsists of three separate but interrelated parts

classification – arrangement of organisms into groups (taxa; s.,taxon)nomenclature – assignment of names to taxaidentification – determination of taxon to which an isolate belongs

Importance of taxonomyallows to organize huge amounts of knowledgeallows to make predictions and frame hypothesesabout organismsfacilitating scientific communicationessential for accurate identification of organismsSystematics

study of organisms with the ultimate object of characterizing and arranging them in an orderly manner

Microbial Evolution and DiversityEarth formed ~ 4.6 billion years ago (bya) when life began to arise soon after planet cooledAppearance of life

first procaryotes arose at least 3.5 to 3.8 bya

fossilized remains found in stromatolites and sedimentary rocksprobably anaerobic

stromatolites –formed by incorporation of mineral sediments into microbial mats

Evolution of eucaryotesarose from procaryotes ~ 1.4 byatwo major hypotheses

nuclei, mitochondria, and chloroplasts arose by invagination of plasma membranesendosymbiotic hypothesis

arose from a fusion of ancient bacteria and archaeachloroplasts arose from free-living phototrophic bacterium that entered symbiotic relationships with primitive eucaryotesmitochondria arose by similar mechanism

3 Domains: Universal phylogenetic tree

work of Carl Woese and collaborators in 1970s

2.5-3.0 bya

Professor of Microbiology at the University of Illinois at Urbana-Champaigncentered on genomic analysis and emphasis on understanding the

evolutionary significance of horizontal gene transfer (HGT):

1. Phylogenies of the aminoacyl-tRNA synthetases and the effect on HGT 2. Construct a model (theory) of how the archaeal, eubacterial, and eukaryotic

cells have evolved from the RNA-world

Carl Richard WoeseBorn July 15, 1928

-1967, the originator of the RNA worldhypothesis

-1977, define the Archaea by phylogenetic taxonomy of 16S rRNA

5 Kingdoms(Whittaker)

Multi-cellular and unicellular, walledeucaryotic cells

- unicellular walledeucaryoticcells

all procaryotes

Fig. 19.16a

Taxonomic Ranksmicrobiologists often use informal names

purple bacteriaProteobacteria

enterobacteria

Spirochetesmethane-oxidizing bacteria

19.3

Figure 19.7

genus – well defined group of one or more species that is clearly separate from other genera

Species

two definitions suggestedcollection of strains that share many stable properties and differ significantly from other groups of strainscollection of strains with similar G + C composition and ≥ 70% sequence similarity

(Table 19.6)

Strainspopulation of organisms that is distinguishable from others within a taxondescended from a single organism or pure culture isolatevary from each other in many ways

biovars – differ biochemically and physiologicallymorphovars – differ morphologicallyserovars – differ in antigenic properties

Type strainusually one of first strains of a species studiedoften most fully characterizednot necessarily most representative member of species

Binomial nomenclature

devised by Carl von Linné (Carolus Linnaeus)each organism has two names

genus name – italicized and capitalized Escherichia

species epithet – italicized but not capitalized coli

can be abbreviated after first use Escherichia coli E. coli

General nomenclatureSalmonella typhiSalmonella typhimuriumKlebsiella pneumoniaeShigella dysenteryHelicobacter pyloriLegionella pneumonphilaRickettsia prowazekii

Classification Systemsnatural classification- share many characteristics- reflects biological nature of organisms

two methods for constructionPhenetically (Table 19.4)

grouped together based on overall similarityPhylogenetically

grouped based on probable evolutionary relationships

Phenetic Classificationbased on mutual similarity of phenotypes

motility and flagella (Table 19.4)

can reveal evolutionary relationships but doesn’t weight charactersbest systems compare as many attributes as possible

Numerical Taxonomyphenetic classification systemsMulti-step process

code information1 = has trait; 0 = no trait

use computer to compare organisms on ≥ 50 charactersdetermine association coefficientconstruct similarity matrix

- dendrograms系統樹圖

Phylogenetic classificationPhylogeny: phyletic classification (Fig. 19.12)

evolutionary development of a speciescomparison of

genetic materialnucleic acid base composition, nucleic acid hybridization, nucleic acid sequencing (oligonucleotidesignature sequences, MLST), genomic fingerprinting (RFLP, BOX-PCR, ERIC-PCR, and REP-PCR)

Fig. 19.11

gene productscomparison of proteins (amino acid sequencing)

Molecular Chronometersnucleic acids (rRNA) or proteins used as “clocks” to measure amount of evolutionary change over timebased on several assumptions

sequences gradually change over timechanges are selectively neutral and relatively randomamount of change increases linearly with time

Problems with molecular chronometersrate of sequence change can vary over timedifferent molecules and different parts of molecules can change at different rates

Creating phylogenetic treesalign sequencesdetermine number of positions that are differentexpress difference

evolutionary distance

use measure of difference to create treeorganisms clustered based on relatednessparsimony – fewest changes from ancestor to organism in question

Indicators of phylogenyrRNA, DNA, and protein indicators do not always produce the same phylogenetic trees

DNA most effective for comparing organisms at species and genus level

proteinsless affected by organism-specific differences in G + C contenteasier to do sequence alignmentproteins evolve at different rates

Polyphasic Taxonomyuse of all possible data to determine phylogeny

genotypic and phenotypic information

data used depends on desired level of resolution

serological data – resolve strainsprotein electrophoretic patterns – resolve speciesDNA hybridization and % G + C – resolve at genus and species level

Figure 19.14

Variations in the design of the “tree of life”

Impact of horizontal transferextensive horizontal gene transfer has occurred within and between domainspattern of microbial evolution is not as linear and treelike as once thought

Fig. 19.15

Bergey’s manual of systematic bacteriologyDomain Bacteria

metabolically and morphologically diversedivided into 23 phyla

The first editionprimarily phenetic and cell wall characteristics play

important role

The second editionlargely phylogenetic rather than phenetic