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