1Figure 19.3procaryotic,bacterial rRNA,diacyl glyceroldiesterlipidsprocaryotic, archaeal rRNA,isoprenoid glycerol diether ordiglycerol tetraether lipidseucaryotic,eucaryotic rRNA,diacyl glyceroldiester lipids2Taxonomic Ranks• microbiologists often use informal names– e.g., purple bacteria, spirochetes, methane-oxidizing bacteria3Figure 19.4genus – well defined group of one ormore species that is clearly separatefrom other genera4Defining procaryotic species• can’t use definition based on interbreeding because procaryotes are asexual• possible definitions:– collection of strains that share many stable properties and differ significantly from other groups of strains– collection of strains with similar G + C composition and ≥ 70% sequence similarity– collection of organisms that share the same sequences in their core housekeeping genes5Strains• population of organisms that is distinguishable from others within a taxon• descended from a single organism or pure culture isolate• vary from each other in many ways– biovars – differ biochemically and physiologically– morphovars – differ morphologically– serovars – differ in antigenic properties6Type strain• usually one of first strains of a species studied• often most fully characterized• not necessarily most representative member of species7Binomial system of nomenclature• devised by Carl von Linné (Carolus Linnaeus)• each organism has two names– genus name – italicized and capitalized (e.g., Escherichia)– species epithet – italicized but not capitalized (e.g., coli)• can be abbreviated after first use (e.g., E. coli)8Classification Systems• natural classification– arranges organisms into groups whose members share many characteristics– most desirable system because reflects biological nature of organisms• two methods for construction– phenetically• grouped together based on overall similarity– phylogenetically• grouped based on probable evolutionary relationships9Phenetic Classification• groups organisms together based on mutual similarity of phenotypes• can reveal evolutionary relationships, but not dependent on phylogenetic analysis– i.e., doesn’t weight characters• best systems compare as many attributes as possible10Phylogenetic Classification• also called phyletic classification systems• phylogeny– evolutionary development of a species• usually based on direct comparison of genetic material and gene products11Major Characteristics Used in Taxonomy• two major types– classical characteristics– molecular characteristics12Classical Characteristics• morphological• physiological and metabolic• ecological• genetic analysis131415Molecular Characteristics• comparison of proteins• nucleic acid base composition• nucleic acid hybridization• nucleic acid sequencing16Nucleic acid sequencing• usually comparison of rRNA genes• increasingly, comparison of entire genomes17Molecular Chronometers• nucleic acids or proteins used as “clocks” to measure amount of evolutionary change over time• use based on several assumptions– sequences gradually change over time– changes are selectively neutral and relatively random– amount of change increases linearly with time18Problems with molecular chronometers• rate of sequence change can vary over time• different molecules and different parts of molecules can change at different rates19rRNA, DNA, and Proteins as Indicators of Phylogeny• all are used• do not always produce the same phylogenetic trees20DNA and proteins•DNA – most effective for comparing organisms at species and genus level• proteins– less affected by organism-specific differences in G + C content– easier to do sequence alignment– proteins evolve at different rates21The Major Divisions of Life• based primarily on rRNA analysis• currently held that there are three domainsof life– Bacteria– Archaea– Eucarya2223Impact of horizontal transfer• extensive horizontal gene transfer has occurred within and between domains• pattern of microbial evolution is not as linear and treelike as once thought24Figure