BIOL 3702 Lecture OutlinePage 1 of 7Copyright  2004 by Chester R. Cooper, Jr.Chapter 19 - Microbial Taxonomy and PhylogenyOverview The extraordinary diversity of the microbes is fascinating, yet very complex Due to the diverse nature of living organisms, it is desirable to categorize them intogroups based upon their similarities Taxonomy - the science of biological classification Classification - arrangement of organisms into groups or taxa (s., taxon) basedupon similarities or evolutionary relatedness Nomenclature - assignment of names to taxonomic groups using special rules Identification - determining to which recognized taxon a particular organismbelongs Why is taxonomy important? Permits the organization of huge amounts of information Allows predictions and hypotheses to be made upon this information Places organisms in useful groups with precise names that permit effectivecommunication between investigators Essential for the identification of organisms The term systematics is often used in synonymy with “taxonomy” This term is better defined as “the scientific study of organisms with the ultimateobject of characterizing and arranging them in an organized manner” Actually encompasses other disciplines including morphology, ecology,epidemiology, biochemistry, molecular biology, and physiologyMicrobial Evolution Earth is estimated to be 4.6 billion years old First procaryotic cells, as evident from fossilized remains, appeared about 3.5-3.8billion years ago and were likely anaerobic Subsequent evolution of cyanobacteria and oxygenic photosynthesis occurred 2.5-3.0 billion years ago Microbial diversity increased as an oxygen-rich environment developed Carl Woese and colleagues, studying rRNA sequences, suggest that procaryotesdivided into two distinct lineages early in the earth’s evolution These workers also suggested that all living things can be placed into one of threedomainsBIOL 3702 Lecture Outline Chapter 19Page 2 of 7Copyright  2004 by Chester R. Cooper, Jr. Domains - placed above the phylum and kingdom levels of classification Bacteria - procaryotic Archaea - procaryotic Eucarya - eucaryotic Eucaryotes arose from procaryotes 1.4-2.7 billion years ago Two hypotheses for the evolution of eucaryotic cells Organelles arose within procaryotes from the invagination of the plasmamembrane Endosymbiotic hypothesis Fusion of ancient true bacteria and archaea to form a nucleus and a Golgiapparatus Mitochondria and chloroplasts develop later from a permanent symbioticrelationship with other bacteria, e.g., cyanelle (cyanobacterium) living inside theprotist Cyanophora paradoxaTaxonomic Ranks Classification of an organism requires that it be placed (ranked) in a group (taxon)and given a specific name Informal names - lactic acid bacterium Formal names - Lactobacillus acidophilus Groups are hierarchical in nature Classification of an organism requires that it be placed (ranked) in a group (taxon)and given a specific name Informal names - lactic acid bacterium Formal names - Lactobacillus acidophilus Groups are hierarchical in nature Categories used in any rank unites groups under it based upon common properties In procaryotes (in ascending order), some ranks have characteristic suffixes Species (Note: do not capitalize first letter) Genus Family (suffix = -aceae) Order (suffix = -iales) Class Phylum DomainBIOL 3702 Lecture Outline Chapter 19Page 3 of 7Copyright  2004 by Chester R. Cooper, Jr. Species - basic taxonomic group In higher organisms, a species is defined based upon sexual reproduction Not a good criteria for bacteria - many procaryotes do not reproduce sexually Procaryotic species - collection of strains that share many stable properties and differsignificantly from other groups of strains Strain - population of organisms that is distinct from other populations within aparticular taxonomic category and is typically descended from a single organism or apure culture Biovars - biochemical or physiological Morphovars - shape Serovars - antigenic properties Type strain - “standard”, but not always the most representative member Genus - a well-defined group of one or more species that is clearly distinct from othergenera Naming of microbes uses a binomial system developed by Carolus Linnaeus Genus - Escherichia Species - coli Abbreviated - E. coli, but only after the full name/epithet is used once; never starta sentence with an abbreviationClassification Systems Two basic types of classification systems are used: Phenetic classification Natural classification system that groups organisms together based uponmutual similarity of their phenotypic characteristics May be used to infer possible evolutionary relationships Phylogenetic (phyletic) classification Based solely on evolutionary relationships Has been difficult to use in the past for procaryotes due to a lack of a fossilrecord Modern methods instead use gene sequences (e.g., RNA genes) or theirproducts (proteins) to estimate phylogenetic relationshipsBIOL 3702 Lecture Outline Chapter 19Page 4 of 7Copyright  2004 by Chester R. Cooper, Jr.Taxonomic Characteristics Classical characteristics Morphology Physiological/metabolic Ecological Genetic analysis Transformation Conjugation Plasmid content Molecular characteristics Proteins Sequencing of conserved proteins Physical, kinetic, and regulatory properties Nucleic acids Base composition Hybridization Sequencing of conserved genes, e.g., rRNA because it is generally stable yetchanges over long periods of timeMicrobial Phylogeny There are a number of methods used to assess the phylogeny of microbes Molecular chronometers - assumes that changes in conversed proteins or genesoccurs over time without destroying or altering the molecules function Phylogenetic trees - compares molecular sequence differences of a conservedgene or protein between organisms to generate a “tree” that expresses thedifferences as an evolutionary distance Signature sequence - particular groups of microbes will possess uniquenucleotides at specific locations in 16S rRNA molecules Signature sequence - particular groups of microbes will possess uniquenucleotides at specific locations in 16S rRNA molecules