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Universities » California State University - Lo.. » MICR - Microbiology » 211 - General Microbiology » Flash Cards

CH 17: Microbial Taxonomy & Evolution of Diversity.. - Flashcards

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Class:	MICR 211 - General Microbiology
Subject:	Microbiology
University:	California State University - Long Beach
Term:	Spring 2011

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Microbial Taxonomy

Science of biological classification
3 parts:

Classification
Nomenclature
Identification

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Classification

Arrangement of organisms into groups (taxa)

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Nomenclature

Assignment names to taxa

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Identification

Determination of taxon to which an isolate belongs

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Natural Classification

Arranges organisms into groups whose members shares many characteristics
Developed by Linnaeus(Based on anatomical characteristic)
Does not necessarily provide info on evolutionary relatedness

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Polyphasic Taxonomy

Determine genus & species of a newly discovered prok.
Incorporates info fr genetic, phenotypic, & phylogenetic analysis

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Phenetic Classification

Groups organisms together based on mutual similarity of phenotypes
Can reveal evolutionary relationships, but NOT dependent on phylogenetic analysis
BEST systems compare as many attributes as possible

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Phylogenetic Classification

Aka Phyletic Classification Systems
Phylogeny: evo development of a species
Based on direct comparison of genetic material & gene product

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Genotypic Classification

Comparison of genetic similarity between organisms
Individuals genes or whole genomes can be compared
70% homologous belong to same species

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Taxonomic Ranks

Microbes placed in hierarchical levels w/each level sharing a common set of specific features
Highest rank is domain
W/in domain: phylum, class, order, family, genus, species, epithet

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Species

Collection of strains that share many stable properties & differ significantly from other groups of strains
Collection of organisms that share same sequences in their core housekeeping genes

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Strains

Descended from a single, pure microbial culture
Vary from each other in many ways:
-biovars, morphovars, serovars

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Biovars

differ biochemically & physiologically

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Morphovars

Differ morphologically

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Serovars

Differ in antigenic properties

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Type Strain

Usually one of first strains of a species studied
Fully characterized
Not necessarily most representative member of species

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Genus

Well defined group of one or more strains
Clearly separate from other genera
Often disagreement among taxonomists about the assignment of a specific species to a genus

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Binomial System of Nomenclature

Devised by Carl von Linne
Each organism has two names:
--genus name: italicized & capitalized
--species epithet: italicized
Can be abbreviated after first use (E. coli)

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Techniques for Determining Microbial Taxonomy & Phylogeny

Morphological
Physiological
Biochemical
Ecological
Genetic

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Ecological Characteristics

Life-cycle patterns
Symbiotic relationships
Ability to cause disease
Habitat preferences
Growth requirements

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Molecular Characteristics

Nucleic acid base composition
Nucleic acid hybridization
Nucleic acid sequencing
Genomic fingerprinting
AA sequencing

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Molecular Approaches

Allows for the collection of a large & accurate data set from many organisms
Phylogenic inferences based on these provide the best analysis of microbial evolution currently available

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Evolution of the 3 Domains of Life

Hypothesize that when RNA became enclosed in a lipid sphere, the 1st primitive life forms were generated

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Last Universal Common Ancestor (LUCA)

Root of the tree of life, based on SSU rRNA, shows the earlies region is on the bacterial branch
Thought that Archaea & Eukarya evolved independently of Bacteria

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Steps in Endosymbiotic Hypothesis

Ancestral eukaryotic cell had lost cell wall
Engulfment of an endosymbiote occured: produced ATP
Genome reduction occured
Evolution of organelles: Mitochondria, hydrogenosome, chloroplast

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Mitochondria & Chloroplast

Descended from Rickettsiae & Prochlorococcus
Became engulfedin a precursor cell
Provided essential function for host
--engulfed organism thought to be aerobic, thereby eliminating oxygen toxicity to the host cell
--host provided nutrients & a safe environment for engulfed organism

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Hydrogenosomes

Assert that the alpha-proteobacterium endosymbiont was an anaerobic bacterium that produced H2 & CO2 as fermentation end products
Host lacking external H2 source became dependent on endosymbiont which make ATP by substrate level phosphorylation

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Eukaryotic Nucleus Evolution: Hypothesis 1

Archaean & Bacterium living in close association (symbiosis) fused
Evolution of organelles included nucleus

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Eukaryotic Nucleus Evolution: Hypothesis 2

Endosymbiosis: archaean engulfs bacterium
nucleus, mitochondria, chloroplast evolve

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Map & Direction of a Microbial Species

Cant use specific definition based on interbreeding bc bacteria & archaea are asexual
"gold standard" for species assignment may not be applicable for microorganisms

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Bergey's Manual

Accepted system of bacterial taxonomy
Detailed work containing descriptions of all bacterial species currently identified
1st edition: 1984

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Microbial Taxonomy	Science of biological classification 3 parts: Classification Nomenclature Identification
Classification	Arrangement of organisms into groups (taxa)
Nomenclature	Assignment names to taxa
Identification	Determination of taxon to which an isolate belongs

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Koofers.com

Natural Classification	Arranges organisms into groups whose members shares many characteristics Developed by Linnaeus(Based on anatomical characteristic) Does not necessarily provide info on evolutionary relatedness
Polyphasic Taxonomy	Determine genus & species of a newly discovered prok. Incorporates info fr genetic, phenotypic, & phylogenetic analysis
Phenetic Classification	Groups organisms together based on mutual similarity of phenotypes Can reveal evolutionary relationships, but NOT dependent on phylogenetic analysis BEST systems compare as many attributes as possible
Phylogenetic Classification	Aka Phyletic Classification Systems Phylogeny: evo development of a species Based on direct comparison of genetic material & gene product

Generated by

Koofers.com

Genotypic Classification	Comparison of genetic similarity between organisms Individuals genes or whole genomes can be compared 70% homologous belong to same species
Taxonomic Ranks	Microbes placed in hierarchical levels w/each level sharing a common set of specific features Highest rank is domain W/in domain: phylum, class, order, family, genus, species, epithet
Species	Collection of strains that share many stable properties & differ significantly from other groups of strains Collection of organisms that share same sequences in their core housekeeping genes
Strains	Descended from a single, pure microbial culture Vary from each other in many ways: -biovars, morphovars, serovars

Generated by

Koofers.com

Biovars	differ biochemically & physiologically
Morphovars	Differ morphologically
Serovars	Differ in antigenic properties
Type Strain	Usually one of first strains of a species studied Fully characterized Not necessarily most representative member of species

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Koofers.com

Genus	Well defined group of one or more strains Clearly separate from other genera Often disagreement among taxonomists about the assignment of a specific species to a genus
Binomial System of Nomenclature	Devised by Carl von Linne Each organism has two names: --genus name: italicized & capitalized --species epithet: italicized Can be abbreviated after first use (E. coli)
Techniques for Determining Microbial Taxonomy & Phylogeny	Morphological Physiological Biochemical Ecological Genetic
Ecological Characteristics	Life-cycle patterns Symbiotic relationships Ability to cause disease Habitat preferences Growth requirements

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Koofers.com

Molecular Characteristics	Nucleic acid base composition Nucleic acid hybridization Nucleic acid sequencing Genomic fingerprinting AA sequencing
Molecular Approaches	Allows for the collection of a large & accurate data set from many organisms Phylogenic inferences based on these provide the best analysis of microbial evolution currently available
Evolution of the 3 Domains of Life	Hypothesize that when RNA became enclosed in a lipid sphere, the 1st primitive life forms were generated
Last Universal Common Ancestor (LUCA)	Root of the tree of life, based on SSU rRNA, shows the earlies region is on the bacterial branch Thought that Archaea & Eukarya evolved independently of Bacteria

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Koofers.com

Steps in Endosymbiotic Hypothesis	Ancestral eukaryotic cell had lost cell wall Engulfment of an endosymbiote occured: produced ATP Genome reduction occured Evolution of organelles: Mitochondria, hydrogenosome, chloroplast
Mitochondria & Chloroplast	Descended from Rickettsiae & Prochlorococcus Became engulfedin a precursor cell Provided essential function for host --engulfed organism thought to be aerobic, thereby eliminating oxygen toxicity to the host cell --host provided nutrients & a safe environment for engulfed organism
Hydrogenosomes	Assert that the alpha-proteobacterium endosymbiont was an anaerobic bacterium that produced H2 & CO2 as fermentation end products Host lacking external H2 source became dependent on endosymbiont which make ATP by substrate level phosphorylation
Eukaryotic Nucleus Evolution: Hypothesis 1	Archaean & Bacterium living in close association (symbiosis) fused Evolution of organelles included nucleus

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Koofers.com

Eukaryotic Nucleus Evolution: Hypothesis 2	Endosymbiosis: archaean engulfs bacterium nucleus, mitochondria, chloroplast evolve
Map & Direction of a Microbial Species	Cant use specific definition based on interbreeding bc bacteria & archaea are asexual "gold standard" for species assignment may not be applicable for microorganisms
Bergey's Manual	Accepted system of bacterial taxonomy Detailed work containing descriptions of all bacterial species currently identified 1st edition: 1984

Generated by

Koofers.com

List View: Terms & Definitions

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	Front	Back
	Microbial Taxonomy	Science of biological classification 3 parts: Classification Nomenclature Identification
	Classification	Arrangement of organisms into groups (taxa)
	Nomenclature	Assignment names to taxa
	Identification	Determination of taxon to which an isolate belongs
	Natural Classification	Arranges organisms into groups whose members shares many characteristics Developed by Linnaeus(Based on anatomical characteristic) Does not necessarily provide info on evolutionary relatedness
	Polyphasic Taxonomy	Determine genus & species of a newly discovered prok. Incorporates info fr genetic, phenotypic, & phylogenetic analysis
	Phenetic Classification	Groups organisms together based on mutual similarity of phenotypes Can reveal evolutionary relationships, but NOT dependent on phylogenetic analysis BEST systems compare as many attributes as possible
	Phylogenetic Classification	Aka Phyletic Classification Systems Phylogeny: evo development of a species Based on direct comparison of genetic material & gene product
	Genotypic Classification	Comparison of genetic similarity between organisms Individuals genes or whole genomes can be compared 70% homologous belong to same species
	Taxonomic Ranks	Microbes placed in hierarchical levels w/each level sharing a common set of specific features Highest rank is domain W/in domain: phylum, class, order, family, genus, species, epithet
	Species	Collection of strains that share many stable properties & differ significantly from other groups of strains Collection of organisms that share same sequences in their core housekeeping genes
	Strains	Descended from a single, pure microbial culture Vary from each other in many ways: -biovars, morphovars, serovars
	Biovars	differ biochemically & physiologically
	Morphovars	Differ morphologically
	Serovars	Differ in antigenic properties
	Type Strain	Usually one of first strains of a species studied Fully characterized Not necessarily most representative member of species
	Genus	Well defined group of one or more strains Clearly separate from other genera Often disagreement among taxonomists about the assignment of a specific species to a genus
	Binomial System of Nomenclature	Devised by Carl von Linne Each organism has two names: --genus name: italicized & capitalized --species epithet: italicized Can be abbreviated after first use (E. coli)
	Techniques for Determining Microbial Taxonomy & Phylogeny	Morphological Physiological Biochemical Ecological Genetic
	Ecological Characteristics	Life-cycle patterns Symbiotic relationships Ability to cause disease Habitat preferences Growth requirements
	Molecular Characteristics	Nucleic acid base composition Nucleic acid hybridization Nucleic acid sequencing Genomic fingerprinting AA sequencing
	Molecular Approaches	Allows for the collection of a large & accurate data set from many organisms Phylogenic inferences based on these provide the best analysis of microbial evolution currently available
	Evolution of the 3 Domains of Life	Hypothesize that when RNA became enclosed in a lipid sphere, the 1st primitive life forms were generated
	Last Universal Common Ancestor (LUCA)	Root of the tree of life, based on SSU rRNA, shows the earlies region is on the bacterial branch Thought that Archaea & Eukarya evolved independently of Bacteria
	Steps in Endosymbiotic Hypothesis	Ancestral eukaryotic cell had lost cell wall Engulfment of an endosymbiote occured: produced ATP Genome reduction occured Evolution of organelles: Mitochondria, hydrogenosome, chloroplast
	Mitochondria & Chloroplast	Descended from Rickettsiae & Prochlorococcus Became engulfedin a precursor cell Provided essential function for host --engulfed organism thought to be aerobic, thereby eliminating oxygen toxicity to the host cell --host provided nutrients & a safe environment for engulfed organism
	Hydrogenosomes	Assert that the alpha-proteobacterium endosymbiont was an anaerobic bacterium that produced H2 & CO2 as fermentation end products Host lacking external H2 source became dependent on endosymbiont which make ATP by substrate level phosphorylation
	Eukaryotic Nucleus Evolution: Hypothesis 1	Archaean & Bacterium living in close association (symbiosis) fused Evolution of organelles included nucleus
	Eukaryotic Nucleus Evolution: Hypothesis 2	Endosymbiosis: archaean engulfs bacterium nucleus, mitochondria, chloroplast evolve
	Map & Direction of a Microbial Species	Cant use specific definition based on interbreeding bc bacteria & archaea are asexual "gold standard" for species assignment may not be applicable for microorganisms
	Bergey's Manual	Accepted system of bacterial taxonomy Detailed work containing descriptions of all bacterial species currently identified 1st edition: 1984

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