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19
Microbial
Taxonomy and the
Evolution of
Diversity
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Copyright © McGraw-Hill Global Education Holdings, LLC. Permission required for reproduction or display.
19.1 Introduction to Microbial Taxonomy
1. Explain the utility of taxonomy and systematics
2. Draw a concept map illustrating the differences
between phenetic (外表), phylogenetic (系統發生；演
化), and genotypic (遺傳) classification
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Introduction to
Microbial Taxonomy
• Taxonomy (分類學)
– science of biological classification
– consists of three separate but interrelated parts
• Classification (分類)– arrangement of organisms into groups
(taxa; s., taxon)
• Nomenclature (命名)– assignment of names to taxa
• Identification (識別)– determination of taxon to which an
isolate belongs
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Natural Classification
• Arranges organisms into groups whose members
share many characteristics
• first such classification in 18th century developed by
Linnaeus
– based on anatomical characteristics
• This approach to classification does not necessarily
provide information on evolutionary relatedness
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Polyphasic Taxonomy
• Used to determine the genus and species of a newly
discovered prokaryote
• Incorporates information from genetic, phenotypic,
and 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
– i.e., doesn’t weigh characters
• Best systems compare as many attributes as
possible
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Phylogenetic Classification
• Also called phyletic classification systems
• Phylogeny (系統發育學)
– evolutionary development of a species
• Usually based on direct comparison of genetic
material and gene products
– Woese and Fox proposed using small subunit (SSU) rRNA
nucleotide sequences to assess evolutionary relatedness
of organisms
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Genotypic Classification
• Comparison of genetic similarity between
organisms
– individual genes or whole genomes can be compared
– 70% homologous belong to the same species
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19.2 Taxonomic Ranks
1. Outline the general scheme of taxonomic hierarchy
2. Explain how the binomial system of Linnaeus is used
in microbial taxonomy
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Taxonomic Ranks - 1
• Microbes are placed in hierarchical taxonomic
levels with each level or rank sharing a common set
of specific features
• Highest rank is domain
– Bacteria and Archaea – microbes only
– Eukarya – microbes and macroorganisms
• Within domain
– phylum, class, order, family, genus, species epithet, some
microbes have subspecies
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(綱)
(目)
(科)
(屬)
(種)
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Species (菌種)
• Definition
– collection of strains that share many stable properties and
differ significantly from other groups of strains
• Also suggested as a definition of species
– collection of organisms that share the same sequences in
their core housekeeping genes
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Strains (菌株)
• Descended from a single, pure microbial culture
• Vary from each other in many ways
– biovars – differ biochemically and physiologically
– morphovars – differ morphologically
– serovars – differ in antigenic properties
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Type Strain
• Usually one of first strains of a species studied
• Often most fully characterized
• Not necessarily most representative member of
species
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Genus (屬)
• 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 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)
• A new species cannot be recognized until it has been
published in the International Journal of Systematic and
Evolutionary Microbiology
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19.3 Exploring Microbial Taxonomy
and Phylogeny
1. Review the approaches commonly used to determine
taxonomic classification
2. Assess the impact molecular methods have had on
the field of microbial taxonomy and phylogeny
3. Compare and contrast nucleotide sequencing and
non-sequencing based molecular approaches use in
microbial taxonomy and phylogeny
4. Select an appropriate technique to identify a
microbial genus, species, and strain
5. Predict the basic biological as well as public health
implications of microbial taxonomic identification
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Techniques for Determining
Microbial Taxonomy and Phylogeny
• Classical characteristics
– Morphological: Table 19.1
– Physiological: Table 19.2
– Biochemical: requiring pure culture for testing
– 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 Approaches
• Extremely important because almost no fossil
record was left by microbes
• Allows for the collection of a large and accurate
data set from many organisms
• Phylogenetic inferences based on these provide the
best analysis of microbial evolution currently
available
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Molecular Characteristics
• Nucleic acid base composition: %GC content
• Nucleic acid hybridization: measure of sequence
homology
• Nucleic acid sequencing: sequence of the small
subunit rRNAs (SSU rRNAs) is the most commonly
used
• Genomic fingerprinting
• Amino acid sequencing
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Nucleic Acid Base Composition
• G + C content
– Mol% G + C = (G + C/G +
C + A + T)100
– usually determined
from melting
temperature (Tm)
– variation within a
genus usually <10%
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Nucleic Acid Hybridization
• DNA-DNA hybridization
– measure of sequence homology
• Common procedure
– bind nonradioactive DNA to nitrocellulose filter
– incubate filter with radioactive single-stranded DNA
– measure amount of radioactive DNA attached to filter
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Nucleic Acid Sequencing
• Small subunit rRNAs (SSU rRNAs)
– sequences of 16S and 18S rRNA most powerful and direct
method for inferring microbial phylogenies and making
taxonomic assignments at genus level
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Comparative Analysis of 16S
rRNA Sequences
• Oligonucleotide signature sequences found
– short conserved sequences specific for a phylogenetically
defined group of organisms
• Either complete or, more often, specific rRNA
fragments can be compared
• When comparing rRNA sequences between 2
organisms, their relatedness is represented by
percent sequence homology
– 70% is cutoff value for species definition
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Small Subunit rRNAs
Bacteria
Archaea
Eukaroya
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Genomic Fingerprinting
• Used when the sequences are not available
• Used for microbial classification and determination
of phylogenetic relationships
• Requires analysis of genes that evolve more quickly
than rRNA encoding genes
– multilocus sequence analysis (MSLA)
• the sequencing and comparison of 5 to 7 housekeeping genes
is done to prevent misleading results from analysis of one
gene
• Can be used between different species
– multilocus sequence typing (MLST)
• discriminates among strains
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Restriction Fragment Length
Polymorphism (RFLP)
• Used when the sequences are not available
• Uses restriction enzymes to recognize specific
nucleotide sequences
– cleavage patterns are compared
• Ribotyping
– similarity between rRNA genes is determined by RFLP rather
than sequencing
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Single Nucleotide Polymorphism
(SNP)
• Looks at single nucleotide changes, or
polymorphisms, in specific genes
• 16S rRNA focuses on one specific gene
• Regions targeted because they are normally
conserved, so single changes in a base pair reveal
evolutionary change
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The Coverage and resolution of
Taxonomic Approaches
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19.4 Phylogenetic Trees
1. Paraphrase the rationale underpinning the
construction of phylogenetic trees
2. Compare and contrast rooted and unrooted trees
3. Outline the general considerations used in building a
phylogenetic tree
4. Characterize the challenges horizontal gene transfer
introduces in the study of microbial evolution
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Phylogenetic Trees
• Show inferred evolutionary relationships in the
form of multiple branching lineages connected by
nodes
• Identified sequences at tip of branches
– operational taxonomic unit
• Nodes represent a divergence event
• Length of branch represents number of molecular
changes between two nodes
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Creating Phylogenetic Trees
from Molecular Data
• Align sequences
• Determine number of positions that are different
• Express difference
– e.g., evolutionary distance
• Use measure of difference to create tree
– organisms clustered based on relatedness
– parsimony – fewest changes from ancestor to organism in
question
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Phylogenetic Trees
• Rooted tree
– has node that serves as common ancestor
• Unrooted tree
– represents a phylogenetic relationship but does not
provide an evolutionary path
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Phylogenetic Trees
• Extensive horizontal gene transfer has occurred
within/between domains
• Pattern of microbial evolution is not as linear and
treelike as once thought
• Some trees attempt to display HGT
– resemble web or network with many lateral branches
linking various trunks
– each branch representing the transfer of one or a few
genes
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Core and Pan Genomes
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19.5 Evolutionary Processes and the
Concept of a Microbial Species
1. Diagram the endosymbiotic theory of the origin of
mitochondria and chloroplasts
2. Compare and contrast the two theories that address
the origin of the nucleus
3. Explain why the concept of a microbial species is
difficult to define
4. List the “gold standard” data currently applied to
species designation
5. Explain the importance of adaptive mutations in
giving rise to new ecotypes
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Evolution of the
Three Domains of Life
• Hypothesized that when RNA became enclosed in a
lipid sphere, the first primitive life forms were
generated
• Table 19.4 showing the differences between the
three domains
• Last universal common ancestor (LUCA)
– the root of the tree of life, based on SSU rRNA, shows the
earliest region is on the bacterial branch
– thought that Archaea and Eukarya evolved independently
of Bacteria
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Steps in Endosymbiotic Hypothesis
• Ancestral eukaryotic cell had lost cell wall
• Engulfment of an endosymbiote occurred
– produced needed product such as ATP
• Genome reduction occurred
• Evolution of organelles
– mitochondria
– hydrogenosome
– chloroplasts
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Mitochondria and Chloroplasts
• Believed to be descended
from Rickettsiae and
Prochlorococcus, engulfed in
a precursor cell
– provided essential function
for host
• engulfed organism thought to
be anaerobic, thereby
eliminating oxygen toxicity to
the host cell
• host provided
nutrients/safety for engulfed
organism
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Hydrogenosomes
• An organelle found in protists that produce ATP by
fermentation
• Asserts that the a-proteobacterium endosymbiont
was an anaerobic bacterium that produced H2 and
CO2 as fermentation end products
– hosts lacking external H2 source became dependent on
endosymbiont which made ATP by substrate level
phosphorylation
– symbiont ultimately evolved into a mitochondrion or a
hydrogenosome
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The Concept and Definition
of a Microbial Species
• Can’t use species definition based on interbreeding
because bacteria and archaea are asexual
• “Gold standard” for species assignment may not be
applicable for microorganisms
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Microbial
Evolutionary
Processes
• Bacteria and Archaea are asexual
• Heritable changes occur
– mutation and natural selection
– gene loss or gain
– intragenomic recombination
– horizontal gene transfer (HGT) not as
important for initial evolution
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Anagenesis Model
of Microbial Diversity
• Microevolution
– also known as genetic drift
• Small, random genetic changes over generations
which slowly drive either speciation or extinction,
both of which are forms of macroevolution
– only adaptive mutants are selected
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Ecotype Model for
Microbial Diversity
• Ecotype: microbes that are genetically similar
population of microbes is ecologically distinct
• Members of specific ecosystem diversify and gain
adaptive mutation to compete for resources
• Extinction occurs in other ecosystems and reduced
genetic variation
• Punctuated equilibria
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Horizontal Gene Transfer (HGT)
Model for Microbial Diversity
• Pan-genome is complete gene repertoire of a taxon
– includes the core genome plus “housekeeping” and dispensable
genes
– pan-genome genes acquired through HGT
– requires genetically heterogeneous group of microbes
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19.6 Bergey’s Manual of Systematic
Bacteriology
1. Employ Bergey’s Manual to investigate the defining
taxonomic elements used for a bacterium or
archaeon that is unfamiliar to you
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Bergey’s Manual of Systematic
Bacteriology
• Accepted system of bacterial taxonomy
• Detailed work containing descriptions of all
bacterial species currently identified
• First edition published in 1984, with significantly
updated editions since
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Homework
1. Define ‘serovars’, ‘biovars’, ‘core and pan genomes’, and ‘genetic drift’.
2. Why has the use of 16S rRNA sequencing as a taxonomic tool
expanded the currently accepted number of microbial phyla? Why is
16S rRNA sequence so suitable for determining relatedness?
3. The endosymbiotic theory hypothesizes that mitochondria were
derived from an α-proteobacterium whereas the chloroplasts were
derived from cyanobacteria. On what evidence is this hypothesis
based?
4. Which do you think would have a pan-genome more closely related to
its core genome: a microbial species whose strains are obligate
intracellular symbionts, or a species whose strains constitute the
normal flora of the mammalian gut? Explain your answer.
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