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Chapter 17
Microbial Taxonomy and
the Evolution of Diversity
1
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Introduction to Microbial
Taxonomy
• taxonomy
– science of biological classification
– consists of three separate but interrelated
parts
• classification – arrangement of organisms into
groups (taxa; s., taxon)
• nomenclature – assignment of names to taxa
• identification – determination of taxon to which
an isolate belongs
2
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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
3
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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
– evolutionary development of a species
• usually based on direct comparison of
genetic material and gene products
– Woese and Fox proposed using small subunit
(16S or 18S 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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Taxonomic Ranks - 1
• microbes are placed in hierarchical (a system of
ranking and organizing thing)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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Figure 17.1
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Species
• 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
• 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
• 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
13
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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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Techniques for Determining Microbial
Taxonomy and Phylogeny
• classical characteristics
–
–
–
–
–
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morphological
physiological
biochemical
ecological
genetic
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Table 17.1
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Table 17.2
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Ecological Characteristics
•
•
•
•
•
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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
•
•
•
•
•
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nucleic acid base composition
nucleic acid hybridization
nucleic acid sequencing
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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Figure 17.2
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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 singlestranded DNA
– measure amount of radioactive DNA
attached to filter
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Table 17.4
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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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Figure 17.3
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Genomic Fingerprinting
• 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
• used for more heterogeneous collection of microbes
– multilocus sequence typing (MLST)
• discriminates among strains
• used for same pathogenic species
28
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Restriction Fragment Length
Polymorphism (RFLP)
• uses restriction enzymes to recognize
specific nucleotide sequences
– cleavage patterns are compared
• ribotyping
– similarity between rRNA genes is
determined by RFLP rather than
sequencing
29
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Figure 17.4
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Single Nucleotide
Polymorphism (SNP)
• Originally was designed for human
• 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
• Distinguish between strains of B. anthracsis
(탄저병균) and M. tuberculosis (결핵균)
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Figure 17.5
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Amino Acid Sequencing
• amino acid sequences reflect mRNA sequence
and therefore of the gene which encodes that
protein
• amino acid sequencing of proteins such as
cytochromes, histones, and heat-shock proteins
has provided relevant taxonomic and
phylogenetic information
• cannot be used for all proteins because
sequences of proteins with different functions
often change at different rates
33
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Figure 17.6
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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
35
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Figure 17.7
considering mutation
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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
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– organisms clustered based on relatedness
– assuming that the methods include maximum
parsimony, meaning the fewest changes exist
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
38
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Figure 17.8
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Phylogenetic Trees
• extensive horizontal gene transfer has
occurred within and 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
40
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Figure 17.9
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Evolutionary Processes and
the Concept of a Microbial
Species
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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
• 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
43
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Figure 17.10
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Table 17.5
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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
46
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Mitochondria and Chloroplasts
• believed to be descended from
Rickettsiae and Prochlorococcus
– became engulfed in 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 and a safe
environment for engulfed organism
47
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Hydrogenosomes
• 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
• organelle found in protists that produce ATP by
fermentation
48
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Eukaryotic Nucleus Evolution
• hypothesis 1
– archaean and bacterium living in close
association (symbiosis) fused
– evolution of organelles included nucleus
• hypothesis 2
– endosymbiosis – archaean engulfs bacterium
– nucleus, mitochondria, chloroplast evolve
49
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Figure 17.11
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The Map 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
51
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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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Figure 17.12
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Anagenesis Model of
Microbial Diversity
• Anagenesis : genetic drift, small random
genetic changes that occurs over generation
• 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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Metapopulation Model for
Microbial Diversity
• groups of microbes live in separate patches
that represent slightly different niches
• population in one patch diversifies into
heterogenous group
• scarce resources cause mingling between
different patches
• genetic divergence occurs
55
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Ecotype Model for Microbial
Diversity
• 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: Evolution is periodically
interrupted by rapid bursts of speciation driven
by abrupt changes in the environment.
56
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Horizontal Gene Transfer
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
horizontal gene transfer
– requires genetically heterogeneous
group of microbes
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Figure 17.13
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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
59
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The First Edition of
Bergey’s Manual of
Systematic Bacteriology
• published in 1984 and is currently in
its ninth edition
• it contained descriptions of all
known prokaryotic species
60
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The Second Edition of
Bergey’s Manual of
Systematic Bacteriology
• largely phylogenetic rather than
phenetic
• prokaryotes are divided between two
domains
61
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Table 17.6
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