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Brock Biology of
Microorganisms
Twelfth Edition
Madigan / Martinko
Chapter 14
Dunlap / Clark
Microbial Evolution and Systematics
Lectures by Buchan & LeCleir
Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings
I. Early Earth and the Origin and Diversification of Life
 14.1 Formation and Early History of Earth
 14.2 Origin of Cellular Life
 14.3 Microbial Diversification: Consequences for
Earth’s Biosphere
 14.4 Endosymbiotic Origin of Eukaryotes
Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings
14.1 Formation and Early History of Earth
 The Earth is ~ 4.5 billion years old
 First evidence for microbial life can be found in
rocks ~ 3.86 billion years old (southwestern Green
land)
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Ancient Microbial Life
3.45 billion-year-old rocks, South Africa
Figure 14.1
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14.1 Formation and Early History of Earth
 Stromatolites
 Fossilized microbial mats consisting of layers of filamentous
prokaryotes and trapped sediment
 Found in rocks 3.5 billion years old or younger
 Comparisons of ancient and modern stromatolites provide
evidence that
 Anoxygenic phototrophic filamentous bacteria formed ancient
stromatolites (relatives of the green nonsulfur bacterium
Chloroflexus)
 Oxygenic phototrophic cyanobacteria dominate modern
stromatolites
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Ancient and Modern Stromatolites
3.5 billion yrs old
1.6 billion yrs old
Figure 14.2
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More Recent Fossil Bacteria and Eukaryotes
1 billion yrs old rocks
prokaryotes
eukaryotic cells
Figure 14.3
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14.2 Origin of Cellular Life
 Early Earth was anoxic and much hotter than
present day (over 100 oC)
 First biochemical compounds were made by abiotic
systems that set the stage for the origin of life
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14.2 Origin of Cellular Life
 Surface Origin Hypothesis
 Contends that the first membrane-enclosed, selfreplicating cells arose out of primordial soup rich in
organic and inorganic compounds in ponds on Earth’s
surface
 Dramatic temperature fluctuations and mixing from
meteor impacts, dust clouds, and storms argue against
this hypothesis
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14.2 Origin of Cellular Life
 Subsurface Origin Hypothesis
 States that life originated at hydrothermal springs on
ocean floor
 Conditions would have been more stable
 Steady and abundant supply of energy (e.g., H2 and H2S)
may have been available at these sites
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Submarine Mound Formed at Ocean Hydrothermal Spring
Cooler, more oxidized, more
acidic ocean water
Hot, reduced, alkaline
hydrothermal fluid
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Figure 14.4
14.2 Origin of Cellular Life
 Prebiotic chemistry of early Earth set stage for selfreplicating systems
 First self-replicating systems may have been RNAbased (RNA world theory)
 RNA can bind small molecules (e.g., ATP, other
nucleotides)
 RNA has catalytic activity; may have catalyzed its own
synthesis
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A Model for the Origin of Cellular Life
Last Universal Common Ancestor
Figure 14.5
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14.2 Origin of Cellular Life
 DNA, a more stable molecule, eventually became
the genetic repository
 Three-part systems (DNA, RNA, and protein)
evolved and became universal among cells
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14.2 Origin of Cellular Life
 Other Important Steps in Emergence of Cellular
Life
 Build up of lipids
 Synthesis of phospholipid membrane vesicles that
enclosed the cell’s biochemical and replication
machinery
 May have been similar to montmorillonite clay vesicles
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Lipid Vesicles Made in the Laboratory from Myristic Acid
vesicle
RNAs
Vesicles formed on Montmorillonite clay particles
Figure 14.6
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14.2 Origin of Cellular Life
 Last Universal Common Ancestor (LUCA)
 Population of early cells from which cellular life may
have diverged into ancestors of modern day Bacteria
and Archaea
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14.2 Origin of Cellular Life
 As early Earth was anoxic, energy-generating
metabolism of primitive cells was exclusively
 Anaerobic and likely chemolithotrophic
(autotrophic)
 Obtained carbon from CO2
 Obtained energy from H2; likely generated by H2S
reacting with FeS or UV light
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Major Landmarks in Biological Evolution
Figure 14.7
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A Possible Energy-Generating Scheme for Primitive Cells
Figure 14.8
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14.2 Origin of Cellular Life
 Early forms of chemolithotrophic metabolism would
have supported production of large amounts of organic
compounds
 Organic material provided abundant, diverse, and
continually renewed source of reduced organic carbon,
stimulating evolution of various chemoorganotrophic
metabolisms
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14.3 Microbial Diversification
 Molecular evidence suggests ancestors of Bacteria
and Archaea diverged ~ 4 billion years ago
 As lineages diverged, distinct metabolisms developed
 Development of oxygenic photosynthesis dramatically
changed course of evolution
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14.3 Microbial Diversification
 ~ 2.7 billion years ago, cyanobacterial lineages developed
a photosystem that could use H2O instead of H2S,
generating O2
 By 2.4 billion years ago, O2 concentrations raised to 1 part
per million; initiation of the Great Oxidation Event
 O2 could not accumulate until it reacted with abundant
reduced materials in the oceans (i.e., FeS, FeS2)
 Banded iron formations: laminated sedimentary rocks;
prominent feature in geological record
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Banded Iron Formations
Iron oxides
Figure 14.9
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14.3 Microbial Diversification
 Development of oxic atmosphere led to evolution of
new metabolic pathways that yielded more energy
than anaerobic metabolisms
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14.3 Microbial Diversification
 Oxygen also spurred evolution of organellecontaining eukaryotic microorganisms
 Oldest eukaryotic microfossils ~ 2 billion years old
 Fossils of multicellular and more complex eukaryotes
are found in rocks 1.9 to 1.4 billion years old
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14.3 Microbial Diversification
 Consequence of O2 for the evolution of life
 Formation of ozone layer that provides a barrier against
UV radiation
 Without this ozone shield, life would only have continued
beneath ocean surface and in protected terrestrial
environments
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14.4 Endosymbiotic Origin of Eukaryotes
 Endosymbiosis
 Well-supported hypothesis for origin of eukaryotic cells
 Contends that mitochondria and chloroplasts arose
from symbiotic association of prokaryotes within
another type of cell
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14.4 Endosymbiotic Origin of Eukaryotes
 Two hypotheses exist to explain the formation of
the eukaryotic cell
1) Eukaryotes began as nucleus-bearing lineage that
later acquired mitochondria and chloroplasts by
endosymbiosis
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Models for the Origin of the Eukaryotic Cell
Figure 14.10a
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14.4 Endosymbiotic Origin of Eukaryotes
 Two hypotheses exist to explain the formation of
the eukaryotic cell (cont’d)
2) Eukaryotic cell arose from intracellular association
between O2-consuming bacterium (the symbiont),
which gave rise to mitochondria and an archaean host
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Models for the Origin of the Eukaryotic Cell
Figure 14.10b
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14.4 Endosymbiotic Origin of Eukaryotes
 Both hypotheses suggest eukaryotic cell is chimeric
 This is supported by several features
 Eukaryotes have similar lipids and energy metabolisms
to Bacteria
 Eukaryotes have transcription and translational
machinery most similar to Archaea
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Major Features Grouping Bacteria or Archaea with Eukarya
Table 14.1
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II. Microbial Evolution
 14.5 The Evolutionary Process
 14.6 Evolutionary Analysis: Theoretical Aspects
 14.7 Evolutionary Analysis: Analytical Methods
 14.8 Microbial Phylogeny
 14.9 Applications of SSU rRNA Phylogenetic Methods
Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings
14.5 The Evolutionary Process
 Mutations
 Changes in the nucleotide sequence of an organism’s
genome
 Occur because of errors in the fidelity of replication, UV
radiation, and other factors
 Adaptative mutations improve fitness of an organism,
increasing its survival
 Other genetic changes include gene duplication,
horizontal gene transfer, and gene loss
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14.6 Evolutionary Analysis: Theoretical Aspects
 Phylogeny
 Evolutionary history of a group of organisms
 Inferred indirectly from nucleotide sequence data
 Molecular clocks (chronometers)
 Certain genes and proteins that are measures of
evolutionary change
 Major assumptions of this approach are that nucleotide
changes occur at a constant rate, are generally neutral, and
random
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14.6 Evolutionary Analysis: Theoretical Aspects
 The most widely used molecular clocks are small
subunit ribosomal RNA (SSU rRNA) genes
 Found in all domains of life
 16S rRNA in prokaryotes and 18S rRNA in eukaryotes
 Functionally constant
 Sufficiently conserved (change slowly)
 Sufficient length
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Ribosomal RNA
16S rRNA
from E. coli
Figure 14.11
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14.6 Evolutionary Analysis: Theoretical Aspects
 Carl Woese
 Pioneered the use of SSU rRNA for phylogenetic
studies in 1970s
 Established the presence of three domains of life:
 Bacteria, Archaea, and Eukarya
 Provided a unified phylogenetic framework for Bacteria
Copyright © 2009 Pearson Education Inc., publishing as Pearson Benjamin Cummings
14.6 Evolutionary Analysis: Theoretical Aspects
 The Ribosomal Database Project (RDP)
 A large collection of rRNA sequences
 Currently contains > 409,000 sequences
 Provides a variety of analytical programs
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14.7 Evolutionary Analysis: Analytical Methods
 Comparative rRNA sequencing is a routine
procedure that involves
 Amplification of the gene encoding SSU rRNA
 Sequencing of the amplified gene
 Analysis of sequence in reference to other sequences
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PCR-Amplification of the 16S rRNA Gene
Figure 14.12
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General PCR Protocol
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14.7 Evolutionary Analysis: Analytical Methods
 The first step in sequence analysis involves
aligning the sequence of interest with sequences
from homologous (orthologous) genes from other
strains or species
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Alignment of DNA Sequences
Figure 14.13
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14.7 Evolutionary Analysis: Analytical Methods
 BLAST (Basic Local Alignment Search Tool)
 Web-based tool of the National Institutes of Health
 Aligns query sequences with those in GenBank
database
 Helpful in identifying gene sequences
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14.7 Evolutionary Analysis: Analytical Methods
 Phylogenetic Tree
 Graphic illustration of the relationships among
sequences
 Composed of nodes and branches
 Branches define the order of descent and ancestry of
the nodes
 Branch length represents the number of changes that
have occurred along that branch
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Phylogenetic Trees: Unrooted (a) and Rooted (b-d) Forms
Figure 14.14
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14.7 Evolutionary Analysis: Analytical Methods
 Evolutionary analysis uses character-state methods
(cladistics) for tree reconstruction
 Cladistic methods
 Define phylogenetic relationships by examining changes in
nucleotides at individual positions in the sequence
 Use those characters that are phylogenetically informative
and define monophyletic groups (a group which contains all
the descendants of a common ancestor; a clade)
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Identification of Phylogenetically Informative Sites
Dots: neutral sites.
Arrows: phylogenetically informative sites.
Figure 14.15
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14.7 Evolutionary Analysis: Analytical Methods
 Common cladistic methods
 Parsimony
 Maximum likelihood
 Bayesian analysis
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14.8 Microbial Phylogeny
 The universal phylogenetic tree based on SSU rRNA genes
is a genealogy of all life on Earth
Animation: Generating Phylogenetic Trees
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Universal Phylogenetic Tree as Determined by rRNA Genes
Figure 14.16
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14.8 Microbial Phylogeny
 Domain Bacteria
 Contains at least 80 major evolutionary groups (phyla)
 Many groups defined from environmental sequences
alone
 i.e., no cultured representatives
 Many groups are phenotypically diverse
 i.e., physiology and phylogeny not necessarily linked
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14.8 Microbial Phylogeny
 Eukaryotic organelles originated within Bacteria
 Mitochondria arose from Proteobacteria
 Chloroplasts arose from the cyanobacterial phylum
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14.8 Microbial Phylogeny
 Domain Archaea consists of two major groups
 Crenarchaeota
 Euryarchaeota
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14.8 Microbial Phylogeny
 Each of the three domains of life can be
characterized by various phenotypic properties
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Major Features Distinguishing Prokaryotes from Eukarya
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Major Features Distinguishing Prokaryotes from Eukarya
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14.9 Applications of SSU rRNA Phylogenetic Methods
 Signature Sequences
 Short oligonucleotides unique to certain groups of organisms
 Often used to design specific nucleic acid probes
 Probes
 Can be general or specific
 Can be labeled with fluorescent tags and hybridized to rRNA
in ribosomes within cells
 FISH: fluorescent in situ hybridization
 Circumvent need to cultivate organism(s)
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Fluorescently Labeled rRNA Probes: Phylogenetic Stains
Stained with universal
rRNA probe
Stained with a
eukaryotic rRNA probe
Figure 14.17
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14.9 Applications of SSU rRNA Phylogenetic Methods
 PCR can be used to amplify SSU rRNA genes from
members of a microbial community
 Genes can be sorted out, sequenced, and analyzed
 Such approaches have revealed key features of
microbial community structure and microbial
interactions
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14.9 Applications of SSU rRNA Phylogenetic Methods
 Ribotyping
 Method of identifying microbes from analysis of DNA
fragments generated from restriction enzyme digestion
of genes encoding SSU rRNA
 Highly specific and rapid
 Used in bacterial identification in clinical diagnostics
and microbial analyses of food, water, and beverage
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Ribotyping
Figure 14.18
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III. Microbial Systematics
 14.10 Phenotypic Analysis
 14.11 Genotypic Analysis
 14.12 Phylogenetic Analysis
 14.13 The Species Concept in Microbiology
 14.14 Classification and Nomenclature
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14.10 Phenotypic Analysis
 Taxonomy
 The science of identification, classification, and
nomenclature
 Systematics
 The study of the diversity of organisms and their
relationships
 Links phylogeny with taxonomy
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14.10 Phenotypic Analysis
 Bacterial taxonomy incorporates multiple methods
for identification and description of new species
 The polyphasic approach to taxonomy uses three
methods
1) Phenotypic analysis
2) Genotypic analysis
3) Phylogenetic analysis
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14.10 Phenotypic Analysis
 Phenotypic analysis examines the morphological,
metabolic, physiological, and chemical characters
of the cell
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Some Phenotypic Characteristics of Taxonomic Value
Table 14.3
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Some Phenotypic Characteristics of Taxonomic Value
Table 14.3
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14.10 Phenotypic Analysis
 Fatty Acid Analyses (FAME: fatty acid methyl ester)
 Relies on variation in type and proportion of fatty acids
present in membrane lipids for specific prokaryotic
groups
 Requires rigid standardization because FAME profiles
can vary as a function of temperature, growth phase,
and growth medium
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Fatty Acid Methyl Ester (FAME) Analysis
Figure 14.19a
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Fatty Acid Methyl Ester (FAME) Analysis
Figure 14.19b
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14.11 Genotypic Analysis
 Several methods of genotypic analysis are
available and used
 DNA-DNA hybridization
 DNA profiling
 Multilocus Sequence Typing (MLST)
 GC Ratio
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Some Genotypic Methods Used in Bacterial Taxonomy
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14.11 Genotypic Analysis
 DNA-DNA hybridization
 Genomes of two organisms are hybridized to examine
proportion of similarities in their gene sequences
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Genomic Hybridization as a Taxonomic Tool
Figure 14.20a
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Genomic Hybridization as a Taxonomic Tool
Figure 14.20b
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Genomic Hybridization as a Taxonomic Tool
Figure 14.20c
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14.11 Genotypic Analysis
 DNA-DNA hybridization
 Provides rough index of similarity between two
organisms
 Useful complement to SSU rRNA gene sequencing
 Useful for differentiating very similar organisms
 Hybridization values 70% or higher suggest strains
belong to the same species
 Values of at least 25% suggest same genus
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Relationship Between SSU rRNA and DNA Hybridization
97
95
25
Figure 14.21
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14.11 Genotypic Analysis
 DNA Profiling
 Several methods can be used to generate DNA
fragment patterns for analysis of genotypic similarity
among strains, including
 Ribotyping: focuses on a single gene
 Repetitive extragenic palindromic PCR (rep-PCR)
and Amplified fragment length polymorphism (AFLP):
focus on many genes located randomly throughout
genome
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DNA Fingerprinting with rep-PCR
Figure 14.22
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14.11 Genotypic Analysis
 Multilocus Sequence Typing (MLST)
 Method in which several different “housekeeping genes”
from an organism are sequenced (~450-bp)
 Has sufficient resolving power to distinguish between
very closely related strains
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Multilocus Sequence Typing
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14.11 Genotypic Analysis
 GC Ratios
 Percentage of guanine plus cytosine in an organism’s
genomic DNA
 Vary between 20 and 80% among Bacteria and
Archaea
 Generally accepted that if GC ratios of two strains differ
by ~ 5% they are unlikely to be closely related
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14.12 Phylogenetic Analysis
 16S rRNA gene sequences are useful in taxonomy;
serve as “gold standard” for the identification and
description of new species
 Proposed that a bacterium should be considered a new
species if its 16S rRNA gene sequence differs by more
than 3% from any named strain, and a new genus if it
differs by more than 5%
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14.12 Phylogenetic Analysis
 The lack of divergence of the 16S rRNA gene limits its
effectiveness in discriminating between bacteria at the
species level, thus, a multi-gene approach can be used
 Multi-gene sequence analysis is similar to MLST, but
uses complete sequences and comparisons are made
using cladistic methods
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14.12 Phylogenetic Analysis
 Whole-genome sequence analyses are becoming
more common
 Genome structure; size and number of chromosomes,
GC ratio, etc.
 Gene content
 Gene order
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14.13 The Species Concept in Microbiology
 No universally accepted concept of species for
prokaryotes
 Current definition of prokaryotic species
 Collection of strains sharing a high degree of similarity
in several independent traits
 Most important traits include 70% or greater DNA-DNA
hybridization and 97% or greater 16S rRNA gene
sequence identity
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Taxonomic Hierarchy for Allochromatium warmingii
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14.13 The Species Concept in Microbiology
 Biological species concept not meaningful for
prokaryotes as they are haploid and do not undergo
sexual reproduction
 Genealogical species concept is an alternative
 Prokaryotic species is a group of strains that based on
DNA sequences of multiple genes cluster closely with
others phylogenetically and are distinct from other
groups of strains
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Multi-Gene Phylogenetic Analysis
16S rRNA genes
gyrB genes
luxABFE genes
Figure 14.24
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14.13 The Species Concept in Microbiology
 Ecotype
 Population of cells that share a particular resource
 Different ecotypes can coexist in a habitat
 Bacterial speciation may occur from a combination
of repeated periodic selection for a favorable trait
within an ecotype and lateral gene flow
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A Model for Bacterial Speciation
Figure 14.25
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14.13 The Species Concept in Microbiology
 This model is based solely on the assumption of
vertical gene flow
 New genetic capabilities can also arise by horizontal
gene transfer; the extent among bacteria is variable
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14.13 The Species Concept in Microbiology
 No firm estimate on the number of prokaryotic
species
 Nearly 7,000 species of Bacteria and Archaea are
presently known
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14.14 Classification and Nomenclature
 Classification
 Organization of organisms into progressively more
inclusive groups on the basis of either phenotypic
similarity or evolutionary relationship
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14.14 Classification and Nomenclature
 Prokaryotes are given descriptive genus names and
species epithets following the binomial system of
nomenclature used throughout biology
 Assignment of names for species and higher groups of
prokaryotes is regulated by the Bacteriological Code
- The International Code of Nomenclature of Bacteria
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14.14 Classification and Nomenclature
 Major references in bacterial diversity
 Bergey’s Manual of Systematic Bacteriology (Springer)
 The Prokaryotes (Springer)
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14.14 Classification and Nomenclature
 Formal recognition of a new prokaryotic species
requires
 Deposition of a sample of the organism in two culture
collections
 Official publication of the new species name and description
in the International Journal of Systematic and Evolutionary
Microbiology (IJSEM)
 The International Committee on Systematics of
Prokaryotes (ICSP) is responsible for overseeing
nomenclature and taxonomy of Bacteria and Archaea
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Some National Microbial Culture Collections
KCCM
Korean Culture Center of Microorganisms
Seoul, Korea
http://www.kccm.or.kr
KACC
Korean Agricultural Culture Collection
Suwon, Korea
http://kacc.rda.go.kr
Table 14.6
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