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LECTURE PRESENTATIONS
For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION
Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark
Chapter 16
Lectures by
John Zamora
Middle Tennessee State University
© 2012 Pearson Education, Inc.
Microbial Evolution
and Systematics
I. Early Earth and the Origin and
Diversification of Life
• 16.1 Formation and Early History of Earth
• 16.2 Origin of Cellular Life
• 16.3 Microbial Diversification: Consequences
for Earth’s Biosphere
• 16.4 Endosymbiotic Origin of Eukaryotes
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16.1 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 (Figure 16.1)
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Figure 16.1
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16.1 Formation and Early History of Earth
• Stromatolites
– Fossilized microbial mats consisting of layers of
filamentous prokaryotes and trapped sediment
(Figure 16.2)
– Found in rocks 3.5 billion years old or younger
– Comparisons of ancient and modern
stromatolites
• Anoxygenic phototrophic filamentous bacteria
formed ancient stromatolites
• Oxygenic phototrophic cyanobacteria dominate
modern stromatolites
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Figure 16.2
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16.2 Origin of Cellular Life
• Early Earth was anoxic and much hotter than
present day
• First biochemical compounds were made by
abiotic systems that set the stage for the
origin of life
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16.2 Origin of Cellular Life
• Surface origin hypothesis
– The first membrane-enclosed, self-replicating
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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16.2 Origin of Cellular Life
• Subsurface origin hypothesis (Figure 16.4)
– 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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Figure 16.4
Evolutionary
events
Early
Bacteria
Early
Archaea
(0.3 to 0.5 billion years)
Time
Dispersal to
other habitats
Diversification
of molecular
biology, lipids,
and cell wall
structure
LUCA
Mound:
precipitates of clay,
metal sulfides, silica,
and carbonates
DNA
Ocean water
RNA and
proteins
(20°C, containing
metals, CO2 and
PO42)
RNA life
Flow of substances
up through mound
Prebiotic
chemistry
Amino
acids
Nitrogen
bases
Sugars
Ocean crust
Nutrients in hot
hydrothermal water
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16.2 Origin of Cellular Life
• Prebiotic chemistry of early Earth set stage for
self-replicating systems
• First self-replicating systems may have been
RNA-based (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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16.2 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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16.2 Origin of Cellular Life
• Other Important Steps in Emergence of
Cellular Life
– Buildup of lipids
– Synthesis of phospholipid membrane vesicles
that enclosed the cell’s biochemical and
replication machinery
• May have been similar to montmorillonite clay
vesicles (Figure 16.5)
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Figure 16.5
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16.2 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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16.2 Origin of Cellular Life
• As early Earth was anoxic, energy-generating
metabolism of primitive cells was exclusively
anaerobic and likely chemolithotrophic
(autotrophic; Figure 16.6)
– Obtained carbon from CO2
– Obtained energy from H2; likely generated by
H2S reacting with H2S or UV light (Figure 16.7)
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Figure 16.6
Eon
BYA Organisms,
events
0
O2
level
Extinction of the
dinosaurs
Cambrian
Phanaerozoic
0.5
Early animals
1.0
Multicellular
eukaryotes
Metabolic
highlights
Precambrian
20%
10%
Proterozoic
1.5
2.0
First eukaryotes
with organelles
Ozone shield
2.5
Great oxidation
event
1%
Endosymbiosis?
0.1% Aerobic respiration
Oxygenic photosynthesis
(2H2O  O2  4H)
Cyanobacteria
3.0
Archaean
Sulfate reduction
Fe3 reduction
3.5
Purple and green
bacteria
Anoxygenic photosynthesis
Anoxic
Bacteria/Archaea
divergence
4.0
First cellular life; LUCA
Formation of
crust and oceans
4.5
Formation of Earth
Hadean
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Acetogenesis
Methanogenesis
Sterile Earth
Figure 16.7
Alternative source of H2
Primitive
ATPase
Primitive
hydrogenase
Cytoplasmic
membrane
S0 reductase
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Out
In
16.2 Origin of Cellular Life
• Early forms of chemolithotrophic metabolism
would have supported production of large
amounts of organic compounds
• Organic material provided an abundant,
diverse, and continually renewed source of
reduced organic carbon, stimulating evolution
of various chemoorganotrophic metabolisms
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16.3 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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16.3 Microbial Diversification
• ~2.7 billion years ago, cyanobacteria 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 (e.g.,
FeS, FeS2)
– Banded iron formations: laminated sedimentary
rocks; prominent feature in geological record
(Figure 16.8)
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Figure 16.8
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16.3 Microbial Diversification
• Development of oxic atmosphere led to evolution
of new metabolic pathways that yielded more
energy than anaerobic metabolisms
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16.3 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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16.3 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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16.4 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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16.4 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 (Figure 16.9a)
2. Eukaryotic cell arose from intracellular
association between O2-consuming bacterium
(the symbiont), which gave rise to mitochondria,
and an archaeal host (Figure 16.9b)
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Figure 16.9
Bacteria
Eukarya Archaea
Animals
Ancestor of
chloroplast
Ancestor of
mitochondrion
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Bacteria
Plants
Nucleus
formed
Eukarya
Animals
Ancestor of
chloroplast
Engulfment of a
H2-producing cell
of Bacteria by a
H2-consuming cell
of Archaea
Nucleus
formed
Archaea
Plants
16.4 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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II. Microbial Evolution
•
•
•
•
•
16.5 The Evolutionary Process
16.6 Evolutionary Analysis: Theoretical Aspects
16.7 Evolutionary Analysis: Analytical Methods
16.8 Microbial Phylogeny
16.9 Applications of SSU rRNA Phylogenetic
Methods
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16.5 The Evolutionary Process
• Mutations
– Changes in the nucleotide sequence of an
organism’s genome
– Occur because of errors in 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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16.6 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 are random
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16.6 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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Figure 16.11
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16.6 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
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16.6 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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16.7 Evolutionary Analysis: Analytical
Methods
• Comparative rRNA sequencing is a routine
procedure that involves the following
(Figure 16.12):
– Amplification of the gene encoding SSU rRNA
– Sequencing of the amplified gene
– Analysis of sequence in reference to other
sequences
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Figure 16.12
Isolate DNA
16 S gene
Amplify 16S
gene by PCR
Run on agarose
gel; check for
correct size
Kilobases 1
3.0–
2
3
4
5
2.0–
1.5–
1.0–
0.5–
Sequence
A C G G T
Align sequences;
generate tree
Ancestral
cell
Distinct
species
Distinct
species
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16.7 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 (Figure 16.13)
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Figure 16.13
Nonidentities
Before
alignment
Species 1
Number of
sequence
matches
9
Species 2
Gaps
After
alignment
Species 1
15
Species 2
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16.7 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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16.7 Evolutionary Analysis: Analytical
Methods
• Phylogenetic tree
– Graphic illustration of the relationships among
sequences (Figure 16.14)
– 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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Figure 16.14
Rooted trees
node
Unrooted tree
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16.7 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
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Figure 16.15
Species 1
Species 2
Species 3
Species 4
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16.7 Evolutionary Analysis: Analytical
Methods
• Common cladistic methods:
– Parsimony
– Maximum likelihood
– Bayesian analysis
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16.8 Microbial Phylogeny
• The universal phylogenetic tree based on SSU
rRNA genes is a genealogy of all life on Earth
(Figure 16.16)
Animation: Generating Phylogenetic Trees
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Figure 16.16
PROKARYOTES
EUKARYOTES
Archaea
Bacteria
Eukarya
Animals
Entamoebae
Green nonsulfur
bacteria
Euryarchaeota
Methanosarcina
Mitochondrion
Proteobacteria
Chloroplast
Grampositive
bacteria
Methano-
Crenarchaeota bacterium
Thermoproteus
Pyrodictium
Fungi
Extreme
halophiles
Plants
Ciliates
Thermoplasma
Thermococcus
Cyanobacteria
Flavobacteria
Methanococcus
Slime
molds
Marine
Crenarchaeota
Pyrolobus
Flagellates
Methanopyrus
Trichomonads
Thermotoga
Thermodesulfobacterium
Microsporidia
Aquifex
LUCA
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Diplomonads
(Giardia)
16.8 Microbial Phylogeny
• Domain Bacteria
– Contains at least 80 major evolutionary groups
(phyla)
– Many groups defined from environmental
sequences alone—i.e., there are no cultured
representatives
– Many groups are phenotypically diverse—i.e.,
physiology and phylogeny not necessarily
linked
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16.8 Microbial Phylogeny
• Eukaryotic organelles originated within Bacteria
– Mitochondria arose from Proteobacteria
– Chloroplasts arose from the cyanobacteria
• Domain Archaea consists of two major groups:
– Crenarchaeota
– Euryarchaeota
• Each of the three domains of life can be
characterized by various phenotypic properties
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16.9 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 (Figure
16.17)
– Circumvent need to cultivate organism(s)
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Figure 16.17
Bacillus
Yeast
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16.9 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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16.9 Applications of SSU rRNA
Phylogenetic Methods
• Ribotyping (Figure 16.18)
– 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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Figure 16.18
Lactococcus
lactis
Lactobacillus
acidophilus
Lactobacillus
brevis
Lactobacillus
kefir
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III. Microbial Systematics
•
•
•
•
16.10 Phenotypic Analysis
16.11 Genotypic Analysis
16.12 The Species Concept in Microbiology
16.13 Classification and Nomenclature
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16.10 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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16.10 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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16.10 Phenotypic Analysis
• Phenotypic analysis examines the
morphological, metabolic, physiological, and
chemical characters of the cell
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16.10 Phenotypic Analysis
• Fatty acid analysis (FAME: fatty acid methyl ester)
– Relies on variation in type and proportion of fatty
acids present in membrane lipids for specific
prokaryotic groups (Figure 16.19a and b)
– Requires rigid standardization because FAME
profiles can vary as a function of temperature,
growth phase, and growth medium
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Figure 16.19a
Classes of Fatty Acids in Bacteria
Structure of example
Class/Example
I. Saturated:
tetradecanoic acid
II. Unsaturated:
omega-7-cis
hexadecanoic acid
III. Cyclopropane:
cis-7,8-methylene
hexadecanoic acid
IV. Branched:
13-methyltetradecanoic acid
V. Hydroxy:
3-hydroxytetradecanoic acid
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Figure 16.19b
IDENTIFY ORGANISM
Compare pattern of peaks
with patterns in database
Bacterial culture
Peaks from
various
fatty acid
methyl esters
Extract fatty acids
Gas chromatography
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Amount
Derivatize to form
methyl esters
16.11 Genotypic Analysis
• Several methods of genotypic analysis are
available:
–
–
–
–
DNA–DNA hybridization
DNA profiling
Multilocus sequence typing (MLST)
GC ratio
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16.11 Genotypic Analysis
• DNA–DNA hybridization
– Genomes of two organisms are hybridized to
examine proportion of similarities in their gene
sequences (Figure 16.20)
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Figure 16.20
Organisms to Organism 1
be compared:
Organism 2
Genomic DNA
Genomic DNA
DNA
Shear and label (– P )
preparation
Shear DNA
Heat to
form
single
strands
Hybridization
experiment: Mix DNA, adding unlabeled DNA in excess:
11
Hybridized DNA
12
Hybridized DNA
Results and
interpretation:
Same
species
100
75
Same genus,
but different Different
genera
species
50
25
Percent hybridization
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0
11
12
100%
25%
Same strain
(control)
1 and 2 are likely
different genera
16.11 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 of 70% or higher suggest
strains belong to the same species
• Values of at least 25% suggest same genus
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16.11 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 (repPCR) (Figure 16.21) and amplified fragment
length polymorphism (AFLP): focus on many
genes located randomly throughout genome
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Figure 16.21
1
2
3
4
5
6
7
5.0 kb
2.0 kb
1.0 kb
0.5 kb
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16.11 Genotypic Analysis
• Multilocus sequence typing (MLST)
– Method in which several different
“housekeeping genes” from an organism are
sequenced (Figure 16.22)
– Has sufficient resolving power to distinguish
between very closely related strains
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Figure 16.22
Linkage Distance
Allele analysis
New isolate or
clinical sample
Isolate DNA
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Amplify 6–7
target genes
Sequence
Compare with
other strains
and generate
tree
0.6
0.4
0.2
0
Strains
1–5
New strain
Strain 6
Strain 7
16.11 Genotypic Analysis
• GC ratios
– Percentage of guanine plus cytosine in an
organism’s genomic DNA
– Vary from 20 to 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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16.12 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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16.12 The Species Concept in
Microbiology
• Biological species concept not meaningful as
prokayotes 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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16.12 The Species Concept in
Microbiology
• 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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16.12 The Species Concept in
Microbiology
• Phylogenetic analysis (cont’d)
– The lack of divergence of the 16S rRNA gene
limits its effectiveness in discriminating between
bacteria at the species level; thus, a multigene
approach can be used
– Multigene sequence analysis is similar to MLST,
but uses complete sequences and comparisons
are made using cladistic methods (Figure 16.24)
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Figure 16.24
Multigene Tree
16S rRNA Gene Tree
Photobacterium damselae
50 changes
Photobacterium leiognathi
Photobacterium mandapamensis
FS-2.1
FS-4.2
FS-3.1
FS-5.1
FS-2.2
Photobacterium
phosphoreum
ATCC 11040T
FS-5.2
Photobacterium angustum
Photobacterium phosphoreum
Photobacterium iliopiscarium
ATCC 51761
NCIMB 13476
NCIMB 13478
NCIMB 13481
Photobacterium
iliopiscarium
ATCC 51760T
Photobacterium kishitanii
chubb.1.1
ckamo.3.1
canat.1.2
hstri.1.1
calba.1.1
BAA-1194T
apros.2.1
ckamo.1.1
vlong.3.1
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Photobacterium
kishitanii
16.12 The Species Concept in
Microbiology
• Phylogenetic analysis (cont’d)
• 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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16.12 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 (Figure 16.25)
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Figure 16.25
One microbial habitat
Ecotype II
Ecotype I
Ecotype III
Cell containing
an adaptive
mutation
Periodic selection
Adaptive mutant
survives. Original
Ecotype III wild-type
cells out competed
Population
of mutant
Ecotype III
Repeat process
many times
New species
of Ecotype III
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16.12 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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16.12 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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16.13 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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16.13 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
International Code of Nomenclature of
Bacteria
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16.13 Classification and Nomenclature
• Major references in bacterial diversity:
– Bergey’s Manual of Systematic Bacteriology
– The Prokaryotes
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16.13 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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