Brock Microbiology 13 Lecture Presentation

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CHAPTER 13
Microbial
Evolution and
Systematics
© 2018 Pearson Education, Inc.

I. Early Earth and the Origin and Diversification
of Life
• 13.1 Formation and Early History of Earth
• 13.2 Photosynthesis and the Oxidation of Earth
• 13.3 Living Fossils: DNA Records the History of Life
• 13.4 Endosymbiotic Origin of Eukaryotes

13.1 Formation and Early History of Earth
• Origin of Earth
• Earth is ~4.5 billion years old. (Figure 13.1)
• Liquid water required for life; first appeared ~4.3 billion

years ago.
• evidence for life ~4.1 billion years ago
• Fossilized remains of cells can be found in rocks

~3.86 billion years old. (Figure 13.2)

© 2018 Pearson Education, Inc. Figure 13.1
• Origin of cellular life

• Life may have originated at hydrothermal systems on
ocean floor. (Figure 13.3)
• Conditions would have been more stable.
• Steady and abundant supply of energy (e.g., H2 and H2S)
may have been available at these sites.
• Geochemistry can support abiotic production of molecules
required for life (e.g., amino acids, lipids, sugars, and
nucleotides).
• Mineral structures may have produced compartments for
conserving energy.


• Life may have begun in an RNA world. (Figure 13.4)
• RNA is part of essential cofactors and molecules (e.g.,
ATP, NADH, coenzyme A).
• RNA can bind small molecules (e.g., ATP, other

nucleotides, amino acids).
• RNA has catalytic activity; may have catalyzed its own

synthesis.
• Earliest viruses may have evolved from RNA genome

cell-like structures.


• Proteins eventually replaced RNAs as catalysts.
• DNA (more stable) became genome and template.
• Earliest cells probably had DNA, RNA, protein, and
membrane system for energy conservation.
• Last universal common ancestor (LUCA) existed
3.8–3.7 billion years ago, then Bacteria and Archaea
diverged.

• Metabolic diversification: Consequences for Earth’s
biosphere
• Because early Earth was anoxic, energy-generating
metabolism of primitive cells was exclusively anaerobic.
• obtained carbon from CO2 (autotrophy)
• evolved ability to use N2 (nitrogen fixation)
• obtained energy from H2; S may have been an early
electron acceptor (Figure 13.5)
• Early forms of chemolithotrophic metabolism would have
supported production of large amounts of organic
compounds.
• Accumulated organic material provided conditions needed
for evolution of chemoorganotrophic metabolisms.
• Eventually Earth became highly oxic.

13.2 Photosynthesis and the Oxidation of Earth
• Phototrophs use energy from sun to oxidize H2S, S,

and H2O to synthesize complex organic molecules
from CO2 or simple organics.
• First phototrophs were anoxygenic.
• Cyanobacteria (O2 producers; oxygenic
phototrophs) evolved.
• Stromatolites (fossilized microbial formations) found
in rocks 3.5 billion years old (Figure 13.6)
• phototrophic bacteria (cyanobacteria and Chloroflexus)
from modern stromatolites
• Ancient stromatolites contain fossils similar to modern
phototrophic bacteria. (Figure 13.7a)

• Between 2.5 and 3.3 billion years ago,

cyanobacteria evolved a photosystem that could
use H2O instead of H2S, generating O2.
• Rise of O2 allowed evolution of life to exploit

energy from O2 respiration.

• The rise of oxygen: Banded iron formations
• Most iron would have been reduced (Fe0 and Fe+2) and
dissolved in anoxic oceans.
• O2 produced reacted spontaneously with reduced iron
forming iron oxides instead of accumulating.
• By 2.4 billion years ago, O2 rose to one part per million
(Great Oxidation Event).
• Iron oxides precipitated and formed banded iron
formations: laminated sedimentary rocks. (Figure 13.8)
• Atmosphere gradually became oxic.
• New metabolisms (e.g., sulfide oxidation, nitrification,
other aerobic chemolithotrophy) evolved.
• respiring O2 energetically advantageous because of high
reduction potential, allowing aerobes to reproduce much
faster than anaerobes
• The ozone shield

• formation of ozone (O3) shield that protects Earth’s
surface from UV radiation
• Before, Earth’s surface was inhospitable.
• Ozone shield allowed organisms to range over surface,

exploiting new habitats and evolving diversity.

13.3 Living Fossils: DNA Records the History
of Life
• Phylogeny: Evolutionary history of related DNA
sequences
• Carl Woese and the tree of life
• universal tree of life (Figure 13.9) based on nucleotide
sequence similarity in ribosomal RNA (rRNA)
• genealogy of all life on Earth
• established the presence of three domains of life:
Bacteria, Archaea, Eukarya
• Root represents when all life shared the last universal
common ancestor (LUCA).
• shows first life forms were microorganisms and that
microbes have dominated most of history of life
of Life
• Genomics supports three-domain concept through
analysis of central cellular function genes.
• example: 60+ (including rRNA) genes shared by nearly all
cells and must have been present in universal ancestor
• Of these, eukaryotic and archaeal genes share more
similarity.
• Bacteria and Archaea likely diverged before
Eukarya existed.
• LUCA was likely prokaryotic with DNA genome and ability
to transcribe and translate proteins.

of Life
• other influences affecting phylogeny
• Many genes shared by two of three domains.
• One hypothesis: Horizontal gene transfer was extensive

before primary domains had diverged.
• Barriers likely evolved to maintain genomic stability.
• cells slowly sorted into primary lines of descent
• example: 60+ (including rRNA) genes shared by nearly all

cells and must have been present in universal ancestor

of Life
• other influences affecting phylogeny
• Bacteria and Archaea likely diverged ~3.7 billion years ago.
• Eukarya diverged from Archaea ~1.2–2.7 billion years ago.

13.4 Endosymbiotic Origin of Eukaryotes
• Divergence of Eukarya from Archaea resulted in

membrane-enclosed nucleus, and organelles gave
rise to eukaryotic cell structures.
• Endosymbiosis
• Oxygen also spurred evolution of organelle-containing
eukaryotic microorganisms.
• oldest eukaryotic microfossils ~two billion years old
• Fossils of multicellular and more complex eukaryotes are
found in rocks 1.9 to 1.4 billion years old.
• By 0.6 billion years ago, O2 was near present levels, and
large multicellular organisms (Ediacaran fauna) were
present in sea, then diversified into ancestors of algae,
plants, fungi, animals.
• Endosymbiosis
• endosymbiotic hypothesis: well-supported hypothesis for origin of
eukaryotic cells (Figure 13.10)
• contends that mitochondria arose from stable incorporation of an aerobic
respiring bacterium into the cytoplasm of early eukaryotic cells
• Chloroplasts arose from stable incorporation of a cyanobacterium-like
cell into cytoplasm of a eukaryotic cell, leading to eukaryotic
photosynthesis.
• Oxygen spurred evolution of organelle-containing eukaryotic
microorganisms.
• consumed by mitochondria, produced by chloroplast
• Physiology, metabolism, and genome structures/sequences of
mitochondria and chloroplasts support endosymbiotic hypothesis.
• 70S ribosomes including 16S rRNA
• mitochondria ancestor likely Alphaproteobacteria, chloroplast ancestor
likely Cyanobacteria
• Formation of the eukaryotic cell

• Eukaryotic cell is chimeric and made up of genes from
both Bacteria and Archaea.
• Eukaryotes have transcription and translational machinery
similar to those of Archaea.
• Eukaryotes have metabolisms similar to those of Bacteria.


• Two hypotheses explaining formation
• Serial endosymbiosis hypothesis: Eukaryotes began as
nucleus-bearing line that split from Archaea and later
acquired mitochondria and chloroplasts by endosymbiosis.
(Figure 13.10a)
• Endosymbiosis occurred when line engulfed a bacterial cell
that survived and replicated.
• Eukaryotic genes that resemble bacterial genes were
acquired through gene transfers from endosymbiont to
nucleus.
• does not account for similarities in bacterial and eukaryotic
membrane lipids

• Formation of the Eukaryotic Cell

• Two hypotheses explaining formation
• Symbiogenesis hypothesis: Eukaryotic cell arose from
symbiotic relationship between Bacteria and Archaea;
bacterial partner was engulfed to form mitochondria.
• Hydrogen hypothesis: Eukaryotic cell arose from an
H2-producing bacterium and an H2-consuming Archaea.
• Genes for lipid biosynthesis were transferred from bacterial
symbiont to archaeal host.


• timing of origin of nucleus unclear
• Formation may be associated with evolution of RNA
processing (i.e., Nuclear membrane may have evolved to
separate spliceosomes from ribosomes).
• pioneered the use of rRNA for phylogenetic studies in
the 1970s
• established the presence of three domains of life
• Bacteria, Archaea, and Eukarya
• provided a unified phylogenetic framework for Bacteria

II. Microbial Evolution
• 13.5 The Evolutionary Process
• 13.6 The Evolution of Microbial Genomes

13.5 The Evolutionary Process
• Evolution is a change in allele (alternative version) frequencies in

a population over time.
• Origins of genetic diversity
• mutations: random changes in DNA sequence occurring over time
• Most mutations are neutral or deleterious; some are beneficial.
• several forms including substitutions, deletions, insertions,
duplications
• Recombination breaks and rejoins DNA segments to make new
combinations of genetic material.
• can reassort genetic material already present
• required for integration of acquired DNA
• can be classified as homologous (requiring short flanking segments of
similar sequence) or nonhomologous (does not require high similarity)
• the ability to produce progeny and contribute to genetic makeup of
future generations

• Selection and genetic drift

• Selection is defined by fitness (ability of an organism to
produce progeny and contribute to genetic makeup of
future generations).
• Most mutations are neutral and accumulate over time.
• Deleterious mutations decrease fitness and are removed
by natural selection over time.
• Beneficial mutations increase fitness and are favored by
natural selection.
• Mutations occur by chance; environment selects for
advantageous mutations.

• Selection and genetic drift

• genetic drift: random process that can cause gene
frequencies to change over time, resulting in evolution in
the absence of natural selection (Figure 13.11)
• most powerful in small populations and those experiencing
frequent “bottleneck” events (severe reduction in size
followed by regrowth from remaining cells, such as
pathogens)

• New traits can evolve quickly in microorganisms.

• Environmental change or introduction of new cells can
cause rapid evolutionary changes.
• Microbes form large populations and reproduce quickly.
• example: Rhodobacter
• anoxygenic phototrophic purple bacterium
• In anaerobic culture, bacteriochlorophyll and carotenoids
are synthesized.
• In light, pigments lead to ATP synthesis; in dark, no benefit.
• In constant darkness, mutants with reduced levels of
photopigments have an advantage and rapidly take over
due to fitness. (Figure 13.12)
• In the light, pigment loss is not advantageous, and
mutants are lost.
• New traits can evolve quickly in microorganisms

• example: Escherichia coli
• Long-term evolution experiment (LTEE) started in 1988
and has tracked 12 parallel lines over 50,000+ generations.
• Minimal glucose medium represents an adaptive
environment in which E. coli can evolve over time.
• A marker that colors cells red or white enables
measurement of evolved strains relative to ancestor by
competition. (Figure 13.13a)
• dramatic increase in fitness over first 500 generations, then
slowed down
• New ability to use citrate found in only one of 12 lines.

• Speciation of microorganisms can take a long time.
• Species can posses a variety of individuals with
different traits.
• Sequence changes can be used as a molecular clock to
estimate time since two lineages diverged.
• Major assumptions are that nucleotide changes
accumulate in proportion to time, are generally neutral
and do not interfere with function, and are random.
• most reliable if calibrated with evidence from
geological record
• examples: E. coli harmless K-12 and O157:H7 pathogen
diverged ~4.5 million years ago, E. coli and Salmonella
enterica diverged ~100-140 million years ago

13.6 The Evolution of Microbial Genomes
• Genome sequencing of three strains of Escherichia

coli showed only 39 percent of genes were shared.
(Figure 13.14)
• core genome: shared by all strains of a species
• pan genome: core genome plus genes not shared

and often acquired through horizontal gene transfer

• The dynamic nature of the Escherichia coli genome

• on average 4721 genes (4068–5379)
• core genome: 1976 genes
• only ~60 genes predicted to be universally present in all
Bacteria and Archaea
• Number of unique genes and size of pan genome keeps
increasing as each new strain is sequenced.
• Genomes are highly dynamic and can shrink or
enlarge quickly.
• Prokaryotes regularly sample genes from other microbes
through horizontal gene transfer.

• Gene deletions in microbial genomes

• play important role in genome dynamics
• deletions far more frequent than insertions
• Nonessential and nonfunctional materials are commonly
deleted over time.
• Genetic drift can promote deletion when population sizes
are small or bottleneck.
• deletions streamlined genomes of obligate intracellular
symbionts and pathogens because host provides many
key metabolites

III. Microbial Phylogeny and Systematics
• 13.7 Molecular Phylogeny: Making Sense of

Molecular Sequences
• 13.8 The Species Concept in Microbiology
• 13.9 Taxonomic Methods in Systematics
• 13.10 Classification and Nomenclature

13.7 Molecular Phylogeny: Making Sense of
Molecular Sequences
• Systematics: Study of diversity of organisms and
relationships, links phylogeny with taxonomy
• Taxonomy: Characterizes, names, classifies
organisms
• Bacterial taxonomy incorporates multiple methods
for identifying and describing new species.
• The polyphasic approach to taxonomy uses three
methods:
1. phenotypic (morphological, metabolic, physiological,
chemical characteristics) analysis
2. genotypic (genome) analysis
3. phylogenetic (evolutionary) analysis

Molecular Sequences
• Phylogenetic trees: Diagrams depicting evolutionary
history
• Difference in nucleotide sequence between two organisms
is a function of number of mutations accumulated since
they shared a common ancestor.
• Obtaining DNA sequences
• isolate genomic DNA and sequence directly or use
polymerase chain reaction (PCR)
• SSU (small subunit) ribosomal RNA (rRNA) genes highly
conserved and easily sequenced and analyzed
(Figure 13.15)
• can amplify SSU rRNA from environmental samples or to
sequence environmental using metagenomics
Molecular Sequences
• Sequence alignment
• Phylogeny requires homology (inheritance from common
ancestor).
• Orthologs have same function and originate from a single
ancestral gene in a common ancestor.
• Paralogs have evolved to have different functions resulting
from gene duplication.
• Phylogenetic analyses typically focus on orthologs.
• estimate evolutionary changes from number of sequence
differences across a set of homologous nucleotides
• Sequence alignment adds gaps to establish positional
homology. (Figure 13.17)

Molecular Sequences
• Phylogenetic trees: Composition and construction
• depicts evolutionary history and resembles family tree
• composed of nodes and branches (Figure 13.18)
• Branch tips are species that exist today.
• can have either rooted (show position of ancestor) or
unrooted (do not show most ancestral node) trees
• Nodes show where an ancestor diverged into two
lineages.
• Branch length represents the number of changes that
have occurred along that branch.
• only one correct tree possible, but challenging to build

Molecular Sequences
• Phylogenetic trees: Composition and construction
• structure inferred by applying an algorithm (programmed

series of steps; Figure 13.19) or optimality criteria

Molecular Sequences
• Limitations of phylogenetic trees
• can be difficult to choose true tree if several fit data well
• Bootstrapping can deal with uncertainty; indicates
percentage of time a node is supported by data.
• Homoplasy (convergent evolution) complicates tree

construction when sequence divergence is high.
(Figure 13.20)
• horizontal gene transfer (Figure 13.21)

13.8 The Species Concept in Microbiology
• Species are fundamental units of diversity.
• What constitutes a microbial species remains controversial.
• A Phylogenetic Species Concept for Bacteria and Archaea
• should be genetically and phenotypically cohesive
• should be distinct from other species
• should be monophyletic (should share a recent common
ancestor excluded by other species)
• Phylogenetic species concept incorporates these principles.
• Bacterial and archaeal species are groups of strains sharing a
high degree of similarity and a recent common ancestor for their
SSU rRNA genes.
• 70 percent or less DNA-DNA hybridization (Figure 13.22) and
difference in SSU rRNA of 30 percent or more indicates two
distinct species. (Figure 13.23)
• Distinct genera have greater than five percent dissimilarity in
SSU rRNA.
13.8 The Species Concept in Microbiology
• How many species of Bacteria and Archaea exist?

• no firm estimate on the number of prokaryotic species
• 10,000 species of Bacteria and Archaea currently known
• Nearly all plant and animal species have microbiomes
with countless unique microbes.

13.9 Taxonomic Methods In Systematics
• Gene sequence analyses

• SSU rRNA not always useful for distinguishing closely
related species
• other highly conserved genes (e.g., recA and gyrB)
useful for distinguishing at species level (Figure 13.24)

• Multilocus sequence typing (MLST)

• method in which several different "housekeeping genes"
(essential functions) from an organism are sequenced
(Figure 13.25)
• has sufficient resolving power to distinguish between
very closely related strains
• useful in clinical microbiology (pathogenic strains),
epidemiological studies (tracking), and environmental
studies (geographic distribution)

• Genome fingerprinting
• rapid approach for evaluating polymorphisms
between strains
• ribotyping: method of identifying microbes from analyzing
DNA fragments generated from restriction enzyme
digestion of genes encoding SSU rRNA (Figure 13.26)
generating a pattern called a ribotype
• highly specific and rapid
• used in bacterial identification in clinical diagnostics and
microbial analyses of food, water, and beverages
• Other fingerprinting methods include repetitive extragenic
palindromic PCR (rep-PCR; Figure 13.27) and amplified
fragment length polymorphism (AFLP).

• Multigene and whole genome analyses

• use of multiple genes and entire genomes increasingly
common as sequencing improves and cost declines
• Orthologs can be aligned and examined to determine
average nucleotide identity (typically less than 95
percent between species).
• Analyses of content (presence/absence of genes), order
of genes (synteny), and GC content provide insight into
relationships.

• Phenotypic analysis
• Observable characteristics (phenotype) provide
differentiable traits. (Table 13.1)
• example: fatty acid analysis
• types and proportions of fatty acids in cytoplasmic
membrane lipids and gram-negative outer membrane lipids
often used in taxonomic analyses
• Technique used is FAME (fatty acid methyl ester).
• widespread use in clinical, public health, and food- and
water-inspection laboratories to identify pathogens
• relies on variation in composition of fatty acids in membrane
lipids for specific prokaryotic groups (Figure 13.28)
• analysis by gas chromatography compared with database
• requires rigid standardization because FAME profiles can
vary as a function of temperature, growth phase, and growth
medium
© 2018 Pearson Education, Inc. Table 13.1
13.10 Classification and Nomenclature
• Taxonomy and describing new species

• taxonomy: how organisms are classified and named
• classification: organization of organisms into
progressively more inclusive groups on the basis of
either phenotypic similarity or evolutionary relationship
• Species is one to several strains.
• Genus (genera) groups several species.
• families, orders, classes, domains (Table 13.2)


• Prokaryotes are given descriptive genus names and
species epithets following the binomial system of
nomenclature used throughout biology.
• Assignment of names for new species and higher groups

of prokaryotes is regulated by the International Code of
Nomenclature of Bacteria (the Bacteriological Code).


• New isolate needs to be compared to see if it is sufficiently
different to be described as a new taxon.
• Formal validation of a new prokaryotic species requires
• detailed description of characteristics/traits and
proposed name
• deposition of viable cultures of the organism in at least two
international culture collections (Table 13.3)
• Official publication for taxonomy and classification is
International Journal of Systematic and Evolutionary
Microbiology (IJSEM).
• websites: List of Prokaryotic Names with Standing in
Nomenclature (http://www.bacterion.net) and Prokaryotic
Nomenclature Up-to-Date (http://www.dsmz.de)


• Molecular and genomic techniques can characterize
phenotypic and genotypic characteristics without
cultivation.
• If an organism is well-characterized but not yet cultured,
a provisional taxonomic name with Candidatus can be
used (e.g., Candidatus Pelagibacter ubique).
• The International Committee on Systematics of
Prokaryotes (ICSP) oversees nomenclature and
taxonomy of Bacteria and Archaea.

• Bergey's Manual and The Prokaryotes

• No official classification, but most widely accepted is
Bergey’s Manual of Systematic Bacteriology.
• The Prokaryotes available online

• Culture collections
• National microbial culture collections are an important
foundation.
• catalog and store microorganisms and provide cultures
on request for a fee
• protect diversity
• store viable cultures (frozen or free-dried)
• act as repositories for type strains (serve as
nomenclatural type for future comparison with other
strains of the species)

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© 2018 Pearson Education, Inc.

• 13.2 Photosynthesis and the Oxidation of Earth

• 13.3 Living Fossils: DNA Records the History of Life

• 13.4 Endosymbiotic Origin of Eukaryotes

© 2018 Pearson Education, Inc.

• Liquid water required for life; first appeared ~4.3 billion

• evidence for life ~4.1 billion years ago

• Fossilized remains of cells can be found in rocks

© 2018 Pearson Education, Inc.

• Origin of cellular life

© 2018 Pearson Education, Inc.

• Origin of cellular life

• RNA can bind small molecules (e.g., ATP, other

• RNA has catalytic activity; may have catalyzed its own

• Earliest viruses may have evolved from RNA genome

© 2018 Pearson Education, Inc.

• Origin of cellular life

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc.

• Phototrophs use energy from sun to oxidize H2S, S,

© 2018 Pearson Education, Inc.

• Between 2.5 and 3.3 billion years ago,

• Rise of O2 allowed evolution of life to exploit

© 2018 Pearson Education, Inc.

• The ozone shield

• Before, Earth’s surface was inhospitable.

• Ozone shield allowed organisms to range over surface,

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc.

• One hypothesis: Horizontal gene transfer was extensive

• Barriers likely evolved to maintain genomic stability.

• cells slowly sorted into primary lines of descent

• example: 60+ (including rRNA) genes shared by nearly all

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc.

• Divergence of Eukarya from Archaea resulted in

• Formation of the eukaryotic cell

© 2018 Pearson Education, Inc.

• Formation of the eukaryotic cell

© 2018 Pearson Education, Inc.

• Formation of the Eukaryotic Cell

© 2018 Pearson Education, Inc.

• Formation of the eukaryotic cell

© 2018 Pearson Education, Inc.

• 13.5 The Evolutionary Process

• 13.6 The Evolution of Microbial Genomes

© 2018 Pearson Education, Inc.

• Evolution is a change in allele (alternative version) frequencies in

© 2018 Pearson Education, Inc.

• Selection and genetic drift

© 2018 Pearson Education, Inc.

• Selection and genetic drift

© 2018 Pearson Education, Inc.

• New traits can evolve quickly in microorganisms.

• New traits can evolve quickly in microorganisms

© 2018 Pearson Education, Inc.

© 2018 Pearson Education, Inc.

• Genome sequencing of three strains of Escherichia

• core genome: shared by all strains of a species

• pan genome: core genome plus genes not shared

© 2018 Pearson Education, Inc.

• The dynamic nature of the Escherichia coli genome