MCR 210:

Microbial Evolution and

Systematics

4 September 2010
 Early Earth
 Roughly 4.6 billion years old
 Crust became stable 3.9 billion years
ago
 Oldest known rocks date back to 3.86
billion years ago
 Sedimentary** - presence of liquid water in
the form of oceans or lakes, compatible
with life
 Volcanic
 carbonate
Early cells

 Some ancient rock

contain vaguely
recognizable
microfossils that appear
bacterial shaped
 Early cells arranged in a
filament

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Stromatolites
 In younger rock clear
fossil evidence exists
 Many examples found
in stromatolites
(mounds of fossilized
filamentous
prokaryotes in
sediment)
 From Warrawoona,
2.7 billion years old

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Living stromatolites
 Intact stromatolite
present today in
Shark”s Bay
 Grow in shallow
marine basins and in
hot springs
 -may be formed by
filamentous
phototrophic
bacteria
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 Conditions on early earth
 Atmosphere was slightly reducing
 Little free O2
 H2O was present
 Variety of gases, mainly CH4, CO2, N2,
and NH3
 Much hotter than today

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 Origins of life
 First biochemical compounds were made
by abiotic syntheses
 Earliest life forms probably consisted
of self replicating RNA
 With time, proteins replaced the
catalytic functions of RNA and DNA
replaced the coding function of RNA

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Evolution of cellular life forms from
RNA life forms
 This is a possible
scenario
 Self replicating RNA’s
could have become
cellular entities by being
integrated into liposome
vesicles
 With time, proteins
replaced the catalytic
functions of RNA and
DNA replaced the
coding function of RNA

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 Primitive Energy Generation
 Primitive metabolism was
anaerobic and likely
chemolithotrophic, exploiting
the abundant sources of FeS
and H2S present .

 Electron acceptor in this

reaction would be elemental S
(S0);
 Oxygenic photosynthesis led
to development of banded iron
formations, an oxic
environment, and great bursts
of biological evolution
Landmarks in biological evolution

 For most of earths

history, only
microbial life forms
existed
 Note how
oxygenation of
atmosphere
occurred over a
period of 1.5 billion
years

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• In the mid-1960s Emile Zuckerkandl and Linus Pauling of
the California Institute of Technology conceived of a
revolutionary strategy that could supply the missing
information.

Instead of looking just at anatomy or physiology, they

asked, why not base family trees on differences in the order
of the building blocks in selected genes or proteins?

Their approach, known as molecular phylogeny, is

eminently logical. Individual genes, composed of unique
sequences of nucleotides, typically serve as the blueprints
for making specific proteins, which consist of particular
strings of amino acids.
All genes, however, mutate (change in sequence),
sometimes altering the encoded protein.

Genetic mutations that have no effect on protein function

or that improve it will inevitably accumulate over time.

Thus, as two species diverge from an ancestor, the

sequences of the genes they share will also diverge. And
as time passes, the genetic divergence will increase.

As this protein work was progressing, Carl R. Woese of the

University of Illinois was turning his attention to a powerful
new yardstick of evolutionary distances: small subunit
ribosomal RNA (SSU rRNA).
 Phylogeny
 Phylogeny is the evolutionary history of
organisms
 Fossil record of microbial evolution is
incomplete
 Phylogeny determined by analyzing rRNA

 3 lines of cellular descent were established

leading to the Bacteria, Archae and Eukarya
These features suggested to Woese in the late
1960s that variations in SSU rRNA (or more
precisely in the genes encoding it) would
reliably indicate the relatedness among
any life-forms,
from the plainest bacteria to the most complex
animals.

Small subunit ribosomal RNA could thus serve,

in Woese’s words, as a “universal molecular
chronometer.”
CONSENSUS VIEW of the universal tree of life
holds that the early descendants of life’s last
universal common ancestor—a
small cell with no nucleus—divided into two
prokaryotic (nonnucleated)
groups: the bacteria and the archaea.
Later, the archaea gave rise to organisms
having complex cells containing a nucleus: the
eukaryotes.
Eukaryotes gained valuable energy-generating
organelles—mitochondria and, in the case of
plants, chloroplasts—by taking up, and
retaining, certain bacteria.
“Tree of life”
 Shows the three
domains Bacteria,
Archae and Eukarya
 Origin of life is within
the bacterial domain
(not on branch leading
to Archaeal and
Eukaryal domain)
 Archae diverged
between the Bacteria
and the Eukarya but
closer to the eukaryotes

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Eukaryotes and organelles
 Primitive eukarya were
structurally simple (no
nucleus, mitochondria
and chloroplast)
 Nucleus and mitotic
apparatus probably
arose to ensure
orderly partitioning of
DNA in large-genome
organisms
 Mitochondria and
chloroplasts ex
prokaryotes became
symbiotic within
eukaryotic cells
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The eukaryotic nucleus and mitotic apparatus probably arose
as a necessity for ensuring the orderly partitioning of DNA in
large-genome organisms.
Mitochondria and chloroplasts, the principal energy-producing
organelles of eukaryotes, arose from symbiotic association of
prokaryotes of the domain Bacteria within eukaryotic cells, a
process called endosymbiosis. Assuming that an RNA world
existed, self-replicating entities have populated Earth for over
4 billion years.
 Progenitor cells
 Progenitor organisms established a basis
for heredity, gene expression, material
transfers and cellular energetics before
divergence
 DNA as hereditary material

 Gene expression from DNA to RNA to

protein
 ATP and proton motif force for cell

energetics
 Central metabolic pathways (glycolysis and

TCA cycle)
All evolved prior to divergence of domains
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 Genetic basis for evolution
 those organisms best adapted to survive in a
given environment have a selective advantage
 Mutations introduce variability into genomes
of organisms – changes spread rapidly in
microbial populations
 Many mutations are harmful
 Favorable mutation makes organism more “fit”

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 Genetic exchange,
recombination and evolution
 Mutation introduces variability into DNA
 genetic exchange and recombination are
equally NB
 Recombination forms new allelic combinations
which may be adaptive
 Exchange of genetic info may produce
individuals with multiple attributes making
them “super fit”

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 Natural selection
 This determines which populations can
successfully establish themselves in a community
 Some organisms possess features which makes
them better adapted for survival in a particular
ecosystem
 Less fit organisms are eliminated by natural
selection
 With time, the interactions of genes and the
environment through the process of natural
selection led to continued diversification of living
cells

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 Evolution of physiological
diversity (1)
 3,6 BYA cells were anaerobic heterotrophs
which degraded and derived energy from
abiotically formed organic molecules
 next step: anaerobic autotrophs able to fix
CO2 and turn CO2 and H into organic molecules
 Electron donors initially were H2 and H2S
 Were all thermophiles

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 Physiological diversity (2)
 Energy sources for these autotrophs:
 Chemoautotrophs used chemical energy from

elements in surroundings
 As this E source was depleted, the ability to

capture E from light evolved (phototrophs)

 Initially only anoxic photosynthesis (based on

PSI)

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 Physiological diversity (3)
 Earth’s 1st major crisis:

Electron donors became scarce(H2, H2S)
 Key innovation =/- 2.5 BYA
 oxygenic photosynthesis by cyanobacteria
(PSII)

Uses H20 as electron donor and generates O2

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 Physiological diversity (4)
 With 02 available, aerobes evolved
 Successful since oxidation of organic
compounds generates more energy
 Higher population densities developed
 Increased chance for evolution of new
types of organisms and metabolic
schemes e.g. aerobic respiration

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 The Ozone Shield
 Major consequence of the appearance of
oxygen was the formation of ozone (03)
 03 provides barrier against UV radiation
 In anoxic world only habitats shielded from
direct radiation was habitable (oceans, under
rocks)
 In oxic world, organisms could range over
entire surface of earth

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 11.11 Chemotaxonomy
 Molecular taxonomy involves molecular
analyses of specific cell components.

• These include, among others, DNA:DNA

hybridization (Figure 11.22), ribotyping and
multilocus sequence typing (MLST) and fatty
acid analyses, such as fatty acid methyl ester
(FAME) analysis
 Evolution is the change in a line of
descent over time leading to new species
or varieties. The evolutionary
relationships between life forms are the
subject of the science of phylogeny.
 Using ribosomal RNA sequencing
technology these organelles have been
shown to be highly derived ancestors of
specific lineages of Bacteria .
 Two major treeing algorithms are
distance and parsimony (Figure 11.13).
 Signature sequences can be used to
generate specific phylogenetic probes,
useful for fluorescent in situ
hybridization (FISH) or microbial
community analyses.
 Life on Earth evolved along three major
lines, called domains, all derived from a
common ancestor. Each domain contains
several phyla. Two of the domains,
Bacteria and Archaea, remained
prokaryotic, whereas the third, Eukarya,
evolved into the modern eukaryotic cell.
 Although the three domains of living
organisms were originally defined by
ribosomal RNA sequencing, subsequent
studies have shown that they differ in
many other ways.
 In particular, the Bacteria and Archaea differ
extensively in cell wall and lipid chemistry and in
features of transcription and protein synthesis
 Conventional bacterial taxonomy
places heavy emphasis on analyses of
phenotypic properties of the organism
(Table 11.4).
Conventional bacterial taxonomy places heavy
emphasis on analyses of phenotypic properties of the
organism
 To identify an organism, one must
assess several of its phenotypic
properties, from general to specific
 Determining the guanine plus cytosine
base ratio (GC ratio) of the DNA of the
organism can be part of this process
 Molecular taxonomy involves
molecular analyses of specific cell
components.
 These include, among others,
DNA:DNA hybridization (Figure 11.22),
ribotyping and multilocus sequence
typing (MLST) (Figure 11.23), and fatty
acid analyses, such as fatty acid methyl
ester (FAME) analysis (Figure 11.24).
 Genomic hybridization measures the
degree of sequence similarity in two
DNAs and is useful for differentiating very
closely related organisms where rRNA
sequencing may not be definitive.
 The species concept applies to
prokaryotes as well as eukaryotes, and a
similar taxonomic hierarchy exists.
 Groups of genera (singular: genus) are
collected into families, families into
orders, orders into classes, classes into
phyla (singular: phylum), and so on up to
the highest-level taxon, the domain.
 It has been proposed that a prokaryote
whose 16S ribosomal RNA sequence
differs by more than 3% from that of all
other organisms (that is, the sequence is
less than 97% identical to any other
sequence in the databases), should be
considered a new species (Figure 11.25).
Bacterial
speciation may
occur from a
combination of
repeated periodic
selection for a
favorable trait
within an
ecotype and
lateral gene flow
 Following the binomial system of
nomenclature used throughout biology,
prokaryotes are given descriptive genus
names and species epithets.
 Formal recognition of a new
prokaryotic species requires deposition of
a sample of the organism in a culture
collection and official publication of the
new species name and description.
Bergey's Manual of Systematic
Bacteriology is a major taxonomic
compilation of Bacteria and Archaea.
 Molecular sequencing has also shown
that the major organelles of Eukarya have
evolutionary roots in the Bacteria and has
yielded new tools for microbial ecology and
clinical microbiology.
 Systematics
Broad Evolutionary Picture
 Original organism replicated and
evolved for millions of years, then
gave rise to the universal
ancestor (common to all later
forms of life known to currently
exist on earth)
 Universal ancestor was the result
of considerable evolution of the
original life form and gave rise to
three domains of living things
Bacteria, Archaea and Eukarya,
via considerable evolution
Classification
 Phylogeny vs. Taxonomy -
phylogeny depends upon
genotypic analysis as a basis
of classification, whereas
taxonomy depends upon
phenotypic (generally
biochemical) analysis
 Binomial nomenclature -
organisms are always given
two names; one designates
their species (similar strains),
one their genus (similar
species)