Microbiology

14.4.2015
Helmut Pospiech

Origin and Diversity of Life

Microbial Diversity

PART I.

ORIGIN OF CELLULAR LIFE

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

Brock Biology of Microorganisms, 13th ed.

Origin of Cellular Life

Surface Origin Hypothesis
Based on Urey-Miller experiment
that tried to simulate conditions on
early earth
Contends that the first membraneenclosed, self-replicating cells
arose out of primordial soup rich in
organic and inorganic compounds
in ponds on Earths surface
Dramatic temperature fluctuations
and mixing from meteor impacts,
dust clouds, and storms argue
against this hypothesis
Brock Biology of Microorganisms, 13th ed.

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
Submarine hydrothermal vents that
expell up to 400C hot, mineral-rich
water form chimneys that are called
black smokers

http://www.ridge2000.org/SEAS/for_students/reference/hydrothermal_vent_intro.html

Submarine Mound Formed at Ocean Hydrothermal Spring

Cooler, more oxidized, more

acidic ocean water

Hot, reduced, alkaline

hydrothermal fluid

Figure 14.4

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

A Model for the Origin of Cellular Life

Last Universal Common Ancestor

Brock Biology of Microorganisms, 13th ed.

An alkaline hydrothermal vent

harbours a natural proton gradient

The flux of hydrothermal effluent maintains an

alkaline interior. In the presence of appropriate
proteins, this source of energy could, in principle, be
tapped. The harnessing of naturally preexisting
chemiosmotic gradients before the advent of
genetically specified mechanisms to generate such
gradients would directly explain why ATP synthases of
the F-type (eubacteria) and A-type (archaebacteria)
are universal and conserved, but the mechanisms to
generate proton gradients are not.
Martin Biology Direct 2011 6:36 doi:10.1186/17456150-6-36

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
DNA may have been invented by viruses as an
mechanism to evade host response
current viruses also utilise modified bases for the
same reason

Brock Biology of Microorganisms, 12th ed.

Brock Biology of
Microorganisms,
13th ed.

A model for the transfer of DNA from viruses to cells for

the origin of cellular DNA chromosomes and plasmid
A DNA virus (DNA genome in red) infected
an RNA-cell (RNA genome in blue) (A) and
co-evolved with it in a carrier state (B).
Genes from the cellular RNA genomes are
progressively transferred to the viral DNA
genome by retrotranscription (white
arrow) and the viral genome evolved into
a DNA plasmid of the RNA-cell (C). The
DNA plasmid finally out-competed the
RNA genome and become a cellular DNA
chromosome (D). Infection of a DNA cell
by a DNA virus can led, by a similar
mechanism, to a DNA cell with both a
plasmid and a chromosome (EG). This
scenario should produce a procaryotic
type of cell. For the formation of
eukaryotic cells, the nucleus could have
originated by viral-induced recruitment of
intracellular membranes to produce the
nuclear membrane, by
a mechanism derived from the process
used by large double-stranded DNA
viruses to form their envelopes.

Forterre P. (2005) The two ages of the RNA world, and the transition to
the DNA world: a story of viruses and cells. Biochimie 87, 793-803.

A Model for the Origin of Cellular Life

Viruses may have large
impact on the
development of life
(Eugen Koonin and
Patrick Forterre)
Evidence for multiple
viral lines already at the
time of LUCA
Probably, there existed
two types of early life
forms: capsid-engulfed
(viruses) und lipid
membrane engulfed
(cellular) life
Koonin EV, Senkevich TG, Dolja VV. (2006) The
ancient Virus World and evolution of cells. Biol
Direct 1, 29.

Origin of Cellular Life

Other Important Steps in Emergence of Cellular Life
Build up of lipids
Synthesis of phospholipid
membrane vesicles that

Lipid Vesicles Made in the

Laboratory from Myristic Acid

enclosed the cells

biochemical and replication
machinery
May have been similar
to montmorillonite clay
vesicles
Vesicles formed on Montmorillonite clay particles

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

Energy Metabolism of the First Free

Cells
After establishment of a
cytoplasma membrane
and the release of first
cells from the
clay/serpentine mounds,
the cell had to be able to
establish an own scheme
to produce a proton
gradient
Possible as iron
chemolithotrophs using a
primitive hydrogenase

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

Brock Biology of Microorganisms, 12th ed.

PART II.

MICROBIAL DIVERSIFICATION

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
Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

Banded Iron Formations

Iron oxides

Figure 14.9

Brock Biology of Microorganisms, 12th ed.

Brock Biology of Microorganisms, 12th ed.

Microbial Diversification
Development of oxic atmosphere led to evolution of
new metabolic pathways that yielded more energy
than anaerobic metabolisms
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

Oxygen also spurred evolution of organelle-containing

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

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

Endosymbiotic Origin of Eukaryotes

Different 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

Brock Biology of Microorganisms, 13th ed.

Endosymbiotic Origin of Eukaryotes

Different hypotheses exist to explain the formation of
the eukaryotic cell (contd)
2) Eukaryotic cell arose from intracellular association between
O2-consuming bacterium (the symbiont), which gave rise to
mitochondria and an archaean host

Brock Biology of Microorganisms, 13th ed.

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

But neither of the two hypotheses explains

how the nucleus itself evolved!!!
Brock Biology of Microorganisms, 12th ed.

The Viral Eukaryogenesis Hypothesis

Many large viruses such as poxviruses
replicate their DNA in the cytoplasm in
membrane-engulfed compartments
Poxvirus-related virus that infect
Archaea are known
Condit (2007) Cell Host & Microbe 2, 205 - 207

Bell PJ (2009) The viral eukaryogenesis hypothesis: a key role for viruses in the
emergence of eukaryotes from a prokaryotic world environment. Ann N Y Acad Sci
1178, 91-105.

Viruses and other selfish

genetic elements may
have contributed in
many ways to the
development of the
eukaryotic cell
Nucleus and part of the
nuclear replication apparatus
Mitochondrial DNA
replication apparatus
introns
(retro-)transposons
etc.

Koonin EV, Senkevich TG, Dolja VV. (2006) The ancient Virus
World and evolution of cells. Biol Direct 1, 29.

A new fusion hypothesis for the origin of Eukarya:

better than previous ones, but probably also wrong

P. Forterre (2011) Research in

Microbiology 162, 77e91
Fig. 2. The PTV fusion hypothesis based on the engulfment of a thaumarchaeon by a PVC bacterium followed by viral
invasions. Bacterial and archaeal membranes, cytoplasmic and nuclear components (including circular chromosome) are in
green and purple, respectively. Eukaryal cytoplasmic and nuclear components are in grey to symbolize differences with
their archaeal ancestors. Eukaryal chromosomes (linear) are in orange. Abbreviations are as in Fig. 1. ICM: Intracytoplasmic
membrane. NE: nuclear envelope. PVC: Planctomycetes, Verrucomicrobia, Chlamydiae superphylum. For simplicity the
reticulum endoplasmicmembrane deriving from the ICM of the PVC bacterium has not been indicated.

Fusion or
not fusion
that is the
question
here!

Forterre P (2013)The common

ancestor of archaea and
eukarya was not an archaeon.
Archaea 2013:372396.

The Evolutionary Process

Mutations
Changes in the nucleotide sequence of an organisms
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
Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

Ribosomal RNA

16S rRNA
from E. coli
Figure 14.11

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 13th ed.

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

Brock Biology of Microorganisms, 13th ed.

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

Brock Biology of Microorganisms, 13th ed.

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)

Brock Biology of Microorganisms, 12th ed.

Evolutionary Analysis: Analytical Methods

Identification of Phylogenetically Informative Sites

Dots: neutral sites.

Arrows: phylogenetically informative sites.

Common cladistic methods

Figure 16.15

Parsimony
Maximum likelihood
Bayesian analysis
Brock Biology of Microorganisms, 13th ed.

Universal Phylogenetic Tree as Determined by rRNA Genes

Brock Biology of Microorganisms, 13th ed.

Microbial Phylogeny
Domain Archaea consists of two major groups
Crenarchaeota
Euryarchaeota

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

Brock Biology of Microorganisms, 13th ed.

Each of the three domains of life can be

characterized by various phenotypic properties

Brock Biology of Microorganisms, 13th ed.

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

Brock Biology of Microorganisms, 13th ed.

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

Brock Biology of Microorganisms, 13th ed.

Phenotypic analysis examines the

morphological, metabolic, physiological, and
chemical characters of the cell

Brock Biology of Microorganisms, 13th ed.

Genotypic Analysis
Several methods of genotypic analysis are
available and used
DNA-DNA hybridization
DNA profiling
Multilocus Sequence Typing (MLST) or whole genome
sequencing
GC Ratio

Brock Biology of Microorganisms, 13th ed.

Genotypic Analysis
DNA-DNA hybridization
Genomes of two organisms are hybridized to examine
proportion of similarities in their gene sequences

Brock Biology of Microorganisms, 12th ed.

Genomic Hybridization as a Taxonomic Tool

Figure 14.20a

Brock Biology of Microorganisms, 12th ed.

Genomic Hybridization as a Taxonomic Tool

Figure 14.20b

Brock Biology of Microorganisms, 12th ed.

Genomic Hybridization as a Taxonomic Tool

Figure 14.20c

Brock Biology of Microorganisms, 12th ed.

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%

Brock Biology of Microorganisms, 12th ed.

Phylogenetic Analysis
Whole-genome sequence analyses are becoming
more common
Genome structure; size and number of chromosomes,
GC ratio, etc.
Gene content
Gene order

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

Taxonomic Hierarchy for Allochromatium warmingii

Brock Biology of Microorganisms, 13th ed.

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

Brock Biology of Microorganisms, 12th ed.

Multi-Gene Phylogenetic Analysis

16S rRNA genes

gyrB genes
luxABFE genes

Figure 14.24

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

A Model for Bacterial Speciation

Figure 14.25

Brock Biology of Microorganisms, 12th ed.

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

Brock Biology of Microorganisms, 12th ed.

Trouble with the Tree of Life Concept

Ring of Life rather than a tree of life

since the eukaryotic genome represents a
fusion of a bacterial and archaeal genome
(Riviera and Lake (2004), Nature 431, 152)

A reticulated tree would better describe the

genotypic relationship of organisms due to
vast horizontal gene transfer
(Doolittle (1999), Science 284, 2124; Martin
(1999), BioEssays 21, 99)

Universal common ancestry

of life on earth?

a, The multiple-ancestry possibility: depicted here is life originating from two separate forms,
with proteins with similar functions arising independently. Transfers, by endosymbiosis or by
lateral gene transfers, are shown by dotted lines. b, A single origin (universal common
ancestry), at least after the advent of protein synthesis. Correlations between patterns at
different amino-acid positions are used to test between the two possibilities.
Steel M & Penny D (2010) Nature 465,168.

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

Classification and Nomenclature

Classification
Organization of organisms into progressively more
inclusive groups on the basis of either phenotypic
similarity or evolutionary relationship

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

14.14 Classification and Nomenclature

Major references in bacterial diversity
Bergeys Manual of Systematic Bacteriology (Springer)
The Prokaryotes (Springer)

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