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Microbiology

14.4.2015

Helmut Pospiech

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Origin and Diversity of Life

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Microbial Diversity

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Origin of Cellular Life

• Early Earth was anoxic and much hotter than

present day (over 100 oC)

• First biochemical compounds were made byabiotic systems that set the stage for the origin of

Brock Biology of Microorganisms, 13th ed.

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• Surface Origin Hypothesis – Based on Urey-Miller experiment

that tried to simulate conditions onearly earth

– Contends that the first membrane-enclosed, self-replicating cellsarose out of primordial soup rich inorganic and inorganic compoundsin ponds on Earth’s surface

– Dramatic temperature fluctuationsand mixing from meteor impacts,dust clouds, and storms argueagainst this hypothesis

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• 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

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

Submarine hydrothermal vents thatexpell up to 400°C hot, mineral-rich

water form chimneys that are called

black smokers

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Submarine Mound Formed at Ocean Hydrothermal Spring

Figure 14.4

Hot, reduced, alkaline

hydrothermal fluid

Cooler, more oxidized, more

acidic ocean water

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• 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 ownsynthesis

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A Model for the Origin of Cellular Life

Last Universal Common Ancestor

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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:10.1186/1745-

6150-6-36

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• DNA, a more stable molecule, eventually becamethe genetic repository

• Three-part systems (DNA, RNA, and protein)evolved and became universal among cells

èDNA may have been invented by viruses as an

mechanism to evade host responseè current viruses also utilise modified bases for the

same reason

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Brock Biology of

Microorganisms,13th ed.

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

the origin of cellular DNA chromosomes and plasmidA 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 similarmechanism, to a DNA cell with both a

plasmid and a chromosome (E–G). 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 processused by large double-stranded DNA

viruses to form their envelopes.

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

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Koonin EV, Senkevich TG, Dolja VV. (2006) The

ancient Virus World and evolution of cells. Biol

Direct 1, 29.

A Model for the Origin of Cellular Life• Viruses may have large

impact on thedevelopment of life(Eugen Koonin andPatrick Forterre)

• Evidence for multiple

viral lines already at thetime of LUCA

• Probably, there existedtwo types of early “lifeforms”: capsid-engulfed

(viruses) und lipidmembrane engulfed(cellular) life

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• Other Important Steps in Emergence of Cellular Life

– Build up of lipids

– Synthesis of phospholipid

membrane vesicles thatenclosed the cell’s

biochemical and replication

machinery

• May have been similar to montmorillonite clay

vesicles

Lipid Vesicles Made in the

Laboratory from Myristic Acid

Vesicles formed on Montmorillonite clay particles

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• 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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Energy Metabolism of the First Free

Cells• After establishment of a

cytoplasma membraneand the release of firstcells from theclay/serpentine mounds,the cell had to be able toestablish an own schemeto produce a protongradient

• Possible as ironchemolithotrophs using a

primitive hydrogenase

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• 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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MICROBIAL DIVERSIFICATION

PART II.

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Microbial Diversification

• Molecular evidence suggests ancestors of

Bacteria and Archaea diverged ~ 4 billion

years ago

• As lineages diverged, distinct metabolisms

developed

• Development of oxygenic photosynthesisdramatically changed course of evolution

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• ~ 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

Figure 14.9

Iron oxides

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• Development of oxic atmosphere led to evolution of new metabolic pathways that yielded more energythan anaerobic metabolisms

• Consequence of O2 for the evolution of life

– Formation of ozone layer that provides a barrier against UVradiation• Without this ozone shield, life would only have continued

beneath ocean surface and in protected terrestrialenvironments

• Oxygen also spurred evolution of organelle-containing

eukaryotic microorganisms – Oldest eukaryotic microfossils ~ 2 billion years old

– Fossils of multicellular and more complex eukaryotes arefound in rocks 1.9 to 1.4 billion years old

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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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Endosymbiotic Origin of Eukaryotes• Different hypotheses exist to explain the formation of

the eukaryotic cell1) Eukaryotes began as nucleus-bearing lineage that later

acquired mitochondria and chloroplasts by endosymbiosis

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Endosymbiotic Origin of Eukaryotes• Different 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 tomitochondria and an archaean host

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Endosymbiotic Origin of Eukaryotes

• Both hypotheses suggest eukaryotic cell is

chimeric

• This is supported by several features

– Eukaryotes have similar lipids and energy metabolismsto Bacteria

– Eukaryotes have transcription and translational

machinery most similar to Archaea

• But neither of the two hypotheses explains

how the nucleus itself evolved!!!

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The Viral Eukaryogenesis Hypothesis

• Many large viruses such as poxvirusesreplicate their DNA in the cytoplasm inmembrane-engulfed compartments

• Poxvirus-related virus that infectArchaea are known

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 Sci1178, 91-105.

Condit (2007) Cell Host & Microbe 2, 205 - 207

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Viruses and other selfish

genetic elements may

have contributed inmany ways to the

development of the

eukaryotic cell

Koonin EV, Senkevich TG, Dolja VV. (2006) The ancient Virus

World and evolution of cells. Biol Direct 1, 29.

• Nucleus and part of the

nuclear replication apparatus

• Mitochondrial DNAreplication apparatus

• introns

• (retro-)transposons

• etc.

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A new fusion hypothesis for the origin of Eukarya:

better than previous ones, but probably also wrong

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 thereticulum endoplasmicmembrane deriving from the ICM of the PVC bacterium has not been indicated.

P. Forterre (2011) Research in

Microbiology 162, 77e91

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Forterre P (2013)The common

ancestor of archaea and

eukarya was not an archaeon.Archaea 2013:372396.

Fusion or

not fusion –

that is thequestion

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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 geneduplication, horizontal gene transfer, and

gene loss

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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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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

Ribosomal RNA

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Ribosomal RNA

Figure 14.11

16S rRNA

from E. coli

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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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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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l l l l h d

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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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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 informativeand define monophyletic groups (a group which contains

all the descendants of a common ancestor; a clade)

l l l l h d

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Evolutionary Analysis: Analytical Methods

• Common cladistic methods

– Parsimony

– Maximum likelihood

– Bayesian analysis

Identification of Phylogenetically Informative Sites

Figure 16.15

Dots: neutral sites.

Arrows: phylogenetically informative sites.

Universal Phylogenetic Tree as Determined by rRNA Genes

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Universal Phylogenetic Tree as Determined by rRNA Genes

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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

Each of the three domains of life can be

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Each of the three domains of life can be

characterized by various phenotypic properties

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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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Phenotypic Analysis

• Bacterial taxonomy incorporates multiple methodsfor 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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Phenotypic analysis examines the

morphological, metabolic, physiological, and

chemical characters of the cell

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Genotypic Analysis

• Several methods of genotypic analysis areavailable and used – DNA-DNA hybridization

– DNA profiling

– Multilocus Sequence Typing (MLST) or whole genomesequencing

– GC Ratio

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Genotypic Analysis

• DNA-DNA hybridization – Genomes of two organisms are hybridized to examine

proportion of similarities in their gene sequences

Genomic Hybridization as a Taxonomic Tool

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Figure 14.20a

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Figure 14.20b

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Figure 14.20c

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Phylogenetic Analysis

• 16S rRNA gene sequences are useful intaxonomy; 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 morethan 3% from any named strain, and a new genus if it

differs by more than 5%

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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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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

Taxonomic Hierarchy for Allochromatium warmingii

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• Biological species concept not meaningfulfor prokaryotes as they are haploid and do

not undergo sexual reproduction

• Genealogical species concept is analternative – 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

Mult i-Gene Phylogenetic Analysis

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Figure 14.24

16S rRNA genes

gyrB genes

luxABFE genes

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• Ecotype

– Population of cells that share a particular resource

– Different ecotypes can coexist in a habitat

• Bacterial speciation may occur from acombination of repeated periodic selection for a

favorable trait within an ecotype and lateral gene

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• This model is based solely on the

assumption of vertical gene flow

• New genetic capabilities can also arise byhorizontal gene transfer; the extent among

bacteria is variable

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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

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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.

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• No firm estimate on the number of prokaryotic

species

• Nearly 7,000 species of Bacteria and Archaea arepresently known

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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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• Prokaryotes are given descriptive genusnames and species epithets following thebinomial system of nomenclature usedthroughout 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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• 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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