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Microbiology

3.4.2018Helmut Pospiech

Origin and Diversity of Life

Microbial Diversity

ORIGIN OF CELLULAR LIFEPART I.

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.


• Surface Origin Hypothesis– Based on Urey-Miller experiment

that tried to simulate conditions on early earth

– Contends that 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



• 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 that expell up to 400°C hot, mineral-rich water form chimneys that are called black smokers

Submarine Mound Formed at Ocean Hydrothermal Spring

Figure 14.4

Hot, reduced, alkaline hydrothermal fluid

Cooler, more oxidized, more acidic ocean water



• 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


A Model for the Origin of Cellular Life

Last Universal Common Ancestor


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


• 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


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 (E–G). This scenario should produce a procaryotictype 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, bya 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.

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

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

Origin of Cellular Life• Other Important Steps in Emergence of Cellular Life

– Build up of lipids

– Synthesis of phospholipid

membrane vesicles that

enclosed 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



• 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


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


• Early forms of chemolithotrophic metabolismwould 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


MICROBIAL DIVERSIFICATIONPART II.

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


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


Banded Iron Formations

Figure 14.9

Iron oxides


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


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


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


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 to mitochondria and an archaean host


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!!!


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

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

Viruses and other selfish genetic elements may

have contributed in many 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 DNA replication apparatus

• introns• (retro-)transposons• etc.

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: Intracytoplasmicmembrane. 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.

P. Forterre (2011) Research in Microbiology 162, 77e91

Forterre P (2013)The common ancestor of archaea and eukarya was not an archaeon. Archaea 2013:372396.

Fusion ornot fusion –that is the question

here!

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 gene duplication, horizontal gene transfer, and gene loss


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



• 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

Figure 14.11

16S rRNA from E. coli



• 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


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



• 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


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



• 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)



• 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


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 characterized by various phenotypic properties


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


Phenotypic Analysis• Bacterial taxonomy incorporates multiple methods

for identification and description of new species

• The polyphasic approach to taxonomy uses three methods1) Phenotypic analysis

2) Genotypic analysis

3) Phylogenetic analysis


Phenotypic analysis examines the morphological, metabolic, physiological, and

chemical characters of the cell


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


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

Figure 14.20a



Figure 14.20b



Figure 14.20c


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%


Phylogenetic Analysis

• Whole-genome sequence analyses are becoming more common – Genome structure; size and number of chromosomes,

GC ratio, etc.

– Gene content

– Gene order


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



• 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


Multi-Gene Phylogenetic Analysis

Figure 14.24

16S rRNA genes

gyrB genes

luxABFE genes



• 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


A Model for Bacterial Speciation

Figure 14.25



• 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


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 ancestryof 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.


• 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


• 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– Bergey’s Manual of Systematic Bacteriology (Springer)

– The Prokaryotes (Springer)


• 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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