Microbio Exam 2: Origns, Evolution, Systematics

Chapters 9, 17

Early Life

Microbial life appeared 3.8 billion years ago (soon after the earth formed)

Sedimentary Layers of Limestone (CaCO₃₎

Hold clear fossil evidence of bacterial communities called stromatolites.

Geological Composition of Earth

1. Core

2. the Mantle

3. The thin outer crust

What element are the core and mantle rich with?

Iron

Biosphere

The sum total of all life on Earth.

• Supported by the earth’s thin crust

How were the major elements of biomolecules formed?

Nuclear reactions within stars.

• Which exploded into supernovas before the birth of our own solar system.

Biosignature

The evidence for life in the geological record.

Hadean Eon

First period of Earth’s existence (4.6-4.0 Gyr ago). Meteor bombardment may have killed off incipient life more than once before microbes finally became established.

Archaean Eon (4.0-2.5 Gyr ago)

Earliest geological evidence for life found in this eon.

• Evidence of microbial life includes isotope ratios, stromatolites, microfossils.

Microfossils

Fossils of early microbes (first found 1.2 Gyr), can be compared to microbes that exist today.

• Include filamentous prokaryotes

• Colonial cyanobacteria

Isotope Ratios

Provides a biosignature with quantitative evidence

• If the ratio between certain isotopes is altered by biological activity.

Chemical Biosignatures

Cyanobacterial hopanoids are steroid-like membrane molecules that are particularly durable.

Oxygenic Phototrophs/Sulfate Reducers

Cyanobacteria that split water to form O2 (adjusting to the level of available oxygen).

Banded Iron Formations

Layers of iron oxide, suggesting period of alternating oxygen-rich and anoxic conditions (based on the oxidation states of minerals).

Prebiotic Soup Model

How did the first small organic molecules arise?

Abiotically, from simple reduced chemicals sparked by lighting.

• These produced complex macromolecules that eventually acquired the apparatus for self-replication and membrane compartmentalization.

The RNA World Model

RNA performed all the informational and catalytic roles of today’s DNA and proteins.

• Genome sequences reveal thousands of catalytic and structural RNAs (they require less energy to form and degrade compared to DNA).

Ribozyme Model

Shown to exhibit enzymatic processes analogous to those of proteins.

• RNA may have fulfilled key functions that are now performed by DNA and proteins.

Panspermia

Organic molecules necessary for life (or even microbial cells) may have been transported by comets to Earth.

• Some evidence of organic molecules in comets and asteroids.

• Nearly 50% organic matter by mass gathered from the Rosetta mission from a comet near Jupiter.

Clades

Branching groups of related organisms

Monophyletic Group

Each clade is one of these groups, who share a common ancestor not shared by organisms outside of that clade.

• Each group then branches into smaller groups, and ultimately, species.

Phylogeny

Full descriptor used for branching divergence/diversity of species.

Molecular Clock

The temporal information contained in a macromolecular sequence.

• Based on the acquisition of new random mutations in each round of DNA replication.

Genes that show a consistent measure of evolutionary time

Encode components of the transcription/translation apparatus.

• Ribosomal RNA and proteins

• tRNA

• RNA polymerase

Using a Molecular Clock

Requires the alignment of homologous sequences of divergent species or strains.

Standard assumptions using molecular clocks

1. Minimum number of changes

2. Functional sequences change more slowly

3. Third-base codon positions show more random change.

Phylogenic Trees

Estimates the relative amounts of evolutionary divergence between sequences.

• Divergence data can be used to infer the length of time since two species shared a common ancestor (LUCA)

• Assuming mutation rate is the same.

Maximum Parsimony

The “best fit” tree is defined as the one requiring the fewest mutations to fit the data.

Maximum Likelihood

The probability that such a tree would have produced the observed DNA sequences.

Bayesian Interference

The probability that the tree is correct given the data, the prior and the likelihood model.

Rooted Phylogenetic Trees

Show the position of the last common ancestor, Unrooted trees do not indicate this position.

Carl Woese

First used SSU rRNA phylogeny to reveal the existence of a third kind of life (Archaea).

Similarities Among all Cells on Earth

1. Chromosomal Material (double-stranded DNA)

2. RNA Transcription (Common ancestral RNA polymerase)

3. Translation (Nearly universal genetic code, shared ancestral rRNAs and elongation factors.

4. Protein (Common ancestral functional domains)

5. Cell Structure (Aqueous cell compartment enclosed by a membrane)

Vertical Gene Transfer

The transmission of the entire genome from parent to offspring.

Gene Transfer in Prokaryotes

DNA is transferred through plasmids, transposable elements, and bacteriophages.

Traditional View of Phylogeny

Asserts that the vast majority of genes are transferred vertically and that most lineages are monophyletic.

Alternative View of Phylogeny

Asserts that horizontal gene transfer is so prevalent among microbes that it obscured monophyletic distinctions.

Ways to study Natural Selection

1. Genomic Analysis

2. Strongly Selective Environments

3. Experimental Evolution

Genomic Analysis

Comparing gene sequences (both within and between) genomes.

• Allows us to track how organisms adapted in the past.

Gene Duplications

Provides the opportunity to evolve paralogous genes, or paralogs, with different functions.

Degenerative (Reductive) Evolution

Unneeded genes are lost from the genome

• The organism saves energy by avoiding their replication and expression.

Strongly Selective Environments

Reveal rapid evolution.

• The “fittest” traits depend on the environment in which selection occurs.

• Rapid adaptive evEolution may be enhanced by disabling regulation.

Experimental Evolution/Laboratory Evolution

Experimenter finds a population of bacteria/other organisms that are grown under a chosen set of environmental conditions.

Richard Lenski

1988 - Long Term Evolution Experiment (LTEE)

• He founded 12 populations of E.Coli from a single clone

• The 12 populations were cultured in a medium in which growth was limited by a small amount of glucose

• Every 24 hours, 1% of each population was transferred to fresh medium

• Every 500 generations, samples of each population were frozen for later study.

• The populations have now evolved for more than 60,000 generations, and daily dilutions continue in the lab.

LTEE Findings

The evolution of bacteria that can grow faster than the ancestor and form larger cells (most striking change after 33,000 generations)

• One of the 12 populations suddenly became much denser, they evolved the ability to grow aerobically on citrate (Citrate plus)

LTEE Gene Sequencing

Genome sequencing from 29 clones isolated from the populations frozen fossil record showed the classic model of the stages of evolving a new trait.

Stages of evolving a new trait

1. Potentiation to achieve useful mutations.

2. Actualization of a novel mutant phenotype

3. Refinement, or increasing the degree of the phenotype.

Species (among Eukaryotes)

A group of individuals capable of interbreeding.

Taxonomy

The naming of species.

Classification

Classifying the life-forms into different kinds.

Two main perspectives for microbiologists

1. Phylogeny (based on DNA relatedness)

2. Ecology (based on shared traits and ecological niches)

Working definition/criteria of a species

1. SSU rRNA similarity ≥95% share the same genus.

2. Average nucleotide identity (ANI) of othologs ≥95%

3. Shared ecotype between organisms with 95% or greater identity

Pangenome

The core genome which consists of genes possessed by all isolates of a species.

• Accessory genes (found in some isolates but not others)

Closed Pangenome

Finite set of available genes

Open Pangenome

Infinite number of genes (dominate in nature).

Subcategories of Taxonomy

1. Classification

2. Nomenclature

3. Identification

“Emerging” Organisms

Used to refer to an organisms recently discovered/described.

Naming a Species

Accepted rules for naming species determined by the International Committee on Systematics of Prokaryotes (ICSP)