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Chapter 11Microbial evolution and

systematics

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Earliest life forms• Origin of our galaxy: explosion of

a big star• Gave rise to sun and other

planets• Earth: 4.6 billion years• Stromatolites date back to 3.5

billion years (fossil record)• Nonoxigenic, phototrophs initially• Modern stromatolites live in high

temperature conditions

Conditions on early earth/origin of life

• Very little oxygen (reducing conditions)• Water and variety of gases• Methane most abundant, CO2, N2• Little amounts of CO, NH3 and H2• HCN (Ammonia and methane)• High temperature above 100 C• Early life forms – heat loving• Combination of radiation, lightning and gases result in

formation of AA, sugars, purines and pyrimidines• Polymerize under certain conditions aided supported by

anhydrous surfaces• Hydrothermal vents: good candidates for places with

conditions for the generation of early life forms

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3.5 Billion Year Old Stromatolites

Stromatolites at Shark Bay, Western Australia

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Banded Iron Formations Document O2Evolution (2 Ga)

Bands of iron oxide come from ancient Cyanobacteria

O2 + UV => O3

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Stanley Miller studied the prebiotic synthesis of monomers of the macromolecules.

Origins of Life?

Volcanic gasses + UV (or lightning) => monomers

Precellular “Life”

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RNA world• Theory• Catalytic RNAs

suggest that self replicating molecule

• Enclosed into lipoprotein

• Energy for processes derived from formation of FeS2 (exergonic)

Free energy of formation -42 kJ

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Major landmarks in biological evolution

Cell size (+)

Endosymbiosis

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Evolutionary relationships/molecular phylogeny

• To establish relatedness a good chronometer molecule is required

• 16S rRNA molecule is a good chronometer

• Universal• The same function• Sequence can be aligned• The rate of change in sequence is

very slow

outline

account for either back mutations to the original genotype or additionalforward mutations at the same site

best fit

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...GTGTCAGCCGCCGCGGTAATACCAGCTCCGCGAGTGGTCGGGGTGATTACTGGGCCTAAAGCG...Sulfolobus sulfotaricus

...GTGGCAGCCGCCGCGGTAATACCGGCGGCCCGAGTGGTGGCCGCTATTATTGGGCCTAAAGCG...Thermococcus celer

...GTGCCAGCAGCCGCGGTAATACCGACGGCCCGAGTGGTAGCCACTCTTATTGGGCCTAAAGCG...Methanococcus vannielii

...GTGCCAGCAGCCGCGGTAATACGTAGGGGGCAAGCGTTACCCGGATTTACTGGGCGTAAAGGG...Thermotoga maratima

...GTGCCAGCAGCCGCGGTAATACGGGAGAGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCG...Anacystis nidulans

...GTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCG...Escherichia coli

...GTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAG...corn

...GTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCAGTTAAAAAG...yeast

...GTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAG...human

Microbial ClassificationGram-variable 32% G+C genome thermophilic (85 C optimum) nonspore-forming anaerobic nonphotosyntheticnonmotilerod-shaped prokaryote grows on H2, CO2 and N2no special growth factors required

lack of a natural system. It does not permit the projection of properties of previously described organisms onto new ones that might be closely related, but not identical. it does not help us understand an organism that we have been unable to cultivate in the laboratory. it does not permit studies of the origin and evolution of cellular functions (e.g., drug resistance, aerobiosis orphotosynthesis), because there is no evolutionary (historical) framework.

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Applications

• Diagnostics• Ecosystem studies

– Surveys: specificity– Assessment– Present vs culture

Fluorescent in situ Hybridization (FISH)1. Design Group-specific DNA probe (2-20 bp)2. Tag probe w/ fluorescent moity (e.g. rhodamine)3. Collect environmental sample4. Fix sample to slide, permeabilize cells with ethanol5. Expose cells to fluorescent probe, wash6. View with appropriate fluorescent filter

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FISH Results

a) Phase-contrast b) Universal probe c) Eukarya probeFISH FISH

ProkaryotesUnique Cell membranesand Protein synthesis

Nucleus

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Microbial taxonomy

• In addition to phylogeneticstudies

• Other methods to identify and name microbial species

• Combination of genotypic and phenotypic traits

• Molecular taxonomy– Polyphasic: various methods

GC Range

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Genomic hybridization as a taxonomic tool

labeled

hybridization experiment

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Fatty acid methyl ester (FAME) analysis in bacterial identification

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same species16SDNA Hyb

different species16S DNA hyb

same species16S

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Bacterial species???

• Definition: determined by combination (polyphasic) of methods– Genetic: SSU and genomic hyb.

• Speciation– Ecotype from a give ecological niche undergoes an

adaptive mutation– Better fit to niche…followed by displacement of

previous population followed by several rounds of selection… separation

– Other route to speciation… gene acquisition