Unformatted text preview: Chapter 19: Chapter 19: Microbial Taxonomy, Evolution & Diversity Recognition of Microbes Recognition of Microbes Dates back only about 300 years Small size Boring morphology/ultrastructure few shapes Most microbes defy cultivation Most live as part of a community, not pure cultures What defines species? What defines species? Higher organisms: interbreeding natural populations Bacterial species: Collection of strains that share many stable properties and differ significantly from other groups Strains may possess slight differences: Biovars, morphovars, serovars Taxonomy (Systematics) Taxonomy (Systematics) Consists of: Classification (arranging into groups) Nomenclature (what to name it) Identification (distinguishing features) Ensures that scientists around the world are referring to same entity Organizes vast amounts of information Phenetic (Natural) Classification (Linnaeus) Taxonomic Classification Taxonomic Classification Systems Reflects similar biological nature of organisms Properties dictate groupings Example: all mammals selfregulating temperature hair mammary glands in the female Phylogenetic Classification Reflects evolutionary relationships Followed “On the Origin of Species” in 1859 Genetic basis ribosomal RNA relatedness since fossil record is limited for prokaryotes Phenetic vs. Phylogentic Phenetic vs. Phylogentic Classification Grouped by common traits Example: Home Entertainment Grouped by shared ancestor Example: Video Game Systems Big screen TV Stereo Game systems Pong Atari Xbox Evolution of Taxonomy Evolution of Taxonomy 2 Kingdoms Plants & animals 3 Kingdoms (18661957) Plants, animals, & protists Bacteria were thought to be unicellular plants 5 Kingdoms (until 1970’s) (Whittaker) Plants, animals, protists, fungi, bacteria Note that 4/5 kingdoms were thought to comprise eukaryotes Evolution of Taxonomy Evolution of Taxonomy 2 Kingdoms Plants & animals 3 Kingdoms (18661957) Plants, animals, & protists Bacteria were thought to be unicellular plants 5 Kingdoms (until 1970’s) (Whittaker) Plants, animals, protists, fungi, bacteria Note that 4/5 kingdoms were thought to comprise eukaryotes Evolution of Taxonomy Evolution of Taxonomy Evolution of Taxonomy Evolution of Taxonomy 3 Domains (Current) (Woese) Prokaryotes change from 1/5 of kingdoms to 2/3 of domains Our understanding of molecular biology and biochemistry allows us to look at finer details: Genome sequence, protein sequence, etc. Ribosomal RNA (rRNA) Ribosomal RNA (rRNA) Prokaryotes and eukaryotes have different sized ribosomes Prokaryotic 70S ribosomes (vs. 80S in eukaryotes) 50S subunit 23S and 5S rRNAs 30S subunit 16S rRNA Why rRNA Sequencing? Why rRNA Sequencing? rRNA is universally present in all living organisms rRNA function is identical in all organisms Some rRNA sequences are highly conserved (stable), while others are more variable Distantly related species can be compared using stable sequences Closely related species can be compared using variable sequences Serves as an evolutionary clock to determine relatedness rRNA Comparison rRNA Comparison Bacteria (16S) Archaea (16S) Eukarya (18S) rRNA Sequencing rRNA Sequencing Sequences are aligned so similar (homologous) regions match up = common origins Calculate the number of positions that vary between the sequences Produces an indication of “evolutionary distance” from one organism to another Like organisms are clustered together to produce phylogenetic trees or dendrograms of evolution Rooted trees establish lineages Unrooted trees establish relationships, but not lineages rRNA Sequencing rRNA Sequencing
Top: Unrooted tree 1. A is more closely related to C than it is to either to B or D Bottom: Rooted tree 1. A is more closely related to C than it is to either B or D 1. C diverged from A more recently than A and B diverged from one another. Whole Genome Sequencing Whole Genome Sequencing Shown many genes are shared between the 3 Domains Indicates evolutionary relationship with one another (i.e. endosymbiont theory) Also shown a great number of genes unique to Archaea alone Confirming distinction as a separate Domain from Bacteria Originally classified bacteria primarily on the basis of natural traits such as: Bergey’s Manual of Systematic Bergey’s Manual of Systematic Bacteriology
C, N, and energy sources Cell wall chemistry Motility Cultural requirements & tolerances Storage inclusions Sensitivity to metabolic inhibitors & antibiotics G+C content (DNA base ratios) New edition will include a polyphasic approach to classification: biochemical properties, morphology, protein and gene sequneces Major Groups of Prokaryotes Major Groups of Prokaryotes
Bacteria Planctomycetes Green sulfur bacteria Green nonsulfur bacteria Spirochetes Cyanobacteria Flavobacteria Chlamydia Gram + bacteria & Mycoplasmas Gram – bacteria Deinococci Archaea Methanogens Methanogenhalophiles Extreme halophiles Extreme thermophiles Major Groups of Each Domain Major Groups of Each Domain Endosymbiotic Evolution? Endosymbiotic Evolution? Mitochondria and chloroplasts likely were originally prokaryotic symbiotes of eukaryotic partners Supporting evidence: Obligately intracellular bacteria like Agrobacterium and Rickettsia show an evolutionary link with mitochondrial 16S rRNA Chloroplasts have cyanobacteria (Prochloron) which are symbiotic with many marine invertebrates in their phylogenetic trees The more we learn and look… The more we learn and look… New species in new environments: Hydrothermal vents Mars rocks & Venusian atmosphere Deep in the earth’s sediments Polar seas and glaciers ...
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- Fall '09
- Bacteria, 16s rrna, rRNA Comparison rRNA, rRNA Sequencing, 16S rRNA Chloroplasts