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Bio 280 Evolution, Identification, Classification Evolution, classification, and identification of bacteria Early life on Earth 0 Age of dinosaurs Early life on Earth 1 Naming microorganisms Origin of metazoans Origin of modern eukaryotes Time before present (billions of years) Classifying and identifying microorganisms Major groups of bacteria 2 Origin of oxygenic phototrophs (cyanobacteria) 3 Origin of Life 4 __________ ___________ Formation of the earth ______________ Early life on Earth 0 Age of dinosaurs Origin of metazoans 20% 1 10% Origin of modern eukaryotes Time before present (billions of years) 1% 2 Origin of oxygenic phototrophs (cyanobacteria) 0.1% O2 (% in atmosphere) 3 Origin of Life Anoxic Planktothrix 4 Lyngbya Formation of the earth http://www-cyanosite.bio.purdue.edu/ Early life on Earth Endosymbiosis -- the theory 0 Age of dinosaurs Origin of metazoans that __________________ 20% and __________________ 1 10% are the descendants of Origin of modern eukaryotes Time before present (billions of years) 2 Endosymbiosis Origin of oxygenic phototrophs (cyanobacteria) 1% ancient prokaryotes from 0.1% O 2 (% in atmosphere) 3 Origin of Life 4 Formation of the earth Anoxic the Domain “Bacteria” Bio 280 Evolution, Identification, Classification An example of a new, developing endosymbiosis? The Endosymbiotic Theory Developed mainly by Lynn Margulis (1970s) Strong evidence supports the endosymbiotic origin of mitochondria and chloroplasts Legionella bacteria Newsome et al. Appl Environ Microbiol, May 1998, p. 16881693, Vol. 64, No. 5 è _________ similar to bacteria è Both have their own _______________, which are similar to those of bacteria (“70S” prokaryotic-type) è mitochondria have their own__________, which is similar to that of bacteria The latest hypothesis: ______________ themselves may have once been endosymbiotic bacteria è è Giemsa stain showing the occurrence of bacteria in vacuoles of an amoeba after 24 and 48 h of incubation at 25°C. Characteristic morphological features of the amoeba host cell, such as the nucleus (arrowhead), were intact. Bar, 20 µm. Recently reported ( Nature, 7/26/01) that bacteria live inside other bacteria in the mealybug (not yet known what they are doing or what one does for the other). Margulis theorizes that the nucleus arose when one type of bacterium moved inside another. Naming microorganisms Binomial nomenclature Homo sapiens Escherichia coli Pseudomonas aeruginosa Text, Fig. 1.13 Classifying and identifying microorganisms Taxonomy - study of the classification, organization, and naming of living things. One’s goal may be simply to organize and group by _____________________ with no concern for natural evolutionary relationships. Often referred to (confusingly) as Classification can be based on phenotypic or genotypic characteristics or both • phenotype -- observable _____________________ of an organism: shape, size, metabolism, etc. simply “taxonomy”. Alternatively, one’s goal may be to reconstruct natural, ________________ relationships between organisms. Known as “phylogeny”. • genotype -- the precise ________________ constitution of an organism Bio 280 Evolution, Identification, Classification Classification based on phenotype Classification based on phenotype Examples of phenotypic characteristics used to differentiate prokaryotes: Gram reaction, fermentation of sugar, cell morphology, growth on a specific compound, etc. These characteristics tell us little or nothing about the true evolutionary relationships between organisms. They are used simply (and very usefully) as a method for ___________________ them. Identification methods are usually based on such characteristics Example of methods to be used for identification of a newly isolated enteric bacterium Isolation of bacterium from intestine of warm-blooded animal Obtain pure culture Phylogenetics Gram Reaction Gram negative Gram positive Phylogeny -- The ordering of species into higher ___________ (classification categories) and the rod-shaped not rod-shaped construction of evolutionary trees, all based on evolutionary (natural) relationships. facultative aerobe ferments lactose, producing acids and gas obligately anaerobic does not ferment lactose confirmatory tests: (positive: indole, methyl red, etc. (negative: citrate, Voges-Proskaur, H2S Phylogenetics Escherichia coli http://heg-school.awl.com/bc/companion/cmr2e/activity/AL/AL09b.htm How similar are two organisms at the level of the DNA? 2 primary methods for determining this. In both, the same DNA___________________ from two organisms is compared: ä DNA hybridization i.e. Put strand from one organism together with strand from another. How well do they ________________ to each other? ä DNA sequencing Bio 280 Evolution, Identification, Classification X X X X X X XX X X Constructing a phylogenetic tree from evolutionary distances Calculating the evolutionary distance between DNA molecules The 16S rRNA gene: a most useful molecule for determining evolutionary relationships Overall, not only is the primary sequence of 16S rRNA molecules highly conserved, but the secondary structure is, as well Advantages • Every organism has it (eukaryotes have 18S rRNA, which is related) • It’s “highly conserved” (i.e. it doesn’t ________________ quickly) • There are, however, regions which evolve more _________________ than others It doesn’t get transferred horizontally (or at least transfer is very rare) • But there are differences, and these differences represent phylogenetic and phenotypic differences in the organisms themselves Evolutionary relationships of representative bacteria based on the sequences of their 16S rRNA genes Anabaena cylindrica (Cyanobacteria) Arthrobacter globiformis (Gram-positive) Rhodococcus rhodochrous (Gram-positive) Desulfovibrio desulfuricans (∂-Proteobacteria) Rhodospirillum rubrum ( α-Proteobact.) Sphingomonas paucimobilis ( α-Proteobact.) Agrobacterium tumefaciens ( α-Proteobact.) Rhodoplanes roseus ( GJ10 α-Proteobact.) Aquabacter spiritensis ( α-Proteobact.) Azorhizobium caulinodans ( α-Proteobact.) Ancylobacter aquaticus ( WDD1 α-Proteobact.) Thiobacillus novellus ( α-Proteobact.) Burkholderia cepacia ( β-Proteobact.) Escherichia coli K12 ( γ-Proteobact.) Acinetobacter calcoaceticus ( γ-Proteobact.) Pseudomonas putida ( γ-Proteobact.) Pseudomonas stutzeri ( γ-Proteobact.) "Flavobacterium" lutescens ( γ-Proteobact.) Pseudomonas balearicus ( WDHI Ps.stutzeri ( γ-Proteobact.) 0.1 γ-Proteobact.) Bio 280 Evolution, Identification, Classification Boletus satanas str. TDB-1000 (mushroom) [100] Scypha ciliata (sponge) [120] Tripedalia cystophora (jellyfish) [124] Styela plicata (sea squirt) [158] Alligator mississippiensis [143] Boletus satanas str. TDB-1000 (mushroom) [100] Anabaena cylindrica (Cyanobacteria) Evolutionary relationships of representative Eukaryotes based on the sequences of their 16S rRNA genes Arthrobacter globiformis (Gram-positive) Scypha ciliata (sponge) [120] Rhodococcus rhodochrous (Gram-positive) Tripedalia cystophora (jellyfish) [124] Desulfovibrio desulfuricans (∂-Proteobacteria) Rhodospirillum rubrum ( α-Proteobact.) Styela plicata (sea squirt) [158] Sphingomonas paucimobilis ( α-Proteobact.) Agrobacterium tumefaciens ( α-Proteobact.) Alligator mississippiensis [143] Rhodoplanes roseus ( α-Proteobact.) GJ10GJ10 Gallus gallus (chicken) [145] Gallus gallus (chicken) [145] Aquabacter spiritensis ( α-Proteobact.) Mus musculus (common or house mouse) [150] Mus musculus (common or house mouse) [150] Azorhizobium caulinodans ( α-Proteobact.) Ancylobacter aquaticus ( α-Proteobact.) WDD1 Homo sapiens (human) [149] Homo sapiens (human) [149] Rhinobatos lentiginosus (lesser sand shark) [135] Thiobacillus novellus ( α-Proteobact.) Rhinobatos lentiginosus (lesser sand shark) [135] Burkholderia cepacia ( β-Proteobact.) Bufo valliceps (African toad) [142] Bufo valliceps (African toad) [142] Escherichia coli K12 ( γ-Proteobact.) Acinetobacter calcoaceticus ( γ-Proteobact.) Drosophila melanogaster (fruit fly) [161] Drosophila melanogaster (fruit fly) [161] Pseudomonas putida ( γ-Proteobact.) Crassostrea virginica (oyster) [176] Crassostrea virginica (oyster) [176] Pseudomonas stutzeri ( γ-Proteobact.) "Flavobacterium" lutescens ( γ-Proteobact.) Gyliauchen sp. (flatworm) [192] Gyliauchen sp. (flatworm) [192] Pseudomonas balearicus ( γ-Proteobact.) WDHI WDH1 Glycine max var. Wayne (soybean) [261] Glycine max var. Wayne (soybean) [261] Ps.stutzeri ( γ-Proteobact.) Paramecium tetraurelia (ciliate) [321] 0.1 0.1 Early life on Earth Paramecium tetraurelia (ciliate) [321] 0.1 Three Domains of Life 0 Age of dinosaurs 20% Origin of metazoans 1 10% Origin of modern eukaryotes Endosymbiosis Time before present (billions of years) 1% 2 Origin of oxygenic phototrophs (cyanobacteria) Bacteria 3 Archaea ? 0.1% O 2 (% in atmosphere) Nuclear line (Eucarya) Origin of Life 4 Anoxic BACTERIA ARCHAEA EUCARYA Chemical evolution Formation of the earth The Archaea January 24, 2001 New Group of Microorganisms Discovered in the Open Sea Archaea, one of three separate domains of life on our planet, were undiscovered until 1970. Since then, they had been found mostly in extreme environments such as hightemperature volcanic vents on the ocean floor, continental hot springs and fumeroles, and highly salty or acidic waters. Now, scientists funded by the National Science Foundation (NSF) have found unexpected, astounding numbers of archaea living in Earth's largest biome, the open sea. The researchers--David Karl and Markus Karner of the University of Hawaii, and Edward DeLong of the Monterey Bay Aquarium Research Institute--have published a paper in this week's issue of the journal Nature on their discovery: "Archaeal dominance in the mesopelagic zone of the Pacific Ocean." The concentration of archaea in their study leads the scientists to conclude that archaea are "a large percentage of the biomass of the open ocean," says Karl. "These organisms could make up 50 percent of life in the open sea." The research is the first to note their numerical abundance. Major groups (kingdoms) of the (true) Bacteria