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Evolution, classification, and identification of bacteria Early life on Earth Naming microorganisms Classifying and identifying microorganisms Major groups of bacteria Early life on Earth 0 Age of dinosaurs 1 Origin of metazoans Origin of modern eukaryotes Time before present (billions of years) 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) 3 Origin of Life 4 Formation of the earth 0.1% O2 (% in atmosphere) Anoxic ______________ Planktothrix Lyngbya http://www-cyanosite.bio.purdue.edu/ Early life on Earth 0 Age of dinosaurs Origin of metazoans 20% 1 10% Origin of modern eukaryotes Time before present (billions of years) 2 Endosymbiosis Origin of oxygenic phototrophs (cyanobacteria) 1% 0.1% O2 (% in atmosphere) 3 Origin of Life 4 Formation of the earth Anoxic Endosymbiosis -- the theory that __________________ and __________________ are the descendants of ancient prokaryotes from the Domain “Bacteria” An example of a new, developing endosymbiosis? Legionella bacteria Newsome et al. Appl Environ Microbiol, May 1998, p. 16881693, Vol. 64, No. 5 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. The Endosymbiotic Theory Developed mainly by Lynn Margulis (1970s) Strong evidence supports the endosymbiotic origin of mitochondria and chloroplasts _________ similar to bacteria Both have their own _______________, which are similar to those of bacteria (“70S” prokaryotic-type) mitochondria have their own__________, which is similar to that of bacteria The latest hypothesis: ______________ themselves may have once been endosymbiotic bacteria 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 simply “taxonomy”. Alternatively, one’s goal may be to reconstruct natural, ________________ relationships between organisms. Known as “phylogeny”. Classification can be based on phenotypic or genotypic characteristics or both • phenotype -- observable _____________________ of an organism: shape, size, metabolism, etc. • genotype -- the precise ________________ constitution of an organism 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 Gram Reaction Gram negative rod-shaped facultative aerobe ferments lactose, producing acids and gas Gram positive not rod-shaped obligately anaerobic does not ferment lactose confirmatory tests: (positive: indole, methyl red, etc. (negative: citrate, Voges-Proskaur, H2S Escherichia coli Phylogenetics Phylogeny -- The ordering of species into higher ___________ (classification categories) and the construction of evolutionary trees, all based on evolutionary (natural) relationships. http://heg-school.awl.com/bc/companion/cmr2e/activity/AL/AL09b.htm Phylogenetics 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: DNA hybridization i.e. Put strand from one organism together with strand from another. How well do they ________________ to each other? DNA sequencing X X X X X X X X X X Calculating the evolutionary distance between DNA molecules Constructing a phylogenetic tree from evolutionary distances The 16S rRNA gene: a most useful molecule for determining evolutionary relationships 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) Overall, not only is the primary sequence of 16S rRNA molecules highly conserved, but the secondary structure is, as well But there are differences, and these differences represent phylogenetic and phenotypic differences in the organisms themselves Anabaena cylindrica (Cyanobacteria) Arthrobacter globiformis (Gram-positive) Rhodococcus rhodochrous (Gram-positive) Desulfovibrio desulfuricans (Ž-Proteobacteria) Rhodospirillum rubrum ( -Proteobact.) Sphingomonas paucimobilis ( -Proteobact.) Agrobacterium tumefaciens ( -Proteobact.) -Proteobact.) Rhodoplanes roseus ( GJ10 Aquabacter spiritens is ( Azorhizobium caulinodans ( -Proteobact.) -Proteobact.) Ancylobacter aquaticus ( WDD1 -Proteobact.) Thiobacillus novellus ( -Proteobact.) Burkholderia cepacia ( -Proteobact.) -Proteobact.) Escherichia coli K12 ( Acinetobacter calcoaceticus ( Pseudomonas putida ( -Proteobact.) -Proteobact.) Pseudomonas s tutzeri ( -Proteobact.) "Flavobacterium" lutescens ( -Proteobact.) Pseudomonas balearicus ( WDHI Ps.stutzeri ( -Proteobact.) 0.1 Evolutionary relationships of representative bacteria based on the sequences of their 16S rRNA genes -Proteobact.) Boletus satanas str. TDB-1000 (mushroom) [100] Scypha ciliata (sponge) [120] Tripedalia cystophora (jellyfish) [124] Styela plicata (sea squirt) [158] Alligator mississippiensis [143] Gallus gallus (chicken) [145] Evolutionary relationships of representative Eukaryotes based on the sequences of their 16S rRNA genes Mus musculus (common or house mouse) [150] Homo sapiens (human) [149] Rhinobatos lentiginosus (lesser sand shark) [135] Bufo valliceps (African toad) [142] Drosophila melanogaster (fruit fly) [161] Crassostrea virginica (oyster) [176] Gyliauchen sp. (flatworm) [192] Glycine max var. Wayne (soybean) [261] Paramecium tetraurelia (ciliate) [321] 0.1 Boletus satanas str. TDB-1000 (mushroom) [100] Anabaena cylindrica (Cyanobacteria) Arthrobacter globiformis (Gram-positive) Scypha ciliata (sponge) [120] Rhodococcus rhodochrous (Gram-positive) Desulfovibrio desulfuricans (Ž-Proteobacteria) Tripedalia cystophora (jellyfish) [124] Rhodospirillum rubrum ( -Proteobact.) Styela plicata (sea squirt) [158] Sphingomonas paucimobilis ( -Proteobact.) Agrobacterium tumefaciens ( -Proteobact.) Alligator mississippiensis [143] Rhodoplanes roseus ( -Proteobact.) GJ10GJ10 Gallus gallus (chicken) [145] Aquabacter spiritensis ( -Proteobact.) Mus musculus (common or house mouse) [150] Azorhizobium caulinodans ( -Proteobact.) Ancylobacter aquaticus ( -Proteobact.) WDD1 Homo sapiens (human) [149] Rhinobatos lentiginosus (lesser sand shark) [135] Thiobacillus novellus ( -Proteobact.) Burkholderia cepacia ( -Proteobact.) Bufo valliceps (African toad) [142] Escherichia coli K12 ( -Proteobact.) Drosophila melanogaster (fruit fly) [161] Acinetobacter calcoaceticus ( -Proteobact.) Pseudomonas putida ( -Proteobact.) Crassostrea virginica (oyster) [176] Pseudomonas stutzeri ( -Proteobact.) "Flavobacterium" lutescens ( -Proteobact.) Gyliauchen sp. (flatworm) [192] Pseudomonas balearicus ( -Proteobact.) WDHI WDH1 Glycine max var. Wayne (soybean) [261] Ps.stutzeri ( -Proteobact.) 0.1 Paramecium tetraurelia (ciliate) [321] 0.1 Early life on Earth 0 Age of dinosaurs 20% Origin of metazoans 1 10% Origin of modern eukaryotes Endosymbiosis Time before present (billions of years) 1% 2 0.1% Origin of oxygenic phototrophs (cyanobacteria) Bacteria 3 Archaea ? Origin of Life 4 Chemical evolution Formation of the earth O2 (% in atmosphere) Nuclear line (Eucarya) Anoxic Three Domains of Life BACTERIA ARCHAEA EUCARYA 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