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Evolution, Classification, and Identification of Bacteria Early Life

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Evolution, Classification, and Identification of Bacteria Early Life Bio 280 Evolution, Identification, Classification Evolution, classification, and Early life on Earth identification of bacteria 0 Age of dinosaurs Early life on Earth Origin of metazoans 1 Naming microorganisms Origin of modern eukaryotes Time before 2 Classifying and identifying microorganisms present Origin of oxygenic phototrophs (billions of years) (cyanobacteria) Major groups of bacteria 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 1% Time before 2 present Origin of oxygenic phototrophs 0.1% (billions of (cyanobacteria) years) O2 (% in 3 atmos- phere) Planktothrix Origin of Life Anoxic 4 Lyngbya Formation of the earth http://www-cyanosite.bio.purdue.edu/ Early life on Earth Endosymbiosis -- the theory 0 Age of dinosaurs that __________________ Origin of metazoans 20% 1 and __________________ 10% Origin of modern eukaryotes are the descendants of Endosymbiosis 1% Time before 2 ancient prokaryotes from present Origin of oxygenic phototrophs 0.1% (billions of (cyanobacteria) O2 (% in years) atmosphere) the Domain “Bacteria” 3 Origin of Life Anoxic 4 Formation of the earth 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 è _________ similar to bacteria è Both have their own _______________, which are similar to those of bacteria (“70S” prokaryotic-type) Legionella è mitochondria have their own__________, which is similar to that of bacteria bacteria Newsome et al. The latest hypothesis: ______________ themselves may have once been Appl Environ Microbiol, May endosymbiotic bacteria 1998, p. 1688- 1693, Vol. 64, è Recently reported ( Nature, 7/26/01) that bacteria live inside other bacteria in the No. 5 mealybug (not yet known what they are doing or what one does for the other). è Margulis theorizes that the nucleus arose when one type of bacterium moved Giemsa stain showing the occurrence of bacteria in vacuoles of an amoeba inside another. 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. Naming microorganisms Binomial nomenclature Homo sapiens Escherichia coli Pseudomonas aeruginosa Text, Fig. 1.13 Classifying and identifying microorganisms Classification can be based on phenotypic Taxonomy - study of the classification, organization, and or genotypic characteristics or both naming of living things. One’s goal may be simply to organize and group by • phenotype -- observable _____________________ with no concern for natural _____________________ of an organism: evolutionary relationships. Often referred to (confusingly) as shape, size, metabolism, etc. simply “taxonomy”. • genotype -- the precise ________________ Alternatively, one’s goal may be to reconstruct natural, constitution of an organism ________________ relationships between organisms. Known as “phylogeny”. 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 Phylogenetics Isolation of bacterium from intestine of Obtain pure culture Gram Reaction warm-blooded animal 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 obligately anaerobic aerobe ferments lactose, producing does not ferment lactose acids and gas confirmatory tests: (positive: indole, methyl red, etc. Escherichia coli (negative: citrate, Voges-Proskaur, H2S 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: äDNA hybridization i.e. Put strand from one organism together with strand from another. How well do they ________________ to each other? äDNA sequencing Bio 280 Evolution, Identification, Classification Constructing a phylogenetic tree Calculating the from evolutionary distances X X X evolutionary X XX distance between X X X X DNA molecules The 16S rRNA gene: a most useful molecule Overall, not only is the primary sequence of 16S rRNA molecules for determining evolutionary relationships 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 Anabaena cylindrica (Cyanobacteria) Evolutionary phylogenetic and phenotypic differences in the organisms Arthrobacter globiformis (Gram-positive) relationships of themselves Rhodococcus rhodochrous (Gram-positive) representative Desulfovibrio desulfuricans (¶-Proteobacteria) bacteria based Rhodospirillum rubrum ( a -Proteobact.) Sphingomonas paucimobilis ( a -Proteobact.) on the Agrobacterium tumefaciens ( a -Proteobact.) sequences of Rhodoplanes roseus ( a -Proteobact.) their 16S rRNA GJ10 genes Aquabacter spiritensis ( a -Proteobact.) Azorhizobium caulinodans ( a -Proteobact.) Ancylobacter aquaticus ( a -Proteobact.) WDD1 Thiobacillus novellus ( a -Proteobact.) Burkholderia cepacia ( b-Proteobact.) Escherichia coli K12 ( g-Proteobact.) Acinetobacter calcoaceticus ( g-Proteobact.) Pseudomonas putida ( g-Proteobact.) Pseudomonas stutzeri ( g-Proteobact.) "Flavobacterium" lutescens ( g-Proteobact.) Pseudomonas balearicus ( g-Proteobact.) WDHI Ps.stutzeri ( g-Proteobact.) 0.1 Bio 280 Evolution, Identification, Classification Boletus satanas str. TDB-1000 (mushroom) [100] Boletus satanas str. TDB-1000 (mushroom) [100] Evolutionary Anabaena cylindrica (Cyanobacteria) Arthrobacter globiformis (Gram-positive) Scypha ciliata (sponge) [120] Scypha ciliata (sponge) [120] relationships of Rhodococcus rhodochrous (Gram-positive) representative Tripedalia cystophora (jellyfish) [124] Tripedalia cystophora (jellyfish) [124] Desulfovibrio desulfuricans (¶-Proteobacteria) Eukaryotes based Rhodospirillum rubrum ( a -Proteobact.) Styela plicata (sea squirt) [158] Styela plicata (sea squirt) [158] on the sequences of Sphingomonas paucimobilis ( a -Proteobact.) Agrobacterium tumefaciens ( a -Proteobact.) Alligator mississippiensis [143] Alligator mississippiensis [143] their 16S rRNA Rhodoplanes roseus ( a -Proteobact.) genes Gallus gallus (chicken) [145] Gallus gallus (chicken) [145] GJ10GJ10 Aquabacter spiritensis ( a -Proteobact.) Mus musculus (common or house mouse) [150] Mus musculus (common or house mouse) [150] Azorhizobium caulinodans ( a -Proteobact.) Homo sapiens (human) [149] Ancylobacter aquaticus ( a -Proteobact.) Homo sapiens (human) [149] WDD1 Rhinobatos lentiginosus (lesser sand shark) [135] Rhinobatos lentiginosus (lesser sand shark) [135] Thiobacillus novellus ( a -Proteobact.) Bufo valliceps (African toad) [142] Burkholderia cepacia ( b-Proteobact.) Bufo valliceps (African toad) [142] Escherichia coli K12 ( g-Proteobact.) Drosophila melanogaster (fruit fly) [161] Acinetobacter calcoaceticus ( g-Proteobact.) Drosophila melanogaster (fruit fly) [161] Pseudomonas putida ( g-Proteobact.) Crassostrea virginica (oyster) [176] Crassostrea virginica (oyster) [176] Pseudomonas stutzeri ( g-Proteobact.) Gyliauchen sp. (flatworm) [192] "Flavobacterium" lutescens ( g-Proteobact.) Gyliauchen sp. (flatworm) [192] Pseudomonas balearicus ( g-Proteobact.) Glycine max var. Wayne (soybean) [261] Glycine max var. Wayne (soybean) [261] WDHIWDH1 Ps.stutzeri ( g-Proteobact.) Paramecium tetraurelia (ciliate) [321] Paramecium tetraurelia (ciliate) [321] 0.1 0.1 0.1 Early life on Earth Three Domains of Life 0 Age of dinosaurs Origin of metazoans 20% 1 10% Origin of modern eukaryotes Endosymbiosis 1% Time before 2 present Origin of oxygenic phototrophs 0.1% (billions of (cyanobacteria) O (% in years) 2 Archaea atmosphere) Bacteria Nuclear line 3 ? (Eucarya) ARCHAEA EUCARYA Origin of Life Anoxic BACTERIA 4 Chemical evolution Formation of the earth The Archaea Major groups (kingdoms) of the (true) Bacteria 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 high- temperature 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..
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