Evolution, classification, and identification of bacteria

1. Evolution, classification, and identification of bacteria • Early life on Earth • Naming microorganisms • Classifying and identifying microorganisms • Major groups of bacteria

2. Early life on Earth 0 Age of dinosaurs Origin of metazoans 1 Origin of modern eukaryotes 2 Time before present (billions of years) Origin of oxygenic phototrophs (cyanobacteria) 3 Origin of Life 4 __________ ___________ Formation of the earth

3. 20% 10% 1% Anoxic Early life on Earth 0 Age of dinosaurs Origin of metazoans 1 Origin of modern eukaryotes 2 Time before present (billions of years) 0.1% Origin of oxygenic phototrophs (cyanobacteria) O2 (% in atmos-phere) 3 Origin of Life 4 Formation of the earth

4. ______________ Planktothrix Lyngbya http://www-cyanosite.bio.purdue.edu/

5. Early life on Earth 0 Age of dinosaurs 20% Origin of metazoans 1 10% Origin of modern eukaryotes Endosymbiosis 1% 2 Time before present (billions of years) 0.1% Origin of oxygenic phototrophs (cyanobacteria) O2 (% in atmosphere) 3 Anoxic Origin of Life 4 Formation of the earth

6. Endosymbiosis -- the theory that __________________ and __________________ are the descendants of ancient prokaryotes from the Domain “Bacteria”

7. An example of a new, developing endosymbiosis? Legionella bacteria 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. Newsome et al. Appl Environ Microbiol, May 1998, p. 1688-1693, Vol. 64, No. 5

8. 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.

9. Naming microorganisms • Binomial nomenclature • Homo sapiens • Escherichia coli • Pseudomonas aeruginosa

10. Text, Fig. 1.13

11. 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”.

12. 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

13. Classification based on phenotype

14. 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

15. Isolation of bacterium from intestine of warm-blooded animal Gram negative rod-shaped facultative aerobe ferments lactose, producing acids and gas confirmatory tests: (positive: indole, methyl red, etc. (negative: citrate, Voges-Proskaur, H2S Example of methods to be used for identification of a newly isolated enteric bacterium Obtain pure culture Gram Reaction Gram positive not rod-shaped obligately anaerobic does not ferment lactose Escherichia coli

16. 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

17. Phylogenetics

18. 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

19. Calculating the evolutionary distance between DNA molecules X X X X X X X X X X

20. Constructing a phylogenetic tree from evolutionary distances

21. 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)

22. Overall, not only is the primary sequence of 16S rRNA molecules highly conserved, but the secondary structure is, as well

23. But there are differences, and these differences represent phylogenetic and phenotypic differences in the organisms themselves

24. Evolutionary relationships of representative bacteria based on the sequences of their 16S rRNA genes

25. Evolutionary relationships of representative Eukaryotes based on the sequences of their 16S rRNA genes

26. GJ10 WDH1

27. Archaea Bacteria Nuclear line (Eucarya) Early life on Earth 0 Age of dinosaurs 20% Origin of metazoans 1 10% Origin of modern eukaryotes Endosymbiosis 1% 2 Time before present (billions of years) 0.1% Origin of oxygenic phototrophs (cyanobacteria) O2 (% in atmosphere) ? 3 Anoxic Origin of Life 4 Chemical evolution Formation of the earth

28. Three Domains of Life EUCARYA ARCHAEA BACTERIA

29. 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 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.

30. Major groups (kingdoms) of the (true) Bacteria