1. Microbiology: Principles and Explorations Sixth Edition Chapter 9: An Introduction to Taxonomy: The Bacteria Copyright © 2005 by John Wiley & Sons, Inc. Jacquelyn G. Black

2. Carolus Linnaeus (1707-1778)

3. Taxonomy The science of classification Provides an orderly basis for the naming of organisms Places organisms into a category or taxon (plural: taxa) Carolus Linnaeus: 18 th century Swedish botanist; the Father of Taxonomy

4. Binomial Nomenclature The system used to name all living things The first name designates the genus (plural: genera) and its first letter is capitalized and italized or underlined The second name is the specific epithet الصفة الخاصة, and it is not capitalized but it’s either italized or underlined Together the genus and specific epithet identify the species

5. The Meaning of the Names of Some Microorganisms Escherichia coli : Named after Theodore Escherich in 1888; found in the colon (it’s a gram negative bacteria) Entamoeba histolytica : Ent, intestinal; amoebae, shape/movement; histo, tissue; lytic, lysing or digesting tissue Strain: A subgroup of a species with one or more characteristics that distinguish it from other members of the same species Escherichia coli 015H7 : strain of Escherichia coli holds the Escherichia coli properties in addition to other properties make it categorized in a strain

6. You don’t have to memorize this table but look at it and know how to name the microorganism

7. Classification of Human Dog Wolf and a Bacterium

8. Using a Taxonomic Key Dichotomous Key: A commonly used key to identify organisms. Has paired statements describing characteristics of organisms. Figure 9.4

9. Dichotomous Key for Classifying U.S. Coins

10. Dichotomous Key for Classifying Major Bacterial Groups

11. To identify the microorganism we ask about It’s Microscopic morphology (shape, motility) biochemical properties (gram reaction, aerobic or non-aerobic)

12. The Five Kingdom Classification Contains the bacteria

13. Notes : The unicellular fungi is yeast The cell wall of fungi is formed of chitin The bacteria that does not contain cell wall is mycoplasma Algae (protesta) is photosynthetic The method of asexual reproduction in fungi is the exospores

14. Kingdom Monera The kingdom Monera is also called the kingdom Prokaryotae, consists of all prokaryotic organisms, including the eubacteria (‘‘true bacteria’’), the cyanobacteria, and the archaeobacteria All monerans are unicellular; they lack true nuclei and generally lack membrane-enclosed organelles Some groups of bacteria, such as Rickettsiae and Chlamydiae, contain rather unusual organisms. These two groups are obligate intracellular parasites; that is, they can only grow inside living cells.

15. Some Typical Monerans

16. Monera : prokaryotic (contains the bacteria) Protestaa : eukaryotic (contains mo like plasmodium, amoeba, pramesium) Fungi : eukaryotic

17. Archaeobacteria— Extremophiles able to exploit the unusual habitat of a “black smoker” vent

18. Some Typical Protists

19. Protista are eukaryotic. Most are unicellular, but some are organized into colonies Protests are classifies based on their motility Paramecium moves by cilia Amoeba moves by pseudopodium Trypanosoma moves by flagella it causes sleeping sickness Plasmodium is non motile it causes malaria

20. Some Typical Fungi Eukaryotic Kingdome

21. Kingdom Animalia

22. Ticks, mites, lice, and fleas are arthropods (animalia kingdome) that live on their hosts for at least part of their lives. Ticks, lice, fleas, and mosquitoes can spread infectious microorganisms from their bodies to those of humans or other animals

23. Certain helminths (worms) areparasitic in humans and other animals.Helminths include flukes, tapeworms,and roundworms, which live inside the body of their host. They also include leeches, which live on the surface of their hosts. Microbiologists often need to identify both microscopic and macroscopic forms of helminths

24. Proposed Major Evolutionary Lines of Descent

25. Theory About Three Domains

26. The Three Domains A new category even higher than kingdom Archaea Bacteria Eukarya Prolaryotes Eukarotes

27. Bacteria vs. Archaea Both have cell walls, however, archaea lack peptidoglycan Bacteria have fatty acids present in their membranes; archaea have isoprenes Bacteria lack histones ; archaea have histone- like proteins associated with the chromosome

28. BERGEY’S MANUAL The accepted reference on the identification of microorganisms is commonly referred to as Bergey’s Manual.

29. Criteria for classifying Bacteria Most macroscopic organisms can preliminarily be classified according to observable structural characteristics but many of the bacteria have similar structures Separating the bacteria according to cell shape, size, and arrangement does not produce a very useful classification system Nor does the presence of specific structures such as flagella, endospores, or capsules

30. the Gram stain, were among the first properties other than morphology to be used to classify bacteria. Other properties now in use include features related to growth, nutritional requirements, physiology, biochemistry, genetics, and molecular analysis. These features include properties of DNA and proteins

32. Assume that you are given an unknown bacteria and you are about to classify it.. The steps are : –Isolate this bacteria in a pure culture –Grow the bacteria –Stain it (gram staining) –Test it under the microscope ( gives the morphology) –Biochemical testing –Molecular testing

33. Biochemical Tests for ID of Bacteria depends on the presence of certain enzymes in the microorganisms

34. Accordingly. When a certain microorganism is classified, then it’s given a certain name Spirochete : gram negative bacteria, helical, moves by axial filaments (e.g. Treponema pallidum)

35. Please. It’s very very important to refer to table 9.7

36. Categories of Viruses

37. Stromatolite Mats

38. Fossil Stromatolite Cross Section

39. Filamentous Cyanobacteria-- Paleolyngbya

40. DNA Sequencer

41. DNA Hybridization

42. SDS PAGE SDS PAGE stands for Sodium Dodecyl Sulfate Poly Acrylamide Gel Electrophoreses method, which separates proteins on the basis of molecular size So, SDS PAGE depends on the proteins while Hybridization depends on the DNA

43. Separation of Proteins

49. Phage Typing

50. David H. Bergey (1860-1937)