MCB100 Introductory Microbiology September 21, 2018

1. MCB100 Introductory Microbiology September 21, 2018

2. MCB100 Exam 1 Fall 2018 Friday, September 28, 2018 2:00 – 2:50 pm Covers: chapters 1, 2, 4, 3 & 6 (Chapter 5 is not on exam 1!) Place: If your last name starts with A – M: please take the exam in room 2079 NHB If your last name starts with N – Z: please take the exam in room 100 Noyes Lab Review Session: 7:00 – 7:50 pm, Wednesday, Sept. 26 Place: Room 161 Noyes Lab

3. MCB100 Exam 1 Fall 2018 Practice Exam 1 has been updated. To find the link to the practice exam, go to:www.life.illinois.edu/mcb/100 - Click on: “Exam Information” - Scroll down to find the link to the practice exam. (It downloads as a MS Word Document.)

4. Do you have a conflict for Exam 1, which is scheduled for 2 – 2:50 pm on Friday 9/28/2018? Contact Dr. Chapman by e-mail: kenchap.life.illinois.edu What is the nature of your conflict? The conflict exam will be given at 3 pm on Thursday, 9/27/18 in room 242 Burrill Hall. Does that fit into your schedule? (It's possible to do it earlier in the day but it's more difficult to find a quiet room where a student can take an exam when the lab is being used by a class.)Conflict exams must be taken before the rest of the class takes the test. Sick on the day of the exam? Don’t come and fail the test because you feel so bad you can’t think. See a doctor and take care of your health. Also get an excuse note. There are no make-up exams in MCB100, but in the event of illness or unexpected circumstances your score can be prorated. If you take a test, your score will be counted as it is. You can’t take a test and later decide you’d rather have your score prorated.

5. What type of microscopy was used to acquire this image? A. Bright Field Microscopy B. Immunofluorescence Microscopy C. Dark Field Microscopy D. Transmission Electron Microscopy E. Scanning Electron Microscopy

6. Classification of Living Creatures

7. Classification of Living Creatures The Linnean Taxonomic System 1735 Two Kingdoms Plants Animals

8. Classification of Living Organisms The animal shown in the picture is an example of Canis domesticus. This species is in the class Mammalia. Which of the following questions can you answer just by knowing that the animal is a mammal? Choose the best answer. A. How many chambers does this animal's heart have? (1, 2, 3, 4, more?) B. Does this animal typically maintain a fairly constant body temperature? (yes, no?) C. How many cervical vertebrae does this animal have? (less than 7, 7, more than 7?) D. If you look at an erythrocyte from this animal will you see a nucleus? (yes, no?) E. You can answer all of the above questions by knowing that the animal is a mammal.

9. Seven Layers of Classification in the Linnaean System Most General - Kingdom - Phylum - Class - Order - Family - Genus - Species Most Specific Species: A group of organisms that are capable of mating and producing viable offspring. Genus: A group of related species, several distinct species that share many common traits and from an evolutionary standpoint are closely related with a relatively recent common ancestor Family: A group of closely related genera. Binomial nomenclature (Two names) Genus, specific epithet Examples:Canis lupus: Gray wolf Canis latrans: Coyote Canis domesticus: Dog Canis aureus: Golden jackal Kingdom: Animalia Phylum: Chordata Class: Mammalia Order: Carnivora Family: Canidae Bacteria in the genus: Bacillus Bacillus stearothermophilus Bacillus thuringiensisBacillus anthracis Bacillus subtilis Bacillus cereus All species in the genus Bacillus are Gram positive rods that can produce heat-resistant endospores and grow aerobically.

11. Inadequacies of the Linnean System - Fungi are not plants. They don’t use photosynthesis, they need organic nutrients, cell walls are different. - Euglena are hard to classify. They use photosynthesis, but don’t have cell walls and they are motile. - Bacterial cells are very different from plant cells. They don’t have chloroplasts nor even a proper nucleus.

12. Whittaker System 1969 Five Kingdoms

13. Modern Molecular Phylogeny Phylogeny vs. Taxonomy, the Philosophical Distinction Taxonomy (taxa- = to gather): A taxa is a group of organisms lumped together because they share certain morphological traits Phylogeny (gen- = origins, beginnings): The grouping of organisms is based on their genetic relationships Basis of Comparison of Species: Molecular Phylogeny vs. Classical Taxonomy Molecular Traits vs. Morphological Traits Conserved Gene vs. Arbitrarily Selected Sequences Observable Features

14. The Three Domains of Life Woese, 1978 Based on 16S rRNA Sequence Comparisons

18. What is the big difference between a classical taxonomic scheme and a modern phylogenetic scheme In a taxonomic scheme a genus is a group of species that are similar to each other. (morphology) In a phylogenetic scheme a genus is a group of species that are closely related to each other. (genetics and evolution)

19. Molecular Phylogeny of Various Eukaryotic Organisms From: Wiser @ www.tulane.edu

20. Classification and Identification of Microorganisms Mid 1700s 1950s 1978

21. Taxonomy and Phylogeny Which one of the following statements about taxonomic and phylogenetic schemes is FALSE? A. In the classical Linnean taxonomic scheme species were grouped together into genera based on shared morphological traits. B. A phylogenetic scheme attempts to group species based on genetic relationships and common ancestors. C. The classical Linnean taxonomic scheme was based on the theory of evolution. D. Sometimes scientists will agree to change the accepted name of a species as they learn more about it. E. A molecular phylogenetic scheme is based on a mathematical analysis of nucleic acid sequences (or amino acid sequences from conserved proteins).

22. Identification and Classification of Bacteria Physical Characteristics(useful, but not definitive, for identifying broad groups of bacteria) Microscopic Examination of Cell Morphology: - Shape, Size, Arrangement - Staining Characteristics (determined by cell wall structure and composition) Biochemical Tests(a classical way of differentiating bacterial species) Check for the presence of specific enzymes and metabolic pathways - carbohydrate fermentation, - utilization of specific amino acids or citric acid - production of specific waste products Serological Tests(strain specific identification) Recognition of the bacteria by specific antibodies Phage Typing(strain specific identification) Differentiates strains on the basis of bacteriophage host rage Molecular Analysis - Uses computer programs to calculate phylogenetic relationships - ribosomal RNA sequence comparisons - other gene sequences

23. ClassicalBacterial IdentificationCell Morphology Figure 11.1

24. Arrangements of Cocci Figure 11.6

25. Arrangements of Bacilli Figure 11.7

26. Biochemical Tests as a tool for Identification of Bacteria Carbohydrate Fermentation Tests Uninoculated tubes of carbohydrate fermentation broth are red & translucent, not cloudy. The medium is inoculated with the bacterium and incubated for 24 - 48 hours at an appropriate temperature, usually 37o C. Growth of the bacteria will turn the medium cloudy. If the bacteria can ferment the carbohydrate, they make acid & the medium turns yellow. If the bacteria cannot ferment the carbohydrate the medium will remain red, sometimes turning a deeper shade of red. If the bacterium does not grow on the medium, it is an invalid test. Some carbohydrates commonly used include: sucrose, lactose, mannitol, xylose and arabinose, but many different carbohydrates can be used. uninoculated positive negative broth result results

27. Indole Test The indole test looks for the presence of the enzyme tryptophanase, which catalyzes the conversion of tryptophan to indole. The media used is tryptone broth, which contains amino acids but no sugar. Indole production is detected by adding Kovac’s reagent to a 1-2 day old culture. A red layer forms at the top if the bacterium is able to make indole. tryptophan  indole + ammonia + pyruvate positive negative result result

28. Biochemical Differentiation of Selected Enterobacteriaceae Citrobacter freundii C.f. Enterobacter aerogenes E.a. Esherichia coli E.c. Klebsiella pneumonia K.p. Morganella morganii M.m. Proteus vulgaris P.v. Salmonella cholerasuis S.c. Serratia liquifaciens S.l. Serratia marcescens S.m. Shigella flexneri S.f. TEST KEY C.f. E.a. E.c. K.p. M.m. P.v. S.c S.l. S.m. S.f. Methyl red + - + [-] + + + + [-] + Voges-Proskauer - + - + - - - + + - Indole production - - + - + + - - - d H2S production [+] - - - - + + - - - Phenylalanine deaminase - - - - + + - - - - Lysine decarboxylase - + + + - - + + + - acid from arabinose + + + + - - + + - d acid from lactose d + + + - - - - - - acid from mannitol + + + + - - + + + + acid from sucrose d + d + - + - + + - acid from xylose + + + + - + + + - - Simmons Citrate + + - + - [-] + + + - Lipase - - - - - [+] - [+] + - Urease d - - + + + - - [-] -

29. Enterotubeby BD DiagnosticsDevices such as this, with multiple chambers containing several different media, let clinical microbiologists run many biochemical tests simultaneously, speeding the identification of bacterial cultures. Image from Mesa Community Collegewww.mc.maricopa.edu

30. Bacterial Identification The bacteria Escherichia coli and Enterobacter aerogenesare both in the Enterobacteriaceae family. How can you tell them apart? A. Acid Fast stain - look for differences in their color B. Biochemical tests - look for differences in the production of indole or 2,3-butanediol C. Simple stain - look for differences in their shapes D. Gram stain - look for differences in their color E. Endospore stain - look for the position and shape of the endospores

31. Phage Typing A bacterial lawn inoculated with a selection of bacteriophages Bacteria are spread over the surface of an agar medium and a range of bacteriophage strains are then inoculated onto the lawn and the plate is incubated. Some phages have no effect on the bacteria, others can attack the cells causing the formation of plaques. Different bacterial strains within a species show different bacteriophage susceptibilities. Image from BMB , University of Leeds, UK