Chapter 2 - Review of general microbiology

1. Chapter 2 - Review of general microbiology • Objectives • Basic description of viruses, bacteria, fungi, algae, and protozoa (size, cell components) • Basic functions of a bacterial cell • Importance of the cell wall and cell membrane to a bacterial cell • Major differences between eubacterial and eukaryotic DNA/RNA • Plasmid types and function • Information exchange between bacteria • Understand the four nutritional categories and give an example of a microbe in each category

2. Evolutionary Timeline Oxygen atmosphere forms Microbes appear Earth forms Humans Dinosaurs 4.5 4.0 3.0 2.0 1.0 0 Billions of years

3. Viruses Viroids Prions http://www.astro.washington.edu/endsofworld/

4. Viruses

5. Bacteria A dividing gram positive bacterium DNA Cell membrane Cell wall Size – ranges from 0.3 to 3mm in length depending on the environment 106 bacteria in a pinpoint colony 106 bacteria/gm soil required to observe significant degradation activity

6. Bacterial Strategies for Survival Nitrosomonas vs. Pseudomonas Specialist vs. Jack-of-all-Trades

7. Specializes in ammonia oxidation. These bacteria are important in • the treatment of industrial and sewage waste in the first step of • oxidizing ammonia to nitrate. • NH3 NO2 NO3 • Nitrosomonas europaea • Gram-negative, chemoautotroph • Found in soil, freshwater, sewage, the walls of buildings and on the • surface of monuments especially in polluted areas where air contains • high levels of nitrogen compounds. • Problematic because can reduce availability of nitrogen to plants and • hence limit CO2 fixation. Also may contribute significantly to the global • production of nitrous oxide. • N. europaea strain Schmidt Stan Watson is now completely sequenced. • 2715 predicted genes, 2.80 x 106 bp • overall G+C content = 50.8%

8. Pseudomonas aeruginosa • Gram-negative, chemoheterotroph • Versatile • Found in soil, marshes, coastal marine habitats, • on plants and animals • Problematic for cystic fibrosis, burn victims, • cancer, ICU patients • P. aeruginosa PAO1 is now completely sequenced. • - 5570 predicted genes • - 6.3 x 106 bp (largest sequenced genome to date) • - overall G+C content = 66.6% • - isolated regions with lower G+C content may be result of recent • horizontal gene transfer • - > 500 genes are transcriptional regulators or environmental • sensors. Has more than twice the number of two-component • regulators than E. coli or B. subtilis.

9. The bacterial cell as the basic unit of life What are the basic functions of a microbial cell? • ability to reproduce • ability to use food as an energy source • ability to synthesize new cell components • ability to excrete waste • ability to respond to environmental changes • ability to change through mutation What are the basic components of a microbial cell? • cell envelope • cell membrane • cell wall • glycocalyx • appendages for motility and adhesion • nucleic acids • spores

10. Cell surface meets the outside world Eubacteria have two main types of envelopes, Gram Positive and Gram Negative.

11. Cell surface meets the outside world • Cell wall -The cell wall is a rigid structure composed of peptidoglycan that maintains the characteristic shape of the cell. • permeable to small molecules (<15,000)

12. Cell surface meets the outside world Cell membrane – The cell membrane is a highly selective barrier that enables cells to take in nutrients and excrete waste products • passive diffusion • facilitated diffusion • group translocation • active transport

13. Fig. 2.12 Cell surface meets the outside world How does the cell membrane fit into the cell envelope?

14. Cells can have flagella that allow them to move over short distances (um) either toward nutrients or away from inhibitory substances. Cells can have fimbriae that aid in attachment of cells to surfaces. Flagella Appendages Fimbriae

15. RNA enzyme transcription translation Nucleic acids –A,T (U), C, G DNA (gene) • Bacteria – DNA • 1 closed circular chromosome • plasmid(s) • RNA • 16s-rRNA • 16s-rDNA gene now used for classification • Eukaryotes – DNA • DNA is found within a membrane-bound nucleus • DNA synthesis and RNA transcription occur in the nucleus • RNA • 18s-rRNA • RNA translation (protein synthesis) occurs in the cytoplasm

16. The chromosome of a bacterial cell contains approximately 3 x 106 base pairs. If stretched out, the chromosome is 1 mm in length. In actively growing cells there are 2 to 4 copies of the chromosome since several replicating forks can occur at the same time. Bacterial cells also contain small circular pieces of DNA called plasmids.

17. Plasmid function Cryptic plasmids no known function (most) Resistance plasmids protect against antibiotics, metals, bacteriophage Degradative plasmids encode biodegradation of unusual metabolites Plant interactive plasmids mediate interaction between bacteria and plants (Sym, Ti plasmids) Miscellaneous plasmids involved in a variety of functions, RNA metabolism, conjugation, bacterial cell envelope alteration Types of plasmids Low-copy –number plasmids 1-2 copies/cell, usually > 10 kb High-copy-number plasmids 10 – 100 copies/cell, usually < 10kb Relaxed plasmids not dependent on initiation of cell replication Stringent plasmids synchronized with replication of chromosome Conjugative plasmids self-transmissible between same/different species, tra genes Non-conjugative plasmids not self-transmissible Incompatible plasmids cannot exist in together in the same cell Inc P plasmids exist in a wide variety of bacteria

18. Information exchange between bacteria can occur in three ways: • Conjugation • Transformation • Transduction

19. 1) Conjugation Pilus

20. 2) Transformation

21. 3) Transduction

22. Case Study 3.1 How was information transfer achieved? DiGiovanni et al. 1996. Appl. Environ. Microbiol. 62:2521-2526.

23. Bacterial spore formers: Gram positive bacteria can form spores that are very resistant to heat, UV, and nutrient stress. Spores can even withstand autoclaving. As a result, soil must be autoclaved three times on consecutive days to achieve complete sterilization. This allows spores to germinate in between autoclaving events.

24. Eukaryotes Fungi Algae Protozoa

25. Microbial Nutrition Autotrophs (CO2) Heterotrophs (organic carbon) Carbon source Energy source Phototroph (light) Chemotroph (chemical) CO2 C(H2O) Photosynthesis Oxidation of inorganics Respiration • Light energy is harnessed through photosynthesis • Chemical energy is harnessed through oxidation of organic/inorganic • substances

26. Nutritional classification Viruses – living or nonliving? Eubacteria – Archaebacteria – Cyanobacteria – Algae – Fungi – Protozoa – photoautotrophic photoheterotrophic chemoautotrophic chemoheterotrophic photoautotrophic chemoautotrophic chemoheterotrophic photoautotrophic photoautotrophic chemoheterotrophic chemoheterotrophic photoautotrophic photoheterotrophic

27. Based on nutritional requirements which microbial groups might you find at the soil surface? At 100 ft below the surface? Based on size which microbial groups might you find at the soil surface? At 100 ft below the surface? Discussion Questions Viruses Eubacteria Archaebacteria Cyanobacteria Algae Fungi Protozoa