Microbial Nutrition and Ecology Chapters 6 & Chapter 25 Some topics also covered in lab:

1. Microbial Nutrition and Ecology Chapters 6 & Chapter 25 Some topics also covered in lab: -- O2 requirements -- culture media and conditions In Chapter 25… You are not responsible for -- food preservation will be covered later -- water quality testing is also covered in lab Understand purposes of 1O & 2O wastewater treatment. Prevention of food spoilage will be covered later in the semester Hmmm…? Biological warfare is under “applied microbiology”! Read for general enlightenment Microbial Ecology

2. Numbers of bacteria Some Recent Estimates of Bacteria On humans: 1014 / human On leaves: 1011 / meter2 In oceans: 1029 cells In soils: 1029 cells In Earth’s crust: 1030 cells 1012 = 1 trillion Total carbon allocation: (~ ½ that of plants) Whitman et al, (1998) PNAS 95:6578 From Naturalist, by E.O Wilson “If I could do it all over again, and relive my vision in the twenty-first century, I would be a microbial ecologist. Ten billion bacteria live in a gram of ordinary soil, a mere pinch held between thumb and forefinger. They represent thousands of species, almost none of which are known to science. Into that world I would go with the aid of modern microscopy and molecular analysis. I would …travel in an imagined submarine through drops of water proportionately the size of lakes, and track predators and prey in order to discover new life ways and alien food webs. All this, and I need venture no farther than ten paces outside my laboratory building. (p 364) Microbial Ecology

3. Biofilm on plant surface How does growth in nature differ from growth in the lab? Inter-species interactions Microhabitats prevail “Feast or famine” Biofilms Quorum sensing Cell Density Biofilms Virulence Biofilms Engineered GFP QS Danino et al(2010) Nature 463, 326-330 (Supplementary Movie 5) http://www.nature.com/nature/journal/v463/n7279/full/nature08753.html Microbial Ecology

4. What are the different modes of Microbial Nutrition? All organisms have three fundamental requirements Carbon Energy Mineral nutrients Bacterial Growth and Metabolism

5. Prokaryotes are much more varied in their sources of C and energy Bacterial autotrophs Phototrophs -- photosynthetic bacteria Chemoautotrophs “Lithotrophs” -- mineral oxidizing bacteria Bacterial Growth and Metabolism

6. Bacterial heterotrophs Photoheterotrophs Chemoheterotrophs saprophytic parasitic Generalists vs fastidious bacteria Bacterial Growth and Metabolism

7. Chemoheterotrophic Metabolism Stages of cellular respiration ** Review on your own** Aerobic vs anaerobic metabolism Where does chemiosmotic ATP synthesis occur in prokaryotes? -- no mitochondria! Overview of Cellular Respiration Bacterial Growth and Metabolism

8. Fastidious bacteria often have metabolic deficiencies Auxotrophic bacteria -- need specific organic nutrient(s) ‘Metabolically defective’ bacteria -- often obligate intracellular pathogens Ricketsia ricketsii -- very fastidious; cofactors, -- lacks gens for glycolysis & amino acid synthesis Rocky Mountain Spotted fever -- Tick borne -- vascular endothelium -- hemorraging -- rash Bacterial Growth and Metabolism

9. Chlamydia Chlamydia trachomatis Also metabolically defective -- 1 MB genome (E. coli = 5 MB) -- Incomplete TCA & e-transport pathways -- ATP – Most common STD in US -- 3-5 million annually -- nongonorrheal urethritis -- often undiagnosed Complex life cycle -- elementary bodies (0.3 μm) -- reticulate body (~ 0.8 μm) Also causes Trachoma -- blindness Pathology

10. Bacterial O2 requirements vary widely (covered in lab) Obligate aerobes Facultative anaerobes -- can use O2 if available Microaerophiles Aerotolerant anaerobes -- can grow with O2 but do not use it -- why? Obligate anaerobes -- cannot grow in presence of O2 -- why? Some Anaerobes can use other terminal e- acceptors -- diminishes ATP yield Bacterial Growth and Metabolism

11. Fermentation Functions End products End products important for -- bacterial identification -- food and chemical industries Bacterial Growth and Metabolism

12. Beer production Normal beer: only yeast … boring! Lambic beer … yeast and bacteria! Yeast CO2 production Bacterial Growth and Metabolism

13. Cheese production Involves bacteria (and sometimes fungi) Curdling stage Ripening stage Bacterial Growth and Metabolism

14. Autotrophic bacteria CO2 is carbon source Energy from light (phototrophs) or inorganics (chemoautotrophs) Phototrophs Purple sulfur bacteria -- anoxygenic Ps Cyanobacteria -- oxygenic Ps Bacterial Growth and Metabolism

15. Cyanobacteria “blue-green” pigmentation Habitat Stromatolites Oxygenic photosynthesis Visit NASA’a “Stromatolite Explorer” on-line Bacterial Growth and Metabolism

16. Purple sulfur bacteria Anoxygenic Photosynthesis Habitat Pigmentation Sulfur granules Bacterial Growth and Metabolism

17. Chemoautotrophic bacteria CO2 is source of carbon inorganic minerals are energy source Groups we will examine: Nitrifying bacteria Iron bacteria Sulfur bacteria Chemoautotrophs ‘oxidize’ their energy sources i.e., electrons removed Play important ecological roles Microbial Ecology

18. Iron-oxidizing Chemoautotrophs Thiobacillus ferrooxidans need ferrous (Fe2+) iron obligate acidophiles acid mine drainage Microbial Ecology

19. Biohydrometalurgy of copper Employs chemoautrophs low grade ore, tailings (< 0.4% Cu) Environmental issues Microbial Ecology

20. Bacteria and Biogeochemical Cycles N cycling in aquatic ecosystems The Nitrogen Cycle Nitrification N Assimilation Decomposition & Excretion Denitrificatiion (anaerobes) N fixation Preparation of an aquarium Nitrogen Cycle Microbial Ecology

21. Nitrogen-fixing bacteria Rhizobium Symbionts with legumes Azotobacter Soil inhabitants Microbial Ecology

22. Sulfur cycle -- demonstrated in a Winogradsky column Sergius Winogradsky (1856-1953) Martinus Beijerinck (1851-1931) Important roles of Sulfur assimilation -- all organisms assimilate S into protein Chemoautotrophs -- extract e- from reduced S (H2S, S2) Photoautotrophs -- H2S is e- source Heterotrophic anaerobes -- SO4 is alternative O2 acceptor Microbial Ecology

23. Endosymbiosis in Riftia Sulfur-oxidizing chemoautotrophs Hydrothermal vents Thermal vent Vent Community Microbial Ecology

24. Symbiosis between bacteria and animals is very common Humans Ruminants (cows, sheep, deer, giraffes, goats, etc) - Rumen - Bacterial fermentation - Acid production The incredible hoatzin (pronounced ‘what-seen’) National bird of Guyana Fistulated cow Microbial Ecology