Microbial Ecology Chapter 16 : Microbes and the Environment also Chapter 15 : about ruminants Topics to be covere

1. Microbial Ecology • Chapter 16: Microbes and the Environment • also Chapter 15: about ruminants • Topics to be covered in class • Bacteria in the real world • Autotrophic bacteria • Biogeochemical cycles • Microbes and symbiosis • Read in Chapter 16 • on your own about • Sulfur cycle • Municipal and waste • water treatment 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? Complex interactions Microhabitats prevail “Feast or famine” Biofilms Quorum sensing Cell Density Biofilms Virulence Biofilms Danino et al(2010) Nature 463, 326-330 (Supplementary Movie 5) http://www.nature.com/nature/journal/v463/n7279/full/nature08753.html Engineered GFP QS Microbial Ecology

4. 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

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

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

7. Bacteria and Biogeochemical Cycles N transformation in an aquarium (& aquatic ecosystems) NH3 and NO2 toxicity The Nitrogen Cycle Nitrification N Assimilation Decomposition & Excretion Denitrificatiion (anaerobes) N fixation Nitrogen Cycle Microbial Ecology

8. 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 Chemolithotrophs -- extract e- from reduced S (H2S, S2) PhotoAutotrophs -- H2S is e- source Heterotrophic anaerobes -- SO4 is alternative O2 acceptor Microbial Ecology

9. Endosymbiosis in Riftia Sulfur-oxidizing chemoautotrophs Hydrothermal vents Thermal vent Vent community Microbial Ecology

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

11. Symbiosis between bacteria and animals is very common • Humans • Ruminants • (cows, sheep, deer, • giraffes, goats, etc) • Multiple stomachs • Rumen • Bacterial fermentation • Acid production Fistulated cow Microbial Ecology

12. The incredible hoatzin (pronounced ‘what-seen’) Only known avian ruminant National bird of Guyana Hoatzin Microbial Ecology