1. Microbial Ecology 138023 Oded Beja Introduction Syllabus presentation What is microbial diversity?

3. A two-credit course with one hour of lecture and one hour of discussion each week. The course focuses on the microbial diversity of different environments. The objectives are: (1) to develop an understanding of the morphological, ecological, biochemical and evolutionary diversity of the microbial world; (2) to learn how microbes have evolved to survive under ‘extreme’ conditions; and (3) to learn the molecular biology and genomics methods by which this genetic diversity can be analyzed.

4. What is Microbial Diversity? Methods in microbial ecology. Phylogeny and evolution Fundamental similarities of all living organisms Paper presentation:Extremes of life Phylogenetics and Trees of Life Paper presentation :Lateral gene transfer Microbial genomics Paper presentation:What can we learn from genome sequences? Paper presentation:Complete Genomes Environmental Molecular Microbiology Overview of marine microbial ecology Molecular Methods to assess microbial diversity Paper discussion:marine microbial diversity Oligotrophy and VBNC Paper discussion:Bacterial Rhodopsin and phototrophy

5. Ecology of Extreme Environments Extremophiles and the Archaea:habitats and diversity Paper presentation:Yellowstone National Park Paper presentation:Vent communities Hyperthermophiles: phylogeny,morphology and physiology Genome integrity in hyperthermophiles Paper presentation:DNA Repair The flow of genetic information in hyperthermophilic Archaea Paper presentation :Protein thermostability Paper presentation:regulation Acidophiles:Sulfolobus and viruses Paper presentation:hyperthermophiles genetics

6. Halophiles Halophiles habitats and diversity Halophiles physiology,biochemistry and genetics Paper presentation:Halophiles Marine Archaea Paper presentation:Cold Archaea Psychrophiles Biology of psychrophiles Paper presentation:Microorganisms of Antarctica

7. Methanogens Methanogenic Archaea and consortia Physiology of methanogenesis Paper presentation:Methanogens Microbial photosynthesis and Novell photothrophs Paper presentation: aerobic anoxygenic phototrophs Novell Eukaryotes Paper presentation: unsuspected eukaryotic diversity Exobiology Paper presentation: Magnetofossils from ancient Mars

8. 14/10/13 Introduction 21/10/13 Phylogeny and evolution Woese 2000 PNAS 97:8392-8396 Dunning Hotopp et al. 2011 Trends Genet. 27:157-163 28/10/13 Microbial genomics 4/11/13 Environmental Molecular Microbiology 11/11/13 Ecology of Extreme Environments 18/11/13 Hyperthermophiles: phylogeny, morphology and physiology 25/11/13 Marine Archaea 9/12/13 Halophiles 16/12/13 Psychrophiles 23/12/13 Microbial photosynthesis and Novell photothrophs 30/12/13 Novell Eukaryotes & New cultivation methods 6/1/14 Exobiology

9. Microbial Diversity -cell shapes: rods, cocci, spirals, filaments, amorphous, pleomorphic, star-shaped, lumpy cocci, squares…. -cell organization: multicellular from pairs and tetrads to filaments, sheets, rosettes, microbial mats,… -cells size: average 1 to 5 microns range 0.1 to 660 microns (Thiomargarita namibiensis, giant sulfur bacteruim in Namibian sediments) Morphological diversity

10. Chemotrophs:energy is obtained from chemicals lithotrophs:inorganic chemicals (sulfur, iron, hydrogen) -autotrophs: carbon is obtained by fixing CO 2 (sulfur-reducing Archaea, methanogens) -heterotrophs: carbon is obtained from organic compounds (sulfur-reducing Archaea) organotrophs and heterotrophs: carbon and energy are obtained from organic chemicals (heterotrophs, E.coli, pathogens) Metabolic diversity Phototrophs: energy is obtained from light heterotrophs:carbon is obtained from organic compounds (halophilic Archaea and others) autotrophs: carbon is obtained by fixing CO 2 (most cyanobacteria, photosynthetic bacteria)

11. Ecological diversity -salinity:from fresh water to marine and hypersaline environments (Dead sea and the Great Salt Lake, halophiles) -temperature: from –12 to 113 o C (Pyrolobus) and beyond (121 o C) -pH: from 0 (Thiobacillus thiooxidans) to 13 (Plectonema nostocorum) pH 0 is 1M HCl -redox potential: from –450mV (methanogens)to + 850mV (iron bacteria) -hydrostatic pressure: from 1 to 1400 atm (barophiles)

12. Methods in microbial ecology

18. Boetius et al. 2000Orphan et al. 2001

20. Nanoarchaeum

29. Boetius et al. 2000Orphan et al. 2001

32. Paper presentation for next week: Woese C.R. (2000) PNAS 97:8392-8396 Interpreting the universal phylogenetic tree