microbial ecology 138023 oded beja introduction syllabus presentation what is microbial diversity?
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Microbial Ecology
138023
Oded Beja
•Introduction•Syllabus presentation•What is microbial diversity?
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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.
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What is Microbial Diversity?Methods in microbial ecology.
Phylogeny and evolutionFundamental similarities of all living organismsPaper presentation:Extremes of lifePhylogenetics and Trees of LifePaper presentation :Lateral gene transfer
Microbial genomicsPaper presentation:What can we learn from genome sequences?Paper presentation:Complete Genomes
Environmental Molecular MicrobiologyOverview of marine microbial ecologyMolecular Methods to assess microbial diversityPaper discussion:marine microbial diversityOligotrophy and VBNCPaper discussion:Bacterial Rhodopsin and phototrophy
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Ecology of Extreme EnvironmentsExtremophiles and the Archaea:habitats and diversityPaper presentation:Yellowstone National ParkPaper presentation:Vent communities
Hyperthermophiles: phylogeny,morphology and physiologyGenome integrity in hyperthermophilesPaper presentation:DNA RepairThe flow of genetic information in hyperthermophilic ArchaeaPaper presentation :Protein thermostabilityPaper presentation:regulation
Acidophiles:Sulfolobus and virusesPaper presentation:hyperthermophiles genetics
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HalophilesHalophiles habitats and diversityHalophiles physiology,biochemistry and geneticsPaper presentation:Halophiles
Marine ArchaeaPaper presentation:Cold Archaea
PsychrophilesBiology of psychrophilesPaper presentation:Microorganisms of Antarctica
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MethanogensMethanogenic Archaea and consortiaPhysiology of methanogenesis Paper presentation:Methanogens
Microbial photosynthesis and Novell photothrophsPaper presentation: aerobic anoxygenic phototrophs
Novell EukaryotesPaper presentation: unsuspected eukaryotic diversity
ExobiologyPaper presentation: Magnetofossils from ancient Mars
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14/10/13 Introduction
21/10/13 Phylogeny and evolutionWoese 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
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Microbial Diversity
-cell shapes: rods, cocci, spirals, filaments,amorphous, pleomorphic, star-shaped, lumpy cocci, squares….
-cell organization: multicellular from pairs andtetrads to filaments, sheets, rosettes, microbial mats,…
-cells size: average 1 to 5 micronsrange 0.1 to 660 microns(Thiomargarita namibiensis , giant sulfur bacteruim inNamibian sediments)
Morphological diversity
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•Chemotrophs:energy is obtained from chemicals •lithotrophs:inorganic chemicals (sulfur, iron, hydrogen) -autotrophs: carbon is obtained by fixing CO2
(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 CO2 (most cyanobacteria, photosynthetic bacteria)
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Ecological diversity
-salinity:from fresh water to marine and hypersalineenvironments (Dead sea and the Great Salt Lake, halophiles)
-temperature: from –12 to 113oC (Pyrolobus) and beyond (121oC)
-pH: from 0 (Thiobacillus thiooxidans) to 13 (Plectonemanostocorum) pH 0 is 1M HCl
-redox potential: from –450mV (methanogens)to +850mV (iron bacteria)
-hydrostatic pressure: from 1 to 1400 atm (barophiles)
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Methods in microbial ecology
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Boetius et al. 2000 Orphan et al. 2001
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Nanoarchaeum
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Boetius et al. 2000 Orphan et al. 2001
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Paper presentation for next week:
Woese C.R. (2000) PNAS 97:8392-8396
Interpreting the universalphylogenetic tree