Microbial Ecology

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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 evolution Fundamental
similarities of all living organisms Paper
presentationExtremes of life Phylogenetics and
Trees of Life Paper presentation Lateral gene
transfer Microbial genomics Paper
presentationWhat can we learn from genome
sequences? Paper presentationComplete
Genomes Environmental Molecular
Microbiology Overview of marine microbial
ecology Molecular Methods to assess microbial
diversity Paper discussionmarine microbial
diversity Oligotrophy and VBNC Paper
discussionBacterial Rhodopsin and phototrophy
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Ecology of Extreme Environments Extremophiles and
the Archaeahabitats and diversity Paper
presentationYellowstone National Park Paper
presentationVent communities Hyperthermophiles
phylogeny,morphology and physiology Genome
integrity in hyperthermophiles Paper
presentationDNA Repair The flow of genetic
information in hyperthermophilic Archaea Paper
presentation Protein thermostability Paper
presentationregulation AcidophilesSulfolobus
and viruses Paper presentationhyperthermophiles
genetics
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Halophiles Halophiles habitats and
diversity Halophiles physiology,biochemistry and
genetics Paper presentationHalophiles Marine
Archaea Paper presentationCold
Archaea Psychrophiles Biology of
psychrophiles Paper presentationMicroorganisms
of Antarctica
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Methanogens Methanogenic Archaea and
consortia Physiology of methanogenesis Paper
presentationMethanogens Microbial
photosynthesis and Novell photothrophs Paper
presentation aerobic anoxygenic
phototrophs Novell Eukaryotes Paper
presentation unsuspected eukaryotic
diversity Exobiology Paper presentation
Magnetofossils from ancient Mars
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23/10/12 Introduction 30/10/12 Phylogeny and
evolution Woese C.R. 2000 PNAS 978392-8396,
Dunning Hotopp J.C. 2007 et al. Science
3171753-1756 6/11/12 Microbial
genomics 13/11/12 Environmental Molecular
Microbiology 20/11/12 Ecology of Extreme
Environments 27/11/12 Hyperthermophiles
phylogeny, morphology and physiology 4/12/12
Marine Archaea 11/12/12 Halophiles
18/12/12 Psychrophiles 25/12/12 Microbial
photosynthesis and Novell photothrophs 1/1/13
Novell Eukaryotes New cultivation
methods 8/1/13 Exobiology
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Microbial Diversity
Morphological 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)
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Metabolic diversity
Phototrophs energy is obtained from light
heterotrophscarbon is obtained from organic
compounds (halophilic Archaea and others)
autotrophs carbon is obtained by fixing CO2
(most cyanobacteria, photosynthetic bacteria)
Chemotrophsenergy is obtained from chemicals
lithotrophsinorganic 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)
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Ecological diversity
-salinityfrom fresh water to marine and
hypersaline environments (Dead sea and the Great
Salt Lake, halophiles) -temperature from 12 to
113oC (Pyrolobus) and beyond (121oC) -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)
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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
Interpreting the universal phylogenetic tree
Woese C.R. (2000) PNAS 978392-8396