Microbial Ecology

138023

Oded Beja

•Introduction•Syllabus presentation•What is microbial diversity?

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.

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

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

HalophilesHalophiles habitats and diversityHalophiles physiology,biochemistry and geneticsPaper presentation:Halophiles

Marine ArchaeaPaper presentation:Cold Archaea

PsychrophilesBiology of psychrophilesPaper presentation:Microorganisms of Antarctica

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

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

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

•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)

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)

Methods in microbial ecology

Boetius et al. 2000 Orphan et al. 2001

Nanoarchaeum

Boetius et al. 2000 Orphan et al. 2001

Paper presentation for next week:

Woese C.R. (2000) PNAS 97:8392-8396

Interpreting the universalphylogenetic tree