Download Brief profile about the Faculty Michel Aragno

Brief profile about the Faculty
Michel Aragno, emeritus professor of Microbiology, University of Neuchâtel (Switzerland).
[email protected]
PhD (1973), Post-doc: Paris, Institut Pasteur (1973), Göttingen University (1975-6). Master-assistant,
Neuchâtel University (1973-78).Assistant professor, Neuchâtel University (1978-1981), full professor,
idem (1981-2008).
Main research topics: Ecology and taxonomy of hydrogen-oxidizing bacteria, particularly
thermophiles; bacterial ecology of plant rhizosphere; calcium carbonate biomineralization through
the oxalate-carbonate pathway.
Applied research: anaerobic digestion of organicwastes; landfill microbiology; microbiology and
hygienic aspects of the composting process; crop bio-inoculation (PGPR bacteria).
Main teaching topics: General and environmental microbiology, soil microbiology and enzymology,
biogeochemical cycles, bioenergetics.
1982-88: Vice-chairman, Swiss Academy of Sciences; 1984-96: member of the Swiss National UNESCO
Commission, chairman of the sciences section, vice chairman of the Commission (1992-96).
Invited professor at following universities: Berne, Fribourg + Architecture Academy Mendrisio
(Switzerland); Besançon (France), TERI University (India).
Main hobbies: classical music, medieval architecture, Italian art.
Details about the lecture
The bacteria and their functions in the environment
1. Introduction to the bacterial world2p week 1/1-2
1.1. Origin and evolution of life
1.2. The discovery of microbes
1.3. Some basic characteristics of the microbial world
1.4. Shapes of bacterial cells
1.5. Adaptations to the environment
2. The prokaryotic cell3pweek1/3-5
2.1. Prokaryotes and Eukaryotes
2.2. Bacterial cell composition
2.3. The bacterial genome
2.4. Cell fractionation (ultracentrifugation)
2.5. The cell (plasma) membrane
2.6. The ribosome
2.7. Reserve inclusions
2.8. The cell wall
2.9. Lysozyme and antibiotics
2.10. S-layers
2.11. Exopolysaccharides and capsules
2.12. Flagella and pili
2.13. Bacterial endospores
3. Trophic types, nutrition2pweek 1/6 + week 2/1
3.1.
Basic thermodynamic principles
3.2.
Trophic types
3.3.
Nutrients acquisition
3.4.
Relationships with oxygen
3.5.
Design of culture media
3.6.
Prototrophs and auxotrophs
4. Bacterial growth2p week2/2 -3
4.1. Exponential growth model
4.2. Sequence of events during a real «batch» culture
4.3. Continuous culture
4.4. Immobilized cultures
4.4.1.
Biomass immobilization systems
4.4.2.
Types of bioreactors
5. Enzyme cofactors related to the energy metabolism1p week2/4
5.1. Definitions
5.2. Energy transfer
5.3. Redox cofactors
6. Heterotrophic metabolism, fermentations, respirations3p week3/1-3
6.1. Extracellular hydrolysis of biopolymers (e.g. polysaccharides)
6.2. Glycolysis
6.3. Fermentations
6.4. Aerobic respiration
6.5. Anaerobic respirations
6.6. Respirations vs fermentations: yield comparison
6.7. Bacterial bioluminescence
7. Autotrophy (CO2 fixation)1p week3/4
8. Chemolithotrophy: respiratory oxidation of inorganic, reduced compounds1.5 p week3/5-5.5
8.1. Anaerobic chemolitho-autotrophy
8.2. Aerobic chemolitho-autotrophy
8.3. Nitrification
8.4. Sulfo-oxidation
8.5. Iron oxidation
9. Phototrophy1p week3/5.5-6, week 4/1-1.5
9.1. Principle of anoxygenic photo(litho)autotrophy
9.2. «Green» phototrophs
9.3. Purple phototrophs
9.4. Halobacteria and the purple membrane
9.5. Oxygenic phototrophy: the Cyanobacteria
10. (Di-)nitrogen fixation 1.5p week4/1.5-2
10.1.
Nitrogenase and its function
10.2.
Regulation of nitrogenase and ammonia assimilation
10.3.
N2-fixation in Cyanobacteria
10.4.
Symbiosis between Azollasppand the CyanobacteriumAnabaena azollae
10.5.
Symbiotic fixation in plant nodules
11. The main biogeochemical cycles of redox elements2p week4/3-4
11.1.
Carbon cycle
11.2.
Oxygen cycle
11.3.
Nitrogen cycle
11.4.
Sulfur cycle
11.5.
Iron Cycle
11.6.
Integration of redox cycles
12. Classification of prokaryotes 2p week 4/5-6
12.1.
Phenotypical approach
12.2.
Genomic approach
12.3.
The universal tree of life
12.4.
Domain Bacteria
12.5.
Domain Archaea
13. A look at Eukaryotes, with special regards to Fungi2p week5/1-2
13.1.
Mucorales
13.2.
Entomophthorales
13.3.
Chytridiomycota
13.4.
Glomeromycota
13.5.
The higher Fungi
13.6.
«Fungi Imperfecti» (Deuteromycetes)
13.7.
Ascomycota
13.8.
Basidiomycota
14. Bacteria as tools in biotechnology2p week5/3-4
14.1. Optimization of natural processes using spontaneously developing microbial
communities
14.2.
Bioinoculation of selected organisms to improve microbially mediated processes
14.3. Use of defined microorganisms to apply their metabolic capabilities to a
biotransformation process
14.3.1. Processes first developed empirically
14.3.1.1.
Alcoholic fermentation : wine, beer
14.3.1.2.
Lactic acid fermentation : yoghurt, cheese, sauerkraut
14.3.1.3.
Propionic fermentation: emmental cheese
14.3.1.4.
Acetic acid bacteria: vinegar
14.3.2.
Strictly controlled processes in fermenter with pure cultures: fermentations
and incomplete oxidations
14.4.
Use of pure cultures to produce microbial metabolites
14.5.
Enzymes from microorganisms
14.6. Use of genetically modified organisms to produce compounds from other
organisms
15. Case study 1: biomethanisation and syntrophy, anaerobic strategies1p week5/5
15.1.
Positive feedback 1: Synthesis of hydrolytic enzymes by fermentative bacteria
15.2.
Positive feedback 2: Methanogens to fermentative bacteria
15.3. Positive feedback 3: Methanogens to proton-reducing acetogenic bacteria: The
case of propionate
15.4.
Spatial considerations: ecology introduces to kinetics approach
16. Case study 2: Interactions and rhizosphere microbiology: plant growth promotion2p week5/6 +
week6/1
16.1.
Biological interactions ; general considerations
16.2.
What is the rhizosphere ?
16.3.
The root environment
16.4.
Microorganisms in the rhizosphere
16.4.1.
The «PGPR» : Plant Growth Promoting Rhizobacteria
16.4.2.
Interactions with mycorrhizae
16.4.3.
Protection of plants against parasites
16.4.4.
Importance of bacteria grazers in the rhizosphere
16.5.
The ISCB rhizosphere project
17. Case study 3: CO2 sink in tropical forests through the oxalate-carbonate pathway 2 p week 6/2-3
17.1.
Climatic change: how to trap CO2 out of the atmosphere ?
17.2.
Why acidic tropical soils become alkaline under several tree species?
17.3.
The oxalate-carbonate patwhway
17.4.
Molecular tools to detect oxalotrophic bacteria
17.5.
Role of fungi in the oxalate-carbonate pathway
17.6.
Geographical and plant taxonomical extent of the phenomenon
17.7.
Prospects for applications
18. Overview and conclusions1p week6/4
19. Repetition session 2p week 6/5-6
20. Evaluation/exams
Total : 32 periods