The listing below gives an overview and a few key words of the lectures themes which are currently offered within each part. Please choose the themes which interests you most and submit your selection on the prepared inscription form. The lecture themes are linked to a keyword summary of the contents.

 

 

 

PART I

Evolution to present day microbial diversity

 

1. Diversity among microbes

2. Phenotypic characterization of metabolic versatility

3. Phylogenetics: Evolution of microbial diversity

4. Microbial paleontology

 

 

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PART II

Microbial ecosystems & ecosystem determinants

 

5. Microbially dominated ecosystems (an overview).

6. Ecological determinants which regulate microbial life

7. Carbon cycling and carbonate buffering

8. Simulation of ecological determinants for the cultivation of microorganisms

9. Perception and responses to environmental variability and changes

 

 

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PART III

Energetics determines microbial lifestyles

 

10. Biochemistry of energy metabolism

11. Bridging chemistry and microbial physiology

12. Application of thermodynamics to environmental processes

13. From thermodynamics to bacterial lifestyles

14. Ecoenergetic case studies

 

 

 

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PART IV

Microbial involvement in geochemical cycling

 

15. Geomicrobiological processes in the sulfur cycle

16. Sulfate and sulfur reducing bacteria

17. Coupled phosphorus and iron cycling

18. Global biogeochemical cycling of elements

 

 

 

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PART V

Primary production by microbes

 

A) Photosynthesis

19. Anoxigenic photosynthesis: processes and organisms

20. Ecology of anoxigenic phototrophic bacteria

21. Adaptation to material and energy gradients in microbial mats and biofilms.

22. Oxigenic photosynthesis by cyanobacteria and prochloron

23. Cyanobacteria as sources for secondary metabolites

 

B) Chemosynthesis

24. Diversity of C1-fixation pathways

25. Lithotrophy

 

 

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PART VI

Microbial interactions

 

26. How microbes interact

27. Interactions between prokaryotes

28. Acetogenic prokaryotes in anaerobic food webs

29. Microbe-Macrobe interactions

 

 

 

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PART VII

Applied microbial ecology

 

30. Technically and industrially important processes

31. Ecology of clinically important microbes

 

 

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PART VIII

Deriving concepts from microbial ecology and diversity

 

32. Concepts in microbial ecology

33. Criteria for life: Applications to Exo- and Astrobiology:

34. Levels of abstraction applied to the study of microbial ecology

35. Defining complexity in microbial ecosystems

36. Microbial ecology in the modern era of biology

 

 1. Diversity among microbes

 

1.1 How diverse are microbial communities ?

• Diversity of habitats which selects for biodiversity of microbial communities. Characteristic microbes from specific ecosystems.
• Spacial heterogeneity: patterns of microbial diversity in soils.
• Temporal changes of community composition: patterns of diversity in time.
• Regulation of organismic ecosystem structure: how bacteriaplankton is regulated.
• Amounts of microbial biomass on earth: human gut contains more prokaryotic cells than the entire body consist of eukaryotic cells.
• Biogeography and co-evolution of bacterial diversity.

 

1.2 How can microbial diversity be sampled and quantified?

• Diversity based on cultivation vs. diversity based on molecular phylogenetic techniques.
• Basic molecular techniques: PCR of rDNA, cloning and sequencing, single-cell hybridization, etc.
• Designing primers which anneal to group specific and to universally conserved sequences of 16S-rRNA-genes.
• Analysis of sequence information: software packages for statistical methods.
• Known and unknown diversity: how to account for not yet culturable microorganisms.

 

1.3 Developments in molecular ecology

• 1970s: Discovery of a hidden diversity, the Archaea domain (kingdom).
• 1980s: Use of microbial models to test evolutionary hypotheses.
• 1990s: Application of molecular tools to study microbial diversity in ecosystems: RFLP, T-RFLP, DGGE, FISH, etc.

 

2. Phenotypic characterization of metabolic versatility

 

2.1 Metabolic versatility

• Understanding metabolic diversity in Bacteria, Archaea and microbial Eukarya.
• Re-inventing the prokaryotic cell.
• Assimilative carbon autotrophy and pathways for CO2-fixation.
• Energetic lifestyles: photo- and chemotrophy.

 

2.2 Levels of diversity

• Criteria for phenotypic characterization of Bacteria and Archaea (taxonomy acc. to Bergey's manual).
• Diversity at the level of electron donors and electron acceptors.
• Diversity in pathways for carbohydrate catabolism and the creation of basic metabolites for anabolism.
• How diverse membrane topologies fulfill the same chemiosmotic function.
• Functional diversity within genotypically unique groups.
• Genotypes, phenotypes, phylotypes and ecotypes.

 

3. Phylogenetics: Evolution of microbial diversity

 

3.1 Evolutionary driving forces

• Mutations, horizontal gene transfer (conjugation, transformation, transduction) , selection, symbioses, cellular compartmentalization.
• Consequences of lateral gene transfer on phylogeny, plasmid structures and plasmid propagation, transposable elements.
• Prerequisits for rapid expression of new traits: haploid chromosome, plasmids, DNA-exchange and insertion mechanisms, small genome size (500kb to 10mb), rapid growth rate.
• Evolutionary experiments with microbes.
• Ecology of spreading genes and selection of microbes that carry them.
• The role of high temperatures for early evolutionary processes.
• Evolution of microbial symbioses, incl. symbioses in eukaryotic cells.

 

3.2 Genomic and proteomic data collections

• Biological databases for the study of microbial evolution: physiology, genomics, phylogeny.
• Molecular records of the biosphere: databases containing genome and protein sequences.
• Evolutionary models based on functional bioinformatics.
• How large is the essential genome ?

 

3.3 Phylogenetic developments

• The three domains (kingdoms) of organisms: Bacteria, Archaea and Eukarya.
• What are the forces that select for differentiated cells and not for the unified cell ?
• Criteria defining evolutionary relatedness: what distignuishes the three domains (kingdoms) of life ?
• Phylogenetic trees based on 16S-rRNA, backgrounds and construction.
• Phylogeny and taxonomy: metabolic genomics beyond phylogenetic trees.
• Metabolic phylogeny in the Archaea domain (kingdom), in the Bacteria domain (kingdom).
• Phylogeny of microbial eukaryotes from anoxic environments.
• Environmental evolutionary driving forces: effects of mass extinction phases, new radiations in the tree.

 

3.4 Genome analysis of bacterial communities

• Strategies and methods to analyze mixed population DNA.
• DNA/DNA hybridization for analyses of microbial communities: FISH and Checkerboard-Hybridization.
• Environmental genomics, novel organisms.

 

 

4. Microbial paleontology

4.1 Origin of lifestyles

• Theories about the chemolithoautotrophic origin of life and possible lifestyles of ancient microbes.
• Theories about the chemoorganotrophic origin of life: organic molecules in the "primordial soup" and remineralization of organics from early biomass.
• Hydrothermal synthesis of amino acids, purines and pyrimidines.
• Initial mechanisms: a) "soup metabolism" in the cytoplasm, b) topologies for metabolism: membrane associated electron transport, proton translocation.
• Initial physiologies: fermentation, CO2-reduction to CH4, Fe(II+)-oxidation by photosynthesis, mechanisms for assimilative CO2-fixation.
• The role of mineral surfaces in the evolution of biochemistry: e.g. ironsulfides, clays.

 

4.2 From RNA to RNA/protein to DNA/RNA/protein worlds.

• Early catalytic molecules, catalytic RNA.
• Evolution of bio-cryptography.
• Life was originally prokaryotic and anaerobic.
• How "primitive" prokaryotes shaped 3.5 billion years of evolution.
• Enzyme evolution: metabolism(s) in non-compartmentalized prokaryotic cells.
• Evolutionarily missing microbial ecosystem processes.

 

4.3 Evolution of communities

• Evolution in the absence of other organisms: exploitation of energy and chemicals.
• The necessity for redox cycling of the nutritive elements: development of specialist microbes.
• Exploitable sources of electrons, oxidants and energy.
• The emergence of communities able to do very different things.
• The missing prokaryote that can do everything.
• Ancestral communities were nearly omnipotent: sulfur-, ferric-iron-, sulfate-respiration preceeding fermentation, methanogenesis and photosynthesis.
• Initially abundant electron acceptors: CO2, Fe(III+), S0 (present in traces SO42-, NO3-, O2).
• Initially abundant electron donors: reduced inorganic (and organic ?) compounds in hydrothermal fluids: H2, H2S, Fe(II+), Corg. favouring thermophilic chemolithotrophs.

 

4.4 Evolution from chemotrophic to phototrophic ways of life

• Methanogenesis might have preceeded photosynthesis. Was early photoynthesis recycling methane ?
• Prerequisites for using the energy of sunlight: pigment and protein complexes (light harvesting, reaction centers for near IR-radiation, 700 &endash;1100nm); exploitation of electron sources and aquisition of C-assimilation mechanism.
• How old are the photosystems and when and from where did photosystem II emerge ?
• Possible evolutionary sequence among the phototrophs: Heliobacterium spp. (gram+, low G+C) ý Chloroflexus spp. (diderm, but actually gram+) ý Cyanobacteria (some are gram +) ý Chlorobium spp. ý phototrophic Proteobacteria.
• Did ferrotrophic photosynthesis emerge before or after organotrophic photosynthesis ?
• Energetic prerequisites and advantages of chl-a-based oxic photosynthesis and of using H2O-electrons.
• Developing UV-radiation protection; "sunscreen pigments".
• Developing protection against oxygen poisoning: superoxide dismutases.
• Coping with the chemistry of iron in an oxic world: iron aquisition, siderophores, iron-containing proteins.
• Fundamental metabolic adaptations during the anoxic to oxic transition.

 

4.5 Sedimentary records of biogeochemical processes

• Microbial metabolites (activities) which are preserved in rocks.
• Life's geochemical and geophysical signatures: molecular fossils, biomarkers, hopanoids (bacteria), sterenes (eukarya), polyisokenoates (Archaea), kerogens, black shales, bio-minerals, BIF, sedimentary deposits, precambrian stromatolites, isotope fractionation.

 

4.6 The rock record vs. the genome record of microbial evolution.

• Evolutionary theory with microbial genomes: molecular history with genome sequence information.
• How old is the prokaryotic genome ?
• Genetic approaches to reconstruct geochemical processes.

5. Microbially dominated ecosystems.

 

5.1 Defining microbial ecosystems

• Ecosystems consist of habitats, conditions and organisms. Habitats separated by physically defined boundaries. Conditions are defined by chemical and physical determinants changing in time and space. Organisms, present as communities (= multitude of populations) can change conditions and migrate across boundaries. Cross-boundary transmitting agents: Arthropods, Chordates, Annelids, Protozoa; transport vehicles: water, aerosols, food; transport mechanisms: ingestion, inhalation, surface contact.
• Niches: physiologically defined ecosystem functions changing through the presence and the evolution of organims.
• Barriers are limitations for microbial migration and functioning. Physical barriers: temperature, radiation, pressure, pore size, adhesion attraction; chemical barriers: pH, salinity, oxidant, denaturant, surfactant, toxicity; biological barriers: immune response, trophic competition, predator-prey, viral attack, resistance, surface protection.
• The role of microbes in ecosystem functioning.
• Linking structures with functions in microbial ecosystems.

 

5.2 Biodiversity in functionally stabilized ecosystems (an overview).

• Diversity of aquatic ecosystems in altitudinal gradients and transients: nival zone, alpine, subalpine, highland, lowland, riverine, estuarine, littoral, shelf, continental slope, abyssal.
• Freshwater vs. marine habitats.
• Lakes and reservoirs in temperate and tropic climatic zones.
• Oxic and anoxic sediments of lakes and oceans.
• Subsurface aquifers: oligotrophy and bioremediation.
• Microbial mats and biofilms.
• Hot spring cyanobacterial mats.
• Hydrothermal vent environments.
• Cryoenvironments in snow and ice.
• Endolithic and rock surface environments (e.g. lichens).
• Syntrophy in animal digestive systems: gastro-intestinal tracts, microniches in gut habitats.
• Host-microbe interactions: plant, animal and human hosts for pathogens.
• Skin &endash; a dry hostile environment.

 

6. Ecological determinants which regulate microbial life

 

6.1 Definitions and abbreviations of ecological state parameters.

• Physical and chemical constraints: temperature, proton activity, water activity, hydrostatic pressure, wind forces and mixing of water and air masses, radiation.
• Chemical and trophic determinants: oxygen concentration, electron activity, sources of energy, electrons, mass, trace elements and oxidants.
• Accessibility of solid nutrient compounds from rocks, minerals, precipitates.
• Electron activities: the pe-concept
• Ecologically useful information derived from pe/pH stability diagrams.

 

7. Carbon cycling and carbonate buffering

 

7.1. Geochemistry of the carbon cycle

• Cycling of carbon between inorganic and organic compounds.
• State parameters which are altered by microbial activities in the carbon cycle: CT and ANC.
• Carbonate buffering capacity ß.
• Spacial and temporal changes in CT and ANC as represented in the ANC/CT -diagram.
• Alterations of ANC and CT by various bacterial lifestyles.
• Effects of acid rain on carbonate-buffered microbial ecosystems: e.g. remote mountain lake ecosystems in silicious rock areas.

 

8. Simulation of ecological determinants for the cultivation of microorganisms

 

8.1 Taming and domesticating microbial diversity

• Enrichment and isolation strategies.
• Composition of microbial diets (media).

 

8.2 Simulating conditions for growth in culture

• Static vs. continuous growth.
• Natural enrichments as sources for microorganisms.
• Evaluating diversity through enrichment culturing.
• Active in nature but not culturable yet: a consequence of our limited knowledge of microbial ecology.

 

9. Perception and responses to environmental variability and changes

 

9.1 Microbial strategies to survive environmental changes

• Adaptation and survival strategies, responses to nutrient starvation: cell cycles, resting or dormant stages, spore formation, storage of nutrients and oxidants.
• Life in gradients and transients: responses to environmental stimuli.
• Adaptation to rapid and extreme environmental changes.
• Life in physically and chemically harsh environments.
• Compatible solutes in non-halophilic bacteria as adaptation to osmolality changes.
• Defence: resistance development and propagation.
• Methods of evaluating gene expression in complex microbial ecosystems.

 

11. Bridging chemistry and microbial physiology

 

• Oxidation as the basic energy conversion process in all living organisms.
• Oxidation states of inorganic and organically bound bio-elements.
• Configuration and exchange of outer shell electrons in redox-processes involving bio-elements.
• Flow of electrons and protons in biochemical and geochemical cycles.
• The redox concept, basis of metabolism and global material cycles.
• Why P does not undergo biological redox-cycling.
• From metabolic to global electron sources and sinks.

 

12. Application of thermodynamics to environmental processes

 

• Thermodynamic laws and the calculation of free energies.
• Range of applicability of thermodynamic principles in microbial energetics.
• Free energies of reactions: terms, definitions and abbreviations.
• Application of thermodynamics in ecological processes:
• Direction and probability of reactions, exergonic and endergonic reactions,
• Alterations of ĘGr by microbially mediated processes,
• Influence of pH and temperature on ĘGr,
• Microbial activities which change the ion activity product and the solubility of minerals,
• Activities which alter redox conditions (Ępe).
• Thermodynamic modelling of microbial reactions: application of a simple calculation model.

 

 

13. From thermodynamics to bacterial lifestyles

 

• Microbial diversity emerges from the different ways microorganisms exploit environmental conditions.
• Major metabolic types: respiration, photosynthesis, fermentation.
• Diversity of life styles determined by electron acceptors.
• Life styles determined by electron donors.
• Life styles deduced from ways of carbon-assimilation.
• Life styles based on energy conversion mechanisms.

 

14. Ecoenergetic case studies

 

• Aerobic and anaerobic oxidation of ammonia.
• The missing link: ammonia-based photosynthesis.
• Acetogenic and sulfidogenic methanol utilization.
• Chemolithoautotrophic growth with reduced S-compounds & nitrate as electron acceptor: Thioploca sp.
• Interactions in anaerobic communities: a thermodynamic perspective.
• Syntrophobacter wolinii in association with hydrogenotrophs: predictions based on thermodynamics.
• Thermochemical energy yield from substrate oxidation with different oxidants.
• Anaerobic methane oxidation: a missing organism ?
• Growth efficiency of methanogens.
• Alteration of halogenated hydrocarbons through halorespiration.

 

15. Geomicrobiological processes in the sulfur cycle

 

• Aerobic and anaerobic sections of the sulfur cycle.
• Interaction among a great diversity of prokaryotes which drive sulfur cycling.
• Old and new "sulfur cycle bacteria and Archaea".
• Redox changes and chemical reactivity of sulfur compounds.
• S-cycling in the vicinity of hydrothermal deep sea vents.
• S-cycling in marine upwelling regions and cold seeps.

 

16. The role of sulfate and sulfur reducing bacteria

 

• Biography of S-reducing ¶-proteobacteria.
• Morphological and physiological diversity of a group with unique metabolic traits.
• Respiration with sulfate in comparison with nitrate and ferric iron respiration, etc.
• Complete and incomplete oxidation of substrates with sulfate and sulfur as electron acceptors.
• Pathways of dissimilatory metabolism.
• Efficiency of energy conversion: thermodynamic vs. actual energy yields.

 

17. Coupled phosphorus and iron cycling

 

17.1 The P- and Fe-cycles in sedimentary microbial ecosystems

• Concepts of microbial involvement in the iron and manganese redox cycles.
• Physiological consequences which follow from iron chemistry.
• Forms of sedimentary phosphorus.
• How anaerobic fermentation mediates the formation and dissolution of Fe/P-minerals.

 

17.2 Lake sediments: a case study

• Dynamics of microbial processes affecting P and Fe in sediments of a eutrophic lake: seasonally fluctuating environmental conditions at sediment-water interfaces.
• How to derive information about fluxes and rates from measurements of states at sediment-water interfaces.
• Ferric iron bound phosphorus: scanning EDX microscopy and chemical models for phosphorus integration into ferric iron(oxy)hydroxides.

 

17.3 Constitutive activities and adaptation of ecosystems

• Transition shift experiments in laboratory microcosms.
• Microbiologically mediated electron flow in anoxic sediments: a model on microbially mediated regulation of phosphorus release and retention.

 

18. Global biogeochemical cycling of elements

 

18.1 Biogeochemistry

• Time scales: Precambrian chemistry begins about at 4.6 eons (Gigayears ago); precambrian biology begins about 3.8 Gy ago; stromatolites (most common precambrian fossils) 2.2-3.4 eons; first 2-dimensional animal 1.2 eons.
• Interactions between global cycles of carbon, sulphur, nitrogen, phosphorus, iron and manganese.
• The role of microbes in Hadean to Proterozoic atmosphere and hydrosphere evolution.

 

18.2 Atmosphere/biosphere interactions

• The role of climate oscillations on biological evolution: how was prokaryotic evolution affected ?
• How oxigenic phototrophs changed atmospheric chemistry globally.
• Microbial regulation of atmospheric gases (O2, CO2, CH4, N2, N2O, NOx, DMSO).
• The contribution of aerobic C-1 oxidizers to global budgets of atmospheric trace gases.

 

18.3 Solid-state microbiology

• How microbes interact with mineral surfaces: weathering, corrosion, leaching.
• Natural weathering agents of microbial origin. Disturbance of weathering processes by anthropogenic pollutants.
• Active and passive formation of biominerals: intracellular and extracellular magnetite, nucleation of crystal formation on cell surfaces or inside cells.
• Biologically mediated mineral dissolution: acid-base reactions, redox processes, ligand mediated reactions.
• Microbially mediated formation of hydroxyapatite in sediments: a thermodynamic case study.
• Geomicrobiology and crustal evolution, effects of volcanism, plate tectonics, eustatic sea-level change, glaciation.
• Clay surfaces as early bio-informatic templates.

 

18.4 Carbon sinks and sources

• The microbe's role in "fossil fuel" formation, accumulation and cycling

 

18.5 Prokaryotic extremophiles

• Microbes which make use of redox-labile heavy metals (As, Se, Cr, Cu, Mo, Sb, U, etc.)
• Microbes which thrive under extremes of pH, salinity and temperature
• Strategies to overcome nutrient deprivation: transport efficiency, remaining very small (nanobes).

 

18.6 Metal-microbe interactions

• biosorption of metals
• bioaccumulation
• metal alkylation
• metal solubilization mechanisms
• industrial applications

 

A) Photosynthesis

 

 

19. Anoxigenic photosynthesis: processes and organisms

 

19.1 Light-driven redox processes.

• Electron sources for photosynthesis: oxidation of reduced sulfur, ferro-iron, hydrogen and carbon compounds.
• Missing processes: photosynthesis with methane (?), ammonia (?) are thermodynamically feasible
• Variations of van Niel's unifying concept of photosynthesis.

 

19.2 Morphological and physiological diversity

• Enrichment and isolation of anoxigenic phototrophic bacteria.
• Phylogeny of anaerobic phototrophs, a clue to the evolution of photosynthesis.
• Phenotypic traits of anoxic phototrophs: pigments, metabolism, membrane structures.
• Distinguishing features of Chromatiaceae, Ectothiorhodospiraceae, Chlorobiaceae, Heliobacteriaceae, "Chloroflexaceae" and Rhodospirillaceae.
• Pigment diversity: bacteriochlorophylls and carotenoids.
• Diversity of metabolisms: C-fixation and electron transfer in phototrophs.
• Phototrophs living chemotrophically: How phototrophs survive in the dark.

 

20. Ecology of anoxigenic phototrophic bacteria

• Redfield's formalism to describe photosynthetic biomass formation.
• Electron and carbon storage in phototrophs: sulfur and glycogen.
• Changes in habitat conditions due to photosynthetic activities.
• Natural enrichment of phototrophs in Lago Cadagno - a case study on photrophic bacteria in a meromictic lake: habitat characterization, light and hydrodynamic forces as ecological determinants, natural enrichment of phototrophic bacteria, adaptation and metabolic responses to environmental variability, orientation and swimming in light gradients.

 

21. Adaptation to material and energy gradients in microbial mats and biofilms.

 

• Phototrophic microbial mats as structured ecosystems: arrangements and topology.
• Ecological factors which determine structure and functionalities in mats.
• Consequences of diurnal light regimes.
• Physiology: shifts between sulfurogenic and oxigenic photosynthesis in Microcoleus mats.
• Respiratory activity in mats: shifts between sulfurotrophic and oxitrophic respiration.
• Interactions with other bacteria of the sulfur cycle.

 

22. Oxigenic photosynthesis by cyanobacteria and prochloron

 

• How oxigenic photosynthesis changed the earth's physicochemical environment.
• Geochemical consequences of oxygen release: oxidation of ferrous iron, establishing an ozon layer.
• Classification and distribution of oxigenic prokaryotes and eukaryotes.
• Pigments, photosystems and CO2-fixation mechanisms.
• Evolution of oxigenic photosynthesis in cyanobacteria-like ancestors.
• Phylogeny, diverse physiology, morphologies and universal distribution of cyanobacteria.
• Ancient and recent cyanobacterial stromatolites.

 

23. Cyanobacteria as sources for secondary metabolites

 

• Products of secondary metabolism: structural diversity and pharmacological/physiological effects of cyanobacterial metabolites.
• Distribution of the ability for toxin formation in cyanobacteria.
• Cyanobacterial toxins as "infochemicals".
• Biochemical, molecular and toxicological methods for the detection and identification of cyanobacterial toxins.
• Natural disasters created by toxic cyanobacterial metabolites: toxins in drinking water infiltration ponds and oligotrophic mountain lakes, harmful algal blooms.

B) Chemosynthesis

 

24. Diversity of C1-fixation pathways

 

• Growth on C1-compounds: carbondioxide, carbonmonoxide, methane, methanol, methylamines, formate and formaldehyde.
• Diversity of carboxylation reactions.
• CO2-fixation pathways: Calvin cyle (RuBP pathway), acetyl-CoA-pathway, reductive TCA, serin pathway, RuMP pathway.
• Evolutionary implication of the distribution of C1-fixing key enzymes.

 

25. Lithotrophy

 

• Modern and ancient lithotrophy among Archaea and Bacteria.
• Global appearance and distribution of inorganic energy- and electron sources: N-, S-, H-, C-, Mn- and Fe- compounds.
• Energetics of dissimilation reactions with inorganic electron donors.
• Coupling between chemolithotrophy and carbon assimilation.
• Prokaryotic versatility in creating membrane protentials by oxidizing inorganic electron donors.
• Coupling element cycles &endash; a prerequisite for lithotrophy.
• Evolution of global biogeochemical cycles in the anoxic Precambrium and adaptation to oxic conditions.

 

26. How microbes interact

 

• Communication between microbial cells: signal molecules and signaling.
• Interactions in biofilms, biofilm structures and conditions in biofilms.
• Interactions in gradients and transients: motility, chemotaxis, phototaxis.
• Bacterioplankton diversity on a microscale.
• Environmental influences on structures of microbial assemblages.
• Types of symbiotic interactions; intimacy (ecto-, endo); dependence (obligate, facultative); function (protection, syntrophism, gene exchange); evolution (optimization: rumen, luminescent fish, Rhizobia in leguminous plant roots, Rubbachia spp. in insects; algae, cyanobacteria, fungi and bacteria in lichens)
• Trophic interactions in synergistic symbioses.
• Trophic interactions in predation and parasitism.
• Population control by bacteriophages and viruses.
• Phototrophic consortia.

 

27. Interactions between prokaryotes

 

• Types of symbioses: mutualism, commensalism, antagonisms, neutralism.
• Examples of microbial symbioses: intestinal tracts, mouth, sediments, swamps, paddies, sewage digestors.
• Electron-donor regulated interactions: syntrophy in anaerobic methanogenic food chains.
• Carbon substrate syntrophy between Klebsiella sp. and Desulfovibrio sp.
• Mutualistic electron donor / electron acceptor interactions between sulfidogens and sulfidotrophs.
• Thermodynamically mandatory electron syntrophy: interspecies hydrogen transfer.
• Syntrophies for the anaerobic degradation of aromatic compounds.
• Interactions on the genetic level: gene exchange in nature.

 

28. Acetogenic prokaryotes in anaerobic food webs

 

• The role of acetogens in lake sediment food webs.
• Cytological and physiological differentiation of homoacetogens.
• Acetogenesis vs. methanogenesis: thermodynamics and substrate affinity.
• Broad substrate spectrum and carbohydrate fermentation by acetogens.
• C-Assimilation in the acetyl-CoA pathway in chemolithotrophic acetogens.

 

29. Microbe-macrobe interactions

 

• Eukaryotic microbial diversity.
• Bacterial endosymbioses:
• protozoa consume prokaryotes and create intracellular organelles with them.
• Bacteria interacting with fungi.
• Bacteria interacting with plants: The Agrobacterium-plant interaction.
• Root-microbe interactions.
• Plant pathogens and pests.
• Bacteria interacting with animals.
• Pathogenesis, an antiprotozoal defense of prey bacteria.
• Genetic properties and adaptation of Buchnera as an intracellular symbiont of aphids.
• The role of bacteria in aquatic and terrestrial food webs.

 

 

30. Technically and industrially important processes

 

30.1 Bioremediation

• The ecology of waste water treatment systems.
• Bioremediation with microbes.

 

30.2 Mining with microbes: The "Rock-eaters"

• Microbial mechanisms in copper and gold mining; large scale industrial applications.
• Bioremediation of metal-polluted soils and sediments; economic aspects
• Metal recovery from industrial wastes using microorganisms
• Biological treatment of solid wastes; case studies: fly ash, galvanic sludge, electronic waste

 

30.3 Industrial and medical applications

• Application of microbes with artificially modified genes (GMO).
• Genetic and biochemical stability of process bioreactors.
• Biosensors to study microbial interactions on a microscale.
• Therapeutic agents from microbially produced metabolites.

 

31. Ecology of clinically important microbes

 

31.1 Ecology of diseases

• Vectors, hosts, pathogens.
• Natural boundaries/barriers of human and animal body ecosystems. Health risks associated with pathogens crossing geographical and physical ecosystem-boundaries.
• How bacteria can become pathogens: either the entire organism or a particular product (toxin) are pathogenic. The role of the cell wall structure in pathogenicity.
• Clostridium botulinum: natural habitat soil, pathogenic by its toxin in human intestine.
• Legionella spp.: normal in aquatic habitats, pathogenic in lung after inhalation of aerosols.
• Vibrio cholerae: natural in open water, pathogenic in small intestine, diarrhea, dehydration, death after ingested through drinking water.
• Borrelia spp. living without iron.
• Ecology of old and re-emerging infectious diseases.
• The foodgrowing-transport-processing-nutrition network: Salmonella spp., Cyclosporidia, Hepatitis A.

 

31.2 Ecology of Malaria

• Host (Anopheles spp.), intermediate host (vertebrate erythrocyte), organisms (Plasmodium spp.), ecosystems (open water, insect gut wall, vertebrate blood). Defense strategies: reduce contact between ecological elements.

 

31.3 Defense mechanisms

• Immune response, antimicrobial defensins produced by eukaryotes.
• Mode of action and development of bacterial resistance to antibiotics.

 

31.4 Evolution of pahogenicity

• Models to study benign infections: Vibrio fisheri in the squid light organ.
• Microbial pathogenicity: ongoing evolution in the presence of other organisms.

 

32. Concepts in microbial ecology

 

• What are microbial ecosystems ?
• Characteristics of habitats, hosts, living conditions and composition of organismic populations.
• Ecologic resolution and dimensions: space, reactions in time, interactions between organisms.
• Microbially mediated reactions in global physiology: modern and acient biogeochemical cycles.
• Kinds of interactions between microbial populations.
• Principles of life derived from microbial ecology.
• Basic biological concepts emerging from studying prokaryote ecology.
• Limits for microbial existence are the limits of life.

 

33. Criteria for life: Applications to Exo- and Astrobiology

 

• Where did life originate, where did it evolve ? It must have developed rapidly during the precambrium on earth or it came from elsewhere.
• Searching for life on Mars: what are the facts which justify looking for it and the concepts to search for it ?
• Criteria for extraterrestrial life.
• Unique chemical signatures which identify life processes.
• Essential molecular components of living systems.
• How old is the genetic code ?
• Criteria for life and survival which determine the spreading of microorganisms on earth.

 

34. Levels of abstraction applied to the study of microbial ecology

 

• Why we abstract from nature's complexity.
• Models applicable to microbial ecology.
• Kinds of models, their formulation and what we can learn from them.
• Mathematical description of microcosm models.
• Growth models.

 

35. Defining complexity in microbial ecosystems

 

35.1 Complexity on the ecosystem level

• Microbial ecosystems are more than the sum of individual niches.
• Community structures: populations present, relative abundance of species, levels on which they interact (trophic, food web, genetic).
• Prerequisites for the study of microbial ecosystems: habitat physics, chemical conditions, organismic adaptation, niche diversification, genomic plasticity.
• Mass and energy flow through microbial ecosystems.
• Abiotic, biotic determinants which alter community structures.
• Macroecological patterns and events which regulate microbial ecosystems.
• Reconstructing microbial ecosystems.

 

35.2 Complexity on the cellular level

• Chemical signaling between cells.
• Microbial life cycles.
• Behavior which leads to cell aggregation.
• Features of a hypothetical "minimum cell".

 

36. Microbial ecology in the modern era of biology

 

• Still a microbe-dominated world.
• The microbial ecologist's contributions to discussions on biological risks and safety.
• Balance between microbes and macrobes.
• Epidemiology - ecology of infectious diseases.
• Disease - evolving symbiosis.
• Gene spreading under natural conditions.
• To what extent has horizontal gene transfer affected the evolution towards diversity ?
• Is sex species-restricted in prokaryotes as well or only in eukaryotes ?