Microbiology
Introduction ............................................................................................................................................. 2
Microbial cell structure............................................................................................................................ 4
Microbial locomotion .............................................................................................................................. 7
Microbial growth ..................................................................................................................................... 8
Nutrition and culture of microorganisms .............................................................................................. 13
Metabolism of microorganisms ............................................................................................................. 14
Diversity of bacteria............................................................................................................................... 18
Ecology of microbes............................................................................................................................... 22
Nutrient cycles ....................................................................................................................................... 25
Microbial symbiosis ............................................................................................................................... 26
Viruses ................................................................................................................................................... 30
Microbes in industry .............................................................................................................................. 33
,Introduction
Microbe = what we cannot see by eye (< 100 µm) → bacteria, viruses, yeasts, protists and fungi.
Archaea: look like bacteria but live in more extreme environments.
Relevance
- Easy to grow and manipulate → good models for medicine, agriculture & food, industry,…
- Oldest form of life and high biomass
→ On Earth same biomass as plants.
- Important in biogeochemical processes: carbon, nitrogen,… cycle
→ cells are key reservoirs of essential elements.
→ High amount of O2 because of past microbial activity.
- Other life depends on microbes (hydrothermal vents/rumen microbiota)
- Everywhere, also most extreme conditions: high radiation (black pigment makes growing under
radiation faster → Cryptococcus neoformans: also lives in dishwasher).
Cells
Can be cultivated: each dot is a colony of billions of prokaryotic cells, all originate from the same
individual (genetically identical).
Prokaryotic microbes share same organization: nucleoid (with genetic material), cytoplasmic
membrane (barrier that separates inside from outside) and cell wall (present in most microbes).
→ Fungi, yeast, protists and algae are eukaryotes: more cell organelles and much larger than
prokaryotes (bacteria and archaea).
➔ Metabolism adapts: ability lies in genes.
Genome sequencing with circular genome (1 chromosome).
Pseudomonas looks green-blue in culture: pigment to catch iron.
➔ Inner and outer wheel: blue is coding for protein → 6 mil. base pairs.
➔ Genomes can be easily modified with genes from other organisms.
➔ Plasmids: small circular DNA with few thousand bp → important for evolution: microbes
evolve fast via genetic exchange (conjugation, transformation and transduction).
➔ Genome size small (few mil. bp and few thousand genes), viruses smallest.
➔ High variability within prokaryotes linked to lifestyle: how depended organisms is → free living
needs bigger genomes. Gene loss by relying on host: pathogens have small genome.
Resistance to antibiotics → combine antibiotics to slow down the adaptation.
Microbes can move (motility: taxis), differentiate (spores) and communicate (via chemicals) in their
environment. Ex. test tube with solid medium and bacteria react with medium → black colour to
follow the motility, to know if bacteria is able to move and contains flagella. Dental plaque: example
of biofilm → bacteria communicate to form superstructure. Some bacteria are bioluminescent.
Ecology
Ex. Glacier ecosystem: different habitats (ice, snow, air, streams) including humans (microbiome on
skin, in nose, gut) → characterized by specific microbial community.
Microbial communities are shaped by and shape their environment:
→ pH, nutrients, temperature, humidity, O2, pressure.
→ decomposition, algal blooms in lakes.
, Evolution
Few fossils → use DNA markers from rRNA present in all bacteria.
Genetic marker: reconstruct phylogeny → evolves slowly.
Bacteria, Archaea and eukaryotes are 3 different parts of evolution from LUCA: Last Universal
Common Ancestor.
Microbes are old → time to adapt to all possible habitats = found everywhere: oceanic and terrestrial
surfaces and subsurfaces.
Impact on humans
Both beneficial and harmful:
Lactobacillus bulgaricus → yogurt, versus Streptococcus pneumoniae → pneumonia.
Harmful ones are most known ex. Xylella fastidiosa (on olive trees). But most microbes are beneficial
or neutral.
- Microorganisms affects our agriculture positively and negatively: nitrogen-fixing bacteria,
regeneration of nutrients in soil and water, diseases in plants and animals.
- Microorganisms affects our food positively and negatively: fermentation, spoilage (blue
cheese is made of rotten bread).
- Microorganisms can be used in industry: energy (biofuel), mining, antibiotics, bioremediation
(depollution of water and soil with oyster mushroom).
- Microorganisms can be used in genetic engineering: produce antibiotics, enzymes and
chemicals → Aspergillus niger.
History of microbiology
Beginnings of microscopy by Antoni van Leeuwenhoek and Robert Hooke → illustrated fruiting
structures of mold: no insights on how the organism’s function.
Ferdinand Cohn founded bacterial classification and discovered endospores → functional knowledge
on microorganisms.
Louis Pasteur: developed vaccines and disproved theory of spontaneous generation (“out of thin
air”) → contamination: led to development of methods for controlling growth of microorganisms.
Liquid with microbes: neck of flask sterilised and boiling liquid: sterile for a long time because
microorganisms can’t get to the liquid. Control to contaminate the liquid by tipping the flask.
Robert Koch: link between microbes and infectious diseases like tuberculosis.
Koch’s postulates = population of animals (some are sick), suspected pathogen must be in all sick
animals and not in healthy animals and it must be grown in pure culture (to be able to grow and
isolate it from sick animals → cells will grow outside of the dead animal) and if these cells from
culture are put in a healthy animals they will get sick, if pathogen is isolated from the sick animal and
reisolated it will be the same as the original.
For pathogens we cannot grow → genomics, like black death: extracting DNA from skeletons.
Microbes drive nutrient cycles, chemolithotrophy = gain chemical energy from mineral nutrients, N
fixation = transforming N from the atmosphere into something that can be taken up by organisms.
Introduction ............................................................................................................................................. 2
Microbial cell structure............................................................................................................................ 4
Microbial locomotion .............................................................................................................................. 7
Microbial growth ..................................................................................................................................... 8
Nutrition and culture of microorganisms .............................................................................................. 13
Metabolism of microorganisms ............................................................................................................. 14
Diversity of bacteria............................................................................................................................... 18
Ecology of microbes............................................................................................................................... 22
Nutrient cycles ....................................................................................................................................... 25
Microbial symbiosis ............................................................................................................................... 26
Viruses ................................................................................................................................................... 30
Microbes in industry .............................................................................................................................. 33
,Introduction
Microbe = what we cannot see by eye (< 100 µm) → bacteria, viruses, yeasts, protists and fungi.
Archaea: look like bacteria but live in more extreme environments.
Relevance
- Easy to grow and manipulate → good models for medicine, agriculture & food, industry,…
- Oldest form of life and high biomass
→ On Earth same biomass as plants.
- Important in biogeochemical processes: carbon, nitrogen,… cycle
→ cells are key reservoirs of essential elements.
→ High amount of O2 because of past microbial activity.
- Other life depends on microbes (hydrothermal vents/rumen microbiota)
- Everywhere, also most extreme conditions: high radiation (black pigment makes growing under
radiation faster → Cryptococcus neoformans: also lives in dishwasher).
Cells
Can be cultivated: each dot is a colony of billions of prokaryotic cells, all originate from the same
individual (genetically identical).
Prokaryotic microbes share same organization: nucleoid (with genetic material), cytoplasmic
membrane (barrier that separates inside from outside) and cell wall (present in most microbes).
→ Fungi, yeast, protists and algae are eukaryotes: more cell organelles and much larger than
prokaryotes (bacteria and archaea).
➔ Metabolism adapts: ability lies in genes.
Genome sequencing with circular genome (1 chromosome).
Pseudomonas looks green-blue in culture: pigment to catch iron.
➔ Inner and outer wheel: blue is coding for protein → 6 mil. base pairs.
➔ Genomes can be easily modified with genes from other organisms.
➔ Plasmids: small circular DNA with few thousand bp → important for evolution: microbes
evolve fast via genetic exchange (conjugation, transformation and transduction).
➔ Genome size small (few mil. bp and few thousand genes), viruses smallest.
➔ High variability within prokaryotes linked to lifestyle: how depended organisms is → free living
needs bigger genomes. Gene loss by relying on host: pathogens have small genome.
Resistance to antibiotics → combine antibiotics to slow down the adaptation.
Microbes can move (motility: taxis), differentiate (spores) and communicate (via chemicals) in their
environment. Ex. test tube with solid medium and bacteria react with medium → black colour to
follow the motility, to know if bacteria is able to move and contains flagella. Dental plaque: example
of biofilm → bacteria communicate to form superstructure. Some bacteria are bioluminescent.
Ecology
Ex. Glacier ecosystem: different habitats (ice, snow, air, streams) including humans (microbiome on
skin, in nose, gut) → characterized by specific microbial community.
Microbial communities are shaped by and shape their environment:
→ pH, nutrients, temperature, humidity, O2, pressure.
→ decomposition, algal blooms in lakes.
, Evolution
Few fossils → use DNA markers from rRNA present in all bacteria.
Genetic marker: reconstruct phylogeny → evolves slowly.
Bacteria, Archaea and eukaryotes are 3 different parts of evolution from LUCA: Last Universal
Common Ancestor.
Microbes are old → time to adapt to all possible habitats = found everywhere: oceanic and terrestrial
surfaces and subsurfaces.
Impact on humans
Both beneficial and harmful:
Lactobacillus bulgaricus → yogurt, versus Streptococcus pneumoniae → pneumonia.
Harmful ones are most known ex. Xylella fastidiosa (on olive trees). But most microbes are beneficial
or neutral.
- Microorganisms affects our agriculture positively and negatively: nitrogen-fixing bacteria,
regeneration of nutrients in soil and water, diseases in plants and animals.
- Microorganisms affects our food positively and negatively: fermentation, spoilage (blue
cheese is made of rotten bread).
- Microorganisms can be used in industry: energy (biofuel), mining, antibiotics, bioremediation
(depollution of water and soil with oyster mushroom).
- Microorganisms can be used in genetic engineering: produce antibiotics, enzymes and
chemicals → Aspergillus niger.
History of microbiology
Beginnings of microscopy by Antoni van Leeuwenhoek and Robert Hooke → illustrated fruiting
structures of mold: no insights on how the organism’s function.
Ferdinand Cohn founded bacterial classification and discovered endospores → functional knowledge
on microorganisms.
Louis Pasteur: developed vaccines and disproved theory of spontaneous generation (“out of thin
air”) → contamination: led to development of methods for controlling growth of microorganisms.
Liquid with microbes: neck of flask sterilised and boiling liquid: sterile for a long time because
microorganisms can’t get to the liquid. Control to contaminate the liquid by tipping the flask.
Robert Koch: link between microbes and infectious diseases like tuberculosis.
Koch’s postulates = population of animals (some are sick), suspected pathogen must be in all sick
animals and not in healthy animals and it must be grown in pure culture (to be able to grow and
isolate it from sick animals → cells will grow outside of the dead animal) and if these cells from
culture are put in a healthy animals they will get sick, if pathogen is isolated from the sick animal and
reisolated it will be the same as the original.
For pathogens we cannot grow → genomics, like black death: extracting DNA from skeletons.
Microbes drive nutrient cycles, chemolithotrophy = gain chemical energy from mineral nutrients, N
fixation = transforming N from the atmosphere into something that can be taken up by organisms.
