In all layers of the ground, microorganisms are diverse and abundant. They feed off dead organic material that they cut into fine particles, making the material easily assimilated by all types of plants. As the decomposers of organic waste and the agents of demineralisation, microorganisms are responsible for the cycling of matter on Earth.

Microorganisms of the deep

Soils are characterized by layers of variable thickness and structure. Each layer differs from the preceding and following ones in colour, texture, structure, porosity, pH, and organic and mineral content. These distinct characteristics then influence the humidity, as well as the gaseous and biological contents of the different layers of soil. A layer rich in organic matter, where great biological activity exists, is quite different from a stone layer with little organic content and therefore little biological activity.

Bacteria live thousands of metres under the surface of the earth, in the underground petroleum reservoirs. Some bacteria use gaseous hydrogen as an energy source as well as the Read More
In all layers of the ground, microorganisms are diverse and abundant. They feed off dead organic material that they cut into fine particles, making the material easily assimilated by all types of plants. As the decomposers of organic waste and the agents of demineralisation, microorganisms are responsible for the cycling of matter on Earth.

Microorganisms of the deep

Soils are characterized by layers of variable thickness and structure. Each layer differs from the preceding and following ones in colour, texture, structure, porosity, pH, and organic and mineral content. These distinct characteristics then influence the humidity, as well as the gaseous and biological contents of the different layers of soil. A layer rich in organic matter, where great biological activity exists, is quite different from a stone layer with little organic content and therefore little biological activity.

Bacteria live thousands of metres under the surface of the earth, in the underground petroleum reservoirs. Some bacteria use gaseous hydrogen as an energy source as well as the carbon from carbon dioxide, even though it is inorganic. These bacteria excrete simple organic compounds that are in turn consumed by other bacteria. These microorganisms can live indefinitely without carbon from the surface, since the essential nutrients are constantly renewed in their environment.

In rock formations where energy sources and food are rare, bacteria have adapted by shrinking in size from a few microns to less than one micron. By using their reserves during periods of deprivation, they have permanently slowed down their metabolism. Their cell division occurs only once per century or less, whereas bacteria on the surface reproduce within a few minutes, a few hours, or at most a few months.

The role of microorganisms in recycling

Microorganisms play a key role in preserving life on Earth by acting as a link between animals and plants. Responsible for numerous transformations, they convert dead animals and plants into simple inorganic substances that feed the plants, which in turn will become food for animals. Microorganisms are indispensable for many essential biochemical processes that result in recycling elements such as sulphur, nitrogen, and carbon.

© Armand-Frappier Museum, 2008. All rights reserved.

Some fungi are near the soil surface where oxygen is more easily obtained: Penicillium, Mucor, Rhizopus, Fusarium, Cladosporium, Aspergillus and Trichoderma.

Dennis Kunkel Microscopy, Inc.

© Dennis Kunkel Microscopy, Inc.


Soil bacterium.

Dennis Kunkel Microscopy, Inc.

© Dennis Kunkel Microscopy, Inc.


Pseudomonas spp. are able to grow in extreme environments like carbon or hydrocarbon source.

Dennis Kunkel Microscopy, Inc.

© Dennis Kunkel Microscopy, Inc.


There is very little nitrogen in mineral form, but the atmosphere contains up to 78 million kg of gaseous nitrogen, N2 over every hectare of land. It is very stable and represents 79 % of the atmosphere. Even though it is essential for protein synthesis, nitrogen in its gaseous form cannot be assimilated by most living beings.

Bacteria Azotobacter, Clostridium and blue algae transforming N2 into ammonia (NH3) usable by plants and other bacteria (arrow pointing from NH3 to a plant). Thanks to the food chain, nitrogen then becomes a constituent of animals. Excrement, carcasses, and dead plants are waste products that contain organic nitrogen. These wastes are transformed into ammonia (NH3) by bacteria that participate in the decomposition process. Nitrification is the process by which ammonia is transformed by nitrifying bacteria (e.g. Nitrosomonas into nitrite (NO2-) and then into nitrate (NO3-) by Nitrobacters. These nitrates can then be transformed into N2, which is returned into the atmosphere through a denitrification process carried out b Read More
There is very little nitrogen in mineral form, but the atmosphere contains up to 78 million kg of gaseous nitrogen, N2 over every hectare of land. It is very stable and represents 79 % of the atmosphere. Even though it is essential for protein synthesis, nitrogen in its gaseous form cannot be assimilated by most living beings.

Bacteria Azotobacter, Clostridium and blue algae transforming N2 into ammonia (NH3) usable by plants and other bacteria (arrow pointing from NH3 to a plant). Thanks to the food chain, nitrogen then becomes a constituent of animals. Excrement, carcasses, and dead plants are waste products that contain organic nitrogen. These wastes are transformed into ammonia (NH3) by bacteria that participate in the decomposition process. Nitrification is the process by which ammonia is transformed by nitrifying bacteria (e.g. Nitrosomonas into nitrite (NO2-) and then into nitrate (NO3-) by Nitrobacters. These nitrates can then be transformed into N2, which is returned into the atmosphere through a denitrification process carried out by many bacterial species such as Paracoccus denitrificans. In this way, nitrogen circulates in the biosphere and gets transformed from one organism to the next. Nitrates (NO3-) also fertilize plants, which absorb them through their roots and use them to synthesize amino acids and then proteins.

© Armand-Frappier Museum, 2008. All rights reserved.

Nitrogen cycle

Photo : Chantal Bourgault, Cinémanima inc.

© Chantal Bourgault, Cinémanima inc.


The atmosphere over one hectare of land contains fifty tons of carbon dioxide (CO2), and living organisms return fifty tons to the atmosphere each year. Carbon dioxide can be transformed into organic compounds by green plants, algae, cyanobacteria, purple and green phototrophic bacteria, and chemo-autotrophic bacteria.

These organisms use carbohydrates, which they produce by fixation of CO2, to build complex organic compounds such as cellulose. Bacteria and fungi use two enzymes to degrade cellulose, which is present in dead plants, into glucose. This glucose can then be used by many types of microorganisms. Complete oxidation of glucose produces H2O and CO2. Carbon dioxide is not produced solely by carbohydrate decomposition. It is also generated by decomposition of amino acids from proteolysis and decomposition of fatty acids from the decomposition of lipids.
The atmosphere over one hectare of land contains fifty tons of carbon dioxide (CO2), and living organisms return fifty tons to the atmosphere each year. Carbon dioxide can be transformed into organic compounds by green plants, algae, cyanobacteria, purple and green phototrophic bacteria, and chemo-autotrophic bacteria.

These organisms use carbohydrates, which they produce by fixation of CO2, to build complex organic compounds such as cellulose. Bacteria and fungi use two enzymes to degrade cellulose, which is present in dead plants, into glucose. This glucose can then be used by many types of microorganisms. Complete oxidation of glucose produces H2O and CO2. Carbon dioxide is not produced solely by carbohydrate decomposition. It is also generated by decomposition of amino acids from proteolysis and decomposition of fatty acids from the decomposition of lipids.

© Armand-Frappier Museum, 2008. All rights reserved.

Carbon cycle

Photo : Chantal Bourgault, Cinémanima inc.

© Chantal Bourgault, Cinémanima inc.


In its elementary form, sulphur cannot be used by either plants or animals. Yet some bacteria can oxidize sulphur into sulphate which is easily used by all forms of life. Plants, for example, get the sulphur they need from sulphates in order to synthesize some amino acids (cystine, cysteine, methionine) that are in turn essential for protein synthesis.

Bacteria Thiobacillus thiooxidans oxidize sulphur into sulphate (SO42-). This is an aerobic chemo-autotrophic process during which acid is produced, resulting in a lowering of the pH of alkaline soils. Dead plants and soil microorganisms degrade sulphur-containing proteins into amino acids. These are degraded by an enzyme called desulfurase found in anaerobic bacteria of the genus Desulfotomaculum. Sulphur is released as hydrogen sulphide (H2S). Some species of green and purple phototrophic bacteria can oxidize hydrogen sulphide produced by sulphate reduction and amino acid decomposition. This oxidation process produces elemental sulphur (S).
In its elementary form, sulphur cannot be used by either plants or animals. Yet some bacteria can oxidize sulphur into sulphate which is easily used by all forms of life. Plants, for example, get the sulphur they need from sulphates in order to synthesize some amino acids (cystine, cysteine, methionine) that are in turn essential for protein synthesis.

Bacteria Thiobacillus thiooxidans oxidize sulphur into sulphate (SO42-). This is an aerobic chemo-autotrophic process during which acid is produced, resulting in a lowering of the pH of alkaline soils. Dead plants and soil microorganisms degrade sulphur-containing proteins into amino acids. These are degraded by an enzyme called desulfurase found in anaerobic bacteria of the genus Desulfotomaculum. Sulphur is released as hydrogen sulphide (H2S). Some species of green and purple phototrophic bacteria can oxidize hydrogen sulphide produced by sulphate reduction and amino acid decomposition. This oxidation process produces elemental sulphur (S).

© Armand-Frappier Museum, 2008. All rights reserved.

Sulphur cycle

Photo : Chantal Bourgault, Cinémanima inc.

© Chantal Bourgault, Cinémanima inc.


Microorganisms are found as transient and variable inhabitants of the air. The air carries dust and water drops from the surface of the earth, the oceans and other bodies of water, which are loaded with microorganisms. These particles can settle rapidly or be carried for metres, even kilometres. Some microorganisms die in fractions of a second once in the atmosphere, while others survive for years. Algae, protozoa, yeasts, moulds, bacteria, and viruses have been isolated from air. In the urban atmosphere, mould spores, especially those of the genus Cladosporium, are the most common microorganisms.
Microorganisms are found as transient and variable inhabitants of the air. The air carries dust and water drops from the surface of the earth, the oceans and other bodies of water, which are loaded with microorganisms. These particles can settle rapidly or be carried for metres, even kilometres. Some microorganisms die in fractions of a second once in the atmosphere, while others survive for years. Algae, protozoa, yeasts, moulds, bacteria, and viruses have been isolated from air. In the urban atmosphere, mould spores, especially those of the genus Cladosporium, are the most common microorganisms.

© Armand-Frappier Museum, 2008. All rights reserved.

Microorganisms are naturally present on the skin and in some ecological niches of the human body. They are generally harmless if they are controlled and balanced. Their presence could even provide some protection, by preventing pathogenic microorganisms from invading.
Microorganisms are naturally present on the skin and in some ecological niches of the human body. They are generally harmless if they are controlled and balanced. Their presence could even provide some protection, by preventing pathogenic microorganisms from invading.

© Armand-Frappier Museum, 2008. All rights reserved.

Inhabitants of the human body

Armand-Frappier Museum

© Armand-Frappier Museum, 2008. All rights reserved.


Learning Objectives

The learner will:
  • familiarize himself with the vocabulary used in microbiology;
  • explain the relationship between developments in imaging technology and the current understanding of the cell;
  • identify which microorganisms are infectious, how the immune system fights against them, and the reinforcements of modern medicine;
  • describe the benefits of microorganisms .

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