microorganisms in their environment and in pure culture,
which, although microorganisms have been isolated from
their environment, can permit to understand them from a
functional point of view and thus their metabolic potential.
It is through these global studies that scientists have been able
to demonstrate the key role of microorganisms in the balance
of biogeochemical cycles, in the restoration of environments
polluted by various chemicals, in the biodegradation or biotransformation of persistent organic pollutants, of heavy
metals, etc. Thus, microbial ecology is now becoming an
important discipline whose practical implications are obvious
and at the service of human activities that aim at maintaining
our environment livable and make development sustainable.
2.2
On the Path to Discovery
of Microorganisms
Although microorganisms are present all over the earth
where they are the most abundant living beings, it was not
until the mid-seventeenth century with the invention of the
microscope that they were actually seen. An English philosopher, Robert Hooke, was the first to observe and to describe
in 1655, using a microscope, various types of fungi (molds)
and protozoa. However, it appears he was not able to observe
bacteria, given the low quality of the lens he used. Soon
after, a French scientist Louis Joblot (1645–1723) constructed different types of microscopes with which he
observed the morphologies of many microorganisms. Born
in Bar-le-Duc, he was appointed “Royal” professor of mathematics and taught mathematics and geometry at the Royal
Academy of Painting and Sculpture in Paris; he devoted
much of his time to develop microscopes with which he
described many “animalcules” and other microscopic
“snakes, fish and eels” he observed in infused preparations
of various plants or vinegar, and “the largest part is invisible
to the ordinary scope of our eyes.” He published his
descriptions and drawings in a book published in 1718:
“Descriptions and uses of several new microscopes and
New observations on many insects, and on Animalcules
which are present in prepared liquors and those are not so”
(Lechevalier 1976; Le Coustumier 2010). Among unicellular microorganisms, he observed probably bacteria (“tiny
eels and snakes of vinegar”).
At the same time, Antoni van Leeuwenhoek (1674–1723,
Fig. 2.1a), a cloth merchant and amateur scientist from Delft
(Holland), created a very simple type of microscope with
higher magnification (Leeuwenhoek microscope, Fig. 2.1b)
to control the quality of the threads of sheets and other
woven wares for commercial purposes (Dobell 1923). By
observing different samples (pond water, maceration of
plants, biological fluids, etc.), he was surprised to find
through his microscopic lenses tiny organisms with
particular forms “apparently moving with a purpose.” He
thus watched many types of single-celled eukaryotes and
even bacteria. In a series of letters to the Royal Society in
London, he described and drew different bacterial forms
(cocci, rods, spirilla), indicating their movement and behavior when they were placed under different physicochemical
conditions, paving the way for the first microbial ecology
observations. With his observations and discoveries of
microbes in different biotopes, he firmly opposed the
supporters of spontaneous generation, who at that time,
believed that microorganisms resulted from the decay of
organic matter and not the reverse. For example, in that
perspective, meat “engendered” microorganisms through
its own decay. A century later, the Italian naturalist Lazzaro
Spallanzani (1729–1799), in order to disprove this theory,
showed that the decomposition of organic substances was
caused by microorganisms that were not spontaneous but
that these multiplied by cell division and could be eliminated
by heating. He tried to explain to proponents of spontaneous
generation that substances heated and separated from ambient air in a tight manner could not decompose and yield
microorganisms, but could be kept without microbial
attacks. However, his works were not totally conclusive
because some samples contained bacteria capable of
withstanding the heat treatments he used (spore-forming or
heat-resistant bacteria). These results have provided
arguments for the theory of spontaneous generation which
persisted in spite of that work. Charles Cagniard-Latour
(1838), Theodor Schwann (1837), and Friedrich Ku ¨tzing
(1837) have, in turn, attempted to disprove this theory by
highlighting the role of yeasts in the fermentation of sugars
to alcohol: fermentation was shown not to occur in the
absence of yeast. They described the yeasts present in
fermenting wine and beer and showed their role in the
fermentation of sugars. In addition, Schwann (1837)
demonstrated the role of airborne microorganisms in the
breakdown of sugars by an experimental setup (vials with a
narrow tube heated to incandescence), which allowed to
leave sugars in contact with air while preventing the penetration of microbes in the heated and sterilized tubing. In a
control flask open to air, organic matter was decomposed
while in the bottle with the heat-sterilized narrow tube,
organic matter in contact with sterilized air did not decompose. However, these experiences were not enough to convince supporters of the spontaneous generation theory who
persisted in maintaining that heating of the tubes to incandescence modified the air quality in the bottles and that
“disturbed air prevented the phenomenon of decomposition
and spontaneous generation.” It was not until the work of
Louis Pasteur, who confirmed in a series of experiments
(Pasteur 1857, 1860) the role of microorganisms in fermentation, that the theory of spontaneous generation was definitely disproved. Using narrow tubing vials, curved (swan
10
P. Caumette et al.
which, although microorganisms have been isolated from
their environment, can permit to understand them from a
functional point of view and thus their metabolic potential.
It is through these global studies that scientists have been able
to demonstrate the key role of microorganisms in the balance
of biogeochemical cycles, in the restoration of environments
polluted by various chemicals, in the biodegradation or biotransformation of persistent organic pollutants, of heavy
metals, etc. Thus, microbial ecology is now becoming an
important discipline whose practical implications are obvious
and at the service of human activities that aim at maintaining
our environment livable and make development sustainable.
2.2
On the Path to Discovery
of Microorganisms
Although microorganisms are present all over the earth
where they are the most abundant living beings, it was not
until the mid-seventeenth century with the invention of the
microscope that they were actually seen. An English philosopher, Robert Hooke, was the first to observe and to describe
in 1655, using a microscope, various types of fungi (molds)
and protozoa. However, it appears he was not able to observe
bacteria, given the low quality of the lens he used. Soon
after, a French scientist Louis Joblot (1645–1723) constructed different types of microscopes with which he
observed the morphologies of many microorganisms. Born
in Bar-le-Duc, he was appointed “Royal” professor of mathematics and taught mathematics and geometry at the Royal
Academy of Painting and Sculpture in Paris; he devoted
much of his time to develop microscopes with which he
described many “animalcules” and other microscopic
“snakes, fish and eels” he observed in infused preparations
of various plants or vinegar, and “the largest part is invisible
to the ordinary scope of our eyes.” He published his
descriptions and drawings in a book published in 1718:
“Descriptions and uses of several new microscopes and
New observations on many insects, and on Animalcules
which are present in prepared liquors and those are not so”
(Lechevalier 1976; Le Coustumier 2010). Among unicellular microorganisms, he observed probably bacteria (“tiny
eels and snakes of vinegar”).
At the same time, Antoni van Leeuwenhoek (1674–1723,
Fig. 2.1a), a cloth merchant and amateur scientist from Delft
(Holland), created a very simple type of microscope with
higher magnification (Leeuwenhoek microscope, Fig. 2.1b)
to control the quality of the threads of sheets and other
woven wares for commercial purposes (Dobell 1923). By
observing different samples (pond water, maceration of
plants, biological fluids, etc.), he was surprised to find
through his microscopic lenses tiny organisms with
particular forms “apparently moving with a purpose.” He
thus watched many types of single-celled eukaryotes and
even bacteria. In a series of letters to the Royal Society in
London, he described and drew different bacterial forms
(cocci, rods, spirilla), indicating their movement and behavior when they were placed under different physicochemical
conditions, paving the way for the first microbial ecology
observations. With his observations and discoveries of
microbes in different biotopes, he firmly opposed the
supporters of spontaneous generation, who at that time,
believed that microorganisms resulted from the decay of
organic matter and not the reverse. For example, in that
perspective, meat “engendered” microorganisms through
its own decay. A century later, the Italian naturalist Lazzaro
Spallanzani (1729–1799), in order to disprove this theory,
showed that the decomposition of organic substances was
caused by microorganisms that were not spontaneous but
that these multiplied by cell division and could be eliminated
by heating. He tried to explain to proponents of spontaneous
generation that substances heated and separated from ambient air in a tight manner could not decompose and yield
microorganisms, but could be kept without microbial
attacks. However, his works were not totally conclusive
because some samples contained bacteria capable of
withstanding the heat treatments he used (spore-forming or
heat-resistant bacteria). These results have provided
arguments for the theory of spontaneous generation which
persisted in spite of that work. Charles Cagniard-Latour
(1838), Theodor Schwann (1837), and Friedrich Ku ¨tzing
(1837) have, in turn, attempted to disprove this theory by
highlighting the role of yeasts in the fermentation of sugars
to alcohol: fermentation was shown not to occur in the
absence of yeast. They described the yeasts present in
fermenting wine and beer and showed their role in the
fermentation of sugars. In addition, Schwann (1837)
demonstrated the role of airborne microorganisms in the
breakdown of sugars by an experimental setup (vials with a
narrow tube heated to incandescence), which allowed to
leave sugars in contact with air while preventing the penetration of microbes in the heated and sterilized tubing. In a
control flask open to air, organic matter was decomposed
while in the bottle with the heat-sterilized narrow tube,
organic matter in contact with sterilized air did not decompose. However, these experiences were not enough to convince supporters of the spontaneous generation theory who
persisted in maintaining that heating of the tubes to incandescence modified the air quality in the bottles and that
“disturbed air prevented the phenomenon of decomposition
and spontaneous generation.” It was not until the work of
Louis Pasteur, who confirmed in a series of experiments
(Pasteur 1857, 1860) the role of microorganisms in fermentation, that the theory of spontaneous generation was definitely disproved. Using narrow tubing vials, curved (swan
10
P. Caumette et al.