or nitrite, coupling it to the release of energy (cf. Sect. 3.3.
2).
2. Chemolithotrophic prokaryotes are autotrophic.
3. The demonstration of the physiological process of bacterial nitrogen fixation previously discovered by Beijerinck
in 1888.
Before concluding this summary of the work of S.
Winogradsky, it is necessary to present his thoughts on the
main methods to study microorganisms in the environment;
based on the recommendations stated in his monograph, he
initiated a number of research themes in contemporary
microbial ecology.
Without underestimating the value of pure cultures, he
insisted on the limitations of axenic cultures, “absolutely
impossible in nature,” that moreover remove a microorganism
from its biotic and abiotic environment and place it under
artificial conditions, “sometimes bordering on pathology”.
Another disadvantage of this approach is that the study of
population dynamics is impossible. Moreover, “protected as
it is in its jar,” the organism is not subject to competition, and
more generally it eliminates interactions with other organisms.
From these remarks, he stressed the difficulty of extrapolating
the results obtained in pure culture to the natural environment.
He was also aware of the diversity of the microflora of the
natural environment “that provides a habitat for a swarming
mass of microscopic organisms, a variety that defies imagination.” He showed that few organisms can be isolated in axenic
culture: the culture, on “conventional” media, thus only
providing an overview of diversity. For example, he found
that direct counting by microscopic examination yielded
counts of billions of cells per gram of soil, while the counting
of bacterial colonies on standard culture media did not exceed
several tens of millions. He concluded that “therefore only a
small part, comprising only 10 to 5 %, sometimes less, of the
total population.” It is now well established (thanks to molecular biology techniques) that only 0.1–1 % of bacteria are
grown on media conventionally used in microbiology.
He also drew attention to the fact that in the natural
environment, namely, the soil, “the vast majority of germs,
at some point, are in a state of latent life, only a minority
being in an active state.” This question led to the notion of
the physiological state of a microorganism that will determine its activity level and survival, in particular, its ability to
grow on a culture medium, some microorganisms being
“viable” but “nonculturable,” unable to divide while
retaining some of their physiological functions (cf. Sect.
15.8). About survival, especially under conditions of dietary
deficiency, he felt that “the activity of the soil microbial
population seems resistant to adverse conditions.”
He concluded that it was necessary to use culture media
that allow the development of microorganisms capable of
performing a specific function and the elimination of the
majority of microorganisms unable to fulfill this function;
culture by enrichment is the most effective because it
“reveals the diversity of functions of microbes, and allows
to isolate the agents capable of fulfilling most functions
including in soils: oxidation of nitrite and nitrate, oxidation
of sulfur and ferrous salts, fixing gaseous nitrogen, anaerobic
decomposition of cellulose and pectic substances, to name
only the most interesting.”
Despite reservations about classic techniques of microbiology, Winogradsky was aware that “research in Biochemistry provides us with notions of great importance in
showing us the intimate ways and the chemical mechanism
of life processes.” Indeed, the cultivation of a microorganism fulfilling a specific function, free from competition, is
essential to know its physiology (e.g., its optimum growth
conditions), biochemistry (e.g., understanding the metabolic
pathways of degradation of an organic compound), and
genetics (e.g., presence of a gene responsible for an activity).
Culture under controlled artificial conditions provides valuable clues about the ecological role of a microorganism. He
also questioned the activity levels measured in the laboratory: these measures provide an estimate of the potential
activity, but not the actual activity that is expressed in situ.
For him, “the method of analysis of actual activities of
microorganisms in nature must be based not on the behavior
of isolated species outside the natural environment, but on
the reactions of the entire microbial community, in this
environment.” It was almost impossible to achieve this at
the time of Winogradsky. Technological developments
presented in Chap. 17 show that serious answers are made
to what remains a major concern for microbial ecologists.
Another school of soil microbiology developed in parallel
in the Netherlands. Dutch microbiologist Martinus
Beijerinck (1851–1931, Fig. 2.6) developed from 1905 a
laboratory of microbiology at the University of Delft, the
birthplace of Antoni van Leeuwenhoek. Long before the
emergence of microbial ecology, he wrote that his “approach
of the microbial world was within microbial ecology, that is
to say the relationship between environmental conditions
and forms of life that exist.” He was led to the discovery of
nitrogen-fixing symbiotic and nonsymbiotic bacteria
(Beijerinck 1888) and was the first to isolate sulfatereducing bacteria. He demonstrated the important processes
of recycling of sulfur and nitrogen compounds in soil,
highlighting the importance of biotransformations in terrestrial ecosystems and their roles in soil fertility (Beijerinck
1895). His work contributed greatly to our understanding of
biogeochemical cycles and of microbial biotransformations
on a global scale. Associated with the work of Winogradsky,
Beijerinck’s work showed the significant role of microorganisms in the recycling of elements and the balance of
ecosystems necessary for the maintenance of environmental
16
P. Caumette et al.
2).
2. Chemolithotrophic prokaryotes are autotrophic.
3. The demonstration of the physiological process of bacterial nitrogen fixation previously discovered by Beijerinck
in 1888.
Before concluding this summary of the work of S.
Winogradsky, it is necessary to present his thoughts on the
main methods to study microorganisms in the environment;
based on the recommendations stated in his monograph, he
initiated a number of research themes in contemporary
microbial ecology.
Without underestimating the value of pure cultures, he
insisted on the limitations of axenic cultures, “absolutely
impossible in nature,” that moreover remove a microorganism
from its biotic and abiotic environment and place it under
artificial conditions, “sometimes bordering on pathology”.
Another disadvantage of this approach is that the study of
population dynamics is impossible. Moreover, “protected as
it is in its jar,” the organism is not subject to competition, and
more generally it eliminates interactions with other organisms.
From these remarks, he stressed the difficulty of extrapolating
the results obtained in pure culture to the natural environment.
He was also aware of the diversity of the microflora of the
natural environment “that provides a habitat for a swarming
mass of microscopic organisms, a variety that defies imagination.” He showed that few organisms can be isolated in axenic
culture: the culture, on “conventional” media, thus only
providing an overview of diversity. For example, he found
that direct counting by microscopic examination yielded
counts of billions of cells per gram of soil, while the counting
of bacterial colonies on standard culture media did not exceed
several tens of millions. He concluded that “therefore only a
small part, comprising only 10 to 5 %, sometimes less, of the
total population.” It is now well established (thanks to molecular biology techniques) that only 0.1–1 % of bacteria are
grown on media conventionally used in microbiology.
He also drew attention to the fact that in the natural
environment, namely, the soil, “the vast majority of germs,
at some point, are in a state of latent life, only a minority
being in an active state.” This question led to the notion of
the physiological state of a microorganism that will determine its activity level and survival, in particular, its ability to
grow on a culture medium, some microorganisms being
“viable” but “nonculturable,” unable to divide while
retaining some of their physiological functions (cf. Sect.
15.8). About survival, especially under conditions of dietary
deficiency, he felt that “the activity of the soil microbial
population seems resistant to adverse conditions.”
He concluded that it was necessary to use culture media
that allow the development of microorganisms capable of
performing a specific function and the elimination of the
majority of microorganisms unable to fulfill this function;
culture by enrichment is the most effective because it
“reveals the diversity of functions of microbes, and allows
to isolate the agents capable of fulfilling most functions
including in soils: oxidation of nitrite and nitrate, oxidation
of sulfur and ferrous salts, fixing gaseous nitrogen, anaerobic
decomposition of cellulose and pectic substances, to name
only the most interesting.”
Despite reservations about classic techniques of microbiology, Winogradsky was aware that “research in Biochemistry provides us with notions of great importance in
showing us the intimate ways and the chemical mechanism
of life processes.” Indeed, the cultivation of a microorganism fulfilling a specific function, free from competition, is
essential to know its physiology (e.g., its optimum growth
conditions), biochemistry (e.g., understanding the metabolic
pathways of degradation of an organic compound), and
genetics (e.g., presence of a gene responsible for an activity).
Culture under controlled artificial conditions provides valuable clues about the ecological role of a microorganism. He
also questioned the activity levels measured in the laboratory: these measures provide an estimate of the potential
activity, but not the actual activity that is expressed in situ.
For him, “the method of analysis of actual activities of
microorganisms in nature must be based not on the behavior
of isolated species outside the natural environment, but on
the reactions of the entire microbial community, in this
environment.” It was almost impossible to achieve this at
the time of Winogradsky. Technological developments
presented in Chap. 17 show that serious answers are made
to what remains a major concern for microbial ecologists.
Another school of soil microbiology developed in parallel
in the Netherlands. Dutch microbiologist Martinus
Beijerinck (1851–1931, Fig. 2.6) developed from 1905 a
laboratory of microbiology at the University of Delft, the
birthplace of Antoni van Leeuwenhoek. Long before the
emergence of microbial ecology, he wrote that his “approach
of the microbial world was within microbial ecology, that is
to say the relationship between environmental conditions
and forms of life that exist.” He was led to the discovery of
nitrogen-fixing symbiotic and nonsymbiotic bacteria
(Beijerinck 1888) and was the first to isolate sulfatereducing bacteria. He demonstrated the important processes
of recycling of sulfur and nitrogen compounds in soil,
highlighting the importance of biotransformations in terrestrial ecosystems and their roles in soil fertility (Beijerinck
1895). His work contributed greatly to our understanding of
biogeochemical cycles and of microbial biotransformations
on a global scale. Associated with the work of Winogradsky,
Beijerinck’s work showed the significant role of microorganisms in the recycling of elements and the balance of
ecosystems necessary for the maintenance of environmental
16
P. Caumette et al.