encompassing actinobacteria such as Streptomyces that the
Russian-born American Selman A. Waksman showed able
to synthesize a whole array of antibiotics like the
aminoglycoside streptomycin that proved active against the
tuberculosis agent Mycobacterium tuberculosis, which
earned him the Nobel Prize for medicine and physiology in
1952. Microbial ecology is based on this type of observation
and thus depends on the development of new methods to
understand precisely such interactions. The idea of wanting
to know the role and behavior of microorganisms in their
biotic and abiotic environments developed from the work of
Sergei Winogradsky (1856–1953, cf. Sect. 2.4) and has
emerged from the 1970s and was instrumental in the emergence of microbial ecology. This discipline has developed
alongside mainstream microbiology disciplines such as
medical microbiology that studies the role of pathogenic
bacteria in the genesis of infectious diseases and food and
industrial microbiology that studies the metabolic role of
certain bacteria for biotechnology.
Parallel to the discovery of bacteria and their role in
infectious diseases, the Russian microbiologist Sergei
Ivanovski (Ivanovski and Polovtsev 1890) was the first to
demonstrate infectious particles of a size much smaller than
that of bacteria. Ivanovski observed in the mosaic disease of
tobacco leaves an infectious process caused by a pathogen
unable to grow using the classical methods of microbiology
and not retained on the candle filters (Chamberland candle
filters made up of porous porcelain) with which one
sterilized liquid by filtration and retention of bacteria on
the filters. He called these particles “filterable viruses” to
refer to infectious agents not retained on the filters of porous
porcelain candles. He was the first to describe the tobacco
mosaic virus (TMV) followed by the American virologist
Rous who discovered the first animal virus in the early
twentieth century (Rous 1911): the retrovirus causing leukemia in chickens. Later, the Canadian Felix d’Herelle
described, in 1917, the first viruses of bacteria, called
bacteriophages (d’He ´relle 1921). It was not until 1939 and
the construction of the electron microscope that these viral
particles could be directly observed.
2.4
The Beginnings of Microbial Ecology
The work of microbiologists mainly focused on pure cultures
have partly contributed to a long-time neglect for ecological
research on microorganisms. In addition, microbial ecology
has had to face major methodological difficulties due to the
small size of microorganisms. Thus, for a long time, mainstream macro-ecology ecologists either considered
microorganisms as static particles or have generally ignored
by considering their communities as “black boxes” in which
their roles in biogeochemical processes are estimated by flux
measurements of organic or inorganic material.
However, pioneering work in the nineteenth century has
permitted to show the importance of knowledge of microorganisms in relation to their environments. In the early
nineteenth century, the Swiss Nicolas-The ´odore de Saussure
(1767–1845) brought to light the capacity of soils to oxidize
hydrogen and worked on various aspects of soil chemistry
(de Saussure 1804). As this hydrogen-oxidizing capacity was
inhibited by heating the soil or following the incorporation of
sulfuric acid, he concluded that the oxidation activity was due
to microorganisms. Similarly, the French Jacques-The ´ophile
Schloesing and Achilles Muntz (1877) showed the oxidation
of ammonium nitrate present in wastewater occurred when
flowing through a sand column. The fact that this activity was
destroyed by chloroform vapors and restored upon addition of
a soil inoculum enabled them to conclude that it was due to
the activity of microorganisms. At the same time, Pasteur
was clearly establishing the role of microorganisms in the
biodegradation of organic substances. He tried unsuccessfully
to prove the role of microorganisms in the transformation of
mineral substances, including the oxidation of ammonium
nitrate, but he could not succeed. All these pioneering studies
were performed on natural samples without the use of isolated
bacteria.
It was not until the great discoveries of the Russian
microbiologist Sergei Winogradsky (1856–1953, Fig. 2.4)
from 1887 to really demonstrate the fundamental role of
microorganisms in pathways of transformation of mineral
compounds. He was the first to speak of the “microbiology
of natural biotopes” and devoted 50 years of his life to
microbiological research. He worked in several European
universities.
In 1885, he left Russia and began his work in the botany
laboratory of the University of Strasbourg. From 1887, he
demonstrated the autotrophic ability of filamentous sulfideoxidizing bacteria of genus Beggiatoa, which constituted one
of his main microbial models (Winogradsky 1887). He
discovered in 1988 (Winogradsky 1888) purple photosynthetic bacteria and sulfide-producing bacteria. He described
taxonomically many anoxygenic phototrophic bacteria
(Fig. 2.5), sulfate-reducing bacteria, and iron-oxidizing, nitrifying, denitrifying, and nitrogen-fixing bacteria. He thus
discovered many metabolic pathways and showed the great
diversity of microbial metabolisms. To elucidate the
interactions between bacteria of the sulfur cycle, he designed
an experimental device, called a “Winogradsky column” in
which he was able to control the flow of nutrients and light
(cf. Box 14.13). He could thus follow the appearance of sulfide
production and development of sulfide-oxidizing purple and
colorless bacteria and establish conditions for development of
these microorganisms (cf. Sect. 14.4.3). These experiments
allowed him to grow simultaneously communities of
14
P. Caumette et al.
Russian-born American Selman A. Waksman showed able
to synthesize a whole array of antibiotics like the
aminoglycoside streptomycin that proved active against the
tuberculosis agent Mycobacterium tuberculosis, which
earned him the Nobel Prize for medicine and physiology in
1952. Microbial ecology is based on this type of observation
and thus depends on the development of new methods to
understand precisely such interactions. The idea of wanting
to know the role and behavior of microorganisms in their
biotic and abiotic environments developed from the work of
Sergei Winogradsky (1856–1953, cf. Sect. 2.4) and has
emerged from the 1970s and was instrumental in the emergence of microbial ecology. This discipline has developed
alongside mainstream microbiology disciplines such as
medical microbiology that studies the role of pathogenic
bacteria in the genesis of infectious diseases and food and
industrial microbiology that studies the metabolic role of
certain bacteria for biotechnology.
Parallel to the discovery of bacteria and their role in
infectious diseases, the Russian microbiologist Sergei
Ivanovski (Ivanovski and Polovtsev 1890) was the first to
demonstrate infectious particles of a size much smaller than
that of bacteria. Ivanovski observed in the mosaic disease of
tobacco leaves an infectious process caused by a pathogen
unable to grow using the classical methods of microbiology
and not retained on the candle filters (Chamberland candle
filters made up of porous porcelain) with which one
sterilized liquid by filtration and retention of bacteria on
the filters. He called these particles “filterable viruses” to
refer to infectious agents not retained on the filters of porous
porcelain candles. He was the first to describe the tobacco
mosaic virus (TMV) followed by the American virologist
Rous who discovered the first animal virus in the early
twentieth century (Rous 1911): the retrovirus causing leukemia in chickens. Later, the Canadian Felix d’Herelle
described, in 1917, the first viruses of bacteria, called
bacteriophages (d’He ´relle 1921). It was not until 1939 and
the construction of the electron microscope that these viral
particles could be directly observed.
2.4
The Beginnings of Microbial Ecology
The work of microbiologists mainly focused on pure cultures
have partly contributed to a long-time neglect for ecological
research on microorganisms. In addition, microbial ecology
has had to face major methodological difficulties due to the
small size of microorganisms. Thus, for a long time, mainstream macro-ecology ecologists either considered
microorganisms as static particles or have generally ignored
by considering their communities as “black boxes” in which
their roles in biogeochemical processes are estimated by flux
measurements of organic or inorganic material.
However, pioneering work in the nineteenth century has
permitted to show the importance of knowledge of microorganisms in relation to their environments. In the early
nineteenth century, the Swiss Nicolas-The ´odore de Saussure
(1767–1845) brought to light the capacity of soils to oxidize
hydrogen and worked on various aspects of soil chemistry
(de Saussure 1804). As this hydrogen-oxidizing capacity was
inhibited by heating the soil or following the incorporation of
sulfuric acid, he concluded that the oxidation activity was due
to microorganisms. Similarly, the French Jacques-The ´ophile
Schloesing and Achilles Muntz (1877) showed the oxidation
of ammonium nitrate present in wastewater occurred when
flowing through a sand column. The fact that this activity was
destroyed by chloroform vapors and restored upon addition of
a soil inoculum enabled them to conclude that it was due to
the activity of microorganisms. At the same time, Pasteur
was clearly establishing the role of microorganisms in the
biodegradation of organic substances. He tried unsuccessfully
to prove the role of microorganisms in the transformation of
mineral substances, including the oxidation of ammonium
nitrate, but he could not succeed. All these pioneering studies
were performed on natural samples without the use of isolated
bacteria.
It was not until the great discoveries of the Russian
microbiologist Sergei Winogradsky (1856–1953, Fig. 2.4)
from 1887 to really demonstrate the fundamental role of
microorganisms in pathways of transformation of mineral
compounds. He was the first to speak of the “microbiology
of natural biotopes” and devoted 50 years of his life to
microbiological research. He worked in several European
universities.
In 1885, he left Russia and began his work in the botany
laboratory of the University of Strasbourg. From 1887, he
demonstrated the autotrophic ability of filamentous sulfideoxidizing bacteria of genus Beggiatoa, which constituted one
of his main microbial models (Winogradsky 1887). He
discovered in 1988 (Winogradsky 1888) purple photosynthetic bacteria and sulfide-producing bacteria. He described
taxonomically many anoxygenic phototrophic bacteria
(Fig. 2.5), sulfate-reducing bacteria, and iron-oxidizing, nitrifying, denitrifying, and nitrogen-fixing bacteria. He thus
discovered many metabolic pathways and showed the great
diversity of microbial metabolisms. To elucidate the
interactions between bacteria of the sulfur cycle, he designed
an experimental device, called a “Winogradsky column” in
which he was able to control the flow of nutrients and light
(cf. Box 14.13). He could thus follow the appearance of sulfide
production and development of sulfide-oxidizing purple and
colorless bacteria and establish conditions for development of
these microorganisms (cf. Sect. 14.4.3). These experiments
allowed him to grow simultaneously communities of
14
P. Caumette et al.