Studies of these abiotic interactions should consider, on
the one hand, how both physical and chemical properties of
the environment may affect the presence, spatial distribution, and also the growth and activity of microorganisms
and, on the other hand, the feedback of microorganisms on
their environment. Among the environmental parameters
interacting with microorganisms, the most important are
pH, pressure, light intensity and wavelength, and the electron donor and acceptor concentration. These donors and
acceptors are most often heterogeneously distributed in the
natural environment and/or present at low concentration. As
a consequence, they do not allow the maximum development of microorganisms and their survival under environmental conditions that are not adapted to their physiology. In
most environments, microorganisms are most often living
under nutrient starvation, leading to long periods of dormancy. They adapt to these starvation conditions by developing nutrient storage systems or other mechanisms
(chemotactic, phototactic, magnetotactic) enabling them an
easier access to nutrients. More generally, microorganisms
must continuously adapt to survive to regular and sometimes
fast changes of the environmental parameters.
The interaction of microorganisms with natural surfaces
(soil or sediment particles, leaves and roots, digestive tract
of humans and animals, skin, etc.) must also be considered.
In the natural environment, many microorganisms are not
free-living organisms, but they attach to most surfaces
through the secretion of extracellular compounds such as
polysaccharides that allow them to form biofilms or microbial mats (Fenchel et al. 2000).
6. Their extraordinary capacity to degrade pollutants, especially xenobiotics, as a service to ecosystems and to the
bioremediation of contaminated sites
Microbial ecology can provide solutions to many environmental problems currently faced by human societies
whose relationships with the environment have changed
dramatically during the last centuries due to an important
increase of the world population, to the settlement of
populations over an extended range of biotopes, and more
recently to the industrial development and, therefore, to the
production of more and more domestic and industrial wastes,
leading to an increasing pollution of environmental sites.
Nowadays, pollution has reached such levels that it
endangers the survival of a large number of species on
Earth. An important goal in microbial ecology is to enhance
the metabolic properties of microorganisms to degrade most
pollutants that affect our planet. Microbial ecology is also
concerned by public health problems such as an increasing
need to produce drinking water, food contamination, dispersion, and changes in the behavior of pathogens in the
environment (emerging infectious diseases, viable but
nonculturable state of pathogens, antibiotics resistance, etc.).
These are the objectives of microbial ecology, at the
interface between microbiology and ecology. To achieve
these goals, it is important to develop appropriate and
efficient methods, sometimes specific to the study of
microorganisms in natural environments. In this matter,
real-time methods are more and more requested to develop
early warning detection systems. Sergei Winogradsky, the
first microbiologist that has introduced the expression “environmental microbiology,” pointed out the limitations and
drawbacks of the methods that are commonly used in medical and industrial microbiology. Based on the study of
microorganisms that have been isolated and grown under
controlled conditions, most of these methods cannot be used
to investigate the life and physiology of environmental
microorganisms. This vision was especially appropriate
since it is now well established that many microorganisms
that are present in the environment are unknown and only
1–10 % of microbes present in natural biotopes have been
grown in pure culture (Singh 2011).
Techniques have been developed that allow a direct
access (without any cultivation step) to microbial
populations and communities in the environment thanks to
the increased performances of microscopy instruments and
analytical chemistry techniques (development of fluorescence techniques and biomarkers*, identification of metabolic pathways), development of microelectrodes to assess
the distribution and activity of microorganisms at the microscale, use of isotopic techniques, development of techniques
to determine the activity of microorganisms under conditions very close to those encountered in the natural environment (e.g., hyperbaric instruments that generate high
pressure, temperature, and oligotrophic conditions that exist
in the deep ocean, etc.), and development and improvement
of flow cytometry instruments to access the properties of
individual cells (numbers, physiological state, presence or
absence of certain metabolic activities, etc.).
Nevertheless, the main technological revolution in this
field was the implementation, development, and use of
molecular biology techniques: DNA fingerprinting, DNA
chips (taxonomic and functional), metagenomic libraries,
transcriptomic and proteomic studies, full genome sequencing, etc. Environmental genomics has allowed the detection,
identification, and quantification of microorganisms in the
natural environment after DNA extraction, with access to
non-cultivable species. They also provided access to the
physiological state of cells and were a considerable contribution to our knowledge of the diversity of microorganisms
(taxonomic, functional, and genetic diversity), their phylogeny, activities, and interactions.
This book aims to address all issues related to this discipline. It consists of 19 chapters that are organized into 5 parts.
– The first part is devoted to “General Chapters.” After an
introduction (Chap. 1, “The Thematic Fields of Microbial
Ecology”), the next chapters present a brief history of the
discipline, including an introduction to the work of
Winogradsky (Chap. 2, “Some Historical Elements of
1 The Thematic Fields of Microbial Ecology
5
the one hand, how both physical and chemical properties of
the environment may affect the presence, spatial distribution, and also the growth and activity of microorganisms
and, on the other hand, the feedback of microorganisms on
their environment. Among the environmental parameters
interacting with microorganisms, the most important are
pH, pressure, light intensity and wavelength, and the electron donor and acceptor concentration. These donors and
acceptors are most often heterogeneously distributed in the
natural environment and/or present at low concentration. As
a consequence, they do not allow the maximum development of microorganisms and their survival under environmental conditions that are not adapted to their physiology. In
most environments, microorganisms are most often living
under nutrient starvation, leading to long periods of dormancy. They adapt to these starvation conditions by developing nutrient storage systems or other mechanisms
(chemotactic, phototactic, magnetotactic) enabling them an
easier access to nutrients. More generally, microorganisms
must continuously adapt to survive to regular and sometimes
fast changes of the environmental parameters.
The interaction of microorganisms with natural surfaces
(soil or sediment particles, leaves and roots, digestive tract
of humans and animals, skin, etc.) must also be considered.
In the natural environment, many microorganisms are not
free-living organisms, but they attach to most surfaces
through the secretion of extracellular compounds such as
polysaccharides that allow them to form biofilms or microbial mats (Fenchel et al. 2000).
6. Their extraordinary capacity to degrade pollutants, especially xenobiotics, as a service to ecosystems and to the
bioremediation of contaminated sites
Microbial ecology can provide solutions to many environmental problems currently faced by human societies
whose relationships with the environment have changed
dramatically during the last centuries due to an important
increase of the world population, to the settlement of
populations over an extended range of biotopes, and more
recently to the industrial development and, therefore, to the
production of more and more domestic and industrial wastes,
leading to an increasing pollution of environmental sites.
Nowadays, pollution has reached such levels that it
endangers the survival of a large number of species on
Earth. An important goal in microbial ecology is to enhance
the metabolic properties of microorganisms to degrade most
pollutants that affect our planet. Microbial ecology is also
concerned by public health problems such as an increasing
need to produce drinking water, food contamination, dispersion, and changes in the behavior of pathogens in the
environment (emerging infectious diseases, viable but
nonculturable state of pathogens, antibiotics resistance, etc.).
These are the objectives of microbial ecology, at the
interface between microbiology and ecology. To achieve
these goals, it is important to develop appropriate and
efficient methods, sometimes specific to the study of
microorganisms in natural environments. In this matter,
real-time methods are more and more requested to develop
early warning detection systems. Sergei Winogradsky, the
first microbiologist that has introduced the expression “environmental microbiology,” pointed out the limitations and
drawbacks of the methods that are commonly used in medical and industrial microbiology. Based on the study of
microorganisms that have been isolated and grown under
controlled conditions, most of these methods cannot be used
to investigate the life and physiology of environmental
microorganisms. This vision was especially appropriate
since it is now well established that many microorganisms
that are present in the environment are unknown and only
1–10 % of microbes present in natural biotopes have been
grown in pure culture (Singh 2011).
Techniques have been developed that allow a direct
access (without any cultivation step) to microbial
populations and communities in the environment thanks to
the increased performances of microscopy instruments and
analytical chemistry techniques (development of fluorescence techniques and biomarkers*, identification of metabolic pathways), development of microelectrodes to assess
the distribution and activity of microorganisms at the microscale, use of isotopic techniques, development of techniques
to determine the activity of microorganisms under conditions very close to those encountered in the natural environment (e.g., hyperbaric instruments that generate high
pressure, temperature, and oligotrophic conditions that exist
in the deep ocean, etc.), and development and improvement
of flow cytometry instruments to access the properties of
individual cells (numbers, physiological state, presence or
absence of certain metabolic activities, etc.).
Nevertheless, the main technological revolution in this
field was the implementation, development, and use of
molecular biology techniques: DNA fingerprinting, DNA
chips (taxonomic and functional), metagenomic libraries,
transcriptomic and proteomic studies, full genome sequencing, etc. Environmental genomics has allowed the detection,
identification, and quantification of microorganisms in the
natural environment after DNA extraction, with access to
non-cultivable species. They also provided access to the
physiological state of cells and were a considerable contribution to our knowledge of the diversity of microorganisms
(taxonomic, functional, and genetic diversity), their phylogeny, activities, and interactions.
This book aims to address all issues related to this discipline. It consists of 19 chapters that are organized into 5 parts.
– The first part is devoted to “General Chapters.” After an
introduction (Chap. 1, “The Thematic Fields of Microbial
Ecology”), the next chapters present a brief history of the
discipline, including an introduction to the work of
Winogradsky (Chap. 2, “Some Historical Elements of
1 The Thematic Fields of Microbial Ecology
5