(Fungi, Alveolates, Mycetobiontes, etc.), play an essential
role in the functioning of aquatic and terrestrial
ecosystems. From this point of view, pelagic aquatic
ecosystems are particularly original since primary production is only due to microbial communities who provide
most of the biomass in these ecosystems. After an overview of MFWs and their main players, the various bottomup (resources) and top-down (predators) factors controlling
microorganisms are presented. Differences and similarities
between aquatic and terrestrial MFWs are described.
Chapter 14, “Biogeochemical Cycles,” concerns the role
of microorganisms in the functioning of natural and anthropogenic ecosystems by studying detailed processes and
mechanisms that are involved in the main biogeochemical
cycles (carbon, nitrogen, sulfur, phosphorus, silicate,
metals), in soils and in freshwater and marine ecosystems.
The exchanges and biotransformations of organic and mineral components between the oxic and anoxic zones of the
different biotopes are presented.
Chapter 15 presents “Environmental and Human Pathogenic Microorganisms” involved in humans or animal
diseases through a large diversity of infectious mechanisms.
The diversity of these pathogenic microorganisms, their
mode of infection, and dissemination but also their behavior
in the environment as well as the specific methods used for
their detection are reported.
“Applied Microbial Ecology and Bioremediation”
(Chap. 16) concerns the use microorganisms for preventive
remediation (wastewater treatment plants, treatment of gaseous effluents) or bioremediation in contaminated sites (bioaugmentation, biostimulation, rhizostimulation, bioleaching).
Most of the processes used to recover contaminated soils,
sediments, and coastal effluents of treatment plants are
reported. An important part of this chapter is devoted to the
description of main pollutants in the environment as well as
natural attenuation processes due to microbial activities (biodegradation and/or biotransformation).
– The fifth part “Tools the Microbial Ecology” describes the
“Methods to Study Microorganisms in the Environment”
(Chap. 17): sampling, microbial biomass and activity
measurements, structure and diversity of microbial populations, and communities using cultural and noncultural
techniques and laboratory studies. These methods are
described for different types of microorganisms (prokaryotes and eukaryotes, heterotrophs and autotrophs) and
different types of biotopes (water, soil, sediment, biofilms,
etc.) providing informations on their advantages and
limitations and using varied approaches and instruments
such as cytometry, molecular biology, biochemistry, and
isotopic and molecular electrochemistry.
Chapter 18 focuses on “Contributions of Genomics and
Proteomics in Microbial Ecology” for studying the organization and functioning of complex microbial communities as
a whole. Genomics and related methods (transcriptomics,
proteomics, metabolomics) are addressed from historical
and technical points of view. Some examples of the contribution of these techniques to the knowledge on microorganisms are reported, addressing their physiology and
ecology in different environments.
Actually, the growing interest in microbial ecology also
requires the quantification of microbial activities and biotic
and abiotic interactions.
Chapter 19 on “The Modeling Microbial Ecology” aims
to provide informations on the development of models in
various fields of microbial ecology through some examples
but also to highlight the current limitations of modeling in
this field. The second objective of this chapter is to provide
the reader the necessary bases to understand the scientific
literature related to microbial ecology and for which
mathematical modeling should be seen as a tool that
complements more traditional methods of investigation
(molecular biology, culture, genomics, etc.).
At the end of each chapter, a list of references including
general books and major articles related to the different
topics may help the reader to complete the scientific information presented in the chapter. Words in bold with an
asterisk in the text are defined in a glossary at the end of
the book, before the index.
References
Brock TD (1966) Principles of microbial ecology. Prentice-Hall,
Englewood Cliffs
Fenchel T, King GM, Blackburn TH (2000) Bacterial biogeochemistry.
Academic Press, San Diego
Margulis L (1981) Symbiosis in cell evolution. W.H. Freeman, San
Francisco
Singh SN (2011) Microbial degradation of xenobiotics. Environmental
science and engineering. Springer, Heidelberg
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
1 The Thematic Fields of Microbial Ecology
7
role in the functioning of aquatic and terrestrial
ecosystems. From this point of view, pelagic aquatic
ecosystems are particularly original since primary production is only due to microbial communities who provide
most of the biomass in these ecosystems. After an overview of MFWs and their main players, the various bottomup (resources) and top-down (predators) factors controlling
microorganisms are presented. Differences and similarities
between aquatic and terrestrial MFWs are described.
Chapter 14, “Biogeochemical Cycles,” concerns the role
of microorganisms in the functioning of natural and anthropogenic ecosystems by studying detailed processes and
mechanisms that are involved in the main biogeochemical
cycles (carbon, nitrogen, sulfur, phosphorus, silicate,
metals), in soils and in freshwater and marine ecosystems.
The exchanges and biotransformations of organic and mineral components between the oxic and anoxic zones of the
different biotopes are presented.
Chapter 15 presents “Environmental and Human Pathogenic Microorganisms” involved in humans or animal
diseases through a large diversity of infectious mechanisms.
The diversity of these pathogenic microorganisms, their
mode of infection, and dissemination but also their behavior
in the environment as well as the specific methods used for
their detection are reported.
“Applied Microbial Ecology and Bioremediation”
(Chap. 16) concerns the use microorganisms for preventive
remediation (wastewater treatment plants, treatment of gaseous effluents) or bioremediation in contaminated sites (bioaugmentation, biostimulation, rhizostimulation, bioleaching).
Most of the processes used to recover contaminated soils,
sediments, and coastal effluents of treatment plants are
reported. An important part of this chapter is devoted to the
description of main pollutants in the environment as well as
natural attenuation processes due to microbial activities (biodegradation and/or biotransformation).
– The fifth part “Tools the Microbial Ecology” describes the
“Methods to Study Microorganisms in the Environment”
(Chap. 17): sampling, microbial biomass and activity
measurements, structure and diversity of microbial populations, and communities using cultural and noncultural
techniques and laboratory studies. These methods are
described for different types of microorganisms (prokaryotes and eukaryotes, heterotrophs and autotrophs) and
different types of biotopes (water, soil, sediment, biofilms,
etc.) providing informations on their advantages and
limitations and using varied approaches and instruments
such as cytometry, molecular biology, biochemistry, and
isotopic and molecular electrochemistry.
Chapter 18 focuses on “Contributions of Genomics and
Proteomics in Microbial Ecology” for studying the organization and functioning of complex microbial communities as
a whole. Genomics and related methods (transcriptomics,
proteomics, metabolomics) are addressed from historical
and technical points of view. Some examples of the contribution of these techniques to the knowledge on microorganisms are reported, addressing their physiology and
ecology in different environments.
Actually, the growing interest in microbial ecology also
requires the quantification of microbial activities and biotic
and abiotic interactions.
Chapter 19 on “The Modeling Microbial Ecology” aims
to provide informations on the development of models in
various fields of microbial ecology through some examples
but also to highlight the current limitations of modeling in
this field. The second objective of this chapter is to provide
the reader the necessary bases to understand the scientific
literature related to microbial ecology and for which
mathematical modeling should be seen as a tool that
complements more traditional methods of investigation
(molecular biology, culture, genomics, etc.).
At the end of each chapter, a list of references including
general books and major articles related to the different
topics may help the reader to complete the scientific information presented in the chapter. Words in bold with an
asterisk in the text are defined in a glossary at the end of
the book, before the index.
References
Brock TD (1966) Principles of microbial ecology. Prentice-Hall,
Englewood Cliffs
Fenchel T, King GM, Blackburn TH (2000) Bacterial biogeochemistry.
Academic Press, San Diego
Margulis L (1981) Symbiosis in cell evolution. W.H. Freeman, San
Francisco
Singh SN (2011) Microbial degradation of xenobiotics. Environmental
science and engineering. Springer, Heidelberg
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
1 The Thematic Fields of Microbial Ecology
7