Microbial Ecology”) and a description of the structure
and microbial metabolisms (Chap. 3 “Structure and
Functions of Microorganisms; Production and Use of
Material and Energy”). Indeed, understanding the role
of microorganisms in the environment requires that their
metabolism be known to understand their action in the
transformation of organic and inorganic compounds
within biogeochemical cycles or wastewater treatment
processes (catabolism pathways, energy metabolism), as
well as their action in interactions and food webs (anabolism pathways, biosynthesis). The remarkable metabolic
diversity of prokaryotes, which is developed in this
chapter (different aerobic and anaerobic respirations,
fermentations, and photosynthesis), has allowed them to
colonize and to be very active in all habitats of our planet
and perhaps other planets.
– The second part “Taxonomy and Evolution” starts with a
chapter entitled “For Three Billion Years, Microorganisms
Were the Only Inhabitants of the Earth” (Chap. 4), where a
description is presented of the last universal common
ancestor (LUCA), different hypotheses of the emergence
of three kingdoms that make up the living world today
(Bacteria, Archaea, Eukarya), and the main stages of the
evolution of microorganisms, in particular the main evolutionary scenarios that can explain the emergence of
eukaryotic organization.
Chapter 5, “Systematic and Evolution of Microorganisms: General Concepts” presents general concepts
related to this topic. In eukaryotes, it addresses primary
endosymbioses at the origin of mitochondria and
chloroplasts (in the kingdom of plants) and perhaps of the
kinetic processes and secondary and tertiary endosymbioses
causing photosynthesis in other eukaryotic kingdoms.
The “Taxonomy and Phylogeny of Prokaryotes” are
presented in Chap. 6. The description of criteria used for
phenotypic and genotypic characterization leads to a discussion of the problems associated to the definition of species in
prokaryotes. The characteristics of the two prokaryotic
kingdoms Bacteria and Archaea are defined. The current
phylogeny of their major taxa is also presented.
Chapter 7, entitled “Taxonomy and Phylogeny of Unicellular Eukaryotes,” suggests a unified terminology for the
description of the cytology, morphology, reproduction, and
biological cycles of eukaryotes. Major taxa of unicellular
eukaryotes are presented with a focus on specific biochemical and cytological markers for each of them. Their position
in the eukaryotic phylogenetic tree is specified.
– The third part “Microbial Habitats: Diversity, Adaptation,
and Interactions” focuses on the study of “Biodiversity
and Microbial Ecosystems Functioning” (Chap. 8).
Microbial biodiversity is a concept that emerged a few
years ago to identify all the players in the microbial biotopes.
This concept is first discussed in a historical perspective in
relation to the paradigms in ecology. Then, mathematical
approaches that are used to characterize all microbial actors
are presented as well as the technical tools developed to
quantify microbial biodiversity. Approaches to explore the
relationship between biodiversity and taxonomic functional
biodiversity are described for major ecosystems (soil, water,
etc.) and the main functions (respiration, photosynthesis,
fixation, and use of nitrogen). Finally, in the conclusion,
there is a discussion of the prospects offered by the tools
under development.
Chapter 9, “Adaptations of Prokaryotes to Their Biotopes
and to Physicochemical Conditions in Natural or
Anthropized Environments,” concerns the adaptive processes developed by prokaryotic cells (two components regulatory systems, chemotaxis, etc.) and their metabolic and
genetic responses to adapt to physicochemical conditions
prevailing in the terrestrial and aquatic habitats.
Chapter 10, “The Extreme Conditions of Life on the Planet
and Exobiology,” deals with the microbial life in ecosystems of
the planet that are characterized by extreme physicochemical
conditions. In the first part, the great diversity of prokaryotes is
described that colonize such environments, which were most
often seen in the past as hostile to life. The ecological, physiological, and taxonomic properties of these indigenous
extremophiles microorganisms are then exposed with particular emphasis on psychrophilic, thermophilic, acidophilic,
alkalophilic, halophilic, and piezophilic microorganisms.
Chapter 11, “Microorganisms and Biotic Interactions,”
describes the interactions (cooperation, commensalism, competition, mutualism or symbiosis, parasitism, predation)
involving microorganisms and their significance in microbe/
microbe, microorganism/plant, and microorganism/animal or
man interactions. It describes molecular and evolutionary
mechanisms of bipartite and/or multi-interactions. The
biological functions involved in these interactions are
addressed in terms of impact on matter and energy fluxes in
the environment, biotechnology, agronomy, and public
health.
Chapter 12, “Horizontal Gene Transfer in Microbial
Ecosystems,” describes general features of horizontal gene
transfer (HGT) (mechanisms, discovery, etc.). HGT are
discussed from a qualitative point of view in relation to the
adaptive response of microorganisms in the environmental
conditions but also from a quantitative point of view, as a
major evolutionary mechanism in microorganisms.
– The fourth part, “Role and Functioning of Microbial
Ecosystems,”
discusses
the
intervention
of
microorganisms in “Microbial Food Webs in Aquatic and
Terrestrial Ecosystems” (Chap. 13). The organisms
involved in microbial food webs (MFWs), including
viruses, Archaea, Bacteria, and many eukaryotic taxa
6
J.-C. Bertrand et al.
and microbial metabolisms (Chap. 3 “Structure and
Functions of Microorganisms; Production and Use of
Material and Energy”). Indeed, understanding the role
of microorganisms in the environment requires that their
metabolism be known to understand their action in the
transformation of organic and inorganic compounds
within biogeochemical cycles or wastewater treatment
processes (catabolism pathways, energy metabolism), as
well as their action in interactions and food webs (anabolism pathways, biosynthesis). The remarkable metabolic
diversity of prokaryotes, which is developed in this
chapter (different aerobic and anaerobic respirations,
fermentations, and photosynthesis), has allowed them to
colonize and to be very active in all habitats of our planet
and perhaps other planets.
– The second part “Taxonomy and Evolution” starts with a
chapter entitled “For Three Billion Years, Microorganisms
Were the Only Inhabitants of the Earth” (Chap. 4), where a
description is presented of the last universal common
ancestor (LUCA), different hypotheses of the emergence
of three kingdoms that make up the living world today
(Bacteria, Archaea, Eukarya), and the main stages of the
evolution of microorganisms, in particular the main evolutionary scenarios that can explain the emergence of
eukaryotic organization.
Chapter 5, “Systematic and Evolution of Microorganisms: General Concepts” presents general concepts
related to this topic. In eukaryotes, it addresses primary
endosymbioses at the origin of mitochondria and
chloroplasts (in the kingdom of plants) and perhaps of the
kinetic processes and secondary and tertiary endosymbioses
causing photosynthesis in other eukaryotic kingdoms.
The “Taxonomy and Phylogeny of Prokaryotes” are
presented in Chap. 6. The description of criteria used for
phenotypic and genotypic characterization leads to a discussion of the problems associated to the definition of species in
prokaryotes. The characteristics of the two prokaryotic
kingdoms Bacteria and Archaea are defined. The current
phylogeny of their major taxa is also presented.
Chapter 7, entitled “Taxonomy and Phylogeny of Unicellular Eukaryotes,” suggests a unified terminology for the
description of the cytology, morphology, reproduction, and
biological cycles of eukaryotes. Major taxa of unicellular
eukaryotes are presented with a focus on specific biochemical and cytological markers for each of them. Their position
in the eukaryotic phylogenetic tree is specified.
– The third part “Microbial Habitats: Diversity, Adaptation,
and Interactions” focuses on the study of “Biodiversity
and Microbial Ecosystems Functioning” (Chap. 8).
Microbial biodiversity is a concept that emerged a few
years ago to identify all the players in the microbial biotopes.
This concept is first discussed in a historical perspective in
relation to the paradigms in ecology. Then, mathematical
approaches that are used to characterize all microbial actors
are presented as well as the technical tools developed to
quantify microbial biodiversity. Approaches to explore the
relationship between biodiversity and taxonomic functional
biodiversity are described for major ecosystems (soil, water,
etc.) and the main functions (respiration, photosynthesis,
fixation, and use of nitrogen). Finally, in the conclusion,
there is a discussion of the prospects offered by the tools
under development.
Chapter 9, “Adaptations of Prokaryotes to Their Biotopes
and to Physicochemical Conditions in Natural or
Anthropized Environments,” concerns the adaptive processes developed by prokaryotic cells (two components regulatory systems, chemotaxis, etc.) and their metabolic and
genetic responses to adapt to physicochemical conditions
prevailing in the terrestrial and aquatic habitats.
Chapter 10, “The Extreme Conditions of Life on the Planet
and Exobiology,” deals with the microbial life in ecosystems of
the planet that are characterized by extreme physicochemical
conditions. In the first part, the great diversity of prokaryotes is
described that colonize such environments, which were most
often seen in the past as hostile to life. The ecological, physiological, and taxonomic properties of these indigenous
extremophiles microorganisms are then exposed with particular emphasis on psychrophilic, thermophilic, acidophilic,
alkalophilic, halophilic, and piezophilic microorganisms.
Chapter 11, “Microorganisms and Biotic Interactions,”
describes the interactions (cooperation, commensalism, competition, mutualism or symbiosis, parasitism, predation)
involving microorganisms and their significance in microbe/
microbe, microorganism/plant, and microorganism/animal or
man interactions. It describes molecular and evolutionary
mechanisms of bipartite and/or multi-interactions. The
biological functions involved in these interactions are
addressed in terms of impact on matter and energy fluxes in
the environment, biotechnology, agronomy, and public
health.
Chapter 12, “Horizontal Gene Transfer in Microbial
Ecosystems,” describes general features of horizontal gene
transfer (HGT) (mechanisms, discovery, etc.). HGT are
discussed from a qualitative point of view in relation to the
adaptive response of microorganisms in the environmental
conditions but also from a quantitative point of view, as a
major evolutionary mechanism in microorganisms.
– The fourth part, “Role and Functioning of Microbial
Ecosystems,”
discusses
the
intervention
of
microorganisms in “Microbial Food Webs in Aquatic and
Terrestrial Ecosystems” (Chap. 13). The organisms
involved in microbial food webs (MFWs), including
viruses, Archaea, Bacteria, and many eukaryotic taxa
6
J.-C. Bertrand et al.