8.1
Introduction
The existence of a plurality of species in ecosystems,
identified as biodiversity, has become a research topic of
general interest important nationally and internationally
since Wilson published his groundbreaking eponymous
book “Biodiversity” (1988). The word “biodiversity” has
subsequently received different interpretations, e.g., Gast
and collaborators (1991) defined it as the variety, distribution, and structure of plant and animal communities,
including all age groups, arranged in space and time. In
addition, Wilcox (1984) added the concept of genetic
diversity.
Takacs (1996) illustrated the rise of the concept by the
fact that in 1988, “biodiversity” was not used as keyword
in biological abstracts, and the expression “biological
diversity” appeared in them only once. In 1993, 5 years
later, “biodiversity” had 72 occurrences, and “biological
diversity” 19. Fifteen years later, it would be difficult to
quantify the use of these terms in daily use by scientists,
politicians, journalists, and the general public. A Google
search (www.google.com) in June 2013 showed more than
53 million websites where the word is used.
This word is now used very broadly, by environmentalists
who want to designate the whole of the organisms of a
biotope or the functions they perform, by evolutionists who
thus designate all members of a phylogenetic clade with
their variations, by molecular biologists who study the
variations of an enzyme to better understand the motifs
that are important for a biological function or the structure
of a protein or metabolite, and by population geneticists who
want to quantify the rate of genetic exchange or the range of
morphological features of a taxon.
Regarding microbial biodiversity, one faces several
problems when characterizing it:
• The question of what kind of biodiversity should be
targeted: global diversity of taxa (bacteria, fungi present,
etc.), diversity within functional groups, diversity of
functional groups, etc.
• The problems of representativity of the samples to use. It
has thus been estimated that the Earth is home to about
10
30 prokaryotes (Whitman et al. 1998). One gram of soil
may contain 10
4 or even 10
5 different taxa.
• The difficulty to cultivate most microorganisms, which
limits our ability to understand their diversity using this
approach.
These problems overlap with issues that arise about
approaches and criteria for characterization of microbial
activities carried out by consortia or other complex sets of
complementary microorganisms. Despite these complexities
and difficulties, studies of microbial biodiversity are increasing rapidly for several reasons that this chapter will seek to
explain.
8.2
The Pertinence of the Paradigms of
Biodiversity and Ecosystem Functioning
for Microbial Ecology
Biological variability between populations and communities
of organisms (macroorganisms and microorganisms) is the
result of selection pressures imposed by the physical and
biological conditions of the environment coupled with
mutations or recombinations of the genome of these
organisms. Many of the processes that create biological
variety occur on timescales or under environmental
conditions that are difficult to reproduce in the laboratory.
Biodiversity of populations or communities is an archive of
the adaptive history of these organisms. It reflects complex
phenomena creating diversity by spontaneous point
mutations, duplications or gene losses, lateral transfers, and
selection by the environment. A major reason to study biodiversity is to open these archives to understand the factors
controlling the ecology and evolution of organisms and how
this biodiversity is related to the way ecosystems function.
This information is essential for managing the biodiversity
of organisms on our planet, to limit the spread of pests, to
better exploit organisms that have industrial or medical
applications, or to preserve the organisms involved in important ecosystem processes.
It is clear that natural populations of organisms do not
grow infinitely either in terms of the number of individuals
or in the abundance of different taxa (species, races,
biotypes, etc.). The twentieth century saw intense debates
about the processes governing growth and diversification of
populations and species. These discussions helped to establish ecology as a discipline with a fluctuating set of
paradigms on control processes. These paradigms have
been developed based almost exclusively on works on
macroorganisms, and few were assessed for their relevance
to microorganisms. A challenge to the discipline of microbial ecology is to evaluate the relevance of these paradigms
for communities of microorganisms.
Among the processes that regulate population growth and
the composition, structure, and functioning of communities,
the concepts of niche, food webs, succession, and the link
between biodiversity and ecological stability of a community or ecosystem functioning as a whole are particularly
262
P. Normand et al.
Introduction
The existence of a plurality of species in ecosystems,
identified as biodiversity, has become a research topic of
general interest important nationally and internationally
since Wilson published his groundbreaking eponymous
book “Biodiversity” (1988). The word “biodiversity” has
subsequently received different interpretations, e.g., Gast
and collaborators (1991) defined it as the variety, distribution, and structure of plant and animal communities,
including all age groups, arranged in space and time. In
addition, Wilcox (1984) added the concept of genetic
diversity.
Takacs (1996) illustrated the rise of the concept by the
fact that in 1988, “biodiversity” was not used as keyword
in biological abstracts, and the expression “biological
diversity” appeared in them only once. In 1993, 5 years
later, “biodiversity” had 72 occurrences, and “biological
diversity” 19. Fifteen years later, it would be difficult to
quantify the use of these terms in daily use by scientists,
politicians, journalists, and the general public. A Google
search (www.google.com) in June 2013 showed more than
53 million websites where the word is used.
This word is now used very broadly, by environmentalists
who want to designate the whole of the organisms of a
biotope or the functions they perform, by evolutionists who
thus designate all members of a phylogenetic clade with
their variations, by molecular biologists who study the
variations of an enzyme to better understand the motifs
that are important for a biological function or the structure
of a protein or metabolite, and by population geneticists who
want to quantify the rate of genetic exchange or the range of
morphological features of a taxon.
Regarding microbial biodiversity, one faces several
problems when characterizing it:
• The question of what kind of biodiversity should be
targeted: global diversity of taxa (bacteria, fungi present,
etc.), diversity within functional groups, diversity of
functional groups, etc.
• The problems of representativity of the samples to use. It
has thus been estimated that the Earth is home to about
10
30 prokaryotes (Whitman et al. 1998). One gram of soil
may contain 10
4 or even 10
5 different taxa.
• The difficulty to cultivate most microorganisms, which
limits our ability to understand their diversity using this
approach.
These problems overlap with issues that arise about
approaches and criteria for characterization of microbial
activities carried out by consortia or other complex sets of
complementary microorganisms. Despite these complexities
and difficulties, studies of microbial biodiversity are increasing rapidly for several reasons that this chapter will seek to
explain.
8.2
The Pertinence of the Paradigms of
Biodiversity and Ecosystem Functioning
for Microbial Ecology
Biological variability between populations and communities
of organisms (macroorganisms and microorganisms) is the
result of selection pressures imposed by the physical and
biological conditions of the environment coupled with
mutations or recombinations of the genome of these
organisms. Many of the processes that create biological
variety occur on timescales or under environmental
conditions that are difficult to reproduce in the laboratory.
Biodiversity of populations or communities is an archive of
the adaptive history of these organisms. It reflects complex
phenomena creating diversity by spontaneous point
mutations, duplications or gene losses, lateral transfers, and
selection by the environment. A major reason to study biodiversity is to open these archives to understand the factors
controlling the ecology and evolution of organisms and how
this biodiversity is related to the way ecosystems function.
This information is essential for managing the biodiversity
of organisms on our planet, to limit the spread of pests, to
better exploit organisms that have industrial or medical
applications, or to preserve the organisms involved in important ecosystem processes.
It is clear that natural populations of organisms do not
grow infinitely either in terms of the number of individuals
or in the abundance of different taxa (species, races,
biotypes, etc.). The twentieth century saw intense debates
about the processes governing growth and diversification of
populations and species. These discussions helped to establish ecology as a discipline with a fluctuating set of
paradigms on control processes. These paradigms have
been developed based almost exclusively on works on
macroorganisms, and few were assessed for their relevance
to microorganisms. A challenge to the discipline of microbial ecology is to evaluate the relevance of these paradigms
for communities of microorganisms.
Among the processes that regulate population growth and
the composition, structure, and functioning of communities,
the concepts of niche, food webs, succession, and the link
between biodiversity and ecological stability of a community or ecosystem functioning as a whole are particularly
262
P. Normand et al.