A more systematic application of these approaches, for the
most part recent ones, will teach us a lot about the importance
of the diversity of microbial communities in the functioning
of ecosystems and the underlying mechanisms. More generally, the microorganisms will become fabulous models to test
ecological theories. Their short generation time implies that
the responses of microbial communities functioning in the
environment include both functional mechanisms, demographic and evolutionary aspects. In this context, the analysis
of relationships between diversity and functioning requires to
combine the approaches of functional ecology and evolutionary ecology.
8.5.1 Soils
Issues that arise with respect to the soil relate to plant
pathogens, to the capacity to metabolize agrochemical
products, better use of microbial communities for a sustainable agriculture and forestry, or effect of transgenic plants on
microbial communities and on various biogeochemical
cycles. It was found in recent years that soils and sediments
were the biotopes with the richest microbial diversity
(Torsvik et al. 2002). In these heterogeneous biotopes, the
most adapted taxa can multiply without eliminating the less
adapted, so they can remain at very low levels in some
microhabitats waiting for more appropriate conditions, i.e.,
until the arrival of the symbiotic plant or recalcitrant substrate. The DNA of dead microorganisms can also be
maintained on charged soil components such as clay for
years (Picard et al. 1992) until a competent bacterium
integrates it in its genome and modifies its metabolic
capabilities.
Inventory by PCR sequencing of bacteria in a typical soil
shows an abundance of Proteobacteria (alpha, gamma), of
actinobacteria, and of acidobacteria (Herrera et al. 2007), the
latter being essentially a taxonomic group of bacteria very
rarely grown in pure culture and thus poorly characterized.
This distribution changes depending on soil conditions and
the addition of compounds such as nickel in soils around
mining sites in New Caledonia decreases the relative
proportion of alphaproteobacteria and increases that of
betaproteobacteria (Hery et al. 2005).
8.5.2 Microbial Mats
Microbial mats, laminated structures of microorganisms that
thrive in coastal areas, are particularly vulnerable to pollution by hydrocarbons. By their extreme metabolic wealth,
these structures are considered model bacterial ecosystems
to study the degradation of hydrocarbons. To estimate the
impact of pollutants on the structure of microbial mats, mats
from Camargue and from the Etang de Berre were studied.
The Camargue mat, considered unpolluted, is located in a
pre-concentration basin of seawater in the salt marshes of
Salins-de-Giraud. The Etang de Berre mat is located close to
an outlet from a treatment plant from an oil refinery and is
therefore considered to be highly contaminated.
The vertical structure of microbial mats from Camargue
was defined by combining molecular approaches, analysis of
lipids, and confocal microscopy (Fourcans et al. 2004). Then
the dynamics (Fourcans et al. 2006) and the phototrophic
communities of sulfate-reducing bacteria (SRB) were
highlighted during a circadian cycle. Population dynamics
of anoxygenic purple bacteria (APB) were followed by
T-RFLP targeting the pufM genes coding for a protein of
the photosynthesis reaction center. Despite the identification
of possible horizontal transfer of this gene, it remains, on the
whole, a good genetic marker for monitoring APB
(Achenbach et al. 2001). CCA on the T-RFLP data showed
that the distribution of anoxygenic phototrophic bacteria
(APB) was directly influenced by the abundance of
cyanobacteria and Microcoleus chthonoplastes and
Halomicronema excentricum and indirectly through their
metabolism (Fig. 8.5). The main parameters influencing the
vertical migration of APB are pH and oxygen
concentrations, suggesting that the mechanisms of air and
energy taxis control the positioning of these bacteria in the
depth of the mat (Fourcans et al. 2006).
SRB analysis was performed by targeting specific
sequences of the 16S rRNA genes. Since the SRB are
divided into five classes, pairs of primers were designed to
specifically target each of these classes (Daly et al. 2000).
The SRB can be targeted by specific functional genes such as
those involved in sulfate reduction. The dsrAB genes
encoding subunits of the disulfite reductase are most commonly used because they allow on the one hand to follow the
same phylogenetic relationships as the 16S rRNA and on the
other hand many sequences are available in databases
(Wagner et al. 1998). Oxygen and sulfur are the main
parameters influencing the behavior of SRB. Molecular
analyses of diversity helped highlight new populations of
SRB tolerant to high concentrations of oxygen. The study of
such bacterial strains will help to understand the
mechanisms of resistance to oxygen.
These mats (Fig. 8.6) were maintained in laboratory
microcosms to assess the impact of oil on bacterial
communities and in turn their effect on degradation
(Bordenave et al. 2007) as they are on the front line of
marine pollution. The most important observation from this
study was the resilience of the bacterial community following contamination. The bacterial community structure
changed after more than a month. However, the analysis of
the active community (rRNA analysis) showed that the
change occurred upon addition of the pollutant.
280
P. Normand et al.
most part recent ones, will teach us a lot about the importance
of the diversity of microbial communities in the functioning
of ecosystems and the underlying mechanisms. More generally, the microorganisms will become fabulous models to test
ecological theories. Their short generation time implies that
the responses of microbial communities functioning in the
environment include both functional mechanisms, demographic and evolutionary aspects. In this context, the analysis
of relationships between diversity and functioning requires to
combine the approaches of functional ecology and evolutionary ecology.
8.5.1 Soils
Issues that arise with respect to the soil relate to plant
pathogens, to the capacity to metabolize agrochemical
products, better use of microbial communities for a sustainable agriculture and forestry, or effect of transgenic plants on
microbial communities and on various biogeochemical
cycles. It was found in recent years that soils and sediments
were the biotopes with the richest microbial diversity
(Torsvik et al. 2002). In these heterogeneous biotopes, the
most adapted taxa can multiply without eliminating the less
adapted, so they can remain at very low levels in some
microhabitats waiting for more appropriate conditions, i.e.,
until the arrival of the symbiotic plant or recalcitrant substrate. The DNA of dead microorganisms can also be
maintained on charged soil components such as clay for
years (Picard et al. 1992) until a competent bacterium
integrates it in its genome and modifies its metabolic
capabilities.
Inventory by PCR sequencing of bacteria in a typical soil
shows an abundance of Proteobacteria (alpha, gamma), of
actinobacteria, and of acidobacteria (Herrera et al. 2007), the
latter being essentially a taxonomic group of bacteria very
rarely grown in pure culture and thus poorly characterized.
This distribution changes depending on soil conditions and
the addition of compounds such as nickel in soils around
mining sites in New Caledonia decreases the relative
proportion of alphaproteobacteria and increases that of
betaproteobacteria (Hery et al. 2005).
8.5.2 Microbial Mats
Microbial mats, laminated structures of microorganisms that
thrive in coastal areas, are particularly vulnerable to pollution by hydrocarbons. By their extreme metabolic wealth,
these structures are considered model bacterial ecosystems
to study the degradation of hydrocarbons. To estimate the
impact of pollutants on the structure of microbial mats, mats
from Camargue and from the Etang de Berre were studied.
The Camargue mat, considered unpolluted, is located in a
pre-concentration basin of seawater in the salt marshes of
Salins-de-Giraud. The Etang de Berre mat is located close to
an outlet from a treatment plant from an oil refinery and is
therefore considered to be highly contaminated.
The vertical structure of microbial mats from Camargue
was defined by combining molecular approaches, analysis of
lipids, and confocal microscopy (Fourcans et al. 2004). Then
the dynamics (Fourcans et al. 2006) and the phototrophic
communities of sulfate-reducing bacteria (SRB) were
highlighted during a circadian cycle. Population dynamics
of anoxygenic purple bacteria (APB) were followed by
T-RFLP targeting the pufM genes coding for a protein of
the photosynthesis reaction center. Despite the identification
of possible horizontal transfer of this gene, it remains, on the
whole, a good genetic marker for monitoring APB
(Achenbach et al. 2001). CCA on the T-RFLP data showed
that the distribution of anoxygenic phototrophic bacteria
(APB) was directly influenced by the abundance of
cyanobacteria and Microcoleus chthonoplastes and
Halomicronema excentricum and indirectly through their
metabolism (Fig. 8.5). The main parameters influencing the
vertical migration of APB are pH and oxygen
concentrations, suggesting that the mechanisms of air and
energy taxis control the positioning of these bacteria in the
depth of the mat (Fourcans et al. 2006).
SRB analysis was performed by targeting specific
sequences of the 16S rRNA genes. Since the SRB are
divided into five classes, pairs of primers were designed to
specifically target each of these classes (Daly et al. 2000).
The SRB can be targeted by specific functional genes such as
those involved in sulfate reduction. The dsrAB genes
encoding subunits of the disulfite reductase are most commonly used because they allow on the one hand to follow the
same phylogenetic relationships as the 16S rRNA and on the
other hand many sequences are available in databases
(Wagner et al. 1998). Oxygen and sulfur are the main
parameters influencing the behavior of SRB. Molecular
analyses of diversity helped highlight new populations of
SRB tolerant to high concentrations of oxygen. The study of
such bacterial strains will help to understand the
mechanisms of resistance to oxygen.
These mats (Fig. 8.6) were maintained in laboratory
microcosms to assess the impact of oil on bacterial
communities and in turn their effect on degradation
(Bordenave et al. 2007) as they are on the front line of
marine pollution. The most important observation from this
study was the resilience of the bacterial community following contamination. The bacterial community structure
changed after more than a month. However, the analysis of
the active community (rRNA analysis) showed that the
change occurred upon addition of the pollutant.
280
P. Normand et al.