8.5.8 Deep Earth
Analysis of aquifers and deep environments requires the
development of appropriate sampling methods. Contamination of the samples, where diversity is low, can be a major
problem. Nevertheless, an adapted sampling method based
on T-RFLP analysis of bacterial communities has been
developed (Basso et al. 2005). Bacterial communities were
characterized by molecular inventories and cultivation
methods. This approach has allowed access to a new source
of diversity, including bacterial strains trapped in geological
layers, permitting to address issues of paleomicrobiology
and the origins of life on earth. Energy sources and carbon
are limited in this environment, apart from hydrothermal
vents, where hydrogen flow from the thermolysis of water
allows chemolithotrophic bacteria (hydrogen, reduced iron)
to thrive (Kimura et al. 2005). Sources of carbon and nitrogen are rare but nevertheless constitute hot spots where
many taxa are active and have been thriving probably for
considerable periods of time (Parkes et al. 2005).
8.5.9 Agricultural and Forestry Systems
The effects of agricultural and forestry practices on the
functioning and diversity of soil microbial communities
have been quantified in many studies. Some studies have
characterized the impact of agricultural practices and land
uses on key microbial functional groups such as denitrifiers
or nitrifiers and the possible feedbacks for agroecosystem
functioning and services (Attard et al. 2011; Philippot et al.
2007). Similarly, forestry practices and tree species have
been demonstrated to influence taxonomic and functional
diversity of soil bacteria and fungi (Buee et al. 2009).
8.5.10 Polluted Environments: The Case of Acid
Mine Drainages
Acid mine drainages (AMD) are considered extreme
environments because on the one hand they have low pH
and on the other they have high concentrations of toxic
compounds. These environments that are hostile to life are
also sometimes considered good models to address the
problem of the origin of life on earth. The composition
of bacterial communities in the AMD of a former
lead mine was followed in relation to seasonal variations
and with changes in the concentration of dissolved oxygen
in the water. These acidic waters (pH ~ 2) are rich in
arsenic (300 mg/L), iron (20,000 mg/L), and sulfate
(7,500 mg/L). The main bacteria isolated from this
environment belonged to the genera Acidithiobacillus and
Thiomonas, genera frequently encountered in these
environments (Bruneel et al. 2006). T-RFLP analyses
showed a low diversity. The molecular inventory has
highlighted the role of sulfate-reducing bacteria (SRB) in
this environment (Bruneel et al. 2006). Efforts are underway to isolate SRB strains that play a role in the transformation of arsenic. More recent metagenomic studies
allowed to identify putative bacteria involved in the AMD
functioning (Bertin et al. 2011), and the challenge is now
to isolate such bacteria and characterize their role.
8.6
Conclusion
Biodiversity is increasingly seen as a resource to be
preserved, and microbial biodiversity is no exception to
this rule. Microbial biodiversity has given us antibiotics,
beer, cheese, and bioactive molecules of many kinds, and it
also allows wastewater treatment and the growth of plants
in soil (Box 8.4). It is moreover an overall indicator of the
status of certain biotopes impacted by anthropogenic
pressures, biotopes that must be preserved so that they
can fulfill various functions and deliver services, on
which our well-being depends. This is why it is important
to quantify and compare the different disturbances that
biotopes can withstand before reaching tipping points.
The approaches used to study microbial biodiversity
should also make significant progress both technically
due to the tools currently developed, e.g., for highthroughput sequencing, and analytically because of new
websites which democratize mathematical and bioinformatic approaches.
Microbial biodiversity should continue to be addressed
by scientists for basic reasons but also due to societal issues
linked to pollution, sustainable agriculture and forestry,
health and productivity of oceans and freshwaters, or
global change. Fundamental work should further seek to
establish the causal link between microbial diversity and
ecosystem functioning. In this context, the capacity to
acquire and analyze very large data sets is a major challenge, but sequencing of nucleic acids increases continuously with associated bioinformatic approaches, rapidly
offering new perspectives. These approaches should help
identify taxa present in a given biotope but also to understand which genes are expressed in a given situation.
A sticking point is our ability to identify the function(s)
of genes; this bottleneck will certainly not be broken for
years, which is the time necessary to do solid work on
microbial physiology. More generally, the functional traits
concept used in ecology has been increasingly used in
8 Biodiversity and Microbial Ecosystems Functioning
285
Analysis of aquifers and deep environments requires the
development of appropriate sampling methods. Contamination of the samples, where diversity is low, can be a major
problem. Nevertheless, an adapted sampling method based
on T-RFLP analysis of bacterial communities has been
developed (Basso et al. 2005). Bacterial communities were
characterized by molecular inventories and cultivation
methods. This approach has allowed access to a new source
of diversity, including bacterial strains trapped in geological
layers, permitting to address issues of paleomicrobiology
and the origins of life on earth. Energy sources and carbon
are limited in this environment, apart from hydrothermal
vents, where hydrogen flow from the thermolysis of water
allows chemolithotrophic bacteria (hydrogen, reduced iron)
to thrive (Kimura et al. 2005). Sources of carbon and nitrogen are rare but nevertheless constitute hot spots where
many taxa are active and have been thriving probably for
considerable periods of time (Parkes et al. 2005).
8.5.9 Agricultural and Forestry Systems
The effects of agricultural and forestry practices on the
functioning and diversity of soil microbial communities
have been quantified in many studies. Some studies have
characterized the impact of agricultural practices and land
uses on key microbial functional groups such as denitrifiers
or nitrifiers and the possible feedbacks for agroecosystem
functioning and services (Attard et al. 2011; Philippot et al.
2007). Similarly, forestry practices and tree species have
been demonstrated to influence taxonomic and functional
diversity of soil bacteria and fungi (Buee et al. 2009).
8.5.10 Polluted Environments: The Case of Acid
Mine Drainages
Acid mine drainages (AMD) are considered extreme
environments because on the one hand they have low pH
and on the other they have high concentrations of toxic
compounds. These environments that are hostile to life are
also sometimes considered good models to address the
problem of the origin of life on earth. The composition
of bacterial communities in the AMD of a former
lead mine was followed in relation to seasonal variations
and with changes in the concentration of dissolved oxygen
in the water. These acidic waters (pH ~ 2) are rich in
arsenic (300 mg/L), iron (20,000 mg/L), and sulfate
(7,500 mg/L). The main bacteria isolated from this
environment belonged to the genera Acidithiobacillus and
Thiomonas, genera frequently encountered in these
environments (Bruneel et al. 2006). T-RFLP analyses
showed a low diversity. The molecular inventory has
highlighted the role of sulfate-reducing bacteria (SRB) in
this environment (Bruneel et al. 2006). Efforts are underway to isolate SRB strains that play a role in the transformation of arsenic. More recent metagenomic studies
allowed to identify putative bacteria involved in the AMD
functioning (Bertin et al. 2011), and the challenge is now
to isolate such bacteria and characterize their role.
8.6
Conclusion
Biodiversity is increasingly seen as a resource to be
preserved, and microbial biodiversity is no exception to
this rule. Microbial biodiversity has given us antibiotics,
beer, cheese, and bioactive molecules of many kinds, and it
also allows wastewater treatment and the growth of plants
in soil (Box 8.4). It is moreover an overall indicator of the
status of certain biotopes impacted by anthropogenic
pressures, biotopes that must be preserved so that they
can fulfill various functions and deliver services, on
which our well-being depends. This is why it is important
to quantify and compare the different disturbances that
biotopes can withstand before reaching tipping points.
The approaches used to study microbial biodiversity
should also make significant progress both technically
due to the tools currently developed, e.g., for highthroughput sequencing, and analytically because of new
websites which democratize mathematical and bioinformatic approaches.
Microbial biodiversity should continue to be addressed
by scientists for basic reasons but also due to societal issues
linked to pollution, sustainable agriculture and forestry,
health and productivity of oceans and freshwaters, or
global change. Fundamental work should further seek to
establish the causal link between microbial diversity and
ecosystem functioning. In this context, the capacity to
acquire and analyze very large data sets is a major challenge, but sequencing of nucleic acids increases continuously with associated bioinformatic approaches, rapidly
offering new perspectives. These approaches should help
identify taxa present in a given biotope but also to understand which genes are expressed in a given situation.
A sticking point is our ability to identify the function(s)
of genes; this bottleneck will certainly not be broken for
years, which is the time necessary to do solid work on
microbial physiology. More generally, the functional traits
concept used in ecology has been increasingly used in
8 Biodiversity and Microbial Ecosystems Functioning
285