16.1 Introduction
Industrial development and increasing population are the
cause of environmental pollution that occurs globally and
affects all terrestrial and aquatic ecosystems. The deleterious
effects of pollution on human health, the functioning of
biogeochemical cycles, erosion of biodiversity and more
broadly on the entire biosphere, have become a major concern for modern societies. Awareness of the seriousness of
this situation has led to the implementation of actions against
environmental pollution at local, regional, national and
international levels.
Microorganisms are key players in the depollution of the
environment. Indeed, because of the huge diversity of their
metabolic capabilities (cf. Chap. 3), expressed whatever environmental conditions are, including the most extreme
conditions (cf. Chap. 10), microorganisms can process almost
all natural pollutants when sufficient time is allowed. They are
also able, in most cases, to deal with artificial substances,
xenobiotics* that never existed in nature. The mechanisms
involved are numerous and diverse: biodegradation*, biotransformation*, cometabolism*, syntrophy*, bioaccumulation*, bioimmobilization, and bioleaching. The adaptive
capacities of microbial communities to pollutants are explained
by their ability to express enzymatic tools via genetic changes
such as mutations, endogenous rearrangements or acquisition
of exogenous DNA fragments, etc. These changes include the
horizontal gene transfers (HGTs) which play an important role
in enabling the spread of catabolic genes often located on
conjugative and integrative plasmids, integrative transposons,
or conjugative integrative elements. These elements can exist
in the form of plasmids (linear or circular) or are integrated at
dedicated chromosomal sites of the “host organism.”
Thus, research in microbial ecology has important practical implications for environmental depollution. In
elucidating the mechanisms by which microorganisms
attack pollutants, this research use the decontaminating
power of microorganisms in the development of many
biological processes that lead to the elimination or mitigation of pollution.
Treatments by microbes depend on the pollutant and the
biotope (water, soil, sediment, air) and can be broadly
grouped into two domains of application. The first domain is
the preventive treatment of pollution for which the organic
(domestic or industrial sewage*, wastes, etc.) or mineral
pollutant is either totally or partially eliminated or
transformed into a nontoxic product (compost or biogas)
having a market value or is reduced to an acceptable level
before discharge into the environment. The second domain of
application is the use of microorganisms to rehabilitate a site
contaminated with one or more pollutants. During the implementation of this type of biotechnology known as bioremediation, the pollutant of organic or inorganic origin can be
treated in situ (without excavation) or ex situ (after excavation) (Iwamoto and Nasu 2001; Pandey et al. 2009). In the
latter case, the treatment of the pollutant can be done on site or
off-site after transport to a depollution center.
In addition to these two applications of microbial
activities, microorganisms can be used in the preservation
of food, management of agricultural soil, and the fight
against biodeterioration (metals, paints, concrete, etc.) or in
the control and prevention of pollution through qualitative
and quantitative highlighting of microbial pathogens in the
environment (cf. Sect. 15.6).
In all cases, the development of a microbial-based
depollution technique cannot be considered without thorough knowledge of:
(i) The chemical structure of the pollution source and the
products formed during its degradation, which most
often require the implementation of sophisticated analytical techniques.
(ii) Its origin and its concentration in the environment;
waste.
(iii) Its behavior, i.e., of its biogeochemical cycle.
(iv) The degradation mechanisms of pollutant by microorganisms which can only be elucidated by experiments
conducted in the laboratory that should simulate, as
realistically as possible, the environmental conditions
in which the microorganisms will be subjected to in the
environment; this step involves studies on the physiology, biochemistry, and genetics of the involved
microorganisms.
(v) The effects of the implemented treatment on the flora,
fauna, and humans.
In this chapter, the following are described:
(i) The chemical structure and the origin of the major
pollutants
(ii) The natural biogeochemical cycles (i.e., without human
action) of the major pollutants, emphasizing the role of
microorganisms in their natural elimination, which
include all physicochemical and biological processes
to which pollutants are subjected in the natural
environment
(iii) The major microbiological treatments that may be
applied both for prevention and rehabilitation of a polluted environment
(iv) Examples of the treatment of major sources of pollution
using microbial-based techniques that enhance natural
attenuation*.
660
J.-C. Bertrand et al.
Industrial development and increasing population are the
cause of environmental pollution that occurs globally and
affects all terrestrial and aquatic ecosystems. The deleterious
effects of pollution on human health, the functioning of
biogeochemical cycles, erosion of biodiversity and more
broadly on the entire biosphere, have become a major concern for modern societies. Awareness of the seriousness of
this situation has led to the implementation of actions against
environmental pollution at local, regional, national and
international levels.
Microorganisms are key players in the depollution of the
environment. Indeed, because of the huge diversity of their
metabolic capabilities (cf. Chap. 3), expressed whatever environmental conditions are, including the most extreme
conditions (cf. Chap. 10), microorganisms can process almost
all natural pollutants when sufficient time is allowed. They are
also able, in most cases, to deal with artificial substances,
xenobiotics* that never existed in nature. The mechanisms
involved are numerous and diverse: biodegradation*, biotransformation*, cometabolism*, syntrophy*, bioaccumulation*, bioimmobilization, and bioleaching. The adaptive
capacities of microbial communities to pollutants are explained
by their ability to express enzymatic tools via genetic changes
such as mutations, endogenous rearrangements or acquisition
of exogenous DNA fragments, etc. These changes include the
horizontal gene transfers (HGTs) which play an important role
in enabling the spread of catabolic genes often located on
conjugative and integrative plasmids, integrative transposons,
or conjugative integrative elements. These elements can exist
in the form of plasmids (linear or circular) or are integrated at
dedicated chromosomal sites of the “host organism.”
Thus, research in microbial ecology has important practical implications for environmental depollution. In
elucidating the mechanisms by which microorganisms
attack pollutants, this research use the decontaminating
power of microorganisms in the development of many
biological processes that lead to the elimination or mitigation of pollution.
Treatments by microbes depend on the pollutant and the
biotope (water, soil, sediment, air) and can be broadly
grouped into two domains of application. The first domain is
the preventive treatment of pollution for which the organic
(domestic or industrial sewage*, wastes, etc.) or mineral
pollutant is either totally or partially eliminated or
transformed into a nontoxic product (compost or biogas)
having a market value or is reduced to an acceptable level
before discharge into the environment. The second domain of
application is the use of microorganisms to rehabilitate a site
contaminated with one or more pollutants. During the implementation of this type of biotechnology known as bioremediation, the pollutant of organic or inorganic origin can be
treated in situ (without excavation) or ex situ (after excavation) (Iwamoto and Nasu 2001; Pandey et al. 2009). In the
latter case, the treatment of the pollutant can be done on site or
off-site after transport to a depollution center.
In addition to these two applications of microbial
activities, microorganisms can be used in the preservation
of food, management of agricultural soil, and the fight
against biodeterioration (metals, paints, concrete, etc.) or in
the control and prevention of pollution through qualitative
and quantitative highlighting of microbial pathogens in the
environment (cf. Sect. 15.6).
In all cases, the development of a microbial-based
depollution technique cannot be considered without thorough knowledge of:
(i) The chemical structure of the pollution source and the
products formed during its degradation, which most
often require the implementation of sophisticated analytical techniques.
(ii) Its origin and its concentration in the environment;
waste.
(iii) Its behavior, i.e., of its biogeochemical cycle.
(iv) The degradation mechanisms of pollutant by microorganisms which can only be elucidated by experiments
conducted in the laboratory that should simulate, as
realistically as possible, the environmental conditions
in which the microorganisms will be subjected to in the
environment; this step involves studies on the physiology, biochemistry, and genetics of the involved
microorganisms.
(v) The effects of the implemented treatment on the flora,
fauna, and humans.
In this chapter, the following are described:
(i) The chemical structure and the origin of the major
pollutants
(ii) The natural biogeochemical cycles (i.e., without human
action) of the major pollutants, emphasizing the role of
microorganisms in their natural elimination, which
include all physicochemical and biological processes
to which pollutants are subjected in the natural
environment
(iii) The major microbiological treatments that may be
applied both for prevention and rehabilitation of a polluted environment
(iv) Examples of the treatment of major sources of pollution
using microbial-based techniques that enhance natural
attenuation*.
660
J.-C. Bertrand et al.