In addition to the spontaneous solubilization in the
aqueous phase (Table 16.6), transfer may take place through
a cell-substrate contact that depends on the cell intrinsic
adherence capacities. Another transfer mode that is the
most widespread brings into play production of tensioactive
molecules, synthesized by microorganisms, called biosurfactants, that emulsify hydrocarbons or increase their solubilization and, consequently, favor their assimilation. The
chemical nature of biosurfactants is highly variable and
depends on the organism that synthesize them (phospholipids, glycolipids, lipopolysaccharides, lipoproteins,
etc.) (Rosenberg and Ron 2000).
Aerobic Biodegradation
Microorganisms that biodegrade hydrocarbons under aerobiosis are ubiquitous (van Hamme et al. 2003; Prince 2010;
Prince et al. 2010) and essentially belong to Proteobacteria:
Gammaproteobacteria (genus Acinetobacter, Alcanivorax,
Pseudomonas, Marinobacter, Mycobacterium, Nocardia,
Rhodococcus, Streptomyces, etc.), Betaproteobacteria
(genus Achromobacter, Alcaligenes, Burkholderia, etc.),
Alphaproteobacteria (genus Sphingomonas); Firmicutes
(genus Bacillus, Geobacillus), as well as some eukaryotic
microorganisms (genus Candida, Hansenula, Saccharomyces, Aspergillus, Fusarium, etc.) are also able to biodegrade hydrocarbons. Biodegradation by cyanobacteria
was not established. However, within some microbial mats
and biofilms, these organisms seem to act indirectly by
producing dioxygen, which would favor the activity of
hydrocarbonoclastic microorganisms. A number of review
were dedicated to biodegradation mechanisms leading to
hydrocarbon mineralization (van Hamme et al. 2003;
Berthe-Corti and Ho ¨pner 2005; Vandecasteele 2008).
These mechanisms will not be described into details, only
hydrocarbon primary oxidation will be described as it is the
essential step of catabolic pathways for these compounds
(Fig. 16.36).
From a chemical point of view, alkanes are relatively
inert molecules. To make possible their degradation, they
must be activated before undergoing other metabolic stages.
Under aerobic conditions, in most cases, n-alkanes are
oxidized by monooxygenases/hydroxylases to form the
corresponding primary alcohol; thus an oxygen atom is
inserted into the molecule. The substrate attack is usually
terminal, but may take place in biterminal or subterminal
position (Fig. 16.36a–c). Depending on the alkane carbon
chain length, different enzymatic systems will be necessary
to insert dioxygen within the substrate and initiate biodegradation. For instance, for alkanes with chain length over 4
carbon atoms, different enzyme families are involved, such
as cytochrome P450-like enzymes (e.g., bacterial enzymes
CYP153) and membranous hydroxylases (pAHs). This last
type of enzyme corresponds to monooxygenases with
nonhemic iron with dinuclear active site of AlkB type,
enabling a number of actinomycetal proteobacteria to use
C 5 –C 16 n-alkanes. These enzymes work within a complex
containing two electron transporters, one rubredroxin and
one rubredroxin reductase enabling electron transfer from
NADH to the active site of the alkane hydroxylase
(Fig. 16.37). After the initial oxidation of the n-alkane,
the corresponding alcohol is then oxidized by an alcohol
dehydrogenase to produce aldehyde and finally the corresponding fatty acid. The latter serves as substrate to acyl-CoA
synthetase and the formed acyl-CoA is then transformed by
β-oxidation.
In the case of aromatic compounds, two key steps
take place in the aerobic biodegradation of mono- or polycyclic aromatic hydrocarbons. In the first step, stable
benzene rings are activated by incorporation of one or
two oxygen atoms upon the action of monooxygenases or
dioxygenases, respectively (Fig. 16.36d, e). For instance,
in the case of naphthalene, this reaction involves the
naphthalene-dioxygenase (NDO) system that usually
comprises one NADH oxidoreductase, ferredoxin, and
one oxygenase containing the catalytic site. This system
Box 16.4 (continued)
optimizing mechanisms used in planktonic growth
mode, such as the secretion of biosurfactants. If it has
been noticed that strains growing as a biofilm on the
hydrocarbon–water interface do not release
bioemulsifiers or biosurfactants in the environment, it
is quite conceivable that biosurfactants would be produced within the biofilm and could accumulate in the
matrix without diffusing into the surrounding medium.
Thus biosurfactants could easily reach a concentration
above their CMC (Critical Micelle Concentration)
which would allow the formation of micelles, ensuring
a fast diffusion of hydrocarbons within the biofilm.
Polymers of the biofilm matrix could also serve as
adsorbents for hydrocarbons making them possibly
more accessible to the cells.
The biofilm mode of growth is characterized by a
profound change in the physiology and in the behavior
of cells, requiring regulation of the expression of
hundreds of genes. The metabolic activities of cells
with diffusion processes generate microchemical
gradients which in turn affect cell physiology (Stewart
and Franklin 2008). As a result, biofilms are highly
heterogeneous structures, containing cells with
different phenotypes, metabolism, and physiological
states. Given such a functional and structural
remodeling, it is not difficult to imagine that the
biofilm lifestyle offers the possibility of several
mechanisms to increase the mass transfer of
hydrocarbons.
722
J.-C. Bertrand et al.
aqueous phase (Table 16.6), transfer may take place through
a cell-substrate contact that depends on the cell intrinsic
adherence capacities. Another transfer mode that is the
most widespread brings into play production of tensioactive
molecules, synthesized by microorganisms, called biosurfactants, that emulsify hydrocarbons or increase their solubilization and, consequently, favor their assimilation. The
chemical nature of biosurfactants is highly variable and
depends on the organism that synthesize them (phospholipids, glycolipids, lipopolysaccharides, lipoproteins,
etc.) (Rosenberg and Ron 2000).
Aerobic Biodegradation
Microorganisms that biodegrade hydrocarbons under aerobiosis are ubiquitous (van Hamme et al. 2003; Prince 2010;
Prince et al. 2010) and essentially belong to Proteobacteria:
Gammaproteobacteria (genus Acinetobacter, Alcanivorax,
Pseudomonas, Marinobacter, Mycobacterium, Nocardia,
Rhodococcus, Streptomyces, etc.), Betaproteobacteria
(genus Achromobacter, Alcaligenes, Burkholderia, etc.),
Alphaproteobacteria (genus Sphingomonas); Firmicutes
(genus Bacillus, Geobacillus), as well as some eukaryotic
microorganisms (genus Candida, Hansenula, Saccharomyces, Aspergillus, Fusarium, etc.) are also able to biodegrade hydrocarbons. Biodegradation by cyanobacteria
was not established. However, within some microbial mats
and biofilms, these organisms seem to act indirectly by
producing dioxygen, which would favor the activity of
hydrocarbonoclastic microorganisms. A number of review
were dedicated to biodegradation mechanisms leading to
hydrocarbon mineralization (van Hamme et al. 2003;
Berthe-Corti and Ho ¨pner 2005; Vandecasteele 2008).
These mechanisms will not be described into details, only
hydrocarbon primary oxidation will be described as it is the
essential step of catabolic pathways for these compounds
(Fig. 16.36).
From a chemical point of view, alkanes are relatively
inert molecules. To make possible their degradation, they
must be activated before undergoing other metabolic stages.
Under aerobic conditions, in most cases, n-alkanes are
oxidized by monooxygenases/hydroxylases to form the
corresponding primary alcohol; thus an oxygen atom is
inserted into the molecule. The substrate attack is usually
terminal, but may take place in biterminal or subterminal
position (Fig. 16.36a–c). Depending on the alkane carbon
chain length, different enzymatic systems will be necessary
to insert dioxygen within the substrate and initiate biodegradation. For instance, for alkanes with chain length over 4
carbon atoms, different enzyme families are involved, such
as cytochrome P450-like enzymes (e.g., bacterial enzymes
CYP153) and membranous hydroxylases (pAHs). This last
type of enzyme corresponds to monooxygenases with
nonhemic iron with dinuclear active site of AlkB type,
enabling a number of actinomycetal proteobacteria to use
C 5 –C 16 n-alkanes. These enzymes work within a complex
containing two electron transporters, one rubredroxin and
one rubredroxin reductase enabling electron transfer from
NADH to the active site of the alkane hydroxylase
(Fig. 16.37). After the initial oxidation of the n-alkane,
the corresponding alcohol is then oxidized by an alcohol
dehydrogenase to produce aldehyde and finally the corresponding fatty acid. The latter serves as substrate to acyl-CoA
synthetase and the formed acyl-CoA is then transformed by
β-oxidation.
In the case of aromatic compounds, two key steps
take place in the aerobic biodegradation of mono- or polycyclic aromatic hydrocarbons. In the first step, stable
benzene rings are activated by incorporation of one or
two oxygen atoms upon the action of monooxygenases or
dioxygenases, respectively (Fig. 16.36d, e). For instance,
in the case of naphthalene, this reaction involves the
naphthalene-dioxygenase (NDO) system that usually
comprises one NADH oxidoreductase, ferredoxin, and
one oxygenase containing the catalytic site. This system
Box 16.4 (continued)
optimizing mechanisms used in planktonic growth
mode, such as the secretion of biosurfactants. If it has
been noticed that strains growing as a biofilm on the
hydrocarbon–water interface do not release
bioemulsifiers or biosurfactants in the environment, it
is quite conceivable that biosurfactants would be produced within the biofilm and could accumulate in the
matrix without diffusing into the surrounding medium.
Thus biosurfactants could easily reach a concentration
above their CMC (Critical Micelle Concentration)
which would allow the formation of micelles, ensuring
a fast diffusion of hydrocarbons within the biofilm.
Polymers of the biofilm matrix could also serve as
adsorbents for hydrocarbons making them possibly
more accessible to the cells.
The biofilm mode of growth is characterized by a
profound change in the physiology and in the behavior
of cells, requiring regulation of the expression of
hundreds of genes. The metabolic activities of cells
with diffusion processes generate microchemical
gradients which in turn affect cell physiology (Stewart
and Franklin 2008). As a result, biofilms are highly
heterogeneous structures, containing cells with
different phenotypes, metabolism, and physiological
states. Given such a functional and structural
remodeling, it is not difficult to imagine that the
biofilm lifestyle offers the possibility of several
mechanisms to increase the mass transfer of
hydrocarbons.
722
J.-C. Bertrand et al.