Box 16.3: Involvement of Horizontal Gene Transfer
in Chlorinated Compounds Biological Degradation:
Example of the Biological Degradation of Lindane
Sibel Berger, Maude M. David, Timothy M. Vogel,
and Pascal Simonet
Utilization and Toxicity of Lindane
Lindane (gamma-hexachlorocyclohexane) is a wide
activity spectrum pesticide against plant eating, soil
living insects, and man and animal parasites. It was
extensively used in forest industry, agriculture, and in
treatments against parasites. Because of a low solubility in water (7 mg∙L
À1 ), lindane can persist in soil
for months (half-life varying from 30 to 300 days),
leading to its accumulation in numerous environmental compartments. In addition, the Cancer International Research Center classifies lindane as a potential
carcinogenic agent for humans (class 2B, IARC,
1991). Effects on the nervous, respiratory, digestive,
and endocrine (reproduction) systems were reported
leading to its ban in most western countries. However,
lindane is still used in numerous developing countries
because of its low cost.
Biological Degradation of Lindane
Only one degradation pathway of lindane under aerobic
conditions was identified in bacteria that belong to
only one genus, Sphingobium. The complete lindane
degradation pathway in Sphingobium japonicum
involves successively LinA to LinJ enzymes, the
regulator LinR, and a putative ABC-type transporter,
LinKLMN (Box Fig. 16.6) (Nagata et al. 2007).
The corresponding coding genes (lin genes) are well
conserved among all Sphingobium isolates that degrade
lindane whatever the country the strains were isolated
(Lal et al. 2006). Under laboratory conditions, the
degradation phenotype can be detected by a halo
surrounding colonies developing on solidified rich
media supplemented with lindane. The degradation
phenotype is very instable with, for instance, in
Sphingobium francense sp.+ (Thomas et al. 1996), a
very high mutation frequency leading to the loss of the
degradation capacity in up to 4 % of cells (Ce ´re ´monie
et al. 2006). Molecular characterization of mutants
revealed significant genomic rearrangements including
deletions or insertion sequence (IS) movements
S. Berger (*) M.M. David T.M. Vogel P. Simonet
Environ. Microb. Genom. Group, E ´ cole Centrale de Lyon,
UMR CNRS 5005, Laboratoire Ampe `re, E ´ cully, France
(continued)
Box 16.3 (continued)
affecting lin genes and particularly the dehydrochlorinase encoding linA gene, a key enzyme in lindane
degradation pathway. This gene was found to be
affected by mutations occurring at high frequency in
addition to a strong plasticity of the Sphingobium
francense genome involving mobile genetic elements.
Putative Origin of Xenobiotic Compound
Degradation Genes
Studies on xenobiotic compound-contaminated
ecosystems, including lindane, confirm that these
compounds are highly recalcitrant to biological degradation because of the lack of degrading bacteria in the
soil. Conventional or DNA-based microbiological
studies systematically lead to negative results regarding detection of degrading bacteria or their genes in
most soils. However, some degradation-adapted bacteria were successfully isolated on sites polluted for
years by the xenobiotic compounds. The hypothesis of
HGT and genetic recombination involving the soil
bacterial community DNA pool were proposed to
explain the assembly of new catabolic genes in some
bacterial cells. The experimental demonstration that
linA and other new catabolic genes result from the
natural and recent shuffling of DNA fragments
initially spread in various bacteria would confirm the
major adaptive role of HGT. The assembly of such
new genes would indicate the extremely high frequency of transfer of DNA fragments occurring at
random among soil bacteria necessary to provide
enough different genetic combinations including the
one corresponding to a catabolic gene susceptible to
increase the fitness of its bacterial host in presence of
the xenobiotic compound.
In Silico and Experimental Approach
The molecular origin of the new degrading genes
can be deduced from their similarity level with
proteins in other catabolic pathways. For instance,
linD, linE, and linF genes share some similarity with,
respectively, pcpC, pcpA, and pcpE genes involved in
pentachlorophenol degradation in Sphingobium
chlorophenolicum, suggesting that they could have
been acquired from this host. In addition, presence of
mobile genetic elements (IS) in the vicinity of the lin
genes and their localization on plasmids suggest the
role of HGT events for spreading them among soil
bacteria including Sphingobium francense (Ce ´re ´monie
et al. 2006; Nagata et al. 2006). However, the
(continued)
16 Applied Microbial Ecology and Bioremediation
705
in Chlorinated Compounds Biological Degradation:
Example of the Biological Degradation of Lindane
Sibel Berger, Maude M. David, Timothy M. Vogel,
and Pascal Simonet
Utilization and Toxicity of Lindane
Lindane (gamma-hexachlorocyclohexane) is a wide
activity spectrum pesticide against plant eating, soil
living insects, and man and animal parasites. It was
extensively used in forest industry, agriculture, and in
treatments against parasites. Because of a low solubility in water (7 mg∙L
À1 ), lindane can persist in soil
for months (half-life varying from 30 to 300 days),
leading to its accumulation in numerous environmental compartments. In addition, the Cancer International Research Center classifies lindane as a potential
carcinogenic agent for humans (class 2B, IARC,
1991). Effects on the nervous, respiratory, digestive,
and endocrine (reproduction) systems were reported
leading to its ban in most western countries. However,
lindane is still used in numerous developing countries
because of its low cost.
Biological Degradation of Lindane
Only one degradation pathway of lindane under aerobic
conditions was identified in bacteria that belong to
only one genus, Sphingobium. The complete lindane
degradation pathway in Sphingobium japonicum
involves successively LinA to LinJ enzymes, the
regulator LinR, and a putative ABC-type transporter,
LinKLMN (Box Fig. 16.6) (Nagata et al. 2007).
The corresponding coding genes (lin genes) are well
conserved among all Sphingobium isolates that degrade
lindane whatever the country the strains were isolated
(Lal et al. 2006). Under laboratory conditions, the
degradation phenotype can be detected by a halo
surrounding colonies developing on solidified rich
media supplemented with lindane. The degradation
phenotype is very instable with, for instance, in
Sphingobium francense sp.+ (Thomas et al. 1996), a
very high mutation frequency leading to the loss of the
degradation capacity in up to 4 % of cells (Ce ´re ´monie
et al. 2006). Molecular characterization of mutants
revealed significant genomic rearrangements including
deletions or insertion sequence (IS) movements
S. Berger (*) M.M. David T.M. Vogel P. Simonet
Environ. Microb. Genom. Group, E ´ cole Centrale de Lyon,
UMR CNRS 5005, Laboratoire Ampe `re, E ´ cully, France
(continued)
Box 16.3 (continued)
affecting lin genes and particularly the dehydrochlorinase encoding linA gene, a key enzyme in lindane
degradation pathway. This gene was found to be
affected by mutations occurring at high frequency in
addition to a strong plasticity of the Sphingobium
francense genome involving mobile genetic elements.
Putative Origin of Xenobiotic Compound
Degradation Genes
Studies on xenobiotic compound-contaminated
ecosystems, including lindane, confirm that these
compounds are highly recalcitrant to biological degradation because of the lack of degrading bacteria in the
soil. Conventional or DNA-based microbiological
studies systematically lead to negative results regarding detection of degrading bacteria or their genes in
most soils. However, some degradation-adapted bacteria were successfully isolated on sites polluted for
years by the xenobiotic compounds. The hypothesis of
HGT and genetic recombination involving the soil
bacterial community DNA pool were proposed to
explain the assembly of new catabolic genes in some
bacterial cells. The experimental demonstration that
linA and other new catabolic genes result from the
natural and recent shuffling of DNA fragments
initially spread in various bacteria would confirm the
major adaptive role of HGT. The assembly of such
new genes would indicate the extremely high frequency of transfer of DNA fragments occurring at
random among soil bacteria necessary to provide
enough different genetic combinations including the
one corresponding to a catabolic gene susceptible to
increase the fitness of its bacterial host in presence of
the xenobiotic compound.
In Silico and Experimental Approach
The molecular origin of the new degrading genes
can be deduced from their similarity level with
proteins in other catabolic pathways. For instance,
linD, linE, and linF genes share some similarity with,
respectively, pcpC, pcpA, and pcpE genes involved in
pentachlorophenol degradation in Sphingobium
chlorophenolicum, suggesting that they could have
been acquired from this host. In addition, presence of
mobile genetic elements (IS) in the vicinity of the lin
genes and their localization on plasmids suggest the
role of HGT events for spreading them among soil
bacteria including Sphingobium francense (Ce ´re ´monie
et al. 2006; Nagata et al. 2006). However, the
(continued)
16 Applied Microbial Ecology and Bioremediation
705