1. Recent or ancient HGT
2. HGT occurring between close or distant lineages
3. HGT among genomes with different or similar genomic
features
4. HGT leading to the replacement of preexisting genes or
the acquisition of new genes, etc.
12.4 A Major Evolutionary Mechanism?
HGT is considered a major evolutionary mechanism by
many evolutionists and microbiologists. Indeed, although
point mutations are the only mechanism creating genetic
diversity, HGT is a powerful and efficient vector for gene
and allele dissemination in populations and ecosystems.
At the population level, the probability of fixation of a
new gene (or allele) is very low. This probability depends on
the selective advantage it confers. In a population of N
haploid cells, the probability of fixation of a neutral allele
(i.e., one that does not confer any particular selective advantage or disadvantage) is equal to 1/N. This process would
require in average 2 N generations. If the allele is not neutral,
that is to say, it is associated to a coefficient of selection s, its
fixation will require (2/s)ln(N) generations. This number of
generation decreases as the selective advantage brought by
the allele increases. For instance, in a population of 10
6
haploid individuals having a generation time of 24 h, the
probability of fixation of a new neutral allele is equal to 10
À6
and will require 2 Â 10
6 days (~5,480 years) in average. If
the new allele confers a selective advantage of 1 %
(s ¼ 0.01), it will be fixed in (2/0.01)ln(10
6 ) generations,
that is, 2,763 days (~7.6 years). This example shows that
even in the case of a haploid population of relatively small
size, the time required to fix a gene or allele under positive
selection can be relatively high.
HGT may accelerate the rate of diffusion and thus of
fixation of genes and alleles in microbial populations. Beyond
intrapopulation diffusion, conjugation and natural transformation allows the transfer of genetic material among species
living in similar environments. As a consequence, if a gene
conferring a strong selective advantage appears in a given
ecosystem, it may be transferred to other organisms living in
the same ecosystem. Finally, transduction allows HGT across
organisms and species also living in distant ecosystems.
12.4.1 HGT in Prokaryotes
12.4.1.1 HGT and Adaptation
Irrespective of its frequency, HGT is considered as an
important way for microorganisms to adapt to their habitats,
allowing for instance the acquisition of resistance to toxic
compounds or phages or the acquisition of metabolic
capabilities allowing the use of new resources and the conquest of new ecological niches. The scientific literature on
the adaptive role of HGT in prokaryotes is extremely rich.
Therefore, the few examples that will be developed here
should not be considered as exhaustive.
From a historical perspective, the adaptive role of HGT
was uncovered in the 1950s following the worldwide emergence of antibiotic resistant strains (Barlow 2009) (cf. Sect.
9.5). From a biological point of view, antibiotic resistance
can have different origins: alterations or changes in the
regulation of enzymes targeted by the antibiotics; changes
in the permeability of the membrane to antibiotics, either
through a decrease in influx or an increase in efflux
capacities; activation of secondary metabolic pathways
bypassing the enzymes targeted by the antibiotics; presence
of competitors presenting a stronger affinity to the antibiotic
compared to its target, etc. The literature on this subject is
very abundant and a few examples will be detailed here. The
interested reader may refer to Lambert (2005).
Irrespective of their origin, it has been clearly shown that
HGTs have played a major role in the dissemination of
antibiotic resistance among microorganisms. Although
mechanisms involved in HGT vary from one species to
another (e.g., conjugation in enterococci, natural transformation in streptococci, transduction or conjugation in
staphylococci) (Barlow 2009), the dissemination of antibiotic
resistance is rapid even among different strains and species
and over large geographical areas. For instance, recent
surveys suggest that less than 3 years are required between
the time of emergence of resistance factors in bacterial
populations and their worldwide dissemination (for additional
details, see references in Barlow 2009). Such rapidity is
linked to the fact that antibiotics induce very strong selection
pressures on microorganisms. As a consequence, carrying
resistance genes provides a strong advantage that favors the
fixation of the corresponding genes in microbial populations
through both vertical and horizontal gene transfer. Therefore,
the appearance of resistance factors in a very small number of
individuals may be a sufficient starting point for their dissemination over large scales through HGT.
Recombination events, which are common in prokaryotic
genomes, are another factor explaining the rapidity of dissemination of antibiotic resistance. Recombination may approach
in the same genome region genes carrying various resistances,
leading to the formation of groups (or cassettes) of resistance
genes. For instance, such a cassette has been characterized in
a bird pathogenic strain of E. coli (Gilmour et al. 2004), which
contains resistance factors to the following:
– Various aminoglycosides (e.g., amikacin, gentamicin,
kanamycin, neomycin, netilmicin, paromomycin, streptomycin, tobramycin, etc.)
– Sulbactam a β-lactamase inhibitor
466
C. Brochier-Armanet and D. Moreira
2. HGT occurring between close or distant lineages
3. HGT among genomes with different or similar genomic
features
4. HGT leading to the replacement of preexisting genes or
the acquisition of new genes, etc.
12.4 A Major Evolutionary Mechanism?
HGT is considered a major evolutionary mechanism by
many evolutionists and microbiologists. Indeed, although
point mutations are the only mechanism creating genetic
diversity, HGT is a powerful and efficient vector for gene
and allele dissemination in populations and ecosystems.
At the population level, the probability of fixation of a
new gene (or allele) is very low. This probability depends on
the selective advantage it confers. In a population of N
haploid cells, the probability of fixation of a neutral allele
(i.e., one that does not confer any particular selective advantage or disadvantage) is equal to 1/N. This process would
require in average 2 N generations. If the allele is not neutral,
that is to say, it is associated to a coefficient of selection s, its
fixation will require (2/s)ln(N) generations. This number of
generation decreases as the selective advantage brought by
the allele increases. For instance, in a population of 10
6
haploid individuals having a generation time of 24 h, the
probability of fixation of a new neutral allele is equal to 10
À6
and will require 2 Â 10
6 days (~5,480 years) in average. If
the new allele confers a selective advantage of 1 %
(s ¼ 0.01), it will be fixed in (2/0.01)ln(10
6 ) generations,
that is, 2,763 days (~7.6 years). This example shows that
even in the case of a haploid population of relatively small
size, the time required to fix a gene or allele under positive
selection can be relatively high.
HGT may accelerate the rate of diffusion and thus of
fixation of genes and alleles in microbial populations. Beyond
intrapopulation diffusion, conjugation and natural transformation allows the transfer of genetic material among species
living in similar environments. As a consequence, if a gene
conferring a strong selective advantage appears in a given
ecosystem, it may be transferred to other organisms living in
the same ecosystem. Finally, transduction allows HGT across
organisms and species also living in distant ecosystems.
12.4.1 HGT in Prokaryotes
12.4.1.1 HGT and Adaptation
Irrespective of its frequency, HGT is considered as an
important way for microorganisms to adapt to their habitats,
allowing for instance the acquisition of resistance to toxic
compounds or phages or the acquisition of metabolic
capabilities allowing the use of new resources and the conquest of new ecological niches. The scientific literature on
the adaptive role of HGT in prokaryotes is extremely rich.
Therefore, the few examples that will be developed here
should not be considered as exhaustive.
From a historical perspective, the adaptive role of HGT
was uncovered in the 1950s following the worldwide emergence of antibiotic resistant strains (Barlow 2009) (cf. Sect.
9.5). From a biological point of view, antibiotic resistance
can have different origins: alterations or changes in the
regulation of enzymes targeted by the antibiotics; changes
in the permeability of the membrane to antibiotics, either
through a decrease in influx or an increase in efflux
capacities; activation of secondary metabolic pathways
bypassing the enzymes targeted by the antibiotics; presence
of competitors presenting a stronger affinity to the antibiotic
compared to its target, etc. The literature on this subject is
very abundant and a few examples will be detailed here. The
interested reader may refer to Lambert (2005).
Irrespective of their origin, it has been clearly shown that
HGTs have played a major role in the dissemination of
antibiotic resistance among microorganisms. Although
mechanisms involved in HGT vary from one species to
another (e.g., conjugation in enterococci, natural transformation in streptococci, transduction or conjugation in
staphylococci) (Barlow 2009), the dissemination of antibiotic
resistance is rapid even among different strains and species
and over large geographical areas. For instance, recent
surveys suggest that less than 3 years are required between
the time of emergence of resistance factors in bacterial
populations and their worldwide dissemination (for additional
details, see references in Barlow 2009). Such rapidity is
linked to the fact that antibiotics induce very strong selection
pressures on microorganisms. As a consequence, carrying
resistance genes provides a strong advantage that favors the
fixation of the corresponding genes in microbial populations
through both vertical and horizontal gene transfer. Therefore,
the appearance of resistance factors in a very small number of
individuals may be a sufficient starting point for their dissemination over large scales through HGT.
Recombination events, which are common in prokaryotic
genomes, are another factor explaining the rapidity of dissemination of antibiotic resistance. Recombination may approach
in the same genome region genes carrying various resistances,
leading to the formation of groups (or cassettes) of resistance
genes. For instance, such a cassette has been characterized in
a bird pathogenic strain of E. coli (Gilmour et al. 2004), which
contains resistance factors to the following:
– Various aminoglycosides (e.g., amikacin, gentamicin,
kanamycin, neomycin, netilmicin, paromomycin, streptomycin, tobramycin, etc.)
– Sulbactam a β-lactamase inhibitor
466
C. Brochier-Armanet and D. Moreira