11.2.2.3 Cooperation
Trophic relations such as the ones above would correspond
to cooperation if facultative. One of the main cases of cooperation between microorganisms is quorum sensing. Bacteria have mechanisms that allow them to control certain
physiological functions (such as conjugation) according to
cell density, which is useful to ensure success. This quorum
sensing mechanism is based on synthesis and perception of
signals such as N-acyl homoserine lactone (described in
details in Sect. 9.3) and is sometimes disturbed by higher
plants or algae (Teplitski et al. 2000; Bauer and Robinson
2002). Thus, it has been shown that gamma-amino butyric
acid (GABA) (synthesized by plants upon wounding or
infection by Agrobacterium) induces the catabolism of Nacyl homoserine lactone and thus may modulate quorum
sensing (Chevrot et al. 2006). Quorum sensing may also be
affected by bacteria that synthesize lactonases, especially
Bacillus thuringiensis and Agrobacterium tumefaciens, a
mechanism that is being evaluated for biological control of
various infectious agents.
11.2.2.4 Commensalism
It is difficult to identify situations of true commensalism
between microorganisms, i.e., where a taxon derives benefits
from an interaction but the other derives none. This could be
the case of bacteria involved in nitrification, a process that
occurs in two steps. Chemolithotrophic ammonia-oxidizing
archaea and bacteria convert ammonium to nitrite, while
nitrite-oxidizing bacteria Nitrobacter and Nitrospira convert
nitrite into nitrate. Nitrite oxidizers obviously depend on the
provision of nitrite by ammonia oxidizers, while the benefit
for the latter is less obvious. However, nitrite is toxic for
many taxa, including certain ammonia oxidizers, which
would then benefit from nitrite removal. The interaction
involved would rather be a cooperation in this case.
In many habitats, an element is limiting for bacterial
growth and taxa with access to this element will be at the
base of a food chain. This is the case of cyanobacteria
capable of fixing carbon dioxide through photosynthesis,
which are trophic partners of marine bacteria particularly
those of the microbial loop (cf. Chap. 13). This is also the
case for nitrogen-fixing bacteria in the rhizosphere and soils.
There are other examples of commensalism, in particular,
E. coli that is optionally aerobic, consumes oxygen, and
renders the intestinal tract anaerobic and therefore suitable
for Bacteroides, a strict anaerobe. Similarly, bacteria
involved in milk souring have a fermentative metabolism
and release acidic compounds that acidify the medium and
provide favorable growth conditions for acid-tolerant lactic
acid bacteria.
Plants and microorganisms also synthesize and secrete
compounds that are toxic to many microorganisms. In the
same vein, many toxic compounds from human activity are
found in the environment, where they selectively inhibit
microbial taxa. Various microorganisms may degrade
them, as illustrated with olive wastes metabolized by
composting (Zenjari et al. 2006) or pentachlorophenol used
as a wood treatment that is degraded by Sphingobium (Dams
et al. 2007). These biodegrading microorganisms enable or
enhance the growth of others.
11.2.2.5 Horizontal Gene Transfer
Horizontal gene transfer (cf. Chap. 12) may be mutually
beneficial and would fall within the framework of cooperation but is not easy to qualify in terms of ecological interaction. The best-known case is that of antibiotic treatment in a
medium comprising more than one microbial taxon, where
initially most bacteria are sensitive to a compound to which
they have never been in contact. Mutants resistant to this
antibiotic will proliferate. Finally, the DNA fragment conferring resistance to the antibiotic may be transferred to
sensitive cells of the same taxon or belonging to a remote
taxon. One of the first described cases of transfer of resistance genes took place in Birmingham, England, in 1960. A
care unit for burn victims found waves of nosocomial
infections starting initially with Klebsiella aerogenes resistant to carbenicillin and carrying a resistance plasmid (RK2),
followed by a second wave of Pseudomonas aeruginosa also
carrying a closely related resistance plasmid. It has been
shown that this phenomenon involved conjugative plasmid
transfer (Ingram et al. 1973). Such cases of transfer of
antibiotic resistance genes are common nowadays; they
threaten our ability to curb infections and are one of the
public health problems of greatest concern (Fig. 11.6).
Another case of gene transfer following a massive chemical selection pressure was found regarding mercury, a metal
present in the bedrock and abundant in many natural or manmade habitats such as hydroelectric reservoirs or gold panning workshops. It was shown that mer genes carried by
conjugative plasmids or transposons and conferring the ability to volatilize mercury were transferred between phylogenetically distant bacteria by conjugation (Mindlin et al. 2002).
A similar phenomenon has also been observed with manmade compounds such as atrazine, currently the most widely
used herbicide in the USA (cf. Sect. 16.7.2). When the
herbicide is added to a field and ends up in the soil, it induces
massive transfer to the soil microbiota of a plasmid carrying
genes atz and trz for atrazine degradation (Devers et al.
2005). atz and trz are often on plasmids, but also on the
chromosome near insertion sequences, suggesting that transposition plays an important role in the dispersion of this
metabolic competence (cf. Sect. 16.7.2).
Maintaining large plasmids is not neutral in terms of
fitness if they do not carry essential genes, which is reflected
in the existence of strains having lost their plasmids in the
soil, as is the case for many bacteria in particular
404
Y. Moe ¨nne-Loccoz et al.
Trophic relations such as the ones above would correspond
to cooperation if facultative. One of the main cases of cooperation between microorganisms is quorum sensing. Bacteria have mechanisms that allow them to control certain
physiological functions (such as conjugation) according to
cell density, which is useful to ensure success. This quorum
sensing mechanism is based on synthesis and perception of
signals such as N-acyl homoserine lactone (described in
details in Sect. 9.3) and is sometimes disturbed by higher
plants or algae (Teplitski et al. 2000; Bauer and Robinson
2002). Thus, it has been shown that gamma-amino butyric
acid (GABA) (synthesized by plants upon wounding or
infection by Agrobacterium) induces the catabolism of Nacyl homoserine lactone and thus may modulate quorum
sensing (Chevrot et al. 2006). Quorum sensing may also be
affected by bacteria that synthesize lactonases, especially
Bacillus thuringiensis and Agrobacterium tumefaciens, a
mechanism that is being evaluated for biological control of
various infectious agents.
11.2.2.4 Commensalism
It is difficult to identify situations of true commensalism
between microorganisms, i.e., where a taxon derives benefits
from an interaction but the other derives none. This could be
the case of bacteria involved in nitrification, a process that
occurs in two steps. Chemolithotrophic ammonia-oxidizing
archaea and bacteria convert ammonium to nitrite, while
nitrite-oxidizing bacteria Nitrobacter and Nitrospira convert
nitrite into nitrate. Nitrite oxidizers obviously depend on the
provision of nitrite by ammonia oxidizers, while the benefit
for the latter is less obvious. However, nitrite is toxic for
many taxa, including certain ammonia oxidizers, which
would then benefit from nitrite removal. The interaction
involved would rather be a cooperation in this case.
In many habitats, an element is limiting for bacterial
growth and taxa with access to this element will be at the
base of a food chain. This is the case of cyanobacteria
capable of fixing carbon dioxide through photosynthesis,
which are trophic partners of marine bacteria particularly
those of the microbial loop (cf. Chap. 13). This is also the
case for nitrogen-fixing bacteria in the rhizosphere and soils.
There are other examples of commensalism, in particular,
E. coli that is optionally aerobic, consumes oxygen, and
renders the intestinal tract anaerobic and therefore suitable
for Bacteroides, a strict anaerobe. Similarly, bacteria
involved in milk souring have a fermentative metabolism
and release acidic compounds that acidify the medium and
provide favorable growth conditions for acid-tolerant lactic
acid bacteria.
Plants and microorganisms also synthesize and secrete
compounds that are toxic to many microorganisms. In the
same vein, many toxic compounds from human activity are
found in the environment, where they selectively inhibit
microbial taxa. Various microorganisms may degrade
them, as illustrated with olive wastes metabolized by
composting (Zenjari et al. 2006) or pentachlorophenol used
as a wood treatment that is degraded by Sphingobium (Dams
et al. 2007). These biodegrading microorganisms enable or
enhance the growth of others.
11.2.2.5 Horizontal Gene Transfer
Horizontal gene transfer (cf. Chap. 12) may be mutually
beneficial and would fall within the framework of cooperation but is not easy to qualify in terms of ecological interaction. The best-known case is that of antibiotic treatment in a
medium comprising more than one microbial taxon, where
initially most bacteria are sensitive to a compound to which
they have never been in contact. Mutants resistant to this
antibiotic will proliferate. Finally, the DNA fragment conferring resistance to the antibiotic may be transferred to
sensitive cells of the same taxon or belonging to a remote
taxon. One of the first described cases of transfer of resistance genes took place in Birmingham, England, in 1960. A
care unit for burn victims found waves of nosocomial
infections starting initially with Klebsiella aerogenes resistant to carbenicillin and carrying a resistance plasmid (RK2),
followed by a second wave of Pseudomonas aeruginosa also
carrying a closely related resistance plasmid. It has been
shown that this phenomenon involved conjugative plasmid
transfer (Ingram et al. 1973). Such cases of transfer of
antibiotic resistance genes are common nowadays; they
threaten our ability to curb infections and are one of the
public health problems of greatest concern (Fig. 11.6).
Another case of gene transfer following a massive chemical selection pressure was found regarding mercury, a metal
present in the bedrock and abundant in many natural or manmade habitats such as hydroelectric reservoirs or gold panning workshops. It was shown that mer genes carried by
conjugative plasmids or transposons and conferring the ability to volatilize mercury were transferred between phylogenetically distant bacteria by conjugation (Mindlin et al. 2002).
A similar phenomenon has also been observed with manmade compounds such as atrazine, currently the most widely
used herbicide in the USA (cf. Sect. 16.7.2). When the
herbicide is added to a field and ends up in the soil, it induces
massive transfer to the soil microbiota of a plasmid carrying
genes atz and trz for atrazine degradation (Devers et al.
2005). atz and trz are often on plasmids, but also on the
chromosome near insertion sequences, suggesting that transposition plays an important role in the dispersion of this
metabolic competence (cf. Sect. 16.7.2).
Maintaining large plasmids is not neutral in terms of
fitness if they do not carry essential genes, which is reflected
in the existence of strains having lost their plasmids in the
soil, as is the case for many bacteria in particular
404
Y. Moe ¨nne-Loccoz et al.