2009). Bacteria have developed resistance to many toxic
metals. Resistant bacteria were detected and isolated mainly
in natural metallic sites, for example, copper in the mining area
of Katanga in Congo (Monchy et al. 2006) and arsenic in India
or Portugal (Muller et al. 2006). Among the mechanisms of
resistance described, a few should be mentioned: specific
metal carrier or broad spectrum, oxidases or reductases that
transform metal into a volatile compound as in the case of
mercury (Barkay and Wagner-Dobler 2005) or in a less toxic
compounds as in the case of arsenic (Cervantes et al. 1994), or
even the formation of structures able to immobilize toxic
compound such as in the case of the uranium fixed by extracellular melanin (Turick et al. 2008).
The official dumps or wild bioreactors are very efficient for
the selection of new strains able to degrade xenobiotic
compounds, which were still unknown 60 years ago. Thus,
lindane (cyclohexane hexachloride) is an insecticide widely
used around the world for agriculture, forestry, or even in
shampoo for the elimination of lice. Bacteria belonging to the
genera Pseudomonas or Sphingomonas (Suar et al. 2004;
Manickam et al. 2008) have been described as capable of
degrading this new compound. The mechanism by which this
biodegradation pathway seems to have been obtained is the
result of the mixing of gene domains, yielding new enzymes
with novel functionalities. Several genes are grouped and carried by plasmids, which leads to their dispersion by conjugation
into vulnerable ecosystems (cf. Sect. 11.2.2). The addition of
synthetic pesticides to the environment is thus a powerful catalyst for the selection of recombinant bacteria (Davison 1999).
Anthropisation also affects habitats beyond the introduction of new chemical compounds. The intensive use of
fertilizers, as well as urbanization with little or untreated
wastes discharged, results in the addition of considerable
amounts of nitrogen and phosphorus to rivers and the
ocean. These additions cause eutrophication with algal
blooms, some of which are toxic to humans.
A current problem concerns radioactive waste. Since the
discovery of radioactivity by Marie Curie in 1898, many
applications have been developed as weapons (bomb uranium
or plutonium, H-bomb, depleted uranium munitions), power
plants, accelerators, and medical care that all create wastes.
These wastes are dumped in soils, sediments, and water courses
where they create difficult conditions for microorganisms due
to their chemical toxicity described above or due to the fact that
they emit radiation and cause damage mainly to nucleic acids.
The influence of radiation on microbial ecosystems has been
well explored, in particular to identify taxa that are most
resistant to gamma irradiation. Soils exposed to high doses of
gamma radiation permit to select bacteria belonging mainly to
the well-known genus Deinococcus, but also Geodermatophilus, etc. (Rainey et al. 2005). Deinococcus seems to
have been selected in environments exposed to drought causing
a strong oxidative stress at the origin of damages to DNA
(Fredrickson et al. 2008). Gamma radiation causes direct damage to DNA by breaking the phosphodiester bridge, while UV
damages DNA by fusion of neighboring thymidine bases, thus
blocking replication fork of DNA and indirectly generating
reactive species of oxygen which also attack the DNA. Different mechanisms of DNA repair have been described (Cox
1998) in bacteria and in archaea (Grogan 2004). Deinococcus
combines the traditional mechanisms and the existence of
multiple copies of the chromosome per cell, copies that complement each other in order to recreate an intact chromosome.
The mode of resistance of other taxa remains unknown for now
(Minton 1994).
9.9
Conclusion
Adaptation of microorganisms to different biotopes constitutes
one of the most fascinating research domains of modern microbiology. Extreme environments have of course provided numerous examples of unusual metabolisms (cf. Chap. 10), and many
more discoveries from genomes studies are expected.
Microorganisms from complex biotopes such as soil, sediments,
or the digestive tract should also yield their share of new
metabolites and new regulation modes. All these approaches
should also provide us with an overview of the adaptability of the
microbial world, yielding new metabolites and new ways to fight
pathogens.
References
Abu-Qarn M, Eichler J, Sharon N (2008) Not just for Eukarya anymore:
protein glycosylation in Bacteria and Archaea. Curr Opin Struct
Biol 18:544–550
Altuvia S (2007) Identification of bacterial small non-coding RNAs:
experimental approaches. Curr Opin Microbiol 10:257–261
Amikam D, Galperin MY (2006) PilZ domain is part of the bacterial cdi-GMP binding protein. Bioinformatics 22:3–6
Anderson JAH, Hooper MJ, Zak JC, Cox SB (2009) Molecular and
functional assessment of bacterial community convergence in
metal-amended soils. Microb Ecol 58:10–22
Andrews SC, Robinson AK, Rodriguez-Quinones F (2003) Bacterial
iron homeostasis. FEMS Microbiol Rev 27:215–237
Bainton NJ, Stead P, Chhabra SR, Bycroft BW, Salmond GP, Stewart
GS, Williams P (1992) N-(3-oxohexanoyl)-L-homoserine lactone
regulates carbapenem antibiotic production in Erwinia carotovora.
Biochem J 288:997–1004
Barkay T, Wagner-Dobler I (2005) Microbial transformations of mercury: potentials, challenges, and achievements in controlling mercury toxicity in the environment. Adv Appl Microbiol 57:1–52
Barrat JA, Gillet P, Lecuyer C, Sheppard HM, Lesourd M (1998)
Formation of carbonates in the meteorite Tatahouine. Science
280:412–414
Bentley SD et al (2002) Complete genome sequence of the model
actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147
Benzerara K, Menguy N, Guyot F, Dominici C, Gillet P (2003)
Nanobacteria-like calcite single crystals at the surfaces of the meteorite Tataouine. Proc Natl Acad Sci U S A 100:7438–7442
346
P. Normand et al.
metals. Resistant bacteria were detected and isolated mainly
in natural metallic sites, for example, copper in the mining area
of Katanga in Congo (Monchy et al. 2006) and arsenic in India
or Portugal (Muller et al. 2006). Among the mechanisms of
resistance described, a few should be mentioned: specific
metal carrier or broad spectrum, oxidases or reductases that
transform metal into a volatile compound as in the case of
mercury (Barkay and Wagner-Dobler 2005) or in a less toxic
compounds as in the case of arsenic (Cervantes et al. 1994), or
even the formation of structures able to immobilize toxic
compound such as in the case of the uranium fixed by extracellular melanin (Turick et al. 2008).
The official dumps or wild bioreactors are very efficient for
the selection of new strains able to degrade xenobiotic
compounds, which were still unknown 60 years ago. Thus,
lindane (cyclohexane hexachloride) is an insecticide widely
used around the world for agriculture, forestry, or even in
shampoo for the elimination of lice. Bacteria belonging to the
genera Pseudomonas or Sphingomonas (Suar et al. 2004;
Manickam et al. 2008) have been described as capable of
degrading this new compound. The mechanism by which this
biodegradation pathway seems to have been obtained is the
result of the mixing of gene domains, yielding new enzymes
with novel functionalities. Several genes are grouped and carried by plasmids, which leads to their dispersion by conjugation
into vulnerable ecosystems (cf. Sect. 11.2.2). The addition of
synthetic pesticides to the environment is thus a powerful catalyst for the selection of recombinant bacteria (Davison 1999).
Anthropisation also affects habitats beyond the introduction of new chemical compounds. The intensive use of
fertilizers, as well as urbanization with little or untreated
wastes discharged, results in the addition of considerable
amounts of nitrogen and phosphorus to rivers and the
ocean. These additions cause eutrophication with algal
blooms, some of which are toxic to humans.
A current problem concerns radioactive waste. Since the
discovery of radioactivity by Marie Curie in 1898, many
applications have been developed as weapons (bomb uranium
or plutonium, H-bomb, depleted uranium munitions), power
plants, accelerators, and medical care that all create wastes.
These wastes are dumped in soils, sediments, and water courses
where they create difficult conditions for microorganisms due
to their chemical toxicity described above or due to the fact that
they emit radiation and cause damage mainly to nucleic acids.
The influence of radiation on microbial ecosystems has been
well explored, in particular to identify taxa that are most
resistant to gamma irradiation. Soils exposed to high doses of
gamma radiation permit to select bacteria belonging mainly to
the well-known genus Deinococcus, but also Geodermatophilus, etc. (Rainey et al. 2005). Deinococcus seems to
have been selected in environments exposed to drought causing
a strong oxidative stress at the origin of damages to DNA
(Fredrickson et al. 2008). Gamma radiation causes direct damage to DNA by breaking the phosphodiester bridge, while UV
damages DNA by fusion of neighboring thymidine bases, thus
blocking replication fork of DNA and indirectly generating
reactive species of oxygen which also attack the DNA. Different mechanisms of DNA repair have been described (Cox
1998) in bacteria and in archaea (Grogan 2004). Deinococcus
combines the traditional mechanisms and the existence of
multiple copies of the chromosome per cell, copies that complement each other in order to recreate an intact chromosome.
The mode of resistance of other taxa remains unknown for now
(Minton 1994).
9.9
Conclusion
Adaptation of microorganisms to different biotopes constitutes
one of the most fascinating research domains of modern microbiology. Extreme environments have of course provided numerous examples of unusual metabolisms (cf. Chap. 10), and many
more discoveries from genomes studies are expected.
Microorganisms from complex biotopes such as soil, sediments,
or the digestive tract should also yield their share of new
metabolites and new regulation modes. All these approaches
should also provide us with an overview of the adaptability of the
microbial world, yielding new metabolites and new ways to fight
pathogens.
References
Abu-Qarn M, Eichler J, Sharon N (2008) Not just for Eukarya anymore:
protein glycosylation in Bacteria and Archaea. Curr Opin Struct
Biol 18:544–550
Altuvia S (2007) Identification of bacterial small non-coding RNAs:
experimental approaches. Curr Opin Microbiol 10:257–261
Amikam D, Galperin MY (2006) PilZ domain is part of the bacterial cdi-GMP binding protein. Bioinformatics 22:3–6
Anderson JAH, Hooper MJ, Zak JC, Cox SB (2009) Molecular and
functional assessment of bacterial community convergence in
metal-amended soils. Microb Ecol 58:10–22
Andrews SC, Robinson AK, Rodriguez-Quinones F (2003) Bacterial
iron homeostasis. FEMS Microbiol Rev 27:215–237
Bainton NJ, Stead P, Chhabra SR, Bycroft BW, Salmond GP, Stewart
GS, Williams P (1992) N-(3-oxohexanoyl)-L-homoserine lactone
regulates carbapenem antibiotic production in Erwinia carotovora.
Biochem J 288:997–1004
Barkay T, Wagner-Dobler I (2005) Microbial transformations of mercury: potentials, challenges, and achievements in controlling mercury toxicity in the environment. Adv Appl Microbiol 57:1–52
Barrat JA, Gillet P, Lecuyer C, Sheppard HM, Lesourd M (1998)
Formation of carbonates in the meteorite Tatahouine. Science
280:412–414
Bentley SD et al (2002) Complete genome sequence of the model
actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147
Benzerara K, Menguy N, Guyot F, Dominici C, Gillet P (2003)
Nanobacteria-like calcite single crystals at the surfaces of the meteorite Tataouine. Proc Natl Acad Sci U S A 100:7438–7442
346
P. Normand et al.