is a few mm or cm, and others that grow on the coral reefs in
tropical lagoons and called “Koparas” in local language can
reach thicknesses of several tens of cm up to 40 cm thicker.
In these microbial mats, cyanobacteria form the basic structure
of the belt in producing the EPS matrix. They are only active in
the surface of the mat where they receive enough light to grow
and produce oxygen through their oxygenic photosynthesis
(cf. Sect. 3.3.4). At a few mm below the anoxic obscure
zone, the structure of the mat is due to dead cyanobacterial
filaments stuck in the mucoid matrix. Indeed, these microbial
mats have developed over the years and even centuries with
the accretion of a new layer of cyanobacteria in surface every
year. In coastal marine microbial mats, gradients of oxygen,
sulfide, and light determine the distribution of strata with
metabolically different bacterial groups (Fig. 9.31; cf. Sect.
14.4.4 and Fig. 14.44). At the surface of the mat, the metabolically active cyanobacteria produce excess oxygen forming a
gradient with reduced oxygen in deeper layers, generally a few
mm below. In deeper anoxic layers, the concentration of
organic material from dead cyanobacteria promotes the development of fermentative and sulfate-reducing bacteria that are
stimulated by high concentrations of seawater sulfate. In the
intermediate zone, the chemolithotrophic aerobic sulfuroxidizing bacteria (Beggiatoa, Thiobacilli, etc.) develop at
the interface between the upper part containing oxygen and
the deeper part with sulfide. If the light reaching the anoxic
zone is sufficient in quantity and quality, the sulfur-oxidizing
purple bacteria can grow and form a purple layer (Figs. 9.31
and 14.44). Thus, these mats are vertical models of cooperation based on trade between bacteria of the biogeochemical
sulfur cycle (cf. Sect. 14.4.4).
Microbial mats and biofilms are well-structured systems
where different prokaryotic and eukaryotic microorganisms
coexist on the basis of trophic interactions. Man has exploited
these capabilities in purification processes such as the formation of biofilms in trickling filters or biodiscs used for the
biological purification of wastewater treatment plants. The
ability of biofilms and microbial mats to trap specific
molecules including organic pollutants and heavy metals can
also be exploited to improve water decontamination processes.
9.7.4 Air
Air contains many microorganisms from soil, water,
animals, or plants in response to gusts, especially in situations
of partial canopy as in the steppes and deserts. Microorganisms
which are carried by the wind and suspended in the air can
travel great distances, thousands of kilometers away from
some dust sources (Sahara Desert, Gobi Desert) to sites
where precipitations will bring them to the ground (Central
Europe, the Pacific Islands). These microorganisms are more
easily carried away as they are smaller, the diameter of a
bacterial cell varying by several orders of magnitude. The
smaller cells are the spores that are favored here and will
therefore be carried farther. A second factor that will affect
the ability for traveling of microorganisms is their resistance to
ionizing radiation to which they are subjected in the atmosphere. Again microorganisms capable of synthesizing spores
can survive the journey as well as Deinococcus and
Geodermatophilus found in soils after gamma irradiation
(Rainey et al. 2005). In addition, microorganisms must withstand solar radiation including UV which causes cellular damage by photooxidation. Microorganisms that produce
carotenoid pigments can withstand the effects of photooxidation due to radiation by diverting a portion of the solar energy
and acting as photocatalysts, thus protecting the cell. In fact, in
prokaryotic communities suspended in the air, the percentage
of pigmented cells (carotenoids) is generally very high.
Finally, the microorganisms must complete the trip and so
get down to the earth. This will happen when they join the
regions where the temperature and the concentration of water
vapor will condense them into droplets or snowflakes. Moreover, some microorganisms (Pseudomonas) contain proteins
that facilitate this condensation and therefore the process
whereby they can be brought to the ground (Morris et al.
2008). Sampling microorganisms in precipitation, glaciers,
or in the air has begun to be published (Xiang et al. 2005).
9.8
Adaptation to Manmade Environments
(cf. Chap. 16)
Man has profoundly changed the different biotopes in the world
especially since the beginning of the industrial age. This effect
called “human impact” was made in different ways, for example, the synthesis of new molecules called “xenobiotics” in
agriculture (herbicides, fungicides, etc.) or industry (PCBs,
PAHs), or by intensive use of natural molecules like metals in
agriculture (copper) or in industry (mercury, nickel), or organic
compounds such as aromatics. All these compounds are found
in soils, sediments, or water bodies, where they alter microbial
activities and end up in the food chain, causing many problems
that are beyond the scope of this text. The use of reactive
molecules such as copper in agriculture dates back more than
a century, especially in the Bordeaux mixture (copper sulfate
neutralized with lime) against various fungal pathogens of
grapevine as downy mildew. As this compound is allowed at
levels of up to 6 kg Cu/ha/year by “organic” agriculture charters,
it should continue to be used in large quantities in the coming
years despite the toxicity observed for microorganisms, for
ground animals (snails), and even for grapes and yeasts that
are responsible for the aroma of wine. This metal is therefore
found in the soil where it accumulates over the years; it changes
the composition of microbial communities and has a cumulative effect on their activity (Ranjard et al. 2006; Anderson et al.
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
345
tropical lagoons and called “Koparas” in local language can
reach thicknesses of several tens of cm up to 40 cm thicker.
In these microbial mats, cyanobacteria form the basic structure
of the belt in producing the EPS matrix. They are only active in
the surface of the mat where they receive enough light to grow
and produce oxygen through their oxygenic photosynthesis
(cf. Sect. 3.3.4). At a few mm below the anoxic obscure
zone, the structure of the mat is due to dead cyanobacterial
filaments stuck in the mucoid matrix. Indeed, these microbial
mats have developed over the years and even centuries with
the accretion of a new layer of cyanobacteria in surface every
year. In coastal marine microbial mats, gradients of oxygen,
sulfide, and light determine the distribution of strata with
metabolically different bacterial groups (Fig. 9.31; cf. Sect.
14.4.4 and Fig. 14.44). At the surface of the mat, the metabolically active cyanobacteria produce excess oxygen forming a
gradient with reduced oxygen in deeper layers, generally a few
mm below. In deeper anoxic layers, the concentration of
organic material from dead cyanobacteria promotes the development of fermentative and sulfate-reducing bacteria that are
stimulated by high concentrations of seawater sulfate. In the
intermediate zone, the chemolithotrophic aerobic sulfuroxidizing bacteria (Beggiatoa, Thiobacilli, etc.) develop at
the interface between the upper part containing oxygen and
the deeper part with sulfide. If the light reaching the anoxic
zone is sufficient in quantity and quality, the sulfur-oxidizing
purple bacteria can grow and form a purple layer (Figs. 9.31
and 14.44). Thus, these mats are vertical models of cooperation based on trade between bacteria of the biogeochemical
sulfur cycle (cf. Sect. 14.4.4).
Microbial mats and biofilms are well-structured systems
where different prokaryotic and eukaryotic microorganisms
coexist on the basis of trophic interactions. Man has exploited
these capabilities in purification processes such as the formation of biofilms in trickling filters or biodiscs used for the
biological purification of wastewater treatment plants. The
ability of biofilms and microbial mats to trap specific
molecules including organic pollutants and heavy metals can
also be exploited to improve water decontamination processes.
9.7.4 Air
Air contains many microorganisms from soil, water,
animals, or plants in response to gusts, especially in situations
of partial canopy as in the steppes and deserts. Microorganisms
which are carried by the wind and suspended in the air can
travel great distances, thousands of kilometers away from
some dust sources (Sahara Desert, Gobi Desert) to sites
where precipitations will bring them to the ground (Central
Europe, the Pacific Islands). These microorganisms are more
easily carried away as they are smaller, the diameter of a
bacterial cell varying by several orders of magnitude. The
smaller cells are the spores that are favored here and will
therefore be carried farther. A second factor that will affect
the ability for traveling of microorganisms is their resistance to
ionizing radiation to which they are subjected in the atmosphere. Again microorganisms capable of synthesizing spores
can survive the journey as well as Deinococcus and
Geodermatophilus found in soils after gamma irradiation
(Rainey et al. 2005). In addition, microorganisms must withstand solar radiation including UV which causes cellular damage by photooxidation. Microorganisms that produce
carotenoid pigments can withstand the effects of photooxidation due to radiation by diverting a portion of the solar energy
and acting as photocatalysts, thus protecting the cell. In fact, in
prokaryotic communities suspended in the air, the percentage
of pigmented cells (carotenoids) is generally very high.
Finally, the microorganisms must complete the trip and so
get down to the earth. This will happen when they join the
regions where the temperature and the concentration of water
vapor will condense them into droplets or snowflakes. Moreover, some microorganisms (Pseudomonas) contain proteins
that facilitate this condensation and therefore the process
whereby they can be brought to the ground (Morris et al.
2008). Sampling microorganisms in precipitation, glaciers,
or in the air has begun to be published (Xiang et al. 2005).
9.8
Adaptation to Manmade Environments
(cf. Chap. 16)
Man has profoundly changed the different biotopes in the world
especially since the beginning of the industrial age. This effect
called “human impact” was made in different ways, for example, the synthesis of new molecules called “xenobiotics” in
agriculture (herbicides, fungicides, etc.) or industry (PCBs,
PAHs), or by intensive use of natural molecules like metals in
agriculture (copper) or in industry (mercury, nickel), or organic
compounds such as aromatics. All these compounds are found
in soils, sediments, or water bodies, where they alter microbial
activities and end up in the food chain, causing many problems
that are beyond the scope of this text. The use of reactive
molecules such as copper in agriculture dates back more than
a century, especially in the Bordeaux mixture (copper sulfate
neutralized with lime) against various fungal pathogens of
grapevine as downy mildew. As this compound is allowed at
levels of up to 6 kg Cu/ha/year by “organic” agriculture charters,
it should continue to be used in large quantities in the coming
years despite the toxicity observed for microorganisms, for
ground animals (snails), and even for grapes and yeasts that
are responsible for the aroma of wine. This metal is therefore
found in the soil where it accumulates over the years; it changes
the composition of microbial communities and has a cumulative effect on their activity (Ranjard et al. 2006; Anderson et al.
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
345