9.7
Adaptation to Biotopes
9.7.1 Soil
Soil is the substrate (together with sediments) that supports
the greatest microbial diversity with 20,000 different microbial genome equivalents per gram (Torsvik et al. 2002).
This means that soil is a permissive biotope for a large
number of microbial taxa and that it contains a varied array
of trophic resources. It is however a selective biotope
because of hydric alternances and mainly because it is
heavily populated by diverse microflora with which must
deal any newcomer. In this biotope are particularly present
filamentous bacteria (Actinobacteria), gliding bacteria,
spore-forming bacteria (Firmicutes, Actinobacteria), and
bacteria producing antibiotics (Actinobacteria).
Soil is considered as a homogeneous habitat, but there are
hundreds of soils that vary for a number of parameters
including the concentration of organic matter, sand, acidity,
concentration of nutrients, trace elements, and pollutants.
However, most soils experience alternating daily or seasonal
water regime. These fluctuations mean that microorganisms
spend part of their lives with an abundance of water and
therefore hypoxia or at the other extreme with limiting water
and thus dehydration.
Hypoxia is a physicochemical condition to which
microorganisms adapt via the synthesis of electron transport
alternatives that use nitrate or sulfate as the final acceptor.
Such systems are widespread in soil microorganisms, such
as nitrite reductase (nirS) and nitrate reductase (NarGHIJ),
especially in rhizosphere microorganisms that have access
to a large amount of carbon substrates compared to the
electron acceptors available, oxygen, nitrate, and nitrite.
The heterogeneous structure of the soil with numerous
discontinuities also seems to have selected a particular
morphology, filamentous morphology, to move through the
soil to areas more favorable for growth. This filamentous
structure is of course also found in cyanobacteria in
the ocean or animal or plant pathogens, but it is particularly
prevalent among actinobacteria, oomycetes, and fungi
(basidiomycetes, ascomycetes). Hyphae allow not only to
grow faster (in terms of tip speed) but also to overcome the
discontinuities in the soil.
9.7.2 Water and Sediment
9.7.2.1 Adaptation to Aquatic Environment
The Prokaryotic Form
In water, prokaryotes must swim or float. Cocci are generally
not motile with rare exceptions; they are less numerous
than rods (straight, curved, or spiral) that are most numerous
in the aquatic environment. These may represent up to
80–90 % of the prokaryotic community of aquatic
environments. These forms are generally motile in the
presence of flagella or gas vacuoles (cf. Sect. 3.1); it is the
cell forms best adapted to aquatic life.
Movement
In prokaryotes that move through water, the movement is
due to the presence of flagella or vacuoles (vesicles) of gas.
• Prokaryotes motile with flagella
These are mostly rods, straight, curved, or spiral.
According to the positioning or flagella, these microorganisms are called monotrichous (single polar flagellum), lophotrichous (a tuft of polar flagella),
amphitrichous (two tufts of flagella, one at both ends),
or peritrichous (flagella distributed over the entire cell)
(cf. Sect. 3.1.1). Flagella grow at their tips: flagellin
molecules synthesized in the cytoplasm passing through
the hollow filament of the flagellum and assembled to
each other at the end of the flagellum, thereby forming a
“rigid” structure consisting of subunits of the same type.
In E. coli, flagella are two to three times as long as the
cell, approximately 5–7 μm. They are constantly built.
Flagella are activated by a basal body consisting of
various proteins inserted in the cell envelope and
extending through a rigid hook which constitutes the
base of the flagellum. The basal body is like a motor
that drives the hook and so all coiled flagellum. The
energy required comes from the proton motive force
(cf. Sect. 3.1.1; Figs. 3.6b and 3.4). The fastest movement
recorded is 200 rotations per second. Spirilla are among
the faster bacteria.
The energy required to activate the basal body of
the flagellum is about 1,200 protons per rotation of the
flagellum (Khan 1992). The rotary movement is known
only to the flagellum prokaryotes. Because of this, movement may be bidirectional. The change of direction is
instantaneous. Periods of activation of the flagellum
are generally one second, interspersed with stop periods
Box 9.2 (continued)
The analysis of the diversity of microorganisms
in hot deserts makes us think it represents the true
treasure of the desert: both for coping with water
stress it imposes of all life forms and also for new
molecules of medical interest, food and agriculture
still hidden in it.
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
339
Adaptation to Biotopes
9.7.1 Soil
Soil is the substrate (together with sediments) that supports
the greatest microbial diversity with 20,000 different microbial genome equivalents per gram (Torsvik et al. 2002).
This means that soil is a permissive biotope for a large
number of microbial taxa and that it contains a varied array
of trophic resources. It is however a selective biotope
because of hydric alternances and mainly because it is
heavily populated by diverse microflora with which must
deal any newcomer. In this biotope are particularly present
filamentous bacteria (Actinobacteria), gliding bacteria,
spore-forming bacteria (Firmicutes, Actinobacteria), and
bacteria producing antibiotics (Actinobacteria).
Soil is considered as a homogeneous habitat, but there are
hundreds of soils that vary for a number of parameters
including the concentration of organic matter, sand, acidity,
concentration of nutrients, trace elements, and pollutants.
However, most soils experience alternating daily or seasonal
water regime. These fluctuations mean that microorganisms
spend part of their lives with an abundance of water and
therefore hypoxia or at the other extreme with limiting water
and thus dehydration.
Hypoxia is a physicochemical condition to which
microorganisms adapt via the synthesis of electron transport
alternatives that use nitrate or sulfate as the final acceptor.
Such systems are widespread in soil microorganisms, such
as nitrite reductase (nirS) and nitrate reductase (NarGHIJ),
especially in rhizosphere microorganisms that have access
to a large amount of carbon substrates compared to the
electron acceptors available, oxygen, nitrate, and nitrite.
The heterogeneous structure of the soil with numerous
discontinuities also seems to have selected a particular
morphology, filamentous morphology, to move through the
soil to areas more favorable for growth. This filamentous
structure is of course also found in cyanobacteria in
the ocean or animal or plant pathogens, but it is particularly
prevalent among actinobacteria, oomycetes, and fungi
(basidiomycetes, ascomycetes). Hyphae allow not only to
grow faster (in terms of tip speed) but also to overcome the
discontinuities in the soil.
9.7.2 Water and Sediment
9.7.2.1 Adaptation to Aquatic Environment
The Prokaryotic Form
In water, prokaryotes must swim or float. Cocci are generally
not motile with rare exceptions; they are less numerous
than rods (straight, curved, or spiral) that are most numerous
in the aquatic environment. These may represent up to
80–90 % of the prokaryotic community of aquatic
environments. These forms are generally motile in the
presence of flagella or gas vacuoles (cf. Sect. 3.1); it is the
cell forms best adapted to aquatic life.
Movement
In prokaryotes that move through water, the movement is
due to the presence of flagella or vacuoles (vesicles) of gas.
• Prokaryotes motile with flagella
These are mostly rods, straight, curved, or spiral.
According to the positioning or flagella, these microorganisms are called monotrichous (single polar flagellum), lophotrichous (a tuft of polar flagella),
amphitrichous (two tufts of flagella, one at both ends),
or peritrichous (flagella distributed over the entire cell)
(cf. Sect. 3.1.1). Flagella grow at their tips: flagellin
molecules synthesized in the cytoplasm passing through
the hollow filament of the flagellum and assembled to
each other at the end of the flagellum, thereby forming a
“rigid” structure consisting of subunits of the same type.
In E. coli, flagella are two to three times as long as the
cell, approximately 5–7 μm. They are constantly built.
Flagella are activated by a basal body consisting of
various proteins inserted in the cell envelope and
extending through a rigid hook which constitutes the
base of the flagellum. The basal body is like a motor
that drives the hook and so all coiled flagellum. The
energy required comes from the proton motive force
(cf. Sect. 3.1.1; Figs. 3.6b and 3.4). The fastest movement
recorded is 200 rotations per second. Spirilla are among
the faster bacteria.
The energy required to activate the basal body of
the flagellum is about 1,200 protons per rotation of the
flagellum (Khan 1992). The rotary movement is known
only to the flagellum prokaryotes. Because of this, movement may be bidirectional. The change of direction is
instantaneous. Periods of activation of the flagellum
are generally one second, interspersed with stop periods
Box 9.2 (continued)
The analysis of the diversity of microorganisms
in hot deserts makes us think it represents the true
treasure of the desert: both for coping with water
stress it imposes of all life forms and also for new
molecules of medical interest, food and agriculture
still hidden in it.
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
339