environments, the proportion of these three phases can rapidly change as a function of the climatic conditions. This
implies that the organisms in the soil need a large degree of
adaptability and adapt quickly. As an example that will be
treated in more detail later, protozoa in soils need a water
film particularly to exert their predatory activity. These
protozoa become inactive and form cysts when the water
content drops below a certain level (Bardgett 2005a).
Finally, as in many other ecosystems, the large majority of
the microorganisms in the soil cannot be cultured using the
currently available techniques. Admittedly, the recent development of molecular techniques (which are independent of
culturing) allows exploring the reel diversity of the
microorganisms in the environment (Bardgett 2005b; cf.
Sect. 17.6). Nonetheless, the efficient extraction of DNA
from soils remains an important methodological problem
to overcome.
13.2 Biological Components in the
Microbial Food Webs
13.2.1 Microorganisms in Pelagic Ocean
and Lake Ecosystems
Progress in techniques for identifying, counting, and measuring metabolic activity, in particular using epifluorescence
microscopy and molecular biology, has allowed a glimpse of
the extraordinary diversity of microorganisms, the extent of
their living conditions, and their abundances hitherto largely
underestimated, especially in aquatic environments. In addition, the sensible improvement of various chromatographic
methods allowed to describe the biochemical composition of
communities and address the qualitatively transfer of matter
in the food webs.
In pelagic marine and lake ecosystems, planktonic lifestyle (floating) is best adapted. Prokaryotic or eukaryotic
planktonic microorganisms may be heterotrophs,
mixotrophs*, or autotrophs. These microorganisms provide
almost all of the biomass production and ensure a large part
of the pelagic ecosystem functions. More generally, pelagic
marine and lake ecosystems are the only ecosystems that the
biomass is mainly microbial.
Differentiation by size classes of microorganisms, as
mentioned in the introduction, is a practical way to study
and is also linked to the functional role of these
microorganisms in pelagic environments. The major
components in the pelagic microbial food webs (Table 13.1)
are presented according to the classification of Sieburth et al.
(1978): femtoplankton (0.02–0.2 μm), picoplankton
(0.2–2 μm), nanoplankton (2–20 μm), microplankton
(20–200 μm), and mesoplankton (0.2–20 mm). The main
methods of counting and estimating biomass of
pelagic microorganisms are flow cytometry and
epifluorescence microscopy for pico- and nanoplankton
and for microplankton is reversed optical microscopy. The
high-performance liquid chromatography (HPLC) is also
used to estimate phytoplankton biomass from the quantification of pigments.
13.2.1.1 Femtoplankton
In addition to very small archaea and bacteria, the
femtoplankton is mainly composed of virioplankton or
virus-like particles (VLP) which are ubiquitous and the
most abundant biological entities in aquatic environments
with concentrations ranging from 10
4 to 10
8 mL
À1 (SimeNgando 1997; Sime-Ngando et al. 2003; cf. Sect. 13.4.1).
13.2.1.2 Picoplankton
Picoplankton is composed of prokaryotic and eukaryotic
organisms: archaea, heterotrophic bacteria, picophytoplankton (cyanobacteria and eukaryotic autotrophs), and
heterotrophic picoflagellates. More specifically, the
bacterioplankton is represented by two main domains:
Archaea and Bacteria. Archaea are not confined
environments called “extreme” and can represent up to
30 % of prokaryotes counted in oxygenated euphotic zones
of lake (Jardillier et al. 2005) and marine ecosystems
(Delong 1992).
The abundance of heterotrophic bacteria in pelagic
marine and lake ecosystems varies from 10
5 to 10
7 mL
À1
in very oligotrophic (poor in nutrients) and more eutrophic
(rich in nutrients) ecosystems, respectively. Generally, a
weak seasonal variability of the heterotrophic bacteria abundance is observed with, however, a significantly higher biomass during spring development of phytoplankton. The
abundance of cyanobacteria in coastal marine environments
is highly variable but is generally about 10
4 mL
À1
(7–13 Â 10
4 mL
À1 in Northwestern Mediterranean Sea
and can reach 17 Â 10
4 mL
À1 in Mediterranean lagoons).
The abundance of eukaryotic picoplankton as Ostreococcus
tauri is approximately 10
3 mL
À1 , particularly in coastal
marine environments (lagoon).
In lake environments, the abundance of autotrophic
picoplankton (picocyanobacteria and eukaryotic autotrophic
picoplankton) fluctuates between 10
3 and 10
6 ml
À1 in oligotrophic and eutrophic lakes, respectively. However, autotrophic picoplankton is a major part (20–50 %) of picoplankton
biomass due to a mean cell biovolume higher than heterotrophic bacteria.
The density of autotrophic eukaryotic picoplankton is
generally highest during spring because of their welladapted pigments to low irradiance of this period, while
picocyanobacteria develop preferentially in summer when
temperature rises.
488
B. Mostajir et al.
implies that the organisms in the soil need a large degree of
adaptability and adapt quickly. As an example that will be
treated in more detail later, protozoa in soils need a water
film particularly to exert their predatory activity. These
protozoa become inactive and form cysts when the water
content drops below a certain level (Bardgett 2005a).
Finally, as in many other ecosystems, the large majority of
the microorganisms in the soil cannot be cultured using the
currently available techniques. Admittedly, the recent development of molecular techniques (which are independent of
culturing) allows exploring the reel diversity of the
microorganisms in the environment (Bardgett 2005b; cf.
Sect. 17.6). Nonetheless, the efficient extraction of DNA
from soils remains an important methodological problem
to overcome.
13.2 Biological Components in the
Microbial Food Webs
13.2.1 Microorganisms in Pelagic Ocean
and Lake Ecosystems
Progress in techniques for identifying, counting, and measuring metabolic activity, in particular using epifluorescence
microscopy and molecular biology, has allowed a glimpse of
the extraordinary diversity of microorganisms, the extent of
their living conditions, and their abundances hitherto largely
underestimated, especially in aquatic environments. In addition, the sensible improvement of various chromatographic
methods allowed to describe the biochemical composition of
communities and address the qualitatively transfer of matter
in the food webs.
In pelagic marine and lake ecosystems, planktonic lifestyle (floating) is best adapted. Prokaryotic or eukaryotic
planktonic microorganisms may be heterotrophs,
mixotrophs*, or autotrophs. These microorganisms provide
almost all of the biomass production and ensure a large part
of the pelagic ecosystem functions. More generally, pelagic
marine and lake ecosystems are the only ecosystems that the
biomass is mainly microbial.
Differentiation by size classes of microorganisms, as
mentioned in the introduction, is a practical way to study
and is also linked to the functional role of these
microorganisms in pelagic environments. The major
components in the pelagic microbial food webs (Table 13.1)
are presented according to the classification of Sieburth et al.
(1978): femtoplankton (0.02–0.2 μm), picoplankton
(0.2–2 μm), nanoplankton (2–20 μm), microplankton
(20–200 μm), and mesoplankton (0.2–20 mm). The main
methods of counting and estimating biomass of
pelagic microorganisms are flow cytometry and
epifluorescence microscopy for pico- and nanoplankton
and for microplankton is reversed optical microscopy. The
high-performance liquid chromatography (HPLC) is also
used to estimate phytoplankton biomass from the quantification of pigments.
13.2.1.1 Femtoplankton
In addition to very small archaea and bacteria, the
femtoplankton is mainly composed of virioplankton or
virus-like particles (VLP) which are ubiquitous and the
most abundant biological entities in aquatic environments
with concentrations ranging from 10
4 to 10
8 mL
À1 (SimeNgando 1997; Sime-Ngando et al. 2003; cf. Sect. 13.4.1).
13.2.1.2 Picoplankton
Picoplankton is composed of prokaryotic and eukaryotic
organisms: archaea, heterotrophic bacteria, picophytoplankton (cyanobacteria and eukaryotic autotrophs), and
heterotrophic picoflagellates. More specifically, the
bacterioplankton is represented by two main domains:
Archaea and Bacteria. Archaea are not confined
environments called “extreme” and can represent up to
30 % of prokaryotes counted in oxygenated euphotic zones
of lake (Jardillier et al. 2005) and marine ecosystems
(Delong 1992).
The abundance of heterotrophic bacteria in pelagic
marine and lake ecosystems varies from 10
5 to 10
7 mL
À1
in very oligotrophic (poor in nutrients) and more eutrophic
(rich in nutrients) ecosystems, respectively. Generally, a
weak seasonal variability of the heterotrophic bacteria abundance is observed with, however, a significantly higher biomass during spring development of phytoplankton. The
abundance of cyanobacteria in coastal marine environments
is highly variable but is generally about 10
4 mL
À1
(7–13 Â 10
4 mL
À1 in Northwestern Mediterranean Sea
and can reach 17 Â 10
4 mL
À1 in Mediterranean lagoons).
The abundance of eukaryotic picoplankton as Ostreococcus
tauri is approximately 10
3 mL
À1 , particularly in coastal
marine environments (lagoon).
In lake environments, the abundance of autotrophic
picoplankton (picocyanobacteria and eukaryotic autotrophic
picoplankton) fluctuates between 10
3 and 10
6 ml
À1 in oligotrophic and eutrophic lakes, respectively. However, autotrophic picoplankton is a major part (20–50 %) of picoplankton
biomass due to a mean cell biovolume higher than heterotrophic bacteria.
The density of autotrophic eukaryotic picoplankton is
generally highest during spring because of their welladapted pigments to low irradiance of this period, while
picocyanobacteria develop preferentially in summer when
temperature rises.
488
B. Mostajir et al.