Chironomidae, Ephemeroptera), and oligochaetes (e.g.,
Lawrence et al. 2002; Majdi et al. 2012b).
In sediments, the extraction techniques are focused on
some groups of microorganisms. However, to date, none of
these techniques allow to obtain all resuspended benthic
microorganisms neither to totally separate them from sediment and detrital particles. Thus, the efficiency of the extraction techniques are variable according to the studied groups,
and consequently, samples of benthic microorganisms collected using resuspension techniques are not totally representative of the diversity of benthic microbial communities.
Moreover, it can be noticed that classification of benthic
microorganisms according to their size is rarely used in
contrast to pelagic systems. Determination of benthic
microorganisms is based on morphology, cell functioning,
or phylogenetic studies using microscopic techniques, biochemistry, or DNA fingerprints.
13.2.2.1 Microalgae and Cyanobacteria
Among microorganisms, microalgae (eukaryotic cell) and
cyanobacteria (prokaryotic cell) are the primary producers.
Filamentous pluricellular forms of cyanobacteria and
diatoms are commonly present in benthic systems. Photoautotrophic microorganisms are able to perform oxygenic photosynthesis. They can be studied using either direct
microscopic observation since they have very characteristic
cell morphologies or indirect methods based on HPLC
analyses of signature photosynthetic pigments (e.g.,
Buffan-Dubau and Carman 2000). Dioxygen production
can be quantified using microsensors and CO 2 uptake using
14 C or
13 C isotopic tracers (cf. Chap. 17).
Among microalgae, diatoms and particularly pennate
diatoms with a raphe are common in superficial sediments
and biofilms. Pennate diatoms and most of filamentous
cyanobacteria are able to migrate by sliding through the
benthic community. These organisms produce important
amounts of extracellular polymeric substances (EPS).
These EPS may be present under different forms:
1. Characteristic sheath-like structures
2. Structured mucus masses enveloping the cells
3. Mucus masses spread in the environment
Except diatoms, other microalgal taxa belonging to the green
microalgal group are commonly observed in biofilms and in
superficial sediments.
13.2.2.2 Phototrophic Anoxygenic Bacteria
Anoxygenic photrophic bacteria represent another group of
phototrophic microorganisms in benthic systems. Because
these organisms have very characteristic pigments (bacteriochlorophylls and specific carotenoids), it is possible to reveal
their presence by HPLC pigment analyses when they are
abundant. Instead of water, these organisms use another
electron donor for their photosynthesis as H 2 S, S 2 O 3
2À , or
small organic molecules; they use CO 2 or dissolved small
organic molecules as the source of carbon. While these
organisms convert also light energy into biomass, they differ
from the classical oxygenic primary producers by the fact
that they use electron donors from biological origin which
have a higher energy content than the water used by oxygenic phototrophs. Therefore, these organisms have sometimes been described as para-primary producers. Hence, the
energy for the fixation of the CO 2 is partially delivered by
the electron donor and partially by the photons.
Many species of anoxygenic phototrophic bacteria have a
very characteristic morphology that can be recognized by
optical microscopy. Examples include the Chromatiaceae
(which store sulfur intracellularly) and the green filamentous
phototrophic bacteria. The latter may, however, be confounded with the very thin filamentous cyanobacteria (e.g.,
Leptolyngbya). In contrast, the morphology of other
anoxygenic phototrophic bacteria including the green sulfur
bacteria (Chlorobiaceae), Ectothiorhodospiraceae, and purple nonsulfur bacteria are easily confounded with the
chemoheterotrophic and chemolithoautotrophic bacteria.
13.2.2.3 Chemolithotrophic Bacteria
The chemolithoautotrophic bacteria comprise different functional groups that all fix CO 2 and are distinguished according
to different electron donors, i.e., H 2 , H 2 S and other reduced
inorganic sulfur compounds, NH 4
+
, and NO 2
À
. Only a very
small number of sulfur-oxidizing bacteria have a morphology that is easily recognizable under the light microscope (e.
g., the members of the Beggiatoa and Thioploca genus). This
functional group also comprises some giant bacteria, which
are visible to the naked eye as some members of Beggiatoa,
Thioploca, and Thiomargarita (Schulz and Jorgensen 2001;
cf. Chap. 5).
13.2.2.4 Heterotrophic Bacteria and Archaea
The chemoorganoheterotrophic prokaryotes (hereafter
referred to as heterotrophs) use organic compounds as the
electron donor and as the carbon source. They comprise a
large number of functional groups, which can be defined
according to the electron acceptor used for energy generation (O 2 , NO 3
À , organic compounds, metal oxides [Mn
4+ ,
Fe
3+ ], SO 4
2À
, and CO 2 ; cf. Chap. 3). In general, microscopic
observation does not allow determining to which functional
group they belong.
Within the sediment, the counting of prokaryotes may be
difficult and problematic because of the large quantities of
detritus. Nevertheless, their quantification has improved a lot
since the introduction of specific fluorochromes (DAPI) and
the use of epifluorescent microscopy (cf. Chap. 17). The
density of prokaryotes in the sediment varies in the surface
layers between 10
8 and 10
10 cells mL
À1 . Prokaryotes that
still occur in oceanic sediment columns below 500 m depth
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
491
Lawrence et al. 2002; Majdi et al. 2012b).
In sediments, the extraction techniques are focused on
some groups of microorganisms. However, to date, none of
these techniques allow to obtain all resuspended benthic
microorganisms neither to totally separate them from sediment and detrital particles. Thus, the efficiency of the extraction techniques are variable according to the studied groups,
and consequently, samples of benthic microorganisms collected using resuspension techniques are not totally representative of the diversity of benthic microbial communities.
Moreover, it can be noticed that classification of benthic
microorganisms according to their size is rarely used in
contrast to pelagic systems. Determination of benthic
microorganisms is based on morphology, cell functioning,
or phylogenetic studies using microscopic techniques, biochemistry, or DNA fingerprints.
13.2.2.1 Microalgae and Cyanobacteria
Among microorganisms, microalgae (eukaryotic cell) and
cyanobacteria (prokaryotic cell) are the primary producers.
Filamentous pluricellular forms of cyanobacteria and
diatoms are commonly present in benthic systems. Photoautotrophic microorganisms are able to perform oxygenic photosynthesis. They can be studied using either direct
microscopic observation since they have very characteristic
cell morphologies or indirect methods based on HPLC
analyses of signature photosynthetic pigments (e.g.,
Buffan-Dubau and Carman 2000). Dioxygen production
can be quantified using microsensors and CO 2 uptake using
14 C or
13 C isotopic tracers (cf. Chap. 17).
Among microalgae, diatoms and particularly pennate
diatoms with a raphe are common in superficial sediments
and biofilms. Pennate diatoms and most of filamentous
cyanobacteria are able to migrate by sliding through the
benthic community. These organisms produce important
amounts of extracellular polymeric substances (EPS).
These EPS may be present under different forms:
1. Characteristic sheath-like structures
2. Structured mucus masses enveloping the cells
3. Mucus masses spread in the environment
Except diatoms, other microalgal taxa belonging to the green
microalgal group are commonly observed in biofilms and in
superficial sediments.
13.2.2.2 Phototrophic Anoxygenic Bacteria
Anoxygenic photrophic bacteria represent another group of
phototrophic microorganisms in benthic systems. Because
these organisms have very characteristic pigments (bacteriochlorophylls and specific carotenoids), it is possible to reveal
their presence by HPLC pigment analyses when they are
abundant. Instead of water, these organisms use another
electron donor for their photosynthesis as H 2 S, S 2 O 3
2À , or
small organic molecules; they use CO 2 or dissolved small
organic molecules as the source of carbon. While these
organisms convert also light energy into biomass, they differ
from the classical oxygenic primary producers by the fact
that they use electron donors from biological origin which
have a higher energy content than the water used by oxygenic phototrophs. Therefore, these organisms have sometimes been described as para-primary producers. Hence, the
energy for the fixation of the CO 2 is partially delivered by
the electron donor and partially by the photons.
Many species of anoxygenic phototrophic bacteria have a
very characteristic morphology that can be recognized by
optical microscopy. Examples include the Chromatiaceae
(which store sulfur intracellularly) and the green filamentous
phototrophic bacteria. The latter may, however, be confounded with the very thin filamentous cyanobacteria (e.g.,
Leptolyngbya). In contrast, the morphology of other
anoxygenic phototrophic bacteria including the green sulfur
bacteria (Chlorobiaceae), Ectothiorhodospiraceae, and purple nonsulfur bacteria are easily confounded with the
chemoheterotrophic and chemolithoautotrophic bacteria.
13.2.2.3 Chemolithotrophic Bacteria
The chemolithoautotrophic bacteria comprise different functional groups that all fix CO 2 and are distinguished according
to different electron donors, i.e., H 2 , H 2 S and other reduced
inorganic sulfur compounds, NH 4
+
, and NO 2
À
. Only a very
small number of sulfur-oxidizing bacteria have a morphology that is easily recognizable under the light microscope (e.
g., the members of the Beggiatoa and Thioploca genus). This
functional group also comprises some giant bacteria, which
are visible to the naked eye as some members of Beggiatoa,
Thioploca, and Thiomargarita (Schulz and Jorgensen 2001;
cf. Chap. 5).
13.2.2.4 Heterotrophic Bacteria and Archaea
The chemoorganoheterotrophic prokaryotes (hereafter
referred to as heterotrophs) use organic compounds as the
electron donor and as the carbon source. They comprise a
large number of functional groups, which can be defined
according to the electron acceptor used for energy generation (O 2 , NO 3
À , organic compounds, metal oxides [Mn
4+ ,
Fe
3+ ], SO 4
2À
, and CO 2 ; cf. Chap. 3). In general, microscopic
observation does not allow determining to which functional
group they belong.
Within the sediment, the counting of prokaryotes may be
difficult and problematic because of the large quantities of
detritus. Nevertheless, their quantification has improved a lot
since the introduction of specific fluorochromes (DAPI) and
the use of epifluorescent microscopy (cf. Chap. 17). The
density of prokaryotes in the sediment varies in the surface
layers between 10
8 and 10
10 cells mL
À1 . Prokaryotes that
still occur in oceanic sediment columns below 500 m depth
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
491