sensitivity to methods of sampling and fixing commonly
used. With the improvement of these methods, over 7,000
species of ciliates, free or parasites, have been described in
aquatic ecosystems. This is a group characterized by the
presence of a ciliate cortex in the form of simple cilia, or
ciliated structures which are much more complex. Most
ciliates also have a nuclear dimorphism because they have
a macronucleus and usually several micronuclei.
Some groups of ciliates, such as Oligotrichia,
Scuticociliates, and Haptoria, are particularly well
represented in the lakes. Their size ranges from 5–10 to
over 200 μm. Their nutritional mode is very diverse being
mixotroph, bacterivore, algaevore, detritivore, or even omnivore. Their abundance in marine and lake ecosystems is an
average of 1 cell mL
À1 . Temperature, available light, and
nutrient resources induce a heterogeneous vertical distribution of ciliates through the water column. Their abundance
also varies according to nutrient concentrations.
13.2.1.4 Micro- and Mesoplankton
The microphytoplankton contributes significantly to primary
production in pelagic environments. Generally, the biomass
is estimated by inverted microscopy cell counts or by measuring chlorophyll (Chl) or other pigment biomarkers by
HPLC (cf. Chap. 17). It is very difficult to determine an
average value for the phytoplankton biomass in the marine
environment, while Chl a concentrations fluctuated between
0.1 and 70 μg Chl a mL
À1 in coastal lagoons. The phytoplankton biomass in the lake environments ranges from
<1 to > 25 mg m
À3 according to nutrient concentrations.
13.2.1.5 Microscopic Fungi
Recent environmental 18S-rDNA surveys of microbial
eukaryotes have unveiled major infecting agents in pelagic
systems, consisting primarily of the fungal order of
Chytridiales (chytrids) (Lefe `vre et al. 2007). Chytrids are
considered the earlier branch of the Eumycetes and produce
motile, flagellated zoospores, characterized by a small size
(2–6 μm) and a single, posterior flagellum. The existence of
these dispersal propagules includes chytrids within the socalled group of zoosporic fungi, which are particularly
adapted to the plankton lifestyle where they infect a wide
variety of hosts, including fishes, eggs, zooplankton, algae,
and other aquatic fungi but primarily freshwater phytoplankton (Sime-Ngando 2012). In Lake Pavin (France), chytrid
zoospores can contribute up to 40 % of the total diversity and
60 % of the total abundance of small-sized heterotrophic
flagellates in the plankton. These flagellates are exclusively
considered as grazers of prokaryotes. Ecological
implications are huge because parasitic chytrids can also
kill their hosts, but release substrates for microbial processes, and provide nutrient-rich particles as zoospores
(Kagami et al. 2007) and short fragments (from the fragmentation of filamentous inedible hosts) for the grazer food
chain. Furthermore, based on the observation that phytoplankton chytridiomycosis preferentially impacts the larger
size species, blooms of such species (e.g., filamentous
cyanobacteria) may not totally represent trophic bottlenecks.
In the case of chytrid epidemics, this can also represent an
important driving factor in phytoplankton seasonal
successions and maturation, in addition to the sole seasonal
forcing (Sime-Ngando 2012).
It is thus becoming evident that non-bacterivorous heterotrophic microbial eukaryotes such as chytrids, but also
the members of the genus Perkinsus or alveolates, which are
parasites or saprotrophs, represent an important but as yet
overlooked ecological driving force in aquatic food web
dynamics. In addition to being able to resist adverse
conditions and use different sources of carbon and nutrients,
these parasites can indeed affect the plankton food web
functions and ecosystem properties and topology, such as
stability and trophic transfer efficiency (Grami et al. 2011).
We are perhaps approaching a new paradigm-shift point in
the development of aquatic microbial ecology (SimeNgando and Niquil 2011).
13.2.2 Microorganisms of Benthic Ocean
and Lake Ecosystems
Benthic consumers of microorganisms are unicellular and
metazoan organisms. Unicellular consumers, such as heterotrophic ciliates, are important potential consumers of benthic
microalgae and bacteria. Their density can reach up to 5,000
and 11,000 ind.cm
3 in marine and freshwater sediments,
respectively. Other groups such as amoebozoan and benthic
foraminifera are also present. Microbial biofilms constitute
one of their typical microhabitats (Giere 2009).
Most of metazoan consumers of microorganisms belong
to meiofauna (benthic invertebrates which pass through a
1 mm mesh and are retained on a 40 μm mesh sieve). They
are abundant and diversified in superficial sediments (on
average 10
6 ind.m
2 ). The patchy spatial distribution of
meiofauna is associated with that of microorganisms in
superficial sediments. These invertebrates are particularly
abundant in phototrophic microbial aggregates which serve
them both as refuge against flow (Majdi et al. 2012a) and as
food source (Majdi et al. 2012b). Moreover, the patchy
distribution of meiofauna and benthic microorganisms is
associated in superficial sediments (Giere 2009). Meiofauna
are generally dominated, in terms of density and biomass, by
free-living nematodes, harpacticoid copepods, and rotifers.
Among macrobenthic invertebrates (larger than
meiofaunal invertebrates), consumers of microorganisms
mainly belong to gastropods, insect larvae (e.g.,
490
B. Mostajir et al.
used. With the improvement of these methods, over 7,000
species of ciliates, free or parasites, have been described in
aquatic ecosystems. This is a group characterized by the
presence of a ciliate cortex in the form of simple cilia, or
ciliated structures which are much more complex. Most
ciliates also have a nuclear dimorphism because they have
a macronucleus and usually several micronuclei.
Some groups of ciliates, such as Oligotrichia,
Scuticociliates, and Haptoria, are particularly well
represented in the lakes. Their size ranges from 5–10 to
over 200 μm. Their nutritional mode is very diverse being
mixotroph, bacterivore, algaevore, detritivore, or even omnivore. Their abundance in marine and lake ecosystems is an
average of 1 cell mL
À1 . Temperature, available light, and
nutrient resources induce a heterogeneous vertical distribution of ciliates through the water column. Their abundance
also varies according to nutrient concentrations.
13.2.1.4 Micro- and Mesoplankton
The microphytoplankton contributes significantly to primary
production in pelagic environments. Generally, the biomass
is estimated by inverted microscopy cell counts or by measuring chlorophyll (Chl) or other pigment biomarkers by
HPLC (cf. Chap. 17). It is very difficult to determine an
average value for the phytoplankton biomass in the marine
environment, while Chl a concentrations fluctuated between
0.1 and 70 μg Chl a mL
À1 in coastal lagoons. The phytoplankton biomass in the lake environments ranges from
<1 to > 25 mg m
À3 according to nutrient concentrations.
13.2.1.5 Microscopic Fungi
Recent environmental 18S-rDNA surveys of microbial
eukaryotes have unveiled major infecting agents in pelagic
systems, consisting primarily of the fungal order of
Chytridiales (chytrids) (Lefe `vre et al. 2007). Chytrids are
considered the earlier branch of the Eumycetes and produce
motile, flagellated zoospores, characterized by a small size
(2–6 μm) and a single, posterior flagellum. The existence of
these dispersal propagules includes chytrids within the socalled group of zoosporic fungi, which are particularly
adapted to the plankton lifestyle where they infect a wide
variety of hosts, including fishes, eggs, zooplankton, algae,
and other aquatic fungi but primarily freshwater phytoplankton (Sime-Ngando 2012). In Lake Pavin (France), chytrid
zoospores can contribute up to 40 % of the total diversity and
60 % of the total abundance of small-sized heterotrophic
flagellates in the plankton. These flagellates are exclusively
considered as grazers of prokaryotes. Ecological
implications are huge because parasitic chytrids can also
kill their hosts, but release substrates for microbial processes, and provide nutrient-rich particles as zoospores
(Kagami et al. 2007) and short fragments (from the fragmentation of filamentous inedible hosts) for the grazer food
chain. Furthermore, based on the observation that phytoplankton chytridiomycosis preferentially impacts the larger
size species, blooms of such species (e.g., filamentous
cyanobacteria) may not totally represent trophic bottlenecks.
In the case of chytrid epidemics, this can also represent an
important driving factor in phytoplankton seasonal
successions and maturation, in addition to the sole seasonal
forcing (Sime-Ngando 2012).
It is thus becoming evident that non-bacterivorous heterotrophic microbial eukaryotes such as chytrids, but also
the members of the genus Perkinsus or alveolates, which are
parasites or saprotrophs, represent an important but as yet
overlooked ecological driving force in aquatic food web
dynamics. In addition to being able to resist adverse
conditions and use different sources of carbon and nutrients,
these parasites can indeed affect the plankton food web
functions and ecosystem properties and topology, such as
stability and trophic transfer efficiency (Grami et al. 2011).
We are perhaps approaching a new paradigm-shift point in
the development of aquatic microbial ecology (SimeNgando and Niquil 2011).
13.2.2 Microorganisms of Benthic Ocean
and Lake Ecosystems
Benthic consumers of microorganisms are unicellular and
metazoan organisms. Unicellular consumers, such as heterotrophic ciliates, are important potential consumers of benthic
microalgae and bacteria. Their density can reach up to 5,000
and 11,000 ind.cm
3 in marine and freshwater sediments,
respectively. Other groups such as amoebozoan and benthic
foraminifera are also present. Microbial biofilms constitute
one of their typical microhabitats (Giere 2009).
Most of metazoan consumers of microorganisms belong
to meiofauna (benthic invertebrates which pass through a
1 mm mesh and are retained on a 40 μm mesh sieve). They
are abundant and diversified in superficial sediments (on
average 10
6 ind.m
2 ). The patchy spatial distribution of
meiofauna is associated with that of microorganisms in
superficial sediments. These invertebrates are particularly
abundant in phototrophic microbial aggregates which serve
them both as refuge against flow (Majdi et al. 2012a) and as
food source (Majdi et al. 2012b). Moreover, the patchy
distribution of meiofauna and benthic microorganisms is
associated in superficial sediments (Giere 2009). Meiofauna
are generally dominated, in terms of density and biomass, by
free-living nematodes, harpacticoid copepods, and rotifers.
Among macrobenthic invertebrates (larger than
meiofaunal invertebrates), consumers of microorganisms
mainly belong to gastropods, insect larvae (e.g.,
490
B. Mostajir et al.