production enters the food web as detritus. Benthic
macrofauna comprise shredders that only consume this matter partially and cut the larger detritus into smaller pieces
that can be colonized by heterotrophic microorganisms.
These microorganisms are subsequently consumed by
small heterotrophic eukaryotes and invertebrates.
So far, little is known about the quantitative importance
of predation on prokaryotes and trophic transfer in
sediments. One of the reasons why the microbial food web
has been less studied in sediment systems compared to the
water column is that some of the classical techniques like
dilution and retrieval of specific size classes by filtration
cannot be used in sediments without complete destruction
of the spatial structure of the sediments. Novel techniques
based on the use of stable isotopes as tracers are promising.
Carbon dioxide and specific organic compounds can be
enriched in
13 C and added to the benthic system as substrates
for oxygenic phototrophs and heterotrophic bacteria, respectively. Their fate in the food web can be followed by studying the
13
C/
12 C ratio in the different trophic compartments.
After a certain incubation time, specimens of the main
macrofauna and meiofauna are collected and analyzed for
their ∂
13 C signatures by mass spectrometry. In contrast, it is
very difficult or often impossible to physically separate
sufficient microalgae and cyanobacteria from the heterotrophic bacteria. The ∂
13 C signatures for these functional
groups can be evaluated by using group specific biomarkers
and measuring the ∂
13 C signatures for these compounds by
using LC-MS or GC-MS. The addition of NaH
13 CO 3 to a
diatom biofilm in intertidal sediments has allowed to detect a
progressive increase of the
13 C tracer in the diatoms during
the first 4 h and a measurable trophic transfer of
13 C to the
nematodes from t ¼ 1 h to 3 days of incubation. Simultaneously, some fatty acids that are specific to heterotrophic
bacteria also became enriched in
13 C; their labeling peaked
after 1 day of incubation (Middelburg et al. 2000). This
shows that there is a quick trophic transfer of OM from
diatoms to heterotrophic bacteria, probably through the
EPS compartment (Fig. 13.5). In another experiment, heterotrophic bacteria have been labeled by adding
13 C glucose
to the same type of biofilms. This way it has been estimated
that the heterotrophic bacteria constitute 8 % and 11 % of the
diet of meiofauna and macrofauna, respectively.
13.3.4 Functioning of Microbial Food Webs in
Terrestrial Ecosystems
The major actors constituting the terrestrial food webs have
been presented in the Sect. 13.2.3. Here, we focus on the
functional role of these actors and their interactions. It is
now widely accepted that the structure of the soil food webs
has a direct impact on its functioning in general (Beare et al.
1995). The biotic components contribute to functional soil
processes via direct and indirect mechanisms. Direct
mechanisms are the result of metabolic degradation of complex molecules and release of energy, C, N, and minerals
through respiration, excretion, and chemotrophy. Indirect
mechanisms include many effects of feedback and agencies
are classified as ecosystem engineers (Anderson 2000).
13.3.4.1 Decomposition of Organic Matter in Soils
The function of decomposing of OM is obviously one of the
major roles of the food webs in soil ecosystems. The decomposition of OM produces CO 2 but also soluble compounds
such nutrients for plants. In natural unfertilized soils, almost
all the nitrogen needs and part of the phosphorus needs come
from the decomposition of OM. Even in amended systems*,
the role of the decomposition of OM remains central in
maintaining an acceptable biological production in soils.
In uncultivated areas, 80–90 % of the primary production
returns to the soil as litter and dead roots. Heterotrophic
fungi and prokaryotes are the main actors in decomposing
these plant incomes. Through fragmentation and ingestion,
the detritivorous fauna essentially play a facilitating role for
the subsequent microbial activity (mainly through the
increase of the colonization surfaces). The incredible range
of metabolic capabilities of microorganisms allows them to
be able to substantially degrade almost all the molecules
present in plants. In many ecosystems, fungi are the most
abundant “primary” decomposers. Compared to bacteria,
they are better adapted to start the decomposition of insoluble plant materials, due to their hyphae which can penetrate
and proliferate inside plant cells. Like bacteria, they exhibit
a wide range of metabolic capabilities that, in particular,
allow them to degrade recalcitrant components of plant
cells, such as lignin. In addition, being able to mobilize
nutrients across their hyphae networks gives to fungi the
opportunity to exploit new substrates, even when the local
levels of P and N are low. These characteristics of active use
of substrates by fungi contrast with the immobility or passive
mobility (e.g., the movements of water in the soil) of bacteria. As a result, the latter are probably more frequently
inactive due to lack of resources in their immediate
environment.
13.3.4.2 Role of Selective Predation
Fungi and heterotrophic prokaryotes are the main actors of
the MO transformation in soils, particularly, for its degradation by mineralization. However, the organisms belonging to
higher trophic levels strongly affect the activity of these
microorganisms (Bardgett 2005a).
Selective feeding of microorganisms can modify the
abundance, structure, and activity of fungal and bacterial
communities. Although a number of studies report the generalist and/or opportunistic feeding characteristics of
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
499
macrofauna comprise shredders that only consume this matter partially and cut the larger detritus into smaller pieces
that can be colonized by heterotrophic microorganisms.
These microorganisms are subsequently consumed by
small heterotrophic eukaryotes and invertebrates.
So far, little is known about the quantitative importance
of predation on prokaryotes and trophic transfer in
sediments. One of the reasons why the microbial food web
has been less studied in sediment systems compared to the
water column is that some of the classical techniques like
dilution and retrieval of specific size classes by filtration
cannot be used in sediments without complete destruction
of the spatial structure of the sediments. Novel techniques
based on the use of stable isotopes as tracers are promising.
Carbon dioxide and specific organic compounds can be
enriched in
13 C and added to the benthic system as substrates
for oxygenic phototrophs and heterotrophic bacteria, respectively. Their fate in the food web can be followed by studying the
13
C/
12 C ratio in the different trophic compartments.
After a certain incubation time, specimens of the main
macrofauna and meiofauna are collected and analyzed for
their ∂
13 C signatures by mass spectrometry. In contrast, it is
very difficult or often impossible to physically separate
sufficient microalgae and cyanobacteria from the heterotrophic bacteria. The ∂
13 C signatures for these functional
groups can be evaluated by using group specific biomarkers
and measuring the ∂
13 C signatures for these compounds by
using LC-MS or GC-MS. The addition of NaH
13 CO 3 to a
diatom biofilm in intertidal sediments has allowed to detect a
progressive increase of the
13 C tracer in the diatoms during
the first 4 h and a measurable trophic transfer of
13 C to the
nematodes from t ¼ 1 h to 3 days of incubation. Simultaneously, some fatty acids that are specific to heterotrophic
bacteria also became enriched in
13 C; their labeling peaked
after 1 day of incubation (Middelburg et al. 2000). This
shows that there is a quick trophic transfer of OM from
diatoms to heterotrophic bacteria, probably through the
EPS compartment (Fig. 13.5). In another experiment, heterotrophic bacteria have been labeled by adding
13 C glucose
to the same type of biofilms. This way it has been estimated
that the heterotrophic bacteria constitute 8 % and 11 % of the
diet of meiofauna and macrofauna, respectively.
13.3.4 Functioning of Microbial Food Webs in
Terrestrial Ecosystems
The major actors constituting the terrestrial food webs have
been presented in the Sect. 13.2.3. Here, we focus on the
functional role of these actors and their interactions. It is
now widely accepted that the structure of the soil food webs
has a direct impact on its functioning in general (Beare et al.
1995). The biotic components contribute to functional soil
processes via direct and indirect mechanisms. Direct
mechanisms are the result of metabolic degradation of complex molecules and release of energy, C, N, and minerals
through respiration, excretion, and chemotrophy. Indirect
mechanisms include many effects of feedback and agencies
are classified as ecosystem engineers (Anderson 2000).
13.3.4.1 Decomposition of Organic Matter in Soils
The function of decomposing of OM is obviously one of the
major roles of the food webs in soil ecosystems. The decomposition of OM produces CO 2 but also soluble compounds
such nutrients for plants. In natural unfertilized soils, almost
all the nitrogen needs and part of the phosphorus needs come
from the decomposition of OM. Even in amended systems*,
the role of the decomposition of OM remains central in
maintaining an acceptable biological production in soils.
In uncultivated areas, 80–90 % of the primary production
returns to the soil as litter and dead roots. Heterotrophic
fungi and prokaryotes are the main actors in decomposing
these plant incomes. Through fragmentation and ingestion,
the detritivorous fauna essentially play a facilitating role for
the subsequent microbial activity (mainly through the
increase of the colonization surfaces). The incredible range
of metabolic capabilities of microorganisms allows them to
be able to substantially degrade almost all the molecules
present in plants. In many ecosystems, fungi are the most
abundant “primary” decomposers. Compared to bacteria,
they are better adapted to start the decomposition of insoluble plant materials, due to their hyphae which can penetrate
and proliferate inside plant cells. Like bacteria, they exhibit
a wide range of metabolic capabilities that, in particular,
allow them to degrade recalcitrant components of plant
cells, such as lignin. In addition, being able to mobilize
nutrients across their hyphae networks gives to fungi the
opportunity to exploit new substrates, even when the local
levels of P and N are low. These characteristics of active use
of substrates by fungi contrast with the immobility or passive
mobility (e.g., the movements of water in the soil) of bacteria. As a result, the latter are probably more frequently
inactive due to lack of resources in their immediate
environment.
13.3.4.2 Role of Selective Predation
Fungi and heterotrophic prokaryotes are the main actors of
the MO transformation in soils, particularly, for its degradation by mineralization. However, the organisms belonging to
higher trophic levels strongly affect the activity of these
microorganisms (Bardgett 2005a).
Selective feeding of microorganisms can modify the
abundance, structure, and activity of fungal and bacterial
communities. Although a number of studies report the generalist and/or opportunistic feeding characteristics of
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
499