The coastal marine environment is regularly enriched
with nutrients that come from rivers and the rain. This
leads to the predominance of herbivorous food web in
coastal zone (with high phytoplankton biomass) relative to
oceanic area which is characterized generally by a microbial
food web. Environmental forcing factors do change the
structure of the food web for the benefit of microorganisms
that best adapt to the new environment. This temporal
change is close to the concept of ecological succession.
The succession of food webs may lead, reversibly, from
the microbial loop to microbial, multivorous, and herbivorous food webs.
The notion of “equilibrium change and status reversibility” between different food webs means that a situation can
switch from one to the other as a result of environmental
forcing factors. The consequences of the dominance of a
food web relative to another one are very important because
they lead to the ecosystem completely different in terms of
production, regeneration, material flow, grazing, sequestration, or export of matter (fisheries can be considered as an
exportation of biomass). Herbivorous food web and the
microbial loop would be transitory and unstable systems,
while multivorous and microbial food webs are much more
stable and sustainable (Legendre and Rassoulzadegan 1995).
Apart from climate forcing factors (wind, temperature,
light, etc.), two main groups of factors controlling pelagic
microbial food webs are usually considered. The “bottomup” factors consist of resources and affect more the growth
rate of organisms than their biomass. The “top-down”
factors are represented by all the predation pressure that
leads to biomass removal.
By extension, all factors affecting the biomass, such as
viral lysis or parasitism, are considered as top-down factors,
although their effects on the structure and functioning of the
food webs are fundamentally different. According to
McQueen et al. (1989), the bottom-up and top-down factors
are not exclusive and the relative intensity of each type of
control varies in space and time. Predation on picoplankton
communities and nutrient recycling within the food webs
and the microbial loop are discussed in Sects. 13.3.1 and
13.3.2; only control via viral lysis is discussed below.
13.4.1.1 Viruses in Aquatic Microbial Food Webs
Abundance and Diversity
Since the discovery two to three decades ago that viruses of
microbes are abundant in marine ecosystems (Bergh et al.
1989), aquatic viral ecology has grown increasingly to reach
the status of a full scientific discipline in environmental
sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms (http://www.isvm.org/),
was recently launched. Viruses are omnipresent components
of the microbial food web dynamics in a great variety of
marine (Fuhrman 1999; Suttle 2005, 2007) and freshwater
ecosystems (Sime-Ngando and Colombet 2009). They often
represent the most abundant biological entity in pelagic and
benthic habitats where abundances generally fluctuate
between 10
4 and 10
8 viruses mL
À1 , that is, 10–1,000-fold
higher than the abundances of prokaryotes. The highest
abundances (10
8 to 10
10 viruses mL
À1 ) were reported in
the sediments of Lake Gilbert, Canada (Maranger and Bird
1996). Values generally increase with the increasing productivity of aquatic ecosystems and, as a consequence, decrease
from freshwater to marine ecosystems, from costal to oceanic zones and from the surface to the bottom of the euphotic
layer. The abundance of viruses in individual aquatic
systems appears to be independent of salinity but is related
to the biomass of primary and secondary producers, as well
as to the seasonal forcing (Weinbauer 2004; Mann 2003).
The most recent 9th report of the International Committee
on Taxonomy of Viruses (ICTV, http://www.ictvonline.org/
index.asp?bhcp ¼ 1) includes 6 orders, 87 families, 19
subfamilies, 349 genera, and 2,284 viral types or “species.”
This is mostly based on isolated viral hosts in laboratory
cultures which, in the case of environmental samples, may
not exceed 1 % of the total prokaryotes. This implies that the
diversity of environmental viruses is huge, although the bulk
of the estimated 10
31 viruses in the biosphere remains
unknown. We now consider that environmental viruses represent the greatest reservoir of noncharacterized genetic
resources on earth (Suttle 2007). In aquatic samples, viral
phenotypes are limited, mainly including tailed or untailed
particles with capsid heads characteristic of bacteriophages
(Fig. 13.6). Tailed phages belong to the order Caudovirales
(Ackermann 2003), all of which are double-stranded DNA
viruses that generally represent about 10–50 % of the total
abundance of viruses in aquatic systems. Within
Caudovirales, three families emerge as quantitatively dominant: Siphoviridae with long noncontractile tails (e.g., phage
lambda), Podoviridae with a short noncontractile tail (e.g.,
phage T7), and Myoviridae with contractile tails of variable
length (e.g., phage T4). Phenotypic traits and viral morphs in
aquatic viruses are cryptic of the selective pressures faced by
these communities and provide insight into host range, viral
replication, and function (Suttle 2005). For instance,
myoviruses are mostly lytic with a large spectrum of sensitive hosts, which is a competitive advantage that can be
assimilated to r-strategist* species thriving with high proliferation rates in fluctuating environments. In contrast,
podoviruses are more highly specific to their hosts, with
siphoviruses being intermediate between myo- and
podoviruses. In addition, several siphoviruses can encode
their genome into their hosts for several generations (lysogeny), which can be rather assimilated to K-strategist* species’ characteristics of stable environments. Combined with
the capacity of viruses to potentially face almost all types of
environments and the related interfaces, the ability of viruses
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
501
with nutrients that come from rivers and the rain. This
leads to the predominance of herbivorous food web in
coastal zone (with high phytoplankton biomass) relative to
oceanic area which is characterized generally by a microbial
food web. Environmental forcing factors do change the
structure of the food web for the benefit of microorganisms
that best adapt to the new environment. This temporal
change is close to the concept of ecological succession.
The succession of food webs may lead, reversibly, from
the microbial loop to microbial, multivorous, and herbivorous food webs.
The notion of “equilibrium change and status reversibility” between different food webs means that a situation can
switch from one to the other as a result of environmental
forcing factors. The consequences of the dominance of a
food web relative to another one are very important because
they lead to the ecosystem completely different in terms of
production, regeneration, material flow, grazing, sequestration, or export of matter (fisheries can be considered as an
exportation of biomass). Herbivorous food web and the
microbial loop would be transitory and unstable systems,
while multivorous and microbial food webs are much more
stable and sustainable (Legendre and Rassoulzadegan 1995).
Apart from climate forcing factors (wind, temperature,
light, etc.), two main groups of factors controlling pelagic
microbial food webs are usually considered. The “bottomup” factors consist of resources and affect more the growth
rate of organisms than their biomass. The “top-down”
factors are represented by all the predation pressure that
leads to biomass removal.
By extension, all factors affecting the biomass, such as
viral lysis or parasitism, are considered as top-down factors,
although their effects on the structure and functioning of the
food webs are fundamentally different. According to
McQueen et al. (1989), the bottom-up and top-down factors
are not exclusive and the relative intensity of each type of
control varies in space and time. Predation on picoplankton
communities and nutrient recycling within the food webs
and the microbial loop are discussed in Sects. 13.3.1 and
13.3.2; only control via viral lysis is discussed below.
13.4.1.1 Viruses in Aquatic Microbial Food Webs
Abundance and Diversity
Since the discovery two to three decades ago that viruses of
microbes are abundant in marine ecosystems (Bergh et al.
1989), aquatic viral ecology has grown increasingly to reach
the status of a full scientific discipline in environmental
sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms (http://www.isvm.org/),
was recently launched. Viruses are omnipresent components
of the microbial food web dynamics in a great variety of
marine (Fuhrman 1999; Suttle 2005, 2007) and freshwater
ecosystems (Sime-Ngando and Colombet 2009). They often
represent the most abundant biological entity in pelagic and
benthic habitats where abundances generally fluctuate
between 10
4 and 10
8 viruses mL
À1 , that is, 10–1,000-fold
higher than the abundances of prokaryotes. The highest
abundances (10
8 to 10
10 viruses mL
À1 ) were reported in
the sediments of Lake Gilbert, Canada (Maranger and Bird
1996). Values generally increase with the increasing productivity of aquatic ecosystems and, as a consequence, decrease
from freshwater to marine ecosystems, from costal to oceanic zones and from the surface to the bottom of the euphotic
layer. The abundance of viruses in individual aquatic
systems appears to be independent of salinity but is related
to the biomass of primary and secondary producers, as well
as to the seasonal forcing (Weinbauer 2004; Mann 2003).
The most recent 9th report of the International Committee
on Taxonomy of Viruses (ICTV, http://www.ictvonline.org/
index.asp?bhcp ¼ 1) includes 6 orders, 87 families, 19
subfamilies, 349 genera, and 2,284 viral types or “species.”
This is mostly based on isolated viral hosts in laboratory
cultures which, in the case of environmental samples, may
not exceed 1 % of the total prokaryotes. This implies that the
diversity of environmental viruses is huge, although the bulk
of the estimated 10
31 viruses in the biosphere remains
unknown. We now consider that environmental viruses represent the greatest reservoir of noncharacterized genetic
resources on earth (Suttle 2007). In aquatic samples, viral
phenotypes are limited, mainly including tailed or untailed
particles with capsid heads characteristic of bacteriophages
(Fig. 13.6). Tailed phages belong to the order Caudovirales
(Ackermann 2003), all of which are double-stranded DNA
viruses that generally represent about 10–50 % of the total
abundance of viruses in aquatic systems. Within
Caudovirales, three families emerge as quantitatively dominant: Siphoviridae with long noncontractile tails (e.g., phage
lambda), Podoviridae with a short noncontractile tail (e.g.,
phage T7), and Myoviridae with contractile tails of variable
length (e.g., phage T4). Phenotypic traits and viral morphs in
aquatic viruses are cryptic of the selective pressures faced by
these communities and provide insight into host range, viral
replication, and function (Suttle 2005). For instance,
myoviruses are mostly lytic with a large spectrum of sensitive hosts, which is a competitive advantage that can be
assimilated to r-strategist* species thriving with high proliferation rates in fluctuating environments. In contrast,
podoviruses are more highly specific to their hosts, with
siphoviruses being intermediate between myo- and
podoviruses. In addition, several siphoviruses can encode
their genome into their hosts for several generations (lysogeny), which can be rather assimilated to K-strategist* species’ characteristics of stable environments. Combined with
the capacity of viruses to potentially face almost all types of
environments and the related interfaces, the ability of viruses
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
501