to develop along the r-K-selection continuum, i.e., from
typical r (e.g., prokaryotes) to typical K (e.g., vertebrates)
strategist organisms, may help to explain their ubiquity,
hence the notion of virosphere (i.e., viral biosphere).
From a genomic point of view, whole genome
comparisons have shown that there are conserved genes
shared among all members within certain viral taxonomic
groups (Breitbart and Rohwer 2005). These conserved genes
can be targeted using PCR-amplification and sequencing for
diversity studies of groups of cultured and environmental
viruses. Examples of such genes are structural proteins such
as gp20 which codes for the capsid formation in T4 phagelike viruses, DNA polymerases for T7-like podophages, or
the RNA-dependent RNA polymerase fragment, which has
been used to identify novel groups of marine viruses. For the
whole environmental communities, molecular fingerprinting
approaches that separate polymerase chain reaction PCRgenerated DNA products, such as denaturing gradient gel
electrophoresis (DGGE) and pulse-field gel electrophoresis
(PFGE), have been widely used but with limited results,
restricted to double-stranded DNA viruses. With this
approach, the genome size of aquatic viruses fluctuates
from 10 to about 900 kb, with mean ranges of 10–650 kb
in marine and freshwater pelagic systems. Finally,
metagenomics has revolutionized microbiology by paving
the way for a culture-independent assessment and exploitation of microbial and viral communities present in complex
environments (Edwards and Rohwer 2005). Metagenomic
analyses of 184 viral assemblages collected over a decade
and representing 68 sites in four major oceanic regions
showed that most of the viral DNA and protein sequences
were not similar to those in the current databases (Angly
et al. 2006). Global diversity was very high, presumably
several hundred thousand “species” and regional richness
varied on a north–south latitudinal gradient. However,
most viral “species” were found to be widespread,
supporting the idea that viruses are widely dispersed and
that local environmental conditions enrich for certain viral
types through selective pressure.
Overall, genomic approaches suggest that environmental
viral diversity is high and essentially uncharacterized. They
also suggest novel patterns of evolution and are increasingly
changing the existing ideas on the composition of the virus
world, while revealing novel groups of viruses and virus-like
agents. The gene composition of aquatic DNA viromes (i.e.,
metagenomes of viruses) is dramatically different from that
of known bacteriophages.
Roles of Viruses in Aquatic Systems
Environmental viruses exhibit various lifestyles that intimately depend on the deep-cellular mechanisms and are
ultimately replicated by all members of the three domains
of cellular life (Bacteria, Eukarya, Archaea), as well as by
some giant viruses of eukaryotic cells. Most of the freeoccurring viruses in aquatic systems are infectious and this
infectivity can last for a long time, several tens of years for
benthic viruses, for example (Suttle 2005). This establishes
lytic viruses as major players in key ecological processes
such as microbial mortality and the related biogeochemical
cycling of nutrients and OM (Fuhrman 1999). It is now well
accepted that the energy requirement for the lytic lifestyle of
viruses is one of the main causes of microbial mortality in
aquatic systems. Based on the direct observation of infected
cells (Fig. 13.6), viral-mediated mortality averages 10–50 %
of the daily production of heterotrophic prokaryotes and
approximately equals the bacterivory from grazers, primarily in both fresh and marine pelagic waters. In the benthos,
viral abundances are largely higher compared to the water
column, but, paradoxically, few visible infected cells were
reported in the sediments (Filippini et al. 2006). Viral lysis
of cells has the strong feedback effect of preventing species
dominance and enhanced species cohabitation within microbial communities, i.e., the so-called phage kills the winner
hypothesis (Thingstad 2000). By this way, viruses also play
major role in governing microbial diversity and structuring
microbial food webs through complex mechanisms that are
summarized in Fig. 13.7 (Weinbauer and Rassoulzadegan
2004).
It was estimated that the absolute abundance of oceanic
viruses results in about 10
29 infection events per day, causing the release of 10
8 –10
9 tons of carbon per day from the
living biological pool (Suttle 2005, 2007). By exploding
microbial cells, lytic viruses are strong catalyzers of the
transformation of living organisms to detrital and dissolved
phases available to noninfected microbes (Fig. 13.7). This
biogeochemical reaction increases the retention time of OM
and its respiration in the water column and weakens the
trophic efficiency of the food web but also provides nutrients
(e.g., directly or indirectly from mineralization and
photodegradation of DOM) to primary producers. For example, it has been shown that the iron content in the viral lysis
products could fulfill the metabolic requirements of marine
phytoplankton. Primary production in the size fraction
2–200 nm can be depleted by about half due to an increase
in viral abundance as low as 20 %. Similarly, a modeling
exercise suggested that viral lysis of 50 % of bacterial
production could increase bacterial respiration by 27 %
while decreasing the grazing efforts from protists and
metazooplankton by 37 and 7 %, respectively. When adding
7 % of viral-mediated loss of phytoplankton and 3 % grazing
of viruses by phagotrophic flagellates, bacterial respiration
increases to 33 % (Fuhrman 1999).
One of the key explanations for the omnipresence of
viruses in natural ecosystems is undoubtedly through the
existence of several lifestyles, of which two major pathways,
namely, lysis and lysogeny, are prevalent in aquatic systems.
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
503
typical r (e.g., prokaryotes) to typical K (e.g., vertebrates)
strategist organisms, may help to explain their ubiquity,
hence the notion of virosphere (i.e., viral biosphere).
From a genomic point of view, whole genome
comparisons have shown that there are conserved genes
shared among all members within certain viral taxonomic
groups (Breitbart and Rohwer 2005). These conserved genes
can be targeted using PCR-amplification and sequencing for
diversity studies of groups of cultured and environmental
viruses. Examples of such genes are structural proteins such
as gp20 which codes for the capsid formation in T4 phagelike viruses, DNA polymerases for T7-like podophages, or
the RNA-dependent RNA polymerase fragment, which has
been used to identify novel groups of marine viruses. For the
whole environmental communities, molecular fingerprinting
approaches that separate polymerase chain reaction PCRgenerated DNA products, such as denaturing gradient gel
electrophoresis (DGGE) and pulse-field gel electrophoresis
(PFGE), have been widely used but with limited results,
restricted to double-stranded DNA viruses. With this
approach, the genome size of aquatic viruses fluctuates
from 10 to about 900 kb, with mean ranges of 10–650 kb
in marine and freshwater pelagic systems. Finally,
metagenomics has revolutionized microbiology by paving
the way for a culture-independent assessment and exploitation of microbial and viral communities present in complex
environments (Edwards and Rohwer 2005). Metagenomic
analyses of 184 viral assemblages collected over a decade
and representing 68 sites in four major oceanic regions
showed that most of the viral DNA and protein sequences
were not similar to those in the current databases (Angly
et al. 2006). Global diversity was very high, presumably
several hundred thousand “species” and regional richness
varied on a north–south latitudinal gradient. However,
most viral “species” were found to be widespread,
supporting the idea that viruses are widely dispersed and
that local environmental conditions enrich for certain viral
types through selective pressure.
Overall, genomic approaches suggest that environmental
viral diversity is high and essentially uncharacterized. They
also suggest novel patterns of evolution and are increasingly
changing the existing ideas on the composition of the virus
world, while revealing novel groups of viruses and virus-like
agents. The gene composition of aquatic DNA viromes (i.e.,
metagenomes of viruses) is dramatically different from that
of known bacteriophages.
Roles of Viruses in Aquatic Systems
Environmental viruses exhibit various lifestyles that intimately depend on the deep-cellular mechanisms and are
ultimately replicated by all members of the three domains
of cellular life (Bacteria, Eukarya, Archaea), as well as by
some giant viruses of eukaryotic cells. Most of the freeoccurring viruses in aquatic systems are infectious and this
infectivity can last for a long time, several tens of years for
benthic viruses, for example (Suttle 2005). This establishes
lytic viruses as major players in key ecological processes
such as microbial mortality and the related biogeochemical
cycling of nutrients and OM (Fuhrman 1999). It is now well
accepted that the energy requirement for the lytic lifestyle of
viruses is one of the main causes of microbial mortality in
aquatic systems. Based on the direct observation of infected
cells (Fig. 13.6), viral-mediated mortality averages 10–50 %
of the daily production of heterotrophic prokaryotes and
approximately equals the bacterivory from grazers, primarily in both fresh and marine pelagic waters. In the benthos,
viral abundances are largely higher compared to the water
column, but, paradoxically, few visible infected cells were
reported in the sediments (Filippini et al. 2006). Viral lysis
of cells has the strong feedback effect of preventing species
dominance and enhanced species cohabitation within microbial communities, i.e., the so-called phage kills the winner
hypothesis (Thingstad 2000). By this way, viruses also play
major role in governing microbial diversity and structuring
microbial food webs through complex mechanisms that are
summarized in Fig. 13.7 (Weinbauer and Rassoulzadegan
2004).
It was estimated that the absolute abundance of oceanic
viruses results in about 10
29 infection events per day, causing the release of 10
8 –10
9 tons of carbon per day from the
living biological pool (Suttle 2005, 2007). By exploding
microbial cells, lytic viruses are strong catalyzers of the
transformation of living organisms to detrital and dissolved
phases available to noninfected microbes (Fig. 13.7). This
biogeochemical reaction increases the retention time of OM
and its respiration in the water column and weakens the
trophic efficiency of the food web but also provides nutrients
(e.g., directly or indirectly from mineralization and
photodegradation of DOM) to primary producers. For example, it has been shown that the iron content in the viral lysis
products could fulfill the metabolic requirements of marine
phytoplankton. Primary production in the size fraction
2–200 nm can be depleted by about half due to an increase
in viral abundance as low as 20 %. Similarly, a modeling
exercise suggested that viral lysis of 50 % of bacterial
production could increase bacterial respiration by 27 %
while decreasing the grazing efforts from protists and
metazooplankton by 37 and 7 %, respectively. When adding
7 % of viral-mediated loss of phytoplankton and 3 % grazing
of viruses by phagotrophic flagellates, bacterial respiration
increases to 33 % (Fuhrman 1999).
One of the key explanations for the omnipresence of
viruses in natural ecosystems is undoubtedly through the
existence of several lifestyles, of which two major pathways,
namely, lysis and lysogeny, are prevalent in aquatic systems.
13 Microbial Food Webs in Aquatic and Terrestrial Ecosystems
503