Lake Pavin History, geology, biogeochemistry, and sedimentology of a deep meromictic maar lake

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viral constituents, including the replication of the viral
genetic material. A number of progeny viruses are then pro-
duced and released in the environment by fatal bursting of
the host cell. In the chronic cycle, the progeny viruses are
episodically or constantly released from the host cell by bud-
ding or extrusion, without immediate lethal events. This
cycle is less known in the plankton, but is common in meta-
zoan viruses such as Herpes and Hepatitis viruses or
Rhabdoviruses. Chronic viral infection is a dynamic and
metastable equilibrium process (Virgin et al. 2009 ) which
ends by the lysis of the host cell after serial budding of lipid
membrane coated viruses, as known from the marine
Emiliana huxleyi host (Mackinder et al. 2009 ). Recently,
chronic infection without host lysis has been reported for the
fi rst time in the marine primary producer Ostreococcus tauri ,
where the low rate of viral release through budding (1–3
viruses cell −1 day −1 ) allows cell recovery and stable coexis-
tence of the viruses and their hosts (Clerissi et al. 2012 ).
In the lysogenic cycle, the viral genome integrates the
genome of the host cell to form a ‘ prophage’ which can stay
in a dormant/latent state for extended periods until an envi-
ronmental stress to the immune host cell set off a switch to a
lytic cycle. Unlike lytic infection, lysogeny provides a mean
of persistence for viruses when the abundance of the host
cells is very low (Weinbauer et al. 2003 ). Prophages may

also affect the metabolic properties of host cells which can

acquire immunity to superinfections and new phenotypic

characteristics, such as antibiotic resistance, antigenic

changes, and virulence factors. A variant to the lysogenic

cycle is the so-called carrier state or pseudolysogenic cycle

where the viral genome is not integrated to the host genome

but rather remains in an ‘inactive state’ within the host cell.

There is no replication of the viral DNA which is segregated

unequally into progeny cells, likely for few generations.

Pseudolysogenic viruses likely occur in very poor nutrient

conditions where host cells are in starvation and cannot offer

the energy necessary to the viral gene expression (Ripp and

Miller 1997 ; Łoś and Węgrzyn 2012 ).

14.3 Methodological Considerations :

Abundance, Basic Infectivity

Parameters and Concentration

of Viruses for Quantitative

and Genomic Studies

Ecological investigations rely on biomass, diversity, and com-

position of organisms, which, in the case of microbial com-

munities are, primarily, gathered using microscopy and

molecular genetic approaches. The diminutive size of viruses

Pradeep Ram et al

CHRONOLOGY OF VIRAL INVESTIGATIONS IN LAKE PAVIN

(^199620022004)
2007
2012
2000 2003 2005
2006 2008
2009
2010
2011
2013
Sime-Ngando et al
First observaons of
viruses from Lake Pavin
with transmission electron
microscope
Bearel et al
Colombet et al
Sime-Ngando et al
Review on viruses in
freshwaters
Bearel et al
Integraon of viral
lysis into carbon
budget
Bearel et al
Bearel et al
Flagellate grazing
on viruses
Bearel et al
Roux et al
Colombet et al
Depth-related gradients in
virioplankton
Pradeep Ram & Sime-Ngando
Colombet et al
Seasonal Depth-
Related Gradients in
Pelagic Viruses
Borrel et al
Viruses of deep-dark
permanently anoxic freshwaters
and sediments
Colombet & Sime-Ngando
Seasonal depth-related
gradients in viral lysis
Roux et al
Bearel et al
First viral
counts in
epifluorescence
Jardillier et al
Effects of viruses and
predators on prokaryoc
community composion
Nutrient effects on the trade-off
between lyc versus lysogenic
viruses
Variable viral and grazer control
of prokaryoc growth efficiency
in temperate lakes
Nycthemeral
dynamics of
viruses
Seasonal dynamics in
viral abundance
Metagenomics of
freshwater viral
communies
Metavir set up Top down regulaonof prokaryoc growth
efficiency
Virioplankton
’pegylaon’
Sime-Ngando & Colombet
Review on viruses and
prophages in aquac
ecosystems
Seasonal dynamics in
lyc infecon
Colombet & Sime-Ngando
Use of PEG to characterize the
diversity of environmental
viruses
2014 2016
Pradeep Ram et al
Pradeep Ram et al
Viral and grazer regulaon
of prokaryoc diversity
and mortality
Sime-Ngando & Pradeep Ram
Grazer effects on
prokaryotes and viruses
Pradeep Ram & Sime-Ngando
Grazer and nutrient effects
on prokaryotes and viruses
Palesse et al
Sime-Ngando et al
Linking host prokaryoc
physiology to viral
lifestyle dynamics
Springer
Monograph
2016
20152015
Fig. 14.1 Chronogram of ecological studies of freshwater viruses in Lake Pavin
14 Ecology of Viruses in Lake Pavin
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