230
ment cores, and their vertical distribution correlated with both viral and prokaryotic abun-
dances. Pleomorphic ellipsoid VLPs were visible in fi lamentous cells tentatively identifi ed
as representatives of the archaeal genus Methanosaeta , a major group of methane producers
on Earth.Keywords
Lake Pavin • Viruses • Seasonal and depth related variability • Viral lysis • Lysogeny •
Microbial loop14.1 Introduction
With the discovery, few decades ago, that viruses of microbes
are abundant in marine ecosystems (Torrella and Morita
1979 ; Bergh et al. 1989 ), aquatic viral ecology has increas-
ingly grown to reach the status of full scientifi c discipline in
environmental sciences, with the recent launch of a dedi-
cated society, i.e. the International Society for Viruses of
Microorganisms (ISVM) ( http://www.isvm.org/ ). As infec-
tious agent of potentially all types of living cells, viruses are
the most abundant biological entity in the biosphere. They
are an ubiquitous component of the microbial food web
dynamics in a great variety of environments, including the
most extreme ecosystems (Sime-Ngando and Colombet
2009 ). Moreover, in spite of the diffi culties to routinely
observe and describe biological nanoparticles, combined
with the absence of conserved evolution tracers such as RNA
ribosomal genes, we now consider that viruses represent the
greatest reservoir of non-characterized genetic diversity and
resources on the earth (Suttle 2007 ). They contain genes that
code for essential biological functions such as photosynthe-
sis (Lindell et al. 2005 ), making their hosts powerful vehicles
for genetic exchanges in the environment. Because lytic
viruses kill their hosts, they play fundamental roles in cycling
nutrients and organic matter, structuring microbial food
webs , governing microbial diversity and, to a lesser extent,
by being a potential food source for protists (Bettarel et al.
2005 ). Viruses can also form long-lived association with
their specifi c hosts, reducing their fi tness, or allowing
infected hosts to remain strong competitors through mutual-
istic symbioses (Roossinck 2011 ). In addition, the discovery
and characterization of the unique group of archaeal viruses
are infl uencing the fi eld of prokaryotic virology, increasing
our knowledge on viral diversity and changing perspectives
on early stages of evolution (Prangishvili et al. 2006 ).
The majority of the studies on the ecology of wild viruses
in aquatic systems was conducted in marine systems, although
some of the original work was done in freshwater systems
(Miller et al. 1992 ). The present chapter sought to review the
literature on viruses in freshwater ecosystems , focusing on
data collected in a pioneer site, the oligo- mesotrophic Lake
Pavin located in the temperate French Massif Central, where
studies on freshwater viral ecology had started about two
decades ago. These data encompassed different aspects of the
whole aquatic viral ecology (Fig. 14.1 ), including (i) methods
for concentrating and counting free-fl oating and infectious
viruses via transmission electron and epifl uorescence micros-
copy (Sime-Ngando et al. 1996 ; Bettarel et al. 2000 ;
Wommack et al. 2010 ; Colombet et al 2007 ; Colombet and
Sime-Ngando 2012a ), (ii) seasonal and depth-related vari-
ability in viral diversity, metagenomics , abundance and both
lytic and lysogenic activities (Bettarel et al. 2003a ; Colombet
et al. 2009 ; Colombet and Sime- Ngando 2012a ; Roux et al.
2012 ), (iii) the role of nutrient inputs on the trade-off between
the two major lifestyles (i.e. lysis and lysogeny ) of planktonic
viruses (Pradeep Ram and Sime-Ngando 2010 ) (iv) the sea-
sonal contribution of viral bacteriolysis vs protistan bacteriv-
ory to the fate of prokaryotes and the related biogeochemical
cycling (Bettarel et al. 2003b , 2004 ; Pradeep Ram et al.
2014 ), (v) the signifi cance of viruses as food source for
phagotrophic protists (Bettarel et al. 2005 ), and (vi) the
impact of viruses on the metabolism (Pradeep Ram et al.
2013 ) and community composition (Jardillier et al. 2005 ) of
prokaryotes. Recently, unexpected and novel putative viruses,
primarily viruses of Archaea, have also been discovered in the
deep-dark permanently anoxic water and sediments of Lake
Pavin (Borrel et al. 2012 ).14.2 Basic Knowledge on Viruses
Viruses are biological entities consisting each of a single- or
a double stranded DNA or RNA surrounded by a protein and,
for some of them, a lipid coat. In mesophilic aquatic systems,
most virus-like particles (VLPs) are tailed or untailed phages,
with capsid diameter typically smaller than 100 nm, based
on direct observation with transmission electron microscope
(TEM). Viruses have no intrinsic metabolism and for all pro-
cesses requiring energy, they need the intracellular machinery
of a living and sensitive host cell. They have various life
cycles, all starting by fi xation on specifi c receptors (often
transporter proteins ) present on the surface of host cells,
followed by injection of the viral genome in the cytosol. In
the lytic cycle , the viral genome induces the synthesis ofT. Sime-Ngando et al.