23714.5 Standing Stocks and Seasonal
Patterns in Viral Dynamics
The fi rst seasonal studies on viruses in Lake Pavin were con-
ducted in 2000 (Bettarel et al. 2003b ) following a diel cycle
study in 1998 (Bettarel et al. 2002 ), corresponding to one of
the earliest attempts in freshwater ecology that established
viruses as ubiquitous, abundant and dynamic component
whose role in the functioning of aquatic ecosystems needs to
be assessed. At seasonal time scale, the abundances of free-
fl oating viruses in the mixolimnion of Lake Pavin typically
ranged from 1 to 6 × 10^7 viruses ml −1 , which is within the
range of those found in other pelagic environments
(Wommack and Colwell 2000 ). Similarly, a small peak was
noted in spring followed by a more or less progressive
increase during the period of thermal stratifi cation , espe-
cially between May and October in Lake Pavin (Fig. 14.6A ),
which also corresponded to the seasonal patterns in other
lakes of the region and in other freshwater and marine envi-
ronments as well, where an autumnal peak is characteristic
of the seasonal abundances of aquatic viruses. Wommack
and Colwell ( 2000 ) interpreted this peak as the consequence
of the autumnal phytoplankton bloom. As a consequence, the
virus-to-bacteria ratio (VBR) in Lake Pavin (range 3–13,
mean 7) also peaked in spring and in autumn, and corre-
sponded to the typical values (range 3–10) reported in pelagic
environments (Wommack and Colwell 2000 ). Typically the
VBR is higher; the low VBRs are usually due to bad storage
conditions for viruses. The calculated burst size from visi-
bly infected cells observed under TEM ranges from 15 to 50,
mean 25 viruses cell −1. Part of the lytic viral production in
the plankton is rapidly removed by complex environmental
processes, such as adsorption on particles, enzyme digestion
via proteolysis, destruction by UV raditions, grazing etc...
The seasonal abundances of viruses and bacteria in Lake
Pavin and other pelagic environments are rather homeostatic
as they do not generally vary by more than ten-fold at a sea-
sonal scale. Both variables are generally correlated, suggest-
ing that most viruses are bacteriophages. In our seasonal
studies, we found a closer linear relationship between viruses
and bacteria in the oligotrophic Lake Pavin (R^2 = 0.59) com-
pared with the eutrophic Lake Aydat (R^2 = 0.13) (Fig. 14.6B ),
indicating a stronger interdependence between these two
communities in less productive lakes (Bettarel et al. 2003b ).
We expected a stronger coupling of bacterial and viral abun-
dances at high bacterial density in productive ecosystems ,
given the fact that virus-mediated mortality of cells generally
increases with increasing bacterial host density. However,
we found an opposite situation which we explain by: (i) an
increasing output of dissolved organic matter (DOM) from
viral lysis in the more oligotrophic system where DOM from
phytoplankton exudates may be a limiting factor for bacterial
production, or (ii) an increasing relative abundance of non-
bacteriophage viruses, such as cyanophages , in productive
lakes where planktonic communities are often dominated by
cyanobacteria.Fig. 14.5 Composition and taxonomic affi liations of Lake Pavin virome
reads as determined by similarity to known sequences. ( a ) The percent
of “known” virome sequences when compared to the non redundant
(NR) protein database. ( b ) Breakdown of the “known” sequences into
Viruses, Bacteria, Archaea, or Eukarya using similarity results against
NR. Hatched parts were reads having a best BLAST hit against a non-
viral sequence, but still presenting signifi cant similarities against a com-
plete virus genome sequence and thus designated as reads “similar to at
least one viral sequence”. ( c ) Taxonomic composition at the viral family
level of these reads “similar to at least one viral sequence”. The “Other”
category pools families which represented less than 1 % of the full
virome sequences. For more details see Roux et al. ( 2012 )14 Ecology of Viruses in Lake Pavin