251the epilimnion and the oxycline of the Lake Pavin were low
suggesting that lacustrine oxic water layers are not an obliga-
tory hotspot for archaeal ammonia oxidation and that MGI
could use another metabolic pathway as an energy source.
Indeed, it has been proposed that these microorganisms
present a large metabolic plasticity, from autotrophy to
potential mixotrophic lifestyles (Ingalls et al. 2006 ).
Nevertheless, further works are necessary to better under-
stand the role of Thaumarchaeota in ammonia oxidation or
other metabolic pathways.
15.4 Metagenomics and Meta-Analysis
for Deciphering the Viral Diversity
15.4.1 Viral Richness and Composition
For studying the diversity of viruses in lakes, two viromes
from freshwater temperate lakes were generated from sam-
ples collected in the epilimnion (at 5 m depth) of lacustrine
ecosystems (lakes Pavin and Bourget, Roux et al. 2012a ).
The genetic diversity and composition of these datasets were
assessed and compared to those of published viromes from
different ecosystems. Subsequently, two families of single
stranded DNA (ssDNA) viruses retrieved in the virome of
Lake Pavin were further analyzed : the Microviridae (Roux
et al. 2012b ) and chimeric viruses (Roux et al. 2013 ).
Species richness (number of different virotypes), gene
richness (number of different genes) and the viral gene com-
position were cross-compared between a large set of viromes
(>30) including viromes of Lakes (Roux et al. 2012a ).
Whereas the species richness remains identical through the
different ecosystems, the gene richness varies greatly
between the different environments. Among aquatic data sets,
genetic richness of marine viromes was higher in average
than that of freshwater ones. However, Lake Bourget and
Lake Pavin viromes harbor very different genetic richness, as
the one from Lake Bourget is comparable to marine viromes
and the one from Lake Pavin is much lower (Roux et al.
2012a ). These observations are tentatively explained by the
general relation between trophic status and microbial rich-
ness (Horner-Devine et al. 2003 ) that impacted the viral rich-
ness through the number of hosts.
Despite these differences in terms of genetic richness, the
comparison of the 31 viromes reveals potential genetic links
between viral communities according to the ecosystem
investigated (Roux et al. 2012a ). This analysis was here per-
formed using recently published viromes (Hurwitz and
Sullivan 2013 ; Fancello et al. 2013 ) and the resulting hierar-
chical clustering tree highlights a clear distinction between
seawater and freshwater viral-communities (Fig. 15.3a ).
In addition to these differences between datasets, the two
lacustrine viromes made it possible to assess the composi-
tion and diversity of temperate freshwater viral communities
(Roux et al. 2012a ). Firstly, the Lake Pavin dataset has a very
small “known” viral-gene fraction (<15 %) illustrating that
viruses in this ecosystem are a huge source of so-far unchar-
acterized genetic diversity. Secondly, considering sequences
that match known viruses and in accordance with electronic
microscope observations, Caudovirales ( Myo -, Sipho - and
Podoviridae ) were retrieved in Lake Pavin virome (Fig.
15.3b ). Furthermore, a high proportion of ssDNA viruses
( Micro -, Circo - and Nanoviridae ) virus was recorded. These
different families of ssDNA viruses gained more of our
attention because they might play an important role in a
broad spectrum of environments as they were found in great
number among the viral fraction from freshwater to human
gut samples (Roux et al. 2012b ).15.4.2 The Pichovirinae, a New Group
Among the Microviridae FamilyMicroviridae are small icosahedral viruses with circular
ssDNA genomes that infect bacteria. Based on structural and
genomic differences, members of this family were divided
into three subgroups: Microvirinae , Gokushovirinae and
Alpavirinae (Krupovic and Forterre 2011 ). Out of the 81
complete Microviridae genomes assembled from viromes
originating from various ecosystems (Roux et al. 2012b ),
three were generated out of the Lake Pavin virome (Fig.
15.3c top). The phylogenetic analysis of the major capsid
protein revealed that one of these three new genomes was
affi liated to the Gokushovirinae. Among this diverse and
cosmopolitan subfamily (Hopkins et al. 2014 ), the genome
from the Lake Pavin was grouped with other freshwater
Microviridae , demonstrating that these viruses are specifi c to
this environment. The phylogeny of the other two complete
Microviridae genomes from the Lake Pavin virome led to the
description of a new group, the Pichovirinae. Furthermore,
all genomes of this new group have an organization of the
three core genes different from the rest of the Microviridae.
Thus, this group that encompasses viruses from various eco-
systems (coral, microbialites, marine and freshwater sys-
tems) has probably diverged from the common Microviridae
ancestor a long time ago (Roux et al. 2012b ). Therefore, the
description of these new genomes expands the existing
knowledge on genome evolution, diversity and environmen-
tal distribution of this viral family.15.4.3 Chimeric Viruses: Implication
for Viral Evolution?Small ssDNA viruses encoding replication proteins (Reps)
related to known eukaryotic viruses have been repeatedly15 Omic Approaches for Studying Microorganisms and Viruses