252isolated from diverse environments, including marine
(Dunlap et al. 2013 ) and freshwater systems (López-Bueno
et al. 2009 ). Recently, one such Rep-encoding genome,
recovered in an extreme environment, was suggested to be a
recombination between unrelated groups of ssRNA and
ssDNA viruses (Diemer and Stedman 2012 ). The validity of
the assembled viral genome and its presence in the lake sedi-
ment pore water were confi rmed by PCR amplifi cation
(Diemer and Stedman 2012 ). Since this study, 13 chimeric
viral genome (CHIV) were assembled from 103 published
viromes (Roux et al. 2013 ) and were grouped according to
the type of Rep they encode : Circo- , Gemini- or Nano-
viridae like Rep groups. As many as 3 of these 13 CHIV
genomes were assembled from the Lake pavin virome (Fig.
15.3c , bottom). These 3 genomes were each affi liated to a
different group, highlighting the diversity of these viruses in
the Lake Pavin. Analysis of these new genomes indicate asingle event of capsid protein gene capture from an RNA
virus in the history of this virus group. Such hints on the
evolution of this viral family raise some exciting horizons in
our understanding of the connections between viruses in the
biosphere.15.5 Summary
Molecular based analyses of microbial communities through
metagenomics are a proxy to investigate the metabolic poten-
tial and evolutionary trajectory of organisms that are still to
be cultured. Here, we have illustrated advances that have
been made using these approaches on three compartments of
freshwater aquatic microorganisms that are of peculiar inter-
est as they correspond to either dominant, rare or unexplored
living bodies.Fig. 15.3 ( a ) Virome hierarchical clustering tree based on sequence
similarity. This tree was computed from tBLASTx comparisons of
virome subsamples. Marines and freshwater viromes are colored
respectively in blue and green. ( b ) Taxonomic composition of the Lake
Pavin virome at the viral family level, determined by similarity to com-
plete virus genomes of the RefseqVirus database (tBLASTx using
thresholds of 10 −3 on e-value and 50 on bit score). The “Other” category
pools families which represented less than 1 % of the full virome
sequences. ( c ) Genomic maps of the three Microviridae and chimeric
viruses assembled out the Lake Pavin virome. Conserved genes are col-
ored for each of these two families, the colour key being provided in the
fi gureG. Bronner et al.