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lakes are affi liated to fungi. This percentage is around 20 %
for the lake Pavin whatever the methods used (Sanger
sequencing (Lefèvre et al. 2008 ) and pyrosequencing
(Monchy et al. 2011 ). In this lake, statistic analysis showed
the distribution of fungi to be related to depth (Lepère et al.
2010 ). In lake Pavin, chytrids infected diverse phytoplankton
host communities, primarily diatoms, chlorophytes, and
colonial and fi lamentous cyanobacteria (Rasconi et al. 2009 ).
The data on the prevalence and intensity of chytrid infection
show that the prevalence increased with increasing trophic
status and ranged from <1 to 16 % in lake Pavin (oligomeso-
trophic) and from 1 to 24 % in lake Aydat (eutrophic).
Cryptomycota (Jones et al. 2011 ) were detected in several
lakes, with an average of 195 cells ml −1 (3.3 % of total
picoeukaryotes (i.e eukaryotic cell <5 μm)) (Lepère et al.
2010 ). Globally, the highest abundance along vertical pro-
fi les was found in the meta- or hypolimnion, even though
they were not specifi cally found in the anoxic zone as sug-
gested by Lara et al. ( 2010 ). In lake Bourget, they could rep-
resent up to 51 % of the small heterotrophs targeted in the
deeper zone of the column water (110 m) (Lepère et al.
2010 ). Members of the new phylum Cryptomycota were pro-
posed to represent intermediate fungal forms, lacking a chi-
tinous cell wall during feeding and known almost exclusively
from ubiquitous environmental ribosomal RNA sequences
that cluster at the base of the fungal tree (Jones et al. 2011 ;
Lara et al. 2010 ). By using a culture of the only described
genus assigned to Cryptomycota, Rozella, James et al.
( 2014 ) sequenced the fi rst Cryptomycotan genome (the
endoparasite Rozella allomycis) and unite the Cryptomycota
with another group of endoparasites, the microsporidia,
based on phylogenomics and shared genomic traits. Tyramide
signal amplifi cation coupled with group-specifi c fl uores-
cence in situ hybridization reveals that they are picoeukary-
otes of 3–5 μm in length, capable of forming a
microtubule-based fl agellum. Co-staining with cell wall
markers demonstrates that representatives from this clade do
not produce a chitin-rich cell wall during any of the life cycle
stages observed and therefore do not conform to the standard
fungal body plan (Jones et al. 2011 ).Although their func-
tional role is still unknown, these organisms seem to be asso-
ciated with the decomposition of phytoplanktonic organisms
(microalgae and cyanobacteria), and could therefore contrib-
ute to the decomposition of organic compounds in oligotro-
phic and oligo-mesotrophic systems (Van Hannen et al.
1999 ). Recently, Lara et al. ( 2010 ) reported that the
Cryptomycota encompassing Rozella form the deepest
branching clade in the fungi and highlighted the hypothesis
that the two groups might be composed to a large extent (if
not entirely) of parasites. Only one study (Jones et al. 2011 )
showed Cryptomycota associated with diatoms
(Phytoplankton). Even if it would be premature to draw any
conclusion on the lifestyle and ecology of these organisms
on the basis of only environmental sequences, a number of
open questions arose about Cryptomycota ecological role
and phylogenetic position.
Among putative parasitic groups, the Perkinsozoa (for a
review see Mangot et al. 2011 ), already known to play a sig-
nifi cant role as parasite in marine systems (Moore et al.
2008 ; Norén et al. 1999 ) is of special interest, since it has
only recently been detected in lakes by constructing 18S
clone libraries (Lefranc et al. 2005 ; Lepère et al. 2008 ).
Using Sanger technique, sequences affi liated to the
Perkinsozoa can account for up to 15.2 % of the OTUs. In
lake Pavin the greatest abundance was found by TSA-FISH
in the epilimnion with an average of 178 cells ml −1. In marine
systems, this group is known for parasiting molluscs or phy-
toplanktonic species, but their functional importance in
freshwater environments is still largely unknown. Only one
study showed an infection of a cryptophyte by a Perkinsozoa
( Rastrimonas subtilis ) in a river environment (Brugerolle
2002 , 2003 ). This group of putative parasites detected in
pelagic environment is characterized by a zoospore stage
(Mangot et al. 2011 ). Recent studies show the quantitative
importance of these zoospores in euphotic zones of several
lakes (Lepere et al. 2010 ; Mangot et al. 2013 ) and their activ-
ity inferred by the sequencing of transcripts (RNA) and the
high RNA/DNA ratios associated to Perkinsozoan sequences
(unpublished data). In lakes environment, the phytoplankton
is certainly the most likely host for Perkinsozoans (Mangot
et al. 2013 ), however, despite of certain indications (eg phy-
logenetic position, punctual microscopic observations), the
identifi cation of the host remains incomplete and so their
putative role as pathogens remains unknown.
Another lineage relatively well represented in 18S SSU
rDNA databanks in lakes is the Cercozoa, a group defi ned by
Cavalier-Smith ( 1998 ). Environmental sequences affi liated
to these organisms were found in all studied lakes with rela-
tively important proportions both in the euphotic and deeper
zones (Lefèvre et al. 2007 ). These microorganisms can rep-
resent more than half of characterized OTUs in the epilim-
nion of the lake Pavin in summer (Lepère et al. 2006 ) and
more than a third of the sequences in the Autumnal oxycline
of the same lake (Lefèvre et al. 2007 ). Three different clades
were determined among these Cercozoa, two are strictly
environmental, the third one contain sequences affi liated to
the order of Cercomonadida and more exactly to the genus
Cercomonas and Heteromita (Lepère 2007 ). Broadly bacte-
rivores with thecamebians and the order of Cercomonadida,
Cercozoa can also be parasites of phytoplankton. This is the
case in particular of the genus Cryothecomonas, which are
nanofl agellates , found associated with diatoms (Schnepf and
Kühn 2000 ).
Of course the diversity mentioned in this section is far
from being exhaustive and some other groups are also
retrieved such as Chrysophyceae and ciliates. ChrysophyceaeC. Lepère et al.