317microbial diversity and spatial distribution. One of the fi rst
model lake used to study picoeukaryotes was the lake Pavin
(Carrias et al. 1996 ). The lake Pavin is a typical crater moun-
tain lake with a maximum depth of 92 m. It is characterized
by the presence of two permanent stratifi ed layers. The upper
layer (mixolimnion) and the deepest layer (monimolimnion),
which is characterized by anoxic conditions (for more
description of the lake, see Chap. 1 ). Picoeukaryotes are pres-
ent throughout the water column (including the anoxic zone).
19.2.1 Black Box of Non-pigmented
Picoeukaryotes: Unexpected
Importance of Parasites
Since the emergence of the ‘microbial loop’ concept (Azam
et al. 1983 ; Amblard et al. 1995 ) heterotrophic fl agellates have
received particular attention as grazers in aquatic ecosystems
(Boenigk and Arndt 2002 ). These microorganisms have his-
torically been considered incorrectly as a homogeneous group
of bacterivorous protists (e.g Carrias et al. 1996 ; Massana
et al. 2009 ). More recently, environmental rDNA surveys in
the pelagic zone of lake ecosystems showed that dominant
phyla found by molecular studies differed from morphological
studies and a substantial part of the sequences cannot be
assigned to bacterivorous but to parasitic and saprophytic
organisms, such as zoosporic true fungi (chytrids) and alveo-
late parasites (Perkinsozoa) (Lepere et al. 2008 ; Lefèvre et al.
2008 ). These fi ndings changed our view of the trophic web
and highlight the potential importance of the parasitism usu-
ally left out of aquatic trophic network functioning.
In freshwater lakes, fungi were discovered a long time
ago (Canter and Lund, 1948 ), and culture collections have
been steadily supplemented by freshwater fungi in the last 50
years however not with many chytrids. The advent of molec-
ular methods highlighted a high diversity of fungal sequences
in lakes and most of them were affi liated to chytrids (Lefranc
et al. 2005 ; Lefèvre et al. 2008 ; Lepère et al. 2008 ; Monchy
et al. 2011 ). These fungi are inferred based on phylogenetic
position as zoosporic organisms. These fungi were obviously
overlooked in previous conventional microscopic studies
because of their small size and the lack of conspicuous ultra-
structural features (Lefèvre et al. 2008 ; Lepere et al. 2008 ).
Jobard et al. ( 2010 ) showed by using FISH method that these
fungi contributed up to 60 % of the total abundance of het-
erotrophic fl agellates in lake Pavin. Multiple roles for zoo-
sporic fungi in lake ecosystems have been suggested,
including parasitism, especially with chytrids, which can
parasite a wide range of phytoplanktonic hosts (For more
details on Fungi role, please see the Chap. 20 ). Fungi 18S
rDNA sequences were identifi ed in lakes with a large range
of trophic level (from oligotrophic to eutrophic lakes). In
lake Pavin and in other lakes, Fungi OTUs (Operational
Taxonomic Units) were for the majority affi liated by phylo-
genetic analyses with the lineage of chytrids, although
Basidiomycota and Ascomycota were also found. On aver-
age 25 % of the picoeukaryotes sequences (all sequences
including pigmented and non pigmented picoeukaryotes) inFig. 19.2 Model of
carbon fl ows between
primary producers,
grazers zooplankton,
and microorganisms in
lacustrine pelagic
ecosystems.
HF:heterotrophic
fl agellates; DOM:
dissolve organic matter19 Diversity and Biogeography of Lacustrine Picoeukaryotes