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the presence of a nucleus, an endomembrane system (endo-
plasmic reticulum, Golgi, and vesicles), mitochondria, and
in the case of photosynthetic picoeukaryotes, a chloroplast.
Due to this small size, picoeukaryotes are largely
indistinguishable by light microscopy and their study was
restricted to the use of electronic microscopy until the revo-
lution of molecular techniques. Consequently, very few
picoeukaryotes have been characterized. The picoeukaryote
assemblage is formed by picoalgae, which participate in pri-
mary production (Stockner and Antia 1986 ), by colorless
heterotrophic cells, mostly fl agellates, which are considered
to be important grazers of prokaryotic and eukaryotic cells
(Caron et al. 1999 ) and also play a signifi cant role in the min-
eralization of organic matter, and fi nally by some eukaryotes
which can be mixotrophs (Hartman et al. 2013 ) and parasites
(Guillou et al. 2008 ; Lepère et al. 2008 ) (Fig. 19.2 ).
Among picoplankton the relative abundance of eukary-
otic cells fl uctuates according to the systems (open ocean,
coastal, lakes), the trophic states, and the spatio-temporal
dynamics of these communities. Epifl uorescence micros-
copy as well as fl ow cytometry allowed the determination of
the abundance and the distribution of picoeukaryotes from a
wide range of regions (Andersen et al. 1996 ). The densities
of picoeukaryotes reach typically 10^2 to 10^4 cells. ml −1 in the
euphotic zone of lakes and oceans (Caron et al. 1999 ). In
lacustrine environments, picoeukaryotes abundances deter-
mined by TSA-FISH (Tyramide Signal Amplifi cation-
Fluorescent in situ hybridisation) varied on average from
5285 cells ml −1 (1414–9428 cells ml −1 in the oligomesotro-
phic lake Pavin) to 31593 cells ml −1 (16452–42832 cellsml −1
in the eutrophic lake Aydat) (Lepère et al. 2010 ). When the
lake is stratifi ed (summer period) a clear gradient of densities
is generally observed from the top to the bottom of the water
column (Lepère et al. 2010 ; Comte et al. 2006 ).19.2 Lacustrine Picoeukaryotes Diversity
A main goal in microbial ecology is to assess how individu-
als are organized in taxonomic units and how they contribute
to ecological processes. Picoeukaryotes are integral mem-
bers of aquatic ecosystems in terms of cell abundance, activ-
ity, and diversity and therefore play crucial roles in trophic
food webs and biogeochemical cycles (Fig. 19.2 ). Diversity
and physiology of microorganisms in lakes, especially
picoeukaryotes, are poorly studied compared with other eco-
systems, such as the marine environment.
Lakes provide unique sentinels and integrators of events in
their catchments and airsheds and in the total landscapes in
which they are embedded (Schindler 2009 ). Furthermore,
these ecosystems, which can be viewed as interconnected
islands, are de facto excellent models of choice to studyFig. 19.1 Phylogenetic breadth among microbial eukaryotes adapted from Baldauf ( 2008 ). Groups where environmental picoeukaryote SSU
rDNA sequences sampled from freshwater lakes have been found are highlighted by a star
C. Lepère et al.