331food web dynamics, as well as the methodological chal-
lenges we had to face for their study. We conclude that phy-
toplankton chytridiomycosis represents an important but still
overlooked ecological driving force in aquatic food web
dynamics.
20.2 Molecular Diversity Studies of Small
Eukaryotes in Lake Pavin Revealed
a High Occurrence of Putative
Parasitoids in the Plankton
Our molecular surveys of small eukaryotes in Lake Pavin
were stimulated by the fact that most studies that used tradi-
tional microscopy to characterize HNF community composi-
tion cluster HNF smaller than 5 μm together as ‘unidentifi ed
HNF’ (Carrias et al. 1996 ). In addition, grazing experiments
showed that the bulk of the ‘unidentifi ed HNF’, which were
considered as main bacterivores in aquatic systems until
early in this century (Strom 2000 ), were unable to ingest
bacterial-size particles (Fig. 20.1 ). Our surveys were also
motivated by a comparative study conducted by Gasol and
Vaqué ( 1993 ) demonstrating a lack of trophodynamic cou-
pling between HNF and their presumed bacterial preys in a
range of marine and freshwater habitats. Major hypotheses
proposed to explain this lack of correlation were that HNF (i)
were not the only organisms that feed on bacteria, (ii) they
could also ingest viruses (see Chap. 14 ) and colloidal organic
matter (Sherr 1988 ), and (iii) were not a phylogenetically
coherent group since they included organisms from many
branches of the eukaryotic tree of life (Patterson 1993 ). From
the above observations, we hypothesized that the so-called
‘unidentifi ed HNF’ group could be hiding an unexplored
diversity and as yet unknown trophic modes. Therefore, in
order to characterize the diversity of these small unidentifi ed
HNF, pelagic samples from Lake Pavin were repeatedly col-
lected during autumn 2004 and spring/summer 2005, and the
eukaryotic community within the size range of 0.6 and 5 μm
characterized using the cloning and sequencing of their 18S
rDNA (Lefèvre et al. 2007 , 2008 ).
Unexpectedly, most of the retrieved sequences affi liated
to 8 major eukaryotic phyla, among which three taxonomic
groups represented 66 % of the detected diversity: Alveolates
(33 %), Fungi (19 %), and Stramenopiles (14 %) (Lefèvre
et al. 2007 , 2008 ). Each of the fi ve other groups (i.e.,
Cryptomonads, Chlorophyceae, Cercozoa, Telonemia, and
Choanozoa) represented less than 10 % of the total diversity
(i.e. non redundant OTU s or Operational Taxonomic
Units ), and affi liated to HNF taxa previously detected using
more traditional microscopic methods. Among Alveolates,
75 % of our sequences belonged to lineages known to con-
tain members of small colorless fl agellates with two unequal
fl agella during the motile stage of their life cycle (i.e.,
Perkinsea and Dinophyceae ). Among the Fungi kingdom,
75 % of the sequences were related to the parasitic or sapro-
trophic Chytridiomycota phylum, which contains organisms
that produce small unifl agellated cells ( zoospores ) during
their life cycle. Among Stramenopiles, 75 % of our sequences
were affi liated to the small heterotrophic bifl agellated
Bicosoecids and unifl agellated Hyphochytrids. Overall,
between 50 and 70 % of the sequences retrieved in Lake
Pavin fell into ecologically important taxonomic groups
known to contain small heterotrophic fl agellated forms:
Alveolates , Fungi, Stramenopiles , Cercozoa and Telonemia.
Unlike with previous studies conducted in other aquatic
environment, our sequences affi liated to known lineages
(Lefèvre et al. 2007 , 2008 ). However, 83 % of our sequences
were not highly similar to any previously published
sequences, and included 23 sequences that belonged to novel
clades (i.e. currently containing no cultured representatives),
suggesting that eukaryotic microbial diversity was still
poorly described in freshwater environments.Fig. 20.1 Typical micrographs
of heterotrophic nanofl agellates
(HNF) observed under UV light
for the whole phenotypic
visualisation ( A , forms and
fl agella) and under blue light
for visualization of ingested
bacterial particles within
vacuoles ( B , the yellow spots in
two large cells). White arrows
show that the smallest
undetermined forms cannot
ingest bacteria
20 Chytrid Parasites of Phytoplankton in Lake Pavin