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importance, and functional roles of planktonic chytrids. We primarily focus on parasitic
chytrids of phytoplankton, the potential ecological implications for food web dynamics, as
well as the methodological challenges related to their study. We conclude that phytoplank-
ton chytridiomycosis is an important but still overlooked ecological driving force in aquatic
food web dynamics.
Keywords
Lake Pavin • Zoosporic fungi • Chytrids • Microbial parasites • Phytoplankton hosts • Food
webs • Microbial ecology • Aquatic ecosystems20.1 Introduction
Since the emergence of the ‘ microbial loop ’ concept, het-
erotrophic nanofl agellates (HNF) have received particular
attention as grazers in aquatic ecosystems (Amblard et al.
1998 ). These protists have historically been wrongly regarded
as a homogeneous group of bacterivorous protists , most of
which (>90 % of the total abundance) includes motile, non-
photosynthetic and pigmented microbes with a diameter of
approximately 5 μm (Strom 2000 ). However, in terms of
trophic modes, HNF were considered a black box until the
early 2000s. The introduction of molecular methods to the
study of prokaryotes in the mid-1980s (Pace et al. 1986 ), and
their application to small eukaryotes in the early 2000s
(Lopez-Garcia et al. 2001 ; Moon-van der Staay et al. 2001 ),
allowed the detection of uncultured microbes in diverse natu-
ral environments and greatly improved our knowledge on
microbial diversity and putative functions. More recently,
progresses made in sequencing technologies and the rapid
development of high throughput sequencing platforms
have revealed an even more impressive taxonomic, genetic
and functional diversity hidden in natural aquatic ecosystems
(Sogin et al. 2006 ; Huse et al. 2008 ). The resulting method-
ological, conceptual and empirical progresses made in
aquatic microbial ecology are arguably the greatest advances
in environmental sciences.
The fi rst molecular surveys of small eukaryotes, mostly
conducted in marine environments and based on the cloning
and sequencing of 18S rDNA , revealed an unexpected high
diversity of eukaryotic microbes in the plankton (Moreira
and Lopez-Garcia 2002 ). In freshwater environments, simi-
lar surveys, including the ones we conducted in Lake Pavin
and other lakes in the vicinity, also revealed a high diversity
of novel small eukaryotes (Lefranc et al. 2005 ; Lefèvre
et al. 2007 ) and provided new insights in the understanding
of microbial food web functioning. Our most remarkable
results are that: (i) the dominant phyla in these studies dif-
fered signifi cantly from those found using traditional
microscopy, (ii) the majority of the retrieved phylotypes
affi liated generally to well-established eukaryotic clades,
but represented a diverse and novel diversity within these
clades and (iii) a substantial part of the retrieved sequences
more than likely belonged to parasitic and saprophytic
organisms, such as zoosporic true fungi (chytrids), other
fungi , fungus-like organisms ( stramenopiles) , and parasitic
alveolates ( Perkinsozoa and Amoebophrya spp.). All these
microorganisms are known to produce small fl agellated
zoospores during the dispersive phase of their life cycle.
Owing to their small size and the lack of distinct morpho-
logical features, we hypothesized that zoosporic species had
probably often been misidentifi ed as bacterivorous protists
in previous studies (Lefèvre et al. 2007 , 2008 ). Indeed,
many zoospores are approximately 5 μm in diameter and the
thallus of zoosporic fungi (i.e., sporangia) is hardly distin-
guishable from the lorica of sessile fl agellates such as cho-
anofl agellates and bicosoecids (Rasconi et al. 2009 ). These
observations provided evidence that HNF thriving in pelagic
systems are not restricted to protists or bacterivores , and
suggest that parasitism and saprophytism represent impor-
tant functions in freshwater ecosystems (Sime-Ngando et al.
2011 ).
Both 18S rDNA environmental cloning surveys (Lefèvre
et al. 2007 , 2008 ; Jobard et al. 2012 ) and the use of SSU
rRNA hypervariable tag sequencing (Monchy et al. 2011 ) for
the study of microbial eukaryotes unveiled major infectious
agents in Lake Pavin, which consisted primarily of zoosporic
fungal order of Chytridiales (chytrids). Chytrids are external
eucarpic parasites that infect diverse eukaryotic and prokary-
otic species, primarily diatoms and fi lamentous phytoplank-
ton (Rasconi et al. 2011 ; Sime-Ngando 2012 ). They produce
specialized rhizoidal systems through host cells, i.e. the
nutrient conveying system for the formation of fruit bodies
(sporangia) from which propagules (motile unifl agellated
zoospores ) are released into the environment. These fi ndings
have stimulated our efforts to study microbial parasites of
phytoplankton, and we primarily directed our focus towards
their community structure, and their quantitative importance
and functional roles in the pelagic system. This also included
methodological developments, which have been crucial for
the study of these inconspicuous eukaryotic parasites. In this
chapter, we primarily focus on parasitic chytrids of phyto-
plankton, discussing the potential ecological implications forT. Sime-Ngando et al.