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T. Sime-Ngando et al. (eds.), Lake Pavin, DOI 10.1007/978-3-319-39961-4_19
Diversity and Biogeography
of Picoeukaryotes: New Insights into
the Rare BiosphereCécile Lepère , Isabelle Domaizon , and Didier Debroas
Abstract
Picoeukaryotes (unicellular eukaryotes smaller than 5 μm) are recognized as important
members of microbial assemblages in aquatic ecosystems in terms of both biomass and
activity. During the past decade, molecular techniques have begun to provide insights into
the structure of picoeukaryote communities in various lacustrine environments. In particu-
lar, cloning and sequencing of nuclear small subunit rRNA genes have revealed a very high
diversity within this assemblage and the presence of many novel eukaryotes. Understanding
the spatial distribution of aquatic microbial diversity and the underlying mechanisms that
underpin differences in community composition is a challenging and central goal for ecolo-
gists. Recent insights into picoeukaryotes diversity and ecology are increasing the debate on
their spatial distribution. The application of novel high-throughput sequencing technologies
have provided new data and new perspectives on this debate, allowing improved sampling
of phylotype diversity and demonstrating a community structure composed of a complex
rare biosphere. Understanding the activities of the rare biosphere may (or may not) be the
key to deriving predictive models of picoeukaryotes community structure and function.Keywords
Picoeukaryotes • Lakes • Diversity • Biogeography • Rare biosphere • 18S rRNA •
Metagenetics • Pyrosequencing19.1 Introduction
Planktonic microorganisms are categorized into classes
based on their size for operational purposes. Initially, only
prokaryotes were included in the smallest class (picoplank-
ton: cells 0.2 to 5 μm) and microbial eukaryotes were
included in the nanoplankton (5 to 20 μm) or microplankton
(20 to 200 μm). This changed radically with the advent of
molecular tools, particularly culture-independent sampling
of ribosomal RNA encoding gene sequences. The fi rst stud-
ies on the in situ diversity of picoeukaryotes by cloning and
sequencing environmental 18S rRNA genes were published
in 2001 and were focused on marine ecosystems (Lopez-
garcia et al. 2001 ; Moon-van der Staay et al. 2001 ). These
studies showed that aquatic picoeukaryotes include a large
phylogenetic diversity and many novel lineages. In fact,
environmental picoeukaryote SSU rDNA sequences sampled
from freshwater lakes are distributed throughout the eukary-
otic tree (Fig. 19.1 ).
Picoeukaryotes have a typical eukaryotic cell structure in
a miniaturized cell. The smallest known eukaryote,
Ostreococcus tauri , has a diameter of 0.8 μm. This includesC. Lepère (*)
LMGE, Laboratoire Microorganismes: Génome et Environnement,
6023 , Université Clermont-Auvergne, Université Blaise Pascal , BP
80026 , 63177 Aubière Cedex , France
CNRS , UMR 6023, LMGE , F-63171 Aubière , France
e-mail: [email protected]
I. Domaizon
INRA , UMR 42 CARRTEL , F-74200 Thonon les Bains , France
D. Debroas
LMGE, Laboratoire Microorganismes: Génome et Environnement,
6023 , Université Clermont-Auvergne, Université Blaise Pascal , BP
80026 , 63177 Aubière Cedex , France