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Protist Diversity and Geographical Distribution 25
“Missing” protists: a molecular prospective
Slava Epstein · PuriWcación López-García 
Originally published in the journal Biodiversity and Conservation, Volume 17, No 2, 261–276.
DOI: 10.1007/s10531-007-9250-y © Springer Science+Business Media B.V. 2007
Abstract Molecular ecology methods based on 18S rRNA ampliWcation and sequencing
have revealed an astounding diversity of microbial eukaryotes in every environment sam-
pled so far. This is certainly true of new species and genera, as essentially every new survey
discovers a wealth of novel diversity at this level. This is almost certain for taxa that are
higher in taxonomic hierarchy, as many molecular surveys reported novel clades within
established protistan phyla, with some of these clades repeatedly conWrmed by subsequent
studies. It may also be that the molecular approaches discovered several lineages of the
highest taxonomic order, but this claim has not been vigorously veriWed as yet. Overall, the
Weld of protistan diversity remains in its infancy. The true scale of this diversity is
unknown, and so are the distribution of this diversity, its patterns, spatial and temporal
dynamics, and ecological role. The sampled diversity appears to be just the tip of the ice-
berg, and this oVers outstanding opportunities for microbial discovery for the purposes of
both basic and applied research.
Keywords 18S rRNA · Cryptic species · Eukaryotic phylogeny · Molecular ecology · 
Species richness
Introduction
Molecular analyses based on the rRNA approach have become an aVordable and practical
tool that is used routinely to study microbial diversity in environmental samples. This type
Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.
S. Epstein
Marine Science Center, Northeastern University, Nahant, MA 01908, USA
e-mail: slava.epstein@gmail.com
P. López-García (&)
Unité d’Ecologie, Systématique et Evolution, CNRS UMR8079, Université Paris-Sud,
Orsay Cedex 91405, France
e-mail: puri.lopez@u-psud.fr
W. Foissner et al. (eds.), Protist Diversity and Geographical Distribution
DOI: 10.1007/978-90-481-2801-3_3 27
28 W. Foissner et al. (eds)
of analyses was designed to bypass inability to cultivate the majority of prokaryotic organ-
isms in vitro, and provided an excellent tool to classify the organisms by placing the
sequences of this marker gene in a phylogenetic tree of life (Olsen et al. 1986; Woese
1987). Results accumulated over the past two decades are impressive. They are more than
“just” 300,000 SSU rDNA prokaryotic sequences now available from GenBank,—they
have changed our view of the biosphere (Pace 1997).
Compared to prokaryotes, the application of the SSU rRNA gene-based approach to study
protistan diversity is very recent (Díez et al. 2001; López-García et al. 2001; Moon-van der
Staay et al. 2001; Moreira and López-García 2002). However, even the limited information
obtained so far shows certain similarities as well as dissimilarities with what is known about
prokaryotic molecular diversity. Contrary to prokaryotic microbiologists, some protozoologists
maintain that the principal protistan taxa have been identiWed during the era of �-taxonomy,
and they question the very possibility of discovering novel high ranking candidate protistan
taxa (e.g. Finlay 2002; Cavalier-Smith 2004). This is not necessarily so for novel subgroups, at
perhaps the class level down to species, where the newly discovered diversity appears impres-
sive (Moreira and López-García 2002; Berney et al. 2004; Richards and Bass 2005). Further-
more, although still quite unstudied, the genetic diversity within protist morphospecies might
be surprisingly high as revealed by SSU rRNA gene sequences (Boenigk et al. 2005), the com-
bination of these with intergenic spacer sequences (ITS) (Katz et al. 2005; Rodriguez et al.
2005), and multilocus sequence analysis (Katz et al. 2006; Slapeta et al. 2006a, b). These Wnd-
ings call into question the validity of the phenotype only-based species concept, and open new
avenues to explore protist biogeography (Foissner 2006), ecological specialization, and mech-
anisms underlying protist speciation. In the present review, we brieXy summarize recent data
on the molecular diversity of microbial eukaryotes.
The molecularly identiWed but undescribed diversity

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