321microorganisms are likely on their way to local extinction or
are transient taxa in an environment; others may be active at
low abundance, providing important functions in the sys-
tems; others may be dormant or inactive, awaiting favorable
environmental conditions to grow (Shade et al 2014 ). These
rare inactive microbial eukaryotes (ie. dormant taxa) have
indeed been observed to become dominant with changing
environmental conditions according to the model of Jones
and Lennon ( 2010 ). Therefore, this study shows that the vari-
ation of total phosphorus had no effect on the proportion of
dormant microbial eukaryotes that were detected by T-RFLP
in lakes, and the transition between activity and dormancy
plays a more important role in shaping bacterial communi-
ties than eukaryotic communities. The contrast between both
domains could be due to the ability to form resting stages or
to the differential sinking rates. The switch between active
and dormant stages could be insignifi cant for protists, and
this fact could have an effect on the activity of rare eukaryote
taxa that have not been studied with the exception of a recent
work in marine environments (Logares et al. 2014 ).
Picoeukaryotes were characterized by numerous new lin-
eages as underlined in the previous section and a biogeogra-
phy of the rarest taxa discussed thereafter. Thus, the richness
would be higher than expected and additional lineages could
be likely found when described from supplemental molecu-
lar inventories.
To display a general view of the picoeukaryote rare bio-
sphere in lakes, the pyrosequencing data obtained from tem-
poral dynamics (1-year period) of the lake Pavin were
analysed with those from the lake Bourget (lake located in
Alps 45°44’N; 5°51’E). After discarding the singletons and
OTUs included only rRNA reads, 6446 OTUs were defi ned
representing 229723 reads (rRNA and rDNA). The taxo-
nomic annotation was conducted according two ways: the
nearest neighbour and the last common ancestror (methods.
The closest OTUs defi ned monophyletic groups also named
phylogenetic units. These OTUs delineated 686 monophy-
letic groups in term of OTUs number, the main taxonomic
groups were the Alveolta (1923 OTUs), Fungi (1564),
Stramenopiles (1165) and Viridiplantae (776). The rDNA1(^1763515267018761051122614011576175119262101227624512626280129763151332635013676385140264201437645514726490150765251542656015776595161266301)
0
0.5
1
1.5
2
2.5
3
OTUs
Relative proportion of rDNA reads (%)
0
0.5
1
1.5
2
2.5
3
A
B
C
Alveolata
Others
Stramenopiles
Viridiplantae
Rhizaria
Haptophyceae
Fungi
Cryptophyta
Choanoflagellida
Amoeboza
Fig. 19.3 Rank-abundance curves based on the rDNA reads (A and B)
and main active and inactive taxa (C) from the two lakes studied. The
panel B displays the OTU taxonomy for the dominant ones (>1 %). In
the panel C, the outside of the circle corresponds to the active OTUs
(OTUs with rRNA reads) and inside the inactive OTUs (including only
rDNA reads). The data were obtained from pyrosequencing of 18S
rDNA and rRNAamplicons. Primers used amplifi cation conditions and-
bioinformatic tool were described in detail in Taib et al. ( 2013 )
19 Diversity and Biogeography of Lacustrine Picoeukaryotes
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