323from the composition observed in the others categories.
Interestingly, some active PUs constituted exclusively by
always rare OTUs and highly frequent in time were discrimi-
nated (Fig. 19.4 ). The dynamics of these clades at 2 m depth
were negatively correlated to the Cyanobacteria dynamics
(P < 0.05) and, for the PU named “Unclassifi ed (879)” a
positive correlation (P < 0.05) with ammonium concentration
was detected.
The rarest fraction, and more particularly, the always rare
OTUs, represented a signifi cant part of the active picoeu-
karyotes in lacustrine ecosystems. In comparison, the same
fraction among the Archaea represented only 1.6 % of the
total activity measured by the total rRNA reads (Hugoni
et al. 2013 ). Interestingly, all the taxonomic groups defi ned
from the always rare OTUs were active and the activity,
described by the ratio rRNA:rDNA, increased with the rar-
ity: from 0.74 for the abundant OTUs to 2.2 for the always
rare OTUs. The variation in this ratio, generally a decrease,
is expected for species able to produce endospores, cysts,
conidia, etc. Nevertheless, some microbes can reduce metab-
olism without producing specialised cellular structures. This
ratio increased with the rarity in all taxonomic groups defi ned
and particularly in groups known for the presence of resting
stages, such as Fungi, for example, which are known to dis-
seminate in the form of conidia/spores and could have a low
activity (Jones and Lennon 2010 ). The high ratio measured
shows that rare picoeukaryotes were active and likely able to
grow; this was verifi ed over the whole year in both lakes
(Pavin and Bourget) and for both the epilimnion and hypo-
limnion zones. Therefore, these data confi rm the hypothesis
that, in contrast to bacteria, dormancy does not play an
important role in planktonic eukaryote communities (Jones
and Lennon 2010 ).
In conclusion, the rare picoeukaryotes represents an
active fraction in the lacustrine ecosystems, which is more
important than that described for the bacteria and Archaea.
Indeed, the rare picoeukaryotes do not act only as a seed
bank of dormant cells waiting for condition changes (Debroas
et al. 2015 ). Using methodologies that specifi cally target this
rare biosphere should unveil new lineages with new physio-
logical properties.
19.4 Biogeography of Picoeukaryotes: Not
All Is Everywhere
Probably the most important overriding features of microbes
are their exceptional diversity and ability to occupy every
possible habitat for life. Indeed, what we consider possible is
challenged constantly by the discovery of new microbial
communities in habitats previously thought inhospitable, or
carrying out processes that we had no idea. There is consid-
erable debate about the extent of diversity and biogeographi-
cal distribution of microorganisms. It has been argued that
given the huge population sizes and the potential for distant
dispersal, most microbial species must be cosmopolitan and
the total number of species must be relatively low (Massana
2009 ). However, the existence of biogeographic patterns has
been highlighted in microbial ecology mainly by distance–
decay or taxa–area relationships (TAR) (Green and Bohannan
2006 ).
Spatial distribution of microbial eukaryotes has
received much less attention than bacteria, and the studies
have concentrated mainly on a single taxonomic group.
However, their total diversity and distribution in nature
are currently the focus of active debates (Finlay and
Fenchel 2004 ; Foissner 2006 ; Pinel-Alloul and Ghadouani
2007 ; Caron 2009 ; Nolte et al. 2010 ). As well as for bac-
teria, picoeukaryotes are characterized by a tiny size and
are likely to disperse easily (ex: capacity of survival dur-
ing transport for dormant cells) and could have a cosmo-
politan distribution, leading to the classical dictum
‘everything is everywhere, but the environment selects’
(Baas-Becking 1934 ). However, they constitute complex
assemblages, and one can wonder if the concept of bio-
geographic diversity is applicable to small- sized hetero-
geneous group, which is diverse in terms of physiologies,
life cycles, phylogenetic positions, with the ability to
reproduce sexually and with capacities of dispersal–colo-
nization, which are likely not the same (ie cyst, endo-
spores easily transported in atmosphere/aerosols).
In order to test the different hypotheses, Lepère et al.
( 2013 ) analyzed alpha - (richness) and beta (composition)-
diversity of lacustrine picoeukaryotes distribution patterns in
view of geographic distances, lake areas, and habitat vari-
ables, using two molecular methods including high-
throughput sequencing as well as T-RFLP. According to
Martiny et al. ( 2006 ), one can expect that environmental fac-
tors (physical, chemical, and biological local parameters)
tested have signifi cant effects in shaping microbial composi-
tion at regional scale, whereas distance (dispersal limitation)
should be the main structuring factor across continents. In
Lepère et al. ( 2013 ) study, lacustrine picoeukaryotes compo-
sition and richness were fi rst assessed at a regional scale, six
French lakes were considered including lakes Pavin. All
lakes were characterized by stable summer stratifi cation and
were sampled in the epilimnetic zone in the same way.
Moreover, the results are based on an equal sampling effort
and/or a time series, which allowed to take into account tem-
poral variations in the community to analyze both spatial
distribution and environment effects. The study was sec-
ondly extended to 11 worldwide lakes.19 Diversity and Biogeography of Lacustrine Picoeukaryotes