Abstract : Considering the degradation of the ecosystems together with a modification of the structure of the communities, and sometimes an increased disappearance of some species, the major stakes of this century are to study the biodiversity and the factors interacting with biodiversity, and finally to study the functional role of this Biodiversity. In the framework of this global context, this thesis aimed at studying the composition and diversity of eubacterial and cyanophage communities within the pelagic region of several French great Alpine lakes, which are submitted to different anthropogenic pressures. Three research studies have been
undertaken within three lakes differing in their trophic state: lake Annecy is oligotrophic and may be considered as the reference site, whereas lake Bourget and lake Geneva are mesotrophic. Another difference is given by the regular and strong presence of a toxic and
filamentous cyanobacteria, Planktothrix rubescens, which proliferate in lake Bourget since 1998. From a methodological point of view, we studied the eubacterial and cyanophage composition by means of the DGGE (Denaturing Gradient Gel Electrophoresis), whereas the
cloning-sequencing technique was used to identify the taxonomic groups present and to infer phylogenetic relationships. From the first study, it appears, that the essential of the variation of the eubacterial composition in lake Bourget, is situated on a vertical scale rather than on a horizontal scale when the lake is stratified. This vertical variability reflects the presence of different
temperature layers and of different chemical micro-layers (in particular phosphate) favoring
the establishment of communities differently adapted to the conditions they encounter. During the mixing period (winter), the composition of the community is omogeneous within the whole water mass. The influence of the tributaries on the eubacterial composition is
restricted to the mouth of the tributaries. From a practical point of view, these results suggest
that, a small number of samples may be sufficient to provide a reliable and representative idea of the eubacterial community composition in a great lake, as long as the samples are not taken within isolated areas of the lake or near the borders of the lake. The second study provided evidence that the three lakes investigated, harbor typical lake eubacterial communities which are characterized by a weak global diversity. The Actinobacteria are the dominant taxonomic group within those communities. We have also
shown, that no major differences occur according to the season, the geographical origin and the depth. Variation due to local pressures may act on a small proportion of the water massand only sporadically : within the epilimnion in spring and in summer, when phytoplankton biomasses are important. It is likely that the strong resemblance among the eubacterial communities of the three lakes, despite differences in their trophic state, are due to the important volume of these lakes : the hypolimnion represents a great part of those lakes; within this part a great number of different environmental factors and processes are shared.
We conclude that the regional pressures may have a strong influence on the eubacterial community Composition within the three great French Alpine lakes.
The third study has shown that the cyanophage diversity is relatively great. The cyanophage community composition is submitted to seasonal changes which are directly or indirectly linked to the temperature and the chlorophyll a. The analysis of the dynamics of the
different microbial communities shows that the cyanophage sequences we obtained, are likely
to originate from viruses infecting picocyanobacteria rather than microcyanobacteria such as P. rubescens.