A 2-year assessment of the main environmental factors driving the free-living bacterial community structure in Lake Bourget (France).

Despite the considerable attention that has been paid to bacterioplankton over recent decades, the dynamic of aquatic bacterial community structure is still poorly understood, and long-term studies are particularly lacking. Moreover, how the environment governs diversity patterns remains a key issue in aquatic microbial ecology. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified partial 16S rRNA gene fragments and multivariable statistical approaches to explore the patterns of change in the free-living bacterial community in the mesotrophic and mono-meromictic Lake Bourget (France). A monthly sampling was conducted over two consecutive years (2007 and 2008) and at two different depths characterizing the epi- and hypolimnion of the lake (2 and 50 m, respectively). Temporal shifts in the bacterial community structure followed different patterns according to depth, and no seasonal reproducibility was recorded from 1 year to the next. Our results showed that the bacterial community structure displayed lower diversity at 2 m (22 bands) compared to 50 m (32 bands) and that bacterial community structure dynamics followed dissimilar trends between the two depths. At 2 m, five shifts in the bacterial community structure occurred, with the temporal scale varying between 2 and 8 months whereas, at 50 m, four shifts in the bacterial community structure took place at 50 m, with the temporal scale fluctuating between 3 and 13 months. More than 60% of the bacterial community structure variance was explained by seven variables at 2 m against eight at 50 m. Nutrients (PO(4)-P, NH(4)-N and NO(3)-N) and temperature were responsible for 49.6% of the variance at 2 m whereas these nutrients, with dissolved oxygen and chlorophyll a accounting for 59.6% of the variance at 50 m. Grazing by ciliates played also a critical role on the bacterial community structure at both depths. Our results suggest that the free-living bacterial community structure in the epi- and hypolimnion of Lake Bourget is mainly driven by combined, but differently weighted, top-down and bottom-up factors at 2 and 50 m.