The use of preserved DNA to assess historical diatom communities in peri alpine lake Bourget : a paleolimnological approach

Diatoms are of global importance in both freshwater and marine systems, both as abundant primary producers and as indicators of in water quality and nutrient status. Paleolimnological studies have identified diatom remains in sediments to reconstruct the histories of lake communities and nutrient status. However, whereas diatoms are traditionally analysed by morphological identification of their silica shell walls, there is a level of ambiguity in the use of certain characteristics and poorly silicified species are unlikely to be well preserved in lake sediments. In this work, we propose the use of DNA preserved in sediments as an alternative or complementary approach to assess historic diatom communities. DNA was successfully extracted from a sediment core documenting the last 150 years in Lake Bourget and the diatom community was targeted with PCR primers targeting the diatom 18S rRNA gene. Cloning and sequencing was used to compare 3 distinct regions of the core, corresponding to a period of transition from natural oligotrophic conditions to human induced eutrophication (1955-1970); the height of eutrophication (1983-1988); and during recent reoligotrophication (2002-2008). Clear changes in the diatom community were identified between the time points analysed. In particular, the proportion of sequences related to Stephanodiscus spp. was much higher in clone libraries constructed for the transition and reoligotrophication periods than for the eutrophic period. Additional changes in the diatom community of layers containing unusually high mineral deposits reflecting flooding events. However, the use of the 18S rRNA gene doesn't provide sufficient differentiation between different Stephanodiscus and Cyclotella spp., thus subsequent work has focused on the optimisation of approaches targeting more quickly evolving, and therefore more variable, gene markers