We investigate the community composition of small eukaryotes (< 5 µm) of 4 African lakes by metabarcoding sequencing the V4 region of 18S rRNA gene using Roche 454. We sampled in the pelagic zone of Kivu, Edward, Albert and Victoria lakes. Moreover, in the meromictic Lake Kivu, one of the largest CH4 reservoirs, two stations (Gisenyi and Ishungu) was sampled over vertical profiles.

The lakes of East African Valley are unique natural resources that are heavily utilized by their bordering countries. Due to their large size, ecosystem function is dominated by pelagic processes; hence microorganisms are a key component of the aquatic community. Overfishing, eutrophication and climate change altered the diversity and function of these lakes and despite microeukaryotes are important in biochemical cycles, they have been less explored. We investigate the community composition of small eukaryotes (< 5 µm) of 4 African lakes by sequencing the V4 region of 18S rRNA gene. We sampled in the pelagic zone of Kivu, Edward, Albert and Victoria lakes. Moreover, in the meromictic Lake Kivu, one of the largest CH4 reservoirs, two stations (Gisenyi and Ishungu) was sampled over vertical profiles. We obtained 779 representative operational taxonomic units (OTUs) (99 % identity) grouped in 9 high-rank taxonomic groups and 58 classes; being Alveolata (31 %), Opistokonta (20%) and Stramenopiles (17%) the most representative. At a superficial level, abundances differed amongst lakes, according to physical and chemical variables. The cluster analysis (Bray-Curtis similarity index) showed Lake Victoria as most dissimilar, which presented the lowest abundances and the greater species richness. Lake Kivu exhibited the highest abundance at 15 m at both sites; differing in composition. Overall, we found extremely high OTUs (40.56 %) with low similarity (< 90 %) with reported sequences in public databases, mostly in depths of Lake Kivu; suggesting a high potential for novel diversity, probably associated with their particular physical and chemical characteristics.