Comparative 16s RRNA sequencing analysis of the composition of the bacterial communities in contrasting freshwater ecosystems in France and Burkina Faso

Abstract

International audienceWe compared the composition of the freeliving eubacterioplankton communities in the pelagic zone of three large French sub-Alpine lakes (Annecy, Bourget and Geneva) and of six small reservoirs located in Burkina Faso. More than 1,100 sequences of a 16S rRNA fragment were obtained from 25 clone libraries. In all these freshwater ecosystems, Actinobacteria was the dominant phylum (>40%), followed by Alpha- and Beta-proteobacteria. These three groups contain between 60 and 90% of the sequences retrieved. Picocyanobacteria were found in variable proportions (0-25%), and the remaining sequences were mainly affiliated to Bacteroidetes or Gammaproteobacteria. Despite contrasting trophic levels (oligotrophic to meso-eutrophic), there was no significant difference in the global composition of the bacterioplankton communities of the alpine lakes at the scale of the year. On the other hand, significant differences were found between reservoirs in Burkina Faso, suggesting the presence of local drift in the global composition of the bacterial communities in these small ecosystems. Operational Taxonomic Units (OTUs) were defined on the basis of a taxon resolution of at least 98% sequence similarity. At this taxonomic level, the diversity of the bacterial communities in small African reservoirs, estimated using the Shannon and the Chao1 estimators, was generally greater than the diversities found in Alpine lakes. Finally, a small number of OTUs belonging to the Alphabroteobacteria and to Actinobacteria phyla were found in all the ecosystems studied. It will be very interesting to go on to isolate and characterize these ubiquitous species, which probably play key functional roles in freshwater ecosystems