Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river.

Geneviève Bricheux (1) , Loïc Morin (2) , Gwenaël Le Moal (1) , Gérard Coffe (1) , Damien Balestrino (1) , Nicolas Charbonnel (1) , Jacques Bohatier (1) , Christiane Forestier (1)

1 LMGE - Laboratoire Microorganismes : Génome et Environnement
2 IGM - Institut de génétique et microbiologie [Orsay]

Despite the recent and significant increase in the study of aquatic microbial communities, little is known about the microbial diversity of complex ecosystems such as running waters. This study investigated the biodiversity of biofilm communities formed in a river with 454 Sequencing™. This river has the particularity of integrating both organic and microbiological pollution, as receiver of agricultural pollution in its upstream catchment area and urban pollution through discharges of the wastewater treatment plant of the town of Billom. Different regions of the small subunit (SSU) ribosomal RNA gene were targeted using nine pairs of primers, either universal or specific for bacteria, eukarya, or archaea. Our aim was to characterize the widest range of rDNA sequences using different sets of polymerase chain reaction (PCR) primers. A first look at reads abundance revealed that a large majority (47-48%) were rare sequences (<5 copies). Prokaryotic phyla represented the species richness, and eukaryotic phyla accounted for a small part. Among the prokaryotic phyla, Proteobacteria (beta and alpha) predominated, followed by Bacteroidetes together with a large number of nonaffiliated bacterial sequences. Bacillariophyta plastids were abundant. The remaining bacterial phyla, Verrucomicrobia and Cyanobacteria, made up the rest of the bulk biodiversity. The most abundant eukaryotic phyla were annelid worms, followed by Diatoms, and Chlorophytes. These latter phyla attest to the abundance of plastids and the importance of photosynthetic activity for the biofilm. These findings highlight the existence and plasticity of multiple trophic levels within these complex biological systems.

Mots clés: Aquatic communities; biofilm; pyrosequencing.; pyrosequencing

Domaines: Biodiversité et Ecologie

Geneviève Bricheux, Loïc Morin, Gwenaël Le Moal, Gérard Coffe, Damien Balestrino, et al.. Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river.. MicrobiologyOpen, 2013, epub ahead of print. ⟨10.1002/mbo3.80⟩. ⟨hal-00812657⟩