Bacterial diversity of the rhizosphere and nearby surface soil of rice (Oryza sativa) growing in the Camargue (France)

Bacterial communities present in the rhizosphere of different plants, including rice (Oryza sativa), play an essential key role in biogeochemical cycles, plant nutrition and disease biocontrol. The Camargue area of France, part of the Rhône river delta flowing into the Mediterranean Sea, is considered a saline ecosystem. In order to understand the soil bacterial ecology of the Camargue rice growing areas, we collected samples from six different sites, from the rhizosphere of two rice varieties (Arelate and Gageron) at late stages of growth, plus adjacent bulk soil samples, during 2013 and 2014. We used pyrosequencing of PCR amplified V3-V4 regions of the 16S rRNA gene from total extracted DNA to identify the bacterial communities present, and found that the principal bacterial phyla were composed of members belonging to the Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes and Gemmatimonadetes phyla. While the relative abundance of these phyla did not differ between the rhizosphere and bulk soil samples, the abundances varied significantly among sites and between the years of collection. The most abundant bacterial groups at both the phylum and genus levels were similar to those found in other rice growing soils, though only one halophilic genus was present in significant numbers. Our work also suggests that the challenges of rice cultivation in proximity to relatively high-salt soils can likely be overcome by current irrigation and crop-rotation strategies.