Plant and soil microbe interactions in controlled conditions: rhizosphere protozoa and bacterial community structure

Plants influence the soil system by the large proportion of photosynthesized matters translocated to the roots and secreted into the soil. This root exudation provides an abundant energy source for rhizosphere living microorganisms. Plants are also strongly affected, positively and negatively, by the presence of soil microbiota, particularly bacteria, protozoa and fungi. Throughout the experiments conducted in this work, we aimed to better understand the influence of protozoa on plant growth. The first part of this work focused on the development of a microcosm method. Firstly, physical soil sterilization methods (autoclaving (A) gamma-ray irradiation (i) and both successively (AI)) were tested to eliminate the soil microbiota and their resistance form (spores and cysts). Although all sterilization methods tested were efficient to eliminate protozoa, AI was the only efficient method to eliminate aerobic heterotrophic cultivable bacteria without changing the soil pH. However the release of NH4+ in the soil after AI sterilization was higher than for other methods. Secondly, a procedure to re-inoculate the sterilized soil with a complex microbial community without protozoa was developed. The protozoa-free bacterial suspension was obtained from rhizosphere soil by subsequent filtering steps to exclude protozoa. The structure of bacterial communities characterised by 16SrDNA PCR-DGGE in the protozoa-free bacterial suspension was similar to that of the native soil. Diversity (Shannon) and evenness indexes increased with time in the sterile soil inoculated with the protozoa-free bacterial suspension. However the final bacterial community composition after 2 months of incubation in the re-inoculated soil presented a lower diversity as compared to the native soil. The second part of this work focused on the plant-microbiota interactions and on protozoa effects on plant growth. The microcosms developed in the first part of the work were re-inoculated wit