Tag-encoded pyrosequencing analysis of the effects of fungicide application and plant genotype on rhizobacterial communities

The application of fungicide on field crops may have unexpected non-target effects on the agro-ecosystem. We analyzed the effects of four foliar fungicide application programs and sequenced the rhizobacterial community of two chickpea cultivars over the course of two years using the 454 GS FLX amplicon pyrosequencing technology. Fungicide treatments modified the composition of the rhizobacterial communities without affecting its richness level. Correspondence analyses showed that the treatments differentially affected the rhizobacterial communities associated with different chickpea cultivars. The effects of fungicide treatment were particularly pronounced in the dry summer of 2009, when rhizobacterial richness was reduced. The influences of chickpea genotype on the fungicide effects suggest an indirect influence of the fungicide treatments through the plant secondary metabolism. In addition, the detection of boscalid residues in rhizosphere soil suggests a direct effect of fungicide. We conclude that the application of foliar fungicide influences the composition of rhizobacterial communities and this influence can be modified by plant genotype and environmental conditions.

► High intensity fungicide usage affected chickpea rhizosphere bacterial community. ► Effects of fungicide treatments differed with chickpea genotype. ► Environmental factors also affect bacteria growth after fungicide application.