Analysis of the microbiome associated to the common bean root system

Abstract

Here, we present a plan for an abroad research internship, which is complementary to the ongoing postdoctoral project (FAPESP 2014/03217-3). For this internship we propose two main activities, first, use the bioinformatics platform and know-how from the Netherlands Institute of Ecology (NIOO) to analyze the data generated in our experiments conducted in Brazil, and second, we propose an additional experiment for the analysis of the endophytic microbial community of the common bean resistant to the soil borne pathogen Fusarium oxysporum. Therefore, the first objective is the analysis of the sequencing data, i.e. 16S rRNA amplicons, shotgun metagenome and metatranscriptome, from the common bean rhizosphere microbial communities. The sequences are being obtained from mesocosms experiments using four common bean varieties, with different levels of resistance to the soil borne pathogen Fusarium oxysporum. Bioinformatics tools will be used to process and annotate the sequences, and statistical software for comparison and interpretation of the data. The second objective is to perform a new experiment to be run at NIOO, in order to assess the effect of F. oxysporum inoculation in the rhizospheric and endophytic microbial community of the resistant common bean variety IAC Milênio. This second objective will add a new dimension to the original ongoing project including the analysis of the endophytes, which was not initially planned, but represents an important contribution to achieve the overall objective of the project. In conclusion, the approval of this proposal will significantly foster the identification of potential microbial groups in the root system of common bean that is related to the suppression of the soil pathogen F. oxysporum. (AU)