Fungal communities analysis and development of an analytical approach in the wheat rhizosphere microbiome

Abstract

The rhizosphere microbiome is essential for health and development of plants, providing protection against pests and diseases. In our ongoing project, we proposed the hypothesis that domestication of plant species may have affected the biodiversity of microbial communities in ancestral plant roots compared to the modern plants, which may have impacted the plant-microbiome defense mechanism. Thus, we promote the enrichment of the rhizosphere microbiome in contrasting materials for resistance against the soil-borne pathogen. Rhizosphere community structure was assessed through 16S rRNA gene parallel amplicon sequencing. The diversity and community structure was assessed through initial exploratory multivariate analysis. In order to develop a consistent statistical pipeline congruent with the integration in the "Back to the Roots" initiative, we propose fungal microbiome identification (based on ITS region gene) using next-generation sequencing and the application of a pipeline developed for microbiome analysis. Given the complexity of the dataset, the proposed analytical workflow that includes: constrained ordination according to ecological variables, network analysis and differential analysis of fold change in count data to improve interpretability of estimates. We also propose investigate whether compounds released by the fungal groups or by the plant roots (upon infection) could create a stress environment that elicits the responses of certain groups of bacteria with signal abilities. Through these analysis, we intend to identify factors (cycles, genotypes and pathogen) with higher influence in rhizosphere community structure and establish a standard pipeline for microbiome analysis.