Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures

Audrey Weber,Sylvain Santoni,Patrice This,Jean-Pierre Péros,Prashant Singh

doi:10.1038/s41598-019-50839-0

Abstract

Impacts of plant genotype on microbial assemblage in the phyllosphere (above-ground parts of plants, which predominantly consists of the set of photosynthetic leaves) of Vitis vinifera cultivars have been studied previously but the impact of grape species (under the grape family Vitaceae) was never investigated. Considering the fact, that the phyllosphere microbiome may have profound effects on host plant health and its performance traits, studying the impact of grape species in microbial taxa structuring in the phyllosphere could be of crucial importance. We performed 16S and ITS profiling (for bacteria and fungi respectively) to access genus level characterization of the microflora present in the leaf phyllosphere of five species within this plant family, sampled in two successive years from the repository situated in the Mediterranean. We also performed α and β-diversity analyses with robust statistical estimates to test the impacts of grape species and growing year, over a two-year period. Our results indicated the presence of complex microbial diversity and assemblages in the phyllosphere with a significant effect of both factors (grape species and growing year), the latter effect is being more pronounced. We also compared separate normalization methods for high-throughput microbiome data-sets followed by differential taxa abundance analyses. The results suggested the predominance of a particular normalization method over others. This also indicated the need for more robust normalization methods to study the differential taxa abundance among groups in microbiome research.

Highlights

Plant phyllosphere is the niche of a disparate group of microbial communities of prokaryotes, eukaryotes, and viruses that interact with each other and with their host plant[1]
Grape associated epiphytes have been recently established as promising biocontrol agents (BCA) against fungal pathogens[14] of Vitis vinifera, the species level variation could offer us hints of new potential players for BCA
If the genotype is a major driver of the phyllosphere microbiome assemblage, we, expected increasing differences in microbial assemblages according to the genetic distance between plant species

Summary

Introduction

Plant phyllosphere is the niche of a disparate group of microbial communities of prokaryotes, eukaryotes, and viruses that interact with each other and with their host plant[1]. Phyllosphere has been largely overlooked in most of the grape related microbiome studies and researches were mainly focused on rhizosphere (root and soil colonizers) and endosphere (inside tissue colonizers)[4,5,6,7,8,9] Most of these studies including few in phyllosphere[10,11,12] analyzed the main drivers for microbial assemblage on Vitis vinifera, the most widely cultivated species for wine and raisins. They suggested that the environmental conditions at different geographic locations (or terroir) and growing seasons are important drivers in the rhizosphere, endosphere or phyllosphere[10,11]. We used few recently published data transformation methods of cumulative sum scaling (CSS)[24], DESeq[225] and log ratio to normalize our zero-inflated taxa abundance data and compared estimates of differentially abundant genera between two growing years and grape species

Methods

Results

Conclusion