Exploring the Temporal Dynamics of the Fungal Microbiome in Rootstocks, the Lesser-Known Half of the Grapevine Crop

Abstract

Rootstocks are the link between the soil and scion in grapevines, can provide tolerance to abiotic and biotic stresses, and regulate yield and grape quality. The vascular system of grapevine rootstocks in nurseries is still an underexplored niche for research, despite its potential for hosting beneficial and pathogenic microorganisms. The purpose of this study was to investigate the changes in the composition of fungal communities in 110 Richter and 41 Berlandieri rootstocks at four stages of the grapevine propagation process. Taxonomic analysis revealed that the fungal community predominantly consisted of phylum Ascomycota in all stages of the propagation process. The alpha-diversity of fungal communities differed among sampling times for both rootstocks, with richness and fungal diversity in the vascular system decreasing through the propagation process. The core microbiome was composed of the genera Cadophora, Cladosporium, Penicillium and Alternaria in both rootstocks, while the pathogenic genus Neofusicoccum was identified as a persistent taxon throughout the propagation process. FUNguild analysis showed that the relative abundance of plant pathogens associated with trunk diseases increased towards the last stage in nurseries. Fungal communities in the vascular system of grapevine rootstocks differed between the different stages of the propagation process in nurseries. Numerous genera associated with potential biocontrol activity and grapevine trunk diseases were identified. Understanding the large diversity of fungi in the rootstock vascular tissue and the interactions between fungal microbiota and grapevine will help to develop sustainable strategies for grapevine protection.

Soil composition and rootstock genotype drive the root associated microbial communities in young grapevines

“…The role of nurseries and propagation process as a primary source of GTDs inoculum has been previously documented ( Aroca et al, 2010 ; Gramaje and Armengol, 2011 ; Nerva et al, 2019 ; Gramaje et al, 2022 ; Lade et al, 2022 ). Special care is taken during the grafting and propagation processes to limit the presence of GTDs related to fungi and viruses.…”

Fungal trunk diseases of fruit trees in Europe: pathogens, spread and future directions

“…HTS methods are probably the most significant advances in molecular biology since the advent of the PCR process. Microbial/fungal genome sequencing or metagenomics/ metabarcoding become a routine analysis and using the latest technology it is possible to generate near complete genomes (Robert-Siegwald et al, 2017;Eichmeier et al, 2022) or whole spectra of microbial/fungal communities (Eichmeier et al, 2018;Bruez et al, 2020;Gramaje et al 2022). There are also other applications of HTS technology which can serve understanding of the plant pathogen interaction as transcriptomics (Romeo-Oliván et al, 2022) or small RNA sequencing (Eichmeier et al, 2019).…”

The functional microbiome of grapevine throughout plant evolutionary history and lifetime

“…All the manipulations and treatments experienced by scions and rootstocks in the nursery can influence the initial grapevine microbiome and its future trajectory of assembly. Gramaje et al (2022) analyzed the fungal microbiome associated with rootstocks harvested in two mother plots located 800m appart. No difference in fungal community composition between these two locations was detected, but the fungal communities varied along the grafting process (after cutting from mother plants, after cold storage and hydration, after grafting and callusing, and in dormant grafted plants).…”

“…Functions of bacteria colonizing necrotic and non-necrotic tissues differed, as they metabolized differently the carbon substrates. Over the last decade, next-generation sequencing (Del Frari et al, 2019;Eichmeier et al, 2018;Gramaje et al, 2022;Lade et al, 2022) and metatranscriptomic analyses (Nerva et al, 2022;Paolinelli et al, 2022) provided deeper resolution in the grapevine wood fungal and bacterial microbiomes. Depending on the grapevine organs, years, seasons and wood health status (i.e.…”