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

Abstract

Soil microbiota plays a significant role in plant development and health and appears to be a major component of certain forms of grapevine decline. A greenhouse experiment was conducted to study the impact of the microbiological quality of the soil and grapevine rootstock genotype on the root microbial community and development of young plants. Two rootstocks heterografted with the same scion were grown in two vineyard soils differing in microbial composition and activities. After 4 months, culture-dependent approaches and amplicon sequencing of bacterial 16S rRNA gene and fungal ITS were performed on roots, rhizosphere and bulk soil samples. The root mycorrhizal colonization and number of cultivable microorganisms in the rhizosphere compartment of both genotypes were clearly influenced by the soil status. The fungal diversity and richness were dependent on the soil status and the rootstock, whereas bacterial richness was affected by the genotype only. Fungal genera associated with grapevine diseases were more abundant in declining soil and related root samples. The rootstock affected the compartmentalization of microbial communities, underscoring its influence on microorganism selection. Fluorescence in situ hybridization (FISH) confirmed the presence of predominant root-associated bacteria. These results emphasized the importance of rootstock genotype and soil composition in shaping the microbiome of young vines.

Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions

“…The structures of the fungal and bacterial communities from root endosphere were distinct from those found in soil. Consistent with previous research on grapevines, reduced bacterial and fungal richness as well as diversity were found in the root endosphere compared to soil samples ( D’Amico et al., 2018 ; Marasco et al., 2018 ; Carbone et al., 2021 ; Swift et al., 2021 ; Darriaut et al., 2022a ). The fungal root microbiome was influenced by soil status, revealing its sensitivity to soil composition.…”

“…From the subgroup of fresh root samples that were not surface sterilized, 30 subsamples of fresh roots were used to evaluate their colonization by mycorrhizal fungi. These roots were stained using the modified ink-KOH-H 2 O 2 method (Phillips and Hayman, 1970), and arbuscular mycorrhizal colonization was estimated as described in Darriaut et al (2022a). Briefly, the samples were rinsed in sterile water, incubated in 10% KOH for 30 min at 95°C, and depigmented with 3% H 2 O 2 .…”

“…Among the studied plots, bulk soils in the S areas showed different bacterial and fungal profiles with increased metabolic activities (Darriaut et al, 2021) combined with higher abundances of putative pathogenic fungi and potentially beneficial bacteria compared to asymptomatic (AS) areas (Darriaut et al, 2023). The effect of the microbial composition of both soils harvested from one of these plots on young grapevine plant growth and rhizosphere and roots was investigated in a greenhouse experiment (Darriaut et al, 2022a), confirming the microbial dysbiosis inherent to the observed decline. However, the microbiome associated with grapevine roots in situ (i.e., within the plot) has not been analyzed to date, and one can wonder if the microbial dysregulation would occur in this belowground compartment.…”

Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact

“…Actinobacteria are known for their production of secondary metabolites, degradation of organic substances and contribution to plant fitness by acting as PGPR or biocontrol agents [ 48 ]. Relatively similar proportions of bacterial phyla were found in other studies [ 24 , 48 , 49 ]. Interestingly, some studies found a greater abundance of Acidobacteria than Actinobacteriota , and observed several phyla such as Armatimonadetes , Deinococcus - Thermus , Rokubacterua , or Synergistetes , which were not detected in the GreffAdapt plot [ 23 , 26 ].…”

The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina

“…While environmental and anthropogenic-driven changes on the grapevine soil microbiome are interesting and widely studied ( Steenwerth et al., 2008 ; Lumini et al., 2009 ; Schreiner and Mihara, 2009 ; Marasco et al., 2013 ; Holland et al., 2014 ; Vega-Avila et al., 2015 ; Novello et al., 2017 ; Berg and Cernava, 2022 ; Nanetti et al., 2023 ), the microbial biodiversity dynamics across the rootstock choice is relevant but still little explored ( D’Amico et al., 2018 ; Marasco et al., 2018 ; Dries et al., 2021 ; Darriaut et al., 2022a ).…”