Variation in Fungal Community in Grapevine (Vitis vinifera) Nursery Stock Depends on Nursery, Variety and Rootstock

Abstract

Grapevine trunk diseases (GTDs) are caused by cryptic complexes of fungal pathogens and have become a growing problem for new grapevine (Vitis vinifera) plantations. We studied the role of the nursery, variety, and rootstock in the composition of the fungal communities in root collars and graft unions of planting material in Catalonia (NE Spain). We compared necrosis and fungal communities in graft unions and root collars at harvest, and then after three months of cold storage. We evaluated combinations of eleven red and five white varieties with four common rootstocks coming from six nurseries. Fungal communities were characterized by isolation and metabarcoding of the ITS2 region. Our data suggests that nursery followed by rootstock and variety had significant effects on necrosis and fungal community structure in graft and root tissues. Within the plant, we found large differences in terms fungal community distribution between graft and root tissues. Graft unions housed a significantly higher relative abundance of GTD-related Operational Taxonomic Units (OTUs) than root collars. More severe necrosis was correlated with a lower relative abundance of GTD-related OTUs based on isolation and metabarcoding analyses. Our results suggest that nurseries and therefore their plant production practices play a major role in determining the fungal and GTD-related fungal community in grapevine plants sold for planting. GTD variation across rootstocks and varieties could be explored as a venue for minimizing pathogen load in young plantations.

Hot Water Treatment Causes Lasting Alteration to the Grapevine (Vitis vinifera L.) Mycobiome and Reduces Pathogenic Species Causing Grapevine Trunk Diseases

“…The pestles and mortars used for grinding were cleaned between samples using a 5% NaOCl solution to avoid cross-contamination of DNA between samples. DNA extraction was conducted with some adjustments to the NucleoSpin© Plant II protocol by Macherey-Nagel (2018; Düren, Germany) so as to optimize the quality of DNA extracted from the woody material [ 34 ], as further described in Lade, Štraus [ 2 ]. The ITS2 region was used as the metabarcoding marker and, therefore, amplifications were performed using ITS4 and ITS7 tagged forward and reverse primers to enable de-multiplexing following Ihrmark, Bodeker [ 35 ].…”

“…Symptoms will often appear several years after planting vines, when winter pruning begins. Recent next-generation sequencing (NGS) work has revealed that regardless of symptomatology, a high diversity of identified GTD-related fungi is present at outplanting, and that nurseries are the largest source of variation in GTD-related fungal communities [ 2 ]. Therefore, effective measures must be taken to reduce plant infection rates and to improve nursery-stock quality prior to shipment.…”

“…Treatment has been found to eliminate P. chlamydospora completely and to reduce the re-isolation of Phaeoacremonium aleophilum [ 18 ] in some cases, and to eliminate the re-isolation of Diplodia seriata and Diaporthe ampelina in others [ 29 ]. However, cultivation-based methods may not provide a complete picture of the fungal community present in the plant and underestimate species richness [ 2 , 17 ]. Recent work utilizing NGS technology revealed that overall GTD-related species richness decreased (insignificantly) as the temperature of the HWT increased [ 17 ].…”

“…Notably, important GTD-related fungi such as Diaporthe and Phaeoacremonium increased in abundance after the treatment of certain rootstock-scion combinations, and no significant differences were recorded between treatments after one growing season [ 17 ]. These variations in the short-term effects of HWT on plant physiomorphology and fungal community abundance may indicate that a more extensive NGS study is required that considers some of the main factors influencing GTD fungal composition, such as nursery, variety, and rootstock [ 2 ].…”

The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases

“…In a more recent work Lade and colleagues [ 38 ] analyzed and compared necrosis and fungal communities in graft unions and root collars in combinations of eleven red and five white grapevine varieties with four common rootstocks coming from six nurseries in Catalonia (Spain) ( Table 1 ). A total of 732 OTUs were detected.…”