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Plant compartments provide unique niches that lead to specific microbial associations. The microbiota colonizing the endophytic compartment (endorhizosphere) and the rhizosphere contribute to productivity, plant growth, phytoremediation and carbon sequestration. The main objective of this study was to investigate how fungal communities are enriched in different habitats outside and inside of grapevine roots. For this purpose, the spatial dynamics of the fungal communities associated with three soil-plant compartments (bulk soil, rhizosphere and endorhizosphere) were characterized by ITS high-throughput amplicon sequencing (HTAS). Fungal communities were largely affected in their diversity and composition by soil-plant compartments, whereas the spatial variation (i.e. across five vineyards) was low. The endorhizosphere compartment differed most from the other two, suggesting that the root tissues entail a barrier for fungal colonization. The results of functional prediction via FUNGuild suggested an increase in the relative abundances of potential plant pathogens, endophytes and arbuscular mycorrhiza, and a decrease in wood, dung and undefined saprotrophs from bulk soil towards the endorhizosphere. Roots of asymptomatic vines were a microbial niche that is inhabited by soilborne fungi associated with grapevine trunk diseases, which opens up new perspectives in the study of the endophytic role of these pathogens on grapevines. Results obtained in this study provide helpful information to better know how the host shapes its microbiome and the implications for vineyard productivity and management., David Gramaje was supported by the DOC-INIA program from theINIA, co-funded by the European Social Fund. María del Pilar Martínez-Diz was supported by the FPI-INIA program from the INIA.

The grapevine trunk diseases (GTD) Botryosphaeria dieback and esca threaten the sustainability of the grapevine industry worldwide. This study aimed to evaluate and compare the efficacy of various liquid (pyraclostrobin + boscalid and thiophanate methyl) and paste (paste + tebuconazole) formulation fungicide treatments as well as biological control agents (Trichoderma atroviride SC1 and T. atroviride I-1237), for their potential to prevent infection of grapevine pruning wounds by Diplodia seriata and Phaeomoniella chlamydospora in two field trials over two growing seasons. Treatments were applied to freshly pruned wounds following label dosages’ recommendations. After 24 h, wounds were artificially inoculated with 400 spores of D. seriata or 800 spores of P. chlamydospora. Isolations were made from the treated pruning wounds after 12 months to evaluate the efficacy of the treatments. Fungicide formulations were superior to Trichoderma-based treatments for the control of both pathogens during both growing seasons, with mean percent disease control of 44–95% for D. seriata and 46–67% for P. chlamydospora. Pyraclostrobin + boscalid was the most effective treatment. Trichoderma atroviride-based treatments did not reduce infection by D. seriata or P. chlamydospora compared to the untreated inoculated control in both vineyards and seasons. This study represents the first scientific comparative vineyard assessment of both commercial and biological treatments to protect pruning wounds against GTD fungi in Europe and provides growers with tangible preventative control practices to minimize yield losses due to GTD., This work has been funded by European funds in collaboration with the ‘Ministerio de Agricultura, Pesca y Alimentación (MAPA)’ (Spanish Government) and the ‘Xunta de Galicia’ (Regional Government) through the project ‘EVID: Innovative practices to combat grapevine diseases’ (FEADER 2017/003B). The authors acknowledge Bodegas Godeval for the provision of field sites and technical assistance for this study. We also thank Dr. J. Luque for the provision of Diplodia seriata isolate JL-398. M.P. Martínez-Diz was supported by the FPI-INIA program from the INIA (Spain, CPD2015-0188). D. Gramaje was supported by the Ramón y Cajal program, Spanish Government (RYC-2017-23098).

Timing of pruning may affect wound susceptibility to wood-invading fungi, such as those associated with grapevine trunk diseases (GTDs). This study aimed to determine the effect of pruning time on natural fungal infection in six vineyards in Galicia, Spain, during two periods of three months each, from November to February and from February to May by ITS2 high-throughput amplicon sequencing. Fungal microbiome composition did not differ significantly with year of sampling. Pruned canes harboured a core community of fungal species, which appeared to be independent of the infection period. Accumulated rainfall over 8 and 11 weeks after pruning positively correlated with the total fungal microbiome. A seasonal effect on GTD fungal infection was detected for most genera, with a higher percent detected after pruning in February (winter) as compared with that of pruning in November (mid-autumn). Early pruning is recommended to reduce the infections caused by GTD fungi in Galicia., Funding was provided by Ministerstvo Školství, Mládeže a Tělovýchovy (CZ.02.1.01./0.0/0.0/16_017/0002334).