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Towards microbiota-based disease management: analysis of grapevine microbiota in plots with contrasted levels of downy mildew infection. Vers une gestion des maladies basée sur le microbiote : analyse du microbiote de la vigne dans des parcelles présentant des niveaux contrastés d'infection par le mildiou
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International audience. Context and purpose of the study: Vineyards harbor a myriad of microorganisms that interact with each other and with the grapevines. Some microorganisms are plant pathogens, such as the oomycete Plasmopara viticola that causes grapevine downy mildew. Others, such as plant growth promoting bacteria and disease biocontrol agents, have a positive influence on vine health. The present study aims to (1) investigate whether vine-based culture media increase the cultivability of the grapevine microbiota, in comparison to standard culture media and (2) identify and isolate bacterial taxa naturally present in grapevine leaves and significantly more abundant in plots showing low susceptibility to downy mildew.Material and methods: Seven pairs of vineyard plots differing significantly in downy mildew symptoms frequency and intensity were selected based on a long-term epidemiological survey conducted in France by the Institut Français de la Vigne et du Vin (IFV). In each plot, we sampled young leaves before the first fungicide treatments. Leaves wereshredded and washed in a buffer to isolate and cultivate foliar bacteria, yeasts and filamentous fungi. We assessed the abundance (CFU/ml) of cultivable bacterial and fungal cells for several culture media, including a vine-based culture medium. Bacterial isolates were identified using MALDI-TOF MS.Results: Yeasts, filamentous fungi, and bacteria were significantly less abundant on the vine-based culture medium than on the other media. Out of 965 total bacterial isolates analyzed, 597 were identified at least to the genus level by MALDI-TOF MS, and of these, 23% to the species level. Two bacterial genera, Gordonia and Rahnella, wereisolated exclusively on the vine-based culture medium. On the other hand, 10 genera, Rahnella, Paracoccus, Acinetobacter, Nocardia, Achromobacter, Peribacillus, Solibacillu, Xanthomona, Budvicia and Paenibacillus were isolated exclusively from samples collected from plots with low infection levels.
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