Towards microbiota-based disease management: analysis of grapevine microbiota in plots with contrasted levels of downy mildew infection
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 were shredded 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.
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, were isolated exclusively on the vine-based culture medium. On the other hand, 10 genera, Rahnella, Paracoccus, Acinetobacter, Nocardia, Achromobacter, Peribacillus, Solibacillu, Xanthomona, Budvicia andPaenibacillus were isolated exclusively from samples collected from plots with low infection levels.
Issue: GiESCO 2023
1INRAE, Bordeaux Sciences Agro, ISVV, SAVE, 33140 Villenave-d’Ornon, France
2INRAE, Univ Bordeaux, BioGeCo, 33610 Cestas, France
3INRAE, CIRAD, Univ Montpellier, Institut AGRO, AGAP institut, 34398 Montpellier, France
4Univ Bordeaux, UMR oenologie, INRAE, Bx INP, Bordeaux Sciences Agro, ISVV, 33882 Villenave d’Ornon, France
5IFV, 33290 Blanquefort, France
Contact the author*
grapevine, downy mildew, microbial biodiversity, culturomics, phyllosphere, biocontrol