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

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions

Étude de la signalisation liée au stress du réticulum endoplasmique dans l’immunité de la vigne associée aux récepteurs kinases à motifs LysM (VvLYKs)

National audienceDans le contexte de réduction des produits phytosanitaires en agriculture, l’amélioration desconnaissances sur l’immunité et la symbiose des plantes est un enjeu important dans larecherche de nouveaux modes de protection des cultures. Ce projet de thèse vise à améliorernos connaissances sur le rôle des récepteurs kinases à domaine LysM (LYKs) dans la balanceentre immunité et symbiose chez la vigne ainsi qu’à déterminer le rôle de la réponse au stressdu réticulum endoplasmique (Unfolded Protein Response; UPR) dans ces voies. Des travauxantérieurs ont identifié 15 récepteurs VvLYKs chez la vigne et permis de caractériser le rôle deVvLYK1-1 et VvLYK1-2 dans la perception de la chitine. Dans ce contexte, le premier objectifde la thèse est de caractériser la fonction de nouveaux VvLYKs impliqués dans la perceptionde facteurs Myc qui permettent le contournement de l’immunité lors de la mise en place dessymbioses mycorhiziennes. Le second objectif est de caractériser les voies de signalisation del’UPR chez la vigne. En effet, même si le rôle de l’UPR dans l’immunité des plantes n’est plusà démonter, notamment via les facteurs de transcriptions bZIP17, bZIP28 et bZIP60, nosconnaissances restent limitées quant à son fonctionnement chez de nombreuses plantes d’intérêtagronomique, dont la vigne. Pour ce faire, une approche de génomique fonctionnelle par éditiongénomique CRISPR/Cas9 chez la vigne permettra de valider le rôle des récepteurs VvLYKs etdes VvbZIPs dans l’immunité et la symbiose mutualiste

Study of the stress-related signalling of endoplasmic reticulum in grapevine immunity associated to LysM receptor kinases (VvLYKs)

National audienceIn the actual situation of decreasing the use of chemicals in agriculture, enhancing our understanding of plant immunity is a critical task to develop more sustainable plant health protection methods. An interesting strategy is to study how plants, and in particular grapevine, perceives and responds to different microorganisms. Microorganisms are notably recognizedby LysM Receptor-like Kinase (LYKs) and previous works have identified 16 LYKs encoded by the grapevine genome (VvLYKs) (Roudaire et al. 2023). Among them, VvLYK1-1, VvLYK1-2 and VvLYK5-1 are involved in chitin perception and thus play a role in the plant immunity. Interestingly, immune responses are also involved during symbiotic interaction but the receptors involved in this process are still unknown. In addition, it has been demonstrated that the Unfolded Protein Response (UPR), which is activated when unfolded proteins accumulate in the endoplasmic reticulum, is also involved during the plant immune response.It’s therefore important to improve our knowledge about the role of the different grapevine LYK receptors involved in the balance between immunity and symbiosis and in addition to determine the role of stress-related signalling of endoplasmic reticulum and the consequent activation of the UPR in these two different pathways.In this context, we aim to characterize new VvLYKs involved in the perception of Myc-factors which allow the down-regulation of the plant immunity during the establishment of mycorrhizal symbiosis. In addition we also intend to characterize the UPR signalling pathways in grapevinewhich is still unknown and finally ho

Study of the stress-related signalling of endoplasmic reticulum in grapevine immunity associated to LysM receptor kinases (VvLYKs)

National audienceEnhancing our understanding of plant immunity is a critical task to develop more sustainableplant health protection methods. An interesting strategy is to study how plants, and in particulargrapevine, perceives and responds to different microorganisms. Microorganisms are notably recognized by LysM Receptor-like Kinase (LYKs) and previous works have identified 16 LYKs encoded by the grapevine genome (VvLYKs) (Roudaire et al. 2023). Among them, VvLYK1-1, VvLYK1-2 and VvLYK5-1 are involved in chitin perception and thus play a role in the plant immunity. Interestingly, immune responses are also involved during symbiotic interaction but the receptors involved in this process are still unknown. In addition, it has been demonstrated that the Unfolded Protein Response (UPR), which is activated when unfoldedproteins accumulate in the endoplasmic reticulum, is also involved during the plant immune response. It’s therefore important to improve our knowledge about the role of the different grapevine LYK receptors involved in the balance between immunity and symbiosis and in addition to determine the role of stress-related signalling of endoplasmic reticulum and the consequent activation of the UPR in these two different pathways. In this context, we aim to characterize new VvLYKs involved in the perception of Myc-factors which allow the downregulation of the plant immunity during the establishment of mycorrhizal symbiosis. In addition, we also intend to characterize the UPR signalling pathways in grapevine which is still unknown and finally how different biotic factors are involved in the stress-related signalling of endoplasmic reticulum

The grapevine LysM receptor-like kinase VvLYK5-1 recognizes chitin oligomers through its association with VvLYK1-1

International audienceThe establishment of defense reactions to protect plants against pathogens requires the recognition of invasion patterns (IPs), mainly detected by plasma membrane-bound pattern recognition receptors (PRRs). Some IPs, also termed elicitors, are used in several biocontrol products that are gradually being developed to reduce the use of chemicals in agriculture. Chitin, the major component of fungal cell walls, as well as its deacetylated derivative, chitosan, are two elicitors known to activate plant defense responses. However, recognition of chitooligosaccharides (COS) in Vitis vinifera is still poorly understood, hampering the improvement and generalization of protection tools for this important crop. In contrast, COS perception in the model plant Arabidopsis thaliana is well described and mainly relies on a tripartite complex formed by the cell surface lysin motif receptor-like kinases (LysM-RLKs) AtLYK1/CERK1, AtLYK4 and AtLYK5, the latter having the strongest affinity for COS. In grapevine, COS perception has for the moment only been demonstrated to rely on two PRRs VvLYK1-1 and VvLYK1-2. Here, we investigated additional players by overexpressing in Arabidopsis the two putative AtLYK5 orthologs from grapevine, VvLYK5-1 and VvLYK5-2 . Expression of VvLYK5-1 in the atlyk4/5 double mutant background restored COS sensitivity, such as chitin-induced MAPK activation, defense gene expression, callose deposition and conferred non-host resistance to grapevine downy mildew ( Erysiphe necator) . Protein-protein interaction studies conducted in planta revealed a chitin oligomer-triggered interaction between VvLYK5-1 and VvLYK1-1. Interestingly, our results also indicate that VvLYK5-1 mediates the perception of chitin but not chitosan oligomers showing a part of its specificity

Broad-Spectrum Efficacy and Modes of Action of Two Bacillus Strains against Grapevine Black Rot and Downy Mildew

International audienceBlack rot (Guignardia bidwellii) and downy mildew (Plasmopara viticola) are two major grapevine diseases against which the development of efficient biocontrol solutions is required in a context of sustainable viticulture. This study aimed at evaluating and comparing the efficacy and modes of action of bacterial culture supernatants from Bacillus velezensis Buz14 and B. ginsengihumi S38. Both biocontrol agents (BCA) were previously demonstrated as highly effective against Botrytis cinerea in grapevines. In semi-controlled conditions, both supernatants provided significant protection against black rot and downy mildew. They exhibited antibiosis against the pathogens by significantly decreasing G. bidwellii mycelial growth, but also the release and motility of P. viticola zoospores. They also significantly induced grapevine defences, as stilbene production. The LB medium, used for the bacterial cultures, also showed partial effects against both pathogens and induced plant defences. This is discussed in terms of choice of experimental controls when studying the biological activity of BCA supernatants. Thus, we identified two bacterial culture supernatants as new potential biocontrol products exhibiting multi-spectrum antagonist activity against different grapevine key pathogens and having a dual mode of action

DataSheet_1_Microbial dysbiosis in roots and rhizosphere of grapevines experiencing decline is associated with active metabolic functions.pdf

When grapevine decline, characterized by a premature decrease in vigor and yield and sometimes plant death, cannot be explained by pathological or physiological diseases, one may inquire whether the microbiological status of the soil is responsible. Previous studies have shown that the composition and structure of bacterial and fungal microbial communities in inter-row soil are affected in areas displaying vine decline, compared to areas with non-declining vines within the same plot. A more comprehensive analysis was conducted in one such plot. Although soil chemical parameters could not directly explain these differences, the declining vines presented lower vigor, yield, berry quality, and petiole mineral content than those in non-declining vines. The bacterial and fungal microbiome of the root endosphere, rhizosphere, and different horizons of the bulk soil were explored through enzymatic, metabolic diversity, and metabarcoding analysis in both areas. Despite the lower microbial diversity and richness in symptomatic roots and soil, higher microbial activity and enrichment of potentially both beneficial bacteria and pathogenic fungi were found in the declining area. Path modeling analysis linked the root microbial activity to berry quality, suggesting a determinant role of root microbiome in the berry mineral content. Furthermore, certain fungal and bacterial taxa were correlated with predicted metabolic pathways and metabolic processes assessed with Eco-Plates. These results unexpectedly revealed active microbial profiles in the belowground compartments associated with stressed vines, highlighting the interest of exploring the functional microbiota of plants, and more specifically roots and rhizosphere, under stressed conditions.</p