Botrytis cinerea causes different plant responses in grape (Vitis vinifera) berries during noble and grey rot: diverse metabolism versus simple defence.

The complexity of the interaction between the necrotrophic pathogen Botrytis cinerea and grape berries (Vitis vinifera spp.) can result in the formation of either the preferred noble rot (NR) or the loss-making grey rot (GR), depending on the prevailing climatic conditions. In this study, we focus on the functional gene set of V. vinifera by performing multidimensional scaling followed by differential expression and enrichment analyses. The aim of this study is to identify the differences in gene expression between grape berries in the phases of grey rot, noble rot, and developing rot (DR, in its early stages) phases. The grapevine transcriptome at the NR phase was found to exhibit significant differences from that at the DR and GR stages, which displayed strong similarities. Similarly, several plant defence-related pathways, including plant-pathogen interactions as hypersensitive plant responses were found to be enriched. The results of the analyses identified a potential plant stress response pathway (SGT1 activated hypersensitive response) that was found to be upregulated in the GR berry but downregulated in the NR berry. The study revealed a decrease in defence-related in V. vinifera genes during the NR stages, with a high degree of variability in functions, particularly in enriched pathways. This indicates that the plant is not actively defending itself against Botrytis cinerea, which is otherwise present on its surface with high biomass. This discrepancy underscores the notion that during the NR phase, the grapevine and the pathogenic fungi interact in a state of equilibrium. Conversely the initial stages of botrytis infection manifest as a virulent fungus-plant interaction, irrespective of whether the outcome is grey or noble rot.

Destructive and non-destructive early detection of postharvest noble rot (Botrytis cinerea) in wine grapes aimed at producing high-quality wines.

BACKGROUND: Botrytis cinerea (Bc) is the causative agent of gray mold disease in wine grape bunches. Under particular climatic and edaphic conditions, typical of some wine regions, the grapes infected by this fungus can develop noble rot, the basic phenomenon for the production of sweet botrytized wines or some high-quality dry wines, such as Amarone. The possibility of early detection of noble rot on plants and at postharvest is an interesting option for managing botrytized wines. RESULTS: The present work aimed at early detection of noble rot and monitoring its development, at postharvest, on Trebbiano wine grapes by means of destructive and non-destructive analytical approaches (e.g., electronic nose and near-infrared spectroscopy). The development of Bc led to substantial modifications in grape composition, including dehydration, biosynthesis, and accumulation of different compounds due to Bc metabolism, grape stress responses, or both. However, these modifications are appreciable, notably at advanced stages of infection. Consequently, a specific focus was to monitor the infection in the first 72 h post inoculation for testing, potentially through non-destructive technologies, and to identify the real early stages of Bc development. CONCLUSION: The destructive chemical analyses performed over the 16 monitored days confirmed what is widely reported in the literature regarding the metabolic/compositional changes that occur following the development of Bc. Moreover, non-destructive technologies allowed us to identify the evolution of Bc, even at early stages of its presence. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Botrytis cinerea expression profile and metabolism differs between noble and grey rot of grapes.

Botrytis cinerea, the pathogen causing grey rot (GR) with important economic losses in fruit crops, can also cause noble rot (NR) of grape berries under certain environmental conditions, leading to metabolic and physical changes necessary for producing highly regarded botrytized wines. The functional genes involved in biochemical processes in these harmful vs. beneficial berry rot types are still scarcely understood. We generated and analyzed transcriptomic data from healthy (H), NR and GR grape berries collected in the Tokaj wine region in Hungary. Our study shows that B. cinerea is most active in NR, followed by GR and H berries. In addition, expression profiles differed qualitatively between NR and GR, and to a smaller extent between months. Several functional genes expressed during NR were linked to well-known physico-chemical changes in botrytized grape berries, including berry skin degradation and the formation of metabolites favorable for botrytized wine production. In addition, we found that B. cinerea appeared to express genes involved in the biosynthesis of antimicrobials during NR, but not in GR, which likely contributes to the dominance of this fungus during NR.

Redox and Hormonal Changes in the Transcriptome of Grape (Vitis vinifera) Berries during Natural Noble Rot Development.

Noble rot is a favorable form of the interaction between grape (Vitis spp.) berries and the phytopathogenic fungus Botrytis cinerea. The transcriptome pattern of grapevine cells subject to natural noble rot development in the historic Hungarian Tokaj wine region has not been previously published. Furmint, a traditional white Tokaj variety suited to develop great quality noble rot was used in the experiments. Exploring a subset of the Furmint transcriptome redox and hormonal changes distinguishing between noble rot and bunch rot was revealed. Noble rot is defined by an early spike in abscisic acid (ABA) accumulation and a pronounced remodeling of ABA-related gene expression. Transcription of glutathione S-transferase isoforms is uniquely upregulated, whereas gene expression of some sectors of the antioxidative apparatus (e.g., catalases, carotenoid biosynthesis) is downregulated. These mRNA responses are lacking in berries exposed to bunch rot. Our results help to explain molecular details behind the fine and dynamic balance between noble rot and bunch rot development.

Metatranscriptomic Analyses Reveal the Functional Role of Botrytis cinerea in Biochemical and Textural Changes during Noble Rot of Grapevines.

Botrytis cinerea, can lead to the formation of noble rot (NR) of grape berries under certain environmental conditions, resulting in favored metabolic and physical changes necessary for producing highly regarded botrytized wines. The functional genes involved in the textural and biochemical processes are still poorly characterized. We generated and analyzed metatranscriptomic data from healthy (H) berries and from berries representing the four stages of NR from the Tokaj wine region in Hungary over three months. A weighted gene co-expression network analysis (WGCNA) was conducted to link B. cinerea functional genes to grape berry physical parameters berry hardness (BH), berry skin break force (F_sk), berry skin elasticity (E_sk), and the skin break energy (W_sk). Clustered modules showed that genes involved in carbohydrate and protein metabolism were significantly enriched in NR, highlighting their importance in the grape berry structural integrity. Carbohydrate active enzymes were particularly up-regulated at the onset of NR (during the transition from phase I to II) suggesting that the major structural changes occur early in the NR process. In addition, we identified genes expressed throughout the NR process belonging to enriched pathways that allow B. cinerea to dominate and proliferate during this state, including sulphate metabolizing genes and genes involved in the synthesis of antimicrobials.

Laccases 2 & 3 as biomarkers of Botrytis cinerea infection in sweet white wines.

Botrytized sweet wines are made with berries infected by the fungus Botrytis cinerea. The aim of this study was to identify biomarkers of B. cinerea infection in sweet wines with a focus on laccases which are exocellular oxidase enzymes produced by this fungus during fruit contamination. Total proteins from six commercial sweet wines, including three naturally botrytized wines and three non-botrytized wines were analysed by LC-QTOF-MS. Five laccases, namely laccase-1-BcLCC1, laccase-2-BcLCC2, laccase-3-BcLCC7, laccase-8-BcLCC8 and laccase-12-BcLCC12, were identified in both types of wine. Then, a targeted proteomic approach by LC-MRM was used to semi-quantify laccase-2-BcLCC2 and laccase-3-BcLCC7, in the six samples. LC-MRM targeted analysis of the two enzymes allowed the discrimination of botrytized versus non-botrytized sweet white wines.

Correlating Noble Rot Infection of Garganega Withered Grapes with Key Molecules and Odorants of Botrytized Passito Wine.

Experimental passito wines with different percentages of naturally noble-rotten grapes of the Garganega variety were analyzed to evaluate key molecules and odorants related to the typical aroma and sensory profile of botrytized passito wine. Remarkable changes in the concentration of 1-octen-3-ol, 4-terpineol, benzaldehyde, N-(3-methylbutyl)acetamide, and sherry lactone 1 and 2 were observed between sound and noble-rotten wines. Wines were perceived to be different for floral, honey, figs, apricot, and caramel scents. By partial least square regression these descriptors were well correlated to samples. An important positive contribution of sherry lactones, N-(3-methylbutyl)acetamide, vanillin, benzaldehyde, and γ-butyrolactone to honey, apricot, and caramel was observed. It is conceivable that oxidative effects of Botrytis cinerea infection play an important role in the genesis of these chemical and sensory aroma markers. This study provides a predictive tool for winemakers that use natural grape withering to produce wines whose aroma profile is not standardized due to the seasonal variation of noble rot incidence.

Plant and fungus transcriptomic data from grapevine berries undergoing artificially-induced noble rot caused by Botrytis cinerea.

Noble rot is a latent infection of grape berries caused by the necrotrophic fungus Botrytis cinerea, which develops under specific climatic conditions. The infected berries undergo biochemical and metabolic changes, associated with a rapid withering, which altogether offer interesting organoleptic features to sweet white wines. In this paper, we provide RNAseq datasets (raw and normalized counts as well as differentially expressed genes lists) of the transcriptome profiles of both grapevine berries (Vitis vinifera cv. Garganega) and B. cinerea during the establishment of noble rot, artificially induced in controlled conditions. The sequencing data are available in the NCBI GEO database under accession number GSE116741. These data were exploited in a comprehensive meta-analysis of gene expression during noble rot infection, gray mold and post-harvest withering. This highlighted an important common transcriptional reprogramming in different botrytized grape berry varieties and led to the identification of key genes specifically modulated during noble rot infection, which are described in the article entitled "Specific molecular interactions between Vitis vinifera and Botrytis cinerea are required for noble rot development in grape berries" Lovato et al., 2019.

Filamentous fungi associated with natural infection of noble rot on withered grapes.

The effects of noble rot infection of grapes on the characteristics of different types of wine, including Italian passito wine, are well known. Nevertheless, there is still little information on filamentous fungi associated with noble-rotten grapes. In this study, withered Garganega grapes for passito wine production, naturally infected by noble rot, were analyzed and compared to sound grapes. Skin morphology and fungal population on berry surfaces were analyzed. Scanning electron microscopy analysis revealed microcracks, germination conidia and branched hyphae on noble-rotten berries. Penicillium, Aureobasidium and Cladosporium were the most frequent genera present. Analysis of single berries displayed higher heterogeneity of epiphytic fungi in those infected by noble-rot than in sound berries. Penicillium adametzoides, Cladosporium cladospoirioides and Coniochaeta polymorpha were recovered. These, to the best of our knowledge, had never been previously isolated from withered grapes and, for C. polymorpha, from grapevine. This study provided novel data on noble rot mycobiota and suggests that fungi that co-habit with B. cinerea could have an important role on grape and wine quality.

The Induction of Noble Rot (Botrytis cinerea) Infection during Postharvest Withering Changes the Metabolome of Grapevine Berries (Vitis vinifera L., cv. Garganega).

The natural or induced development of noble rot caused by the fungus Botrytis cinerea during the late stages of grapevine (Vitis vinifera L.) berry ripening is used in some traditional viticulture areas to produce high-quality wines such as Sauternes and Tokaji. In this research, we wanted to verify if by changing the environmental conditions during post-harvest withering we could induce the noble rot development on harvested berries in order to positively change the wine produced from withered Garganega berries. Therefore, we exposed the berries to postharvest withering under normal or artificially humid conditions, the latter to induce noble rot. The presence of noble rot symptoms was associated with the development of B. cinerea in the berries maintained under humid conditions. The composition of infected and non-infected berries was investigated by untargeted metabolomics using liquid chromatography/mass spectrometry. We also explored the effects of the two withering methods on the abundance of volatile organic compounds in wine by yeast-inoculated micro-fermentation followed by targeted gas chromatography/mass spectrometry. These experiments revealed significant metabolic differences between berries withered under normal and humid conditions, indicating that noble rot affects berry metabolism and composition. As well as well-known botrytization markers, we detected two novel lipids that have not been observed before in berries infected with noble rot. Unraveling the specific metabolic profile of berries infected with noble rot may help to determine the compounds responsible for the organoleptic quality traits of botrytized Garganega wines.

Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts.

Cell walls are barriers that impair colonization of host tissues, but also are important reservoirs of energy-rich sugars. Growing hyphae of necrotrophic fungal pathogens, such as Botrytis cinerea (Botrytis, henceforth), secrete enzymes that disassemble cell wall polysaccharides. In this work we describe the annotation of 275 putative secreted Carbohydrate-Active enZymes (CAZymes) identified in the Botrytis B05.10 genome. Using RNAseq we determined which Botrytis CAZymes were expressed during infections of lettuce leaves, ripe tomato fruit, and grape berries. On the three hosts, Botrytis expressed a common group of 229 potentially secreted CAZymes, including 28 pectin backbone-modifying enzymes, 21 hemicellulose-modifying proteins, 18 enzymes that might target pectin and hemicellulose side-branches, and 16 enzymes predicted to degrade cellulose. The diversity of the Botrytis CAZymes may be partly responsible for its wide host range. Thirty-six candidate CAZymes with secretion signals were found exclusively when Botrytis interacted with ripe tomato fruit and grape berries. Pectin polysaccharides are notably abundant in grape and tomato cell walls, but lettuce leaf walls have less pectin and are richer in hemicelluloses and cellulose. The results of this study not only suggest that Botrytis targets similar wall polysaccharide networks on fruit and leaves, but also that it may selectively attack host wall polysaccharide substrates depending on the host tissue.

The 'Dr Jekyll and Mr Hyde fungus': noble rot versus gray mold symptoms of Botrytis cinerea on grapes.

Many cryptic species have recently been discovered in fungi, especially in fungal plant pathogens. Cryptic fungal species co-occurring in sympatry may occupy slightly different ecological niches, for example infecting the same crop plant but specialized on different organs or having different phenologies. Identifying cryptic species in fungal pathogens of crops and determining their ecological specialization are therefore crucial for disease management. Here, we addressed this question in the ascomycete Botrytis cinerea, the agent of gray mold on a wide range of plants. On grape, B. cinerea causes severe damage but is also responsible for noble rot used for processing sweet wines. We used microsatellite genotyping and clustering methods to elucidate whether isolates sampled on gray mold versus noble rot symptoms in three French regions belong to genetically differentiated populations. The inferred population structure matched geography rather than the type of symptom. Noble rot symptoms therefore do not seem to be caused by a specific B. cinerea population but instead seem to depend essentially on microclimatic conditions, which has applied consequences for the production of sweet wines.