MicrobiomeSupport: Towards coordinated microbiome R&I activities in the food system to support (EU and) international bioeconomy goals

The use of rootstocks tolerant to soil water deficit is an interesting strategy to cope with limited water availability. Currently, several nurseries are breeding new genotypes, but the physiological basis of its responses under water stress are largely unknown. To this end, an ecophysiological assessment of the conventional 110-Richter (110R) and SO4, and the new M1 and M4 rootstocks was carried out in potted ungrafted plants. During one season, these Vitis genotypes were grown under greenhouse conditions and subjected to two water regimes, well-watered and water deficit. Water potentials of plants under water deficit down to < -1.4 MPa, and net photosynthesis (AN) <5 μmol m-2 s-1 did not cause leaf oxidative stress damage compared to well-watered conditions in any of the genotypes. The antioxidant capacity was sufficient to neutralize the mild oxidative stress suffered. Under both treatments, gravimetric differences in daily water use were observed among genotypes, leading to differences in the biomass of root, shoot and leaf. Under well-watered conditions, SO4 and 110R were the most vigorous and M1 and M4 the least. However, under water stress, SO4 exhibited the greatest reduction in biomass while M4 showed the lowest. Remarkably, under these conditions, SO4 reached the least negative stem water potential (Ψstem), while M1 reduced stomatal conductance (gs) and AN the most. In addition, SO4 and M1 genotypes also showed the highest and lowest hydraulic conductance values, respectively. Our results suggest that there are differences in water use regulation among genotypes, not only attributed to differences in stomatal regulation or intrinsic water use efficiency at the leaf level. Therefore, because no differences in canopy-to-root ratio were achieved, it is hypothesized that xylem vessel anatomical differences may be driving the reported differences among rootstocks performance. Results demonstrate that each Vitis rootstock differs in its ecophysiological responses under water stress.

A large varietal collection including over 1700 varieties was maintained in Conegliano, ITA, since the 1950s. Phenological data on a subset of 400 grape varieties including wine grapes, table grapes, and raisins were acquired at bud break, flowering, veraison, and ripening since 1964. Despite the efforts in maintaining and acquiring data over such an extensive collection, the data set has varying degrees of missing cases depending on the variety and the year. This is ubiquitous in phenology datasets with significant size and length. In this work, we evaluated four state-of-the-art methods to estimate missing values in this phenological series: k-Nearest Neighbour (kNN), Multivariate Imputation by Chained Equations (mice), MissForest, and Bidirectional Recurrent Imputation for Time Series (BRITS). For each phenological stage, we evaluated the performance of the methods in two ways. 1) On the full dataset, we randomly hold-out 10% of the true values for use as a test set and repeated the process 1000 times (Monte Carlo cross-validation). 2) On a reduced and almost complete subset of varieties, we varied the percentage of missing values from 10% to 70% by random deletion. In all cases, we evaluated the performance on the original values using normalized root mean squared error. For the full dataset we also obtained performance statistics by variety and by year. MissForest provided average errors of 17% (3 days) at budbreak, 14% (4 days) at flowering, 14.5% (7 days) at veraison, and 17% (3 days) at maturity. We completed the imputations of the Conegliano dataset, one of the world’s most extensive and varied phenological time series and a steppingstone for future climate change studies in grapes. The dataset is now ready for further analysis, and a rigorous evaluation of imputation errors is included.

Water status impact in viticulture has been widely explored, as it strongly affects grapevine physiology and grape chemical composition. It is considered as a key component of vitivinicultural terroir. Most of the studies concerning grapevine water status have focused on either physiological traits, or berry compounds, or traits involved in wine quality. Here, the response of grapevine to water availability during the ripening period is assessed through non-targeted metabolomics analysis of grape berries by ultra-high resolution mass spectrometry. The grapevine water status has been assessed during 2 consecutive years (2019 & 2020), through carbon isotope discrimination on juices from berries collected at maturity (21.5 brix approx.) for 2 Vitis vinifera cv. Pinot noir (PN) and Chardonnay (CH). A total of 220 grape juices were collected from 5 countries worldwide (Italy; Argentina; France; Germany; Portugal). Measured δ13C (‰) varied from -28.73 to -22.6 for PN, and from -28.79 to -21.67 for CH. These results also clearly revealed higher water stress for the 2020 vintage. The same grape juices have been analysed by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and Liquid Chromatography coupled to Mass Spectrometry (LC-qTOF-MS), leading to the detection of up to 4500 CHONS containing elemental compositions, and thus likely tens of thousands of individual compounds, which include fatty acids, organic acids, peptides, phenolics, also with high levels of glycosylation. Multivariate statistical analysis revealed that up to 160 elemental compositions, covering the whole range of detected masses (100 –1000 m/z), were significantly correlated to the observed gradients of water status. Examples of chemical markers, which are representative of these complex fingerprints, include various derivatives of the known abscisic acid (ABA), such as phaesic acid or abscisic acid glucose ester, which are significantly correlated with higher water stress, regardless of the variety. Cultivar-specific behaviours could also be identified from these fingerprints. Our results provide an unprecedented representation of the metabolic diversity, which is involved in the water status regulation at the grape level, and which could contribute to a better knowledge of the grapevine mitigation strategy in a climate change context.

Measurement of carbon isotope discrimination in berry juice sugars at maturity (δ13C) provides an integrated assessment of water use efficiency (WUE) during the period of berry ripening, and when collected over multiple seasons can be used as an indication of drought stress response. Berry juice δ13C measurements were carried out on 48 different varieties planted in a common garden experiment in Bordeaux, France from 2014 through 2021 and were paired with midday and predawn leaf water potential measurements on the same vines in a subset of six varieties. The aim was to discriminate a large panel of varieties based on their stomatal behaviour and potentially identify hydraulic traits characterizing drought tolerance by comparing δ13C and hydroscapes (the visualisation of plant stomatal behaviour as a response to predawn water potential). Cluster analysis found that δ13C values are likely affected by the differing phenology of each variety, resulting in berry ripening of different varieties taking place under different stress conditions within the same year. We accounted for these phenological differences and found that cluster analysis based on specific δ13C metrics created a classification of varieties that corresponds well to our current empirical understanding of their relative drought tolerances. In addition, we analysed the water potential regulation of the subset of six varieties (using the hydroscape approach) and found that it was well correlated with some δ13C metrics. Surprisingly, a variety’s water potential regulation (specifically its minimum critical leaf water potential under water deficit) was strongly correlated to δ13C values under well-watered conditions, suggesting that base WUE may have a stronger impact on drought tolerance than WUE under water deficit. These results give strong insights on the innate WUE of a very large panel of varieties and suggest that studies of drought tolerance should include traits expressed under non-limiting conditions.

Grapevine trunk diseases including Eutypa dieback are a major factor in the decline of vineyards and may lead to loss of productivity, reduced income, and premature reworking or replanting. Several studies have yielded results indicating that vines may be more likely to express symptoms of vascular disease if their health is already compromised by stress. In Australia and many other wine-growing regions it is a common practice for canes to be wrapped tightly around the cordon wire during the establishment of permanent cordon arms. It is likely that this practice may have a negative effect on health and longevity, as older cordons that have been trained in this manner often display signs of decay and dieback, with the wire often visibly embedded within the wood of the cordon. It is possible that adopting a training method which avoids constriction of the vasculature of the cordon may help to limit the onset of vascular disease symptom expression. A survey was conducted during the spring of two consecutive growing seasons on vineyards in South Australia displaying symptoms of Eutypa lata infection when symptomless shoots were 50–100 cm long. Vines were assessed as follows: (i) the proportion of cordon exhibiting dieback was rated using a 0–100% scale; (ii) the proportion of canopy exhibiting foliar symptoms of Eutypa dieback was rated using a 0–100% scale; (iii) the severity of strangulation was rated using a 0–4 point scale. Images were also taken of each vine for the purpose of measuring plant area index (PAI) using the VitiCanopy App. The goal of the survey was to determine if and to what extent any correlation exists between severity of strangulation and cordon dieback, in addition to Eutypa dieback foliar symptom expression.