Microbial metagenomics of vineyard soils and wine terroir

Stomatal traits determine grapevine water use, carbon supply, and water stress, which directly impact yield and berry chemistry. Breeding for stomatal traits has the strong potential to improve grapevine performance under future, drier conditions, but the trait values that breeders should target are unknown. We used a functional-structural plant model developed for grapevine (HydroShoot) to determine how stomatal traits impact canopy gas exchange, water potential, and temperature under historical and future conditions in high-quality and hot-climate California wine regions (Napa and the Central Valley). Historical climate (1990-2010) was collected from weather stations and future climate (2079-99) was projected from 4 representative climate models for California, assuming medium- and high-emissions (RCP 4.5 and 8.5). Five trait parameterizations, representing mean and extreme values for the maximum stomatal conductance (gmax) and leaf water potential threshold for stomatal closure (Ψsc), were defined from meta-analyses. Compared to mean trait values, the water-spending extremes (highest gmax or most negative Ysc) had negligible benefits for carbon gain and canopy cooling, but exacerbated vine water use and stress, for both sites and climate scenarios. These traits increased cumulative transpiration by 8 – 17%, changed cumulative carbon gain by -4 – 3%, and reduced minimum water potentials by 10 – 18%. Conversely, the water-saving extremes (lowest gmax or least negative Ψsc) strongly reduced water use and stress, but potentially compromised the carbon supply for ripening. Under RCP 8.5 conditions, these traits reduced transpiration by 22 – 35% and carbon gain by 9 – 16% and increased minimum water potentials by 20 – 28%, compared to mean values. Overall, selecting for more water-saving stomatal traits could improve water-use efficiency and avoid the detrimental effects of highly negative canopy water potentials on yield and quality, but more work is needed to evaluate whether these benefits outweigh the consequences of minor declines in carbon gain for fruit production.

Soil is a reservoir of microorganisms playing important roles in biogeochemical cycles and interacting with plants whether in the rhizosphere or in the root endosphere. The composition of the microbial communities thus impacts the plant health. Rhizodeposits (such as sugar, organic and amino acids, secondary metabolites, dead root cells …) are released by the roots and influence the communities of rhizospheric microorganisms, acting as signaling compounds or carbon sources for microbes. The composition of root exudates varies depending on several factors including genotypes. As most of the cultivated grapevines worldwide are grafted plants, the aim of this study was to explore the influence of rootstock and scion genotypes on the microbial communities of the rhizosphere and the root endosphere. The work was conducted in the GreffAdapt plot (55 rootstocks x 5 scions), in which the 275 combinations have been planted into 3 blocks designed according to the soil resistivity. Samples of roots and rhizosphere of 10 scion x rootstock combinations were first collected in May among the blocks 2 and 3. The quantities of bacteria, fungi and archaea have been assessed in the rhizosphere by quantitative PCR, and by cultivable methods for bacteria and fungi. The communities of bacteria, fungi and arbuscular mycorrhizal fungi (AMF) was analyzed by Illumina sequencing of 16S rRNA gene, ITS and 28S rRNA gene, respectively. The level of mycorrhization was also evaluated using black ink coloration of newly formed roots harvested in October. The level of bacteria, fungi and archaea was dependent on rootstock and scion genotypes. A block effect was observed, suggesting that the soil characteristics strongly influenced the microorganisms from the rhizosphere and root endosphere. High-throughput sequencing of the different target genes showed different communities of bacteria, fungi and AMF associated with the scion x rootstock combinations. Finally, all the combinations were naturally mycorrhized. The root mycorrhization intensity was influenced by the rootstock genotype, but not by the scion one. Altogether, these results suggest that both rootstock and scion genotypes influence the rhizosphere and root endophytic microbiomes. It would be interesting to analyze the biochemical composition of the rhizodeposition of these genotypes for a better understanding of the processes involved in the modulation of these microbiomes. Moreover, crossing our data with the plant agronomic characteristics could provide insights into their roles on plant fitness.

The project VINIoT pursues the creation of a new technological vineyard monitoring service, which will allow companies in the wine sector in the SUDOE space to monitor plantations in real time and remotely at various levels of precision. The system is based on spectral images and an IoT architecture that allows assessing parameters of interest viticulture and the collection of data at a precise scale (level of grape, plant, plot or vineyard) will be designed. In France, three subjects were specifically developed: evaluation of maturity, of water stress, and detection of flavescence dorée. For the evaluation of maturity, it has been decided first to work at the berry scale in the laboratory, then at the bunch scale and finally in the vineyard. The acquisition of the spectral hyperstal image as well as the reference analyzes to measure the maturity, were carried out in the laboratory after harvesting the berries in a maturity monitoring context. This work focuses on a case study to predict sugar content of three different grape varieties: Syrah, Fer Servadou and Mauzac. A robust method called Roboost-PLSR, developed in the framework of this work (Courand et al., 2022), to improve prediction model performance was applied on spectra after the acquirement of hyperspectral images. Regarding the evaluation of water stress, to work with a significant variability in terms of water status, it has been worked first with potted plants under 2 different water regimes. The facilities have allowed the supervision of irrigation and micro-climatic conditions. The regression models on agronomic variables (stomatal conductance, water potential, …) are studied. To detect flavescence dorée, the experimental plan has consisted of work at leaf scale in the laboratory first, and then in the field. To detect the disease from hyper-spectral imaging, a combination of multivariate curve resolution-alternating least squares (MCR-ALS) and factorial discriminant analysis (FDA) was proposed. This strategy proved the potential towards the discrimination of healthy and infected leaves by flavescence dorée based on the use of hyperspectral images (Mas Garcia et al., 2021).

In viticulture, a warming climate can have a very significant impact on grapevine development and therefore on the quality and characteristics of wines across different spatial scales, ranging from global to local. In order to adapt wine-growing to climate change, global climate models can be used to define future scenarios, but only at the scale of major wine regions. Despite the huge progress made over the last ten years in terms of the spatial resolution of climate models (now downscaled to a few square kilometres), they are not yet sufficiently precise to account for the local climate variability associated with such parameters as local topography, in spite of these parameters being decisive for vine and wine characteristics. This study describes a method to downscale future climate scenarios to vineyard scale. Networks of data loggers have been used to collect air temperature at canopy level in the Waipara winegrowing region (New Zealand) over five growing seasons. These measurements allow the creation of fine-scale geostatistical models and maps of temperature (at 100 m resolution) for the growing season. In order to model climate change at pilot site scale, these geostatistical models have been combined with regional climate change predictions for the periods 2031-2050 and 2081-2100 based on the RCP8.5 climate change scenario. The integration of local climate variability with regionalized climate change simulations allows assessment of the impacts of climate change at the vineyard scale. The improved knowledge gained using this methodology results from the increased horizontal resolution that better addresses the concerns of winegrowers. The results provide the local winegrowers with information necessary to understand current processes, as well as historical and future viticulture trends at the scale of their site, thereby facilitating decisions about future response strategies.

Vineyards are complex agro-ecosystems with high spatial and temporal variability. An efficient training system may counteract the adverse effects of this variability. Moreover, considering the climate change issues, choosing an efficient training system that enhances water use and protects the vines from radiative thermal stress has become a priority for the farmers. A multidisciplinary approach that assesses the soil-crop-yield-wine relationships of vineyards in a distributed and holistic way could bring added knowledge on the behavior of the different training systems. This ongoing research aimed to implement a multidisciplinary approach to study the behavior of “Aglianico del Vulture” grapevines trained with two different systems: a spurred cordon (SC) and an “Alberello in parete” (AL), grown in a high-quality wine production area of Basilicata region (Italy). The approach merged several methods and scales of soil, ecophysiology, must/wine quality, and spectral data collection to assess the influence of the training system. Homogeneous zones (HZs) in both training systems were defined through a procedure based on geomorphological classification, unmanned aerial vehicles (UAV) images analysis, and a traditional soil survey supported by geophysical scanning. During the 2021 season, TDR probes monitored soil water content, while grapevine health status was assessed using eco-physiological measurements (LWP, chlorophyll content, PSII photosynthetic efficiency, LAI, and point-based field spectroscopy). These grapevine in-vivo measurements validated the spectral vegetation indexes (NDVI, RENDVI, CVI, and TVI) derived from the UAV multispectral imagery, which monitored the grapevine status in a distributed and non-invasive way. Grape yield, quality of berries, must and wine were measured to assess the effects of the training systems. The first experimental year results showed the variability of the vineyards and revealed relationships among soil parameters, crop characteristics, and vegetation indices of the SC and AL training systems. This multidisciplinary study could bring new insights into the vineyard training system’s effects on grape yield and wine quality.