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Abstract Quantifying healthy and degraded inner tissues in plants is of great interest in agronomy, for example, to assess plant health and quality and monitor physiological traits or diseases. However, detecting functional and degraded plant tissues in-vivo without harming the plant is extremely challenging. New solutions are needed in ligneous and perennial species, for which the sustainability of plantations is crucial. To tackle this challenge, we developed a novel approach based on multimodal 3D imaging and artificial intelligence-based image processing that allowed a non-destructive diagnosis of inner tissues in living plants. The method was successfully applied to the grapevine (Vitis vinifera L.). Vineyard’s sustainability is threatened by trunk diseases, while the sanitary status of vines cannot be ascertained without injuring the plants. By combining MRI and X-ray CT 3D imaging with an automatic voxel classification, we could discriminate intact, degraded, and white rot tissues with a mean global accuracy of over 91%. Each imaging modality contribution to tissue detection was evaluated, and we identified quantitative structural and physiological markers characterizing wood degradation steps. The combined study of inner tissue distribution versus external foliar symptom history demonstrated that white rot and intact tissue contents are key-measurements in evaluating vines’ sanitary status. We finally proposed a model for an accurate trunk disease diagnosis in grapevine. This work opens new routes for precision agriculture and in-situ monitoring of tissue quality and plant health across plant species.

Since its identification in 2003, little has been revealed about the spread of grapevine Pinot gris virus (GPGV), an emerging grapevine virus. According to studies from Italy, GPGV transmission in the vineyard can be fast but progressive over the years. To gain new insights into the spread of GPGV infections, we tested 67 grapevines in a single vineyard parcel in southern France. These vines were sampled over 8 years (2013 to 2020) and tested for GPGV by reverse-transcription PCR using a new primer pair designed from the recently described genetic diversity of GPGV worldwide. While focusing on a portion of the samples (n = 20), we observed a drastic increase in newly GPGV-infected vines from 2014 (5%, 1 of 20) to 2015 (80%, 16 of 20) and 2016 (90%, 18 of 20). Infected vines were scattered throughout the vineyard with no distinct pattern of distribution, and some rare vines remained negative through 2020. Using all available genomic information, we performed Bayesian-based phylogeographic analyses that identified a major intravineyard transmission in 2014 to 2015. To test our model, we analyzed 47 additional grapevines and confirmed the outbreak of GPGV in 2015, validating our in silico projection. Interestingly, some grapevines remained negative throughout the study, in spite of their close proximity to infected plants. These results raise questions about the dynamics of vector populations and environmental conditions that may be required for virus spread to occur in the vineyard.

Plants are able to naturally graft or inosculate their trunks, branches and roots together, this mechanism is used by humans to graft together different genotypes for a range of purposes. Grafts are considered successful if functional vascular connections between the two genotypes occur. Various techniques can evaluate xylem connections across the graft interface. However, these methods are generally unable to assess the heterogeneity and three‐dimensional (3D) structure of xylem vessel connections. Here we present the use of X‐ray micro‐computed tomography to characterize the 3D morphology of grafts of grapevine. We show that xylem vessels form between the two plants of natural root and human‐made stem grafts. The main novelty of this methodology is that we were able to visualize the 3D network of functional xylem vessels connecting the scion and rootstock in human‐made stem grafts thanks to the addition of a contrast agent to the roots and improved image analysis pipelines. In addition, we reveal the presence of extensive diagonal xylem connections between the main axial xylem vessels in 2‐year old grapevine stems. In conclusion, we present a method that has the potential to provide new insights into the structure and function of xylem vessels in large tissue samples. Summary statement: Successful grafting requires the formation of functional vascular connections between two different plants. We describe using X‐ray micro‐computed tomography to characterize the network of xylem vessels formed across the graft interface of natural root and human‐made stem grafts of grapevine. [ABSTRACT FROM AUTHOR]

The production of grafted grapevine plant material is a complex process with many steps running over at least one year, from grafting to final sorting in nurseries. To reach the market in France, grafted grapevines must meet three criteria by law: resistance to a manual graft union test (or thumb test), a minimum number of three roots and a woody, lignified stem which has grown from the bud of the scion wood of at least 2 cm long. This study aimed to evaluate the possibility of using visual criteria to select good quality grafted grapevines, without the need to do the thumb test because the thumb test is manual and therefore very subjective; the test depends on the strength applied by the person who realises it. This study was done on 22 scion/rootstock combinations with different degrees of grafting success, i.e., producing different proportions of marketable plants after one year in the nursery. The three legal criteria currently used to select marketable grafted grapevines in France as well as other external and measurable criteria such as the length of lignified stem and diameter, the number of thin and thick roots, and rootstock wood diameter were measured on the 22 scion/rootstock combinations. Variation in the values for these different criteria was observed and correlations between the criteria and the number of marketable plants were studied. This data was then analysed to determine which visible criteria contribute most to identifying marketable grafts. The percentage of marketable grafts was most strongly correlated with the thumb test and positively correlated with the length of the lignified stem. The variables with the highest predictive effect for identifying marketable plants (other than the thumb test) were the number of large roots and the length of the lignified stem. The possibility of using visible criteria to screen for good quality grafted plants is discussed, but no single, or combination of criteria, was sufficiently strongly correlated with the percentage of marketable plants to replace the thumb test.

The recently described member of the genus Trichovirus grapevine Pinot gris virus (GPGV) has now been detected in most grape-growing countries. While it has been associated with severe mottling and deformation symptoms under some circumstances, it has generally been detected in asymptomatic infections. The cause(s) underlying this variable association with symptoms remain(s) subject to speculations. GPGV genetic diversity has been studied using short genomic regions amplified by RT-PCR but not so far at the pan-genomic level. In an attempt to gain insight into GPGV diversity and evolutionary history, a systematic datamining effort was performed on our own high-throughput sequencing (HTS) data as well as on publicly available sequence read archive files. One hundred new complete or near complete GPGV genomic sequences were thus obtained, together with 69 new complete genomes for the other grapevine-infecting Trichovirus, grapevine berry inner necrosis virus (GINV). Phylogenetic and diversity analyses revealed that both viruses likely have their origin in Asia and that China is the most probable country of origin of GPGV. However, despite their common taxonomy, origin, and host, these two trichoviruses display very distinct genetic features and evolutionary traits. GINV shows an important overall genetic diversity, and is likely evolving under a balancing selection in a very restricted region of the world. On the contrary, GPGV shows a worldwide distribution with a modest genetic diversity and presents a strong selective sweep pattern. Taken together, these results show how two closely related trichoviruses differ drastically in their evolutionary history and epidemiological success. Possible causes for these differences are discussed.

Biological invasions are one of the main global threats to biodiversity in terrestrial, freshwater and marine ecosystems worldwide, requiring effective inventorying and monitoring programs. Here, we present an updated list of non-indigenous species in French marine and transitional waters. Focused on eukaryote pluricellular species found throughout the three metropolitan French marine regions (Western Mediterranean Sea, Bay of Biscay and the Northern Seas), a total of 342 non-indigenous, including 42 cryptogenic, species are listed as having been introduced since the 13th century. The majority of the species originated from the temperate Northern Pacific. They mainly arrived through both ballast and hull fouling and also are associated with shellfish farming activities. Most of them have been introduced since the 1970s, a time when maritime and aquaculture trade intensified. Despite important human-aided opportunities for species transfer between the three marine regions (for instance, via recreational boating or aquaculture transfers), only a third of these NIS are common to all regions, as expected due to their environmental specificities.

The recent development and miniaturization of hyperspectral sensors embedded in drones has allowed the acquisition of hyperspectral images with high spectral and spatial resolution. The characteristics of both the embedded sensors and drones (viewing angle, flying altitude, resolution) create opportunities to consider the use of hyperspectral imagery to map and monitor macroalgae communities. In general, the overflight of the areas to be mapped is conconmittently associated accompanied with measurements carried out in the field to acquire the spectra of previously identified objects. An alternative to these simultaneous acquisitions is to use a hyperspectral library made up of pure spectra of the different species in place, that would spare field acquisition of spectra during each flight. However, the use of such a technique requires developed appropriate procedure for testing the level of species classification that can be achieved, as well as the reproducibility of the classification over time. This study presents a novel classification approach based on the use of reflectance spectra of macroalgae acquired in controlled conditions. This overall approach developed is based on both the use of the spectral angle mapper (SAM) algorithm applied on first derivative hyperspectral data. The efficiency of this approach has been tested on a hyperspectral library composed of 16 macroalgae species, and its temporal reproducibility has been tested on a monthly survey of the spectral response of different macro-algae species. In addition, the classification results obtained with this new approach were also compared to the results obtained through the use of the most recent and robust procedure published. The classification obtained shows that the developed approach allows to perfectly discriminate the different phyla, whatever the period. At the species level, the classification approach is less effective when the individuals studied belong to phylogenetically close species (i.e., Fucus spiralis and Fucus serratus).

Beside the well-known fungal pathologies, grapevine virus diseases are of major importance in grapegrowing areas, also due to the limited knowledge by the professionals of the sector. To face this problem, the PAThOGEN training program was developed, with the aims of: (i) building a high-quality Vocational and Education Training program, (ii) improving the skills of the main actors of the wine sector. The pilot courses were developed in two levels (Basic and Advanced) and made available on a dedicated online platform in 4 languages (French, Italian, Spanish and English). Moreover, two field sessions were organized in each of the 3 partner countries in order to complete the theoretical training. A specific feature of this project was the “demand driven approach” used to conceive the courses. Indeed, a panel of experts and 128 “student-testers” were selected in the 3 countries in the different professional categories to test the training program. 98% of the testers evaluated the training course as “interesting” or “very interesting”. The detailed evaluations allowed us to rework the courses both in terms of content and functionality. The elearning training is now available in the four languages, and the field training is annually organized in France, Italy and Spain.

This study aims to evaluate the anthropogenic pressure in the St. Lawrence River by assessing the relationships between composition and chemical contamination of sediments and macroinvertebrate community structure using a selection of indices and metrics. The aims of this study are to (i) determine the composition of macroinvertebrate community in sediments across a gradient of disturbance, (ii) select relevant macroinvertebrate indices and metrics for the assessment of sediment quality, (iii) investigate whether responses of selected indices and metrics differ across habitats and/or sediment quality classes, and finally, (iv) determine the thresholds for critical contaminants related to significant changes in the most relevant indices and metrics. Organic and inorganic contaminants as well as other sediment variables (sediment grain size, total organic carbon, nutrients, etc.) and macroinvertebrate assemblages were determined in 59 sites along the river. Fourteen macroinvertebrate indices and metrics, on the 264 initially selected, were shown to be the most effective to be used in bioassessment for the St. Lawrence River. However, the variation in macroinvertebrate indices and metrics remains strongly explained by habitat characteristics, such as sediment grain size or the level of nutrients. There is also an influence of metals and, to a lesser extent, organic contaminants such as petroleum hydrocarbons. The 14 selected indices and metrics are promising bioassessment tools that are easy to use and interpret in an environmental assessment of sediment quality in the St. Lawrence River.

The nutritional benefits of pomegranate have attracted great scientific interest. The pomegranate, including the pomegranate peel, has been used worldwide for many years as a fruit with medicinal activity, mostly antioxidant properties. Among chronic diseases, osteoporosis, which is associated with bone remodelling impairment leading to progressive bone loss, could eventually benefit from antioxidant compounds because of the involvement of oxidative stress in the pathogenesis of osteopenia. In this study, with in vivo and ex vivo experiments, we investigated whether the consumption of pomegranate peel extract (PGPE) could limit the process of osteopenia. We demonstrated that in ovariectomized (OVX) C57BL/6J mice, PGPE consumption was able to significantly prevent the decrease in bone mineral density (−31.9%; p < 0.001 vs. OVX mice) and bone microarchitecture impairment. Moreover, the exposure of RAW264.7 cells to serum harvested from mice that had been given a PGPE-enriched diet elicited reduced osteoclast differentiation and bone resorption, as shown by the inhibition of the major osteoclast markers. In addition, PGPE appeared to substantially stimulate osteoblastic MC3T3-E1 alkaline phosphatase (ALP) activity at day 7, mineralization at day 21 and the transcription level of osteogenic markers. PGPE may be effective in preventing the bone loss associated with ovariectomy in mice, and offers a promising alternative for the nutritional management of this disease.