Biology subjects

Rossi, J.-P.

Publications and source records attributed to Rossi, J.-P..

6 recordsLinked to original sources

bioRxiv2024

Quantitative assessment and spatial distribution of Plasmopara viticola oospores in vineyard soil

Grapevine downy mildew, caused by the oomycete Plasmopara viticola, is one of the most devastating diseases of grapevine worldwide. Primary inoculum (i.e. oospores) play a decisive role in downy mildew epidemics, but we still know very little about its abundance in vineyard soil. This study presents a novel molecular method for quantifying P. viticola oospore concentration in vineyard soil using digital droplet PCR (ddPCR). The development of this method enabled characterization of both the abundance and spatial distribution of oospores in a vineyard at the onset of the growing season. Following a regular grid, a total of 198 soil samples (0-15cm horizon) were collected in March 2022 in grapevine rows in a 0.22 ha vineyard planted with cv. Merlot and conducted according to French organic viticulture specifications. Additional samples were collected from the same field within five nested sampling plots with three distance levels, including samples collected in the inter-rows. Using ddPCR, we found P. viticola DNA in all soil samples except one, and we estimated that oospore concentration ranged from 0 to 1858 oospores per gram of soil (303 {+/-} 308 on average). The distribution of oospores at field scale was not random but characterized by 15 m-diameter patches of concentrically increasing oospore concentration. Oospores accumulated 5 times more below the vine stocks than in the inter-row. Using a leaf disc bioassay, we found that soil infectious potential significantly increased with oospore concentration assessed by ddPCR. However, the low coefficient of determination of the relationship indicated that DNA-based oospore quantification lacked clear epidemiological significance. Both ddPCR and bioassay methods are valuable tools that could be used to assess reservoirs of P. viticola primary inoculum across different agroclimatic contexts, thereby bringing greater genericity. Further methodological improvement will also help refine the accuracy of DNA-based assessment of primary inoculum reservoir and improve our understanding of the relationship between primary inoculum reservoir and epidemic dynamics. Ultimately, these data will be essential for improving epidemic risk models and evaluating new preventive disease management strategies targeting the primary inoculum. ImportanceGrapevine downy mildew caused by the oomycete Plasmopara viticola, affects leaves and bunches, and leads to important economic losses for viticulturists. Recently, evidences have accumulated that soilborne primary inoculum (i.e. oospores in the soil) importantly contributes to disease progress. The significance of our work is in presenting a direct and sensitive method for assessing soil oospore concentration, as well as quantitative and spatially-explicit data on downy mildew primary inoculum. This opens the way to new research, the evaluation of new disease control strategies based on primary inoculum management and the improvement of epidemic risk models, which will potentially contribute to lower fungicide use in viticulture in fine.

plant biology↗

bioRxiv2024

Insect-habitat-plant interaction networks provide guidelines to mitigate the risk of transmission of Xylella fastidiosa to grapevine in Southern France

O_LIXylella fastidiosa (Xf) is a xylem-limited bacterium that has been recorded in several European countries since its detection in 2013 in Apulia (Italy). Given the prominence of the wine industry in many southern European countries, a big threat is the development of Pierces disease in grapevines. Yet, the insect-habitat and insect-plant interaction networks in which xylem feeders, possible vectors of Xf, are involved around European vineyards are largely unknown. C_LIO_LIHere we describe these networks in three important wine-growing regions of southern France (Provence-Alpes-Cote dAzur, Occitanie, Nouvelle-Aquitaine) to identify the main source habitats of xylem feeders, and to gather information about their specialization degree at the habitat, plant family, and plant species levels. A total of 92 landscapes (and 700 sites) were studied over three sampling sessions in the fall 2020, the spring 2021, and the fall 2021. C_LIO_LIAmong the habitats sampled, meadows hosted the largest xylem feeder communities, followed by alfalfa fields. Vineyard headlands and inter-rows hosted slightly smaller xylem feeder communities, indicating that potential Xf vectors were thriving in the close vicinity of vulnerable plants. Finally woody habitats in general and grapevines in particular hosted very few xylem feeders, showing that transfer on vulnerable plants are rare, but not inexistent. In terms of specialization degrees, Philaenus spumarius, Aphrophora alni, Lepyronia coleoptrata, and Cicadella viridis were all similarly generalists at the habitat, plant family or plant species level. The only specialist was Aphrophora grp. salicina, which was restricted to riparian forests, and more specifically to Salicaceae. Neophilaenus spp. were extremely specialist at the plant family level (Poaceae), but rather generalist at the habitat and plant species levels. All 1017 insects screened for the presence of Xf tested negative, showing that Xf is not widespread in the studied regions. C_LIO_LIOur study provides new basic ecological information on potential vectors of Xf, especially on their specialization and feeding preferences, as well as practical information that may be relevant for the design of epidemiological surveillance plans. C_LI

ecology↗

bioRxiv2020

Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)

Despite their ecological and evolutionary importance as key components of tropical ecosystems, the phylogeny of fig trees is still unresolved. We use restriction-site-associated DNA (RAD) sequencing (ca 420kb) and 102 morphological characters to elucidate the relationships between 70 species of Ficus representing all known subgenera and sections and five outgroups. We compare morphological and molecular results to highlight discrepancies and reveal possible inference bias. We analyse marker and taxon properties that may bias molecular inferences, with existing softwares and a new approach based on iterative principal component analysis to reduce variance between clusters of samples. For the first time, with both molecular and morphological data, we recover a monophyletic subgenus Urostigma and a clade with all gynodioecious fig trees. However, our analyses show that it is not possible to homogenize evolutionary rates and GC content for all taxa prior to phylogenetic inference and that four competing positions for the root of the molecular tree are possible. The placement of the long-branched section Pharmacosycea as sister to all other fig trees is not supported by morphological data and considered as a result of a long branch attraction artefact to the outgroups. Regarding morphological features and indirect evidence from the pollinator tree of life, the topology that divides the genus Ficus into monoecious versus gynodioecious species appears most likely. Active pollination is inferred as the ancestral state for all topologies, ambiguity remains for ancestral breeding system including for the favored topology, and it appears most likely that the ancestor of fig trees was a freestanding tree. Increasing sampling may improve results and would be at least as relevant as maximizing the number of sequenced regions given the strong heterogeneity in evolutionary rates, and to a lesser extent, base composition among species. Despite morphological plasticity and frequent homoplasy of multiple characters, we advocate giving a central role to morphology in our understanding of the evolution of Ficus, especially as it can help detect insidious systematic errors that tend to become more pronounced with larger molecular data sets.

evolutionary biology↗

bioRxiv2019

Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

Recent technical advances combined with novel computational approaches promised the acceleration of our understanding of the tree of life. However, when it comes to hyperdiverse and poorly known groups of invertebrates, studies are still scarce. As published phylogenies will be rarely challenged by future taxonomists, careful attention must be paid to potential analytical bias. We present the first molecular phylogenetic hypothesis for the family Chalcididae, an emblematic group of parasitoid wasps, with a representative sampling (144 ingroups and 7 outgroups) that covers all described subfamilies and tribes and 82% of the known genera. Analyses of 538 Ultra-Conserved Elements (UCEs) with supermatrix (RAxML and IQTREE) and gene-tree reconciliation approaches (ASTRAL, ASTRID) resulted in highly supported topologies in overall agreement with morphology but reveal conflicting topologies for some of the deepest nodes. To resolve these conflicts, we explored the phylogenetic tree space with clustering and gene genealogy interrogation methods, analyzed marker and taxon properties that could bias inferences and performed a thorough morphological analysis (130 characters encoded for 40 taxa representative of the diversity). This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent /divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artefactual results. We highlight a GC-content bias for ML approaches, an artefactual mid-point rooting of the ASTRAL tree and a deleterious effect of high percentage of missing data on gene tree reconciliation methods. Based on the results we propose a new classification of the family into eight subfamilies and 10 tribes that lay the foundation for future studies on the evolutionary history of Chalcididae.

evolutionary biology↗

bioRxiv2018

Climate change and the potential distribution of Xylella fastidiosa in Europe

The bacterium Xylella fastidiosa (Xf) is a plant endophyte native to the Americas that causes worldwide concern. Xf has been recently detected in several regions outside its natural range including Europe. In that context, accurate estimates of its response to climate change are required to design cost-efficient and environment-friendly control strategies. In the present study, we collected data documenting the native and invaded ranges of the three main subspecies of Xf: fastidiosa, pauca and multiplex, as well as two strains of Xf subsp. multiplex recently detected in southern France (ST6 and ST7). We fitted bioclimatic species distribution models (SDMs) to forecast their potential geographic range and impact in Europe under current and future climate conditions. According to model predictions, the geographical range of Xf as presently reported in Europe is small compared to the large extent of suitable areas. The European regions most threatened by Xf encompass the Mediterranean coastal areas of Spain, Greece, Italy and France, the Atlantic coastal areas of France, Portugal and Spain as well as the south-western regions of Spain and lowlands in southern Italy. Potential distribution of the different subspecies / strains are contrasted but all are predicted to increase by 2050, which could threaten several of the most economically important wine-, olive- and fruit-producing regions of Europe, warranting the design of control strategies. Bioclimatic models also predict that the subspecies multiplex might represent a threat to most of Europe under current and future climate conditions. These results may serve as a basis for future design of a spatially informed European-scale integrated management strategy, including early detection surveys in plants and insect vectors, quarantine measures as well as agricultural practices.

ecology↗

bioRxiv2018

Using insects to detect, monitor and predict the distribution of Xylella fastidiosa: a case study in Corsica

We sampled ca 2500 specimens of Philaenus spumarius throughout Corsica without a priori on the presence of symptoms on plants. We screened 448 specimens for the presence of Xylella fastidiosa (Xf) using qPCR and a custom nested PCR. qPCR appeared versatile and under-estimated the prevalence of Xf. Nested PCR showed that Xf was present in all populations. Molecular results were validated by prediction on the distribution of Xf made from tests conducted on plants, which shows the pertinence of using vectors in risk assessment studies. Xf was detected in tenerals and adults. Thus, P. spumarius could acquire Xf from its host plant, mostly Cistus monspeliensis in Corsica, which may act as reservoir for the next season. This contrasts with other observations and suggests that management strategies may have to be adapted on a case-by-case basis. At least two genetic entities and several variants of Xf not yet identified on plants were present in the insects, which suggests ancient introductions of Xf and a probable underestimation of the current diversity of the strains present in Corsica. Interestingly 6% of the specimens carried two subspecies. Studies are wanted to better characterize the strains present in Corsica and know how the disease was introduced, spread and why no sign of a potential epidemic was detected earlier. This study shows that, when sensitive enough methods are implemented, insects can be used to predict and better assess the exact distribution of Xf. Insects are indeed easy to collect, Xf multiply only in their foregut and does not become circulative, which facilitates its detection.\n\nKey messageO_LIInsect vectors can be used to detect, monitor and predict the distribution of Xylella fastidiosa\nC_LIO_LIThe widely used qPCR approach is not sensitive enough to detect low bacterial load\nC_LIO_LIDifferent strains/subspecies of Xf are widely distributed in Corsica which suggests old introduction(s)\nC_LIO_LIStrategies to manage Xf may need to be set up on a case-by-case basis\nC_LIO_LIThere is an urgent need to take stock of the situation in Europe to avoid unnecessary economic pressure on certain geographical areas and agricultural sectors.\nC_LI

ecology↗