Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plantassociated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature

Le pâturage domestique comme outil de gestion de la biodiversité : L’exemple des pelouses sèches de Camargue

National audienc

Refus de pâturage Ecologie et moyens de contrôle

National audienc

High Stocking Density Controls Phillyrea Angustifolia in Mediterranean Grasslands

International audienceExtensive grazing applied in the form of low instantaneous pressure over a long period is a widespread management practice in protected areas. However this kind of stocking method does not always achieve the expected results, in particular because it fails to limit colonization by woody plants.This is the case in the relict xero-halophytic grasslands of the northern Mediterranean coastal region, subjected to widespread colonization by the shrub Phillyrea angustifolia despite the presence of extensive grazing. In this study, we investigated, for an equal annual stocking rate, the respective impact of high stocking density applied over a short period (mob grazing) and low stocking density applied over a long period on both P. angustifolia and herbaceous cover, using an in situ experimental design run for 7 years. Only mob grazing was effective both in controlling the establishment and increasing the mortality of P. angustifolia individuals. We did not find any difference after the 7 years of experimentation between the two stocking methods with regard to the herbaceous community parameters tested: species richness, diversity, evenness, contribution of annual characteristic species. By contrast, the exclusion of domestic grazing led to a strong reduction of these values.The use of mob grazing may be well suited for meeting conservation goals such as maintaining open habitats in these grasslands

Microwave soil heating reduces seedling emergence of a wide range of species including invasives

International audienc

Cressa critica L. (Convolvulaceae), host plant of the weevil Sharpia rubida (Rosenhauer, 1956) (Coleoptera, Curculionidae, Erirrhininae)

In the course of a study on Cressa cretica, an endangered plant living in transient salt marshes, we detected a parasitism involving the rare weevi l Sharpia rubida. The consequences fo r the reprodu ction of the plant may be dramatic, since up to about 90% of the flower buds are destroyed. Ovipos ition and larval developm ent of Sharpia rubida occur in the flower buds between the end of July and the end of Aug ust. The fourth-instar larvae pupate in the soil. Adults emerge in September and overwinter in the surrounding vegetation

Using Microwave Soil Heating to Inhibit Invasive Species Seed Germination

International audienceSuccessful invasive plant eradication is rare, because the methods used target the adult stage, not taking into account the development capacity of a large seedbank. Heating by microwave was considered, because it offers a means to quickly reach the temperature required for loss of seed viability and inhibition of germination. Previous results were not encouraging, because homogeneous and deep-wave penetration was not achieved, and the various parameters that can affect treatment effectiveness were incompletely addressed. This study aimed to determine, under experimental conditions, the best microwave treatment to inhibit invasive species seed germination in terms of power (2, 4, 6 kW) and duration (2, 4, 8 min) of treatments and depending on soil moisture (10%, 13%, 20%, 30%) and seed burial depth (2, 12 cm). Three invasive species were tested: Bohemian knotweed, giant goldenrod, and jimsonweed. The most effective treatments required relatively high power and duration (2kW8min, 4kW4min, 6kW2min, and 6kW4min; 4kW8min and 6kW8min were not tested for technical reasons), and their effectiveness diminished with increasing soil moisture with germination percentage between 0% and 2% for the lowest soil moisture, 0% and 56% for intermediate soil moisture, and 27% and 68% in control treatments. For the highest soil moisture, only 2kW8min and 4kW4min reduced germination percentage between 2% and 19%. Occasionally, germination of seeds located at the 12-cm depth was more strongly affected. Giant goldenrod seeds were the most sensitive, probably due to their small size. Results are promising and justify further experiments before developing a field microwave device to treat large volumes of soil infested by invasive seed efficiently and with reasonable energy requirements. Other types of soil, in terms of texture and organic matter content, should be tested in future experiments, because these factors influence soil water content and, consequently, microwave heating

Cressa critica L. (Convolvulaceae), host plant of the weevil Sharpia rubida (Rosenhauer, 1956) (Coleoptera, Curculionidae, Erirrhininae)

In the course of a study on Cressa cretica, an endangered plant living in transient salt marshes, we detected a parasitism involving the rare weevi l Sharpia rubida. The consequences fo r the reprodu ction of the plant may be dramatic, since up to about 90% of the flower buds are destroyed. Ovipos ition and larval developm ent of Sharpia rubida occur in the flower buds between the end of July and the end of Aug ust. The fourth-instar larvae pupate in the soil. Adults emerge in September and overwinter in the surrounding vegetation

Recasting the dynamic equilibrium model through a functional lens: the interplay of trait-based community assembly and climate

[Departement_IRSTEA]Territoires [TR1_IRSTEA]SEDYVINInternational audience1. According to the dynamic equilibrium hypothesis (DEH), plant species richness is locally controlled by productivity and disturbance. Given that regional conditions widely affect local environmental variables such as soil nutrient availability, the DEH predictions could be improved by considering how climate influences local controls of species richness. Further, a trait-based approach to community assembly has the potential to reveal a deeper, mechanistic understanding of species richness variation across environments. Here, we bring together DEH and trait-based community assembly expectations to examine whether and how local relationships between diversity, disturbance and productivity are affected by habitat filtering and regional climate.2. We specifically tested how gradients of local nutrient availability and disturbance intensity interact with climatic conditions to drive the species richness of grassland communities. Further, we recast the DEH through a functional lens by exploring how disturbance–diversity and nutrient availability–diversity relationships are shaped by the functional space occupied by species in a community and species packing within this functional space.3. The functional space occupied by co-occurring species and the way they are functionally packed are quantified using multi-trait indices calculated with five core plant functional traits. Working with grassland communities spread across differing regional climatic conditions, we used mixed models to test whether the variation in taxonomic and functional metrics corresponded to the DEH predictions as well as to determine the relationship between those metrics.4. Contrary to the expectations based on the relation between species richness and the functional components considered, taxonomic and functional metrics did not vary in accordance along environmental gradients. Climate strongly interacted with the local environment to modulate local diversity patterns, sometimes even inversing a given trend and falsifying the DEH predictions.5. Synthesis. Our findings quantitatively highlight the interplay between regional and local environmental gradients in driving community assembly. We demonstrate that, depending on climatic conditions, observed patterns of both taxonomic and functional community composition can be opposite to expected productivity–diversity and disturbance–diversity relationships. This emphasizes the relevance of multifaceted studies of biodiversity and the need for a more systematic quantification of regional controls in community assembly studies

When does grazing generate stable vegetation patterns in temperate pastures?

International audienceThe stability of grazing-induced spatial patterns of vegetation was analyzed at two spatial scales (25 m × 20 m areas and 1.6 m × 0.8 m grids) in pastures of contrasting productivity (maximum standing biomass: 130–800 gDM/m 2). At both scales, the mosaic of grazed and ungrazed patches was modeled as a Boolean process, calculating cross-variograms to quantify the temporal stability of grazing patterns and its links with local floristic composition were tested. The scale at which stability of vegetation patterns took place in two successive years depended on pasture productivity. Inter-annual stability of large-scale patterns mainly occurred in extensively used fertile pastures grazed by cattle, and in pastures grazed by horses. Less-fertile grasslands were mainly characterized by a fine-scale stability of grazing patterns. Stable fine-scale patterns were often related to the local abundance of legumes and forbs. Stable large-scale patterns of grazing within lightly grazed productive grasslands could result in divergent local vegetation dynamics, which can be seen as an opportunity for restoring biodiversity in fertile grasslands