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Outbreak of cucumber mosaic virus subgroup IB in pepper from the Espelette area (Basque Country, southwestern France) and first report of five taxa as natural hosts of CMV: Outbreak of CMV in the Espelette area
No full textInternational audienceTo better understand the emergence of cucumber mosaic virus (CMV) in the protected designation of origin of Espelette pepper (southwestern France), more than 7,300 samples were collected in and around 36 pepper fields in 2021 and 2022, and diagnosed using ELISA, RT-PCR and partial Sanger sequencing of viral RNAs. This allowed the identification of five new host genera or species among the natural hosts of CMV: Arum italicum, Cerastium glomeratum, Hyacinthoides sp., Lysimachia arvensis and Trifolium incarnatum. A CMV variant belonging to subgroup IB and presenting a low molecular diversity was highly prevalent in the pepper crops (78% of the pepper samples) as well as in naturally growing plants (8% of the non-pepper samples) within the fields. CMV isolates from group II were detected in a single pepper plant as well as in Hyacinthoides sp. (3 samples), Capsella bursa-pastoris (2 samples) and Stachys arvensis (1 sample). To our knowledge, this is the second report of the occurrence of subgroup IB of CMV in France. Investigation of old pepper samples indicate that it was present at least since 2009
StochasticWeatherGenerators.jl: A Julia package to generate weather sequences with Stochastic Weather Generators
No full textAlternative double strand break repair pathways shape the evolution of high recombination in the honey bee, <i>Apis mellifera</i>
No full textInternational audienceSocial insects, particularly honey bees, have exceptionally high genomic frequencies of genetic recombination. This phenomenon and underlying mechanisms are poorly understood. To characterise the patterns of crossovers and gene conversion in the honey bee genome, a recombination map of 187 honey bee brothers was generated by wholegenome resequencing. Recombination events were heterogeneously distributed without many true hotspots. The tract lengths between phase shifts were bimodally distributed, indicating distinct crossover and gene conversion events. While crossovers predominantly occurred in G/C-rich regions and seemed to cause G/C enrichment, the gene conversions were found predominantly in A/T-rich regions. The nucleotide composition of sequences involved in gene conversions that were associated with or distant from crossovers corresponded to the differences between crossovers and gene conversions. These combined results suggest two types of DNA double-strand break repair during honey bee meiosis: non-canonical homologous recombination, leading to gene conversion and A/T enrichment of the genome, and the canonical homologous recombination based on completed double Holliday Junctions, which can result in gene conversion or crossover and is associated with G/C bias. This G/C bias may be selected for to balance the A/Trich base composition of eusocial hymenopteran genomes. The lack of evidence for a preference of the canonical homologous recombination for double-strand break repair suggests that the high genomic recombination rate of honey bees is mainly the consequence of a high rate of double-strand breaks, which could in turn result from the life history of honey bees and their A/T-rich genome
Economic valuation of groundwater over-exploitation in the Maghreb
No full textInternational audienceThe agricultural sector is recognized as particularly vulnerable to the effects of climate change. In semi-arid areas, the performance and durability of irrigated systems are often difficult to manage. Understanding agriculture's response to water scarcity, institutional change and policy interventions is important in order to better define the different agricultural development pathways. The purpose of this paper is to carry out an economic assessment of the costs of groundwater over-exploitation in the Maghreb. This was achieved by using bioeconomic modeling in three case studies: the Saïss plain (Morocco), El Haouaria plain (Tunisia) and Sétif plain (Algeria). A set of indicators (land use, farm gross margin, the dual value of water and labor requirements) was calculated for each case study in two scenarios (a business-as-usual (S_BAU) scenario and a return-toequilibrium (S_RtE) scenario) over a period of 15 years, from 2021 to 2035. Our results show that (i) the state of the aquifer and its over-exploitation level determine the extent of future changes; (ii) in the case of significant groundwater over-exploitation, restoration costs are higher than over-exploitation costs (Saïss plain); on the other hand, in the case where the over-exploitation rate is lower (El Haouaria and Sétif plains), the overexploitation and restoration costs are close; (iii) both scenarios show significant structural and social changes, and without the effective implementation of environmental and social policies, they lead to high economic losses
Linking effect traits of soil fauna to processes of organic matter transformation
No full textInternational audienceSoil organic matter (SOM) transformation processes are regulated by the activities of plants, microbes, and fauna. Compared with plants and microbes, effects of soil fauna are less understood because of their high taxonomic and functional diversity, and mix of direct and indirect effect mechanisms. Trait-based approaches offer a generic perspective to quantify mechanistic relationships between soil fauna and SOM transformations, including decomposition, translocation, and stabilisation of organic carbon. Yet, at present, we lack a consensus concerning relevant key effect traits of soil fauna (i.e. those affecting ecosystem functioning).2. Here, we address this knowledge gap by focusing on relationships between soil fauna effect traits and SOM transformations. Based on existing literature, we identify key processes linked to SOM transformations, and fauna effect traits universally applicable across taxa and soil types, and discuss the process-trait links.3. We define eight SOM transformation processes that are directly affected by soil fauna: (i) litter mass loss, (ii) litter fragmentation, (iii) SOM aggregation in faeces, (iv) SOM aggregation in soil mineral particles, (v) decomposition of faeces, (vi) SOM and mineral translocation, (vii) pore space creation and maintenance and (viii) SOM stabilisation. We link these processes to general effect traits classified into four categories: (a) food selection and ingestion, (b), digestion and excretion, (c) mobility, and (d) body mass and metabolic rate. We also propose proxies when effect trait measurements are laborious.</p
Overall performances of Leucaena leucocephala and Morus alba in high-density protein banks at maturity in western Burkina Faso
No full textInternational audienceThe objective of this work was to carry out long-term monitoring of protein banks (PB) established under the real-low-input-farm conditions of Burkina Faso, characterized by a Sudano-Sahelian climate type with wide variations in rainfall. The PBs, planted in 2016–2017 with Leucaena leucocephala (LL) and Morus alba (MA) at a high density (20,000 plants/ha), were monitored from 2016/2017 to 2021 for their biomass (fodder) production, chemical composition and nutritional value of the edible fodder, and their impacts on soil carbon content. The average annual fodder production of LL for the 6 PBs (1, 2, 3, 4, 5, and 6) was 11.4 ± 2.12 t DM/ha/year, while that of MA was 3.8 ± 1.2 t DM/ha/year for the 3 PB (1, 2, and 3). Such differences are related to higher adaptive capacity for LL in such climatic conditions. Crude protein was higher in LL (19% versus 17%), but dry matter digestibility (65% versus 77%) was superior in MA. Soil carbon increased during the five monitored years, an exciting result for these poor, low-fertility soil conditions. Our results demonstrate the technical and environmental feasibility of establishing this low input agroforestry technology in these conditions and inspire the potential of sustainable agriculture as an agroecological alternative to overcoming feed shortages for local livestock farming. However, the successful management of a PB relies on selecting the right suitable species, protecting them, and managing them during the establishment and fodder production periods with suitable cutting frequency and appropriate post-harvest management
Terre disputée, oasis fragmentée. Partager les ressources, reconfigurer le pouvoir dans les oasis de Tozeur
No full textSource Agritrop Cirad (https://agritrop.cirad.fr/616967/)International audienc
The diversity of Ficus
No full textInternational audienceBackground The influence of Ficus extends beyond its numbers (887 species), and fig trees are often keystone species in their habitats. Ficus fills many tropical forest niches. The past 15 years have witnessed an explosion of research on Ficus and its obligate mutualists in the chalcid family Agaonidae, but also on its wider community of interactants. Long-standing ideas have been challenged, and pathways to speciation have been explored. We aim to stimulate collegiate discussion: why are there not more species of fig? Scope Here, we critically review the literature relating to diversification in Ficus, while presenting a synthetic overview of our current understanding and knowledge gaps. We illustrate key concepts with well-studied groups of Ficus and other obligate mutualisms. Our review is unapologetically detailed and includes extensive botanical insight that is frequently overlooked in the literature. We draw on these details to develop hypotheses relating to the origin of diversity within the genus Ficus. Conclusions We argue that the fig itself represents a new niche and explore the implications of sexual and vegetative traits in driving diversification (species richness) and diversity (in the ecological sense). An increasingly stable backbone phylogeny and the availability of genomic nuclear and chloroplast data have shed dappled light upon the deep evolutionary past. Incidences of potential diversification through introgression exist, but we must be cautious because the tools used were not always suitable for revealing ancient hybridization. An asymmetric genetic sampling of figs and wasps has further influenced our concepts of host specificity in the genus. Our comparative approach evaluates classical models of speciation in Ficus, concluding that adaptive radiations on islands have triggered diversification. We should maintain global research networks and sample widely. It is tempting to overgeneralize results. This leads to misconceptions and missing puzzle pieces. Furthermore, adoption of standard protocols ensures connectivity
<i>Zymoseptoria tritici</i> Effectors Structurally Related to Killer Proteins UmV ‐ KP4 and UmV ‐ KP6 Inhibit Fungal Growth, and Define Extended Protein Families in Fungi
No full textInternational audienceFungal effectors play crucial roles in plant infection. Despite low sequence identity, they were recently discovered to belong to families with similar three-dimensional structures. In this study, we elucidated the structures of Zt-NIP1 and Mycgr3-91409-2 effectors of the wheat fungal pathogen Zymoseptoria tritici using X-ray crystallography and NMR. These effectors displayed a structural homology with, respectively, KP4 and KP6α killer toxins from UmV dsRNA viruses of the maize fungal pathogen Ustilago maydis. Consequently, Zt-NIP1 and Mycgr3-91409-2 were renamed Zt-KP4-1 and Zt-KP6-1. Orthologues and paralogues of Zt-KP4-1 and Zt-KP6-1 were identified in Zymoseptoria, but not in other fungi, except ECP2 effectors related to Zt-KP4-1. Assessment of the biological activities of Zt-KP6-1 and Zt-KP4-1 revealed their ability to inhibit fungal growth, but they were unable to induce wheat leaf necrosis. A novel pipeline relying on cysteine-pattern constrained HMM searches and Foldseek analysis of AlphaFold2 predicted structures from Uniprot generated a comprehensive inventory of KP4 and KP6 proteins in fungi and plants. Their structure-based classification revealed four KP4 and three KP6 structural superfamilies and provided far-reaching hypotheses on their biological function and evolution. This framework highlights the power of structure determination and modelling for the classification of effectors and their functional investigation
Seasonal variability in precipitations drives flow intermittence in headwaters
No full textInternational audienceIntermittent and ephemeral streams are found across different climate, bedrock, and land use types(Messager et al., 2021). Across these gradients and the various size of intermittent catchments, drivers ofintermittency usually result from the complex interaction of meteorology, geology and land cover (Costiganet al., 2015). Climate aridity is a good predictor of flow cessation and occurrence of non-permanent streamsat the global scale while in wet and temperate regions, the occurrence of flow cessation is usually associatedwith small catchment sizes and steeper topography (Messager et al., 2021; Snelder et al., 2013; Sauquet etal., 2021). In this work, we hypothesized that at the scale of headwater catchments (< 20 km2) and targetingnon-permanent streams as recommended by Costigan et al. (2015), it would be possible to identify factorscontrolling flow intermittence across climates, geologies and land covers. We computed several metrics offlow intermittence from long-term flow records at 16 French CZO (OZCAR-RI) catchments and analyzedhow these metrics were correlated with proxies of climate, catchment size, hydrological characteristics, landuse and geology types. We found a diversity of flow intermittence regimes across these 16 catchments and formost of them, the interannual variability at a given catchment was higher than the variability among them.The spatial variability of no-flow metrics among catchments was highly correlated with the seasonal indexfor precipitation, and meteorological indices (e.g. mean annual rainfall, reference ET, temperature). Theinter annual variability was not correlated to the same meteorological variables for all catchments, whichsuggests different processes might be responsible for flow cessation in the different streams. We discuss thesensitivity to threshold values used for no-flow identification and the importance of acquiring accurate lowflow values in Observatories to study climate evolution especially droughts. a more integrated approach ofsuch intermittent streams is needed to investigate whether their diversity can be explained by the characteristicsof groundwater-stream or riparian zone-stream interfaces, and to which extend this diversity of flowregime is associated to different ecological functions.Costigan, K. H., Jaeger, K. L., Goss, C. W., Fritz, K. M., and Goebel, P. C. (2016) Understanding controlson flow permanence in intermittent rivers to aid ecological research: integrating meteorology, geology andland cover. Ecohydrol., 9: 1141–1153. doi: 10.1002/eco.1712.Messager, M.L., Lehner, B., Cockburn, C. et al. (2021) Global prevalence of non-perennial rivers andstreams. Nature 594, 391–397, https://doi.org/10.1038/s41586-021-03565-5Sauquet, E., Shanafield, M., Hammond, J.C., Sefton, C., Leigh, C., Datry, T. (2021). Classification andtrends in intermittent river flow regimes in Australia, northwestern Europe and USA: A global perspective,Journal of Hydrology, 597, 126170, https://doi.org/10.1016/j.jhydrol.2021.126170Snelder, T. H., Datry, T., Lamouroux, N., Larned, S. T., Sauquet, E., Pella, H., and Catalogne, C. (2013)Regionalization of patterns of flow intermittence from gauging station records, Hydrol. Earth Syst. Sci.,17, 2685–2699, https://doi.org/10.5194/hess-17-2685-201