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Main conclusions and perspectives from the collective scientific assessment of the effects of plant protection products on biodiversity and ecosystem services along the land-sea continuum in France and French overseas territories
No full textPreservation of biodiversity and ecosystem services is critical for sustainable development and human well-being. However, an unprecedented erosion of biodiversity is observed and the use of plant protection products (PPP) has been identified as one of its main causes. In this context, at the request of the French Ministries responsible for the Environment, for Agriculture and for Research, a panel of 46 scientific experts ran a nearly 2-year-long (2020–2022) collective scientific assessment (CSA) of international scientific knowledge relating to the impacts of PPP on biodiversity and ecosystem services. The scope of this CSA covered the terrestrial, atmospheric, freshwater, and marine environments (with the exception of groundwater) in their continuity from the site of PPP application to the ocean, in France and French overseas territories, based on international knowledge produced on or transposable to this type of context (climate, PPP used, biodiversity present, etc.). Here, we provide a brief summary of the CSA's main conclusions, which were drawn from about 4500 international publications. Our analysis finds that PPP contaminate all environmental matrices, including biota, and cause direct and indirect ecotoxicological effects that unequivocally contribute to the decline of certain biological groups and alter certain ecosystem functions and services. Levers for action to limit PPP-driven pollution and effects on environmental compartments include local measures from plot to landscape scales and regulatory improvements. However, there are still significant gaps in knowledge regarding environmental contamination by PPPs and its effect on biodiversity and ecosystem functions and services. Perspectives and research needs are proposed to address these gaps
Ethnolinguistic and genetic diversity of fonio (Digitaria exilis) in Senegal
Get PDFSocietal Impact Statement Fonio (Digitaria exilis—Kippist—Stapf) is a neglected cereal crop that plays a crucial role in the food and nutritional security of sub-Saharan populations. Currently threatened with extinction in many countries, fonio, like other minor species, could help give insights into the history of African agriculture and provide clues to past social interactions. Highlighting and preserving genetic diversity that can be used to develop improved varieties improves food security. By recognizing the role of indigenous people and local communities (IPLCs) in agrobiodiversity creation and management, this study provides support for strengthening the rights of rural communities and promoting their food and seed sovereignty as outlined in the United Nations UNDROP Declaration. Summary Fonio (Digitaria exilis) is a neglected cereal crop that plays a crucial role in the food and nutritional security of sub-Saharan populations. It is an excellent candidate to diversify agricultural and food systems beyond Africa because of its adaptability and hardiness. However, fonio is threatened with extinction and the factors that organize its genetic diversity remain unknown, despite the fact that this knowledge is necessary to define conservation strategies and uses to achieve sustainable agriculture. Here, we combined social anthropology and population genetics analysis of 158 fonio landraces, thereby generating insight into the genetic diversity, population structure and evolutionary history of fonio cultivation in Senegal. We noted a spatial structure of genetic diversity at two embedded levels, with the first corresponding to the genetic differentiation between ethnic groups and the second to the demographic history of the Mande and Atlantic Congo linguistic families. Selection and seed exchange practices have contributed to shaping fonio genetic diversity at the ethnic level, while the migration of Fulani people over the last 500 years has fragmented the Mandinka kingdom, hence leaving a fonio diversity imprint. Our study highlighted that social factors are pivotal in structuring diversity and should be taken into greater consideration in research and conservation projects to dovetail local and regional scales. It also showed that neglected species such as fonio—which are seldom used in breeding and dissemination programmes—are key markers of the history of African agriculture
Advancing biomonitoring of eDNA studies with the Anaconda R package: Integrating soil and One Health perspectives in the face of evolving traditional agriculture practices
Get PDFSoil health and One Health are global concerns, necessitating the development of refined indicators for effective monitoring. In response, we present the Anaconda R Package, a novel tool designed to enhance the analysis of eDNA data for biomonitoring purposes. Employing a combination of different approaches, this package allows for a comprehensive investigation of species abundance and community composition under diverse conditions. This study applied the Anaconda package to examine the impact of two types of duration fire-fallow cropping systems, using natural forests as a reference, on soil fungal and bacterial communities in Maré Island (New Caledonia). Condition-specific taxa were identified, particularly pathogenic fungi and bacteria, demonstrating the importance of long-term fallowing efforts. Notably, this package also revealed the potential contributions of beneficial soil microbes, including saprophytes and plant-endophyte fungi, in suppressing soil-borne pathogens. Over-represented microbial ASVs associated with both plant and animal pathogens, including those of potential concern for human health, were identified. This underscores the importance of maintaining intrinsic balance for effective disease suppression. Importantly, the advanced analytical and statistical methods offered by this package should be harnessed to comprehensively investigate the effects of agricultural practice changes on soil health within the One Health framework. Looking ahead, the application of this method extends beyond the realm of One Health, offering valuable insights into various ecological scenarios. Its versatility holds promise for elucidating complex interactions and dynamics within ecosystems. By leveraging this tool, researchers can explore the broader implications of agricultural practice modifications, facilitating informed decisions and sustainable environmental management
New, complete circularized genomes of Xanthomonas citri pv. mangiferaeindicae produced from short- and long-read co-assembly shed light on strains that emerged a decade ago on mango and cashew in Burkina Faso
No full textWe report high-quality genomes of three strains of Xanthomonas citri pv. mangiferaeindicae, the causal agent of mango bacterial canker disease, including the pathotype strain of this pathovar and two strains from Burkina Faso that emerged a decade ago. These strains hosted two to three plasmids of sizes ranging from 19 to 86 kb. Genome mining revealed the presence of several secretion systems and effectors involved in the virulence of xanthomonads with (i) a type I secretion system of the hlyDB group; (ii) xps and xcs type II secretion systems; (iii) a type III secretion system with several type III effectors, including transcription activator-like effectors; (iv) several type IV secretion systems associated with plasmid or integrative conjugative elements mobility; (v) three type V secretion system subclasses (Va, Vb, and Vc); and (vi) a single i3* type VI secretion system. The two strains isolated in Burkina Faso from mango (Mangifera indica) and cashew (Anacardium occidentale) differed by only 14 single-nucleotide polymorphisms and shared identical secretion systems and type III effector repertoires. Several transcription activator-like effectors were identified in each strain, some of which may target plant genes previously found implicated in disease development in other xanthomonad-associated pathosystems. These results support the emergence in Burkina Faso a decade ago of very closely related strains that became epidemic on mango and cashew (i.e., two distinct host genera of a same plant family). These new genomic resources will contribute to better understanding the biology and evolution of this agriculturally major crop pathogen
New results related to residual fertility and re-mating in the sterile insect technique against fruit flies
No full textThe sterile insect technique (SIT) is an old autocidal control method used to fight pest and vectors of diseases [6]. Most of SIT models are dedicated to mosquitoes, like [1–4], while very few models have been developed for other pest, like fruit flies [5]. In fact, fruit flies do not have the same biological cycle than mosquitoes. In particular, contrary to mosquitoes, fruit flies can re-mate, between, so-called, refractory periods. This re-mating can have multiple consequences on SIT efficiency. Based on [5], we build a new model taking into residual fertility, double re-mating, different refractory periods related to an initial mating with a wild or a sterile male, and also the fact that the competitiveness of sterile males may change between the first mating and the second mating. We explore the impact of all these issues, theoretically and numerically, on SIT efficiency. This presentation stands within the framework of an ongoing project in Réunion island, AttracTIS [7], which aims at studying a combination of control tools against the oriental fruit fly, Bactrocera dorsalis, that invaded Réunion island in 2017 and, since then, has impacted significantly the production of fruits, in particular mangos
Molecular diagnosis of Phlebovirus riftense Infection using an L-Segment-BasedReal-TimeRT-PCR method
No full textRift Valley fever (RVF) is one of the main vector-borne zoonotic diseases that affects a wide range of ruminants and humans in Africa and the Arabian Peninsula. Several techniques involving cell culture and molecular biology methods have been developed to diagnose RVF infection. Success partly relies on sending samples to a national or reference laboratory in good conditions and having the capacity to perform the appropriate diagnostic test in the matrix of interest during the period of viremia where high loads of viral particles are present. Conventional and duplex/multiplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assays are currently the most rapid and sensitive molecular tests for the detection and quantification of Rift Valley fever virus (RVFV) during outbreaks. The one-step real-time duplex RT-PCR technique that is detailed in this chapter is based on the L segment of RVFV. Results must be carefully validated and interpreted, taking into account the results of both positive and negative controls
On the tracks of an uninvited guest, the Asian tiger mosquito, Aedes albopictus in Cyprus
Get PDFBackground: Aedes albopictus, the Asian tiger mosquito, which is listed among the world's 100 most dangerous invasive species, is the main vector of chikungunya, dengue and Zika viruses. This mosquito species has rapidly dispersed and invaded much of the globe assisted by its life history traits and high propagule pressure driven by human activities. Aedes albopictus is currently widespread across mainland Europe and the Mediterranean region, including the islands. Cyprus remained free of Ae. albopictus until October 2022, when specimens were recorded for the first time in Limassol district, including the port area. Understanding the processes associated with the introduction, expansion and establishment of this vector in Cyprus is of primary importance to mitigate its dispersal on the island, and to implement control methods to prevent disease outbreaks. A genetic analysis of these invasive specimens collected in Limassol district and in areas from the Central Mediterranean was performed to obtain a genetic portrait of the demographic history of the invasive mosquitoes on Cyprus. Methods: We applied highly polymorphic simple sequence repeat (SSR) markers to the Ae. albopictus mosquitoes collected in Cyprus and to specimens from Italy, France, Switzerland, the Balkans, Greece and Turkey to construct an SSR individual genotype dataset that would enable the invasion pattern of Ae. albopictus in Cyprus to be traced. Bayesian clustering analyses using STRUCTURE and BayesAss version 3 were employed to derive information on the degree of ancestry among Cypriot and Mediterranean mosquitoes and on recent mosquito movements both within Cyprus and between Cyprus and the Central Mediterranean areas. Results: The Cypriot mosquitoes appear to be highly polymorphic with no signs of genetic drift due to recent founder effects. An ongoing mosquito dispersal within the Limassol district was detected, suggesting the presence of established, hidden adventive populations. These mosquitoes share a high degree of ancestry with those in the Balkans and parts of northern Italy that border the Adriatic Sea. Conclusions: Considering the trade connections of Limassol port, Cyprus with the Balkans and the Adriatic Italian region, we hypothesise that these areas may be involved in the incursion of Ae. albopictus into Cyprus. As the Balkan and Italian mosquitoes display high competence for CHIKV, questions arise about possible arbovirus outbreaks in Cyprus and highlight the need to implement surveillance and control measures
Effects of vegetation growth on soil microstructure and hydro-mechanical behaviour
No full textLiterature studies are presenting counterposed effects of vegetation on soil hydraulic behaviour. Besides, root impacts at the micro-scale are rarely correlated to phenomenological observations due to the complexity of adopting up-scaling factors. In this study, the microstructural causes behind observed changes in vegetated compacted clayey sand's hydraulic and volume change behaviour were explored. Laboratory experiments were carried out on compacted samples seeded with Cynodon dactylon. Significant changes in soil water-saturated permeability, water retention and shrinkage upon drying were observed after root growth. Laboratory measurements were complemented by the quantification of root morphological features and observations at the micro-scale for different soil hydraulic states. X-ray scans and mercury intrusion porosimetry allowed to cover seven orders of magnitude of pore sizes, shedding light on soil fabric changes at the soil–root interface and the clay aggregate scale. The effects of roots on the soil pore size distribution consisted of Multiphysics phenomena: fissure generation, void clogging and soil aggregation due to roots' chemical interaction. Furthermore, a good correlation was found between the normalised volume of roots and the micro-pores volume. This new expression was included in a framework to predict soil water retention behaviour considering the aggregated structure and soil–root hydro-chemical interactions
Limited transmission of avian influenza viruses, avulaviruses, coronaviruses and Chlamydia sp. at the interface between wild birds and a free-range duck farm
Get PDFRecent outbreaks of highly pathogenic avian influenza in Europe have raised questions regarding the epidemiological role of commensal wild birds on free-range poultry farms. This study aimed to assess the prevalence of avian influenza viruses (AIV), avulaviruses, coronaviruses and Chlamydia sp. in commensal wild birds on a free-range duck farm in southwestern France and to evaluate possible transmission events at the wild‒domestic interface. From 2019 through 2021, a longitudinal study was conducted on wild birds, domestic ducks and their shared environment on farms. Commensal wild birds were captured and sampled for blood and swabs, and fresh feces from cattle egrets visiting the farm were collected. In parallel, domestic ducks were sampled, and environmental samples were collected. The presence of the four pathogens was tested by q(RT-)PCR, and the immunity of wild birds to AIV and Newcastle disease virus (NDV) was tested by ELISA. Wild birds were found to shed AIV and Chlamydia only, with a low prevalence (< 3%). The seroprevalence rates were less than 10% for AIV and less than 4.5% for NDV. No significant temporal trend was identified. Ducks and their environment frequently test simultaneously positive for the same pathogens (19 to 44% of flocks), mostly during fall‒winter. In addition to unrelated temporal patterns, the identification of pathogens in wild birds seemed unrelated to that in domestic ducks. These results suggest a low transmissibility of the avian pathogens tested in our study at the wild‒domestic interface and highlight the limited contribution of commensal wild birds in comparison with free-range poultry to the global microbiological pressure on the environment