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A ribodepletion and tagging protocol to multiplex samples for RNAsseq based virus detection: Application to the cassava virome
Get PDFBackground: Cassava (Manihot esculenta, Crantz), is a staple food and the main source of calories for many populations in Africa, but the plant is beset by several damaging viruses. So far, eight families of virus infecting cassava have been identified; the Geminiviridae (ssDNA viruses responsible for cassava mosaic disease, CMD) and Potyviridae (ssRNA + viruses responsible for cassava brown streak disease, CBSD) families being the most damaging to cassava in Africa. In several cassava-growing regions, the co-existence of species and strains from these two families results in a complex epidemiological situation making it difficult to correctly identify the viruses in circulation and delaying the implementation of disease management schemes. Nevertheless, the development of next generation sequencing (NGS) methods has revolutionized plant virus detection and identification. One NGS method that has been successfully used in virus detection and identification is ribodepleted RNA sequencing. Unfortunately, the relatively high cost makes it difficult to upscale this method to large epidemiological surveys and limits its adoption as a diagnostic tool. Results: Here, we develop a high-throughput sequencing protocol, named Ribo-M-Seq, that combines plant rRNA ribodepletion, cDNA synthesis, tagging with a 96 multiplexing scheme and Illumina sequencing. We evaluated the protocol on a series of cassava samples with a known assemblage of viruses. After confirming that the protocol was suitable for ribodepletion, we demonstrated it was possible to detect RNA and DNA viruses via identification of near full-size genomes. Additional phylogenetic analyses confirmed the presence of begomoviruses and ipomoviruses responsible for CMD and CBSD, respectively. We also detected a recently described ampelovirus (Manihot esculenta-associated virus) that was not detected in previous analyses. Conclusions: The use of the Ribo-M-Seq protocol will pave the way for large-scale sample analyses of collections with potentially complex viromes, such as those collected in the West African cassava integrated pest management program
Text mining methods for automated data extraction to create a tropical weeds traits database
No full textWeeds are among the most significant biotic reducing factors to crop production, causing major yield losses, particularly in tropical agroecosystems where they benefit from favorable climate conditions. However, the high diversity of tropical weeds (more than 1,700 species observed) is still poorly known, especially from a trait-based perspective. Beyond impeding their identification, this knowledge gap strongly limits our understanding of how they respond to the environment and agricultural practices, which significantly compromises the development of appropriate agroecological management. Currently, quantitative data on tropical weed traits are scarce and often difficult to extract. Moreover, qualitative data are heterogeneous from a semantic, syntactic and structural point of view and come from various sources (e.g., databases or herbarium websites such as TRY, GBIF, Kew Garden, WIKTROP, Seed Information Database) in various formats (e.g., numeric, textual, graphical) making them difficult to access, integrate, analyze and model. Though, there is a need to gather, consolidate and standardize the existing knowledge on tropical weed traits to better understand how biotic and abiotic filters influence their growth, development, and effects on cropping systems performances. Our work aims to create a global trait database dedicated to tropical weeds based on existing online sources. Based on an extensive list of tropical weed species, we use and compare different web scraping and text mining algorithms to collect, sort out, clean and organize relevant qualitative and quantitative data on plant traits in a large sense (i.e. information on plants and organs morphology, growth, physiology, phenology, ecology) from various pre-identified data sources. Using these methods provides access to nonnumerical data (e.g. plant reproduction habits) and allows us to explore “grey literature” to enrich our database. Then, the information gathered is filtered and standardized into a database to enable comparative analyses of species traits. We then address the benefits of our approach in the context of weed science. Drawing on recent data science methods, this work represents a crucial step towards filling in the knowledge gaps concerning these numerous tropical weed species and should help the development of sustainable weed management practices in tropical cropping systems
Global carbon markets and rural development in Madagascar
Get PDFNature-based carbon offset initiatives have proliferated across the Global South through the voluntary carbon market (VCM). Although often framed as “win-win” solutions for both climate mitigation and local development, evidence from Madagascar suggests that the VCM's development potential should be ap- proached with caution due to three key constraints. The sector comprises a diverse range of actors, including governmental agen- cies, non-governmental organisations, and private sector entities. The latter often prioritise corporate profit over development outcomes for local commu- nities. Notably, dominant carbon standards remain silent on stringent bene- fit-sharing mechanisms, allowing companies to establish projects with mini- mal community engagement. There is often a significant gap between investment commitments and actual implementation, raising concerns about the scale and durability of such pro- jects, as well as their impact on local communities and territories. Even for community-based initiatives, the financial sustainability and scala- bility of projects remains uncertain due to the volatility of carbon-credit prices and structural barriers on the ground. At the same time, many rural commu- nities in Madagascar live below the international poverty line, and enabling their participation in carbon markets can serve as a valuable strategy for di- versifying income portfolios
When farmers' knowledge matters: Improving epidemiological understanding of Peste des petits ruminants in northern Nigeria
Get PDFPeste des petits ruminants (PPR) is an endemic disease of sheep and goats in Nigeria and represents a major threat to the livelihoods of smallholders. Understanding the epidemiology of this disease and its management by livestock farmers is essential for developing appropriate surveillance and control programmes. This study aimed to enhance the knowledge about PPR by conducting a large-scale survey in 52 villages in Plateau, Bauchi and Kano states in the northern part of Nigeria. Our approach involved holding focus group discussions with farmers, both men and women, to collect their knowledge about the disease and to understand their perspectives on its management. The results showed that farmers use several different terms to refer to diseases that are likely to be PPR, and that these same terms might also be used to refer to diseases caused by other infectious agents. Farmers rarely call on veterinary services to prevent the disease and vaccination is seldom practiced. Disease control is attempted using conventional treatments, with or without veterinary supervision, or using traditional therapies. There is limited or poor implementation of good farming practices such as biosecurity measures. This study has increased our understanding of PPR and its management in areas with limited public and private veterinary services. In addition, it has also fostered trust between scientists and communities, paving the way for future participatory action research programmes
Theoretical study of human-environment interactions in a peri-forest context
No full textIn Central Africa, the settlement of population and the development of new infrastructures, like industrial complex or roads, negatively impact the forest ecosystems. This anthropization of the natural landscape has consequences on wild-life, which is, on the other hand, threaten by over-hunting [1]. The de- cline in the abundance of the wild fauna raises concerns about the ecosystem's sustainability and the food security of forest dependent communities [2]. We present and study a dynamical system to model human-environment interactions. Based on the fact that the human population relies on food avail- ability provided either from domestic sources (agriculture, breeding) or from hunt, we assume that the interactions between human population and the envi- ronment are limited to hunting activities, which reflect what happens in South Cameroon [3]. Depending on the functional used, the theoretical analysis is done using the theory of monotone systems [4], or is simplified using quasi steady state assumption [5]. In both cases, the analysis shows that di↵erent kind of dynamics are possible, including the convergence towards a limit cycle [6]. We identify the conditions on the hunting rate under which humans and wild fauna can coexist, as well as how anthropization may a↵ect those conditions. Numerical simulations supplement the theoretical work
Carbon payment strategies in coffee agroforests shape climate and biodiversity outcomes
Get PDFAgricultural supply chains increasingly mitigate climate change and biodiversity loss through initiatives that either plant trees or protect threatened carbon stocks on farmlands. We conducted a global meta-analysis to evaluate how these programs may impact carbon and biodiversity outcomes across coffee agriculture, which spans a vegetation complexity gradient from monoculture to biodiverse agroforestry. For aboveground carbon, we estimated coffee farms currently hold 481.59 TgC globally and could sequester an additional 81.53-86.50 TgC under different agroforestry adoption scenarios. However, more than twice as much aboveground carbon could be lost under intensification scenarios (174.23-221.45 TgC). While tree diversity supports overall biodiversity in agroforestry, we found it does not independently increase carbon, indicating carbon and biodiversity outcomes may be decoupled. Ultimately, tree planting programs in coffee can sequester meaningful carbon volumes but may fail to achieve global carbon and biodiversity goals if they do not also protect existing agroforestry and diversify planting efforts
Co-designing zoonotic diseases prevention practices when people depend on wild meat
Get PDFIn the face of the escalating frequency of diseases emergences originating from wildlife, the development of reliable strategies for controlling zoonotic diseases transmission at the interface between wildlife and human is becoming a global priority. Rural communities whose subsistence is based on hunting for wild meat extraction are natural targets of such interventions, because of their regular contacts with wildlife. To date there have been few attempts at building preventive sanitary strategies taking into account the socioeconomic and institutional constraints in which wild meat systems operate. The study presented here, conducted in eastern Gabon, aimed at conceiving risk-reduction strategies of zoonotic diseases transmitted from wildlife in a two-phase approach, namely (1) an assessment phase, based on a survey on risk knowledge and practices conducted with members of communities living on wild meat, and (2) a co-design phase based on focus group discussions to identify acceptable prevention strategies aimed at limiting the contacts creating the major risks of exposure to zoonoses infections. The use of participatory methods aiming at eliciting issues and solutions from the participants, enabled the conception of strategies that were adapted to the context and well accepted by stakeholders at different stages, namely the track, capture, transport of wild animals, the butchering of carcasses, cooking and consumption process. However, some limitations to the effective application of the strategies can be anticipated notably because of (1) the current low and biased perception of zoonotic risks by wild meat actors, and (2) the economic incentives for maintaining risky behaviors like the capture and trade of live animals and the consumption or sale of animals found dead or displaying signs of disease infection
Compte-rendu de l'évaluation agronomique de 31 variétés de patate douce réunionnaises cultivées sur la station Cirad de Bassin-Plat pendant la saison fraiche 2024
No full textOld foe, New host: Epidemiology, genetic diversity, and pathogenic characterization of maize streak virus in rice fields from Burkina Faso
Get PDFRice is of critical significance regarding food security worldwide, including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus (Solemoviridae) and the rice stripe necrosis virus (Benyviridae). Using viral metagenomics, we aimed at broadening knowledge on interacting communities associated with plants in rice landscapes and exploring the diversity and epidemiological status of viruses circulating in rice fields from Burkina Faso. We performed an epidemiological survey in this country between 2016 and 2019 involving 57 small farmers' rice fields under two production systems: rainfed lowlands and irrigated areas. More than 2,700 rice samples were collected without regard to disease symptoms following a regular scheme. Wild and cultivated Poaceae (maize and sugarcane) growing in nearby rice fields were also collected. Unexpectedly, metagenomics detected maize streak virus (MSV) (Geminiviridae) in analyzed rice samples. Further molecular analyses using rolling circle amplification-polymerase chain reaction showed that MSV was widely distributed and highly prevalent in both rainfed lowlands and irrigated rice areas. MSV-A and MSV-G strains were identified. MSV-G, exclusively identified thus far in wild grasses, was the most prevalent strain, whereas MSV-A, known to cause severe symptoms in maize, was sporadically identified. Using infectious clones in experimental conditions, we confirmed the pathogenicity of both MSV strains in rice. Thus, in addition to contributing to the epidemiological surveillance of rice production in Africa, our results illuminate new epidemiological and pathogenic aspects of one of the most studied plant viruses with significant economic consequences in Africa