Biology subjects

Filloux, D.

Publications and source records attributed to Filloux, D..

3 recordsLinked to original sources

bioRxiv2023

Old foe, new host: epidemiology, genetic diversity and pathogenic characterization of maize streak virus in rice fields from Burkina Faso.

Rice 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 exploring the diversity of viruses circulating in Burkina Faso rice fields. 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 2700 rice samples were collected without a priori (not based on symptom observation) following a regular scheme. In addition, wild and cultivated (maize and sugarcane) Poaceae growing nearby rice fields were also collected. Unexpectedly, metagenomics detected maize streak virus (MSV, Geminiviridae) in analyzed rice samples. Further molecular analyses using RCA-PCR showed that MSV is 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 so far in wild grasses, was the most prevalent strain while MSV-A, known to cause severe symptoms in maize, was sporadically identified. No genetic differentiation was detected between MSV isolates either infecting wild or cultivated plant species. Using infectious clones in experimental conditions, we confirmed the pathogenicity of both MSV strains on rice. Thus, in addition to contribute 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. FundingFrench National Research Agency < > program (ANR-10-LABX-001-01), Agropolis Fondation (ANR-16-IDEX-006), French National Research Agency "young researchers" program (ANR-20-CE35-0008-01), CGIAR Research Program on Rice Agri-food Systems (RICE), Cooperation and cultural action department of the French Embassy (SCAC) in Burkina Faso.

pathology↗

bioRxiv2023

Long term anthropic management and associated loss of plant diversity deeply impact virome richness and composition of Poaceae communities

Modern agriculture has influenced plant virus emergence through ecosystem simplification, introduction of new host species, and reduction in crop genetic diversity. Therefore, it is crucial to better understand virus distributions across cultivated and uncultivated communities in agro-ecological interfaces, as well as virus exchange among them. Here we advance fundamental understanding in this area by characterizing the virome of three co-occurring replicated Poaceae community types that represent a gradient of grass species richness and management intensity, from highly managed crop monocultures to little-managed, species-rich grasslands. We performed a large-scale study on 950 wild and cultivated Poaceae over two years combining untargeted virome analysis down to virus species level with targeted detection of three plant viruses. Deep sequencing revealed i) a diversified and largely unknown Poaceae virome (at least 51 virus species/taxa), with an abundance of so-called persistent viruses; ii) an increase of virome richness with grass species richness within the community; iii) a stable virome richness over time but a large viral intraspecific variability; and iv) contrasted patterns of virus prevalence, co-infections and geographical distribution among plant communities and species. Our findings highlight the complex structure of plant virus communities in nature and suggest the influence of anthropic management on viral distribution and prevalence.

genomics↗

bioRxiv2022

African army ants at the forefront of virome surveillance in a remote tropical forest

In this study, we used a predator-enabled metagenomics strategy to sample the virome of a remote and difficult-to-access densely forested African tropical region. Specifically, we focused our study on the use of army ants of the genus Dorylus that are obligate collective foragers and group predators that attack and overwhelm a broad array of animal prey. Using 209 army ant samples collected from 29 colonies and the virion-associated nucleic acid-based metagenomics approach, we showed that a broad diversity of bacterial, plant, invertebrate and vertebrate viral sequences were accumulated by army ants: including sequences from 157 different viral genera in 56 viral families. This suggests that using predators and scavengers such as army ants to sample broad swathes of tropical forest viromes can shed light on the composition and the structure of viral populations of these complex and inaccessible ecosystems.

microbiology↗