Biology subjects

Massart, S.

Publications and source records attributed to Massart, S..

6 recordsLinked to original sources

bioRxiv2023

Biological characterization of an emergent virus infecting vegetables in diversified production systems: physostegia chlorotic mottle virus

With the emergence of high throughput sequencing (HTS) technologies, the discovery of new plant viruses has outpaced their biological characterization. However, it is crucial to understand the biology of these viruses to evaluate the risks they pose for the production of crops and natural ecosystems and to manage them properly. In 2018, Physostegia chlorotic mottle virus (PhCMoV) was detected in Austria in a Physostegia plant (Lamiaceae) using HTS, and subsequent prepublication data sharing associated the presence of the virus with severe fruit symptoms on important crops like tomato, eggplant, and cucumber across nine European countries. This discovery led to a collaborative effort to understand better the viruss genetic diversity, host range, symptomatology, and distribution. Still, specific knowledge gaps remained. In this study, the authors address these gaps by examining the transmission mode, prevalence, and disease severity of PhCMoV. Bioassay and field survey confirmed the causal association between the presence of the virus and symptoms on tomato and eggplant. The investigation also mapped out the historical and geographic footprint of the virus, spanning back 30 years and including a new location, Switzerland. Based on field survey, PhCMoV was found to naturally infect 11 new host plant species across seven families, extending the host range of PhCMoV to 20 plant species across 14 plant families. Greenhouse assays with mechanical inoculation showed that yield losses could reach 100% depending on the phenological stage of the plant at the time of infection. The study also identified a polyphagous leafhopper species (Anaceratagallia sp.) as the natural vector of PhCMoV. PhCMoV was widespread in diversified vegetable farms in Belgium where tomato is grown in soil, occurring in approximately one-third of such farms. However, outbreaks were sporadic and it can be suggested that they were associated with specific cultural practices, such as the cultivation of perennial plants in tomato tunnels that can serve as a host for both the virus and its vector. To further explore this phenomenon and better manage the virus, studying the ecology of the Anaceratagalliae vector would be beneficial.

plant biology↗

bioRxiv2023

Cont-ID:Detection of samples cross-contamination in viral metagenomic data

BackgroundHigh Throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples. Cross-contamination management was a key drawback during the development of PCR-based detection and is now adequately monitored in routine diagnostics. HTS technologies are facing similar difficulties due to their very high analytical sensitivity. As a single viral read could be detected in millions of sequencing reads, it is mandatory to fix a detection threshold that will be influenced by cross-contamination. Cross-contamination monitoring should therefore be a priority when detecting viruses by HTS technologies. ResultsWe present Cont-ID, a bioinformatic tool designed to check for cross-contamination by analysing the relative abundance of virus sequencing reads identified in sequence metagenomic datasets and their duplication between samples. It can be applied when the samples in a sequencing batch have been processed in parallel in the laboratory and with at least one external alien control. Using 273 real datasets, including 68 virus species from different hosts (fruit tree, plant, human) and several library preparation protocols (Ribodepleted total RNA, small RNA and double stranded RNA), we demonstrated that Cont-ID classifies with high accuracy (91%) viral species detection into (true) infection or (cross) contamination. This classification raises confidence in the detection and facilitates the downstream interpretation and confirmation of the results by prioritising the virus detections that should be confirmed. ConclusionsCross-contamination between samples when detecting viruses using HTS can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.

bioinformatics↗

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↗

bioRxiv2023

High Throughput Sequencing technologies complemented by growers perception highlight the impact of tomato virome in diversified vegetable farms

The number of small-scale diversified vegetable growers in industrialized countries has risen sharply over the last ten years. The risks associated with plant viruses in these systems have been barely studied in Europe, yet dramatic virus emergence events, such as tomato brown fruit rugose virus, sometimes occur. We developed a methodology that aimed to understand better the implications related to viruses for tomato production in Belgians vegetable farms by comparing growers perception of the presence of viral symptoms (visual inspection) with non targeting detection of nearly all viruses present in the plants by high throughput sequencing technologies (HTS). Virus presence and impact were interpreted considering the farms typology and cultural practices, the growers professional profiles, and visual inspection of plant-viral-like symptoms. Overall, The data indicated that most growers have limited understanding of tomato viruses and are not concerned about them. Field observations were correlated to this perception as the prevalence of symptomatic plants was usually lower than 1%. However, important and potentially emergent viruses, mainly transmitted by insects, were detected in several farms. Noteworthy, the presence of these viruses was correlated with the number of plant species grown per site (diversity) but not with a higher awareness of the growers regarding plant viral diseases or a higher number of symptomatic plants. In addition, both HTS and perception analysis underlined the rising incidence and importance of an emergent virus: Physostegia chlorotic mottle virus. Overall, the original methodology developed here, combining social science with HTS technologies, could be applied to other crops in other systems to identify emergent risks associated with plant viruses and can highlight the communication needed toward growers to mitigate epidemics.

plant biology↗

bioRxiv2022

Diversity and pathobiology of an ilarvirus unexpectedly detected in diverse host plants and in global sequencing data

High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years and implementing them with classical plant virology techniques results to a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (family Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a very diverse host association is atypical for ilarviruses, thus warranted further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared to other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, while the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Kochs postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provided information to better understand the diversity, distribution, and pathobiology of SnIV1, but whether it could emerge as a destructive pathogen remains uncertain. FundingO_LIEU Horizon 2020 Marie Skodowska-Curie Actions Innovative Training Network (H2020 MSCA-ITN) project no. GA 813542 C_LIO_LIAdministration of the Republic of Slovenia for Food Safety, Veterinary Sector and Plant Protection and Slovenian Research Agency (ARRS) funding no. P4-0165, P4-0407, J4-4553 C_LIO_LIBalik Scientist Program (Republic Act 11035) of the Department of Science and Technology- Philippine Council for Agriculture, Aquatic, and Natural Resources Research and Development (DOST-PCAARRD), Republic of the Philippines C_LIO_LIThe Belgian FPS Health Food Chain Safety and Environment under Project RT18/3 SEVIPLANT C_LI

microbiology↗

bioRxiv2021

Multi-omics approach reveals new insights into the gut microbiome of Galleria mellonella (Lepidoptera:Pyralidae) exposed to polyethylene diet

The current plastic pollution throughout the world implies a crucial optimization of its (bio)degradation processes. In order to identify plastic degrading bacteria and associated enzymes, the gut microbiota of insects has raised interest. Some entomological models such as Tenebrio molitor (L. 1758), Plodia interpunctella (Hubner 1813) or Galleria mellonella (L. 1758) have the ability to ingest and degrade polyethylene. Then, it is promising to identify the composition and the role of the gut microbiota in this process. This study takes part in this issue by investigating G. mellonella as a biological model feeding with a polyethylene diet. Gut microbiome samples were processed by high throughput 16S rRNA sequencing, and Enterococcaceae and Oxalobacteraceae were found to be the major bacterial families. At low polyethylene dose, we detect no bacterial community change and no amplicon sequence variant associated with the polyethylene diet suggesting microbiome resilience. The functional analysis of insects gut content was promising for the identification of plastic degrading enzymes such as the phenylacetaldehyde dehydrogenase which participate in styrene degradation. This study allows a better characterization of the gut microbiota of G. mellonella and provides a basis for the further biodegradation study of polyethylene based on the microorganism valorization from insect guts.

microbiology↗