Biology subjects

Massart, S.

Publications and source records attributed to Massart, S..

9 recordsLinked to original sources

bioRxiv2025

Host-specific adaptation and fitness trade-off of Barley Yellow Dwarf Viruses suggested by experimental evolution through aphid inoculation on multiple Poaceae species

Yellow dwarf viruses are damaging viruses infecting cereals. They are able to infect a wide range of host plants belonging to the Poaceae family. The ban of neonicotinoids in Europe has resulted in an increasing disease incidence and triggered the need to better understand their emergence and spread. The ability of a Barley yellow dwarf virus (BYDV) population to adapt to different hosts has never been studied. We performed an experimental evolution of two BYDV species (BYDV-PAS and BYDV-PAV) to study their adaptation to four Poaceae species (wheat, oat, two-row barley, and six-row barley). After four months of evolution (4 passages from plant to plant), the replicative fitness of the final viral populations was estimated, and the complete viral genomes were sequenced by high-throughput sequencing in pools of BYDV populations. Wildly divergent evolutionary trajectories were obtained, with stable or increased fitness, up to extinctions of viral populations within and among plant species. To understand these results, the composition of viral populations was analysed in detail using single nucleotide polymorphism (SNP) calling, clustering, and haplotype reconstruction methods. Interestingly, adaptation to oat and barley was mainly explained by a combination of BYDV-PAV haplotypes showing specific mutations. In contrast, adaptation to wheat was mainly explained by a combination of BYDV-PAS haplotypes harbouring specific mutations. Moreover, these local adaptations were associated to an adaptation cost in other hosts for some viral populations. The presence of adaptation costs in controlled but realistic conditions opens the door for evaluating practices such as crop mixtures or rotations on fields, as a means to mitigate the impact of BYDV. Author summaryThe use of genetically uniform plant resistant varieties in traditional agriculture creates unique environments that facilitate the rapid emergence of highly virulent pathogen populations. In natural ecosystems, host spatial and temporal heterogeneity help limit the outbreak of epidemics. As a result, disease management strategies such as crop mixtures and rotations have been proposed to reduce the selection pressure exerted on pathogen populations and prevent the emergence of "super-infectious" pathogens. These strategies would be particularly relevant against Barley yellow dwarf virus (BYDV), the virus causing the greatest economic losses on cereals, as insecticides controlling the disease are banned in Europe and few resistance genes are currently available. However, the effectiveness of these strategies against BYDV remains to be demonstrated. By experimentally evolving a natural BYDV population on different cereal species through natural transmission (e.g. vector instead of mechanical inoculation), we showed that different combinations of mutations and haplotypes enable the virus to adapt to different cereal species. Moreover, for some viral populations, the combination promoting adaptation to one host resulted in maladaptation in another host. These host-specific adaptations are key elements in the establishment of crop mixtures and rotations in the field. Our results generated in controlled but realistic conditions demonstrate for the first time that these cultural practices could be effective against these viruses.

evolutionary biology↗

bioRxiv2024

Highlighting the complexity of pathogenesis: the host microbiota impacts disease development on apple fruit and is a cornerstone for its biocontrol

Apple fruit is the most produced temperate fruit with a trade value estimated at 7.5 billion $ and is usually stored up to one year after harvest. Postharvest pathogens often compromise storage, responsible for up to 55% of fruit losses, depending on the country and fruit. They are also a source of mycotoxin contamination. A sustainable way to control that pathogen is using beneficial microorganisms called biocontrol agents (BCA). Despite promising efficacy in laboratory conditions, BCAs efficacy is variable and often reduced once applied at a large scale through either orchard or postharvest treatment. We hypothesized that the epiphytic microbiota plays a role in the variability of BCA efficiency (Pichia anomala, strain K) and postharvest disease development due to Botrytis cinerea on apples. A diverse set of 18 epiphytic microbial communities were harvested from apple carposphere and bio-banked. The analysis of their bacterial and fungal taxonomic composition and carbon metabolic footprint confirmed that contrasted microbiotas were harvested. Their impact on B. cinerea disease development was evaluated through a standardized in vivo bioassay. The reduction of B. cinerea rot development ranged from 20% to 80% when the microbiotas were applied alone. In addition, three microbiotas enhanced the biological control efficiency of strain K (up to +100%, whatever the tested microbiota concentrations) while others limited its action (down to -27%). A co-clustering analysis of biocontrol efficacy with carbon profiles or taxonomic composition was carried out. It identified promising molecules whose high metabolization was associated with high biocontrol by the microbiota and taxa with higher abundance in microbiota limiting B. cinerea rot development. Putative beneficial taxa were isolated from the most efficient microbiota. In vivo bioassays confirmed the efficacy of two molecules and two strains belonging to species never mentioned for their biocontrol properties against plant disease. This study demonstrated that natural epiphytic microbiota significantly influences postharvest disease development in apples and cause a variability in biocontrol efficacy. By mining the generated data, our approach identified promising molecules and taxa that enhance biocontrol, offering new insights for sustainable postharvest pathogen management.

microbiology↗

bioRxiv2024

Surveillance and molecular characterization of banana viruses and their association with Musa germplasm in Malawi.

Malawi has local banana germplasm preferred by its population. However, the epidemics of banana bunchy top disease, caused by the banana bunchy top virus (BBTV), is wiping out the most preferred germplasm and limiting its plantation. On the other hand, there needs to be more knowledge on viruses present in Malawi on banana crops. Therefore, a survey was conducted country-wide to characterize banana germplasm and evaluate the presence, incidence and prevalence of banana viruses. The survey covered four country zones, combined farmers structured questionnaire and plant sampling. PCR products from infected germplasm were sequenced and aligned for each detected virus to build a phylogenetic tree. BBTV, BanMMV and BSV species were detected in Malawi. Malawis BBTV isolates belonged to the Pacific Indian Ocean group only and BanMMV isolates clustered to three sub-branches. All the BSV species present in Malawi belonged to clade 1. Among the genetic groups of Musa, the identified banana germplasm belonged to AA, AAA, AB, AAB, and ABB groups with some germplasms unique compared to already genotyped germplasms. The ABB group was dominant in Malawi and was often infected by BSV species (probably originating from endogenous viral sequences), while BBTV more often infected the AAA group. Banana propagule sharing was the primary source of banana planting materials with a higher risk of spreading virus diseases. The survey underlined the need to set up a banana seed industry and policies that promote farmers access to virus-tested planting materials, which will consequently prevent future virus epidemics.

pathology↗

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↗