References of "Massart, Sébastien"
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See detailCharacterisation of a novel virus infecting orchids of the genus Pleione
Kominek, Petr; Massart, Sébastien ULiege; Pham, Khanh et al

in Virus Research (2019), 261

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See detailMinor plant species can be key players of the Poaceae virome at the agroecosystem scale.
Maclot, François ULiege; Candresse, Thierry; Filloux, Denis et al

Conference (2019, May 13)

Prior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions ... [more ▼]

Prior to the domestication of plants, it is hypothesized that plant viruses were co-evolving with uncultivated plants growing in mixed species communities, which probably resulted in complex interactions (antagonism, commensalism, mutualism). The development of agriculture further deeply modified natural ecosystems and land use, creating agroecosystems composed by both cultivated and uncultivated areas. It is postulated that the advent of agriculture has modified the dynamics of virus-plant interactions, which has fostered the occurrence of virus disease emergence events. At the level of natural ecosystems, the relationships between plant communities’ diversity and plant virus diversity, the distribution of plant viruses and the interactions between viruses and their uncultivated hosts, have just started to be explored. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to characterize the virome of Poaceae communities, including minor species, in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We adapted a virion-associated nucleic acids (VANA) metagenomics protocol to sequence at high throughput pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) and per plant species. Over two years, about 4,300 Poaceae plants (corresponding to 24 species) were sampled and processed using the VANA metagenomics approach. The bioinformatic analyses revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seed-borne. Interestingly, minor Poaceae species studied in grasslands contained a wide virus richness, sometimes greater than ecosystemic pools containing 8-11 major plant species. Moreover, some virus genera (e.g. Amalgavirus, Alphaendornavirus, Potyvirus, Sobemovirus) were found only in minor species, underlining the importance of minor plant species as virus reservoirs in wild ecosystems such as grasslands. [less ▲]

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See detailExploring bacterial communities in aquaponic systems
Eck, Mathilde ULiege; Sare, Abdoul Razack ULiege; Massart, Sébastien ULiege et al

in Water (2019), 11(260),

Aquaponics is a production system based on the dynamic equilibrium between fish, plants, and microorganisms. In order to better understand the role of microorganisms in this tripartite relationship, we ... [more ▼]

Aquaponics is a production system based on the dynamic equilibrium between fish, plants, and microorganisms. In order to better understand the role of microorganisms in this tripartite relationship, we studied the bacterial communities hosted in eight aquaponic and aquaculture systems. The bacterial communities were analyzed by 16S rRNA gene deep sequencing. At the phylum level, the bacterial communities from all systems were relatively similar with a predominance of Proteobacteria and Bacteroidetes. At the genus level, however, the communities present in the sampled systems were more heterogeneous. The biofilter samples harbored more diverse communities than the corresponding sump samples. The core microbiomes from the coupled and decoupled systems shared more common operational taxonomic units than with the aquaculture systems. Eventually, some of the taxa identified in the systems could have beneficial functions for plant growth and health, but a deeper analysis would be required to identify the precise functions involved in aquaponics. [less ▲]

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See detailEffect of species composition on virome diversity in various ecosystemic communities of Poaceae
Maclot, François ULiege; Candresse, Thierry; Filloux, Denis et al

Conference (2019, January 28)

Before the domestication of plants, it is hypothesized that plant viruses were co-evolving with wild plants growing in mixed species communities, thereby resulting in complex interactions (antagonism ... [more ▼]

Before the domestication of plants, it is hypothesized that plant viruses were co-evolving with wild plants growing in mixed species communities, thereby resulting in complex interactions (antagonism, commensalism, mutualism). The development of agriculture deeply modified ecosystems, which is postulated to have altered the dynamics of virus-plant pathosystems and accelerated the rate of virus evolution and emergence. In this context, we are conducting a study in the Natural Park “Burdinale-Mehaigne” (Belgium) using high throughput sequencing technologies in order to examine the impact of species diversity (in terms of richness and density) on the virome of Poaceae communities in contrasted agricultural ecosystems (cereal monocultures, grazed pastures and natural grasslands). We developed a metagenomic approach consisting in virus particles purification, virion-associated nucleic acids (VANA) extraction and library preparation for Illumina sequencing and applied it on pools of 50 plant samples per ecosystem (50 samples reflecting plant species composition) or plant species (50 individual plants). Over two years, 4096 Poaceae plants were thus sampled and the bioinformatic analysis revealed the presence of diverse viral communities in wild and cultivated Poaceae, even though they did not present any symptoms. These viruses belong to diverse families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large range of hosts within the Poaceae and transmitted by different vectors (aphids, planthoppers, mites, nematods) or seeds-bornes. Virus richness was compared between ecosystems: limited viral diversity (e.g. Hordeum vulgare endornavirus, Brome mosaic virus) were detected in barley and wheat field s, whereas a larger diversity was found in less anthropic ecosystems. Lolium latent virus (Alphaflexiviridae) and Ryegrass mosaic virus (Potyviridae) were strongly present in grazed pastures, particularly in Lolium perenne L. Several tentative new virus species belonging to the Nepovirus genus and the Partitiviridae family were found in natural grasslands. [less ▲]

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See detailIdentification of a new isolate of Banana mild mosaic virus by high throughput sequencing triggers the development of a new diagnostic primer
Hanafi, Marwa ULiege; Rong, Wei ULiege; Crew, kathy S et al

Poster (2019, January 27)

The Bioversity International Musa Germplasm Transit Centre (ITC) hosts more than 1,500 accessions covering the genetic diversity of the genus Musa. Its objective is to conserve this diversity and supply ... [more ▼]

The Bioversity International Musa Germplasm Transit Centre (ITC) hosts more than 1,500 accessions covering the genetic diversity of the genus Musa. Its objective is to conserve this diversity and supply plant materials to users worldwide. These accessions can be distributed only if virus infection is not detected during indexing. The indexing is carried out by targeted IC-(RT)-PCR for 10 viruses, electron microscopy and symptom observation (De Clerck et al., 2017). One accession (ITC 0763) tested negative by IC-RT-PCR while viral particles were observed by electron microscopy, suggesting the infection by a new virus species or by a divergent viral strain from an existing species. The accession was sequenced as follows: after RNA extraction, the sequencing library was prepared using the Ribo-Zero™ Plant Leaf Kit (Illumina) for ribodepletion followed by the TruSeq Stranded Total RNA Library Prep Kit (Illumina). The sample was sequenced on the Illumina Nextseq 500 platform (Liège University) and a total of 8,683,460 paired reads (2x150 nt) were obtained. Bioinformatics analysis was carried out using Geneious v9.1 software. The nearly complete genome sequence of a banana mild mosaic virus (BanMMV) isolate was identified. The primers used for the detection of BanMMV during indexing at Gembloux Agro-Bio Tech are Poty1 and BanMMCP2 (De Clerck et al., 2017). A careful analysis of the genome sequences complementary to the detection primers revealed four mismatches with BanMMCP2 primer. These mismatches could be the origin of the negative PCR results obtained. To confirm this hypothesis, a new primer was designed at the same genome location as BanMMCP2 but with two additional degenerate bases. Combined with Poty1, the new primer was able to detect the infection by BanMMV. Currently, a retrospective analysis is being carried out on all the banana accessions already indexed to validate the new degenerate primer for use in routine indexing. [less ▲]

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See detailVirome Analysis of Grapevines in German Vineyards
Zarghani, Shaheen Nourinejhad; Ruiz-Garcia, Ana Belen; Olmos, Antonio et al

Poster (2019, January)

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See detailEvaluation of lambda Carrageenan, CpG-ODN, glycine Betaine, Spirulina platensis, and Ergosterol as elicitors for control of Zymoseptoria tritici in wheat
Le Mire, Géraldine; Siah, Ali; Marolleau, Brice et al

in Phytopathology (2019), 109(3), 409-417

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See detailInsights gained from metagenomic shotgun sequencing of apple fruit epiphytic microbiota
Angeli, Dario; Sare, Abdoul Razack ULiege; Jijakli, Haissam ULiege et al

in Postharvest Biology and Technology (2019), 153

The epiphytic plant microbial communities living at the surface of fruit have been the source of most current biocontrol agents (BCAs) and can influence fruit quality during storage. Despite this interest ... [more ▼]

The epiphytic plant microbial communities living at the surface of fruit have been the source of most current biocontrol agents (BCAs) and can influence fruit quality during storage. Despite this interest, their taxonomical and functional composition has been poorly studied so far. This paper describes the use of high-throughput sequencing (HTS) technologies to characterise the microbial phytobiome residing on apple surface at the taxonomic and functional levels through shotgun metagenome sequencing. Apples from the Pinova cultivar bearing no symptom of disease development were sampled in an orchard at harvest, and their epiphytic microbiota was isolated. After DNA extraction, 14.1 Gbases of raw sequences were generated by HTS. These sequences were annotated following two pipelines in parallel: (i) they were individually analysed by the MG-RAST server, and (ii) they were de novo assembled into contigs and the contigs were annotated by the IMG server. Our results showed a very high fungal and bacterial diversity, with a higher proportion of fungal sequences (79.0%) than bacterial sequences (13.8%). Among fungi, the phylum Ascomycota prevailed, while Bacteroides were dominant in the bacterial population. Among them, 24 species corresponded to known apple pathogens like Aspergillus spp., Botrytis spp., Sclerotinia spp., and Penicillium spp. for fungi, and Erwinia spp. and Agrobacterium spp. for bacteria. Moreover, several contigs were assigned to species of known BCA strains belonging to the following genera: Filobasidiella spp., Talaromyces spp, Candida spp., Saccharomyces spp., Bacillus spp., and Enterobacter spp. The functional analysis showed similar patterns of abundance and function in all samples, identified genes potentially involved in biocontrol properties, but also underlined the complexity of datum interpretation and the incompleteness of current databases. [less ▲]

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See detailFirst report of grapevine rupestris vein feathering virus in grapevine in Germany
Daldoul, S.; Massart, Sébastien ULiege; Ruiz-Garcia, A.B. et al

in Plant Disease (2018), 102(10), 2053

Detailed reference viewed: 32 (4 ULiège)
See detailImpact of ecosystem diversity on the Poaceae virome
Maclot, François ULiege; Filloux, Denis; Roumagnac, Philippe et al

Conference (2018, November 26)

This STSM was dedicated to the study of the viral diversity of different agro-ecological systems by metagenomic analyses. Indeed, before the domestication of plants, it is hypothesized that plant viruses ... [more ▼]

This STSM was dedicated to the study of the viral diversity of different agro-ecological systems by metagenomic analyses. Indeed, before the domestication of plants, it is hypothesized that plant viruses were co-evolving with wild plants growing in mixed species communities, thereby resulting in complex interactions. The development of agriculture deeply modified ecosystems, which is postulated to have altered the dynamics of virus-plant pathosystems and accelerated the rate of virus evolution and emergence. In this context, the objective of my PhD is to study the impact of ecosystems with contrasted biodiversity (monoculture, pastures and grasslands of the Natural Park “Burdinale-Mehaigne”, Belgium) on the virome of Poaceae plant species using high throughput sequencing technologies. We developed a metagenomic approach consisting in virus particles purification, virion-associated nucleic acids (VANA) extraction and library preparation for Illumina sequencing applied on pools of 50 plant samples per ecosystem. Bringing my data with me, I visited for one month (March 2018) the team of Professor Philippe Roumagnac (MicroQuar, UMR BGPI, CIRAD, Montpellier, France) in order to discuss the statistical approaches used to characterize viral dynamics in ecosystems and to develop knowledge in the bioinformatic tools adapted to virus detection. The bioIT analysis of my VANA samples revealed the presence of viral communities in wild and cultivated Poaceae. These viruses belong to a quite diverse set of families (e.g. Endornaviridae, Luteoviridae, Partitiviridae, Potyviridae, Reoviridae, Secoviridae), infecting a large host range within the Poaceae and transmitted by various vectors (aphids, planthoppers, mites, nematods, seeds). This STSM had a very positive impact on (1) my work by allowing me to develop my own bioIT pipeline which is still used and optimized in the framework of my ongoing analyses, and (2) my lab with whom a new collaboration was initiated with the MicroQuar team. The preliminary results obtained will be presented. [less ▲]

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See detailIdentification of a novel virus in citrus samples exhibiting impietratura disease symptoms by HTS technology
Beris, Despoina; Malandraki, Ionna; Kektsidou, Oxana et al

Conference (2018, November)

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See detailAfter the data deluge: biological characterization of the new variants and viral species identified by HTS
Massart, Sébastien ULiege; Candresse, Thierry; Gil, José et al

Conference (2018, August 03)

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See detailMolecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species
Koloniuk, Igor; Thekke-Veetil, Thanuja; Reynard, Jean-Sébastien et al

in Viruses (2018), 10(369),

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See detailEcological relations inside plant microbiota can improve the efficacy of biocontrol agents: The case of Pichia anomala strain K against Botrytis cinerea on apple
Sare, Abdoul Razack ULiege; Ait-A, Nawel; Jijakli, Haissam ULiege et al

Conference (2018, May 22)

Pichia anomala strain K is a Biological Control Agents (BCA) against apple two postharvest pathogens (Penicillium spp. and Botrytis cinerea). Progress have been made during the past two decades to ... [more ▼]

Pichia anomala strain K is a Biological Control Agents (BCA) against apple two postharvest pathogens (Penicillium spp. and Botrytis cinerea). Progress have been made during the past two decades to understand its modes of action through various studies. To further improve and stabilize its efficacy, Massart et al. (2015) suggested to focus on benefic interactions inside host microbiota to favor BCAs. Indeed, once applied, BCAs will face a complex microbiota where ecological interactions such as competition, parasitism, mutualism and commensalism occur. In this study, we investigated the potential of apple microbiota to improve the efficacy of strain K against B. cinerea. Sampling were carried out in Belgium, by harvesting fruits of fifteen apple varieties grown in four disease management practices [no phytosanitary treatment (conservation orchard), light-organic, organic and conventional]. Epiphytic microbiota were collected by 15 min sonication and by washing apples with a phosphate buffer (pH=7.4). Apple washing solutions were stored at -80°C to generate a microbiota bank made up with eighteen different microbiota. The quantity of microorganisms (bacteria and fungi/yeast) in each microbiota type was first estimated by plating. Afterward, biological assays on wounded apple fruits have been carried out by co-inoculating each apple microbiota with the strain K, then with B. cinerea 24h later. The results show that apple skin harbors around 2 x104 ± 1,5 x104 microorganisms/cm2. The biological assays revealed that the apple microbiota can either raise till 100%, drop or have no effect on the efficacy of strain K. Thanks to next generation sequencing that makes the microbiota profiling possible, studies are ongoing to identify ecological strains/species or groups of taxa which are benefic to the strain K efficacy. [less ▲]

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