Biology subjects

Laval, V.

Publications and source records attributed to Laval, V..

10 recordsLinked to original sources

bioRxiv2025

Uromyces plumbarius first reported on Oenothera lindheimeri in Europe with widespread distribution and association with the rust hyperparasite Sphaerellopsis sp.

The rust fungus Uromyces plumbarius Peck was reported in Europe for the first time on Oenothera lindheimeri (Engelm. & A. Gray) W.L. Wagner & Hoch (Lindheimers beeblossom), a highly popular ornamental plant widely cultivated since the 2000s. The fungus was found in 11 locations across France and two locations in the Netherlands. The identification was based on an analysis of morphological characteristics and 28S rDNA sequences. The pathogenicity was confirmed through reinoculation using fresh urediniospores. This represents the first record of U. plumbarius outside its native range in North America. Its widespread distribution in France appears to result from rapid dissemination, likely facilitated by the plant trade between nursery gardeners. The discovery of U. plumbarius was accompanied by the detection of the hyperparasitic fungus Sphaerellopsis sp. and fungivorous larvae of Mycodiplosis sp.--two native, non-specific natural enemies which may play a role in limiting the impact of rust infections.

microbiology↗

bioRxiv2023

Development of a tool combining multiplex PCR and high-throughput sequencing to study the polymorphism of eight Leptosphaeria maculans avirulence genes and its application to field surveys in France

Leptosphaeria maculans is a fungal pathogen causing stem canker of oilseed rape (Brassica napus). The disease is mainly controlled by the deployment of varieties with major resistance genes (Rlm). Rlm genes can rapidly become ineffective following the selection of virulent isolates of the fungus, i.e. with deletions or mutations in the corresponding avirulence genes (AvrLm). Reasoned and durable management of Rlm genes relies on the detection and monitoring of virulent isolates in field populations. Based on previous knowledge of AvrLm gene polymorphism, we developed a tool combining multiplex PCR and Illumina sequencing to characterise allelic variants for eight AvrLm genes in field L. maculans populations. We tested the method on DNA pools of 71 characterised L. maculans isolates and of leaf spots from 32 L. maculans isolates. After multiplex-PCR and sequencing with MiSeq technology, reads were mapped on an in-house AvrLm sequence database. Data were filtered using thresholds defined from control samples included in each run. Proportions of each allelic variant per gene, including deletions, perfectly correlated with expected ones. The method was then applied to around 1300 symptoms (42 pools of mainly 32 leaf spots) from nine B. napus fields. The proportions of virulent isolates estimated by sequencing leaf spot pools perfectly correlated with those estimated by pathotyping. In addition, the proportions of allelic variants determined at the national scale also correlated with those previously determined following individual sequencing of AvrLm genes in a representative collection of isolates. Finally, the method also allowed us to detect still undescribed and rare allelic variants. Despite the diversity of mechanisms generating virulent isolates and the gene-dependant diversity of AvrLm gene polymorphism, the method proved suitable for large-scale and regular monitoring of L. maculans populations, which will make it possible to choose effective Rlm genes and to detect resistance breakdowns at early stages.

molecular biology↗

bioRxiv2022

Identifying fungal leaf spots on oilseed rape: could pictures help?

From sowing in late summer until harvest in following summer, oilseed rape can be infected by several fungi, which foliar symptoms (leaf spots) coexist on the crop. Training an expert at their identification is quick for the typical symptoms with characteristic appearance. However, in many cases the size, colour and morphology are similar and for the atypical symptoms, there is a risk of confusion or in-decidability. Also, scouting the fields for expert training is not possible at all seasons and all diseases might not be seen in all years and all places. The aim of our study was to produce large sets of pictures annotated by several experts, from which tables illustrating the diversity of symptom appearance were chosen. These tables will enable assistance to diagnostic and expert training.

ecology↗

bioRxiv2022

NGS data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici

The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. This resource announcement provides fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves differing in the presence of symptoms caused by Z. tritici. Tissues were sampled from three wheat commercial varieties on three sampling dates during a cropping season. Weeds around wheat fields were sampled as well. In total, more than 450 leaf samples were collected. The pathogen Z. tritici was quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata associated to each sample (sampling date, wheat variety and tissue health condition), a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis.

microbiology↗

bioRxiv2021

Synergy of culture-dependent molecular identification and whole-community metabarcode sequencing for characterizing the microbiota of arable crop residues

This study is the first to compare culture-dependent (strain isolation plus molecular identification) and culture-independent (whole-community metabarcode sequencing) approaches for characterizing the microbiota of crop residues. We investigated the diversity of fungal and bacterial communities in wheat and oilseed rape residues, using two different culture-dependent strategies to cover the maximum diversity for each kingdom: broad substrate sampling coupled with low-throughput isolation and diversity analysis for fungi, and reduced substrate sampling coupled with high-throughput isolation and diversity analysis for bacteria. The proportion of cultivable microorganisms was neither as low as the 1% paradigm long associated with the rhizosphere microflora, nor as high as the 50% sometimes reported for the phyllosphere microflora. It was, thus, intermediate between the values for soil and plants. This finding is consistent with residues being considered to constitute an ecotone, at the interface between soil and phyllosphere. Isolation and metabarcoding provided consistent complementary information: they revealed close community profiles, leading to the identification of several common and specific amplicon sequence variants (ASVs). The power of the culture-independent approach was thus confirmed. By contrast the culture-dependent approach was less weak than anticipated. Firstly, it provided complementary information about microbial diversity, with several ASVs not retrieved by metabarcoding being identified after isolation in the community-based culture collection. Secondly, this approach made it possible to preserve and test different taxa either individually or after the creation of synthetic communities, for deciphering the ecological functions of communities beyond merely descriptive aspects.

microbiology↗

bioRxiv2020

Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: the case of the Leptosphaeria maculans-Brassica napus pathosystem

Oilseed rape residues are a crucial determinant of stem canker epidemiology, as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterise the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify micro-organisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterised by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify micro-organisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonisation of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial ASVs (amplicon sequence variants). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex may be considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote micro-organisms with beneficial effects against residue-borne pathogens, and more broadly, to decipher the complex interactions between multi-species pathosystems and other microbial components in crop residues.

microbiology↗

bioRxiv2019

Differential dynamics of microbial community networks help identify microorganisms interacting with residue-borne pathogens: the case of Zymoseptoria tritici in wheat

BackgroundWheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues, and to identify microorganisms interacting with it. We used metabarcoding to characterize the microbiome associated with wheat residues placed outdoors, with and without preliminary Z. tritici inoculation, comparing a first set of residues in contact with the soil and a second set without contact with the soil, on four sampling dates in two consecutive years.\n\nResultsThe diversity of the tested conditions, leading to the establishment of different microbial communities according to the origins of the constitutive taxa (plant only, or plant and soil), highlighted the effect of Z. tritici on the wheat residue microbiome. Several microorganisms were affected by Z. tritici infection, even after the disappearance of the pathogen. Linear discriminant analyses and ecological network analyses were combined to describe the communities affected by infection. The number of fungi and bacteria promoted or inhibited by inoculation with Z. tritici decreased over time, and was smaller for residues in contact with the soil. The interactions between the pathogen and other microorganisms appeared to be mostly indirect, despite the strong position of the pathogen as a keystone taxon in networks. Direct interactions with other members of the communities mostly involved fungi, including other wheat pathogens. Our results provide essential information about the alterations to the microbial community in wheat residues induced by the mere presence of a fungal pathogen, and vice versa. Species already described as beneficial or biocontrol agents were found to be affected by pathogen inoculation.\n\nConclusionsThe strategy developed here can be viewed as a proof-of-concept focusing on crop residues as a particularly rich ecological compartment, with a high diversity of fungal and bacterial taxa originating from both the plant and soil compartments, and for Z. tritici-wheat as a model pathosystem. By revealing putative antagonistic interactions, this study paves the way for improving the biological control of residue-borne diseases.

microbiology↗

bioRxiv2018

Crop residues in wheat-oilseed rape rotation system: a pivotal, shifting platform for microbial meetings

Crop residues are a crucial ecological niche with a major biological impact on agricultural ecosystems. In this study we used a combined diachronic and synchronic field experiment based on wheat-oilseed rape rotations to test the hypothesis that plant is a structuring factor of microbial communities in crop residues, and that this effect decreases over time with their likely progressive degradation and colonization by other microorganisms. We characterized an entire fungal and bacterial community associated with 150 wheat and oilseed rape residue samples at a plurennial scale by metabarcoding. The impact of plant species on the residue microbiota decreased over time and our data revealed turnover, with the replacement of oligotrophs, often plant-specific genera (such as pathogens) by copiotrophs, belonging to more generalist genera. Within a single cropping season, the plant-specific genera and species were gradually replaced by taxa that are likely to originate from the soil. These changes occurred more rapidly for bacteria than for fungi, known to degrade complex compounds. Overall, our findings suggest that crop residues constitute a key fully-fledged microbial ecosystem. Taking into account this ecosystem, that has been neglected for too long, is essential, not only to improve the quantitative management of residues, the presence of which can be detrimental to crop health, but also to identify groups of beneficial micro-organisms. Our findings are of particular importance, because the wheat-oilseed rape rotation, in which no-till practices are frequent, is particularly widespread in the European arable cropping systems.

microbiology↗

bioRxiv2018

Optimized real-time qPCR assays for detecting and quantifying the Fusarium and Microdochium species responsible for wheat head blight, as defined by MIQE guidelines

In order to better understand the Fusarium head blight disease, reliable real-time PCR assays for detection and quantification of fungal species belonging to the Fusarium and Microdochium genus are needed. Specific qPCR assays were developed for nine of those species. All criteria required for reproducing the assays are presented. The assays were species specific and allow quantification of at least 5 pg of fungal DNA and detection of 0.5 pg of fungal DNA per PCR reaction. Moreover we showed that the quantification performances of the tests were not altered in the presence of DNA of closely related species in the sample. The assays were tested on field samples and have been already used in greenhouse experiments.

molecular biology↗

bioRxiv2017

Stability in the genetic structure of a Zymoseptoria tritici population from epidemic to interepidemic stages at a small spatial scale

Subpopulations of the wheat pathogen Zymoseptoria tritici (26 sample groups composed of 794 strains) were collected in two nearby wheat fields in the Paris basin, during both epidemic and inter-epidemic periods of three successive years (2009-2013). In addition to the type of inoculum (ascospores vs. pycnidiospores), the alternative presence of wheat debris allowed taking into account its putative origin (local vs. distant). We used a molecular epidemiology approach, based on population genetic indices derived from SSR marker analysis, to describe putative changes in the structure and genotypic diversity of these subpopulations over three years, at a spatiotemporal scale consistent with epidemiological observations. Genetic structure was stable over time (within and between years) and between fields. All subpopulations displayed very high levels of gene and genotypic diversity. The low levels of linkage disequilibrium and the very low clonal fraction at all stages were consistent with the regular occurrence of sexual reproduction in the two fields. A significant increase of the MAT1-1/MAT1-2 ratio was observed over the course of the epidemics, suggesting a competitive advantage of MAT1-1 strains consistently with their greater pathogenicity reported in the literature. Finally, we found that the period, the type of inoculum and its putative origin had little effect on the short term evolution of the local population of Z. tritici. Fungal population size and diversity are apparently large enough to prevent genetic drift at this fine spatiotemporal scale, and more likely short distance migration contributes strongly to the stabilization of genetic diversity among and within plots.

epidemiology↗