Biology subjects

Vimont, N.

Publications and source records attributed to Vimont, N..

4 recordsLinked to original sources

bioRxiv2025

Environmental context as a key driver of Pseudomonas biocontrol activity against Salmonella.

Salmonella poses a significant threat to food security, with frequent outbreaks reported worldwide. A large percentage of these outbreaks are associated with fresh produce intended for raw consumption. Plant microbiomes harbour diverse microbial communities, including commensal microbes such as Pseudomonas that sometimes exhibit biocontrol activity against plant pathogens. However, little is known about whether Pseudomonas strains can effectively suppress foodborne pathogens and the mechanisms they employ. In this study, we identified and characterised food derived Pseudomonas isolates capable of inhibiting Salmonella growth in vitro and in planta. The identified isolates were active against a range of Salmonella serovars, and additionally E. coli isolates derived from food. We demonstrated that dynamics of the interaction between Pseudomonas and Salmonella are environment and application dependant. To uncover the mechanisms Pseudomonas employs to suppress Salmonella, we used transcriptomics coupled with pathway analysis in the two different settings. We showed that Pseudomonas metabolism undergoes significant environment-specific changes in the presence of Salmonella, implicating different pathways responsible for the control of the pathogen in the two different settings. Our results highlight the plasticity of Pseudomonas metabolism in response to Salmonella in two distinct environments and provide evidence that Pseudomonas biocontrol activity is multifactorial and environment dependent.

microbiology↗

bioRxiv2019

From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy

BackgroundBud dormancy is a crucial stage in perennial trees and allows survival over winter to ensure optimal flowering and fruit production. Recent work highlighted physiological and molecular events occurring during bud dormancy in trees. However, they usually examined bud development or bud dormancy in isolation. In this work, we aimed to further explore the global transcriptional changes happening throughout bud development and dormancy onset, progression and release.\n\nResultsUsing next-generation sequencing and modelling, we conducted an in-depth transcriptomic analysis for all stages of flower buds in several sweet cherry (Prunus avium L.) cultivars that are characterized for their contrasted dates of dormancy release. We find that buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are defined by the expression of genes involved in specific pathways, and these are conserved between different sweet cherry cultivars. In particular, we found that DORMANCY ASSOCIATED MADS-box (DAM), floral identity and organogenesis genes are up-regulated during the pre-dormancy stages while endodormancy is characterized by a complex array of signalling pathways, including cold response genes, ABA and oxidation-reduction processes. After dormancy release, genes associated with global cell activity, division and differentiation are activated during ecodormancy and growth resumption. We then went a step beyond the global transcriptomic analysis and we developed a model based on the transcriptional profiles of just seven genes to accurately predict the main bud dormancy stages.\n\nConclusionsOverall, this study has allowed us to better understand the transcriptional changes occurring throughout the different phases of flower bud development, from bud formation in the summer to flowering in the following spring. Our work sets the stage for the development of fast and cost effective diagnostic tools to molecularly define the dormancy stages. Such integrative approaches will therefore be extremely useful for a better comprehension of complex phenological processes in many species.

plant biology↗

bioRxiv2018

Hormonal balance finely tunes dormancy status in sweet cherry flower buds

In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiological, transcriptional analyses, quantification of abscisic acid (ABA) and gibberellins (GAs), and modelling to further investigate how these signaling pathways are associated with dormancy progression in the flower buds of two sweet cherry cultivars. Our results demonstrated that GA-associated pathways have distinct functions and may be differentially related with dormancy. In addition, ABA levels rise at the onset of dormancy, associated with enhanced expression of ABA biosynthesis PavNCED genes, and decreased prior to dormancy release. Following the observations that ABA levels are correlated with dormancy depth, we identified PavUG71B6, a sweet cherry UDP-GLYCOSYLTRANSFERASE gene that up-regulates active catabolism of ABA to ABA-GE and may be associated with low ABA content in the early cultivar. Subsequently, we modelled ABA content and dormancy behavior in three cultivars based on the expression of a small set of genes regulating ABA levels. These results strongly suggest the central role of ABA pathway in the control of dormancy progression and open up new perspectives for the development of molecular-based phenological modelling.

plant biology↗

bioRxiv2018

Chromatin immunoprecipitation-sequencing and RNA-sequencing for complex and low-abundance tree buds

Chromatin immunoprecipitation-sequencing (ChIP-seq) is a robust technique to study interactions between proteins, such as histones or transcription factors, and DNA. This technique in combination with RNA-sequencing (RNA-seq) is a powerful tool to better understand biological processes in eukaryotes. We developed a combined ChIP-seq and RNA-seq protocol for tree buds (Prunus avium L., Prunus persica L Batch, Malus x domestica Borkh.) that has also been successfully tested on Arabidopsis thaliana and Saccharomyces cerevisiae. Tree buds contain phenolic compounds that negatively interfere with ChIP and RNA extraction. In addition to solving this problem, our protocol is optimised to work on small amounts of material. Furthermore, one of the advantages of this protocol is that samples for ChIP-seq are cross-linked after flash freezing, making it possible to work on trees growing in the field and to perform ChIP-seq and RNA-seq on the same starting material. Focusing on dormant buds in sweet cherry, we explored the link between expression level and H3K4me3 enrichment for all genes, including a strong correlation between H3K4me3 enrichment at the DORMANCY-ASSOCIATED MADS-box 5 (PavDAM5) loci and its expression pattern. This protocol will allow analysis of chromatin and transcriptomic dynamics in tree buds, notably during its development and response to the environment.

plant biology↗