Biology subjects

BARRET, M.

Publications and source records attributed to BARRET, M..

5 recordsLinked to original sources

bioRxiv2026

Seed Microbiota Diversity and Culture Collection of Four Major Crops Covering Different Genotypes and Production Modes

Seed microbiota play a crucial role in plant health and development, yet remain understudied compared to other plant-associated microbial communities. This study aimed to characterize seed microbiota diversity across four major crops (common bean, rapeseed, tomato, and wheat) and establish a comprehensive strain collection of seed-borne microorganisms (bacteria and fungi). We employed a combination of culture-dependent and culture-independent approaches to analyze 68 seed samples representing diverse genotypes and production modes. Our results revealed highly variable seed microbiota, with bacterial colonization ranging from 10 to 100 million bacterial CFUs per gram of seeds, and microbial richness varying from 4 to 351 bacterial and 16 to 138 fungal amplicon sequence variants (ASVs) per sample. Both plant genotype and production mode significantly influenced microbiota composition, with each seed sample produced harboring a distinct microbial assemblage. Interestingly, seeds produced in confined environments exhibited lower bacterial colonization but higher microbial richness compared to field-produced seeds. We observed divergent ecological drivers shaping bacterial and fungal communities. Bacterial assemblages were more host-specific and variable, while fungal communities showed greater stability and a substantial core microbiome shared across plant species. Our culturomics approach yielded a collection of 2,510 bacterial and 837 fungal isolates, representing 10-21% of the seed microbiota diversity detected by metabarcoding and the majority of the prevalent and abundant taxa. Notably, 44-60% of cultured bacterial isolates were not detected by metabarcoding, highlighting the complementary nature of these approaches to detect rare or under amplified taxa in PCR. This study provides insights into the complexity and variability of seed microbiota across different crops and production conditions. Our findings emphasize the importance of combining culturomics and sequencing methods for comprehensive characterization of seed microbiota to uncover the potential of seed-borne microorganisms as bioinoculants for sustainable agriculture.

ecology↗

bioRxiv2026

Flow constraints at infection site shape multiplication-dissemination trade-offs and opposite regulatory programs of Xanthomonas and Ralstonia xylem pathogens

Pathogens rely on multiple pathogenicity traits, such as proliferation, adhesion, motility and the production of virulence factors, to successfully colonize their host. The expression of virulence functions is often finely regulated to mitigate resource allocation trade-offs due to their cost for the cell. The ways in which constraints encountered inside the host shape strategies for mitigating the trade-off between pathogenicity traits remain poorly understood. Xanthomonas campestris pv. campestris (Xcc) and Ralstonia solanacearum (Rs) are two bacterial phytopathogens that can colonize the same plant habitat, the xylem vessel, from two different infection sites, leaf and root, respectively. Analyses of the virulent regulatory networks (VRN) of Xcc and Rs revealed differences in the expression of their virulence programs in a cell density-dependent manner. Notably, swimming motility and exopolysaccharide production were regulated using opposite strategies. Simulation of bacterial dispersion in the vascular system through spatial model showed that these VRNs were adapted to the constraint of xylem sap flow. This study reports how strong environmental constraints, such as the direction of xylem sap flow, can shape opposite regulatory programs and strategies for mitigating trade-offs for pathogens colonizing the same ecological niche. ImportanceThe regulation of pathogen virulence programs and how differences in their execution confer invasion advantages remain poorly understood. Because the expression of pathogenicity traits is costly in terms of energy, pathogens must carefully control their deployment to proliferate efficiently within the host. This work uses a systems-level approach to provide a comprehensive understanding of the sequential expression of pathogenicity traits in two xylem pathogens Ralstonia solanacearum (Rs) and Xanthomonas campestris pv. campestris (Xcc) during xylem colonization. Moreover, computational analysis of their dispersal within xylem vessels highlights the significance of strategies that mitigate trade-offs to ensure effective colonization, despite the strong physical constraints imposed by xylem sap flow. Together, these results provide new insight into how distinct regulatory strategies influence the success of pathogen invasion and enhance our understanding of bacterial adaptation to host vascular environments.

systems biology↗

bioRxiv2025

Genotype-Specific Root Morphology and Metabolic Traits Shape Bacterial Communities and Tolerance to Fusarium Root Rot in Wheat

Plant genotype plays a critical role in shaping root-associated microbial communities and in modulating plant tolerance to soilborne diseases such as Fusarium root rot (FRR). In this study, we investigated how four wheat (Triticum aestivum) varieties, whose tolerance to FRR differs, influence the composition and structure of bacterial communities in the rhizosphere and root endosphere. We evaluated root traits that may contribute to the genotype-specific assembly of bacterial communities across the four wheat genotypes. The variety Concret exhibited the highest FRR tolerance, whereas Pilier was the most susceptible. Analyses of root morphology revealed significant genotype-dependent differences in root length and volume, which were positively correlated with the abundance of some rhizosphere bacteria affiliated with Bacillus, Lysobacter, and Sphingomonas. Untargeted metabolomics identified 879 features, with 20 key metabolites distinguishing the wheat genotypes, including alkaloids and benzoate- and benzoxazinoid-derived compounds. Correlation analysis revealed significant relationships between these root metabolites and key bacterial taxa. Our findings demonstrate that wheat genotypes influence the assembly of the root microbiota through genotype-based morphological and metabolic traits, providing valuable insights into traits that modulate the plant microbiome to improve wheat resistance to FRR.

ecology↗

bioRxiv2025

Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations

Drought is a critical risk in developing countries for staple crops like common bean (Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither response of the Red Hawk microbiomes to drought, nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity. This study demonstrates that rhizosphere microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries, while difficult to implement, are useful to inform generalities and build theory towards prediction on microbiome responses to global change.

microbiology↗

bioRxiv2025

Lactuchelins: New lipopeptide siderophores from Pseudomonas lactucae inhibit Xanthomonas campestris pv. campestris 8004

Seeds harbor diverse microbial communities, including beneficial microbes that play a vital role in protecting plants from seed-borne pathogens. Despite their critical importance, the molecular mechanisms driving intermicrobial competition within the seed microbiome remain poorly understood, limiting the potential to optimize seed inoculation strategies. In this study, we evaluated the inhibitory potential of 30 seed-borne bacterial strains against the phytopathogen Xanthomonas campestris pv. campestris 8004 (Xcc8004). We identified Pseudomonas lactucae CFBP13502 as a potent inhibitor of Xcc8004, mediated by exometabolites specifically induced in the presence of Lysobacterales (formerly Xanthomonadales). Transcriptomic analysis of CFBP13502 revealed upregulation of a gene cluster involved in the biosynthesis of a lipopeptide siderophore biosynthesis. Gene deletion confirmed that this cluster is essential for the growth inhibition of Xcc8004. Furthermore, iron supplementation abolished this inhibitory effect, providing strong evidence for the role of iron chelation. Through comparative metabolomics, we elucidated the structure of a novel family of lipopeptide siderophores, which we named lactuchelins, produced by CFBP13502. Our findings provide the first molecular evidence of competitive exclusion mechanisms at the seed microbiome interface, highlighting lactuchelins as a promising avenue for the development of seed-based biocontrol strategies against seed-borne phytopathogens.

microbiology↗