Biology subjects

SIMONIN, M.

Publications and source records attributed to SIMONIN, M..

3 recordsLinked to original sources

bioRxiv2026

Seed-applied multi-kingdom synthetic communities selectively reshape bacterial communities and highlight key criteria for strain selection

Defined microbial communities (also known as synthetic communities) are showing promising results for plant health but are lacking an efficient lab to field transition. This is the due to limited knowledge on how to efficiently modulate plant microbiota by considering complex environments and multi-kingdom interactions. In this study, we aimed to better understand the transmission and impact of multi-kingdom synthetic communities (SynComs) from the seed to seedling stage. We constructed 20 different SynComs using both a priori and random approaches, from pool of diverse strains including 24 bacteria, 11 yeasts and 10 filamentous fungi. SynComs were inoculated on Brassica napus seeds and we monitored both transmission and impact on the microbiota of 15-day-old seedlings grown in non-sterile soil. Optimization of the inoculation protocol showed that alginate coating improved bacterial, yeast and filamentous fungi concentrations by more than 2 log compared with other approaches. With this inoculation method, we observed contrasted seedling colonization profiles, with SynComs members representing between 1.1-45.7% of bacterial community and 3.2-36.6% of fungal community. Our multiple SynCom design revealed that strain selection is a more critical determinant of SynCom performance than assembly strategy. Even randomly assembled communities performed well, as long as they are drawn from a pool of ecologically relevant, well-adapted taxa. Based on these evidences, we identified key bacterial and fungal traits explaining efficient seedling colonization such as high abundance on inoculated seed and low in vitro lag-time. Despite low colonization levels, we observed that SynCom inoculation altered seeding bacterial community assembly in 14 SynComs. A total of 82 native bacterial ASVs were identified as responsive to SynCom inoculation, most likely originating from the soil. This shift indicates that SynComs influence community assembly by modulating the recruitment of environmental taxa, especially when SynCom strains were more integrated in multi-kingdom network structures. Finally, we identified four distinct SynComs profiles which either colonized strongly or not seedlings while shifting of not native microbiota. Altogether, these findings provide actionable directions for improving SynCom design, suggesting that leveraging ecological processes such as host adaptation, optimal inoculation density, and network integration could enhance both colonization efficiency and plant phenotypic outcomes.

microbiology↗

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↗