Ronnie de Jonge

This study identifies bacterial secretion systems enriched in the rhizosphere and their associated taxa, suggesting potential applications for bioinoculant optimization.

This study shows that Pseudomonas protegens CHA0 maintains its multi-host lifestyle and key traits after serial passage through insect larvae, with only minor and limited changes observed.

The paper investigates how Arabidopsis, Barley, and Lotus plants recruit specific bacteria from synthetic communities, finding that functional capacities drive microbiota assembly.

The paper uses protein foundation models to predict microbial root competence across bacteria, finding that these models outperform traditional methods when predicting traits in evolutionarily distant species.

ASVNet improves microbial community analysis by clustering 16S rRNA amplicon sequences into biologically relevant groups that better reflect actual organisms than traditional OTUs or ASVs.

This study identifies two distinct functional states in synthetic plant root bacterial communities driven by Bacilli abundance and microbial interactions.

SyFi improves the accuracy of SynCom member identification by using genomic and amplicon-based fingerprints, enhancing resolution for closely related isolates.

The paper uses pangenome graph analysis of 19 spinach downy mildew isolates to study the evolution of resistance-breaking traits and identifies effector candidates associated with resistance breakdown.

This study uses a modified Pseudomonas syringae strain to identify key effectors contributing to disease in spinach, enabling high-throughput analysis of effector function.

The paper predicts next-season potato vigor based on seed tuber microbiome composition using a Random Forest model trained on microbiome and crop development data.

The paper constructs a pangenome graph for Peronospora effusa, revealing extensive copy-number variation in pathogenicity genes and transposable elements contributing to genomic diversity.

This study quantifies the rhizosphere effect along a soil-root gradient in Arabidopsis thaliana, showing microbial community convergence driven by selection and priority effects.