Corné M. J. Pieterse

The plant hormones salicylic acid (SA) and jasmonic acid (JA) are major regulators of plant defense. They can antagonize each other’s activity, enabling an optimized defense response. The SA master regulator NPR1 is a key player in this SA/JA crosstalk, although the mechanisms of NPR1-mediated SA/JA crosstalk remain only partly understood, especially regarding the ethylene-coregulated ERF branch of the JA pathway. Here, we investigated the function of NPR1 in SA/JA crosstalk using several Arabidopsis npr1 mutant variants. Assays using the NPR1-HBD and npr1-nls lines, expressing only cytosolic NPR1, revealed that NPR1 has a nuclear role in SA/JA crosstalk. RNA-seq analysis of lines expressing NPR1 mutated in residues Cys ⁸² or Cys ²¹⁶ , in which repression of the JA pathway was impaired while SA pathway induction remained mostly intact, identified 32 SA-responsive genes with reduced expression compared to Col-0, including four WRKY transcription factor genes. Of these, WRKY53 and WRKY70 could suppress expression of the JA marker gene PDF1.2 induced by ORA59, the master regulator of the ERF branch of the JA pathway, in a protoplast system. Additional SA-inducible WRKYs (WRKY50, WRKY54, WRKY63, and WRKY67) similarly suppressed ORA59-induced PDF1.2 expression, implicating WRKY63 and WRKY67 for the first time in SA/JA crosstalk and confirming earlier reports on the role of the other WRKY TFs. WRKY53 and WRKY67 were further shown to reduce accumulation of the ORA59 protein in protoplasts. Thus, our study indicated that NPR1 can regulate SA/JA crosstalk in the nucleus via transcriptional activation of genes encoding specific JA-repressing WRKY transcription factors. MAIN CONCLUSION: NPR1 has a nuclear function in regulating salicylic acid/jasmonic acid crosstalk by activating specific WRKY transcription factors that suppress the jasmonic acid pathway, likely in part by reducing ORA59 accumulation.

Harnessing plant microbiomes for sustainable agriculture requires understanding not only whether they can boost crop performance, but also how ecological processes govern their assembly, stability, and functional contributions across environments. While we previously showed that seed tuber microbiomes can predict potato vigour using machine learning, it remained unclear how ecological processes shape tuber microbiome stability and functionality across host genotypes, tuber compartments, soil types, and years. Here, we analyzed the national‐scale dataset of 240 field‐collected potato seedlots, spanning six genotypes, two soil types, and two growing years, with a focus on the spatially distinct heel and eye compartments of the potato tuber. By profiling over 1200 bacterial and fungal communities and linking microbiome composition to plant performance, we show that plant genotype and tuber compartment are the strongest determinants of microbial diversity and composition. Compartment‐specific enrichment of functional traits revealed spatial partitioning of microbial functions, with organic compound conversion and nitrogen cycling dominant in the heel, and energy metabolism enriched in the eye. Applying a macroecological abundance–occupancy framework, we identified a stable core microbiome of bacterial and fungal taxa that persisted across all environments and years. These core members were more strongly associated with plant growth‐related traits than non‐core taxa, and core taxa in different tuber compartments showed distinct correlations with taxa of potential pathogenic relevance. Together, our findings demonstrate that tuber compartments act as ecological filters that structure persistent, functionally specialised microbiomes linked to plant growth‐related traits across environments. By providing an ecological and functional framework for compartment‐resolved, stable core microbiomes, this study advances mechanistic understanding of plant–microbe interactions and identifies stable microbial partners as promising targets for improving potato resilience and productivity.

Alkaline salinity is an expanding soil constraint that severely impairs crop productivity through combined osmotic, ionic, and pH-driven stresses, with iron (Fe) limitation as a major constraint. We characterize the plant growth–promoting (PGP) potential of the alkaline-saline-adapted rhizosphere microbiome (MSAT) of Brassica fruticulosa, together with four bacterial strains (R60, T7, E1, E14) isolated from this microbiome and evaluate their capacity to improve salt-sensitive Sinapis alba performance under combined NaCl/NaHCO₃ stress (Salt-Alk). Reciprocal transplant experiments showed that MSAT enhanced shoot biomass, chlorophyll content, and proline accumulation in salt-sensitive B. fruticulosa populations, without detectable changes in leaf ionome, indicating a microbiome-mediated tissue-tolerance strategy rather than ion exclusion. All four isolates retained PGP traits under Salt-Alk, though performance was strain-specific. In S. alba, R60 and T7 promoted shoot and root biomass under Salt-Alk, while R60, T7, and E1 reduced leaf Na⁺ accumulation. Long-term assays identified T7 as the most effective inoculant, enhancing fitness under neutral and alkaline salinity, whereas E1 benefited plants specifically under combined stress. Consortium inoculations showed strain-dependent outcomes, highlighting the complexity of multistrain interactions.Using Arabidopsis thaliana to investigate the mechanisms underlying T7-mediated growth promotion, we found that T7 rescues growth and photosynthetic efficiency under Fe deficiency, even under Salt-Alk stress. T7 inoculation increased FRO2 expression and repressed the coumarin-related genes F6'H1 and MYB72, suggesting selective modulation of Strategy I Fe-deficiency responses. These findings identify T7 as a promising bioinoculant for alkaline-saline conditions and suggest that T7-mediated improvement of plant performance is associated with changes in Fe acquisition responses.

Induced systemic resistance (ISR) is activated in leaves upon root colonization by beneficial microbes, yet the signals linking rhizosphere perception to shoot immunity remain unknown. In the Arabidopsis thaliana-Pseudomonas simiae WCS417 model interaction, the root-specific transcription factor MYB72 and its target gene BGLU42 regulate ISR and the production, activation, and root secretion of coumarins, specialized metabolites involved in plant iron (Fe) acquisition and rhizosphere microbiome assembly. Overexpression of BGLU42 confers constitutive ISR in leaves, suggesting a link between coumarin metabolism and systemic immunity. Here, two-photon multispectral imaging and targeted metabolite profiling revealed that, under Fe-sufficient conditions, WCS417 induces a distinct spatial pattern of F6’H1-dependent coumarin accumulation along the root system. These WCS417-induced coumarin signatures differed from those observed under Fe deficiency, indicating activation of a microbiota-specific coumarin metabolic program. Increased coumarin accumulation in roots was followed by a rise in coumarin levels in shoots. Time-resolved transcriptome profiling supported this metabolic reprogramming, showing rapid activation of Fe acquisition and coumarin biosynthesis genes in roots, including F6’H1, MYB72, and BGLU42 , followed by delayed but similar transcriptional responses in shoots. Functional analyses demonstrated that coumarin biosynthesis is required for WCS417-ISR: the f6’h1 mutant failed to mount systemic resistance, whereas F6’H1 overexpression conferred constitutive resistance to bacterial and fungal pathogens. In addition, WCS417-mediated coumarin accumulation systemically modulated flg22-triggered reactive oxygen species production in leaves in an F6’H1-dependent manner. Together, our results identify coumarins as key mediators linking rhizobacterial perception in roots to systemic immune signaling and resistance in leaves.

Consortia of microbial isolates, also known as synthetic communities (SynComs), are increasingly used to study and harness microbe-microbe and microbe-host interactions. Since “synthetic” potentially evokes negative connotations, we propose adopting the term “Defined Microbial Community” for practical applications.

Background: Root competence, the ability of soil bacteria to establish and grow on plant roots, is a key ecological trait influencing plant nutrition, growth, and health. However, identifying genomic determinants of root competence across bacteria remains challenging, in part because model generalisability depends strongly on how genomes are represented. Traditional approaches based on curated annotations are incomplete and biased toward well-characterised organisms and functions, limiting generalisation. Sequence-similarity clustering improves coverage but yields high-dimensional features relative to dataset size, hindering training. Foundation models offer an alternative by learning com-pact representations without relying on prior annotation. Results: Here, we compared pretrained genome representations from protein and DNA foundation models (ESM-2, Bacformer, DNABERT-S) with annotation- and clustering-based features (KEGG orthology, OrthoFinder protein families) for predicting root competence using synthetic microbial community data from Arabidop-sis thaliana and assessed generalisability across bacteria. When training and test sets contained taxonomically related bacteria, most approaches performed similarly. However, when test bacteria belonged to phyla entirely absent from training, reflecting high evolutionary separation across all levels of bacterial classification, only pretrained protein representations retained predictive performance. Bacformer-derived representations, which incorporate genomic context, supported the strongest generalisation, suggesting that conserved genomic organisation contributes to predicting root competence. Feature attribution quantifying protein contributions to model decisions linked root competence to TonB/SusD-dependent receptors, small-molecule transporters, and unannotated proteins with conserved regulatory motifs and homology to carbon starvation-response loci. Conclusions: Protein foundation models support generalisation across evolutionarily distant bacteria and identify genomic determinants of root competence, including unannotated proteins.

Summary: Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and plants. While their potential as plant growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remain poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress Arabidopsis seedlings were exposed to VOCs emitted by Pseudomonas strains under control and osmotic stress conditions. Plant biomass and root architecture were evaluated. Root transcriptomics analysis was performed and validated using Arabidopsis mutants and metabolomics. Volatile organic compounds effects were also tested on soil‐grown Brassica oleracea and on its rhizosphere microbiome. Pseudomonas VOCs promoted plant growth under both axenic and soil conditions in A. thaliana and in B. oleracea , and under control and drought conditions. Transcriptomics, metabolomics, and functional analysis revealed interactions between Pseudomonas VOCs, glucosinolates, and ABA signalling, as well as a positive association between VOC exposure and coumarin biosynthesis. VOC treatment also reshaped the rhizosphere microbiome under drought, leading to a community composition more similar to that of well‐watered plants. Overall, Pseudomonas VOCs promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.

Summary: Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and with plant roots. While their potential as plant-growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remains poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress. Arabidopsis thaliana plants were exposed to VOCs emitted by Pseudomonas strains under both control and osmotic-stress conditions. VOC exposure generally enhanced plant growth, and this effect was even more pronounced under both drought and salt stress. Transcriptomic analysis revealed that VOC exposure modulates key stress-responsive pathways, including those related to abscisic acid biosynthesis and signalling, sugar transport, iron uptake, aliphatic glucosinolate biosynthesis, and plant defences. Using Arabidopsis mutants, we identified abscisic acid and aliphatic glucosinolates as important components in mediating the plant response to VOCs. SWEET11/12 sugar transporters and ABA signaling genes were downregulated by VOCs exposure, in order to allow for a positive regulation of lateral root numbers (in case of SWEET genes) and plant growth in general under drought stress. In summary, using metabolomics, transcriptomics and functional analysis, we showed a negative cross-talk between the effects of VOCs on plant growth and glucosinolate production, whereas a positive interaction was observed between the biosynthesis of coumarins and VOCs. Notably, VOCs also improved drought tolerance in soil-grown Brassica oleracea plants. We showed that VOC treatment altered the root-associated microbiome under drought, leading to a community composition more similar to that of well-watered plants. Our results show that Pseudomonas emitted VOCs can promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.

Plants can respond to pathogen attack by assembling disease-suppressive microbiomes. In Arabidopsis thaliana, infection by the obligate foliar downy mildew pathogen Hyaloperonospora arabidopsidis (Hpa) consistently led to the formation of a soil microbial community, referred to as “soilborne legacy” (SBL), that enhanced resistance in subsequent plant populations grown in the same soil. Previous work identified an enrichment of specific “Hpa-associated microbiota” (HAM) in the phyllospheres of infected plants, which suppressed pathogen proliferation. Here, we demonstrate how the assembly of protective HAM in the phyllosphere contributes to a disease-suppressive SBL. We identified a community of 25 core-HAM that consistently dominated the phyllospheres of 14 sets of distinct Hpa-infected plant populations across six independent experiments. Using HAM-free, gnotobiotic Hpa spores, the infection-driven assembly of a core-HAM representative was recapitulated, showing de novo and progressive enrichment under sustained disease pressure. Despite being transmitted via soil as SBL, HAM are phyllosphere specialists with infected leaves as their primary niche. Disease-induced HAM assembly is initiated in the phyllosphere rather than the rhizosphere, and once transmitted, they particularly accumulate on aboveground tissues. Leaf wash-offs from plant populations that inherited SBL were shown to effectively suppress downy mildew disease when applied to leaves of plants grown in unconditioned soil. These findings reveal that downy mildew disease–suppressive soils transmit a protective core microbiome to the phyllosphere, highlighting a crucial link between belowground and aboveground plant-driven microbiome assembly processes. Paradoxically, the phyllosphere thus emerges as a key assembly hub for disease-suppressive soil microbiomes.