The microbiota of plants is composed of a large diversity of microbes, engaging with their host via various types of interactions, from beneficial to detrimental. Consequently, how plants perceive mutualistic from pathogenic microbes and which molecular pathways drive the outcome of the interaction (partnership or defense) are critical questions for the understanding of plant-microbe interactions. In this study, we evaluated the rice transcriptional response to a diversity of bacteria spanning from root pathogens to plant growth-promoting rhizobacteria (PGPRs) in hydroponic conditions. A transcriptomic analysis of rice leaf and root tissues was performed to identify common and specific transcriptional signatures during interaction with non-plant-isolated (Escherichia coli and Stenotrophomonas maltophilia), plant-isolated (Pseudomonas defensor and Bradyrhizobium sp. ORS278), or rice-isolated bacteria (Azospirillum sp. B510 and Burkholderia plantarii). Among all tested groups, the pools of differentially expressed genes (DEGs) modulated by all bacteria or by the PGPRs represented only a fraction of the total DEGs, highlighting the specificity of response to each bacterium. However, plant-isolated bacteria induced a stronger response than non-plant-isolated bacteria. The rice response to PGPRs, pertaining to growth induction and stress mitigation, allowed us to identify putative marker genes of beneficial interaction. Ten genes (such as OsPR1b and rNBS41, related to defense response) were oppositely regulated: repressed upon pathogenic and induced upon PGPR interactions. These genes could be pivotal to triggering mutualism or immunity signals. These transcriptomic clues to bacterial mitigation of rice health were confirmed in a greenhouse experiment, in which PGPRs demonstrated strong biocontrol potential against a foliar phytopathogen. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Climate change is increasing the overall temperature of the planet and increasing the number of extreme heat waves events. These phenomena are negatively affecting crop production and food security. Thus, under this scenario, understanding the adaptations that encompass the plant response to high temperature will be essential to enhance crop tolerance and yield. Plant responses to elevated temperature rely on both genetic factors and the dynamic interplay with the surrounding microbiota. Recently, the role of root microbiota as a key player in the plant’s response to heat, is gaining significant relevance. This work presents the analysis of fungal microbiota from the rhizosphere and the root-associated fractions of tomato roots in response to high temperature. Although the analyses were done in an enclosed environment, we used the TGRooZ (Temperature Gradient Root Zone) system to mimic field conditions. The TGRooZ generates a temperature gradient like the natural soil during a heat wave event. We found that distinct soil/root compartments assemble a different fungal community, with the rhizosphere fraction exhibiting greater diversity and abundance, while the root-associated fraction was enriched in fewer but more specialized taxa. Notably, the experimental conditions used to analyze heat responses significantly influenced the final microbiome composition. Our data suggest that the TGRooZ system will enable more accurate analysis of plant-microbiome responses to heat stress and help evaluate the potential of beneficial microbes to enhance crop productivity under near-natural conditions.

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Plants, constantly exposed to dynamic environmental conditions, encounter various abiotic stresses that significantly affect their growth and development. In response, plants initiate complex physiological and molecular adjustments, including altered gene expression. One of the most influential factors in mitigating stress impacts is the plant–microbe interaction. Among these, plant growth-promoting rhizobacteria (PGPR) are well-studied for their ability to enhance plant resilience. More recently, microalgae have emerged as potential members of the plant microbiome, although their roles remain comparatively underexplored. This study investigates the transcriptomic responses of Arabidopsis thaliana to inoculation with the PGPR strain Stutzerimonas stutzeri, the green microalgae Chlorella vulgaris, and a consortium of both microorganisms under salt stress conditions. Through RNA-seq analysis, we identified a set of core genes commonly regulated across all inoculation treatments, including SALT OVERLY SENSITIVE 3 (SOS3), the potassium channel AKT2, and CBL-INTERACTING PROTEIN KINASE 5 (CIPK5), suggesting a shared stress-mitigation mechanism. Additionally, we identified genes uniquely regulated in response to the S. stutzeri–C. vulgaris consortium. These included components of the ethylene signaling pathway (EIN3/EIL1), detoxification-associated genes such as β-GLUCOSIDASE (BGLU22), and transcription factors linked to stress response, notably NAC6 and MYB12. Together, these findings provide insight into the specific and overlapping transcriptomic changes induced by bacterial, algal, and combined inoculations, contributing to our understanding of plant–microbe interactions under salt stress. Comparative transcriptomic profiling of Arabidopsis thaliana inoculated with plant growth promoting rhizobacteria, Stutzerimonas stutzeri, green microalgae Chlorella vulgaris, and their consortium under salt stress reveals synergistic transcriptional responses and identifies candidate genes involved in growth promotion and salt stress tolerance.

AbstractPlants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of inter-organismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis ofArabidopsis thalianawith the beneficial root colonizing endophyteSerendipita indicarepresents a well-studied system. Co-colonization of Arabidopsis roots withS. indicasignificantly promotes plant growth. Due to the notable phenotypic alterations of fungus-infected root systems, the involvement of a reprogramming of plant hormone levels, especially that of indole-3-acetic acid, has been suggested earlier. However, until now, the molecular mechanism by whichS. indicapromotes plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis betweenA. thalianaandS. indica. Our experiments revealed the essential role of tightly controlled auxin conjugation in the plant–fungus interaction. It particularly highlighted the importance of twoGRETCHEN HAGEN 3(GH3) genes,GH3.5andGH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of thePIN2auxin transporter gene in roots of Arabidopsis seedlings infected withS. indicaand demonstrate that this transcriptional adjustment affects auxin signaling in roots, which results in increased plant growth.

We conducted a multi-laboratory experiment across five labs to demonstrate reproducible microbiome formation, metabolite production, and plant growth using the EcoFAB 2.0 system. This protocol provided standardized instructions for the participating labs to implement the EcoFAB 2.0 system effectively, ensuring consistency in plant-microbiome experimentation. It includes annotated videos detailing each experimental step, utilizing a model bacterial community and the model grass Brachypodium distachyon in a hydroponic EcoFAB 2.0 setup.

Plants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of interorganismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis of Arabidopsis thaliana with the beneficial root colonizing endophyte Serendipita indica represents a well-studied system. Colonization of Arabidopsis roots with S. indica promotes plant growth and stress tolerance of the host plant. However, until now, the molecular mechanism by which S. indica reprograms plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis between A. thaliana and S. indica. Our experiments revealed the sustained stimulation of auxin signalling in fungus infected Arabidopsis roots and disclosed the essential role of tightly controlled auxin conjugation in the plant-fungus interaction. It particularly highlighted the importance of two GRETCHEN HAGEN 3 (GH3) genes, GH3.5 and GH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of the PIN2 auxin transporter gene in roots of Arabidopsis seedlings infected with S. indica and demonstrate that this transcriptional adjustment affects auxin signalling in roots, which results in increased plant growth.

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon , and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia , which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies. ### Competing Interest Statement P.F.A. and T.R.N. are inventors of patent US11510376B2, held by the University of California, covering an Ecosystem device for determining plant-microbe interactions. In addition, T.R.N. is an advisor to Brightseed Bio. All other authors declare no competing interest.

Global climate change exacerbates abiotic stresses, as drought, heat, and salt stresses are anticipated to increase significantly in the coming years. Plants coexist with a diverse range of microorganisms. Multiple inter-organismic relationships are known to confer benefits to plants, including growth promotion and enhanced tolerance to abiotic stresses. In this study, we investigated the mutualistic interactions between three fungal endophytes originally isolated from distinct arid environments and an agronomically relevant crop, Solanum lycopersicum. We demonstrated a significant increase in shoot biomass under drought conditions in co-cultivation with Penicillium chrysogenum isolated from Antarctica, Penicillium minioluteum isolated from the Atacama Desert, Chile, and Serendipita indica isolated from the Thar Desert, India. To elucidate plant gene modules commonly induced by the different endophytes that could explain the observed drought tolerance effect in tomato, a comprehensive transcriptomics analysis was conducted. This analysis led to the identification of a shared gene module in the fungus-infected tomato plants. Within this module, gene network analysis enabled us to identify genes related to abscisic acid (ABA) signaling, ABA transport, auxin signaling, ion homeostasis, proline biosynthesis, and jasmonic acid signaling, providing insights into the molecular basis of drought tolerance commonly mediated by fungal endophytes. Our findings highlight a conserved response in the mutualistic interactions between endophytic fungi isolated from unrelated environments and tomato roots, resulting in improved shoot biomass production under drought stress.

The plant microbiome has recently emerged as a reservoir for the development of sustainable alternatives to chemical fertilizers and pesticides. However, the response of plants to beneficial microbes emerges as a critical issue to understand the molecular basis of plant-microbiota interactions. In this study, we combined root colonization, phenotypic and transcriptomic analyses to unravel the commonalities and specificities of the response of rice to closely related Burkholderia s.l. endophytes. In general, these results indicate that a rice-non-native Burkholderia s.l. strain, Paraburkholderia phytofirmans PsJN, is able to colonize the root endosphere while eliciting a markedly different response compared to rice-native Burkholderia s.l. strains. This demonstrates the variability of plant response to microbes from different hosts of origin. The most striking finding of the investigation was that a much more conserved response to the three endophytes used in this study is elicited in leaves compared to roots. In addition, transcriptional regulation of genes related to secondary metabolism, immunity, and phytohormones appear to be markers of strain-specific responses. Future studies need to investigate whether these findings can be extrapolated to other plant models and beneficial microbes to further advance the potential of microbiome-based solutions for crop production.

Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.

Burkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth. ABSTRACT Burkholderia vietnamiensis LMG10929 and Paraburkholderia kururiensis M130 are bacterial rice growth-promoting models. Besides this common ecological niche, species of the Burkholderia genus are also found as opportunistic human pathogens, while Paraburkholderia species are mostly environmental and plant associated. In this study, we compared the genetic strategies used by B. vietnamiensis and P. kururiensis to colonize two subspecies of their common host, Oryza sativa subsp. japonica (cv. Nipponbare) and O. sativa subsp. indica (cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days postinoculation. Overall, we detected twice more genes in B. vietnamiensis involved in rice root colonization than in P. kururiensis, including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice toward B. vietnamiensis than toward P. kururiensis. For both strains, the bacterial fitness depends on a higher number of genes when colonizing indica rice compared to japonica. These divergences in host pressure on bacterial adaptation could be partly linked to the cultivars’ differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains, e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain specifically, we detected functions limiting root colonization such as biofilm production in B. vietnamiensis and quorum sensing in P. kururiensis. The involvement of genes identified through the Tn-seq procedure as contributing to root colonization, i.e., ED pathway, c-di-GMP cycling, and cobalamin synthesis, was validated by directed mutagenesis and competition with wild-type (WT) strains in rice root colonization assays. IMPORTANCE Burkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth. However, the closely related Burkholderia genus includes both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat toward other plant hosts or humans. To start answering these questions, we used in this study transposon sequencing to identify genetic traits in Burkholderia vietnamiensis and Paraburkholderia kururiensis that contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.

AbstractBurkholderia vietnamiensisLMG10929 (Bv) andParaburkholderia kururiensisM130 (Pk) are bacterial rice growth-promoting models. Besides this common ecological niche, species of theBurkholderiagenus are also found as opportunistic human pathogens whileParaburkholderiaare mostly environmental and plant-associated species. Here, we compared the genetic strategies used byBvandPkto colonize two subspecies of their common host,Oryza sativa ssp. japonica(cv. Nipponbare) andssp. indica(cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days post inoculation. Overall, we detected twice more genes inBvinvolved in rice roots colonization compared toPk, including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice towardsBvcompared toPk. For both strains, the bacterial fitness depends on a higher number of genes when colonizingindicarice compared tojaponica. These divergences in host pressure on bacterial adaptation could be partly linked to the cultivar’s differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain-specifically, we detected functions limiting root colonization such as biofilm production inBvand quorum sensing inPk.The involvement of genes identified through the Tn-seq procedure as contributing to root colonization i.e., ED pathway, c-di-GMP cycling and cobalamin synthesis, was validated by directed mutagenesis and competition with WT strains in rice root colonization assays.ImportanceBurkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species ofParaburkholderiahave repeatedly been described to stimulate plant growth. However, the closely relatedBurkholderiagenus hosts both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat towards other plant hosts or humans. To start answering these questions, we used here transposon sequencing to identify genetic traits inBurkholderia vietnamiensisandParaburkholderia kururiensisthat contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.

Burkholderia vietnamiensis LMG10929 ( Bv ) and Paraburkholderia kururiensis M130 ( Pk ) are bacterial rice growth-promoting models. Besides this common ecological niche, species of the Burkholderia genus are also found as opportunistic human pathogens while Paraburkholderia are mostly environmental and plant-associated species. Here, we compared the genetic strategies used by Bv and Pk to colonize two subspecies of their common host, Oryza sativa ssp. japonica (cv. Nipponbare) and ssp. indica (cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days post inoculation. Overall, we detected twice more genes in Bv involved in rice roots colonization compared to Pk , including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice towards Bv compared to Pk . For both strains, the bacterial fitness depends on a higher number of genes when colonizing indica rice compared to japonica . These divergences in host pressure on bacterial adaptation could be partly linked to the cultivar’s differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain-specifically, we detected functions limiting root colonization such as biofilm production in Bv and quorum sensing in Pk. The involvement of genes identified through the Tn-seq procedure as contributing to root colonization i.e., ED pathway, c-di-GMP cycling and cobalamin synthesis, was validated by directed mutagenesis and competition with WT strains in rice root colonization assays.Importance Burkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of Paraburkholderia have repeatedly been described to stimulate plant growth. However, the closely related Burkholderia genus hosts both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat towards other plant hosts or humans. To start answering these questions, we used here transposon sequencing to identify genetic traits in Burkholderia vietnamiensis and Paraburkholderia kururiensis that contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.

Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root-soil-microbiome interactions creates emerging properties that impact plant nutrition and health. As a consequence, the rhizosphere can be considered an extended root phenotype, a manifestation of the effects of plant genes on their environment inside and/or outside of the organism. Here, we review current understanding of how plants shape the rhizosphere and the benefits it confers to plant fitness. We discuss future research challenges and how applying their solutions in crops will enable us to harvest the benefits of the extended root phenotype.

Additional file 7: Table S4. Specific core-genomes of B. cenocepacia and Burkholderia sp. nov. Each gene is detailed with its function, abundance within the species and average length. Their presence within a genome is marked with an â Xâ . The genes further described in the study are highlighted in yellow.

Background Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential. Results We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia , and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia , belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence. Conclusion Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.