Comparative transcriptomic analysis reveals distinct responses of beneficial bacterial endophytes to wild and cultivated rice root exudates

Combined transcriptomics and metabolomics reveals the molecular mechanism by which rice responds to Ustilaginoidea virens infection.

The combined transcriptome and metabolome analysis revealed that plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis were significantly enriched in resistant rice varieties, providing valuable information on the molecular mechanisms by which rice defends against U. virens infection.

Integrated genomic and metabolomic insights into sesame rhizosphere-derived multi-trait Pseudomonas aeruginosa SIRJ8 with salinity stress alleviation and biocontrol potential

Although SIRJ8 exhibited multiple plant-beneficial traits, its virulence-associated genomic repertoire precludes its consideration as an agricultural bioinoculant at present and underscores the necessity of comprehensive biosafety evaluation before any practical application.

Habitat-Adapted Fungal Symbionts Promote Salt Stress Tolerance Through Distinct Root Mechanisms and Shared Shoot Regulatory Networks in Arabidopsis thaliana

Salinity is a major constraint to crop productivity. Beneficial plant–fungus interactions represent a promising strategy to enhance stress resilience. Here, we investigated fungal endophytes isolated from the roots of Oryza sativa cultivated in saline-prone marshlands of the Guadalquivir River, Spain. From a collection of 38 isolates, five salt-tolerant strains exhibiting plant growth-promoting activity were identified, including a previously uncharacterized Reticulascus sp. strain S5. Co-cultivation assays with the non-native host plant Arabidopsis thaliana demonstrated that S5 increased the root and shoot biomass under salt stress. To elucidate the underlying molecular mechanisms, a comprehensive RNA-Seq analysis of the roots and shoots under control and saline conditions was performed. Fungal colonization induced pronounced transcriptomic changes, particularly in the shoots, including rewiring of the auxin- and abscisic acid-related pathways and the induction of genes associated with cell wall remodeling. Concurrently, defense-related processes, including glucosinolate biosynthesis and ethylene signaling, were broadly repressed, suggesting attenuated stress perception in colonized plants. In the roots, S5 inoculation suppressed the expression of genes involved in root hair development and cell wall organization, indicating a fungus-driven reconfiguration of root development. Moreover, comparative analysis with Fusarium sp. K-23, a fungus that has previously been demonstrated to promote plant growth under salinity stress, revealed distinct root-associated mechanisms but convergence on a shared regulatory module in shoots involving ABA-responsive transcription factors and osmotic stress regulators. Collectively, our findings demonstrate that Reticulascus sp. S5 enhances plant salt stress tolerance through the coordinated transcriptional reprogramming of growth, hormone signaling, and stress responses, highlighting a possible potential of habitat-adapted endophytes for sustainable crop improvement.

Ceratobasidium sp. GS2 exudates elicit downstream transcriptional and physiological responses in seeds of Gymnadenia conopsea (Orchidaceae)

Abstract Orchidaceae is a highly valuable horticultural and medicinal plant family worldwide; however, large-scale propagation and conservation remain severely limited. Orchid seeds depend on symbiotic fungi for germination, and pre-symbiotic communication is essential for establishing a successful association, a process that remains poorly understood. In this study, exudates were collected from the germination-promoting fungus Ceratobasidium sp. GS2 and applied to seeds of the terrestrial orchid Gymnadenia conopsea to investigate downstream responses. Multi-omics approaches, including RNA-seq, metabolomics, and phylogenetic analysis, combined with biological validation, revealed that the exudates elicited transcriptional and physiological responses in G. conopsea seeds, potentially promoting dormancy release. Exposure to fungal exudates increased the levels of brassinosteroids, cytokinins, and fatty acids in seeds. Exogenous hormone application confirmed that brassinosteroids and cytokinins promote fungal colonization and facilitate symbiotic seed germination. Phylogenetic analysis revealed the conservation of symbiotic genes in partially mycoheterotrophic orchids, and functional characterization confirmed the role of GcRAM2 in G. conopsea. These findings provide new insights into the mechanisms underlying orchid mycorrhizal symbiosis.

Changes in Root Exudate Composition Drive the Evolution of Their Ecological Functions Towards Improved Chemical Defense and Plant-Microbe Interactions.

Alterations in root exudates and their ecological significance across plant evolutionary divergence time remain elusive due to methodological challenges. Herein, we measured root exudate composition of 20 woody species and assessed its associations with root traits and rhizosphere microbiota to investigate the ecological functions of root exudates throughout plant evolution. The root exudates showed increased richness, polarity, unsaturation and aromaticity with divergence time. Furthermore, fungal richness markedly increased with divergence time, accompanied by the rhizosphere enrichment of copiotrophic bacteria (e.g., Bacteroidota and Actinobacteriota), ectomycorrhizal fungi and several functional microbes. Additionally, competitive root traits (e.g., specific root length and root nitrogen concentration) were positively correlated with exudate richness and chemical complexity in ectomycorrhizal (EcM) trees, whereas they were related to the exudation rates in the arbuscular mycorrhizal (AM) trees. Microbial richness and strategies were closely linked to exudate chemistry, and the exudate-microbe interactions were more tightly coupled in the rhizosphere of EcM trees than in that of the AM trees. Shifts in exudate composition and their associated microbial communities may reflect enhanced chemical defense and rhizosphere communication as plants evolve. These results provide evidence that root strategies extend beyond the root itself to include exudates and the rhizosphere, thereby advancing our understanding of root traits-exudate-microbiota associations across plant evolution.

Multi-omics data analysis reveals a novel beneficial role for strigolactones in tomato