Plant-Microbe Symbiosis

The nuclear pore complex controls the movement of proteins into and out of the nucleus, allowing cells to regulate protein localization and abundance. This process influences how organisms respond to environmental stimuli. Components of the nuclear pore complex, including the NUP107-160 sub-complex, NUP133, NUP85, and NENA, are required for root nodulation and arbuscular mycorrhization in Lotus japonicus. However, the specific role of these nucleoporins in symbiotic signaling was poorly understood. Through reverse genetics, we discovered that NUP133 is also required for symbiosis in Medicago truncatula, although the mutant phenotypes were less pronounced than in Lotus. Overexpression of the symbiotic ion channels Medicago DMI1 and Lotus Castor and Pollux in the Lotus Ljnup133, Ljnup85, and Ljnena mutants partially alleviated the nodulation defects. Notably, in NUP107-160 sub-complex mutants of Lotus and Medicago, the accumulation of GFP-labeled Pollux and DMI1 on the inner nuclear membrane was reduced, indicating the NUP107-160 sub-complex plays a key role in regulating the distribution of DMI1 and Pollux on the nuclear envelope. This highlights the extreme sensitivity of nodulation in Lotus to changes in the abundance of Pollux on the inner nuclear membrane. In contrast, Medicago appears to exhibit greater tolerance to alterations in the distribution of DMI1 on the nuclear envelope.

The fossil fuel–driven chemosynthesis of ammonia for nitrogen fertilizers is a major contributor to global greenhouse gas emissions, releasing approximately 1130 million metric tons (MMT) of CO2-equivalent annually. In addition, the extensive use of synthetic nitrogen fertilizers (≈108 MMT annually) results in substantial emissions of nitrous oxide (N2O), while nearly 50% of applied nitrogen is lost through leaching and runoff, leading to widespread nitrate pollution and ecosystem degradation. In contrast, solar-powered biological nitrogen fixation (BNF) by nitrogen-fixing plants offers a sustainable alternative that supports agricultural productivity and healthy ecosystem resilience.
BNF by leguminous and non-leguminous plants plays a critical role in reducing dependence on synthetic nitrogen fertilizers. Legumes alone contribute an estimated ∼32-149kg.hm-2 of fixed nitrogen annually. Beyond legumes, associative, endosymbiotic, and endophytic nitrogen fixation in non-legume plants further expands the ecological and taxonomic scope of BNF. Nitrogen-enriched cropping systems, such as legume–cereal rotations, can reduce greenhouse gas emissions by up to 88%, increase soil organic carbon stocks by approximately 8%, enhance soil microbiome activity by 45%, and provide farmers with 15–25% more stable revenues. Advances in biotechnology offer new opportunities to improve nitrogen fixation efficiency and develop novel nitrogen-fixing crops, including cereals and perennial fruit trees. By integrating nature’s evolutionary solutions (N2-fixing plants) with modern biotechnology, agriculture can transition from a fossil fuel–based chemo-nitrogen economy to a solar-powered bio-nitrogen economy.

Epigenomic processes in arbuscular mycorrhizal fungi are receiving increased attention as a framework for explaining phenotypic variability.
Arbuscular mycorrhizal fungi genomic organization into A and B compartments mirrors that of plant-pathogenic fungi, where genes facilitating host adaptation are isolated within the rapidly evolving B compartment.
Arbuscular mycorrhizal fungi exhibit high levels of DNA methylation, a common pathway across eukaryotes to adjust metabolic processes in response to the environment and transmit these responses to subsequent generations.
Evidence is mounting that arbuscular mycorrhizal fungi deploys noncoding RNA to control gene expression and to interact with plants, where specific RNA molecules could be transmitted to the next generation.
The field is poised to draw from multigenerational studies, as used in other model organisms, to pinpoint epigenomic processes that determine phenotypic plasticity and rapid adaptation.

Sorghum (Sorghum bicolor) serves dual roles as a staple food crop providing energy and nutrition for human’s consumption, and as an economic crop utilized in the production of saccharides, silage, and bioethanol. The biological significance of aerial root mucilage secretion lies in biological nitrogen fixation, through which sorghum acquires approximately 40% of its nitrogen from the atmosphere. Prior transcriptomic data indicated tissue-specific overexpression of ENOD93 in aerial roots. This study presents the characterization of the ENOD93 multigene family in sorghum. Sobic.004G099900 exhibited distinct evolutionary patterns compared to the other six members in chromosomal localization, gene structure, physicochemical properties, domain architecture, subcellular targeting, and phylogenetic reconstruction, suggesting its emergence earlier in evolutionary history. Expression profiling across tissues and stress conditions revealed significant nitrogen responsiveness at the transcriptomic level. Mucilage secretion was positively correlated with the ENOD93 expression level at the developmental stage and immersion in vitro. Collectively, these findings indicate that the ENOD93 multigene family has undergone functional diversification during evolution. The ENOD93 expression may respond to nitrogen fluctuations in the mucilage microenvironment, suggesting it could be a candidate positive genes of aerial root mucilage secretion. This work advances understanding of ENOD93 evolutionary patterns in sorghum and provides some clues for the exploration of genes regulating mucilage secretion in aerial roots.

• Root mucilage is not a homogeneous secretion but a composite of mucilage and substantial border cell biomass.
• Aerial roots of maize secrete ∼4 times more mucilage and release ∼6 times more border cells than primary roots.
• Mucilage secretion is significantly associated with border cell release (R2 = 0.60), indicating coordinated root cap activity.
• Rhizodeposition varies markedly with root type and plant developmental stage, challenging static assumptions.
• Explicit separation of mucilage and border cell contributions is essential for accurate rhizosphere modeling and interpretation of plant-soil interactions.

Microbial exopolysaccharides (EPS) are high-molecular-weight carbohydrate polymers secreted by bacteria (including cyanobacteria) and fungi that have attracted increasing interest as biostimulants for sustainable crop production. Despite a growing body of literature, an integrated analysis connecting EPS structural and physicochemical properties to downstream plant molecular responses has been lacking. This review addresses that gap by adopting a structure–function–omics framework, tracing a sequence from EPS chemical composition, including charge, molecular weight, hydrophilicity, and rheological behavior, through plant perception mechanisms, to the transcriptomic and metabolic changes that follow. In the rhizosphere, EPS contribute to soil aggregate stabilisation, water retention, and heavy metal chelation, improving root-zone conditions under drought, salinity, and metal toxicity. At the plant surface, LysM-domain receptor-like kinases recognize structurally defined EPS and initiate signaling cascades. The outcome, such as symbiosis, immunity, or growth promotion, depends on the EPS structural identity. Transcriptomic and metabolomic studies across multiple crop systems indicate that EPS exposure is associated with modulation of photosynthesis, carbohydrate metabolism, antioxidant defense, and secondary metabolite biosynthesis, including phenylpropanoids, flavonoids, and terpenoids. Phytohormone networks involving salicylic acid, jasmonic acid, abscisic acid, and auxin are also influenced, though evidence for intact high-molecular-weight EPS as direct hormonal regulators remains limited. Dedicated coverage is provided for cyanobacterial EPS, an underexplored source with distinctive structural properties. The review concludes by identifying priority knowledge gaps, notably the complete absence of studies on EPS-mediated epigenetic effects in plants, and outlines directions for translating EPS research into field-applicable biostimulant technologies.

Endosymbiotic interactions in fungi are fundamental to ecological and evolutionary processes; however, despite their potential to elucidate key mechanisms of biological integration, they remain insufficiently explored. This review provides a comprehensive synthesis of the available evidence on these associations across major fungal lineages, encompassing their composition, functional attributes, and breadth across diverse model systems. Additionally, the current state of artificial endosymbiosis is examined, together with its applications in multiple areas of biotechnology, spanning both natural and engineered systems. Finally, a framework of progressive endosymbiosis is proposed to describe the continuum of integration states of endosymbionts within fungal hosts. Together, these insights highlight the central role of fungal endosymbiosis in biological integration and underscore its value as a model for understanding evolutionary transitions and developing innovative biotechnological applications.

Tetracycline (TC), a widely used veterinary antibiotic, frequently accumulates in agricultural soils and disrupts nitrogen (N) cycling, thereby enhancing nitrous oxide (N2O) emissions. However, biologically based mitigation strategies and their underlying mechanisms remain poorly understood. In this study, a soybean pot experiment was conducted with four treatments: control, arbuscular mycorrhizal fungi (AMF) inoculation, TC addition, and AMF combined with TC. By integrating hyphosphere-specific sampling, potential N2O production rate measurements, 16S rRNA gene sequencing, quantitative PCR, metagenomics, and partial least squares path modeling, we systematically elucidated AMF-mediated regulation of N2O production under TC stress. TC significantly increased potential N2O production rate (+21.2%), primarily by selectively suppressing the terminal denitrification step, as evidenced by reduced nitrous oxide reductase (NOS) activity and decreased abundance of the nosZ gene, resulting in denitrification pathway disruption and N2O accumulation. In contrast, AMF inoculation under TC stress reduced potential N2O production rate by 29.5%, restoring it to control levels. Mechanistically, AMF improved hyphosphere soil properties (e.g., increased SOC and TN and enhanced TC dissipation) and selectively enriched functionally competent and TC-tolerant denitrifiers, particularly nosZ-harboring taxa such as Streptomyces, thereby repairing denitrification pathway completeness. Path modeling further demonstrated that AMF mitigated N2O production both directly by enhancing N-cycling microbial functional capacity and indirectly by optimizing soil physicochemical conditions. Our findings reveal the microbial and molecular mechanisms underlying antibiotic-enhanced N2O emissions and highlight AMF as a low-input, nature-based environmental biotechnology strategy to simultaneously remediate antibiotic-contaminated soils and mitigate agricultural greenhouse gas emissions.

Arbuscular mycorrhizal (AM) symbiosis is regulated by carotenoid-derived molecules, including strigolactones and other apocarotenoids. However, the role of root carotene availability remains poorly understood. Here we evaluated AM performance in tomato using two mutants showing contrasting root carotenoid profiles, i.e. cyc-b7, an EMS-derived TILLING mutant carrying a characterized mutation in Cyc-B, and 7458-Y, an uncharacterized mutant line showing high carotenoid accumulation), compared to their related wild type (Red Setter). Not-inoculated and AM fungal inoculated plants were grown under controlled conditions and root colonization parameters were assessed after two months. Root carotenoids were quantified by high-performance liquid chromatography (HPLC), and RNA-seq analysis was performed on root samples to understand the tomato response to the inoculation. Roots of cyc-b7 accumulated significantly lower total carotenoids than Red Setter, including reduced lutein and β-carotene, whereas 7458-Y showed increased β-carotene, together with higher arbuscule abundance than both Red Setter and cyc-b7. Transcriptome profiling revealed a genotype-dependent response to AMF inoculation, with symbiosis-related genes differentially regulated in the two mutant lines. In cyc-b7, AMF inoculation was associated with reduced expression of genes encoding nutrient transporters, as well as of a gene encoding a symbiosis receptor-like kinase (SYMRK), a component of the common symbiosis signaling pathway. By contrast, in 7458-Y, AMF inoculation was associated with up-regulation of a gene encoding a LysM receptor-like kinase involved in AM establishment, and of a gene, SlD27, related to strigolactone biosynthesis. Overall, our results support a link between root carotenoid metabolism and AMF colonization.

Rhizobial bacteria are known for their ability to fix nitrogen for leguminous plants and their essential function for sustainable agriculture. This study characterizes the taxonomic status and functional potential of the Bradyrhizobium B64 isolate using integrated genomic and molecular approaches. The whole genome of the B64 isolate was sequenced via Illumina paired-end technology. Species delimitation was performed using average nucleotide identity (ANI) and digital DNA-DNA Hybridization (dDDH). The NodD1 protein structure was modeled using AlphaFold3 and validated by Ramachandran plot analysis. Molecular docking was then conducted to evaluate interactions between NodD1 and four signaling flavonoids: Apigenin, Daidzein, Genistein, and Naringenin. Genomic analysis revealed a maximum ANI of 94.4% and dDDH values between 51.4 and 62.4%. Since these values fall below the standard prokaryotic thresholds (ANI < 95%; dDDH < 70%), the B64 isolate is identified as a novel species. Physiological assays confirmed nitrogen fixation (1.97 ppm), IAA production (3.67 ppm), and phosphate solubilization (26.10 ppm). Structural validation showed 100% of NodD1 residues in allowed regions, ensuring high model reliability. Docking simulations demonstrated strong binding affinities across all flavonoids, with binding free energies ranging from − 8.8 to − 9.0 kcal/mol. Daidzein exhibited the highest thermodynamic stability (− 9.0 kcal/mol), whereas apigenin showed the most extensive residue interaction network. The B64 isolate is a novel Bradyrhizobium species with a high symbiotic capacity. The stable NodD1-flavonoid interactions provide a molecular basis for efficient nodulation, positioning B64 as a promising candidate for developing lipo-chitooligosaccharide (LCO)-based biofertilizers.

Arbuscular mycorrhizal (AM) symbiosis is a widespread, ancient, mutualistic relationship between plants and fungi that supports nutrient acquisition in more than 80% of plant species (Brundrett and Tedersoo 2018; Sportes et al. 2021). Central to the plant-AM symbiotic relationship is the formation of arbuscules. Arbuscules are finely branched fungal structures that form inside root cortical cells and serve as sites for nutrient exchange (Fig. 1a; Luginbuehl and Oldroyd 2017). Although arbuscules are morphologically well described, their cellular heterogeneity and developmental dynamics have remained difficult to resolve because colonized individual roots contain a mosaic of fungal structures at different stages.

This article traces more than four decades of Eva Kondorosi's personal life and scientific journey in symbiotic nitrogen fixation, from early insights into nitrogenase structure to the molecular mechanisms governing root nodule development and symbiotic cell differentiation in the Medicago–Sinorhizobium meliloti symbiosis. Effective symbiosis depends on precise molecular communication between the partners, beginning in the soil and continuing through a highly coordinated, progressive differentiation program. A defining feature of symbiotic cell development is endoreduplication in both host plant cells and their Rhizobium partners. Host-induced bacterial endoreduplication results in the formation of large, polyploid, noncultivable nitrogen-fixing bacteroids. This terminal differentiation is orchestrated by plant-derived effector peptides, notably nodule-specific cysteine-rich (NCR) and nodulin glycine-rich (nodGRP) peptides, which act sequentially to reprogram bacterial physiology. Together, these findings establish symbiotic nitrogen fixation as a model for cross-kingdom cellular differentiation and highlight NCR and nodGRP peptides as a vast, largely unexplored resource with promising applications in agriculture and medicine.

The establishment of an efficient symbiotic relationship between soybean and rhizobia requires precise regulation of root nodule development. While sugar transporters are known to participate in nutrient allocation during symbiosis, their molecular functions and regulatory mechanisms in this process remain poorly characterized. This study aims to functionally characterize the sugar transporter GmSWEET17 and elucidate its role in soybean-rhizobia symbiosis. Building upon initial yeast library screening that identified GmSWEET17 as a novel interacting partner of the Nod factor receptor GmNFR1α, this study further confirmed their physical interaction through yeast two-hybrid assays and luciferase complementation imaging (LCI) in tobacco leaves. The two proteins were shown to co-localize at the plasma membrane in Arabidopsis mesophyll protoplasts. Rhizobial infection induced GmSWEET17 expression in roots, with dynamic expression patterns showing an initial increase followed by a decrease during nodule development. Promoter activity assays demonstrated specific expression of GmSWEET17 in the vascular tissues of roots and nodules. Heterologous expression in yeast revealed that GmSWEET17 primarily transports glucose. Overexpression of GmSWEET17 in transgenic hairy roots led to reduced nodule number but increased nodule size and enhanced nitrogen fixation activity. Furthermore, GmSWEET17 overexpression up-regulated the expression of key nodulation marker genes. Our results demonstrate that GmSWEET17, a sugar transporter interacting with GmNFR1α, positively regulates soybean nodule development and nitrogen fixation efficiency. This study provides new molecular evidence for the biological function of GmSWEET17 in nodulation and nitrogen fixation, and offers novel insights into the regulatory mechanisms of GmNFR1α in rhizobial symbiosis.

Arbuscular mycorrhizal fungi (AMF) are central components of terrestrial ecosystems and agroecosystems. However, their accurate identification remains methodologically challenging due to their complex biology and the limitations of traditional morphological approaches. Over the past three decades, molecular tools have profoundly reshaped AMF research, shifting from spore-based identification and Sanger sequencing of ribosomal markers toward high-throughput amplicon sequencing and, more recently, metagenomic frameworks that enable community-level and functional analyses. This review critically examines the conceptual and technical evolution of AMF identification strategies, comparing morphological characterization, ribosomal DNA markers (SSU, ITS, LSU), multilocus approaches, metabarcoding, and whole-genome metagenomics. We analyze their taxonomic coverage, resolution, and methodological biases, including primer specificity, intragenomic rDNA variation, database limitations, and bioinformatic pipeline effects. Attention is given to how marker selection influences ecological interpretation, cross-study comparability, and functional inference. Finally, we propose practical guidelines for aligning marker choice with study objectives and outline validation strategies—such as mock communities, curated reference databases, and multi-marker integration—to improve reproducibility and taxonomic robustness. By integrating historical perspective, methodological evaluation, and applied recommendations, this review provides a decision-oriented framework to support more accurate and comparable assessments of Glomeromycota diversity.