Legume–rhizobium symbiosis relies on the precise integration of receptor-mediated signaling with dynamic membrane trafficking to initiate infection threads (ITs) and accommodate bacterial infection via root hairs. Here, we identify the soybean Qa-SNARE GmSYNTAXIN111a (GmSYP111a), a close paralog of the cytokinesis-specific protein KNOLLE, as a critical regulator in symbiotic infection. A kinase client (KiC) assay revealed that GmSYP111a is a direct phosphorylation substrate of the receptor kinase GmSymRKβ (also known as DMI2 or NORK in other legumes), which modifies Ser-8 at its N-terminus. BiFC, co-immunoprecipitation, and in vitro kinase assays confirmed that GmSymRKβ phosphorylates GmSYP111a without disrupting their basal association, but phosphorylation alters the subcellular distribution of the complex. In soybean root hairs, GmSYP111a and GmSymRKβ co-localize to the plasma membrane, and Nod factor perception induces clathrin-mediated endocytosis accompanied by GmSYP111a re-localization into intracellular vesicles. A non-phosphorylatable mutant (GmSYP111aS8A) showed markedly reduced internalization and a corresponding decrease in infection events, resulting in impaired IT formation and a phenotype resembling GmSymRKβ-RNAi roots. In contrast, a phosphomimetic variant (GmSYP111aS8D) displayed partial vesicular recruitment upon infection. Functional analyses further demonstrated that GmSYP111a, but not its paralog SYP111b, is indispensable for nodule initiation in soybean, with this role conserved in Lotus japonicus. Collectively, our results show that GmSymRKβ-mediated phosphorylation of GmSYP111a functions as a molecular switch that links symbiotic signaling to clathrin-dependent endocytosis. This mechanism coordinates localized membrane remodeling at infection sites, parallels the role of KNOLLE in cytokinesis, and highlights how duplication and neo-functionalization of GmSYP111a contributed to the evolution of legume-specific symbiotic pathways.

Arbuscular mycorrhizal (AM) fungi enhance plant nutrient acquisition from soil; however, their ability to exploit organic nutrient forms in the absence of associated microbes capable of mineralization remains unclear. To test if the AM fungi carry their beneficial bacterial partners into nutrient-rich zones, we conducted three controlled experiments manipulating the microbial inputs, diversity and composition in plant–AM fungus–soil systems, ranging from open pots to semi-sterile mesocosms. We manipulated soil microbial diversity by imposing a microbial diversity gradient (complex communities fractionated by size, resulting in fractions passing through 1 µm to 1000 µm sieves) and cultivated Andropogon gerardii in previously sterilized substrate together with a bacterial-free Rhizophagus irregularis. In each experiment, 15N‐labeled chitin or mineral nitrogen (N) compartments were installed in the root‐free zone of each mesocosm. With decreasing microbial inputs into the root-free zone, the N uptake from chitin to plants, facilitated by the AM fungal hyphae, decreased. Upon complete absence of microbes in the root-free zone, AM hyphal foraging preferences assessed by quantitative PCR indicated that exploration of the mineral N compartments was more effective than that of the chitin compartments. AM fungal hyphae were ineffective in priming mineralization of organic N even if provided with complex soil microbiomes at a distance from the compartment. In summary, chitin-enriched compartments become attractive for the AM fungi only when previously mineralized by competent microbes. Such microbes, however, were not effectively transported to spatially restricted organic resources in soil via AM hyphal highways in our experiments.

Symbiotic mycorrhizal fungi are crucial drivers of ecosystem functioning through their associations with plants. Ecosystems dominated by different types of mycorrhizal fungi, such as ectomycorrhizal fungi (EM) and arbuscular mycorrhizal (AM) fungi, often exhibit variation in plant productivity. However, the mechanisms underlying these differences and their dependence on environmental context remain unclear. Furthermore, the lack of robust, fine-scale evidence linking plant productivity to measurable indicators of mycorrhizal colonization or dominance, together with limited information on environmental variables, constrains accurate global-scale modeling of mycorrhizal effects on ecosystem functioning. In this study, we synthesize existing knowledge on the competitive and complementary interactions between the two dominant mycorrhizal types. Building on this synthesis, we propose a new conceptual framework to describe the context-dependent and often idiosyncratic nature of these interactions. We then present case studies and a meta-analysis spanning local to global scales, examining how vegetation biomass is related to mycorrhizal colonization or dominance under different environmental conditions. Our findings indicate that mycorrhizal types and environmental variables interactively shape ecosystem productivity in a dynamic and resilient manner. This work offers a new foundation for spatially explicit, locally informed assessments of how mycorrhizal influence vegetation productivity across contrasting environmental constraints.

Plant–microbe symbioses such as the legume–rhizobium mutualism are vital in the web of ecological relationships within both natural and managed ecosystems, influencing primary productivity, crop yield, and ecosystem services. The outcome of these interactions for plant hosts varies quantitatively and can range from highly beneficial to even detrimental depending on natural genetic variation in microbial symbionts. Here, we take a systems genetics approach, harnessing the genetic diversity present in wild rhizobial populations to predict genes and molecular pathways crucial in determining partner quality, i.e., the benefits of symbiosis for legume hosts. We combine traits, dual-RNAseq of both partners from active nodules, pangenomics/pantranscriptomics, and Weighted Gene Co-expression Network Analysis (WGCNA) for a panel of 20 Sinorhizobium meliloti strains that vary in symbiotic partner quality. We find that genetic variation in the nodule transcriptome predicts host plant biomass, and WGCNA reveals networks of genes in plants and rhizobia that are coexpressed and associated with high-quality symbiosis. Presence–absence variation of gene clusters on the symbiosis plasmid (pSymA), validated in planta, is associated with high or low-quality symbiosis and is found within important coexpression modules. Functionally our results point to management of oxidative stress, amino acid and carbohydrate transport, and NCR peptide signaling mechanisms in driving symbiotic outcomes. Our integrative approach highlights the complex genetic architecture of microbial partner quality and raises hypotheses about the genetic mechanisms and evolutionary dynamics of symbiosis.

Legumes engage in nitrogen-fixing symbiosis with rhizobia, wherein it is well established that host legumes supply dicarboxylates as a carbon source to rhizobia, while rhizobia reciprocate by providing ammonium to the host plants. Apart from the classical model, accumulating evidence suggests that amino acid exchange is also essential to legume-rhizobium symbiosis. However, it remains unclear whether amino acid transporters are present on the symbiosome membrane (SM) to mediate amino acid exchange in symbiotic nitrogen fixation (SNF). In this study, we identified three amino acid transporters in Medicago truncatula—MtCAT1a, MtCAT1b, and MtCAT1c—belonging to a clade of the plant Cationic Amino acid Transporter (CAT) family known for transporting a wide range of amino acids. Notably, MtCAT1b and MtCAT1c are predominantly expressed in infected cells of nodules and are localized to the SM. Genetic analyses further demonstrate that both MtCAT1b and MtCAT1c are required for amino acid exchange on the SM, with additional evidence indicating that metabolism of bacteroids is disturbed in the mutant. Transport assays reveal that both MtCAT1b and MtCAT1c exhibit broad substrate specificity. Collectively, our findings identify MtCAT1b and MtCAT1c as key mediators of cross-kingdom amino acid exchange, essential for maintaining efficient SNF in root nodules.

Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with roots of most terrestrial plants, playing a crucial role in regulating soil organic carbon (SOC) dynamics. While precipitation increase (Pi) is a major facet of climate change, its impacts on root- and AMF-mediated SOC formation and stability remain largely unexplored. Here, we combined a meta-analysis across global grasslands with a multiyear precipitation manipulation experiment in a semiarid grassland on the Loess Plateau to disentangle the relative effects of roots and their associated AMF on microbial communities and SOC as influenced by Pi. We show that Pi induced tradeoffs between roots and AMF, and promoted SOC formation and stability via the mycelium- rather than the root-pathway, leading to an increase of 136% (±40) and 297% (±90) in mycelium-derived C and mineral-associated organic C (MAOC), respectively. Pi altered plant community composition, favoring subshrubs and forbs over grasses. Also, Pi reduced specific root length, but increased root diameter, tissue density, and root colonization and extraradical biomass of AMF. Furthermore, Pi-induced change in AMF shifted the soil bacterial community by favoring K-strategists, increasing bacterial necromass C and promoting MAOC accumulation. Our findings provide direct evidence that Pi enhances AMF-driven SOC sequestration by expanding the mycorrhizosphere and promoting microbiota with high C use efficiency, highlighting a key mechanism by which mycorrhizal fungi mediate SOC formation and stability under shifting precipitation regimes.

The plant rhizosphere, a region interconnecting roots, soil, and microorganisms, is critical for plant resource acquisition, community structure, and the functional stability of ecosystems. Most studies focus primarily on root traits, while overlooking the covariation within the rhizosphere root–soil–microbe continuum and its ecological implications under environmental change. Here, we highlight the necessity of integrating rhizosphere function into a broader theoretical framework encompassing belowground traits, such as the core functional modules of roots, rhizosphere microorganisms (including mycorrhizal fungi), and soil. We further identify critical knowledge gaps and future directions for research on rhizosphere function traits. This framework expands current perspectives on plant belowground functional traits, plant adaptation, and ecosystem stability under changing environments.

In recent years, interest in the role of nutrient cycling in sustainable agriculture has significantly increased. The potential of arbuscular mycorrhizal (AM) fungi (AMFs) in nutrient cycling and plant growth improvement has long been recognized. However, there have been only a few studies on the identification and exploration of AM symbiosis-related plant genes for sustainable agriculture. We have developed a new constructive model for using host plant-derived AM symbiosis-related genes to improve breeding and AMF utilization for sustainable agriculture, particularly in the context of climate change. This model include: 1) the discovery of AM symbiosis-related genes in crop wild-relatives for molecular breeding and 2) the screening and propagation of AMFs that can help improve water-use efficiency and nutrient-use efficiency by crops, thereby reducing chemical fertilizer use in agricultural production. The first approach uniquely facilitates the identification of host plant-derived AM symbiosis-related genes, such as CHITIN ELICITOR RECEPTOR KINASE 1 (OsCERK1) from Dongxiang (DY) wild rice (Oryza rufipogon) (OsCERK1DY), MILDEW RESISTANCE LOCUS 1 (MLO1) from wild barley (Hordeum spontaneum), and WRKY60 from wild soybean (Glycine soja), for breeding purposes. The second one involves identifying soil-borne AMF species, such as Rhizophagus intraradices and Glomus mosseae for practical applications in the field. This suggestive model presents an emerging biotechnological potential for engineering climate-resilient crops.

The demands for food are rising worldwide due to the planet’s finite resources and changing environment. The population of Earth is growing drastically every day, which may be in charge of ensuring global food security, which will ultimately have an impact on farming methods and human habitation. All living things require nitrogen, although it is the most restrictive in ecosystems. Despite the significant contribution of synthetic fertilizers, the amount of nitrogen needed for food production increases yearly, and the misuse of agrochemicals threatens the sustainability of agriculture and the health of the soil. Biological nitrogen fixation (BNF) is one solution to this issue. BNF accounts for about 60% of Earth’s fixed nitrogen. As a result, it is becoming more and more important to optimize BNF in agriculture to satisfy the expanding global demand for food production. BNF offers numerous practical advantages to agroecosystems. It is an essential method for enhancing soil N availability to enhance crop growth and refilling the reservoirs of soil organic N. A thorough understanding of the BNF mechanism would enable the transfer of this capacity to other non-fixing microbes or highly valuable non-leguminous plants. This chapter includes the history and contributions from both global and regional sources, gives the current understanding of BNF, the process of the global nitrogen fixation cycle, advantages of BNF, effectiveness in agriculture, commercialization of nitrogen as biofertilizers, limitations, and their prospects. It also addresses potential ways to increase BNF for potential benefit and draws attention to the opportunities and challenges on the adoption of BNFs.

Introduction: Microbial interactions in the rhizosphere are fundamental to soil health, plant growth, and ecosystem stability. Among these interactions, metabolic cross-feeding, the exchange of metabolites between microorganisms, plays a critical role in shaping microbial community structure and function. This study investigates the metabolic interplay between two PGPR (Priestia megaterium and Bacillus licheniformis), focusing on how metabolite exchange influences bacterial growth and metabolic reprogramming.

Methods: An integrative metabolomics approach was employed to examine metabolic exchanges between P. megaterium and B. licheniformis. Cultures were grown individually and in co-culture, followed by extraction of extracellular metabolites at distinct growth phases. Metabolomic profiling was conducted using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Data preprocessing and feature extraction were followed by molecular networking and multivariate statistical analysis to identify discriminant metabolites. Pathway enrichment and functional annotation were performed using KEGG and MetaboAnalyst to pinpoint key metabolic pathways altered during cross-feeding interactions.

Results and discussion: Metabolomic analysis revealed distinct metabolic shifts driven by reciprocal metabolite exchange between P. megaterium and B. licheniformis. Metabolites secreted by B. licheniformis exhibited a growth-inhibitory effect on P. megaterium, while those from P. megaterium stimulated the growth of B. licheniformis. Multivariate data analysis demonstrated significant variation in the production of amino acids, fatty acids, and cyclic lipopeptides across growth phases. Pathway enrichment identified the phenylalanine, tyrosine, and tryptophan biosynthesis (PTTB) pathway as a central metabolic hub mediating these interactions. The regulation of aromatic amino acid metabolism appeared critical in determining whether interactions were cooperative or competitive. The observed metabolic reprogramming reflects adaptive strategies employed by PGPR to thrive under nutrient-limited conditions, balancing cooperation and competition through selective metabolite secretion. These findings offer systems-level insight into the mechanistic basis of cross-feeding and highlight the potential of integrating metabolomics to guide microbial consortia design for agricultural applications. Understanding these metabolic determinants supports the development of tailored biofertilizer formulations that enhance soil fertility and plant resilience.

Conclusion: This study demonstrates that metabolite cross-feeding induces distinct metabolic reprogramming between Priestia megaterium and Bacillus licheniformis, underpinning adaptive interactions in nutrient-limited environments. These findings provide a mechanistic basis for microbial consortia design and biofertilizer optimization. Future multi-omics and systems-level investigations should elucidate the genetic and regulatory determinants of these metabolic exchanges, advancing sustainable biotechnological innovations aligned with SDGs 9, 12, and 13.

Legume plants have the capacity to incorporate atmospheric nitrogen by establishing an endosymbiotic interaction with soil bacteria resulting in the formation of nitrogen-fixing nodules. Bacteria are internalized through a tightly regulated process that requires membrane remodelling and vesicle trafficking, which are controlled by small GTPases. Members of the ARF family of GTPases mediate vesicle budding in a wide range of biological processes; however, the modulation of ARF members, their subcellular localization and the formation of complexes with other proteins during the root nodule symbiosis has not been investigated. Here, to identify proteins that physically interact with MtARFA1, a yeast two hybrid screening was performed using a cDNA library of Medicago truncatula roots inoculated with Sinorhizobium meliloti. One of the identified MtARF1 interactors is a protein that possesses a BTB/POZ domain. BTB/POZ domains are present in substrate-specific adaptors that form complexes with the Ubiquitin ligase E3 Cullin3 (CUL3), thus the interactor was designated as M. truncatula CUL3 substrate-adaptor protein 1 (MtCSP1). Physical interaction between MtARF1 and MtCSP1 was verified in planta by co-immunopurification assays and bimolecular fluorescence complementation, revealing that the interaction takes place in vesicles of the late endosome. The MtCSP1 promoter is active in lateral roots and in the meristem of indeterminate nodules. Phenotypic analysis of transgenic roots with altered mRNA levels of MtCSP1 evidenced the requirement of this gene for the progression of rhizobial infection and nodule organogenesis. This work establishes a link between small GTPases and protein degradation by the ubiquitin system in the context of the nitrogen-fixing symbiosis.

Background
The trans-kingdom movement of microRNAs (miRNAs) is a key regulatory mechanism in plant biotic interactions, influencing and modulating both pathogenic virulence and symbiotic relationships. This study employed bioinformatic analysis to predict the role of rice (Oryza sativa L.) miRNAs in regulating gene expression during interactions with the pathogenic fungi Rhizoctonia solani (R. solani) and Magnaporthe oryzae (M. oryzae), as well as the symbiotic fungus Rhizophagus irregularis (R. irregularis).

Results
Previously reported and up-regulated rice miRNAs were identified from the literature during inoculation, and their target genes were predicted in the fungal transcriptomes. The KEGG pathway and GO enrichment analyses revealed that rice miRNAs could target genes crucial for pathogen metabolism (e.g., carbohydrate, amino acid, lipid, and xenobiotic), genetic information processing, and essential cellular processes (e.g., signal transduction, transport, catabolism, and cell growth and death), potentially impairing fungal virulence and survival. The osa-miR171 family is predicted to regulate R. irregularis genes involved in protein serine/threonine kinase activity, antiporter activity, cell division, TAP complex binding, and O-acetylhomoserine sulfhydrylase activity during symbiosis. Additionally, the osa-miR171 family targets key rice genes such as phosphate transporter, NSP2, and SCR, involved in nutrient transport, common symbiosis signaling, and root development, respectively, which are likely important for forming and regulating a symbiotic relationship. The qRT‒PCR results confirmed the up-regulation of osa-miR171h (symbiosis-related) and osa-miR167d-5p (pathogen-responsive) in rice roots inoculated with R. irregularis.

Conclusions
These findings highlight the significant role of trans-kingdom RNA regulation in plant–microbe interactions, contributing to understanding the molecular regulation, distinctions, and similarities between pathogenic and symbiotic relationships in plants. This initial study performs the first comparative trans-kingdom sRNA analysis in rice, successfully predicting and distinguishing the molecular mechanisms that drive virulence versus mutualism. This work also lays the groundwork for developing novel strategies to enhance plant disease resistance, foster beneficial symbiotic interactions, and ultimately boost agricultural yields.