Arbuscular mycorrhizal fungi (AMF) can improve nutrient acquisition and stress responses in maize, yet inoculation benefits remain inconsistent across fields. Root colonization alone does not establish effective nutrient transfer or net crop benefit. This critical narrative review examines maize-associated AMF diversity, arbuscule-mediated exchange, host genotype effects, phosphorus availability, stress responses, rhizosphere and hyphosphere interactions, inoculant quality, and field evidence. We define crop-adapted AMF by demonstrated function in a specified maize–soil–management context, rather than fungal origin or colonization percentage alone. Drawing on mechanistic research and contrasting field outcomes, we propose a six-stage Maize–Soil–AMF Fit Framework linking native resource mapping, functional screening, compatibility tests, formulation quality, field integration, and ecological monitoring. The framework distinguishes practical agronomic evidence from advanced mechanistic measurements and permits three decisions: inoculate with a validated product, manage an effective native AMF network, or avoid intervention. It is a conceptual decision aid, not a validated predictive model. Reliable application requires replicated, genotype-aware field tests with appropriate native-AMF controls, prespecified crop outcomes, and transparent assessment of uncertainty and economic value.

Background
Most land plants benefit from the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these ‘non-mycorrhizal’ plants meet their nutritional requirements without this crucial partnership.

Results
Comparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90–122 million years ago. Field surveys of 42 wild populations across seven sites revealed that non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors.

To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57–69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders.

Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions.

Conclusions
Our findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities.

Root colonisation by endomycorrhizal fungi has long been a widely used metric in mycorrhizal studies. However, due to the significant time required to assess colonisation using traditional microscopy techniques, studies of colonisation at large scales are impractical. Machine-learning-based approaches may increase output and facilitate ecosystem assessments. We trained a machine-learning-based tool (MycorrhizaFinder) on 42 field roots (132 unique 1 cm sections, with > 100,000 tiles) and validated on a further 37 sections from grasslands and heathlands hosting common Northern European plants with arbuscular (AM) and ericoid mycorrhizal (ErM) fungal structures, and dark septate endophytes (DSE), also common in field-sourced roots. We incorporated a user-customized confidence threshold to encourage engagement with morphological ambiguities, in e.g. ErM and DSE. A Macro F1 statistic was used to assess the tool’s development performance. We provide a sample workflow from root processing and microscope slide scanning to semi-automated model training and performance evaluation. Our model performance combining all classes, the Macro F1, is conservatively 66% for arbuscular and 57% for ericoid mycorrhizal colonisation assessment. MycorrhizaFinder is user-friendly, requires no programming skills and offers flexibility for advanced agronomists or ecologists to train the tool using their own labelled mycorrhizal root datasets, including images acquired from different instruments or staining protocols. This adaptability allows users to customize the model for specific ecosystems or experimental designs. Leveraged with molecular identification and/or functional traits of fungi (e.g. arbuscules), MycorrhizaFinder supports scalable and repeatable nursery experiments and monitoring across ecosystems to assess mycorrhizal status and track land-use changes over time.

Symbiotic nitrogen fixation efficiency in soybean can be compromised by nodule senescence; however, the mechanisms by which rhizobial type III effectors NopL and NopP─which disrupt plant immune signaling pathways and promote symbiotic compatibility─regulate nodule senescence in soybean remain unclear. Therefore, we investigated this aspect and identified GmPRLP as a key host gene responsive to NopL and NopP, via quantitative trait locus mapping and whole-genome resequencing. Functional analysis using hairy root transformation showed that GmPRLP overexpression accelerated nodule senescence, as evidenced by increased bacteroid degradation and membrane lipid peroxidation, whereas GmPRLP silencing delayed senescence. Transcriptomic profiling and weighted gene coexpression network analysis indicated that GmPRLP promotes nodule senescence by activating ethylene signaling genes, including GmACS7, GmACO, and GmERFs. To conclude, GmPRLP mediates soybean responses to rhizobial effectors and regulates nodule senescence through the ethylene signaling pathway, providing a potential target for improving nitrogen fixation efficiency in soybean breeding.

For a large community of ecosystem ecologists, plant–soil interactions have moved center stage in the understanding of both plant and soil ecology. Frequently, plants are deemed to be the main drivers of these interactions. However, soils existed before the evolution of land plants (i.e., embryophytes), and terrestrial communities were already highly diverse around 400 million years ago (Ma), reflecting an earlier origin of the organisms that populated them. But which organisms were contemporaneous at the origin of soil and in what type of environment they lived is not well established. Here, we trace the development of soil and its biotic components from the beginnings, about one billion years ago (Ga), by using the fossil record and geochemical data. We show that the first terrestrial ecosystems were probably situated near the ocean, where organisms were already adapted to high oxygen pressures and where plants were not yet present. Drawing on this, we discuss the need to rethink the primacy of plants in modern terrestrial ecosystems, considering that persistence of the soil system over deep time could help explain the enormous current biodiversity found in soil. We advocate for a shift in perspective by embracing a vision of terrestrial ecosystems with interdependent and equally important above- and below-ground system compartments. Finally, we highlight the importance of ‘bending the curve’ on the increasing rate of soil degradation and loss of soil health, and we discuss the outlook for the future of soils and their interactions with plants.

Rhizobial nitrogen fixation in legume nodules requires precise spatial and temporal coordination between host and bacterial gene expression. Here, we applied spatial enhanced resolution omics sequencing (Stereo-seq) to profile Medicago nodules across five developmental stages, generating a co-transcriptomic atlas of nodule development. Using a mixed-probe capture strategy, we simultaneously detected host and rhizobial transcripts within the same tissue sections, enabling analysis of host-microbe transcriptional coordination during symbiosis. We identified dynamic changes in host cell composition and developmental trajectories and uncovered two transcription factors, MtERF82 and MtDOF53, required for maintenance of the indeterminate nodule meristem. Rhizobial and host genes exhibited stage- and zone-specific expression patterns along the nodule apex-to-base axis. Notably, reactive oxygen species (ROS)-associated stress responses in both host cells and rhizobia were linked to symbiotic nitrogen fixation. Functional analyses further showed that MtERF71 and MtCBF1 promote nitrogen fixation by regulating ROS homeostasis and activating key symbiotic genes, highlighting stress signaling as an integral component of mutualistic symbiosis.

Nitrogen fertilizers are the foundation of modern agriculture, but they impose severe environmental costs in the form of greenhouse gas emissions and ecological eutrophication. Unlike legumes (which naturally host nitrogen-fixing bacteria), cereals such as maize, rice and wheat — the world’s major calorie-producing crops — require nitrogen fertilizers to support high yields. Crop scientists have long sought a sustainable solution using nitrogen-fixing bacteria (diazotrophs) that colonize cereal roots. However, rigorous evidence of efficacy in the field remains scarce. Here we explore why: the production and release of fixed nitrogen in the form of ammonia are limited by insufficient bacterial colonization of roots, suboptimal environmental conditions and feedback repression of nitrogen fixation. Genetic engineering can force ammonia release, but it also impairs bacterial competitiveness and colonization to levels below what we estimate is required to deliver agronomically relevant quantities of fixed nitrogen. We argue that the field needs a course correction and propose a framework for developing improved cereal biofertilizers.

Climate change threatens crop productivity and soil function, increasing reliance on rhizosphere microbiomes that support plant nutrition, stress tolerance and disease suppression. Plants shape these communities through root exudation, which transfers an estimated 13.4 Pg C yr-1, about 9% of global gross primary productivity, belowground. Yet most studies report exudate composition rather than the concentrations and rates microorganisms perceive. This review synthesises literature published between 2015 and 2026, with emphasis on work from 2020 onward, and proposes a quantitative signalling framework in which absolute concentration, release flux and spatial gradient determine microbial responses at defined activation thresholds. Exudate chemistry, biosynthesis, transport and uptake are first examined, distinguishing passive diffusion sustained by the microbial sink from transporter-mediated release, root re-uptake and phytosiderophore-mediated iron acquisition. Sampling and analytical approaches, including HRMS-based metabolomics, stable isotope tracing, imaging and kinetic modelling, are then evaluated, separating relative from absolute quantification. Because most high-precision flux data derive from hydroponic or sterile systems, where wheat phytosiderophore release exceeds that in soil by about 50-fold, in situ microdialysis, corrections for sorption and degradation, and minimum reporting standards are proposed. Signal-response modules and allelochemical signalling at the root-microbe-soil interface are discussed, followed by multi-omics integration, where static metabolite pools and transcripts cannot resolve flux unless anchored by pulse labelling with LC-MS, stable isotope probing and NanoSIMS. Stress-induced quantitative reprogramming of exudation is interpreted within this framework. Exudation measured in soil is concluded to be a net flux, and unresolved compound-specific thresholds remain the principal barrier to predictive rhizosphere manipulation.

Nitrogen-fixing root nodules develop as lateral organs on legume roots and their formation is restricted by autoregulation of nodulation (AON), a systemic mechanism with unclear evolutionary origins. We identify Lotus japonicus NUCLEAR FACTOR Y subunit A4 (NF-YA4) gene as a central target of the leucine-rich repeat receptor kinase HAR1, which controls both AON and root system architecture. Under nonsymbiotic conditions, HAR1 suppresses expression of NF-YA4 and its close paralog NF-YA1, at least in part through a miR169-dependent mechanism, mirroring the Arabidopsis CLAVATA1/2-miR169-NF-YA module. Loss of HAR1 leads to NF-YA4 overexpression, broad transcriptional reprogramming, and induction of LATERAL ORGAN BOUNDARIES DOMAIN, STYLISH, and YUCCA auxin biosynthesis genes, enhancing auxin signaling and lateral root development. Grafting experiments show that HAR1 constrains NF-YA4-mediated branching both locally in roots and systemically from shoots. Because NF-YA4 functions partly redundantly with NF-YA1 to mediate nodule emergence, our results suggest a model in which duplication and neofunctionalization of an ancestral NF-YA-dependent pathway controlling lateral root development facilitated its recruitment to the nodulation program. They also raise the possibility that AON could have evolved, at least in part, through the co-option of a LRR-RK/miR169/NF-YA regulatory module that limited lateral root development.

Rhizobium inoculation can improve alfalfa performance, but responses depend on both plant genotype and growing environment. We first screened 14 rhizobial strains plus one commercial inoculant with Medicago varia ‘Caoyuan No. 3’ (CY3) in a greenhouse pot experiment, together with an uninoculated control (16 treatments; three pots per treatment). Based on plant height, root length, leaf number, nodule number, and above- and belowground biomass after two months, SJN, HH, and HK were selected as higher-performing strains, whereas XBC, SWL, and XH were retained as lower-performing comparators. These six strains were then evaluated with CY3, Medicago sativa ‘Aohan’ (AH), and M. sativa ‘Adrenalin’ (ADN) in a replicated field experiment. Individual growth and nutritional responses varied among varieties and growth stages. At flowering, XH increased CY3 above-ground biomass by 113% relative to CK, whereas the reported TOPSIS composite ranking placed CY3+XBC first overall. The corresponding composite rankings placed AH+SJN and ADN+SWL first; notably, CK ranked second for ADN. Thus, ‘optimal’ refers to the highest reported composite score across the measured growth, nodulation and nutritional indicators, not superiority for every individual trait. Because symbiotic nitrogen fixation was not measured directly and a pre-sowing physicochemical baseline for the field soil was unavailable, the findings should be interpreted as context-dependent agronomic responses rather than direct quantification of nitrogen fixation or remediation of saline soil.

Indigenous nodule-forming bacteria associated with French bean can differ substantially in functional phenotype, while plant responses to inoculation may also depend on external nitrogen (N) availability. This study evaluated functional variation among nodule-forming bacterial isolates recovered from French bean (Phaseolus vulgaris L.) and examined how selected isolates interacted with four mineral-N levels (0, 30, 60, and 100 kg N ha⁻¹) to influence plant growth, nodulation, N accumulation, physiological responses, and productivity. Fifty probable isolates were initially recovered from French bean nodules and tested for nodule-forming ability. Thirty-five indigenous isolates were authenticated by plant infection tests and subsequently screened in sand culture under net-house conditions. Ten comparatively effective isolates were selected for the mineral-N experiment and evaluated together with Rhizobium leguminosarum MTCC 10,096 and an uninoculated control in a completely randomized design with three biological replications. The isolates exhibited phenotypic, functional, and carbon-substrate-utilization diversity. In the pot experiment, isolate treatment, mineral-N availability, and their interaction influenced several plant traits. Increasing mineral N generally enhanced vegetative growth, biomass production, plant N accumulation, and grain yield while progressively suppressing nodulation. RD20-3 and RK3-1 were among the isolates associated with comparatively favorable responses across several plant traits, although their relative performance varied with trait and N level and nodulation of both declined as mineral N increased. Apparent inoculation-derived nitrogen gain (AING), calculated as the difference in total plant N uptake between inoculated and corresponding uninoculated treatments at the same N level, did not consistently correspond with nodule abundance. Multivariate analysis separated a dominant plant-performance/N-acquisition axis from a nodulation-dominated response axis. These results show that isolate functional differences interact with mineral-N availability to generate contrasting French bean growth, nodulation, N accumulation, and productivity responses. Because molecular identification of the indigenous isolates, nodule-occupancy confirmation, and direct N₂-fixation measurements were not undertaken, the results should not be interpreted as demonstrating taxonomic identity or isolate-specific symbiotic N₂-fixation efficiency.

Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia, a key step in the global nitrogen cycle. The Mo- and V-dependent nitrogenase isozymes are expressed under different environmental conditions, including temperature, yet little is known about how their catalytic behavior changes with temperature. Here, we examine the temperature dependence of total electron flux, electron partitioning into the products NH3 and H2, and estimate ATP energy costs per N2 fixed for purified Mo- and V-nitrogenases from Azotobacter vinelandii over a 10-50 ˚C temperature range. Both isozymes exhibit similar temperature-dependent scaling of total electron flux to all products across the temperature range, but with significantly different distributions of electrons to H2 or NH3 formation. As temperature increases, V-nitrogenase diverts an increasing fraction of electron flux into H2 formation, whereas Mo-nitrogenase maintains a nearly constant electron partitioning to N2 reduction. The estimated ATP molecules hydrolyzed per N2 reduced change little for the Mo-nitrogenase across this temperature range, but rises significantly for the V-nitrogenase with increasing temperature, reaching over 200 ATP per N2 fixed at 50 ˚C. These results demonstrate that, in A. vinelandii, the Mo- and V-nitrogenases exhibit significantly different responses of electron partitioning to products and ATP hydrolyzed per N2 reduced to changes in temperature. These findings suggest environmental conditions under which each isozyme would be optimal, with V- and Mo-nitrogenase both being favorable at low temperatures and Mo-nitrogenase being the only energetically reasonable enzyme at higher temperatures.

Plants function as integral components of soil ecosystems, embedded within diverse microbial consortia that engage in continuous chemical and informational exchange. This molecular dialog governs how plants distinguish harmful, neutral, and beneficial microbes, transforming the rhizosphere into a dynamic signaling interface. Microbial interactions operate along a chemical continuum in which metabolites, volatiles, peptides, and other small molecules act across aqueous, lipidic, and chemically heterogeneous microenvironments to shape recognition and response. The physicochemical organization of rhizosphere metabolites may influence their diffusion, stability, and accessibility, although direct evidence for these effects remains limited. Within this framework, plant recognition is reinterpreted as a fluid, context-dependent communication process rather than a binary separation of immunity and symbiosis. This review synthesizes recent advances in the molecular architecture of this continuum, from receptor-mediated signaling to metabolite-driven ecological filtering, and examines how these overlapping systems determine host specificity, community stability, and adaptive resilience. Special attention is given to the regulatory roles of reactive oxygen species (ROS), phytohormones, and redox metabolites as both stress indicators and inter-organismal communicators. By integrating biochemical, ecological, and systems perspectives, this review highlights implications for developing microbiome-based, climate-smart, and sustainable agricultural practices.

Generating crops that utilize atmospheric nitrogen rather than soil nitrogen requires the transfer of nitrogenase structural genes together with genes required for the biosynthesis of nitrogenase iron−sulfur cofactors. Scaffold proteins, such as NifU, are the starting point of nitrogenase cofactor assembly. While NifU has been successfully produced in plants, its optimal production was achieved with iron supplementation in the nutrient solution. This suggests a faulty connection with the endogenous iron trafficking network, indicating the need for specific elements targeting iron to NifU. Here, we identify bacterioferritin A (BfrA) as an iron donor to NifU. Co-expression with BfrA increases NifU production in Nicotiana benthamiana, leading to doubling the production of NifH, a nitrogenase structural protein that is also required for the synthesis of more complex nitrogenase cofactors. This work underscores the importance of transferring metal delivery systems alongside metalloproteins when engineering heterologous systems.

Atmospheric dinitrogen (N2) is far more abundant than carbon dioxide (CO2), yet photosynthesis has been studied and harnessed predominantly for photosynthetic carbon fixation (PCF), underpinning the global biocarbon economy. In contrast, biological N2 fixation—the natural gateway for atmospheric nitrogen into the biosphere—remains comparatively underexploited. Modern agriculture and industry consequently depend heavily on the fossil-fuel-intensive Haber–Bosch process, with substantial energy and environmental costs. Diazotrophic cyanobacteria offer a fundamentally different paradigm by coupling oxygenic photosynthesis to nitrogenase-mediated N2 fixation. We term this process photosynthetic nitrogen fixation (PNF), which uses solar energy to convert water and atmospheric N2 into bioavailable nitrogen.
Beyond its ecological significance, PNF expands the functional scope of photosynthesis beyond carbon fixation and provides a biological foundation for sustainable nitrogen production, biofertilization, and N2-based biosolar manufacturing. Recent advances in cyanobacterial physiology, ecology, evolution, synthetic biology, and AI-enabled multi-omics are accelerating efforts to harness this potential. This review examines the diversity of diazotrophic cyanobacteria, their strategies for protecting oxygen-sensitive nitrogenase, and emerging approaches for genetic engineering cyanobacteria as programmable platforms for nitrogen production and crop-associated nitrogen delivery. We further propose a roadmap toward a solar-powered BioNitrogen Economy encompassing bioprospecting, synthetic biology, genomic engineering, crop integration, and scalable agricultural and industrial deployment. By expanding photosynthesis from carbon fixation to the solar-powered capture of both carbon and atmospheric nitrogen, PNF could help drive the transition from a fossil-fuel-dependent chemo-nitrogen economy toward a sustainable BioNitrogen Civilization.

Plants form associations with diverse beneficial microbes, including arbuscular mycorrhizal (AM) fungi, rhizobia, and plant growth-promoting bacteria (PGPB). Research on legume-rhizobia symbiosis (LRS) and AM symbiosis has demonstrated that molecular communication between symbiotic partners is essential for initiating these interactions. Genetic and biochemical studies have further identified both plant and microbial signals, as well as host genetic pathways, that regulate these interactions. However, most studies on plant-PGPB interactions have focused on direct application of PGPB to plant roots, leaving the early signaling mechanisms underlying these interactions poorly understood. In this study, we report that diffusible signals from A. brasilense can promote rice growth without direct contact between bacteria and plant roots, 7 days post-treatment (dpt). Using RNA sequencing, we identified 2,516 differentially expressed genes (DEGs) in rice roots in response to diffusible signals from A. brasilense at 1 dpt. We identified differential expression of genes involved in flavonoid synthesis, defense responses, receptor activity, transcription factors, and hormone pathways. Comparative transcriptomic analysis of rice roots with or without contact with A. brasilense revealed both shared and unique gene expression patterns. We observed upregulation of certain defense-response genes (PAL, chitinase, thionin), transcription factors (AP2/ERFs, MYBs, WRKYs, and GRAS), and hormone-related (auxin and ethylene) genes without bacterial contact, but downregulation or no differential expression of these genes upon bacterial contact. This pattern suggests that initial induction followed by subsequent suppression of these genes may be crucial for establishing the interaction with A. brasilense. Our transcriptomic analysis also suggests that flavonoids may be required throughout the interaction, whereas nitrate transporters appear to be involved at later stages and likely require contact between plant roots and bacteria. Collectively, our findings reveal that diffusible signals from A. brasilense can promote rice growth and induce distinct gene expression changes in plant roots. These results provide novel insights into the early phase of rice-A. brasilense interaction and highlight the potential for leveraging plant-PGPB signaling mechanisms to enhance crop growth under adverse environmental conditions.