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.

In bacteria, the auxiliary complex SecDF–YajC participates in the Sec system, facilitating post-translational translocation of preproteins across the membrane through the SecYEG channel. Although YajC homologs are strongly conserved in rhizobial strains and may play important roles in many processes, the functions and mechanisms by which they are involved in the interaction between rhizobia and host legumes are unknown. By constructing Mesorhizobium huakuii yajC mutant, we observed an increase in the strain growth rate, but a reduction in both the biomass and average thickness of the biofilm in the yajC gene mutant compared to the wild type. Deletion of yajC gene results in severe suppression of competitive ability in the plant rhizosphere, alongside a substantial reduction in root hair curling and infection thread initiation during the early infection stages. The yajC-deficient mutant formed more numerous but smaller root nodules, with a 77% decrease in nitrogen-fixing capacity. Scanning electron microscopy analysis revealed that yajC mutant bacteroids displayed, alongside clear hallmarks of cellular deformation, dissociation, and premature senescence. From nodule bacteroid proteomic analysis, we further identified 210 differentially expressed proteins, including 32 transport-related proteins, and 10 associated with nitrogen fixation. Altogether, our findings reveal the importance of YajC-mediated transport and biofilm formation in rhizobial infection and nodule development during M. huakuii-Astragalus sinicus symbiosis.

Microbiome homeostasis is crucial for host health and ecosystem function, yet the molecular and ecological mechanisms underlying community assembly and stability remain elusive. Here we uncover a conserved yeast–oomycete association that promotes their coexistence in the leaf microbiome. Using a continental-scale microbiome survey, we identified an asymmetric mutualistic interaction between two eukaryotic hub microbes: the yeast Dioszegia hungarica and the obligate oomycete Albugo laibachii. We show that Dioszegia facilitates Albugo colonization by supplying thiamine via a dedicated membrane permease, alleviating Albugo’s auxotrophy. Genomic and transcriptomic analyses indicate that natural selection has acted on thiamine production in Dioszegia, shaping this metabolic complementation. In planta assays further suggest that Albugo presence supports Dioszegia persistence under glasshouse conditions. Our study illustrates how the evolution of nutrient cross-feeding mediates microbial coexistence and microbiome stability. Targeting microbial nutrient flows offers new strategies for engineering microbiomes and enhancing plant resilience in natural and agricultural systems. Evolution of nutrient cross-feeding between a yeast and oomycete mediates microbial coexistence and leaf microbiome stability.

Biological nitrogen fixation (BNF) is a sustainable and environmentally friendly approach to nitrogen assimilation that extends beyond leguminous plants

Fungal hyphae form spatially confined interfaces in soil that mediate close associations with bacteria, collectively referred to as the hyphosphere. Despite its recognized ecological importance, experimental access to hyphosphere-associated microbial communities under realistic soil and plant-associated conditions has remained limited. Here, we present a soil-mimetic microcosm that enables controlled recovery of hyphosphere bacterial communities embedded within plant-associated soil. The system integrates field-derived soil, a native soil microbial inoculum, living cotton seedlings, and a spatially constrained fungal inoculum housed within sterile cell-strainer assemblies, permitting hyphal extension into soil while preserving a recoverable fungal-soil boundary. Using the soil-borne plant pathogen Fusarium oxysporum f. sp. vasinfectum as a model filamentous fungus, we show that the microcosm enables reproducible recovery of hypha-associated soil microaggregates containing physically attached bacterial cells. Full-length 16S rRNA profiling revealed pronounced reductions in bacterial richness and evenness in hyphosphere samples relative to bulk and rhizosphere soils (Shannon diversity, Kruskal-Wallis H = 15.25, P = 0.0016, with genus richness declining by 87% in bulk soil and 24% in rhizosphere soil contexts), consistent with recruitment of a restricted subset of the surrounding microbiota. Ordination analyses demonstrated clear compositional separation between soil and hyphosphere compartments (PERMANOVA F = 7.14, R2 = 0.572, P = 0.001), with hyphosphere communities of bulk and rhizosphere origin converging to similar composition despite differing starting soils (R2 = 0.128, P = 0.307). Phylogenetic turnover analyses (βNTI) indicated phylogenetic structuring (exceeding the +2 threshold), whereas taxonomic analyses identified a conserved set of bacterial genera consistently associated with hyphae, alongside compartment-specific taxa influenced by soil and plant context. Together, these findings establish the novel hyphal release-and-capture microcosm as a reproducible, ecologically grounded platform for studying hyphosphere-associated bacterial communities in plant-associated soils.

Symbiosomes are plant membrane–bound, organelle-like structures that enclose single or multiple bacteroids (differentiated rhizobia) within legume cells, serving specifically as the site for N2 fixation. Although isolated symbiosomes have been used to study nitrogen fixation, ion transport, and metabolite translocation, conventional density gradient–based isolation methods for their isolation are labor-intensive. Here, we describe a simplified, density gradient–free protocol for rapid enrichment of symbiosome-containing fractions from mature legume nodules using the Medicago truncatula–Sinorhizobium meliloti symbiosis as an example. The method combines razor blade homogenization, filtration through a 40 μm cell strainer, and sequential low-speed centrifugation to remove debris and enrich symbiosome-associated fractions. The resulting material is compatible with downstream mass spectrometry–based proteomics and mutant phenotypic analyses. Compared with conventional approaches, this protocol is rapid, simple, and suitable for higher-throughput biochemical and proteomic studies of symbiosomes.

The coordination of intracellular carbon and nitrogen levels is essential for optimal bacterial growth and, in rhizobia, for survival in the soil, root colonization, and symbiotic interactions with their host plants. Here, we show that the phosphotransferase system PTSNtr, a global regulator of carbon and nitrogen metabolism, modulates the tricarboxylic acid (TCA) cycle activity and the accumulation of three major carbon storage polymers: glycogen, polyhydroxybutyrate, and exopolysaccharide in Rhizobium leguminosarum. The unphosphorylated form of the effector protein ManX is sufficient for the full activation of the TCA cycle dehydrogenase enzymes. Accordingly, loss of manX reduced dehydrogenase activity and redirected overflow carbon into storage polymers, phenocopying wild-type cells grown under nitrogen starvation. We further demonstrate that carbon metabolism in R. leguminosarum is also tightly regulated by the HPr kinase (HprK) protein. In an hprK mutant, loss of NPr Ser48 phosphorylation favors phosphotransfer through the histidyl arm and is predicted to increase phosphorylation of downstream PTSNtr components. When grown on glucose, the hprK mutant accumulates elevated intracellular pyrimidine levels and exhibits increased malate dehydrogenase and TCA cycle activity, consistent with a misregulated shift toward gluconeogenesis. This mutant also overproduces exopolysaccharide, an effect potentially mediated by crosstalk between phosphorylated PtsN and the ChvI/ChvG two-component regulatory system. Together, these data suggest that HprK exerts pleiotropic control over processes regulated by PTSNtr, influencing central metabolism while repressing exopolysaccharide production, likely by promoting the unphosphorylated state of PtsN.

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.

Fungi have repeatedly delivered transformative advances across industries, from medicine to food to materials, yet these breakthroughs have emerged from a narrow base of organisms and well-studied systems. Although mycology has taken a big leap forward in the past decades because of advances in genomics, multi-omics, engineering, phenotyping and environmental monitoring, much fungal diversity remains taxonomically and functionally under-characterised, and many sustainability-relevant innovations remain limited by lack of investment, sparse infrastructure, and fragmented governance. We now have technologies that make previously inaccessible fungal questions tractable, which can help unlock the next generation of fungal breakthroughs. Informed by a workshop held in December 2025 that convened 20 leading experts across fungal disciplines, here we lay out key bottlenecks to fungal research and innovation through three lenses: functional mycology, human and institutional capacity, and governance. We identify selected sustainability-relevant fungal frontiers and use these to surface the recurrent gaps that cut across domains. We propose four elements of coordinated action across research and development, governance, and advocacy that could contribute to unlocking the full potential of fungi for sustainability transitions.

The formation of nitrogen-fixing symbiotic nodules is a complex process that involves extensive transcriptional reprogramming of legume roots to enable intracellular accommodation of host compatible rhizobia. This process requires coordinated regulation of hundreds to thousands of genes, including the induction of highly expressed genes, traditionally referred to as nodulin genes. While the functions of many nodulins have been elucidated, a substantial number remained poorly characterized, or their functions are still unclear. One such gene, NOD25, was originally identified based on differential hybridization between roots and nodules and is expressed at exceptionally high levels in Medicago nodules. MtNOD25-like proteins in IRLC legumes exhibit a repetitive modular structure flanked by conserved N- and C-terminal regions, with clade-specific repeat organization. To understand the role of NOD25 in symbiotic nitrogen fixation, we generated loss-of-function mutants in Medicago truncatula using CRISPR/Cas9-mediated genome editing. Four independent Mtnod25 mutant lines displayed normal growth under symbiotic conditions and showed no detectable defects in nodule colonization, symbiosome formation, or bacteroid differentiation. These results indicate that MtNOD25 is not essential for symbiosis in M. truncatula under the conditions tested. However, the biological function of MtNOD25 has not yet been elucidated, and its highly specialized evolutionary conservation suggests that it may have a specific, non-essential role in modulating or fine-tuning symbiotic processes under particular environmental or physiological conditions that remain to be defined.

Background and Aims
Actinorhizal root nodule symbioses are formed between a diverse group of mostly woody dicotyledonous plants and nitrogen-fixing soil Actinomycetota of the genus Frankia. Some of the most ecologically relevant actinorhizal plants are Casuarina species, used widely in shelter belts and phytoremediation due to their high tolerance to abiotic stresses and ability to thrive on marginal soils. All sequenced Frankia strains isolated from Casuarina nodules using standard culture techniques show high sequence identity and belong to a single species, Frankia casuarinae. This lack of diversity in nodules is unusual in actinorhizal symbioses. We hypothesized that Casuarina nodules are colonized by Frankia strains that could not be cultivated and exhibit genome erosion.

Methods
To test this, we directly sequenced nodule metagenomes from four countries, followed by reconstruction of metagenome-assembled genomes (MAGs).

Results
Our findings show that the dominant Frankia genotypes in field samples were far more diverse than the isolated strains and included MAGs with substantial genome reduction – one having over 25% reduction compared to F. casuarinae. Notably, we observed erosion of two types of [NiFe] hydrogenases, a phenomenon linked to evolution toward obligate symbiosis in other Frankia groups.

Conclusion
These results indicate that potentially obligate symbionts may dominate nodules in nature but had gone undetected by conventional approaches. For applications such as reforestation or tsunami shelter belts, crushed, nodule-derived strains may offer superior ecological compatibility. We speculate that Frankia strains followed two different evolutionary trajectories; one, towards obligate symbiosis accompanied by strong genome erosion, and two, towards rhizosphere colonization involving limited genome erosion.

The symbiotic relationship between the legume Medicago sativa and the soil bacteria Sinorhizobium meliloti results in the formation of nitrogen-fixing root nodules. Traditional destructive methods, including paraffin sectioning, vibratome sectioning, and cryosectioning, have been applied to visualize how bacteria occupy the nodule, making it extremely difficult to obtain reliable three-dimensional information. These approaches are often combined with fluorescent labeling or staining, which can introduce additional stress affecting plant growth and nodule formation. MicroCT has emerged as a relatively quick, easy, and robust tool for plant biology that can non-destructively visualize plant histological features in three dimensions (3D), thereby avoiding destructive artifacts during sample preparation and ensuring high-fidelity 3D reconstruction. While microCT has been applied to legume root nodules, a detailed established protocol that documents the process from plant harvest and sample preparation to scanning and software visualization is lacking.

Improving the functional benefits of arbuscular mycorrhizal fungi (AMF) is considered an important part of developing more sustainable and resilient cro

Adopting a risk assessment paradigm that is contextualized and strain-specific will be critical to enabling the continued development and safe use...

Here, we aimed to deepen our understanding of the integration between root and shoot signaling during early nodulation by jointly analyzing proteome-level dynamics in roots and leaves of the wild type (WT) and the hypernodulating autoregulation-of-nodulation (AON) mutant, nark. To this end, we performed a time-course shotgun proteomics experiment in soybean roots and leaves of the same plants inoculated with Bradyrhizobium diazoefficiens. In WT roots, we observed proteome changes linked to calcium-dependent signaling, cellular reorganization, and nutrient allocation. In the leaves, isoflavonoid biosynthesis and immunity-associated responses were differentially regulated in the WT and nark mutant during nodulation. We hypothesize that AON signaling involves a complex interplay between isoflavonoids and immunity, which might be associated with jasmonic acid and/or systemic auxin transport.