The trait‑based root economics space provides a fundamental framework for understanding plant belowground adaptation to environmental change, yet it typically omits root exudation that sustains plant resource acquisition and health. Results from a ~3500 km north‑south forest transect demonstrate that arbuscular mycorrhizal (AM) trees have higher root exudation rates than ectomycorrhizal (ECM) trees, with stronger increases under warmer and wetter climates. Root exudation rate is positively related to specific root length and negatively related to root diameter for both mycorrhizal types, but is related to tissue density and nitrogen content only in AM trees. These findings suggest that root exudation may represent an alternative collaboration strategy, facilitating organic nutrient acquisition more strongly for AM species and functioning as a relatively redundant nutrient acquisition mechanism for ECM species. Moreover, mycorrhizal type modulates how exudation rates relate to the “fast–slow” strategy. Overall, our findings refine the conceptual framework of the root economics space and enhance understanding of fine‑root strategies.

Synthetic microbial communities (SynComs) are emerging as promising alternatives to single-strain inoculants in agriculture, offering greater functional robustness and environmental adaptability. However, transforming conceptual studies into engineerable and scalable agricultural practices remains challenging. In this opinion article, we synthesize current research on plant SynComs through a framework that moves from strain-centered assembly toward system-level design, linking the identification of truly stable coexisting communities in natural microbiomes to the elucidation of plant–microbe–soil interaction mechanisms, the development of dynamical models, and the integration of these models into platform-based design and production pipelines. We focus on recent advances that integrate generalized Lotka–Volterra and consumer-resource models with multi-omics data and other system-level constraints, with the aim of introducing model-driven concepts of SynCom design and promoting their large-scale application in agriculture.

Tobacco Fusarium root rot is a widespread soil-borne root-stem disease affecting tobacco in China. Arbuscular mycorrhizal fungi (AMF) can enhance the disease resistance of host plants. A systematic study of tobacco's response to AMF under pathogen attack can lay the foundation for the application of AMF in alleviating tobacco root rot. This study aimed to clarify the effects of pre-inoculation with Claroideoglomus lamellosum (Cl) on tobacco growth, physiology, and root rot resistance, and to identify key AMF-responsive genes in tobacco leaves under Fusarium oxysporum (F) infection. Pot experiments with tobacco K326 included four treatments: control (CK), single Cl inoculation, single F inoculation, and dual Cl + F inoculation. Disease incidence, growth indices, and antioxidant enzyme activities were measured to assess Cl-induced resistance. Transcriptome analysis revealed key gene expression changes in response to Cl under F stress. Compared with CK, Cl formed a stable symbiosis with tobacco and promoted plant growth, as evidenced by increases in total biomass (77.71%), shoot biomass (83.5%), root biomass (107.71%), plant height (33.22%), root length (38.78%), stem diameter (18.67%), and effective leaf number (66.67%). Cl also enhanced leaf activities of superoxide dismutase (30.48%), peroxidase (71.81%), phenylalanine ammonia-lyase (169.25%), polyphenol oxidase (320.22%), and catalase (125.44%). Relative to pathogen treatment alone (F), the Cl + F combination reduced root rot incidence by 57.14% and disease index by 70.61%. In contrast, pathogen infection alone suppressed tobacco growth (6.65–27.64%) and decreased antioxidant enzyme activities (0.65–51.46%) compared with CK. Transcriptome analysis identified 20 050 differentially expressed genes (DEGs), with 2365 DEGs specifically responsive to AMF under pathogen challenge as key genes for AMF-induced resistance. GO and KEGG enrichment indicated that AMF enhanced resistance via plant-pathogen interaction and MAPK signaling pathways, while peroxisome, fatty acid elongation, and other key metabolic pathways also contributed significantly. Cl is an effective strain for enhancing tobacco resistance against root rot. Inoculation with Cl significantly promoted tobacco growth and increased physiological enzyme activities in tobacco leaves. At the transcriptomic level, it was confirmed that the effect of Cl inoculation on tobacco resistance against root rot involves multiple pathways and metabolic routes, forming a tripartite "signaling-membrane transport-metabolism" defense network model, thereby improving tobacco resistance to root rot.

The uptake of nitrogen-fixing bacteria into living plant cells and the intracellular accommodation of arbuscular mycorrhiza (AM) fungi requires the plasma membrane-localised Symbiosis Receptor-like Kinase (SymRK). AM is widespread across terrestrial vascular plant lineages, while the nitrogen-fixing root nodule symbiosis (RNS) is restricted to one clade within the eurosids. This distribution led to the concept that SymRK was adopted during evolution to mediate RNS. Comparative analyses revealed that SymRK orthologs from the eurosid clade support RNS while SymRK from the phylogenetically distant species Solanum lycopersicum (tomato) does not. To dissect the molecular basis for this different functionality, we carried out complementation analyses of the Lotus japonicus symrk-3 mutant which is unable to form AM or RNS. Domains swap chimera from the tomato and L. japonicus SymRK orthologs revealed that the intracellular domain of L. japonicus SymRK is necessary and for cortical infection thread (IT) and symbiosome development at 21 days post inoculation. Notably, this signalling specificity could be overcome by ectopic expression of tomato SymRK, pointing to altered protein dosage as a potential determinant of function. Consistent with this idea, SINA family E3 ubiquitin ligases interacted with and ubiquitinylated L. japonicus SymRK, but not tomato SymRK. In yeast two hybrid analysis, the interaction of SymRK with SINA2 and SINA4 depended on the C-terminal intrinsically disordered tail region of L. japonicus SymRK. We conclude that the SymRK intracellular domain evolved interaction capabilities with SINA E3 ligases which correlates with its ability to support RNS.

While nitrogen fertilizers are widely used in agricultural production, their application incurs significant environmental and energetic costs. In contrast, some crops are less dependent on these fertilizers because they engage in symbioses with rhizobia, nitrogen-fixing bacteria provide ammonium to the plant in exchange for carbon. However, the carbon cost associated with nitrogen fixation can negatively impact crop yields. Improving the efficiency of this metabolic process could alleviate this impact on crop productivity. Mathematical models can help us quantitatively explore metabolic behavior and identify potential targets for metabolic engineering. In this work, we developed a kinetic model of determinate root nodule metabolism, where this symbiotic exchange of carbon from the plant and nitrogen from the bacteria occurs.

We used this model to evaluate how the predicted metabolic behavior differs between inefficient and efficient nodules, and to identify potential engineering targets for improving nitrogen fixation efficiency and rate. We show that the enzymes phosphoenolpyruvate carboxylase and pyruvate kinase have significant influence on the predicted rate and efficiency of nitrogen fixation, especially when their expression is varied in combination with oxidative Pentose Phosphate Pathway enzymes like glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase. The model predicts that pairing a 3-fold decrease in glucose-6-phosphate dehydrogenase activity along with either a 3-fold increase in phosphoenolpyruvate carboxylase activity or decrease in pyruvate kinase activity could increase nitrogen fixation rate by 5.51% while improving nitrogen fixation efficiency by 7.74%.

The relationship between plants and microorganisms has ancient roots. However, only recently we have begun to appreciate the true complexity of the holobiont and its intricate interactions. Fungi, bacteria and viruses residing within or around plants play a crucial role in enhancing their resilience to biotic and abiotic stressful factors. The impact of these interactions is not limited to stress resilience but are strictly correlated with the plant’s life cycle. The recognition of specific effects on plant growth and resilience has driven research towards utilizing microorganisms as sustainable solutions for agricultural challenges. The application of selected microorganisms, combined with the development of SynCom consortia, marks the beginning of a promising strategy for achieving sustainability in agriculture. This chapter explores the hidden world of plant-associated microorganisms, emphasizing their diverse beneficial impacts and providing evidence to support their potential applications in modern agriculture.

Improving the effectiveness of microbial inoculants for soybean is essential to enhance biological nitrogen fixation and reduce fertilizer dependence; however, inoculated Bradyrhizobium strains frequently display inconsistent field performance. Inoculation is usually carried out with single-strain formulations, overlooking the possible influence of the native soil microbiota on nodulation success. This limitation may be addressed by formulating inoculants with consortia that include selected members of the soil microbiota. To this end, a synthetic microbial community (SynCom) was developed through a host-mediated microbiome engineering approach guided by leaf chlorophyll content as a rapid, non-destructive plant trait. The experiment was initiated by inoculating soybean plants with a consortium of 9 Bradyrhizobium spp. and 14 non-rhizobial soil isolates. Across eight consecutive selection rounds under gnotobiotic conditions, rhizosphere communities associated with superior plant performance were pooled and propagated. Recurrent selection induced significant shifts in community composition, consistently favoring Bradyrhizobium diazoefficiens as the dominant nodulating member and enriching taxa from Pseudomonadales, Burkholderiales, and Sphingomonadales. Sequencing-based profiling and network analysis suggested the emergence of a cohesive and functionally enriched community, with increased potential for nitrogen transformations and organic matter turnover. When evaluated in non-sterile soil, the SynCom derived from the sixth selection round increased nodule number and biomass relative to an uninoculated control and a commercial inoculant strain. These results suggest that plant-guided selection can steer rhizosphere community assembly toward beneficial configurations and support the development of improved soybean bioinoculants.

Intercropping is widely practiced on sloping red-soil farmland in Southwest China and helps mitigate soil erosion. However, the mechanisms by which intercropping influences soil aggregate stability remain poorly understood. Based on an 11-year (2013–2024) fixed-location experiment in Yunnan Province, this study examined the effects of maize monoculture (MM), soybean monoculture (SS), and maize–soybean intercropping (IM/IS) on soil aggregate stability and explored how rhizospheric arbuscular mycorrhizal fungi (AMF) dynamics were associated with aggregate stability under different cropping systems.
Results indicated that: (1) compared with monocultures, intercropping significantly increased AMF colonization rates and hyphal density by 8.3–34.9% (P < 0.01) and 0.51–1.20-fold (P < 0.01), respectively, and increased the abundance of Glomus in maize rhizospheres. (2) Intercropping significantly increased glomalin-related soil protein (GRSP), with the increase in easily extractable GRSP (EE-GRSP; 13.11–29.91%) exceeding that of total GRSP (T-GRSP; 2.51–6.85%). GRSP contents were significantly higher at tasseling than at maturity (P < 0.05). (3) Compared with monocultures, intercropping significantly increased xylanase (XYL), N-acetyl-β-D-glucosaminidase (NAG), and acid phosphatase (PHOS) activities by 43.38–61.84%, 39.28–96.03%, and 42.57–101%, respectively (P < 0.05). These biochemical improvements were accompanied by improved soil structure, with >2 mm macroaggregates and mean weight diameter (MWD) increasing by 24.37–38.84% and 11.24–25.26%, respectively (P < 0.05). Structural equation modeling further indicated that hyphal density may indirectly improve soil aggregate stability by increasing EE-GRSP content and hydrolase activity. Overall, maize–soybean intercropping enhanced aggregate formation and stability through AMF-related GRSP and hydrolase pathways, supporting improved acidic red-soil structure on sloping farmland.

Dramatic cytoskeleton modifications are involved in establishing mutualistic bacterial and fungal associations with plants, as new specialized symbiotic structures are formed. A recent study in Science1 explores actin remodeling during the inception of these interactions, potentially creating opportunities to increase mycorrhizal and nodulation efficiency and reduce our need for fertilizers.

Intracellular infection by beneficial microorganisms enables endosymbiosis and remains a challenge in synthetic biology. A new study by Qiao et al. reveals that a formin orchestrates both rhizobial infection in legumes and mycorrhization in diverse plants. Harnessing this mechanism could enable the engineering of microbial entry into crops for sustainable nutrient acquisition.

Development of arbuscular mycorrhiza (AM), a symbiosis between plants and beneficial Glomeromycotan fungi, is largely under plant control. Several genes, required for AM development, are proposed to be regulated by the karrikin signalling module, comprising the alpha/beta hydrolase receptor KARRIKIN INSENSITIVE 2 (KAI2), the F-box protein MORE AXILLARY GROWTH2 (MAX2) and the transcriptional repressor SUPPRESSOR OF MAX2 1 (SMAX1), which is ubiquitylated for proteasomal degradation upon KAI2-ligand-induced binding to the KAI2-MAX2 complex. Rice and Brachypodium distachyon kai2 mutants are incapable of forming AM. Here, we show that in Lotus japonicus, Pisum sativum, and Nicotiana benthamiana, KAI2 only quantitatively affects AM development, indicating angiosperms vary in their requirement for KAI2-signalling to support AM. Comparative transcriptomics of L. japonicus and B. distachyon roots after treatment with fungal signalling molecules revealed some AM-relevant genes respond KAI2-independently in L. japonicus but not in B. distachyon. Consistently we obtained

Nodules cystine-rich (NCR) peptides from legume nodules mediate bacteroid differentiation of Rhizobium sp. This study aimed to characterize NCR peptides of Phaseolus vulgaris, Trifolium repens, Medicago sativa, and Vicia faba, as relevant information on these legumes is still lacking. After exposing the root nodules of four leguminous plants to sonication, the peptides were separated according to their molecular weight by sodium dodecyl gel electrophoresis (SDS-PAGE). The NCR peptide was detected by high-performance liquid chromatography (HPLC), followed by the determination of the protein sequence and amino acid composition and their evolutionary history in terms of the phylogenetic tree by bioinformatics analysis. The results showed these four peptides had the same molecular weight of 60 kDa. The peaks of the curve varied with retention time depending on the legume from which the peptide was extracted. Bioinformatic analysis of the results showed that the amino acid substitutions varied in number and sequence for each species and that these peptides had three distinct wire, ribbon, and surface patterns within the structural modeling of their crystals. Side chains of amino acids in the loops and helices within the grid box may facilitate hydrophobic interactions via tyrosine, phenylalanine, or polar interaction sites via cysteine, histidine, and glutamine. These loops often serve as flexible regions to adapt to binding partners. In general, this study contributed to the characterization of NCR peptides that showed mismatches and differences in amino acid sequences and deletions of some amino acids at different locations depending on the type of legume from which the peptide was extracted.

Background
Phosphate (Pi) is essential for plant growth, but its bioavailability in soil is often limited. Forming symbiotic associations with arbuscular mycorrhizal fungi can significantly enhance the host plant’s root Pi acquisition ability. PHT1 transporters, such as MtPT4, are involved in Pi uptake from arbuscules. It is unknown how Pi is exported from the mycorrhizal root to the vascular bundle.

Results
Here, we found the medicago vascular apoplastic Pi exporter PHO1 proteins not only mediate Pi transport in the direct Pi uptake pathway but also influence arbuscular mycorrhizal symbiosis. MtPHO1s showed Pi export activities when expressed in nicotiana leaves. The MtPHO1.3 tnt1 insertion mutant displayed significant growth inhibition and reduced shoot Pi content. Moreover, AM colonization was lower in the Mtpho1.3 mutant compared to the wild type. Consistent with this, the expression level of the strigolactone biosynthesis gene DWARF27 was suppressed in Mtpho1.3 mutant, and root exudates from the mutant induced less fungal hyphal branching. Furthermore, the Mtpho1.3 mutant exhibited increased arbuscule degeneration, suggesting that Pi levels in the plant are key to regulating arbuscule lifespan.

Conclusion
Our analysis shows that MtPHO1.3 also exerts function in mediating Pi translocation during arbuscular mycorrhizal symbiosis.