Plant-Microbe Symbiosis

Arbuscular mycorrhizal (AM) symbiosis is conserved across land plants and is the default nutrient uptake strategy in nature. Within roots, AM colonisation is tightly patterned and dynamically tuned by nutritional cues. Multiple genetic modules contribute to this regulation, including the phosphate starvation response, DWARF14-LIKE (D14L) karrikin signalling, and the common symbiosis signalling pathway (CSSP). Transcriptional overlap among these has led to the hypothesis that phosphate starvation and D14L signalling act upstream of the CSSP. Here, we examined the epistatic relationship between D14L and CSSP in rice. Overexpression of an autoactive gain-of-function CCaMK (gofCCaMKox) restored AM colonisation and symbiosis marker gene expression in d14l mutants to wild-type levels or above, whereas overexpression of wild-type CCaMK did not, confirming that CSSP operates downstream of D14L signalling. However, gofCCaMKox did not rescue the d14l mesocotyl elongation phenotype, supporting a bifurcation of D14L into developmental and symbiotic outputs. Unexpectedly, gofCCaMKox also expanded fungal access to normally restrictive tissue domains (the meristematic zone and endodermis) assigning a role for CCaMK activation in defining root zone and cell-type competence for AM colonisation. Despite restored colonisation, introduction of gofCCaMKox into d14l produced arbuscules, which however were less developed and had increased hyphal septation, revealing a CCaMK-independent role for D14L in intraradical colonisation and arbuscule development. Transcriptome profiling resolved AM-relevant genes into modules controlled by CCaMK activation alone, in combination with D14L, or requiring additional colonisation-associated cues, and further suggested CCaMK primarily acts through AP2 transcription factors. Together, these findings reinforce CCaMK as a master regulator of AM symbiosis at the genetic, transcriptomic and anatomical levels while uncovering CCaMK-independent functions of D14L in arbuscule development.

In nature, some tree species interact with both arbuscular mycorrhizal (AM) Glomeromycotina fungi and ectomycorrhizal (ECM) Basidiomycota/Ascomycota fungi, and are termed dual mycorrhizal plants. Although the AM-upregulated genes and their functions have been well studied, those of ECM symbiosis remain unclear, despite their essential roles in forest ecosystems. Therefore, this study aimed to compare symbiosis-regulated downstream genes in the dual mycorrhizal model tree, Eucalyptus grandis, during fully developed AM and ECM symbioses. First, we conducted a comparative transcriptomic analysis and found a distinct transcriptional profile between E. grandis AM and ECM roots. Notably, none of the examined AM-related downstream genes were upregulated in the ECM roots. To identify ECM-specific genes and their expression patterns, comparative genomic analysis was performed. This study identified several gene families, including NAC transcription factors, that significantly expanded across the examined ECM lineages. Interestingly, we identified some ECM-promoted NAC transcription factors in the ECM roots of E. grandis, Populus trichocarpa, and Castanea mollissima. Moreover, none of the Eucalyptus NAC genes were transcriptionally promoted during AM symbiosis. Taken together, our results indicate that the downstream pathways necessary for the establishment of AM and ECM symbioses would be distinct.

The stabilization of rhizobia in specialized organelles, called symbiosomes, is an evolutionary hallmark for maintaining high rates of nitrogen fixation in legumes. This is achieved by releasing thousands of bacteria from nodular infection threads within in a single plant cell, which poses a great challenge for the host to keep control over these differentiated bacteria. Considering the importance of proteolytic degradation of antimicrobial proteins or generation of symbiosis-promoting peptides, proteolytic activity may represent a key regulatory system. Indeed, we identified the Medicago truncatula subtilisin-like protease (subtilase, SBT) 12a acting as a novel regulator of symbiosome functionality and maintenance. Loss-of-function mutations in SBT12a led to severe symbiotic defects with nodules of sbt12a being characterized by high level induction of defense/senescence-related genes. Using untargeted proteomic High-efficiency Undecanal-based N-Termini EnRichment (HUNTER) we identified and individually confirmed specific SBT12a target proteins that are involved in plant defense responses and symbiosome maintenance. This positions SBT12a as a central host factor controlling symbiosome performance.

Arbuscular mycorrhizal fungi (AMF) have facilitated the colonization of land by plants some 470 million years ago. The vast majority of land plants have maintained a symbiotic association with these fungi to facilitate the uptake of mineral nutrients, such as phosphorus, at the cost of photosynthates delivered to the fungus in the form of lipids and sugars. Despite their importance for plant nutrient status, plants can refuse AMF if soil nutrient conditions are such that it is less costly for the plants to take up the nutrients by themselves or if environmental conditions are not appropriate. Recently, Hong et al. (2026) revealed how multiple signaling pathways in rice converge on a transcription factor complex involving the GRAS transcription factors NSP1 and NSP2 to control AM colonization. In this spotlight we highlight recent insights into the molecular mechanisms that control the permissiveness of plants to allow AMF entry into their roots (Figure 1fig1).

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.

Symbiosis between legumes and rhizobia is beneficial on nutrient-poor soils, as it enables the fixation of atmospheric N2. To establish this symbiosis, gene expression in both the host plant and the symbiont has to be regulated. To understand the underlying RNA-mediated regulation of host gene expression, we designed experiments to identify competing endogenous networks involving circular RNA, microRNA, and linear transcripts during symbiosis, using wt and symbiosis-deficient Lotus japonicus mutants with the rhizobium Mesorhizobium loti (M. loti).

CircRNA, miRNA, and linear transcripts were identified from Lotus japonicus wildtype and CCamK mutant (ccamk-13; snf-1) seedlings without inoculation or with M. loti inoculation using deep short-read sequencing with rRNA-depletion and random primers.

Differentially expressed miRNAs showed negative correlations to predicted target genes and may regulate symbiotic processes. The symbiosis essential iron-sensor LjnsRING/BRUTUS expresses a circRNA which was upregulated in symbiotic treatments. This circRNA may act as a target mimic and contribute to nodule longevity. CircRNAs are predicted to act predominantly as trans-regulatory molecules with similar frequencies in Arabidopsis thaliania, Oryza sativa, and Lotus japonicus.

We identified novel miRNAs, long noncoding RNAs, and circRNAs, and nominated several as potential new regulatory non-coding RNAs that may act as target mimics to stabilize genes and support symbiosis.

The advent of endosymbiosis underlies evolutionary innovation and ecosystem function. However, whether free-living partners tend to benefit or exploit each other during the early stages of novel endosymbiosis remains a dilemma. Rhizobia soil bacteria can initiate root nodules and fix nitrogen for host plants as endosymbionts due to genes carried on mobile genetic elements such as the symbiosis island (SI). We conjugated marked SIs into the genomes of non-nodulating strains, which was sufficient to generate de novo root nodule-forming endosymbionts. Most novel endosymbionts originated as commensals that incurred no detectable costs to host plants, in contrast to predictions of exploitation. In fact, a third of novel endosymbionts originated as nitrogen-fixing mutualists. Consistent with phylogenetic limits to transfer of mobile genetic element function, novel endosymbionts derived from more closely related SI donor and recipient strains showed greater nitrogen fixation. However, consistent with selection on the SI for broad horizontal transfer, we did not detect phylogenetic limits to SI transmission, and the SI was able to displace other genomic elements residing at its characteristic tRNA gene insertion site. We thus provide genetic, genomic, and functional evidence of how mobile genetic elements can potentiate and constrain major evolutionary transitions to expand bacterial niches, with cascading impacts on the fitness of host organisms.

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.