Mycorrhizal fungi are crucial components of plant rhizosphere microbiota and key players in terrestrial biogeochemical cycles.Arbuscular mycorrhizal(AM)fungi can form symbiotic relationships with more than 70% of terrestrial plants and their origin can be traced back to the Devonian period,460 million years ago.They played an important role in the transition of plants from aquatic to terrestrial environments and continue to profoundly affect the growth performance of plants and their ecosystem functions.In the peri-arbuscular space of AM symbiosis,plants provide carbon fixed by photosynthesis in exchange for mineral nutrients,especially phosphorus and nitrogen.In the hyphosphere,many bacteria are involved in the establishment of AM symbiosis.These bacteria obtain carbon from extraradical hyphal exudates and mineralizing organic compounds to enhance the availability of mineral nutrients for the fungi.Therefore,plants,AM fungi and hyphospheric bacteria form a continuum and are accompanied by top-down carbon flows and bottom-up nutrient flows.In this review,we first introduce the latest research on how plants,AM fungi and the related hyphospheric bacteria exchange carbon from host plants and mineral nutrients from the soil.These exchanges provide energy for microbial partners and deliver nutrients for plants that are necessary for growth and development.Secondly,we analyze in detail the mechanism by which the plant-AM fungi-bacterial continuum maintains cross-kingdom cooperation,which is conducive to a better understanding of the complex ecological relationships between plants,AM fungi and soil bacteria.This provides information on their evolutionary significance and a theoretical basis and technical pathway for sustainable agriculture grounded in plant-microbe interactions.

The traditional model of plant-arbuscular mycorrhizal (AM) fungal coevolution, based solely on interactions between plants and AM fungi, became obsolete with the discovery of the critical roles that belowground microbiomes play in the function of mycorrhizal symbiosis. Based on insights into hyphosphere microbiota, we expand the plant-AM fungus-bacterium continuum into a multipartite AM fungal-orchestrated holobiont (H-AMF) framework, where AM fungi integrate plant roots with soil microbiota into a cross-kingdom ecological unit. A division of labor exists among plants, AM fungi, and hyphosphere microbes in the mycocentric H-AMF perspective. We summarize mechanisms by which AM fungi sustain cooperative relationships with plants and hyphosphere microbiota and propose holobiont-scale methodologies to advance understanding of plant-fungal-microbial interactions and their ecological functions.

Rhizosphere keystone taxa critically drive microbial community stability and soil biogeochemical cycles. However, the manipulation of such taxa remains a challenge. This study simulated plant-mediated modulation of keystone taxa via simplified synthetic root exudates to track their compositional shifts. The combination of luteolin, myristic acid, and glucose enhanced rhizosphere phosphatase activity, significantly enriched Domibacillus indicus D99, and converted it into a keystone taxon. This precise regulation was driven by transcriptional upregulation of C metabolism and an unusual fatty acid assimilation pathway. Additionally, metabolites produced by D. indicus D99 (such as bergapten and lactate) were preferentially utilized by phosphate-mineralizing bacteria, Bacillus sp. C67 and Domibacillus sp. C94. These partner bacteria exhibited less substrate overlap and pronounced resource partitioning, forming an efficient synergistic relationship with D. indicus D99 that amplified rhizosphere phosphatase activity and plant growth. This study highlights opportunities to utilize the ecological roles of keystone taxa in manipulating the microbiome.

Efficient nutrient acquisition in crops depends on coordinated interactions between plant roots and associated microbiota. Arbuscular mycorrhizal (AM) fungi enhance root system plasticity, yet the underlying regulatory mechanisms remain incompletely understood. Here, we investigate AM fungus–induced lateral root development in maize (Zea mays) and identify ethylene-responsive transcription factors (ERFs) as key regulators of pericycle cell division. ERF activity is associated with ethylene biosynthesis genes ACS6 and ACS7 and is required for AM fungus–stimulated lateral root formation. We further observe that AM colonization is accompanied by shifts in flavonoid profiles, including reduced accumulation of flavonols such as kaempferol and quercetin. In addition, the rhizobacterium Massilia associates with fungal hyphae and displays context-dependent effects on root development. Together, these findings support a model in which ethylene signaling and ERF activity contribute to AM-induced root developmental responses, with flavonoid metabolism and hyphosphere-associated bacteria representing additional modulatory components.

Efficient nutrient use in agriculture depends on the dynamic interplay between plant roots, soil, and microbial communities. The root–rhizosphere interface is central to nutrient uptake and serves as a key hub for interactions with beneficial microbes. Arbuscular mycorrhizal (AM) fungi, positioned at the nexus between plant roots and soil microbiota, play a critical role in enhancing crop performance under nutrient-limited conditions. In this study, we dissected the genetic and molecular basis of AM fungi–induced lateral root development in maize ( Zea mays ), focusing on the role of ethylene-responsive transcription factors (ERFs). We identified ERF genes as essential regulators of pericycle cell division, acting downstream of ethylene biosynthesis genes ( ACS6 and ACS7 ) and AM fungal signaling. Our findings reveal that AM fungi promote lateral root initiation by activating ERF expression and reprogramming flavonoid metabolism, particularly reducing the accumulation of flavonols such as kaempferol and quercetin, which otherwise inhibit root development when over-accumulated. Furthermore, we demonstrated that Massilia , a beneficial rhizobacterium, synergizes with AM fungi to enhance lateral root formation by colonizing fungal hyphae, degrading flavonoids, and contributing to auxin production. Together, our results uncover a tripartite signaling network linking ethylene signaling, flavonoid-mediated microbial recruitment, and AM symbiosis. This study highlights ERFs as central integrators of plant–microbe interactions and provides a molecular framework for engineering root architecture and microbiome assembly to improve nutrient acquisition and support sustainable crop productivity.

Nutrient enrichment alters the functioning of grassland ecosystems, but the community structure and functions of microbes associated with the hyphosphere of arbuscular mycorrhizal (AM) fungi under nitrogen (N) and phosphorus (P) amendments remain poorly understood. Using a compartmented microcosm system and 16S rRNA gene and metagenomic sequencing, we studied the effects of AM fungal hyphae on soil microbial community composition, carbohydrate metabolism, and P cycling in four soils subjected to long-term N and/or P amendments. In long-term N-amended soils, AM fungal hyphae markedly altered the composition of the microbial community, improved P uptake and transport, and enriched genes associated with amino acid and secondary metabolite metabolism. Conversely, in long-term P-amended soils, the hyphae significantly reduced the concentration of available P in the soil and decreased the relative abundance of glucosyl transferases. Under combined NP amendments, the hyphae also induced significant changes in the composition of the microbial community and decreased the concentration of available P in the soil. In addition, AM fungal hyphae selectively modulated the abundance of specific genes involved in carbohydrate metabolism and P cycling, with variable effects depending on the soil. These results show that long-term nutrient amendments reshape AM fungal regulation of hyphosphere microbial communities and functions.

Plants engage in intricate interactions with rhizosphere microbes. These interactions are crucial for plant nutrient acquisition and productivity, but the mechanisms by which different nutrient forms shape rhizosphere microbes to enhance nutrient utilization under field conditions remain unclear. We investigated the rhizosphere bacterial communities of wheat and their functions across key growth stages in response to different phosphorus (P) fertilizer forms in a 4-yr field experiment, integrating 16S rRNA gene sequencing, metatranscriptomic sequencing, and soil chemical analyses. In the field, the three P fertilizer forms showed comparable P use efficiency (PUE) over 4 years. At the three-leaf stage, insoluble P fertilizer increased root-associated citrate concentrations, enriched carboxylate-associated bacteria (e.g. Bacillus, Solirubrobacter, and Nitrospira), and resulted in higher transcript abundance of genes involved in citrate metabolism and P acquisition. Polymeric P fertilizer enhanced soil phosphatase activity, increased root-associated succinate concentrations, and had higher transcript abundance of genes involved in succinate metabolism and complex polysaccharide degradation. Soluble P fertilizer increased soil available P and enriched Devosia, favored glycoprotein degradation, while showing a limited response to P mobilization processes. This study suggests that, under field conditions, different P fertilizer forms shape distinct rhizosphere bacterial communities to improve PUE by altering root-associated carboxylate release.

Abstract Plants are best understood as evolutionary holobionts, in which the host and its associated microbiomes operate as an integrated unit to influence growth, health, and stress resilience. This comprehensive review synthesizes the most current knowledge of plant‐associated microbiomes across key ecological compartments, including the rhizosphere, endosphere, phyllosphere, and seeds, highlighting their assembly drivers, functional mechanisms, and translational potential. We dissect the molecular foundations of rhizobial and arbuscular mycorrhizal (AM) symbioses, the plant‐AM fungus‐bacterium continuum, alongside emerging concepts including the aerial root mucilagesphere, phyllosphere homeostasis, and the pathobiome. We further explore host genetic, metabolic, and environmental determinants of microbiome assembly, and present cutting‐edge methodologies ranging from quantitative profiling to artificial intelligence‐driven synthetic community design. Finally, we outline a strategic blueprint for harnessing standardized synthetic microbiomes and precision microbiome engineering to advance sustainable agriculture. This integrative framework bridges fundamental ecology with practical applications, delineating a path toward climate‐resilient crop production.

Soil biota can enhance plant P acquisition, but the extent of this enhancement varies considerably across crop species, and how soil biota modulates root physiological and morphological strategies employed by different crop species for P mobilization remains poorly understood. Eight crop species were cultivated in sterilized and unsterilized soil amended with sodium phytate (100 mg P kg−1) as an organic P source. Multiple parameters were measured to characterize three P mobilization and acquisition strategies: microbial strategies, root physiological strategies, and root morphological strategies. Microbial community composition was analyzed using 16S rRNA and ITS sequencing. Principal component analysis (PCA) was used to evaluate the diversity of P mobilization and acquisition strategies among the crop species. The P content of Zea mays, Cicer arietinum, Arachis hypogaea, and Medicago sativa was higher in unsterilized soil compared to sterilized soil. Soil biota modified other P mobilization and acquisition strategies, including reducing root carboxylate exudation in Glycine max and Medicago sativa. The PCA revealed distinct P mobilization and acquisition strategies with soil biota: Zea mays was closely associated with mycorrhizal symbiosis, Arachis hypogaea and Medicago sativa were associated with specific microorganisms, and Vicia faba mobilized P through root carboxylates. Soil biota significantly enhanced P uptake in microbial dependent species. Moreover, soil biota modulated P acquisition strategies across species. These results suggest that optimizing species-specific plant–microbe interactions could be a practical approach to improve P use efficiency in low P soils.

The reciprocal exchange of carbon (C) and phosphorus (P) in arbuscular mycorrhizal (AM) symbiosis plays a crucial role in regulating soil biogeochemical cycling. However, how chemically fertilized (CF) versus organically fertilized (OF) soils alter AM fungal-driven effects on soil microbiomes and carbon/phosphorus cycling remains poorly understood. We conducted a greenhouse three-compartment microcosm experiment using a CF and OF soil. Amplicon and metagenomic sequencing were employed to investigate how soil microbial communities and functional genes respond to the presence of AM fungal extraradical hyphae. When AM hyphae are absent, the CF and OF soils harbored markedly distinct microbial communities. Hyphae presence triggered highly responsive amplicon sequence variants (ASVs) in both soils. Moreover, hyphae presence significantly altered the OF soil microbial community. AM fungal hyphae decreased Olsen-P and enhanced alkaline phosphatase (ALP) activity. Hyphal effects were soil-dependent: hyphae promoted P-mineralization genes (E3.1.3.1, phoA, phoB) and C-degradation genes in the CF soil, whereas they stimulated P-solubilization genes (ppx-gppA), C-fixation genes, and glycoside hydrolase (GH) families in the OF soil. These findings demonstrate that fertilization regimes (i.e. chemical or organic) dictate the functional trajectories of AM fungal-microbiome interactions, advancing our mechanistic understanding of the AM fungal ecological function under contrasting fertilization regimes.

Colonization of plant roots by symbionts requires substantial morphodynamic reorganization. Examples are actin-scaffolded microcompartments called infection pockets formed during root nodule symbiosis (RNS) by legumes. We demonstrate that the actin-binding formin SYFO2 is indispensable for rhizobial infection in Medicago truncatula, where it drives actin polymerization in phase-separated and symbiosis-specific nanodomains. SYFO2 also regulates symbiotically active arbuscules formed during mycorrhizal symbiosis in plants outside the nodulating clade, indicating that it was additionally recruited to promote rhizobial infections in legumes. As part of our aim to enable nitrogen fixation in nonlegumes, we activated endogenous SYFO2 by stably introducing the RNS master regulator NODULE INCEPTION (NIN) into the natural nonhost tomato. This demonstrates the possibility of recruiting arbuscular mycorrhizae-related genes into an engineered nodulation-specific pathway.

Arbuscular mycorrhizal (AM) fungi are vital plant symbionts in terrestrial ecosystems, yet their community distribution patterns and key drivers in extreme environments remain elusive. Focusing on the unique soda saline-alkaline meadows in the cold region of Northeast China, we established six sampling sites along a 500-km climatic gradient. By integrating traditional microscopic techniques with high-throughput sequencing, we systematically characterized the spatial distribution and drivers of soil AM fungal communities under severe salinealkaline stress. Results indicated that under saline-alkaline stress, abiotic variables overrode host preferences to dominate community structuring. Specifically, high pH significantly suppressed root colonization and extraradical mycelial density, and significantly reduced soil AM fungal Shannon diversity. Nitrate nitrogen (NO3- acted as a critical "diversity filter," showing a significant negative correlation with species richness and phylogenetic diversity. Conversely, soil organic carbon (SOC), total nitrogen (TN), and regional climate synergistically drove community composition divergence. Crucially, the lack of significant correlation between soil AM fungal and plant communities confirmed the primacy of abiotic filtering in these extreme habitats. Further analysis revealed divergent ecological strategies: Regional climate potentially regulated the abundance of the dominant genera Glomus and Scutellospora, whereas Rhizophagus was driven by local nutrient-rich micro-niches (SOC and ammonium nitrogen) and closely associated with plant productivity. This study identifies severe soil abiotic stress as the core driver shaping AM fungal spatial patterns in cold saline-alkaline meadows. These findings deepen our understanding of microbial distribution in stressed habitats and offer critical scientific insights for the restoration of fragile saline-alkaline ecosystems.

The legacy effects of nicotine, alkaloid from tobacco, on soil bacteria and nutrient cycling functions are not fully understood. In this microcosm study using soil from a decade-long tobacco monoculture field. Nicotine exhibited a persistent influence on nitrification for 42 days via direct nicotine-N supply and priming nitrifier activity. Gross nitrification rates and available nitrogen (NH 4 + and NO 3 − ) content were significantly higher at 100 mg kg − 1 nicotine than those at 10 mg kg − 1 . Nicotine significantly altered soil bacterial dynamics (contribution = 0.22) and increased the abundance of Intrasporangiaceae and Bryobacter . Changes in nitrification rates were positively correlated with increases in ammonia-oxidizing bacteria (AOB)- amoA copy numbers. Phylogenetic analysis revealed dominant AOB Operational Taxonomic Units (OTUs) affiliated with the genus Nirosospira , closely related to ‘ Nitrosospira sp. Np 39 − 19’ (99% identity). Dominant ammonia-oxidizing archaea (AOA) include Nitrosopumilaceae (> 70% of sequences) and Nitrosopumilus . This study enhances understanding nicotine’s role in microbial function shifts and suggests potential strategies for rhizodeposition-based nitrogen management in tobacco fields.

Tobacco cultivation leads to nicotine accumulation in soil, but how nicotine affects soil nitrification and ammonia-oxidizing microorganisms remains poorly understood. This study conducted a microcosm incubation using soil collected from a 10-year tobacco monoculture field. The soil was spiked with nicotine at 0, 10, or 100 mg kg−1 (the two concentrations representing realistic root-zone levels and a worst-case residue hotspot, respectively) and incubated for 42 days under controlled conditions. Gross nitrification rates were measured by 15N isotope dilution, and the abundance (qPCR) and community composition (amplicon sequencing) of ammonia-oxidizing bacteria (AOB) and archaea (AOA) were determined at multiple time points. Results showed nicotine at 10 mg kg−1 slightly stimulated nitrification, whereas 100 mg kg−1 caused a transient inhibition (day 1) followed by a sustained stimulation, with gross nitrification rates increased by up to 2-fold compared to the control. Nicotine explained 22% of the variation in bacterial community composition and significantly enriched Intrasporangiaceae and Bryobacter while suppressing Bradyrhizobium. AOB-amoA copy numbers increased within 3 days of nicotine addition and correlated strongly with nitrification rates, whereas AOA-amoA responded only after 6 weeks. Phylogenetic analysis showed that Nitrosospira (cluster Np 39-19) dominated the AOB community. We conclude that nicotine exerts concentration-dependent, biphasic effects on soil nitrification and that AOB, not AOA, drive the nitrification response to nicotine in this agricultural soil. Our findings highlight the potential of nicotine to shape nitrogen cycling in tobacco-cultivated ecosystems and call for field validation under long-term residue conditions.

In nature, cooperation is an essential way for species, whether they belong to the same kingdom or to different kingdoms, to overcome the scarcity of resources and improve their fitness. Arbuscular mycorrhizal fungi are symbiotic microorganisms whose origin date back 400 million years. They form symbiotic associations with the vast majority of terrestrial plants, helping them to obtain nutrients from the soil in exchange for carbon. At the more complex level, soil bacteria participate in the symbiosis between arbuscular mycorrhizal fungi and plants: they obtain carbon from the exudation of hyphae connected to the roots and compensate for the limited saprophytic capacity of arbuscular mycorrhizal fungi by mineralizing organic compounds. Therefore, plants, arbuscular mycorrhizal fungi and soil bacteria constitute a continuum that may be accompanied by multiple forms of cooperation. In this review, we first analyzed the functional complementarities and differences between plants and arbuscular mycorrhizal fungi in arbuscular mycorrhizal symbiosis. Secondly, we discussed the resource exchange relationship between plants and arbuscular mycorrhizal fungi from the perspective of biological market theory and "surplus carbon" hypothesis. Finally, on the basis of mechanisms for maintaining cooperation, direct and indirect reciprocity in the hyphosphere, induced by the availability of external resource and species fitness, were examined. Exploring these reciprocal cooperations will provide a better understanding of the intricate ecological relationships between plants, arbuscular mycorrhizal fungi and soil bacteria as well as their evolutionary implications.

Plants, arbuscular mycorrhizal (AM) fungi and soil bacteria coexist stably in ecosystems. Resource availability can affect the mutualistic relationship between plants and AM fungi, but it is unclear how it affects the reciprocal cooperation between AM fungi and bacteria. Here, we used an in vitro culture system containing a source of organic phosphorus (P) to explore the early-stage reciprocal cooperation between the AM fungus Rhizophagus irregularis and the phosphate-solubilizing bacterium (PSB) Rahnella aquatilis under two different levels of inorganic P. Under low inorganic P availability, the reciprocal cooperation between the AM fungus and the PSB, materialized by carbon (C)-P exchange, was strengthened. This was evidenced at transcriptional level by the activation of multiple C metabolism and P transport and regulation pathways of both partners. Conversely, under high inorganic P availability, the exchange of P for C with plants was slowed down. This was accompanied by the activation of only P transport and regulation pathways and less C metabolism pathway, weakening the reciprocal cooperation with the PSB. In conclusion, the availability of inorganic P can mediate the reciprocal cooperation between AM fungi and bacteria, which could also extend to host plants since they are inseparable in ecosystems.

Arbuscular mycorrhizal (AM) fungi acquire photosynthetically fixed carbon (C) from host plants and transport some of it to hyphosphere bacteria via an extensive extraradical hyphal network. The hyphosphere microbiome, fostered by hyphal exudates, is crucial for AM fungi to access soil organic phosphorus (Po) and enhance plant growth, but the impact of plant-AM fungal combinations is still not well-elucidated. To answer this question, we selected two plant species with differing photosynthetic efficiency, medic (a C3 plant) and maize (a C4 plant), along with 4 AM fungal species, and successfully established various plant-AM fungal combinations. We examined the growth of plants and AM fungi, the mineralization process of soil Po, and the absolute quantity, community composition, and metabolic preferences of the hyphosphere microbiome. Maize-AM fungi combinations exhibited greater abilities to increase soil phosphatase activity and promote Po mineralization compared to medic-AM fungi combinations. This was related to substantial disparities in the hyphosphere core microbiome between maize and medic. Massilia, a pivotal member of the core microbiome and a keystone taxon within the hyphosphere network, showed a notably greater relative abundance in maize-AM fungal systems than in the medic treatment. Thirteen core bacterial strains isolated from the hyphosphere showed a universal ability to secrete phosphatase, with Massilia being the most proficient. Additionally, community level physiological profiles showed that the maize-associated hyphosphere microbiomes had a heightened capacity for metabolizing fructose and glucose, key components of hyphal exudates. Our study demonstrates that different combinations of plants and AM fungal species modulate the relative abundance of the core taxon through hyphal exudates, thus influencing the functionality of hyphosphere microbiomes for Po mineralization in the phytate-enriched soil. This provides novel insights into AM symbiosis for nutrient cycling and underscores the potential of tailored plant-fungal pairings in improving agricultural nutrient management and soil health.

>Improving nutrient use efficiency in agriculture is a major challenge for achieving food security and green development,which is necessary to systematically develop the biological potential of soil-crop-microbe systems. Led by Prof. Fusuo Zhang, China Agricultural University has proposed a broadening of the concept of rhizobiont and the corresponding working strategies to address this key issue. Aiming at the major scientific questions of rhizosphere interaction and nutrient efficiency,

Bacterial composition and functions in the hyphosphere of arbuscular mycorrhizal (AM) fungi are complex because AM fungal hyphae transport carbon compounds from plant photosynthesis which feed bacteria and act as signaling molecules. This function is lost when hyphae separate from roots, a common occurrence in soil. However, the impact of such disturbances on hyphal surface bacteria remains unclear. We used in vitro bi-compartmented Petri plates with carrot roots and the AM fungus Rhizophagus irregularis MUCL 43194, separating root and hyphal compartments. Treatments included hyphae connected to roots (+ AM), no hyphae (-AM), and hyphae cut at different times (C3D and C0D, where C3D indicates hyphae cut 3 days before inoculation and C0D indicates hyphae cut on the day of inoculation) subjected to a bacterial suspension extracted from a field soil. Thirteen bacterial phyla were identified, with Streptomyces, Pseudomonas, Rhodococcus, and Cellulomonas dominating. Hyphae increased bacterial ASV relative abundance, notably enriching Actinobacteria ASVs. After 14 days, α-diversity decreased from -AM to C3D, C0D, and + AM, with fewer Bacteroidetes species in + AM compared to -AM. Root-connected hyphae led to deterministic bacterial assembly, while cut hyphae resulted in stochastic assembly. Our findings show that physical disruption of hyphae significantly affects bacterial diversity and may influence ecological functions.

To efficiently obtain P from soil, most terrestrial plants form symbiosis with arbuscular mycorrhizal(AM) fungi and thus have two P uptake pathways, i.e.,the direct pathway(DP) via roots, particularly root hairs, and the mycorrhizal pathway(MP) via AM fungal hyphae. AM fungi form an extraradical hyphal network to expand their contact area with soil and release carbon-rich compounds, which provide a high-energy habitat for soil bacteria. The bacteria affected by AM fungi support P nutrition of AM fungi by secreting extracellular phosphatases. During the P acquisition process, both DP and MP function and require C fixed by plant photosynthesis to maintain P transport. Plants make trade-offs between DP and MP based on C inputs and P benefits. This review first systematically explores the potential trade-offs between plant C inputs and P gains of DP and MP as well as the factors that influence such trade-offs.Then the response of AM fungi to soil nutrient heterogeneity and the mechanisms by which AM fungi select bacteria to mineralize organic P and increase the P contribution of MP were analyzed. Future studies need to apply emerging methods and technologies to accurately quantify the contribution of DP and MP to plant P absorption under different conditions and provide the theoretical basis for optimizing sustainable agricultural production systems.