Phosphate-solubilizing bacteria are the most fully studied functional group, among which Bacillus and Pseudomonas are the two groups with the greatest application potential. Bacillus (e.g., Bacillus megaterium, Bacillus subtilis) efficiently dissolves inorganic phosphorus such as calcium phosphate by secreting various organic acids and phytases, and simultaneously produces ACC deaminase and plant hormones, possessing both growth-promoting and stress-tolerant functions (Thampi et al., 2023; Wang et al., 2023); Pseudomonas (e.g., Pseudomonas aeruginosa) exhibits excellent performance in promoting crop growth and phosphorus uptake through the synergistic effect of organic acids, siderophores, and plant growth regulators, and its application value has been confirmed in crops such as peanuts and wheat (Anonymous, 2024; Wang et al., 2023). Some strains of Enterobacter also have the potential to remediate heavy metal-contaminated soils by regulating rhizosphere phosphorus cycling to reduce the bioavailability of heavy metals (Bashir et al., 2024; Iftikhar et al., 2024; Li et al., 2023; Wang X. et al., 2025).

Phosphate-solubilizing fungi are the core functional group for phosphorus activation in acidic soils. Their phosphorus-solubilizing advantages stem from two aspects: first, they secrete high-concentration organic acids with strong chelating ability (e.g., oxalic acid, citric acid), which can directly act on the surface of phosphorus minerals (Lu et al., 2025; Šeremešić et al., 2024); second, mycelia can penetrate small soil pores, contact phosphorus mineral particles that are difficult for bacteria to reach, and expand the scope of action (Šeremešić et al., 2024). For example, when Penicillium chrysogenum strain PSF-4 dissolves tricalcium phosphate and iron phosphate, the concentration of soluble phosphorus is significantly positively correlated with the secretion of carboxylic acids, and the phosphorus-solubilizing efficiency in acidic soils is 2–3 times that of bacteria (Jiang et al., 2020; Lu et al., 2025). Some Trichoderma strains also have biocontrol functions, which can inhibit the growth of plant pathogens and achieve a synergistic effect of “phosphorus solubilization+disease prevention” (Wang et al., 2023).

Actinomycetes are a group with insufficient resource exploration. Existing studies have confirmed that Streptomyces and Francisella have phosphorus-solubilizing ability, which activates phosphorus through the synergy of organic acids and phosphatases (Iftikhar et al., 2024; Wang et al., 2023). Due to their strong tolerance to poor nutrition and stress, actinomycetes have unique potential in the ecological remediation of extreme soils such as mine tailings and degraded forestlands. However, current research only stays at the strain screening level, and molecular mechanisms and application effect verification are relatively weak.

The synthesis and secretion of organic acids are the core pathways for PSMs to dissolve inorganic phosphorus. Their molecular regulation involves the synergistic effect of carbon metabolism pathway genes, phosphorus starvation response systems, and transporter protein genes (de Almeida Leite et al., 2024; Lü et al., 2011; Rodríguez and Fraga, 1999). Genomic studies have shown that PSMs generally carry key enzyme genes of glycolysis and tricarboxylic acid (TCA) cycle, such as glucose dehydrogenase (gcd) gene of Pseudomonas and citrate synthase gene of Bacillus. The expression of these genes directly determines the type and yield of organic acids (Campo and San Segundo, 2020; Sharon et al., 2016; Sharma et al., 2021). For example, under low phosphorus conditions, TCA cycle-related genes (e.g., malate dehydrogenase gene) in Pseudomonas aeruginosa are significantly upregulated, driving the increase in the secretion of citric acid and malic acid (Wang et al., 2022); while the expression of gcd gene in Pseudomonas strain JW-SD2 is regulated by environmental phosphorus concentration. Under low phosphorus conditions, the expression level increases by 3.2 times, accompanied by the increase in gluconic acid secretion and medium acidification (Su L. et al., 2023; Wang Y. et al., 2025; Zeng et al., 2015).

The phosphorus starvation response system (e.g., Pho Regulon system in bacteria) is the core regulatory hub for organic acid secretion. Under low phosphorus conditions, the sensor protein PhoR is phosphorylated to activate the response regulator protein PhoB, which binds to the promoter region of organic acid synthesis genes to upregulate gene expression (Sharon et al., 2016). It is worth noting that the regulatory networks of different PSMs have species specificity: the regulation of organic acid secretion in fungi may depend on PHR family transcription factors, which have evolutionary differentiation from the Pho Regulon system in bacteria (Gurbanov et al., 2021; Li et al., 2025); while the relevant regulatory mechanisms of actinomycetes have not been reported, which is a key gap for future research.

The extracellular secretion of organic acids depends on transporter protein genes, such as ABC transporter and proton pump (H⁺-ATPase) genes (Amy et al., 2022). The expression of H⁺-ATPase genes not only provides power for the efflux of organic acids but also directly acidifies the rhizosphere environment, enhancing phosphorus dissolution efficiency (Amy et al., 2022). Currently, only a few transporter protein genes have been identified, and their substrate specificity (e.g., transport preference for different organic acids) is not clear, which limits the efficiency of enhancing organic acid secretion through genetic engineering.

Phosphatases (phytases, phosphomonoesterases) are key enzymes for PSMs to mineralize organic phosphorus, and their expression is also regulated by the phosphorus starvation response system. Under low phosphorus conditions, the phosphorus starvation response genes (e.g., phoD, phoA) of PSMs are activated, driving the synthesis and secretion of phosphatases (Chen et al., 2025; da Silva Rodrigues et al., 2024; Gao et al., 2025; Yang et al., 2022). For example, in phoD gene-harboring microorganisms in karst forest soils, the gene expression level increases by 4.5 times and the acid phosphatase activity increases by 2.8 times under phosphorus limitation (Chen et al., 2024); while the phytase gene (phy) of Bacillus is regulated by PhoB. Under low phosphorus conditions, the expression level is upregulated, the phytase activity is enhanced, and phytic acid salts in soil can be efficiently degraded (Li et al., 2025).

Omics studies have revealed the environmental adaptive regulation of phosphatase production: transcriptome analysis found that the expression profiles of phosphatase genes in PSMs differ significantly between different soil types (acidic vs. alkaline). For example, the expression level of acid phosphatase gene in Penicillium chrysogenum in acidic soil is 2.5 times that in alkaline soil, while the opposite is true for alkaline phosphatase gene (Akbar et al., 2023). This difference ensures the organic phosphorus mineralization ability of PSMs in different environments. However, current related studies are mostly focused on the regulation of a single environmental factor, and the regulatory network under combined stresses (e.g., low phosphorus + heavy metals) is not clear.

In addition to the core mechanisms, compounds secreted by PSMs such as plant growth regulators (IAA, gibberellins) and siderophores indirectly improve phosphorus absorption efficiency by improving plant root development and regulating rhizosphere microenvironment (Timofeeva et al., 2022; Vasques et al., 2024). For example, Bacillus strains promote wheat root branching by secreting IAA, increasing root surface area by more than 30% and phosphorus absorption by 25% (Khan et al., 2009); while siderophores of Pseudomonas chelate Fe^{3 +} to release phosphate ions from iron-phosphate complexes, and simultaneously promote plant iron absorption, achieving a synergistic improvement of “phosphorus-iron” nutrition (Thampi et al., 2023). Multi-omics studies have shown that the genes of these auxiliary mechanisms and core phosphorus-solubilizing genes are regulated by the same phosphorus starvation signal, forming a synergistic regulatory network (Bolan et al., 2025). However, the analysis of the interaction between network nodes is still fragmented.

pH regulates phosphorus-solubilizing efficiency by affecting the metabolic activity of PSMs and the chemical form of insoluble phosphorus. In acidic environments, H⁺ can destroy the lattice structure of calcium phosphate and iron phosphate, and the chelating effect of organic acids is enhanced, significantly improving the dissolution efficiency of inorganic phosphorus (Liu et al., 2023; Pang et al., 2024); in alkaline soils, PSMs need to secrete more organic acids to reduce rhizosphere pH to achieve phosphorus activation, so the screening of high-efficiency PSMs in alkaline soils is more challenging (Naorem et al., 2023). There are differences in the pH adaptation range of different PSM groups: fungi have the best phosphorus-solubilizing efficiency under pH 4.0–6.0, while bacteria are more adaptable to neutral environments with pH 6.5–7.5 (Akbar et al., 2023; Jia et al., 2023). This differentiation is an important driving factor for the community structure of soil PSMs.

Phosphorus concentration regulates PSMs activity through “negative feedback regulation”: under low phosphorus conditions, PSMs activate the phosphorus starvation response system, upregulate the expression of genes related to organic acids and phosphatases, and enhance phosphorus-solubilizing activity (Liu et al., 2023; Richy et al., 2024); under high phosphorus conditions, the phosphorus starvation response system is inhibited, and PSMs do not need to invest energy in synthesizing phosphorus-solubilizing substances, resulting in a significant decrease in phosphorus-solubilizing activity (Zeng et al., 2015). This regulatory mechanism is an evolutionary strategy for PSMs to adapt to environmental phosphorus levels, but it also limits their application effect in high-phosphorus soils.

Carbon source is the energy basis for the metabolic activities of PSMs. Easily utilizable carbon sources (e.g., glucose, sucrose) can significantly increase the secretion of organic acids and phosphatase activity (Liu et al., 2023). The effect of different carbon source types on PSMs activity has species specificity: Pseudomonas has the highest phosphorus-solubilizing efficiency when glucose is used as the carbon source, while Bacillus prefers sucrose (Wang et al., 2023), which provides a basis for the selection of carbon source additives in PSMs biofertilizers.

The species specificity of plant root exudates is the key driving factor for the host preference of PSMs. There are significant differences in the composition of root exudates (e.g., sugars, amino acids, flavonoids) among different crops: leguminous plants (e.g., soybeans) have high levels of flavonoids in their root exudates, which can specifically induce the chemotaxis and colonization of rhizobia-related PSMs (Vasques et al., 2024); while the root exudates of gramineous plants (e.g., wheat) are mainly glucose and organic acids, which are more likely to attract Pseudomonas PSMs (Khan et al., 2024). Transcriptome analysis shows that the expression of chemotaxis factor genes and colonization-related genes (e.g., adhesion protein genes) in PSMs is specific to root exudates, which can only be activated under the induction of exudates from suitable hosts (de Almeida Leite et al., 2024).

Differences in plant root structure also affect interaction efficiency. Fibrous root crops (e.g., wheat) have a large root surface area and more contact sites with PSMs, making it easier to form stable interactions; while taproot crops (e.g., cotton) have a stable rhizosphere microenvironment, which is conducive to the long-term colonization of PSMs (Zhu Y. et al., 2024). In addition, the phosphorus starvation response of plants can also regulate interactions. Under low phosphorus conditions, plants increase the secretion of organic acids in root exudates, further recruiting PSMs colonization (Li et al., 2025).

Host-specific interactions can significantly improve phosphorus absorption efficiency and plant stress resistance. For example, in the specific interaction between soybeans and rhizobia PSMs, PSMs not only dissolve soil phosphorus but also provide nitrogen for soybeans through nitrogen fixation, achieving synergistic supply of “phosphorus-nitrogen,” and soybean yield is increased by 22%–35% (Vasques et al., 2024); in the interaction between wheat and Pseudomonas PSMs, siderophores secreted by PSMs can synergistically improve the absorption of phosphorus and iron by wheat, alleviating the “phosphorus-iron” antagonism (Khan et al., 2024). On the contrary, non-specific PSMs inoculation (e.g., inoculating PSMs suitable for leguminous crops directly into gramineous crops) results in a colonization rate of less than 10% and a phosphorus-solubilizing effect of only 25% of specific inoculation (Zhu Y. et al., 2024).

At present, the molecular signaling pathways of host-specific interactions between PSMs and plants are still unclear. Key scientific issues such as how plants recognize PSMs and how PSMs regulate host root development have not been resolved, which need to be further analyzed through combined metatranscriptome and metabolome analysis.

Screen native PSMs strains with excellent phosphorus-solubilizing ability and environmental adaptability from specific crop varieties or agricultural ecosystems (e.g., saline-alkaline soils, oil palm rhizospheres) (Acevedo et al., 2014; Jiang et al., 2018). These native strains may better adapt to local soil environments, improving colonization and competitiveness. Screen and develop PSMs strains tolerant to abiotic stresses such as salinity, heavy metals, drought, and high temperature to improve their application effects in harsh environments (Cao et al., 2023; Lu et al., 2023). For example, studies have found that certain halophilic PSMs (e.g., Bacillus) can still effectively solubilize phosphate in saline media (Jiang et al., 2018). Use multi-omics methods such as genomics, proteomics, and metabolomics to deeply analyze the phosphorus-solubilizing mechanisms of PSMs and their interaction mechanisms with plants (Kumar et al., 2023; Lu et al., 2023; Park et al., 2020). Conduct genetic improvement of PSMs through synthetic biology, metabolic engineering, and genetic engineering technologies to enhance their phosphorus-solubilizing efficiency, stress resistance, colonization ability, and ability to secrete plant growth-regulating substances (Lovley and Yao, 2021).

Studies have shown that organic materials such as straw compost can be used as effective carriers for PSMs, improving their survival rate and effect in soil (Li C. et al., 2024). Straw compost can improve soil physical and chemical properties, provide a favorable microenvironment for PSMs, thereby promoting the colonization of PSMs in the rhizosphere soil of plants, improving phosphorus-solubilizing efficiency, and further promoting plant phosphorus absorption and growth (Li C. et al., 2024). Use nano/microstructured supramolecular biopolymers as carriers for PSMs to achieve targeted delivery and controlled release of bioactive compounds, improve the stability and bioavailability of PSMs, and improve soil structure and water retention capacity (Saberi Riseh et al., 2024). Combined application of PSMs with other beneficial microorganisms such as Arbuscular Mycorrhizal Fungi (AMF) and Plant Growth-Promoting Microorganisms (PGPM) can exert synergistic effects, more effectively promoting plant growth and nutrient absorption (Cao et al., 2024; Laishram et al., 2024; Sahoo et al., 2024; Trivedi et al., 2021). For example, the combined inoculation of PSMs and AMF can significantly promote the growth of Phyllostachys edulis seedlings in phosphorus-deficient soils (Xing et al., 2023).

Coordinate the application of organic fertilizers, inorganic fertilizers, and PSMs, and implement integrated phosphorus management strategies to improve phosphorus use efficiency, reduce phosphorus fertilizer input and environmental pollution (Bolo et al., 2021; El Attar et al., 2022). For example, improve soil microbial biomass and PSMs abundance by adjusting tillage methods, crop rotation, and residue return (Bolo et al., 2021). Conduct precision fertilization according to soil phosphorus status and crop needs, reduce the use of excessive phosphorus fertilizers, and create a more favorable environment for PSMs to play their roles (El Attar et al., 2022).

Plant secondary metabolites play key roles in plant-environment interactions, including responding to abiotic and biotic stresses (Aggarwal et al., 2024; Clemensen et al., 2020, 2025; He et al., 2026; Mandal, 2025; Shelake et al., 2023; Sun and Fernie, 2024). Studying how PSMs regulate plant phosphorus absorption, stress resistance, and interaction with microorganisms by affecting the synthesis and secretion of plant secondary metabolites will help develop more effective PSMs application strategies (Clemensen et al., 2025; Su Y. et al., 2023). Certain plant secondary metabolites have antibacterial activity and can be used to manage antibiotic resistance of bacteria (Kongkham et al., 2020). Combining PSMs (Phosphate-Solubilizing Microorganisms) with biologically active plant secondary metabolites may enhance plant resistance to diseases and insect pests while improving crop productivity.

Carry out multi-scale field trial studies to systematically evaluate the long-term effects and environmental safety of PSMs in different ecological regions, soil types, and crop systems (Park et al., 2020; Raymond et al., 2020). Use advanced technologies such as high-throughput sequencing, mass spectrometry, metabolomics, and eco-metabolomics to real-time monitor soil microbial community dynamics, plant metabolic changes, and the fate of PSMs in the soil-plant system (Clemensen et al., 2025; Kumar et al., 2023; Lu et al., 2023; Park et al., 2020), and real-time monitor the potential impacts of PSMs release on the environment and native microbiome biodiversity.

To address the limitation of fragmented molecular mechanisms, it is necessary to break through the research paradigm of “single strain - single environment,” rely on the synergistic advantages of multi-omics technologies, and combine single-cell sequencing technology to achieve panoramic and precise analysis of the ternary interaction system of “PSMs - plants - soil microorganisms.” Specifically, the combination of metagenomics and metatranscriptomics can reveal the species composition, dynamic expression of functional genes, and niche differentiation of microbial communities in the ternary interaction system under different environmental conditions (especially combined stresses), clarifying the competitive/synergistic relationships between PSMs and soil microorganisms; metabolome and secretome analysis can accurately identify key signal molecules mediating interactions (e.g., flavonoids in plant root exudates, organic acids secreted by PSMs), constructing an association network of “genes - metabolites - phenotypes”; single-cell genomics/transcriptomics technology can avoid the “average effect” of metagenomics, accurately locate core functional strains in the interaction network, and analyze their specific regulatory pathways. On this basis, focus on breaking through the synergistic regulatory mechanisms under combined stresses (low phosphorus + heavy metals + drought/salinity-alkalinity), clarify the cross-regulatory nodes between the phosphorus starvation response system and stress resistance system of PSMs, identify core target genes that simultaneously improve phosphorus-solubilizing efficiency and stress resistance, and provide theoretical support for the breeding of high-efficiency stress-tolerant strains. At the same time, it is necessary to establish a mechanism verification system of “laboratory simulation - field validation” to ensure that the analyzed molecular mechanisms have ecological authenticity.

To address the limitation of superficial host-specific research, it is necessary to focus on the core chain of “signal recognition - gene regulation - colonization adaptation” to clarify the molecular mechanisms of PSMs-plant interactions. First, through combined transcriptome and proteome analysis, identify specific signal molecules in root exudates of different crops (especially major field crops such as corn and soybeans) and corresponding receptor proteins on the surface of PSMs, analyzing the binding mode of signal molecules and receptor proteins and downstream regulatory pathways; second, verify the function of key signaling pathway genes using synthetic biology technology to clarify the molecular basis of PSMs adapting to different hosts; finally, based on mechanism analysis results, establish a precise matching database of “crops - PSMs,” clarifying the dominant PSMs groups suitable for different crops (e.g., rhizobia for leguminous crops, Pseudomonas for gramineous crops), providing theoretical basis for the precise application of inoculants. In addition, it is necessary to carry out specific interaction experiments under different crop-soil type combinations, evaluate the impact of host specificity on PSMs colonization rate and phosphorus-solubilizing effect, and optimize the matching scheme of “crops - strains - soil.”

To address the limitation of poor field adaptability of PSMs, it is necessary to combine the results of molecular mechanism research and adopt a synergistic strategy of “gene editing + directed domestication” to breed high-quality strains with high-efficiency phosphorus solubilization, broad-spectrum stress resistance, and stable colonization ability. On the one hand, based on the core target genes analyzed by the ternary interaction mechanism, use gene editing technologies such as CRISPR-Cas9 to directionally modify PSMs, for example, enhance the expression of core genes in the phosphorus starvation response system (e.g., PhoB) to increase organic acid secretion; introduce heavy metal and salinity-alkalinity tolerance-related genes to enhance adaptability to combined stresses. At the same time, attention should be paid to the ecological safety evaluation of gene-edited strains to avoid damage to the native soil microbial community. On the other hand, carry out long-term directed domestication experiments, domesticate PSMs for multiple generations under simulated field combined stresses (low phosphorus + heavy metals + drought), and screen strains with strong adaptability and stable phosphorus-solubilizing function, making up for the ecological risk shortcomings of gene editing technology. In addition, the development of compound microbial inoculants should take “functional complementarity” and “interaction compatibility” as the core principles, screen functionally complementary strain combinations (e.g., PSMs + nitrogen-fixing bacteria, PSMs + arbuscular mycorrhizal fungi) through in vitro interaction experiments, and evaluate the interaction effects between strains using metabolomics to avoid competitive inhibition, achieving a synergistic function of “phosphorus solubilization + stress resistance + growth promotion.”

To address the disconnection between basic research and practice, it is necessary to establish a three-level verification system of “laboratory simulation - plot experiment - long-term location trial across ecological regions” to systematically evaluate the long-term application effects of PSMs. First, simulate stress environments of different soil types and climatic conditions in the laboratory to evaluate the phosphorus-solubilizing efficiency and stress resistance of PSMs; second, carry out plot experiments in typical ecological regions to optimize the application rate and method (e.g., seed coating, furrow application) of PSMs inoculants; finally, establish long-term location trials in major agricultural ecological regions such as Northeast black soil, North China saline-alkaline soil, and South red soil, continuously monitor the long-term impact of PSMs on crop yield, soil fertility (e.g., soil organic matter content, available phosphorus content), and soil microbial community structure, and evaluate their ecological safety and sustainability. At the same time, combine meteorological data, soil physical and chemical properties, and crop growth indicators to construct a PSMs application effect prediction model using machine learning technology, realizing precise optimization of application strategies under “soil - crop - climate” conditions, and improving the stability of application effects.

To address industrialization bottlenecks, it is necessary to make breakthroughs in the entire chain of “fermentation process - formulation development - quality control,” reduce application costs, and improve the industrial system. In terms of fermentation process, develop intelligent fermentation technology using agricultural wastes (e.g., corn stover, livestock and poultry manure) as low-cost fermentation substrates, optimize fermentation conditions (temperature, pH, aeration rate), improve strain yield and activity, and reduce fermentation costs; in terms of formulation development, focus on the optimization of carrier materials, develop composite carriers of biochar + trehalose + humic acid, use embedding technology to improve the shelf life and field colonization ability of inoculants, and simplify the application method (e.g., seed coating, foliar spraying) to improve farmers’ acceptance; in terms of quality control, establish a full-chain quality standard system for PSMs biofertilizers, clarify core indicators such as strain activity, purity, shelf life, and heavy metal content, develop rapid detection technologies (e.g., quantitative real-time PCR technology), and realize precise monitoring of product quality. In addition, it is necessary to promote the formulation of international unified quality standards, standardize the market order, and improve the market recognition of PSMs biofertilizers.

In conclusion, as a core biological resource for sustainable phosphorus management, the full exploitation of PSMs application potential depends on the deep integration of basic research and practical research. Future research needs to break through the limitations of existing research paradigms, guide the focus of research directions with critical thinking, and realize the leap of PSMs from “high efficiency in the laboratory” to “stability in the field” through the systematization of mechanism analysis, precision of application technologies, and improvement of industrial systems, providing core support for ensuring food security and promoting the green and sustainable development of agriculture.