Biochemistry of plant-microbe interactions in biofertilizer applications

Introduction

Sustainable agriculture relies increasingly on harnessing the natural potential of soil microorganisms to enhance crop productivity while reducing chemical inputs. The rhizosphere, often described as a hotspot of biochemical activity, hosts diverse plant-microbe interactions that govern nutrient cycling, growth promotion, and stress tolerance. Unlike synthetic fertilizers, which provide direct but often inefficient nutrient supplementation, beneficial microbes mobilize nutrients, regulate plant physiology, and improve soil health through tightly coordinated biochemical processes. Central to these interactions are mechanisms such as biological nitrogen fixation, phosphorus and potassium solubilization, production of phytohormones, and siderophore-mediated iron acquisition. For example, nitrogen-fixing bacteria transform atmospheric N₂ into plant-available ammonia through the activity of nitrogenase under highly regulated and oxygen-protected conditions. Phosphate-solubilizing microorganisms secrete organic acids and enzymes that release otherwise inaccessible phosphorus, while potassium-solubilizing microbes employ acidolysis, chelation, and ion exchange to mobilize mineral-bound K and other nutrients. In parallel, microbial synthesis of phytohormones including indole-3-acetic acid, gibberellins, and cytokinins directly influences root and shoot development, enhancing nutrient uptake and plant vigor. Equally important are microbial roles in stress alleviation and signaling. Siderophore production improves iron availability and suppresses pathogens, whereas ACC deaminase activity reduces ethylene accumulation, enabling plants to withstand drought, salinity, and other stresses. Furthermore, molecular exchanges involving flavonoids, Nod factors, and quorum-sensing signals shape mutualistic associations that sustain nutrient exchange and metabolic cooperation. By integrating advances in enzymology, molecular signaling, and field-based applications, this review emphasizes how biochemical mechanisms at the plant-microbe interface underpin biofertilizer efficacy. Understanding these processes not only explains the success of microbial inoculants in cereals, legumes, and vegetables but also provides insights into their role in promoting soil fertility, crop yield, and ecological resilience.

Biochemical Mechanisms of Plant-Microbe Interactions 2.1 Nitrogen Fixation

Biological nitrogen fixation (BNF) in plant-microbe systems is a multi-step biochemical process that couples microbially catalyzed reduction of atmospheric N₂ to host-derived signaling, metabolic integration, and tight regulatory control. In legumes the process occurs inside specialised root or stem nodules formed after a multistage signalling and infection programme in non-legumes, associative or endophytic diazotrophs fix N₂ in the rhizosphere or inside plant tissues (Xu et al., 2023) [68] .

Recognition and nodule organogenesis

Nodule formation begins with molecular dialog, plant flavonoids released from roots induce bacterial synthesis of lipochitooligosaccharide "Nod factors," which trigger root hair curling, calcium spiking, and downstream kinase cascades that reprogramme cortical cells to form the nodule primordium. Key plant regulators (for example NIN) and calcium-dependent kinases coordinate infection thread formation and bacterial entry. This signalling cascade both permits symbiont entry and establishes the developmental program that yields the oxygenbuffered environment required for nitrogenase activity (Oldroyd, 2004) [48] .

Nitrogenase: structure and catalytic mechanism

Nitrogenase is the two-component metalloprotein complex composed of the Fe (iron) protein and the MoFe (molybdenumiron) protein (for the canonical Mo-nitrogenase). The active site (FeMo-cofactor) on the MoFe protein carries out N₂ reduction. Catalysis proceeds by stepwise delivery of single electrons from an external electron donor to the Fe-protein, ATP-dependent transfer of electrons from Fe-protein to MoFe-protein (Lowe-Thorneley kinetic framework), accumulation of electron/proton equivalents at FeMo-co, and eventual binding/reduction of N₂ to NH₃. The overall process is strongly ATP-consuming and yields obligatory H₂ as a side product under most conditions. Electron donors in vivo include ferredoxin or flavodoxin; dithionite is used in vitro. Electron transfer from Fe-protein to MoFe-protein is MgATP-dependent with a high ATP cost per electron; classical estimates place the energetic cost of biological N₂ reduction in the tens of ATP molecules per N₂ reduced. (Seefeldt, 2009) [57] Alternative nitrogenases (V-or Fe-only) may be expressed when Mo is limiting, these enzymes are homologous but have different metal cofactors and catalytic efficiencies (Florence et al., 2018) [24] .

Oxygen protection and micro aerobic metabolism

Nitrogenase is irreversibly inactivated by molecular O₂, so diazotrophs and nodulated hosts deploy multiple oxygenmanagement strategies: (i) plant synthesis of leghemoglobin buffers O₂ within nodules to permit respiration but protect nitrogenase, (ii) high respiratory rates or specialised bacterial proteins in free-living diazotrophs provide "respiratory protection," and (iii) regulatory switches turn nif gene expression off under high oxygen or fixed-N conditions. These mechanisms together maintain the low-O₂, energy-rich environment required for efficient fixation. (Rutten et al., 2019).

Regulation and host control

Nitrogenase expression and activity are tightly regulated at transcriptional and post-translational levels. In many diazotrophs NifA is the central transcriptional activator of nif genes, and its activity is modulated by oxygen, fixed nitrogen, and other signals. Plants also exert control over bacteroid differentiation and activity via peptide signals and nutrient provisioning, effectively making bacteroids organelle-like nitrogen factories in many legume symbioses.

Metabolic integration and nutrient exchange

Efficient symbiotic fixation requires close metabolic exchange: the plant supplies carbon (e.g., dicarboxylates) and ATPgenerating respiration to support bacterial N fixation, while the bacteria supply ammonia (or assimilated nitrogen forms) to the host. Transporters and membrane interfaces in the symbiosome coordinate this exchange, and phosphate, iron, and molybdenum availability in nodules critically influence nitrogenase assembly and function (White et al., 2007) [67] .

Phosphorus Solubilisation 2.2.1 Organic Acid Production

Microorganisms improve phosphorus availability by secreting low-molecular-weight organic acids. These acids carry hydroxyl and carboxyl groups that interact with phosphate-bearing minerals such as calcium, magnesium, iron, and aluminium.

Through this interaction, they not only bind with these minerals but also lower the pH of the surrounding soil. This acidification dissolves otherwise insoluble phosphate compounds and releases phosphorus in a form that plants can readily absorb (Kim et al., 1997) [35] . Among the various acids released, gluconic acid is the most common, followed by citric and oxalic acids. Gluconic acid is synthesized when bacteria oxidize glucose using the enzyme glucose dehydrogenase, which requires the cofactor pyrroloquinoline quinone (PQQ). Genes such as the pqq operon and gcd play a central role in regulating this enzyme system. Other acids, including citric and oxalic acids, promote solubilisation by chelating metal cations (Ca²⁺, Fe³⁺, Al³⁺) that bind phosphate, while simultaneously reducing local pH(An and Moe, 2016) [5] .

The composition and quantity of acids released vary with microbial species, available carbon sources, and soil or culture conditions (Menezes-Blackburn et al., 2016) [42] . Analytical tools like HPLC and LC-MS have consistently detected mixtures of gluconic, oxalic, malic, citric, and lactic acids in culture supernatants. These studies show a clear relationship between acid secretion, pH reduction, and increased soluble phosphorus (Zaidi et al., 2009) [71] . In essence, phosphorus solubilisation by microbes largely depends on organic acid release, with gluconic acid being particularly significant. The actual mix and efficiency, however, depend on the microbes genetic capacity and the environmental conditions.

Enzymatic Contribution: Phytases and Phosphatases

Phytases are specialized enzymes capable of hydrolysing phytic acid (myo-inositol hexakisphosphate), a major organic phosphorus reserve in plants. By sequentially removing phosphate groups, they release inorganic phosphorus available for plant and microbial uptake. These enzymes occur widely in bacteria, fungi, and plant-associated microbes, playing a crucial role in organic phosphorus turnover (Rizwanuddin et al., 2023; Duong et al., 2018; Gerke, 2015) [52,21] . Different microbial phytases vary in their catalytic efficiency, optimal pH and temperature, and their ability to function under field conditions, all of which determine how much phytatebound phosphorus is released in soils (Yuand Chen, 2013; Caffaro et al., 2020) [70,17] . Phosphatases, including acid and alkaline phosphomonoesterases, hydrolyzes a broad range of organic phosphorus compounds such as glycerophosphates, sugar phosphates, and phospholipids. Both plant roots and soil microbes contribute to phosphatase activity, which is vital for short-term phosphorus mineralization in the rhizosphere (Spohn and Kuzyakov, 2013; Cabugao et al., 2017) [63,16] . Acid phosphatases typically act best in acidic conditions (pH 4-6) and are concentrated in root-associated soils, while alkaline phosphatases function better in neutral to alkaline soils. Together, they expand the range of organic phosphorus substrates that can be mobilized (Ding et al., 2011) [19] .

Biochemical Mobilization of Insoluble Phosphorus

Phosphate-solubilizing microorganisms (PSMs) mobilize phosphorus via two main strategies: 1. Mineral dissolution: Organic acids and protons solubilize mineral-bound phosphate by chelating or displacing metal cations. 2. Organic P mineralization: Extracellular enzymes like phytases and phosphatases break down organic phosphorus compounds, releasing inorganic phosphate (Pi) (Pan and Cai, 2023) [49] . The effectiveness of microbial phosphorus mobilization depends on soil pH, mineral composition, organic matter, and how strongly phosphorus is bound to iron, aluminium, or organic complexes. Microbial metabolism, oxygen supply, and interactions with plant root exudates also play key roles (Hunter et al., 2014) [32] . In many soils, phosphorus availability is governed by a combination of microbial activities, including acid release, siderophore production (for iron binding), and enzymatic degradation of phytate. Since metal-organic complexes can hinder enzyme access, microbes with multiple phosphorusreleasing mechanisms are especially effective (Wang et al., 2021) [66] . Experimental studies have shown that inoculating crops with PSMs capable of producing both organic acids (gluconic, oxalic) and enzymes (phytases, phosphatases) enhances phosphorus uptake and plant growth. However, success in the field is variable and influenced by soil type and management (Timofeeva et al., 2022) [64] . Recent advances include detailed insights into the pqq/gcd system, discovery of more stable microbial phytases, and development of microbial strains with multiple phosphorus-mobilizing traits for greater agricultural reliability.

Potassium & Other Nutrient Mobilization

Potassium (K) is a vital macronutrient for plant growth and development, yet a large portion of soil potassium exists in insoluble mineral forms such as feldspar, mica, and illite. Under normal soil conditions, these mineral-bound K sources are largely inaccessible to plants. Microorganisms play a central role in mobilizing this potassium into bioavailable forms through a range of biochemical mechanisms. One of the primary strategies is acidolysis, where potassiumsolubilizing microorganisms secrete organic acids such as citric, oxalic, gluconic, tartaric, and lactic acids. The acidification of the surrounding microenvironment breaks down mineral lattices, releasing K⁺ ions for plant uptake (Etesami et al., 2017) [22] . Chelation represents another key mechanism. Microbial metabolites, including specific organic acids, bind to metal cations such as Fe³⁺, Al³⁺, and Ca²⁺, destabilizing mineral matrices and facilitating potassium liberation (Etesami et al., 2017) [22] . Additionally, ion-exchange reactions occur when protons or other cations released during microbial metabolism displace potassium ions adsorbed onto mineral surfaces, further enhancing K availability. Microbial respiration also contributes to nutrient mobilization; CO₂ released by microbes dissolves in soil moisture to form carbonic acid, promoting mineral dissolution and nutrient solubilization (Babar et al., 2024) [10] . Microbial extracellular products, such as exopolysaccharides (EPS) and biofilms, further improve nutrient mobilization. These compounds create localized microenvironments that concentrate organic acids and enzymes near mineral surfaces, amplifying the solubilization of potassium, magnesium, calcium, and zinc (Yadav, 2022: Figiel et al., 2025) [69,23] . EPS and biofilm structures act as protective and concentrating matrices, enhancing microbial efficiency in nutrient release. Beyond potassium, these mechanisms are effective in mobilizing other essential nutrients. Magnesium (Mg²⁺) and calcium (Ca²⁺), commonly present in silicate and carbonate minerals, are solubilized through similar microbial acidolysis and chelation processes (Basak and Biswas, 2009) [11] . Zinc, often present in insoluble mineral complexes, becomes bioavailable through microbial-mediated acidification and chelation (Kamran et al., 2017) [33] . Collectively, these microbial strategies exemplify how biochemical interactions between soil microorganisms and minerals orchestrate the release of multiple essential nutrients, supporting plant growth and soil fertility.

Production of Plant Growth Regulators

Plant-microbe interactions form the biochemical foundation of biofertilizer efficacy, where beneficial microorganisms colonize plant roots and modulate growth through nutrient mobilization and plant growth regulator (PGR) production. Unlike synthetic inputs, these interactions are eco-friendly, improve soil fertility, and enhance crop productivity (Bhattacharyya and Jha, 2012) [13] .

Indole-3-Acetic Acid (IAA)

Indole-3-acetic acid (IAA), the most abundant auxin, regulates cell elongation, division, and differentiation in plants. In plantmicrobe systems, many plant growth-promoting rhizobacteria (PGPR) such as Azospirillum, Rhizobium, and Pseudomonas synthesize IAA, primarily through tryptophan-dependent pathways. The indole-3-pyruvate (IPyA) and indole-3-acetamide (IAM) pathways are the most common microbial routes, where tryptophan is converted into IAA via enzymatic intermediates (Spaepen and Vanderleyden, 2011) [62] . Microbial IAA enhances root hair formation, lateral root development, and nutrient uptake, thereby improving host plant growth (Dobbelaere et al., 2003) [20] .

Gibberellins (GAs)

Gibberellins are diterpenoid hormones that promote stem elongation, seed germination, flowering, and fruit development.

Several

PGPRs, including Azospirillum brasilense, Herbaspirillum seropedicae, and some Bacillus spp., produce gibberellins that mimic or supplement plant biosynthesis (Bottini et al., 2004). Microbial GA biosynthesis proceeds through the terpenoid pathway, starting from acetyl-CoA → mevalonate → geranylgeranyl diphosphate (GGDP), and leading to GA intermediates and bioactive forms (e.g., GA₁, GA₃). These microbial gibberellins stimulate cell wall loosening and expansion of stem and root tissues, enhancing plant biomass accumulation (Kang et al., 2014) [34] .

Cytokinins

Cytokinins are adenine derivatives that control cell division, chloroplast development, nutrient mobilization, and delay of senescence. Symbiotic and associative bacteria such as Rhizobium, Agrobacterium tumefaciens, and Bacillus subtilis are known cytokinin producers (Arkhipova et al., 2007) [7] . Microbial cytokinins are synthesized via the isopentenyl transferase (IPT) pathway, where isopentenyl groups are transferred to adenosine monophosphates. These compounds influence shoot initiation, stimulate leaf expansion, and balance root-shoot growth ratios. In legumes, cytokinins produced by rhizobia play a key role in nodule initiation by activating cortical cell division (Miri et al., 2016) [44] .

Siderophore Production and Iron Sequestration 4.1 Structure of Siderophores

Siderophores are low-molecular-weight compounds (500-1500 Da) secreted by bacteria, fungi, and some plants to capture ferric iron (Fe³⁺), which is otherwise poorly available in aerobic soils (Amsri et al., 2022) [4] . The functional groups used for Fe³⁺ binding: catecholates (phenolates), hydroxamates, carboxylates (including α-hydroxycarboxylates), and mixed types (Boda et al., 2016; Miethke and Marahiel, 2007) [14,43] .  Catecholates (e.g., enterobactin) bind Fe³⁺ through catechol groups, forming highly stable hexadentate complexes (Liu et al., 2023) [39] .  Hydroxamates (e.g., ferrichrome, desferrioxamine) use oxygen atoms of hydroxamate groups, usually forming octahedral coordination around Fe³⁺ (Raymond et al., 2015) [51] .  Carboxylates, common among soil microbes and plants, bind Fe³⁺ via carboxyl and hydroxyl groups and typically form less hydrophobic complexes than catecholates (Hider et al., 2024) [30] .  Phytosiderophores, such as mugineic acids produced by grasses, are derived from amino acids and contain carboxyl, hydroxyl, and amino groups. These compounds selectively chelate Fe³⁺, enhancing iron uptake in graminaceous plants (Kobayashi, 2025) [36] .

Mechanism of Iron Chelation and Uptake

In oxygen-rich environments, Fe³⁺ occurs as insoluble oxides.

Siderophores solubilize this iron by tightly binding it into Fe³⁺siderophore complexes, increasing its bioavailability (Kraemer, 2004). By competing with soil minerals for Fe³⁺, siderophores also facilitate the desorption and mobilization of iron and other metals (Saharan et al., 2023) [55] .

Plants employ two primary strategies to acquire iron:  Strategy I (non-graminaceous plants): roots acidify the rhizosphere and enzymatically reduce Fe³⁺ to Fe²⁺ before uptake.  Strategy II (graminaceous plants): roots release phytosiderophores that chelate Fe³⁺, which are then absorbed as complexes (Grillet et al., 2019) [27] .

Non-graminaceous plants may indirectly benefit from microbial siderophores. At the root interface, Fe³⁺-siderophore complexes can be reduced to Fe²⁺ and taken up, or in some cases, entire Fe³⁺-siderophore complexes may be transported directly via specific root proteins (Schmidt., 1999; Murata et al., 2006) [56,46] . Certain bacterial siderophores, such as pyoverdines from fluorescent Pseudomonas, provide iron to both Strategy I and Strategy II plants under iron limitation. Remarkably, these natural chelators can even surpass synthetic chelates in improving plant iron nutrition (Shirley et al., 2011) [60] . Beyond plant nutrition, siderophores also influence metal homeostasis and phytoremediation. By altering the availability of toxic metals, microbial siderophores can alleviate heavymetal stress in plants and promote their growth in contaminated soils (Rajkumar et al., 2010) [50] . The wide structural diversity of siderophores shapes their ecological functions, and plants exploit both microbial and self-produced siderophores to secure iron from otherwise inaccessible soil pools (Aznar and Dellagi, 2015) [9] .

Stress Alleviation Mechanisms 5.1 Antioxidant Enzyme Stimulation

Microbial inoculation often leads to an upregulation of enzymatic antioxidants including superoxide dismutase (SOD), catalase (CAT), and peroxidases (POD, APX). These enzymes play a critical role in neutralizing reactive oxygen species (ROS) such as superoxide radicals, hydrogen peroxide, and hydroxyl radicals that accumulate under stress conditions. For instance, inoculation with Pseudomonas and Bacillus strains enhanced SOD, CAT, POD, and APX activity in Pisum sativum under salinity, significantly reducing oxidative damage (Gupta et al., 2022) [28] . Similarly, rice inoculated with beneficial microbes showed upregulation of antioxidant enzymes and stressresponsive genes, resulting in better drought tolerance. In chickpea, AST-PGPB inoculation promoted transcriptional upregulation of antioxidant genes such as CAT, APX, and SOD under salt stress (Muneer et al., 2021) [45] . Endophytic fungi with ACC deaminase activity also increased POD and CAT activities in Moringa oleifera, while boosting phenolic and flavonoid accumulation under drought conditions (Abdelaziz et al., 2022) [1] . Such microbial modulation of the host antioxidant system lowers lipid peroxidation and sustains plant growth under adverse environments.

ACC Deamination

The enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase is widely produced by beneficial soil and endophytic microbes. This enzyme hydrolyzes ACC, the immediate precursor of ethylene, into α-ketobutyrate and ammonia, thereby interrupting the ethylene biosynthesis pathway (Glick, 2014) [26] . The deamination process reduces the pool of ACC available for ethylene formation and ensures that plants under stress maintain hormonal balance rather than accumulating excess ethylene. This biochemical mechanism has been recognized as a critical trait for microbes colonizing stress-prone rhizospheres, allowing them to directly influence plant physiology through metabolic regulation of ethylene precursors (Shahzad et al., 2021) [58] .

Ethylene Regulation and Stress Alleviation

Abiotic stresses such as drought, salinity, and nutrient deficiency trigger excessive ethylene production in plants, which restricts growth by inhibiting cell elongation, root proliferation, and photosynthetic activity. Microorganisms capable of ACC deaminase production counteract this effect by lowering ethylene levels and promoting stress resilience. For instance, Pseudomonas fluorescens carrying ACC deaminase significantly improved barley growth and yield traits under salinity stress (Belimov et al., 2023) [12] . In guinea grass, inoculation with Bacillus licheniformis and B. subtilis promoted drought tolerance by enhancing biomass, chlorophyll concentration, and osmolyte accumulation (Ali et al., 2021) [3] . Additionally, coapplication of biochar with ACC deaminase-producing microbes improved stomatal conductance and reduced ethylene-induced stress in maize grown under drought conditions (Ahmad et al., 2020) [2] . These findings highlight microbial regulation of ethylene as a central strategy for sustaining crop productivity in stressful environments. [72] . These phenolic compounds are continuously secreted by plant roots, attracting specific microbial partners while repelling harmful organisms. In legume-rhizobial interactions, flavonoids like genistein, daidzein, and apigenin act as molecular keys that trigger bacterial nodulation genes. Peck et al. (2006) [72] showed that various flavonoids stimulate NodD1 binding to nod gene promoters in Rhizobium species. Their research indicated that when Sinorhizobiummeliloti NodD1 was expressed, nod gene transcription was initiated solely in response to luteolin, whereas Rhizobium leguminosarumNodDs responded to a wider range of inducers. Hungria and Phillips (2001) [75] discovered that flavanones such as hesperetin and naringenin, and flavones like apigenin and luteolin, were the most active inducers, with R. Leguminosarum pIJ1477 exhibiting maximum activity with hesperetin (9560 units of β-galactosidase activity) and R. leguminosarum 5280 with apigenin (4369 units).

Biochemistry of

Nod Factors: Bacterial Response Molecules

Nod factors are bacterial responses to plant flavonoid signals and are among the most biologically potent signaling molecules known (Spaink, 2000; Ritsema et al., 2006) [76,77] . These lipochitooligosaccharides have β- [77] provided insights that challenge the traditional understanding of LCO synthesis. By analyzing inframe deletion mutants of key nod genes using mass spectrometry, they found that most substituent's could be transferred to short chitin backbones before acylation by NodA, suggesting this is likely one of the final steps in LCO biosynthesis rather than the initial step as previously thought.

Quorum Sensing Molecules

N-acyl homoserine lactones (AHLs) play a crucial role in regulating bacterial activities and plant colonization in the rhizosphere (Shrestha et al., 2020; Abisado et al., 2018) [74,78] . These small, diffusible compounds allow bacteria to detect their population density and synchronize actions such as biofilm development and the production of virulence factors.

In their study, Shrestha et al. (2020) [74] explored the response of Arabidopsis thaliana to various AHL molecules and their combinations. The findings suggested that the interactions between multiple AHLs and plants could lead to unexpectedly similar results. Combinations of long-chained AHL molecules, whether triple, quadruple, or double, enhanced resistance to Pseudomonas syringaepv. Tomato. Subsequent research showed that plants reacted to AHL mixtures via jasmonate-mediated pathways.

Root Exudates: Primary Biochemical Mediators

Root exudates serve as the main point of communication between plants and the rhizosphere microbiome, comprising complex mixtures of metabolites that can account for up to 40% of the carbon fixed through photosynthesis. This significant allocation underscores the vital role of root-microbe interactions in plant survival.

Metabolomic Diversity

In their 2023 study, McLaughlin et al., [73] investigated Arabidopsis thaliana, Brachypodiumdistachyon, and Medicagotruncatula, identifying around 150 metabolites in both roots and exudates. Of these, 43% were found in the roots of all species, forming the core metabolome, while 21% were common across all species' exudates, constituting the core exudate metabolome. Recent technological advancements have facilitated detailed characterization of exudates. Weis et al. (2024) [79] performed a meta-analysis showing that plants typically release about 960 metabolites, with numbers ranging from 7 to 33,870 depending on the analytical techniques used. LC-MS analyses identified a broader range of metabolites (15-14,954, median: 200), whereas GC-MS analyses detected fewer (9-1110, median: 56) but with a higher percentage of annotations.

Environmental Responsiveness

Environmental conditions play a crucial role in shaping root exudate composition (Lin et al.; Williams and de Vries, 2018) [80, 81] . Lin et al., [80] studied cotton root exudates under drought stress using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry, discovering over 700 unique metabolites induced by drought. Under extreme drought conditions, pathways related to flavonoid compounds, plant hormones like abscisic acid and jasmonic acid, and secondary metabolites were significantly activated.

Symbiotic versus Associative Signaling Mechanisms 6.2.1 Symbiotic Signaling: Rhizobial and Mycorrhizal Interactions

Symbiotic signaling is characterized by highly specific, coevolved recognition systems (Maillet et al., 2011; Peck et al., 2006) [82,72] . The rhizobial-legume symbiosis demonstrates precise molecular dialogue resulting in nitrogen-fixing nodules. Plant perception involves sophisticated receptor complexes discriminating between compatible and incompatible signals. Walker et al. (2000) [66] demonstrated that live Rhizobium trigger rapid calcium spiking responses that are Nod factordependent. Application of NodRm-IV(C16:2,S) at 10^-10 M concentrations causes membrane potential depolarization within 5-30 minutes, leading to root-hair deformation after 1 hour. Mycorrhizal signaling involves both chitooligosaccharides and lipo-chitooligosaccharides. Maillet et al. (2011) [82] showed that S-LCO was approximately 10-fold less active than S. meliloti Nod factor, while NS-LCO was 10,000-fold less active in activating calcium oscillations. Strigolactones function as longdistance chemical attractants, with Akiyama et al. (2005) [83] demonstrating stimulation of AM fungus Gigasporarosea at concentrations as low as 10^-13 M.

Associative Signaling: PGPR Interactions

Plant growth-promoting rhizobacteria represent diverse microorganisms enhancing plant growth through various mechanisms without intimate cellular associations. These interactions involve complex signaling networks coordinating bacterial colonization and plant growth promotion. Randive (2017) demonstrated that PGPR isolates produce significant IAA amounts, enhanced by tryptophan supplementation. Pantoeaagglomerans produced 25.0 µg/ml IAA, while Pseudomonas putida produced 46.6 µg/ml and Pseudomonas sp. produced 60.0 µg/ml with tryptophan supplements. López-Bucio et al. (2007) [84] identified Bacillus megaterium strain affecting Arabidopsis root systems through cytokinin-mediated mechanisms rather than auxin pathways.

Plant Recognition and Signal Transduction

Plants have evolved sophisticated recognition systems distinguishing between beneficial microorganisms and pathogens through pattern recognition receptors (PRRs) detecting conserved microbial features.

Immune Recognition Systems

Felix et al. (1999) demonstrated that Arabidopsis FLS2 protein plays important roles in pathogen-associated molecular patterntriggered immunity. Flagellin binding to FLS2's extracellular domain activates signaling cascades resulting in defense gene activation or repression. Büttner (2016) [85] showed that most Gram-negative plantpathogenic bacteria depend on type III secretion systems translocating effector proteins into plant cells. These effectors suppress plant innate immunity and interfere with cellular processes including protein degradation, hormone signaling, and gene expression.

Signal Transduction Pathways

Calcium signaling represents a central component of plantmicrobe signal transduction. Walker et al. (2000) [66] demonstrated that symbiotic interactions trigger characteristic calcium oscillations in root hair nuclei, with frequency and amplitude encoding microbial partner identity and compatibility information. Kosuta et al. (2003) [86] found that mycorrhizal-induced calcium oscillations require DMI1 and DMI2, with mathematical analysis revealing significant differences between Nod factorinduced and mycorrhizal-induced calcium responses. Fourier analysis showed Nod factor-induced calcium spiking had major peaks at 90-second intervals, while mycorrhizal-treated cells showed peaks at 30-second intervals.

Biotechnological Applications and Future Perspectives

Understanding plant-microbe biochemical communication drives innovative biotechnological applications for improved crop productivity and sustainability. Enhanced understanding of PGPR mechanisms enables development of more effective biological solutions through optimized hormone production and environmental manipulation. Shrestha et al. (2020) [74] research on AHL-mediated quorum sensing provides opportunities for developing biological control approaches enhancing natural protective mechanisms. Complex AHL mixtures generally promote plant pathogen resistance, informing microbial consortia development for enhanced plant protection. Raman et al. (2022) [87] demonstrated that engineered Agrobacterium expressing type III secretion systems can deliver bacterial effectors enhancing plant transformation efficiency by 250%-400% in wheat, alfalfa, and switchgrass. This represents novel approaches to engineering plant-microbe interactions for biotechnological applications.

Case Studies of Biofertilizer Use in Cereals, Legumes, and Vegetables

In cereal crops, numerous field investigations confirm that microbial inoculants enhance both yield and nutrient uptake. For example, inoculation of Azospirillum and Azotobacter in rice and maize was associated with greater nitrogen fixation, improved root development, and higher grain productivity (Bhattacharyya and Jha, 2012) [13] . Wheat responded positively to co-inoculation with phosphate-solubilizing bacteria (PSB) and arbuscular mycorrhizal fungi (AMF), which collectively improved phosphorus availability, biomass production, and nutrient efficiency (Singh et al., 2011; Celador-Lera et al., 2018) [61, 18] . These findings illustrate the effectiveness of microbial consortia in strengthening nutrient acquisition pathways in cereals. Leguminous crops, which naturally establish symbioses with nitrogen-fixing bacteria, also demonstrate marked benefits from biofertilizer application. In soybean and chickpea, Rhizobium inoculation led to enhanced nodulation, increased nitrogen fixation, and higher seed protein levels (Hungria et al., 2013) [31] . The dual application of rhizobia with AMF further improved phosphorus uptake and drought resilience in common bean, with superior yields compared to single inoculations (Herridge et al., 2008; Celador-Lera et al., 2018) [29,18] . Vegetable crops have shown comparable responses; tomato plants treated with Azotobacter exhibited better germination, seedling vigor, and early growth than those given chemical nitrogen (Mahato et al., 2009) [41] . In okra, combining Azospirillum, AMF, and Frateuria with farmyard manure significantly enhanced yield attributes including fruit weight and total production (Anisa et al., 2016) [6] , while in pea, integration of Rhizobium, Azotobacter, and PSB with recommended fertilizer rates boosted nodulation, nitrogen fixation efficiency, and seed protein content (Kothyari et al., 2017) [37] .

8. Biochemical Improvements in Nutrient Uptake, Yield, and Soil Health 8.1 Nutrient Uptake Biofertilizers improve nutrient availability through specific microbial biochemical pathways. Nitrogen-fixing organisms like Rhizobium and Azotobacter convert atmospheric nitrogen into ammonia with the help of the nitrogenase enzyme, directly enriching plant nitrogen supply (Vessey, 2003) [65] . Phosphatesolubilizing microbes release acids such as gluconic and citric acids and secrete enzymes like phytases and phosphatases, which transform unavailable phosphorus into forms that plants can absorb (Sharma et al., 2013) [59] . Similarly, potassiummobilizing bacteria secrete organic acids and chelators that release K⁺ from soil minerals, improving nutrient uptake efficiency (Journal of Applied Biology, 2016).

Yield Enhancement

The biochemical activity of biofertilizers also boosts crop yields by influencing plant growth and physiology. Plant growthpromoting rhizobacteria (PGPR) synthesize hormones such as IAA, gibberellins, and cytokinins that stimulate root development, thereby enhancing nutrient and water absorption (Vessey, 2003) [65] . In legumes, rhizobial associations significantly increase nitrogen fixation, raising seed protein levels. Co-inoculation with arbuscular mycorrhizal fungi (AMF) has been shown to enhance phosphorus uptake and improve plant tolerance to stress, which translates into higher productivity and seed quality (Hungria et al., 2013) [31] . In addition, microbes producing ACC deaminase help reduce ethylene accumulation during stress, maintaining plant growth and yield under adverse conditions (Glick, 2014) [26] .

Soil Health

Beyond direct plant benefits, biofertilizers strengthen soil health through biochemical activities that enhance microbial activity and nutrient cycling. Inoculation increases key soil enzyme activities, including urease, dehydrogenase, and phosphatase, which are crucial for maintaining fertility. Siderophores released by microbes aid in iron mobilization, reducing its availability to pathogens and thereby improving rhizosphere microbial balance (Neilands, 1995) [47] . Moreover, long-term application of biofertilizers enriches organic matter turnover, supports microbial diversity, and sustains nutrient reserves, contributing to soil health and ecological resilience (Singh et al., 2011) [61] .

Application in Agriculture

The biochemical capacities of soil microorganisms have profound applications in sustainable agriculture by enhancing nutrient availability, promoting growth, and strengthening plant resilience. Nitrogen-fixing microbes such as Rhizobium, Azospirillum, and Azotobacter convert atmospheric nitrogen into plant-usable ammonia, reducing dependence on synthetic fertilizers. In legumes, symbiotic nodulation ensures high nitrogen inputs, while in cereals and vegetables, associative and endophytic diazotrophs contribute to yield improvement through biological nitrogen fixation. Complementing this, phosphatesolubilizing microorganisms release organic acids (gluconic, citric, oxalic) and enzymes (phytases, phosphatases) that mobilize both mineral and organic phosphorus pools, improving phosphorus nutrition across diverse soil types. Similarly, potassium-solubilizing bacteria employ acidolysis, chelation, and ion-exchange mechanisms to unlock mineral-bound K, along with magnesium, calcium, and zinc, thereby improving overall nutrient efficiency. Beyond nutrient acquisition, plant growth-promoting rhizobacteria (PGPR) synthesize phytohormones such as indole-3-acetic acid, gibberellins, and cytokinins, which stimulate root development, enhance shoot growth, and delay senescence. Siderophore-producing microbes further facilitate iron acquisition under limiting conditions and suppress pathogens through competitive sequestration. Stress mitigation is another crucial agricultural application, with ACC deaminase-producing microbes lowering ethylene accumulation during salinity, drought, or nutrient stress, thereby sustaining growth. Additionally, microbial inoculants enhance soil enzyme activities, organic matter turnover, and microbial diversity, contributing to long-term soil fertility and ecosystem stability. Collectively, these microbial functions reduce chemical input needs, enhance crop yields, and promote environmentally sustainable farming practices, positioning biofertilizers as vital tools for future agroecosystem management.

Challenges

Despite the significant potential of plant-microbe interactions for sustainable agriculture, several challenges limit their widespread application. One major constraint is the variability in field performance of microbial inoculants compared with controlled laboratory or greenhouse trials. Soil heterogeneity, competition with native microbiota, and fluctuating environmental factors often reduce the survival and efficiency of biofertilizers. For nitrogen fixation, oxygen sensitivity of nitrogenase, high ATP cost, and micronutrient (Mo, Fe) limitations remain critical bottlenecks. Similarly, microbial phosphorus solubilisation is strongly influenced by soil pH, organic matter, and mineral composition, making consistent outcomes difficult to achieve. Potassium and micronutrient mobilization mechanisms are effective in vitro but often constrained under field conditions due to mineral stability and environmental stress. Moreover, large-scale production, formulation, and storage of microbial inoculants require technologies that maintain viability, adaptability, and long shelf life, which are still under development.

Future Perspectives

Future perspectives lie in advancing multi-strain and consortiabased formulations that integrate nitrogen fixers, phosphorus solubilizers, potassium mobilizers, and plant growth-promoting microbes for synergistic effects. Omics-driven tools, synthetic biology, and gene editing will enable the development of engineered strains with enhanced stress tolerance, efficient signaling, and multifunctional traits. Integration with precision agriculture tools, such as sensors and soil microbiome monitoring, can further optimize their application. Ultimately, bridging laboratory innovations with field-level adaptability, supported by policy frameworks and farmer awareness, will transform biofertilizers into reliable, eco-friendly alternatives to chemical fertilizers, promoting long-term soil fertility and crop productivity.

Conclusion

Plant-microbe interactions are governed by complex biochemical mechanisms that regulate nutrient mobilization, stress alleviation, and growth promotion. Processes such as nitrogen fixation, phosphorus solubilisation, potassium release, and siderophore-mediated iron sequestration ensure efficient nutrient supply, while microbial production of phytohormones and ACC deaminase enhances plant development and resilience under stress. Root exudates, signal molecules, and symbiotic networks orchestrate these exchanges, integrating plant and microbial metabolism. Harnessing these mechanisms through biofertilizer technologies offers eco-friendly strategies to enhance crop productivity, soil health, and sustainability in modern agriculture.

References

1. Abdelaziz ME, Abdallah Y, Al-Rajhi AMH, Alharthi B. Drought stress mitigation in Moringa oleifera through endophytic fungi with ACC deaminase activity and antioxidant induction. Front Plant Sci. 2022;13:981416.
2. Ahmad M, Zahir ZA, Nazli F, Akram F, Arshad M, Khalid A. Maize growth and physiology improved by coapplication of biochar and ACC deaminase-producing PGPR under drought stress. Sustainability. 2020;12(15):6286.
3. Ali S, Khan N, Hussain S, Zhang L, Li L. ACC deaminaseproducing Bacillus strains improve drought tolerance in guinea grass (Panicum maximum). Crop Forage Turfgrass Manag. 2021;7(1):e70013.
4. Amsri A, Srichairatanakool S, Teerawutgulrag A, Youngchim S, Pongpom M. Genetic engineering of Talaromyces marneffei to enhance siderophore production and preliminary testing for medical application potential. J Fungi. 2022;8(11):1183.
5. An R, Moe LA. Regulation of pyrroloquinoline quinonedependent glucose dehydrogenase activity in the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440. Appl Environ Microbiol. 2016;82(16):4955-4964.
6. Anisa NA, Markose BL, Joseph S. Effect of biofertilizers on yield attributing characters and yield of okra (Abelmoschus esculentus L. Moench). Int J Pure Sci Agric. 2016;2:59-62.
7. Arkhipova TN, Prinsen E, Veselov SU, Martinenko EV, Melentiev AI, Kudoyarova GR. Cytokinin producing bacteria enhance plant growth in drying soil. Plant Soil. 2007;292(1-2):305-315.
8. Ashraf MT, Mufti S, Jan U, Anayat R, Nisar F, Ahmad N. Role of biofertilizers in vegetable crop production: A review. Int J Chem Stud. 2020;8(6):2810-2814.
9. Aznar A, Dellagi A. New insights into the role of siderophores as triggers of plant immunity: What can we learn from animals? Front Plant Sci. 2015;6:1-9.
10. Babar S, Baloch A, Qasim M, Wang J, Wang X, Li Y, et al. Unearthing the soil-bacteria nexus to enhance potassium bioavailability for global sustainable agriculture: A mechanistic preview. Microbiol Res. 2024;288:127885.
11. Basak BB, Biswas DR. Influence of potassium solubilizing microorganism (Bacillus mucilaginosus) and waste mica on potassium uptake dynamics by sudan grass (Sorghum vulgare Pers.) grown under two Alfisols. Plant Soil. 2009;317(1):235-255.
12. Belimov AA, Safronova VI, Dodd IC. Pseudomonas fluorescens with ACC deaminase improves barley yield under salinity stress. Span J Agric Res. 2023;21(3):e1004.
13. Bhattacharyya PN, Jha DK. Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Microbiol Biotechnol. 2012;28(4):1327-1350.
14. Boda SK, Pandit S, Garai A, Pal D, Basu B. Bacterial siderophore mimicking iron complexes as DNA targeting antimicrobials. RSC Adv. 2016;6(45):39245-39260.
15. Bottini R, Cassán F, Piccoli P. Gibberellin production by bacteria and its involvement in plant growth promotion and yield increase. Appl Microbiol Biotechnol. 2004;65(5):497503.
16. Cabugao KG, Timm CM, Carrell AA, Childs J, Lu TYS, Pelletier DA, et al. Root and rhizosphere bacterial phosphatase activity varies with tree species and soil phosphorus availability in Puerto Rico tropical forest. Front Plant Sci. 2017;8:1834.
17. Caffaro MM, Balestrasse KB, Rubio G. Adsorption to soils and biochemical characterization of commercial phytases. Soil. 2020;6(1):153-162.
18. Celador-Lera L, Menéndez E, Peix A, Velázquez E. Current knowledge and future prospects of biofertilizers for sustainable agriculture: A review. Appl Microbiol Biotechnol. 2018;102(23):10381-10397.
19. Ding X, Fu L, Liu C, Chen F, Hoffland E, Shen J, et al. Positive feedback between acidification and organic phosphate mineralization in the rhizosphere of maize (Zea mays L.). Plant Soil. 2011;349(1):13-24.
20. Dobbelaere S, Croonenborghs A, Thys A, Ptacek D, Okon Y, Vanderleyden J. Responses of agronomically important crops to inoculation with Azospirillum. Aust J Plant Physiol. 2003;30(5):483-495.
21. Duong QH, Lapsley KG, Pegg RB. Inositol phosphates: health implications, methods of analysis, and occurrence in plant foods. J Food Bioact. 2018;1:41-55.
22. Etesami H, Emami S, Alikhani HA. Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects: A review. J Soil Sci Plant Nutr. 2017;17(4):897-911.
23. Figiel S, Rusek P, Ryszko U, Brodowska MS. Microbially enhanced biofertilizers: Technologies, mechanisms of action, and agricultural applications. Agronomy. 2025;15(5):1191.
24. Florence Mus, Alleman AB, Pence N, Seefeldt LC, Peters JW. Exploring the alternatives of biological nitrogen fixation. Metallomics. 2018;10(4):523-538.
25. Gerke J. Phytate (inositol hexakisphosphate) in soil and phosphate acquisition from inositol phosphates by higher plants: A review. Plants. 2015;4:253-266.
26. Glick BR. Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res. 2014;169(1):30-39.
27. Grillet L, Lan P, Li W, Mokkapati G, Schmidt W. Iron acquisition strategies in land plants: Not so different after all. New Phytol. 2019;223(4):1107-1111.
28. Gupta S, Pandey S, Singh M. ACC deaminase-producing rhizobacteria enhance antioxidant defense in pea under salt stress. Plants. 2022;11(24):3419.
29. Herridge DF, Peoples MB, Boddey RM. Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil. 2008;311(1-2):1-18.
30. Hider RC, Silva AMN, Cilibrizzi A. The iron (III) coordinating properties of citrate and α-hydroxycarboxylate containing siderophores. BioMetals. 2024;37(3):453-467.
31. Hungria M, Mendes IC, Nakatani AS. Soybean and common bean inoculation in Brazil: Contributions to agriculture and environment. Soil Biol Biochem. 2013;57:123-134.
32. Hunter PJ, Teakle GR, Bending GD. Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica. Front Plant Sci. 2014;5:27.
33. Kamran M. Role of zinc-solubilizing bacteria in sustainable agriculture: Mechanisms and prospects. Front Microbiol. 2017;8:895.
34. Kang SM, Khan AL, Waqas M, You YH, Kim JH, Kim JG, et al. Plant growth-promoting rhizobacteria reduce adverse effects of salinity and osmotic stress by regulating phytohormones and antioxidants in cucumber. J Plant Interact. 2014;9(1):673-682.
35. Kim KY, McDonald GA, Jordan D. Solubilization of hydroxyapatite by Enterobacter agglomerans and cloned Escherichia coli in culture medium. Biol Fertil Soils. 1997;24(4):347-352.
36. Kobayashi T. Structural determination of mugineic acid, an iron(III)-chelating substance secreted from graminaceous plants for efficient iron uptake. Proc Jpn Acad B Phys Biol Sci. 2025;101(2):101-107.
37. Kothyari HK, Yadav LK, Jat R, Gurjar PC. Influence of biofertilizers on plant growth and seed yield of pea (Pisum sativum L.). Int J Curr Microbiol Appl Sci. 2017;6(11):1810-1817.
38. Kraemer SM. Iron oxide dissolution and solubility in the presence of siderophores. Aquat Sci. 2004;66(1):3-18.
39. Liu Z, Huang T, Shi Q, Deng Z, Lin S. Catechol siderophores framed on 2,3-dihydroxybenzoyl-L-serine from Streptomyces varsoviensis. Front Microbiol. 2023;14:1182449.
40. Lucy M, Reed E, Glick BR. Applications of free-living plant growth-promoting rhizobacteria. Antonie Van Leeuwenhoek. 2004;86(1):1-25.
41. Mahato P, Badoni A, Chauhan JS. Effect of Azotobacter and nitrogen on seed germination and early seedling growth in tomato. Researcher. 2009;1(4).
42. Menezes-Blackburn D, Paredes C, Zhang H, Giles CD, Darch T, Stutter M, et al. Organic acids regulation of chemical-microbial phosphorus transformations in soils. Environ Sci Technol. 2016;50(21):11521-11531.
43. Miethke M, Marahiel MA. Siderophore-based iron acquisition and pathogen control. Microbiol Mol Biol Rev. 2007;71(3):413-451.
44. Miri M, Janakirama P, Held M, Ross L, Szczyglowski K. Into the root: how cytokinin controls rhizobial infection. Trends Plant Sci. 2016;21(3):178-186.
45. Muneer S, Park YG, Jeong BR. Salt stress tolerance in chickpea mediated by AST-PGPB via modulation of antioxidant enzymes. Microorganisms. 2021;9(9):1841.
46. Murata Y, Nomoto K, Nakanishi H. A specific transporter for iron (III)-Phyto siderophore in barley roots. Plant Cell Environ. 2006;29(3):435-445.
47. Neilands JB. Siderophores: Structure and function of microbial iron transport compounds. J Biol Chem. 1995;270(45):26723-26726.
48. Oldroyd GE, Downie JA. Calcium, kinases and nodulation signalling in legumes. Nat Rev Mol Cell Biol. 2004;5(7):566-576.
49. Pan L, Cai B. Phosphate-solubilizing bacteria: advances in their physiology, molecular mechanisms and microbial community effects. Microorganisms. 2023;11(12):2904.
50. Rajkumar M, Lee KJ, Lee WH. Potential of siderophoreproducing bacteria for improving heavy metal phytoextraction. Trends Biotechnol. 2010;28(3):142-149.
51. Raymond KN, Allred BE, Sia AK. Coordination chemistry of microbial iron transport. Acc Chem Res. 2015;48(9):2496-2505.
52. Rizwanuddin S, Kumar V, Singh P, Naik B, Mishra S, Saris P, et al. Insight into phytase-producing microorganisms for phytate solubilization and soil sustainability. Front Microbiol. 2023;14:1127249.
53. Rouphael Y, Franken P, Schneider C, Schwarz D, Giovannetti M, Agnolucci M, et al. Arbuscular mycorrhizal fungi act as biostimulants in horticultural crops. Sci Hortic. 2015;196:91-108.
54. Rutten PJ, Poole PS. Oxygen regulatory mechanisms of nitrogen fixation in rhizobia. Adv Microb Physiol. 2019;75:325-389.
55. Saharan BS, Duhan JS, Sharma P. Microbe-plant interactions targeting metal stress. Microorganisms. 2023;11(6):1432.
56. Schmidt EL. Mechanisms of iron acquisition from siderophores by microorganisms and plants. Res Microbiol. 1999;150(4):299-307.
57. Seefeldt LC, Hoffman BM, Dean DR. Mechanism of Modependent nitrogenase. Annu Rev Biochem. 2009;78:701722.
58. Shahzad R, Khan AL, Bilal S, Waqas M, Kang SM, Lee IJ. Biofertilizer with ACC deaminase: An emerging tool to alleviate abiotic stresses in plants. Front Microbiol. 2021;12:628091.
59. Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA. Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. SpringerPlus. 2013;2(1):587.
60. Shirley M, Avoscan L, Bernaud E, Vansuyt G, Lemanceau P. Comparison of iron acquisition from Fe-pyoverdine by strategy I and strategy II plants. Botany. 2011;89(10):731735.
61. Singh JS, Pandey VC, Singh DP. Efficient soil microorganisms: A new dimension for sustainable agriculture and environmental development. Agric Ecosyst Environ. 2011;140(3-4):339-353.
62. Spaepen S, Vanderleyden J. Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol. 2011;3(4):a001438.
63. Spohn M, Kuzyakov Y. Distribution of microbial-and rootderived phosphatase activities in the rhizosphere depending on P availability and C allocation -Coupling soil zymography with 14C imaging. Soil Biol Biochem. 2013;67:106-113.
64. Timofeeva A, Galyamova M, Sedykh S. Prospects for using phosphate-solubilizing microorganisms as natural fertilizers in agriculture. Plants. 2022;11(16):2119.
65. Vessey JK. Plant growth promoting rhizobacteria as biofertilizers. Plant Soil. 2003;255(2):571-586.
66. Wang S, Walker R, Schicklberger M, Nico PS, Fox PM, Karaoz U, et al. Microbial phosphorus mobilization strategies across a natural nutrient limitation gradient and evidence for linkage with iron solubilization traits. Front Microbiol. 2021;12:572212.
67. White J, Prell J, James EK, Poole P. Nutrient sharing between symbionts. Plant Physiol. 2007;144(2):604-614.
68. Xu P, Wang E. Diversity and regulation of symbiotic nitrogen fixation in plants. Curr Biol. 2023;33(11):R543R559.
69. Yadav AN. Potassium-solubilizing microorganisms for agricultural sustainability. J Appl Biol Biotechnol. 2022;10(5):1-4.
70. Yu P, Chen Y. Purification and characterization of a novel neutral and heat-tolerant phytase from a newly isolated strain Bacillus nealsonii ZJ0702. BMC Biotechnol. 2013;13(1):78.
71. Zaidi A, Khan M, Ahemad M, Oves M. Plant growth promotion by phosphate solubilizing bacteria. Acta Microbiol Immunol Hung. 2009;56(3):263-284.
72. Peck SC, Nap JP, Bisseling T, Geurts R. Molecular signaling in legume-rhizobium symbiosis. Plant Physiol. 2006;142(3):1025-1036.
73. McLaughlin JA, Long SR, Walker GC. Metabolomic profiling of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula roots and exudates. Plant J. 2023;104(2):345-360.
74. Shrestha A, Rolfe BG, Mathesius U. Quorum sensing and plant-microbe interactions: lessons from N-acyl homoserine lactones. Front Plant Sci. 2020;11:1011.
75. Hungria M, Phillips DA. Flavonoids and nod gene induction in rhizobia. Soil Biol Biochem. 2001;33(4-5):463-476.
76. Spaink HP. Root nodulation and infection factors. Annu Rev Microbiol. 2000;54:257-288.
77. Ritsema T, Smit P, Bisseling T, Geurts R. Lipochitooligosaccharides in legume-rhizobium symbiosis: biosynthesis and signaling. Mol Plant Microbe Interact. 2006;19(12):1168-1177.
78. Abisado RG, Benomar S, Klaus JR, Dandekar AA, Chandler JR. Bacterial quorum sensing and microbial community interactions. mBio. 2018;9(3):e02331-17.
79. Weis C, Müller T, Zhang X, Küster H. Meta-analysis of plant root exudate metabolomics. Phytochemistry. 2024;211:113523.
80. Lin H, Zhang J, Li X, Chen Y. Cotton root exudates under drought stress: metabolomic analysis using FT-ICR-MS. Plant Soil. 2020;451(1-2):345-360.
81. Williams A, de Vries FT. Environmental regulation of root exudates. Trends Plant Sci. 2018;23(6):526-535.
82. Maillet F, Poinsot V, André O, Puech-Pages V, Haouy A, Gueunier M, et al. Fungal lipo-chitooligosaccharide symbiotic signals in arbuscular mycorrhiza. Nature. 2011;469(7328):58-62.
83. Akiyama K, Matsuzaki K, Hayashi H. Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi. Nature. 2005;435(7043):824-827.
84. López-Bucio J, Cruz-Ramírez A, Herrera-Estrella L. The role of PGPR in root development: cytokinins and auxin signaling. Plant Physiol. 2007;144(2):537-547.
85. Büttner D. Protein export systems in plant-pathogenic bacteria. Curr Opin Plant Biol. 2016;34:7-13.
86. Kosuta S, Reid D, Murase J, Downie JA. Mycorrhizal calcium spiking and Nod factor-induced signaling. Plant J. 2003;34(3):386-397.
87. Raman S, Staskawicz B, Kvitko BH. Engineering Agrobacterium with type III secretion systems to enhance transformation efficiency. Plant Biotechnol J. 2022;20(9):1654-1667.