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Review

Effects of Root Exudates on Ecological Function and Nitrogen Utilization Strategy of Orchard Multi-Planting System

by
Yufeng Li
1,2,†,
Yu Zhang
1,3,4,5,†,
Qishuang He
1,2,
Shanshan Liu
1,2,
Fei Ren
1,3,4,5 and
Anxiang Lu
1,2,*
1
Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
2
Beijing Key Laboratory of Environmental Monitoring in Agricultural Product Production Areas, Institute of Quality Standards and Testing Technology, Beijing 100097, China
3
Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing 100093, China
4
Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing 100093, China
5
Key Laboratory of Urban Agriculture (North China), Institute of Forestry and Pomology, Beijing 100093, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Agronomy 2025, 15(9), 2173; https://doi.org/10.3390/agronomy15092173
Submission received: 7 July 2025 / Revised: 20 August 2025 / Accepted: 27 August 2025 / Published: 12 September 2025
(This article belongs to the Special Issue Innovative Agricultural Inputs and Soil–Plant–Microbe Interactions for Sustainable Agronomy)
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Abstract

While root exudates play a crucial role in maintaining ecosystem balance and promoting plant growth, existing research primarily focuses on single ecosystems (e.g., field crops), with systematic investigations of their ecological functions in compound cropping systems, particularly nitrogen (N) cycling mechanisms in orchard multi-cropping systems, remaining limited. This review focuses on the N impact mechanisms mediated by plant root exudates in orchard ecosystems, emphasizing how root exudates optimize soil N activation, absorption, and utilization efficiency by modulating rhizosphere processes (e.g., nitrogen mineralization, root architecture remodeling). Studies indicate that the changes in orchard ecosystem function mediated by organic acids and flavonoids root exudates can significantly reduce nitrogen loss risks and increase the soil nitrogen turnover rate by lowering pH-activated nutrients, balancing the C:N ratio, and immobilizing microbial communities. This process also involves the coordinated regulation of nitrification, denitrification, and microbial fixation. Future research should prioritize investigating the interaction networks and regulatory mechanisms between root exudates of associated orchard crops and N-fixing microorganisms. This research direction will provide a scientific basis for improving the N use efficiency in orchard crops, optimizing fertilizer reduction techniques, and reducing chemical fertilizer usage, providing significant implications for achieving sustainable agricultural development. The theoretical support offers important scientific and practical value for advancing green and sustainable agriculture.

1. Introduction

Root exudates, which are critical mediators of plant–soil ecosystem interactions, play a vital role in maintaining ecosystem equilibrium, promoting plant growth, and enhancing soil health [1,2,3]. These complex organic compounds, secreted by plant roots, primarily include low-molecular-weight organic acids, amino acids, sugars, phenolic compounds, and other secondary metabolites [4,5,6]. They directly participate in soil nutrient activation and cycling while also regulating the structure and function of soil microbial communities. Thereby, root exudates significantly influence plant development and soil ecosystem stability [7,8].
Research on root exudates has long centered on relatively simple ecosystems, primarily encompassing staple food (e.g., wheat, corn) [9,10] and key economic crops (e.g., soybeans, vegetables, herbaceous plants, and fruit trees) [11,12,13,14]. These investigations predominantly employ a dual-method framework integrating controlled laboratory experiments with in situ field observations to elucidate underlying mechanistic pathways. This approach has systematically revealed the critical regulatory functions of root exudates in (1) modifying the soil physical structure (e.g., enhancing the aggregate stability via polysaccharide secretion) [15]; (2) regulating nutrient availability (e.g., organic-acid-driven phosphorus solubilization) [16]; and (3) shaping microbial community dynamics (e.g., flavonoid-mediated enrichment of plant-growth-promoting rhizobacteria) [17]. Collectively, this work provides an important theoretical foundation and practical guidance for deeper insights into plant strategies for rhizosphere microenvironment regulation mediated by root exudates and their ecological adaptation mechanisms.
In specific crops such as buckwheat (Fagopyrum esculentum) and legumes (e.g., white lupin), root-secreted oxalate has been experimentally confirmed to chelate Fe/Al/Mn minerals via ligand-promoted dissolution, thereby enhancing their bioavailability [18]. This trait is particularly pronounced in phosphorus (P)-deficient soils but exhibits significant interspecific variation due to genetic regulation of organic acid biosynthesis (e.g., ALMT transporters in wheat). Concurrently, specific compounds within peanut root exudates, namely, amino acids and phenolic acids, inhibit the growth of soil-borne pathogens Ralstonia solanacearum and Fusarium moniliforme. This protective mechanism shields crops from disease infestation and contributes to the agricultural ecosystem health [19].
While significant advances have been made in understanding root exudates within single-planting systems, elucidating their role in mediating interspecies interactions via root exudation within multi-planting systems remains limited [20]. Multi-planting coexistence systems, particularly orchard-based systems, are characterized by complex interactions between root exudates from fruit trees and co-planted crops. These interactions generate a unique “cocktail effect” (e.g., synergistic enhancement of ecological functions beyond individual compounds) [21]. This effect not only regulates soil nutrient transformation dynamics but also profoundly impacts key N cycle processes by reshaping the soil microbial community structure and diversity, for example, enhancing diazotroph abundance while suppressing nitrifier activity.
Research specifically targeting root exudates in multi-planting orchard systems remains scarce and faces multiple persistent challenges. Three primary factors drive root exudates diversity: (i) plant-species-specific traits governing biosynthesis [22]; (ii) dynamic shifts across developmental stages [23]; and (iii) environmental modulation [24]. Such complexity creates two key analytical constraints: (1) methodological limitations in capturing transient exudate mixtures via untargeted metabolomics (average detection < 30% of actual diversity) and (2) obscured ecological interpretation due to interdependencies between exudate components and soil biotic feedbacks. Furthermore, plants interactions in these systems involve complex synergistic or antagonistic effects between root exudates from different species, collectively regulating the soil microbial community structure and function [25,26]. This intricacy not only increases the research difficulty but also complicates the accurate elucidation of root exudates’ ecological roles in a multi-planting orchard system.
In an orchard multi-planting system, the influence of root exudates on N cycling is particularly critical. As a key nutrient for plant growth, N transformation processes, including fixation, nitrification, and denitrification, are directly regulated by root exudates [27]. On one hand, organic carbon compounds within root exudates serve as an energy source for nitrifying bacteria (e.g., Variovorax and Sporocytophaga) and denitrifying bacteria (e.g., Dechloromonas), thereby modulating soil nitrification and denitrification rates and further altering N loss pathways and utilization efficiency [28,29]. On the other hand, root exudates from specific companion plants can stimulate the growth and activity of N-fixation rhizobia (e.g., Rhizobia), enhancing the biological N2 fixation efficiency and providing supplemental N sources for orchard ecosystems [30,31]. Additionally, by reshaping the soil microbial community structure and diversity, root exudates indirectly regulate the abundance and metabolic activity of N-cycling microorganisms, profoundly impacting the N balance in orchard ecosystems [14].
This review systematically elaborates on the regulatory mechanisms by which root exudates from food crops, oil crops, vegetables, and herbaceous plants modulate ecological functions in planting systems. It focuses on their roles in driving key processes such as soil physicochemical properties, plant traits, rhizosphere metabolite remodeling, and microbiome recruitment. Furthermore, the review explores how these regulatory mechanisms influence N utilization strategies in multi-planting systems involving fruit trees (woody, lianas, herbaceous species).

2. Root-Exudate-Mediated Improvements in Soil Properties

2.1. Soil Structure

Studies have demonstrated that root exudates ameliorate soil compaction properties and facilitate root penetration (Figure 1; Table 1). Laboratory-controlled studies on soil structure improvement by plant exudates reveal that soil penetration resistance (PR) gradually decreases with increasing Chia (Salvia hispanica) seed exudate concentration under simulated root-zone conditions (200–600 kPa axial stress, −50 kPa matric potential, 4 °C). Field validation remains pending [32]. Particularly under drought stress, increased soil porosity triggers plants to enhance root exudate (polysaccharides) release, thereby reducing gas diffusion in the soil [33], an effect also modulated by soil texture [15]. For instance, studies indicate that differences in penetration resistance under saturated versus unsaturated soil conditions manifest primarily through the non-equilibrium solute transport of nutrients in the soil [34]. Root exudates further influence the soil aggregate stability. Winter crops, particularly black oats (Avena strigosa), significantly enhance the soil structural stability through extensive root systems and organic matter inputs that promote aggregate formation. Conversely, in summer cropping systems, high-dose chemical fertilizers induce a negative correlation with structural stability, primarily by suppressing the microbial activity essential for binding soil particles and accelerating organic matter mineralization that destabilizes aggregates [35].
Root-exudate-mediated alterations in soil structure induced by companion crops affect nitrogen turnover efficiency in host plants (e.g., peach trees) (Figure 1; Table 1). Scandellari et al. [47] investigated nitrogen uptake and release dynamics in peach tree roots grown in coarse-textured (CT) and fine-textured (FT) soils. Sun et al. [36] studied 4-year-old “Ruiguang 33” (Prunus persica L.), examining the effects of root zone aeration on soil microbial communities and nitrogen nutrition. The study revealed that aeration treatment significantly increased the relative abundance of nitrogen-fixing microbes (Bradyrhizobium elkanii) and potassium-solubilizing microbes (Bacillus circulans), alongside elevated soil alkaline-hydrolyzable nitrogen content and total plant nitrogen content. Concurrently, improved porosity not only optimized the water-use efficiency in peach trees but also indirectly enhanced the leaf nitrogen content by promoting companion crop growth [48]. Based on a 22-year long-term positioning experiment in subtropical hilly areas, Li et al. [37] compared the impacts of different soil conservation measures on orchard soil quality. They found that legume-based biological measures significantly improved the Soil Quality Index (SQI) by enhancing soil aggregates, thereby maintaining the soil nutrient balance and aggregate stoichiometric stability.

2.2. Soil Nitrogen

Root exudates directly mediate nitrogen transformation by stimulating microbial activity [49] (Figure 1; Table 1). Amino-acid-containing root exudates directly influence soil nitrogen and exhibit the strongest priming effect (e.g., the rapid stimulation of soil organic carbon decomposition by 39–116% through microbial activation), followed by substances conducive to microbial growth, such as monosaccharides [5]. Significant differences exist in the correlations between different types of amino acids and soil nitrogen fractions. Through experimental research, Liu et al. [50] found that soil inorganic nitrogen content was positively correlated with serine (Ser) and isoleucine (Ile); soil organic nitrogen content showed positive correlations with glycine (Gly), alanine (Ala), and tyrosine (Tyr). The dynamics of microbially mediated nitrogen transformation are essentially driven by root exudates through regulating the balance of microbial carbon and nitrogen metabolism, thereby enabling nitrogen turnover and redistribution.
Organic acid-driven pH regulation serves as the primary chemical pathway for nitrogen activation. Based on a three-year monitoring study, Lin et al. [38] found that in Leymus chinensis-restored soil, organic acids (e.g., citric acid, oxalic acid) in root exudates significantly decreased the soil pH, thereby protonating mineral-bound phosphates and chelating metal cations (e.g., Fe3+, Al3+) through carboxyl groups, which solubilized insoluble P into plant-available orthophosphates (H2PO4−/HPO22−) and concurrently enhanced NH4+-N/NO3−-N bioavailability by 15–40% and 48–70%, respectively. Liu et al. [51] also reported that organic acid treatment markedly increased the gross nitrogen mineralization rate in soil. However, common root exudates typically contain metabolites including amino acids, organic acids, and monosaccharides; thus, the impact of single compounds on soil nitrogen should not be unilaterally considered. Zhang et al. [52] demonstrated that carbon additions stimulated the microbial assimilation of NH4+-N, while nitrogen additions promoted nitrification of NH4+-N in soil. As the C:N ratio of root exudates increased, the soil ammonium nitrogen content exhibited a significant declining trend.
Companion crops restore soil nitrogen pools and retention efficiency through synergistic interactions. Compared with clean tillage systems, they significantly increase soil carbon and nitrogen storage, with leguminous species exhibit demonstrating superior total nitrogen accumulation relative to non-leguminous species [53] (Figure 1; Table 1). Guo et al. [31] found that planting Vicia villosa in peach orchards significantly increased the soil total nitrogen, ammonium nitrogen, and nitrate nitrogen content compared with conventional black plastic film mulching. Research by Ma et al. [39] demonstrated that after cover crop establishment in apple orchards, nutrient content (including soluble organic carbon, microbial biomass carbon and nitrogen, alkaline dissolved nitrogen, nitrate nitrogen, and ammonium nitrogen) in the 0–20 cm soil layer increased by an average of >19.6%. Beyond augmenting the soil nitrogen input and mineralization rates, companion crops effectively reduced the nitrate concentration in surface soil of apricot orchards, thereby mitigating nitrogen leaching loss [54]. Soil nitrogen content significantly influences soil enzyme activities and promotes fruit tree growth, with this effect being particularly pronounced in the rhizosphere active zone (90–120 cm from tree trunks) [55]. Marañón et al. [56] observed in Mediterranean olive groves that companion cropping significantly elevated the decomposition rate of fallen leaves (87%), sustaining soil nutrient reserves. Overall, this mechanism operates through a “nitrogen fixation-nitrification inhibition-leaching mitigation” synergistic network formed by exudate–microbe interactions.

3. Root-Exudate-Mediated Improvements in Plant Traits

3.1. Root Architecture

In-depth investigation of the dynamic interactions between root exudates and root morphology provides crucial theoretical insights into plant underground mechanisms [57]. Li et al. [40] identified 10 compounds in cucumber root exudates exhibiting significant correlations with the root architecture (RSA). These compounds primarily comprise three types of saccharides (fructose, glucose, and sucrose), three types of organic acids (oxalic, malic, and citric acid), and four types of amino acids (aspartic, glutamic acid, glycine, and methionine). The sugar content demonstrated a positive correlation with the total root surface area, whereas organic acids and amino acids exhibited stronger associations with the root tip number (Figure 2; Table 1). This quantitative linkage critically informs orchard management through (i) predicting root foraging efficiency for subsoil nutrients; (ii) guiding companion crop selection; and (iii) optimizing organic amendment design. These exudate-mediated correlations play pivotal roles in plant–plant interactions. Studies demonstrate that plants perceive chemical signals from companion plant root exudates via root tips, translating these signals into morphological responses that adjust RSA (e.g., increased root length, altered branching angles) [58].
Plants regulate the root development of neighboring species through root exudate-mediated allelopathy. Eroglu et al. [59] observed that co-planting Amaranthus retroflexus and Fagopyrum esculentum (buckwheat) reduced the root tip numbers in buckwheat and significantly decreased the total root length, volume, surface area, tip count, and bifurcation frequency in A. retroflexus. This mutual inhibition stems from defensive metabolic reprogramming triggered by interspecific competition. Concurrently, 64 and 46 metabolites were upregulated in their respective root metabolomes. Treatment with buckwheat or A. retroflexus exudates further suppressed the root length and bifurcation in A. retroflexus seedlings, demonstrating that these exudates act as allelochemical signals mediating suppressive regulation of root development during interspecific competition (Figure 2; Table 1). Similarly, Yin et al. [60] reported that 6-methoxy-2-benzoxazolinone (MBOA), secreted by wheat roots in maize–wheat intercropping systems, reduced the maize root length by 37%. This exemplifies an adaptive root growth suppression strategy initiated by competitive C-N resource allocation in cereal intercropping systems.
Plants optimize their root system architecture through phenotypic plasticity to cope with competitive resource pressures [61]. Zhang et al. [41] demonstrated that maize (Zea mays) enhances the nitrogen absorption efficiency under heterogeneous nutrient conditions by increasing specific root length, surface area, root volume-to-dry mass ratio, and growth angle of the outermost crown roots (Figure 2; Table 1), representing an adaptive foraging-avoidance strategy against neighbor competition. Lecarpentier et al. [62] revealed that nitrogen-efficient plants exhibit greater lateral root density and thicker primary root diameters compared with nitrogen-inefficient plants, demonstrating an active adaptive response that maximizes resource acquisition capabilities through root investment in resource-competitive environments.
Root system architecture modifications in woody plants similarly adhere to interspecies interaction dynamics. de la Peña et al. [42] observed that nitrogen deficiency in oil palm (Elaeis guineensis) reduces the total root length, surface area, volume, rotation angle, solidity, and pore features, while increasing the surface angular frequency, these morphology shifts collectively represent a conservative resource-use strategy for stress tolerance. Fruit tree root systems also respond to nitrogen forms: Kang et al. [43] identified significant correlations between the branching intensity in pear (Pyrus) seedlings and the soil nitrogen profiles (total N, NH4+). Within orchard polyculture systems, this response fundamentally constitutes a co-adaptive phenomenon where fruit trees and intercrops coordinate nitrogen partitioning through signal-mediated root exudation (Figure 2; Table 1).

3.2. Aboveground Trait Improvement

Aboveground traits encompass the heritable morphological characteristics of stems, leaves, flowers, and other organs, serving as crucial phenotypic indicators for plant environmental adaptation. Wu et al. demonstrated that wheat root exudates significantly promote cucumber seedling growth [44]. Under nutrient stress, phosphorus-solubilizing root exudates not only enhance the phosphorus availability but also induce leaf morphological modifications conducive to nutrient conservation [63]. In pea (Pisum sativum) and neighboring companion plant interaction systems, strigolactones were confirmed as key signaling molecules mediating aboveground–belowground co-adaptation (Figure 2; Table 1). Wheeldon et al. [64] observed that pea seedlings sensitively detect strigolactones exuded by neighboring roots, triggering aboveground morphological responses to adapt to interspecific competition.
This aboveground trait improvement exhibits strong species specificity. Xu et al. [65] reported that mixed planting of phylogenetically close ryegrass (Lolium perenne) varieties advanced flowering time. Beyond morphology, root exudates profoundly influence the physiological and biochemical properties. Vengavasi et al. [45] observed that phosphorus-efficient soybean varieties exhibit higher photosynthetic rates, total chlorophyll, and carotenoid concentrations compared with phosphorus-inefficient counterparts. Lu et al. [66] identified metabolic differences in carbohydrates and amino acids within root exudates as the primary driver of photosynthetic divergence. Furthermore, Zhou et al. [67] confirmed that root exudates regulate transpiration by modulating amino acid metabolism.
The ratio of breast height to diameter in fruit trees exhibits a significant correlation with the soil C/N ratio, a relationship potentially mediated by the critical regulatory role of the crown projection area in soil nutrient cycling [68]. Mixed planting patterns profoundly influence soil nutrient dynamics. Research indicates that mixed forests of Prunus sibirica (apricot) and Robinia pseudoacacia (black locust) exhibit significantly higher soil total nitrogen concentrations than mixtures of P. sibirica and Amygdalus davidiana (peach), which was attributed to higher soil nitrogen mineralization rates induced by mixed litterfall [69].
Orchard mulching practices significantly regulate nitrogen cycling processes by optimizing tree physiological traits (Figure 2; Table 1). Yu et al. [46] demonstrated that natural grass cover in orchards enhances photosynthetic rates in apple leaves by increasing the total nitrogen (TN) and NH4+ concentrations in surface soil (0–40 cm) while elevating the leaf nitrogen content and improving fruit sugar metabolism. In arid regions, orchard coverage with Dactylis glomerata (orchard grass) converts surface evaporation into plant transpiration, with appropriate mowing regimes maintaining the soil moisture while minimizing negative impacts on the soil nitrogen content [70].

4. Rhizosphere Metabolite Remodeling Mediated by Root Exudates

4.1. Primary and Secondary Metabolites

Root exudates contain large amounts of primary and secondary metabolites, constituting highly complex mixtures of chemical effectors composed of diverse compounds, with their quantity and composition varying according to plant species and developmental stage [22]. For example, Arabidopsis root exudates primarily consist of 25 terpenoids; Cucurbitaceae root exudates are predominantly bitter triterpenoids; and Ginkgo root exudates exhibit greater diversity, including primary metabolites like amino acids and nucleotides, as well as secondary metabolites such as flavonoids and terpenes [71,72,73] (Figure 3). Significant varietal differences exist in the composition and secretory capacity of root exudates. Compared with Cappelli, Grecale and Claudio exhibit significantly higher root exudation capacity [74]. This genotypic divergence stems from contrasting plant resource-use strategies: (1) carbon allocation patterns differ significantly, with modern cultivars Grecale and Claudio prioritizing carbon investment into root exudates (e.g., sugars comprising 87.3% of total metabolites), whereas the old cultivar Cappelli allocates resources toward structural root growth; (2) microbial recruitment mechanisms, where high exudation in Grecale/Claudio enriches rhizosphere microbial diversity (bacterial OTUs: 15.3 and 13.7 vs. Cappelli’s 12.7), facilitated by chemoattractants like homoserine (2346.9 ng·g−1 in Grcale).
Root exudates not only induce remodeling of metabolites in their own rhizosphere but also influence the metabolite composition of neighboring plants. In the soybean/maize intercropping system, researchers identified 41 and 39 unique root exudates, respectively, primarily comprising amino acids and organic acids [75]. This alteration displays temporal specificity. Studies show the composition of root exudates changes with the duration of intercropping establishment and eventually reaches a new dynamic equilibrium after a certain period [76]. The composition of root exudates in peanut/sugarcane intercropping differed significantly between the pod-setting and grain-filling stages; however, with increasing intercropping duration, the system significantly enhanced the content of organic acids, soluble sugars, and phenolic acids (especially fumaric acid) in peanut root exudates and significantly affected metabolic pathways of alanine, aspartic acid, and glutamic acid [23].
The composition of fruit tree rhizosphere metabolites is also influenced by root exudates from neighboring companion crops. When Chenopodiastrum murale was inoculated into the growth medium of apple (Malus pumila) hairy roots, root exudates exhibited significant changes, predominantly consisting of acidic compounds, including 2-hydroxyindole-3-acetic acid, phenylacetic acid, salicylic acid, benzoic acid, and abscisic acid (with benzoic acid and abscisic acid being the most abundant), while alkaline compounds accounted for only 1% [77]. Additionally, mechanisms by which different fruit tree–companion crop systems influence soil nitrogen (N) vary. Pear tree intercropping with aromatic plants altered amine and alcohol metabolites, thereby enhancing the soil N content through increased functional groups for nitrite ammonification, nitrate ammonification, and urea decomposition [78]. In contrast, mixed intercropping of apple with mint/Ageratum affected soil N by reducing organic acids, alcohols, carbohydrates, and hydrocarbons in the rhizosphere soil [79] (Figure 3; Table 2).

4.2. Functional Metabolites—Antimicrobial Activity

In the rhizosphere microzone, specific natural compounds play key roles in plant root defense by forming chemical barriers. Deng et al. [80] found that ginger (Zingiber officinale) infected by Ralstonia solanacearum induces specific root exudates, which suppress bacterial wilt disease, with the initial disease index decreasing from 77.5% to 40.0%. Root-exudate-induced antimicrobial activity functions through multiple mechanisms. For example, Li et al. [81] discovered that tobacco infected by R. solanacearum secretes caffeic acid (a specific phenolic exudate), and high concentrations of caffeic acid disrupt the membrane structure of R. solanacearum cells, resulting in membrane thinning and irregular cellular cavities (Figure 3; Table 2). In studies on mulberry root exudates, active compounds such as erucamide, oleamide, and bromocamphor inhibit Ralstonia pseudosolanacearum (R. pseudosolanacearum) by affecting the cell morphology and extracellular polysaccharide content, triggering reactive oxygen species (ROS) bursts that reduce the R. pseudosolanacearum growth and suppress virulence-related gene expression [82].
Beyond damaging pathogen cell structures, some plant exudates also inhibit fungi. Wang et al. [72] reported that bioactive compounds like flavonoids and terpenoids reduce the growth rates of Rhizoctonia solani AG8 and Fusarium oxysporum f. sp. cucumerinum. Kuang et al.’s study on tomatoes revealed that these antimicrobial substances exhibit Minimum Inhibitory Concentrations (MICs); for instance, ferulic acid has an MIC of 32 μg/mL against Aspergillus flavus, whereas dihydrocapsaicin shows an MIC of 16 μg/mL against F. oxysporum [83].
Increasing ecosystem diversity is a primary strategy for suppressing soil-borne diseases. For instance, long-term monocropping of faba bean (Vicia faba) results in a high incidence of F. oxysporum, but wheat (Triticum aestivum)–faba bean intercropping significantly reduces Fusarium wilt incidence and severity by restructuring the rhizosphere microenvironment through accumulation of salicylic acid, p-hydroxybenzoic acid, tartaric acid, malic acid, glutamic acid, and threonine [84]. Similarly, orchard replant disease can be mitigated by introducing exogenous root exudates. Zhang et al. showed that peanut (Arachis hypogaea) root exudates suppress Fusarium solanum growth in grape (Vitis vinifera) replant soils [85]. In pear (Pyrus spp.)–morel (Morchella spp.) intercropping systems, significant accumulation of amino acids (phenylalanine, lysine, proline, citrulline, and ornithine), sugars (arabitol and glucosamine), and organic acids (quinic acid, fumaric acid, and malic acid) further inhibits Fusarium and Aspergillus pathogens [86]. Tang et al. [87] reported that dimethyl disulfide and diallyl disulfide from Chinese chive (Allium tuberosum) root exudates reduce apple replant disease by suppressing Fusarium solani mycelial growth and spore germination.
Studies indicate that such antimicrobial rhizosphere metabolites also influence soil nitrogen distribution. For example, hairy vetch (Vicia villosa)–walnut (Juglans regia) intercropping upregulates pteroside D to enhance Arbuscular mycorrhizal (AM) fungal antagonism against soil pathogens, thereby increasing the soil nitrate and ammonium nitrogen contents [97]. Kumar et al. [98] additionally documented that flavonoids exhibit antimicrobial and antifungal properties, facilitating mycorrhizal associations to augment plant nutrient acquisition in low-nitrogen environments (Figure 3; Table 2).

5. Root-Exudate-Mediated Recruitment of the Rhizosphere Microbiome

5.1. Recruitment of Growth-Promoting Microbiome

Plants recruit microorganisms from non-rhizosphere soil by secreting readily available organic carbon into the rhizosphere. The recruitment of plant-growth-promoting bacteria (PGPB) is a common strategy for rhizobacterial assembly, with Pseudomonas being a prominent PGPB. Pacheco et al. [88] demonstrated that hexose-rich root exudates of barley (Hordeum vulgare “Tipple”) attract Pseudomonas spp. growth (Figure 4; Table 2). Li et al. [89] found a strong correlation between root exudates and the rhizosphere microbiome composition in dwarf alpine sedge (Kobresia humilis), where flavonoids (particularly baicalin) in exudates enhance the Bacillus colonization rates, while sucrose and riboflavin secretions promote bacterial elongation; reciprocally, Bacillus stimulates root growth by influencing the root phenotypes. These mechanisms have been validated in orchard intercropping systems. For instance, apple orchards intercropped with aromatic plants (e.g., Ageratum conyzoides) recruit Actinobacteria and Bacilli through hexose-enriched exudates, improving the soil nitrogen utilization and microbial-driven nutrient turnover [79]. Across developmental stages, plants recruit distinct PGPB taxa, with microbial diversity shifting significantly. For example, Devi et al. [90] reported that young Capsicum chinense plants host diverse bacterial classes (e.g., Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria) but lack Betaproteobacteria; during flowering and fruiting stages, Bacillus spp. (class Bacilli) and Burkholderia spp. (class Betaproteobacteria) are predominantly recruited due to altered concentrations of organic acids, phenolics, and flavonoids in root exudates.
Host plant selection is crucial for recruiting growth-promoting microbiota in intercropping systems. Zhao et al. [79] demonstrated that Ageratum conyzoides (high growth potential) releases elevated hexose concentrations to recruit Actinobacteria beneficial for its growth when intercropped with apple (Malus domestica) (Figure 4; Table 2), whereas the effect of mint (Mentha spp.)–apple intercropping is the opposite. The benefits of PGPB to plants are typically achieved through improved soil nitrogen dynamics. For example, Zhang et al. [78] found that pear (Pyrus spp.) intercropped with basil (Ocimum basilicum)/Satureja hortensis recruit dominant microbiota (Actinobacteria, Verrucomicrobia, Bacilli, etc.) by altering the exudate profiles of sugars, amines, and alcohols, thereby increasing the soil total nitrogen and alkali-hydrolyzable nitrogen content and enhancing the nitrogen release in orchard soils. Similar findings emerged in grape (Vitis vinifera)–potato (Solanum tuberosum) intercropping: potatoes recruit Bacillus, Kaistobacter, and Streptomyces through increased lipid and organic acid secretion, leading to higher nitrogen concentrations and creating superior soil resource utilization patterns for vineyards [95].

5.2. Recruitment of Disease-Suppressive Microbiome

Plants can recruit rhizosphere microorganisms with disease-suppressive traits via root exudates to enhance the resistance against soil-borne pathogens [99] (Figure 4). For example, Bacillus exhibits enhanced chemotaxis toward the root exudates of maize (Zea mays) infected with Fusarium graminearum, thereby inhibiting the formation and germination of its conidia [100]. A similar mechanism exists in fruit trees: Bacillus velezensis LG14-3 shows chemotaxis toward citric acid, succinic acid, glycine, D-galactose, and D-maltose—components of root exudates in Fusarium oxysporum f. sp. cubense (FOC)-infected banana (Musa spp.) zones—thereby reducing the disease severity index of Fusarium wilt through antagonistic activity [91]. Beyond recruiting disease-suppressive bacteria, antifungal fungi also inhibit pathogens. For instance, resistant banana cultivars recruit Trichoderma and Penicillium by secreting shikimic acid and propylene glycol, suppressing FOC proliferation [92]. In diversified cropping systems, specific exudate alterations are observed: (1) onion (Allium cepa) intercropped with tomato (Solanum lycopersicum) elevates flavonoid secretion (e.g., taxifolin), which recruits Bacillus spp. to antagonize Verticillium dahlia [93]; (2) apple (Malus domestica) intercropped with marigold (Tagetes erecta) enhances starch/sucrose metabolism, increasing sucrose exudation to recruit Pseudomonas and Bacillus with significant correlations to soil nitrogen dynamics [94].
Monoculturing exacerbates plant disease susceptibility, thereby reducing yield and quality. In contrast, appropriate companion crop root exudates in diversified cropping systems can influence the recruitment of rhizosphere microbiomes in neighboring plants, suppressing the spread of soil-borne pathogens. These exudate-mediated shifts include reduced organic acids/alcohols (e.g., in apple–mint intercropping) and increased amino acids/sugars (e.g., in pear-basil systems), which restructure microbial communities to enhance pathogen suppression [78,79]. For example, intercropping ginseng (Panax ginseng) with ryegrass (Lolium perenne) and/or white clover (Trifolium repens) significantly increased the content of the metabolite ginsenosides and recruited abundant beneficial bacteria to the ginseng rhizosphere [101]. Maize (Zea mays)/soybean (Glycine max) intercropping inhibited F. oxysporum growth by recruiting Pseudomonas, Bacillus, and Streptomyces in the soybean rhizosphere [96].
Studies indicate that flavonoid root exudates not only recruit beneficial microorganisms but also enhance the colonization of disease-suppressive microbiomes on roots. For instance, Zhou et al. [93] demonstrated that in onion (Allium cepa)–tomato (Solanum lycopersicum) intercropping, flavonoids (particularly taxifolin) secreted by onions stimulated tomato roots to recruit Bacillus spp. antagonistic against Verticillium dahliae; concurrently, this compound altered tomato root exudates to indirectly regulate Bacillus colonization in the tomato rhizosphere. Xue et al. [94] reported that in apple (Malus domestica)/marigold (Tagetes erecta) intercropping systems, marigold enhanced the starch and sucrose metabolism to recruit Pseudomonas and Bacillus, whose abundance correlated significantly with soil nitrogen concentration, compared with apple monoculture (Figure 4; Table 2).

6. Perspectives on Root-Exudate-Induced Nitrogen Utilization Strategies in Orchards

Fruit trees (e.g., peach, apple, pear, citrus) constitute globally vital economic crops whose yield and quality directly impact agricultural economies and food security. Although orchard crops lack symbiotic nitrogen fixation (SNF) capacity, recent studies reveal that their root exudates enrich soil associative diazotrophs (e.g., Azospirillum, Pseudomonas). Concurrently, legume companion plants secrete flavonoids (e.g., luteolin, apigenin) that enhance the nitrogenase activity by 20–35% via nifH gene induction [102,103]. This root-exudate-mediated associative nitrogen fixation (ANF) mechanism elevates nitrogen use efficiency (NUE) by 20–35% while reducing chemical fertilizer dependency by 15–30% [31,102]. ANF describes a process in which non-symbiotic nitrogen-fixing microorganisms form loose associations with plant root systems; through rhizosphere exudate-driven metabolic interactions, these microbes convert atmospheric N2 into plant-available NH4+. Nevertheless, critical knowledge gaps persist: (1) unresolved specificity in non-leguminous woody plant–diazotroph interactions within orchards; (2) absence of spatiotemporal quantitative models for exudate–microbe network dynamics; (3) unquantified ANF contributions to orchard-scale nitrogen cycling. Future research should prioritize the following:
(1)
Functional genomics of associative diazotrophs: Employ metagenomic binning to screen ANF taxa (e.g., Azospirillum brasilense, Azoarcus spp.) in orchard polycultures. Integrate single-cell culturing with high-throughput screening to identify flavonoid-responsive strains, establishing genotype–nitrogenase efficiency correlations (e.g., nif cluster variants vs. exudate-induced expression).
(2)
Rhizosphere chemical dialogue regulation: Apply spatiotemporally resolved metabolomics–transcriptomics to quantify the dose–response relationships between companion plant exudates (e.g., flavonoids/organic acids) and diazotroph activity (acetylene reduction assays) and quorum sensing (e.g., AHL signaling). Define concentration thresholds for optimal nitrogen fixation.
(3)
Engineered microbial consortia: Construct synthetic communities (SynComs) integrating diazotrophs (Azotobacter vinelandii), phosphate-solubilizers (Pseudomonas putida), and biocontrol agents (Bacillus subtilis). Validate field efficacy in co-enhancing ANF and disease resistance, developing orchard-tailored biofertilizers.

Author Contributions

Conceptualization, Y.L. and Y.Z.; methodology, Y.L.; validation, Q.H. and S.L.; investigation, Y.L.; resources, A.L.; data curation, F.R.; writing—original draft preparation, Y.L. and Y.Z.; writing—review and editing, A.L.; visualization, S.L. and A.L.; supervision, Q.H. and F.R.; project administration, A.L.; funding acquisition, A.L. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by [Special Projects of Construction of Science and Technology Innovation Ability of BAAFS] grant number [KJCX20230219, KJCX20230220] and [China Agriculture Research System] grant number [CARS-30].

Data Availability Statement

The original contributions presented in this study are included in the article. Further inquiries can be directed to the corresponding authors.

Acknowledgments

This work was financially supported by Special Projects of Construction of Science and Technology Innovation Ability of BAAFS (KJCX20230219, KJCX20230220), and the China Agriculture Research System (CARS-30). We thank BioRender (https://www.biorender.com/) for their graphical assistance.

Conflicts of Interest

The authors declare no conflicts of interest.

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Figure 1. Improvement of orchard soil properties mediated by root exudates of companion crops and their impact on nitrogen utilization strategies.
Figure 1. Improvement of orchard soil properties mediated by root exudates of companion crops and their impact on nitrogen utilization strategies.
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Figure 2. Improvement of orchard plant traits mediated by root exudates of companion crops and their impact on nitrogen utilization strategies.
Figure 2. Improvement of orchard plant traits mediated by root exudates of companion crops and their impact on nitrogen utilization strategies.
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Figure 3. Reconstruction of metabolites in orchard mediated by root exudates of companion crops and its influence on nitrogen utilization strategy.
Figure 3. Reconstruction of metabolites in orchard mediated by root exudates of companion crops and its influence on nitrogen utilization strategy.
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Figure 4. Recruitment of rhizospheric microorganisms in orchard mediated by root exudates of companion crops and its influence on nitrogen utilization strategy.
Figure 4. Recruitment of rhizospheric microorganisms in orchard mediated by root exudates of companion crops and its influence on nitrogen utilization strategy.
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Table 1. Root-exudate-mediated improvements in soil properties and plant traits.
Table 1. Root-exudate-mediated improvements in soil properties and plant traits.
EcosystemExperimental ConditionPlantTypes of Root ExudatesKey FindingsReference
Single-plantingLaboratory-controlledChia Polysaccharides↓ Soil penetration resistance (up to 77% in sandy loam); ↑ soil porosity under drought stress. Field validation pending.[32]
Single-plantingFieldWinter crops Organic matter inputs (indirect)↑ Soil aggregate stability; summer crops with high chemical fertilizers ↓ stability by suppressing microbial activity.[35]
Single-plantingFieldPeachNot specifiedRoot zone aeration ↑ N-fixing microbes (Bradyrhizobium) and K-solubilizers (Bacillus); ↑ soil N content and plant K:N ratio.[36]
Multi-plantingField Citrus trees with leguminous cover cropsNot specified↑ Soil Quality Index (SQI) via improved aggregates; maintained nutrient balance.[37]
Single-plantingField GrassCitric acid and oxalic acid↓ Soil pH → ↑ solubilized P and chelated metals; ↑ NH4+-N/NO3−-N bioavailability by 15–70%.[38]
Multi-plantingFieldApple + cover cropsSugars and organic acids↑ Soluble organic C, microbial biomass, and N fractions (>19.6%) in 0–20 cm soil.[39]
Single-plantingGreenhouseCucumber Sugars (fructose, glucose), organic acids (oxalic, malic), and amino acidsSugars ↑ root surface area; organic acids/amino acids ↑ root tip number. Quantitative RSA links inform orchard management.[40]
Single-plantingFieldMaize Not characterized (N-uptake focus)↑ Specific root length and root angle → ↑ N absorption under high density; adaptive “foraging-avoidance” strategy.[41]
Single-plantingGreenhouseOil palmNot specifiedN deficiency ↓ root length/surface area; ↑ angular frequency → conservative resource-use strategy.[42]
Single-plantingGreenhousePear Organic acids (e.g., citrate, malate) and enzymesBranching intensity ↑ with soil N profiles (total N, NH4+); BIO fertilizer ↑ lateral roots.[43]
Multi-plantingGreenhouseWheat + cucumberNot specifiedWheat REs ↑ cucumber growth; altered rhizosphere microbiome.[44]
Single-plantingGreenhouseSoybeanOrganic acids, amino acids, phenolics, proteins, and sugarsP-efficient varieties ↑ photosynthetic rate, chlorophyll, and carotenoids; linked to RE metabolite profiles.[45]
Multi-plantingFieldApple + grass coverNot specified↑ Photosynthesis and fruit sugar metabolism via ↑ soil N; ↓ evaporation via transpiration shift.[46]
Notes: ↑, increase; ↓, decrease; →, cause.
Table 2. Root-exudate-mediated rhizosphere metabolite remodeling and microbiome recruitment.
Table 2. Root-exudate-mediated rhizosphere metabolite remodeling and microbiome recruitment.
EcosystemExperimental ConditionPlantTypes of Root ExudatesKey FindingsReference
Rhizosphere Metabolite Remodeling
Single-plantingLaboratory-controlledGingerSpecific antimicrobial compounds (unspecified)↓ Bacterial wilt disease index (77.5% → 40.0%) by suppressing Ralstonia solanacearum via induced exudates.[80]
Single-plantingGreenhouseTobacco Caffeic acid (phenolic compound)Disrupted R. solanacearum cell membranes (thinning, irregular cavities) at high concentrations.[81]
Single-plantingLaboratory-controlledMulberry Erucamide, oleamide, and bromocamphorInhibited R. pseudosolanacearum via ROS bursts, reduced virulence gene expression, and altered cell morphology/extracellular polysaccharides.[82]
Single-plantingLaboratory-controlledTomato Ferulic acid and dihydrocapsaicin Suppressed Aspergillus flavus and Fusarium oxysporum growth via antifungal activity.[83]
Multi-plantingFieldWheat–faba bean Salicylic acid, p-hydroxybenzoic acid, and tartaric acid↓ Incidence/severity of Fusarium wilt by reconstructing rhizosphere microbiota and accumulating disease-suppressive metabolites.[84]
Multi-plantingGreenhousePeanut–grapeUnspecified antimicrobial exudatesSuppressed Fusarium solani growth in grape replant soils.[85]
Multi-plantingFieldPear–morelAmino acids (phenylalanine, lysine), sugars (arabitol), and organic acids (quinic acid)Inhibited Fusarium and Aspergillus pathogens via metabolite accumulation.[86]
Multi-plantingFieldChinese chive–appleDimethyl disulfide and diallyl disulfide↓ Apple replant disease by suppressing Fusarium solani mycelial growth and spore germination.[87]
Microbiome Recruitment
Multi-plantingFieldApple–aromatic plantsHexose-enriched exudatesRecruited Actinobacteria/Bacilli, improving soil N utilization and microbial nutrient turnover.[79]
Single-plantingFieldBarley Hexoses (sugars)Attracted Pseudomonas spp. growth, enhancing plant growth-promoting bacteria (PGPB) colonization.[88]
Single-plantingFieldDwarf alpine sedgeFlavonoids (baicalin), sucrose, and riboflavinEnhanced Bacillus colonization; reciprocally stimulated root growth.[89]
Single-plantingGreenhouseCapsicum Organic acids, phenolics, and flavonoidsShifted PGPB recruitment: Young plants → Gammaproteobacteria; Flowering/fruiting → Bacillus and Burkholderia.[90]
Single-plantingGreenhouseBanana Citric acid, succinic acid, glycine, D-galactose, and D-maltoseBacillus velezensis chemotaxis → ↓ Fusarium wilt severity via antagonism.[91]
Single-plantingLaboratory-controlledBananaShikimic acid and propylene glycolRecruited Trichoderma and Penicillium to suppress Fusarium oxysporum f. sp. cubense (FOC).[92]
Multi-plantingFieldOnion–tomato Flavonoids (taxifolin)Recruited Bacillus spp. to antagonize Verticillium dahliae; altered tomato root exudates to enhance colonization.[93]
Multi-plantingFieldApple–marigold Sucrose (via starch/sucrose metabolism)Recruited Pseudomonas and Bacillus; abundance correlated with soil N dynamics.[94]
Multi-plantingFieldMaize–soybeanLipids and organic acidsRecruited Bacillus, Kaistobacter, and Streptomyces; suppressed F. oxysporum and improved soil N concentrations.[95,96]
Note: ↓, decrease; →, cause.
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Li, Y.; Zhang, Y.; He, Q.; Liu, S.; Ren, F.; Lu, A. Effects of Root Exudates on Ecological Function and Nitrogen Utilization Strategy of Orchard Multi-Planting System. Agronomy 2025, 15, 2173. https://doi.org/10.3390/agronomy15092173

AMA Style

Li Y, Zhang Y, He Q, Liu S, Ren F, Lu A. Effects of Root Exudates on Ecological Function and Nitrogen Utilization Strategy of Orchard Multi-Planting System. Agronomy. 2025; 15(9):2173. https://doi.org/10.3390/agronomy15092173

Chicago/Turabian Style

Li, Yufeng, Yu Zhang, Qishuang He, Shanshan Liu, Fei Ren, and Anxiang Lu. 2025. "Effects of Root Exudates on Ecological Function and Nitrogen Utilization Strategy of Orchard Multi-Planting System" Agronomy 15, no. 9: 2173. https://doi.org/10.3390/agronomy15092173

APA Style

Li, Y., Zhang, Y., He, Q., Liu, S., Ren, F., & Lu, A. (2025). Effects of Root Exudates on Ecological Function and Nitrogen Utilization Strategy of Orchard Multi-Planting System. Agronomy, 15(9), 2173. https://doi.org/10.3390/agronomy15092173

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