Stress-induced keystone species facilitate functional microbial community assembly to suppress root-knot nematodes for susceptible plants
Xingqun Liu, Mengyuan Song, Zhicheng Xue, Qiannan Zhang, Lihong Gao, Yongqiang Tian
TL;DR
Stress from nematode infection leads to the recruitment of a key bacterial species that helps build a microbial community to protect plants.
Contribution
Identification of a keystone bacterial strain that drives functional microbial community assembly to suppress nematodes.
Findings
RKN infection restructured the rhizosphere bacterial community in susceptible cucumber plants.
The Rhizobium pusense strain TYQ1 inhibited RKNs and restructured the microbial community.
A TYQ1-centered synthetic community showed efficient and stable nematode suppression.
Abstract
Stresses (e.g. high temperature, drought, and pests) can reshape the structure of root-associated microbial communities, but how to discover functional microbial community assembly to support plant health remains a great challenge. Here, we found that root-knot nematode (RKN) infection restructured the rhizosphere bacterial community in RKN-susceptible cucumber plants, regardless of the soil type. We isolated a Rhizobium pusense strain, TYQ1, which was significantly enriched following RKN infection. This strain not only directly inhibited RKNs but also caused the restructuring of the rhizobacterial community, thereby leading to the enrichment of multiple biomarker species. These enriched microorganisms, in collaboration with TYQ1, enhanced the biofilm-forming ability of the community and established a tightly interconnected metabolic interaction network, further strengthening the…
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Figure 6- —National Natural Science Foundation of China10.13039/501100001809
- —China Agriculture Research System
- —2115 Talent Development Program of China Agricultural University
- —Key Research and Development Program of Ningxia10.13039/100016692
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Taxonomy
TopicsPlant-Microbe Interactions and Immunity · Legume Nitrogen Fixing Symbiosis · Mycorrhizal Fungi and Plant Interactions
Introduction
Root-knot nematodes (RKNs) are an adaptable group of endoparasitic nematodes that infest plants [1]. Their widespread global distribution and destructive impacts pose a significant challenge to the sustainable development of modern agriculture [2]. When RKNs infect plant roots, they trigger the formation of giant cells within vascular cells, ultimately leading to the development of root knots [3]. This not only directly impairs the absorption of water and nutrients but also serves as an entry point for soil-borne pathogens, resulting in substantial losses in crop yield and quality. In agricultural production, chemical nematicides face prominent drawbacks such as nontarget ecological toxicity, residual risks to agricultural product safety, and disruption of soil microbial communities [4, 5]. The breeding and application of resistant plant varieties are frequently restricted by the narrow resistance spectrum and the rapid adaptive evolution of pathogens [1, 2, 6]. For most crop species, there remains a shortage of dominant resistance genes against RKNs [5–7]. Consequently, the development of alternative control strategies that are environmentally friendly, sustainable, and efficient is an urgent necessity.
The rhizosphere microbiome is essential for maintaining plant health [8]. Certain rhizosphere microorganisms carry out multiple beneficial functions including directly secreting plant growth regulators, activating mineral nutrients, inducing systemic resistance, secreting antagonistic metabolites, and competing for ecological niches [9, 10]. All these functions work synergistically to enhance plant adaptability to abiotic or biotic stresses. When plants are exposed to adverse stress, the reprogrammed root exudates specifically enrich or activate a group of key beneficial microbial populations with biocontrol potential [11, 12]. This plant-driven “cry for help” response strategy provides a theoretical foundation for harnessing beneficial microorganisms to improve plant stress resistance [12–14]. Based on this knowledge, certain beneficial microbes (e.g. Rhizobium and Pseudomonas) have been utilized as microbial inoculants [15, 16]. However, single microbial inoculants frequently encounter issues such as unstable functional expression and low colonization success rates within complex field environments [17, 18]. Over the past decade, synthetic communities (SynComs)—rationally designed preselected microbial consortia with plant-beneficial functions—have been extensively studied [5, 11, 19]. They enable precise characterization of host-microbe traits under controlled, reproducible conditions and exhibit higher stability and robustness than single strains [20–22], providing promising solutions for sustainable agriculture. However, their long-term beneficial effects are constrained by inter-strain interactions [18]. Therefore, an in-depth analysis of rhizosphere microbial interaction mechanisms is essential for formulating more effective strategies to optimize SynComs.
The construction of SynComs generally adheres to two fundamental principles (i.e. function and interaction) [19]. During this process, the interactions among strains play a crucial role in the stability of SynComs. The overall function of a SynCom is not merely the sum of the individual functions of its members, but rather, it highly depends on the complex interaction networks formed among them (e.g. mutualism, nutrient chains, quorum sensing, and signal interference) [23]. More importantly, the interactions of SynCom members with soil resident microbiota can play a more important role in determining the efficacy of inoculants. Metabolic cross-feeding is a widely studied form of microbial mutualism defined as an interaction phenomenon where metabolic products of one microbe are utilized as nutrients, signaling molecules, or metabolic precursors by another (or multiple) microbes in a microbial community. Microbial cross-feeding can be utilized to guide the design of SynComs with greater stability and efficacy, thus facilitating the development of innovative agricultural microbial inoculants [24]. Beneficial microorganisms can promote plant adaptability to stresses not only through their direct interactions with host plants but also by reshaping the indigenous microbial community [25, 26]. For instance, inoculation with Bacillus velezensis SQR9 modifies the composition of the rhizosphere bacterial communities, thus further facilitating plant growth [25]. Inoculation with Bacillus megaterium NCT-2 promotes the enrichment of rare rhizosphere microbial groups, further strengthening the plant’s capacity to remediate heavy metals [26]. However, the interaction mechanisms between microbial inoculants and native microorganisms, especially the dynamic changes under RKN stress, remain unknown. Hence, research on microbial inoculants should not be confined to their binary interaction with plants. Instead, it should explore more deeply their interaction with native microbial communities and how this interaction ultimately impacts the functional stability of the applied inoculants [27].
In this study, we isolated Rhizobium pusense TYQ1—an RKN enriched, nematicidal strain—from the rhizosphere of RKN-susceptible cucumber plants and used it as a model single-strain inoculant to investigate how microbial agents enhance plant resistance to RKNs by regulating the indigenous microbial community (a well-established plant defense line against RKNs [5]). Hypothesizing that TYQ1 reshapes rhizobacterial community structure to enrich beneficial groups and synergistically boost resistance, we identified TYQ1-mediated beneficial microbial units, explored their interaction with TYQ1, constructed a TYQ1-centered SynCom via metabolite feeding experiments (based on metabolic interaction networks), and finally elucidated the molecular mechanisms of plant responses to this SynCom using transcriptome and metabolome analyses.
Materials and methods
Preparation of experimental materials
Soils from three regions (Beijing, Shandong, and Zhejiang) with distinct physicochemical properties (Table S1) were used (Fig. 1A). The infective second-stage juveniles (J2s) of Meloidogyne incognita were prepared via egg mass collection and hatching [6], followed by surface sterilization. Susceptible cucumber cultivar Cucumis sativus L. “Zhongnong 26” was selected, with seeds surface sterilized, pre-germinated, and checked for contamination. Details of these assays are provided in the Supplementary Methods.
*Response of the cucumber rhizosphere bacterial community to nematode infection. (A) Locations of the three soil collection sites in China. (B) Relative abundance of bacterial communities at the phylum level. (C) Principal coordinate analysis (PCoA) of bacterial communities based on Bray–Curtis dissimilarity metrics (OTU level) was performed for three soil types collected from Beijing (BJ), Shandong (SD), and Zhejiang (ZJ) province of China. Statistical analysis was performed using ANOSIM (analysis of similarities). Four biological replicates were included per treatment. (D) Heatmap showing the relative abundances of the top 10 bacterial families in the samples (n = 4). (E) Changes in the abundance of rhizobacterial communities (genus level) in response to root-knot nematode inoculation compared to non-inoculated controls. Data points of different colors represent different bacterial genera, and different shapes represent different soils. P values were calculated using Student’s t-test. (F) Comparison of the relative abundance of Rhizobium (Agrobacterium) in the rhizosphere with and without root-knot nematode inoculation. (G) Comparison of the relative abundance of OTU2834 in inoculated and non-inoculated treatments across the three soils. P values were calculated using Student’s t-test (for G and H); *P < .05, **P < .001. For all panels, treatment are defined as follows: Mock, non-inoculated with root-knot nematodes; Mi, inoculated with root-knot nematodes.
Nematode infection and phenotypic measurement
Germinated seedlings were transplanted into sterile pots with sterilized/unsterilized soil and grown in a growth chamber (28°C/18°C day/night, 16 h/8 h light/dark, 280–300 μmol m^−2^ s^−1^). At the two-true-leaf stage, 300 J2s were inoculated per seedling. After 35 days, shoot and root fresh weight (FW) were measured. Nematode infection was assessed by acid fuchsin staining [6], with galls and egg masses quantified per gram of root FW. Details of these assays are provided in the Supplementary Methods.
Rhizosphere soil sampling
Rhizosphere soil was sampled 35 days post-J2 inoculation (for nematode-induced community analysis) and at 7, 21, and 35 days (for TYQ1-induced dynamics). Roots were vortexed in PBS, centrifuged (8000×g, 5 min, 4°C) to collect sediment, flash-frozen in liquid nitrogen, and stored at −80°C. Each treatment included four biological replicates, with each replicate pooling rhizosphere soil from five plants. Details of these assays are provided in the Supplementary Methods.
High-throughput sequencing of rhizosphere soil
Genomic DNA was extracted, and the bacterial 16S rRNA gene V3–V4 region was amplified with primers 338F/806R. PCR products were purified, pooled, and sequenced on a MiSeq System (Illumina) (250 bp paired-end). Reads were merged, quality filtered, clustered into operational taxonomic units (OTUs) (97% similarity), and taxonomically assigned against the SILVA 138.2 database. Chloroplast, mitochondrial, and archaeal OTUs were removed. α-Diversity was analyzed with mothur. Details of these assays are provided in the Supplementary Methods.
Isolation, purification, and identification of culturable single bacterial strains
Rhizosphere soil was serially diluted (10^−3^ to 10^−7^) and plated on TSA and R2A media. The plates were then incubated at 28°C for 3–5 days. Morphologically distinct colonies were purified by three rounds of streaking and stored in 25% glycerol at −80°C. Strains were identified via 16S rRNA gene sequencing (primers 27F/1492R) and NCBI BLASTn (similarity >97%). Details of these assays are provided in the Supplementary Methods.
Detection of plant growth–promoting traits, TYQ1 colonization, chemotaxis, and nematicidal activity
Phosphorus-solubilizing ability on NBRIP medium and IAA secretion via Salkowski reagent assay were tested [28, 29]. Carbon source utilization was analyzed with Biolog GEN III MicroPlate [30]. GFP-labeled TYQ1 (TYQ1-GFP) was constructed [31]. Colonization dynamics were quantified via CFU counting on gentamicin-containing LB plates, and root colonization was visualized by confocal laser scanning microscopy (ZEISS LSM880). TYQ1 chemotaxis to root exudates was assessed via soft agar plate and quantitative assays [32]. Growth kinetics in M9 medium with root exudates was monitored by OD_600_ measurement. In vitro assays included nematode viability, egg hatching, and migration inhibition; pot efficacy was validated by inoculating bacterial suspensions (1 × 10^8^ CFU g^−1^ soil) and quantifying galls/egg masses. Details of these assays are provided in the Supplementary Methods.
Evaluation of synergistic interactions between bacterial strains
An inter-colony attraction assay was performed according to a previously published method [11]. Bacterial suspensions were adjusted to OD_600_ = 1.0 with PBS, and 1-μl aliquots were inoculated in a “V” shape on the surface of TSA medium. The plates were sealed with parafilm and subjected to incubation at 28°C for 7–10 days. The attraction index was determined according to a previously published method [5], with three biological replicates per treatment. Synergistic interactions among bacterial strains were assessed through bacterial pellicle development and inter-colony chemotaxis assays. The biofilm formation assessment was performed following an established protocol [33]. The biofilms were stained with 1% crystal violet and solubilized in ethanol. Biofilm amount was determined by measuring absorbance at 590 nm (OD_590_). The experiment included four biological replicates.
Metabolic interactions and SynCom construction
TSB supplementation and cross-feeding assays were performed to evaluate metabolite-mediated growth promotion. Growth curves were fitted with a logistic model to obtain carrying capacity (K) and maximum growth rate (r). A complete SynCom (TYQ1 + 7 enriched strains) and eight defective SynComs (each lacking one strain) were constructed. SynComs with diversity gradients (0–8 strains) were also generated (85 combinations total). Details of these assays are provided in the Supplementary Methods.
Transcriptome and metabolome profiling of plant roots
Root RNA was sequenced on a HiSeq System (Illumina). Clean reads were mapped to cucumber genome (Cucumis sativus v3.0). DEGs were identified with DESeq2 (FDR < 0.05, |log_2_FC| ≥ 1), followed by GO/KEGG enrichment. Root metabolites were extracted and analyzed via UHPLC-QTOF-MS. DEMs were screened by Student’s t-test (P < .05) and VIP >1. Details of these assays are provided in the Supplementary Methods.
Validation of quantitative real-time PCR
Eighteen defense-related DEGs were selected. Total RNA was extracted, cDNA synthesized, and quantitative PCR (q-PCR) performed with SYBR Green Master Mix. Actin was used as reference gene, and relative expression was calculated via 2^−ΔΔCt^ method (primer sequences in Table S8). Details of these assays are provided in the Supplementary Methods.
Statistical analyses
Statistical analyses were conducted with Microsoft Excel 2021 and SPSS 25.0, incorporating two-sided unpaired t-tests, analysis of variance (ANOVA), and Tukey’s multiple range test for significance. Data visualization was conducted using Origin 2023b. Principal coordinate analysis (PCoA) using Bray–Curtis dissimilarity metrics was conducted to compare microbial community composition, employing the vegan v.2.5.6 and ggplot2 v.4.0.1 packages in R v.4.1.3 [34]. A phylogenetic tree of screened strains was constructed via the maximum-likelihood method (1000 bootstrap replicates) and visualized using ChiPlot (https://www.chiplot.online/). Linear relationships among variables were estimated using an ordinary least squares (OLS) regression model. Metabolic networks were visualized in Gephi 0.10.1 software, with directed edge weights defined as the carrying capacity (K) derived from logistic growth curve fitting.
Results
Meloidogyne incognita infection modifies the structure of the rhizosphere bacterial microbiome
Meloidogyne incognita infection consistently reshaped the rhizobacterial community of RKN-susceptible cucumber plants across three distinct soil types (sandy loam, silty loam, and loam) from different Chinese regions—despite significant variations in soil physicochemical properties (Table S1; Fig. 1A, Fig. S1) and initial microbial composition (Fig. 1B–C, Figs. S2–S3), confirming that nematode-induced community reorganization is soil-type independent.
For further investigation into the bacterial groups specifically enriched in the rhizosphere following M. incognita infection, we compared the differences between nematode treatments (Fig. 1D–E). At the family level, the three soils exhibited distinct enrichment patterns after nematode infection (enriched families: Sphingomonadaceae, Paracoccaceae, Rhizobiaceae, and Chitinophagaceae in Site 1-BJ; Rhizobiaceae and Oxalobacteraceae in Site 2-SD; and Sphingomonadaceae, Chitinophagaceae, Rhizobiaceae, and Comamonadaceae in Site 3-ZJ; Fig. 1D). Rhizobiaceae showed significantly increased abundance in all soils. Further analysis revealed that the Rhizobium genus within the Rhizobiaceae family increased significantly in all soils, with quantified percentage changes of 51.9% in BJ soil, 56.8% in SD soil, and 197.2% in ZJ soil, despite the soil-specific enrichment of other genera (Fig. 1E–F), emphasizing the prominent cross-soil enrichment characteristic of Rhizobium. Considering the common responses of the rhizosphere bacterial microbiome following nematode infection, we further selected the OTUs that were significantly enriched in all soils. The results showed that OTU2834, OTU856, OTU951, OTU2597, and OTU2646 were significantly enriched (Fig. S4). Among them, OTU2834 belonged to the Rhizobium genus, and its abundance exhibited a marked increase of 81.0%, 172.8%, and 247.6% in the three soils, respectively (Fig. 1G).
Meloidogyne incognita–induced rhizobacterium TYQ1 inhibits nematode infection in plants
We isolated Rhizobium pusense TYQ1 via broad screening of culturable rhizobacteria from the RKN-infected cucumber rhizosphere. Phylogenetic analysis confirmed that TYQ1’s 16S rRNA gene sequence shares 100% homology with OTU2834 (Fig. S5)—the most cross-soil enriched Rhizobium OTU identified by 16S rRNA sequencing (Fig. 1E–G). The other four enriched OTUs were not isolated due to low abundance or uncultivability. TYQ1 stably colonized cucumber rhizosphere and root surface, with significantly higher colonization density beginning at 3 days post-RKN infection (Fig. 2A, Fig. S6). To examine whether root exudates induced by nematode infection mediate the enrichment of TYQ1, functional validation was carried out by collecting root exudates from cucumber roots with and without M. incognita inoculation. Growth curve analysis revealed that TYQ1 exhibited a significantly accelerated proliferation rate in the presence of root exudates from M. incognita–infected roots (+Mi) (Fig. 2B). Moreover, TYQ1 demonstrated a strong chemotactic response to root exudates from M. incognita–infected roots (Fig. 2C–F). Collectively, the alterations in root exudate components triggered by nematode infection are the key drivers underlying the rhizosphere-directed recruitment of TYQ1.
*Efficacy of Rhizobium pusense TYQ1 in controlling root-knot nematodes. (A) Colonization dynamics of TYQ1 in the rhizosphere soil with (+Mi) and without (−Mi) nematode inoculation. (B) Growth curve of TYQ1 in M9 minimal medium supplemented with root exudates. Mock, the control with sterile water added; −Mi, root exudates from plants not inoculated with nematodes; +Mi, root exudates from plants inoculated with nematodes. (C–F) Chemotaxis of TYQ1 toward root exudates. Mock, the control with sterile water added; −Mi, root exudates from plants not inoculated with nematodes; +Mi, root exudates from plants inoculated with nematodes. (G) Schematic diagram of the pot experiment. Mock, treated with 10 mM MgSO4 buffer; TYQ1, inoculated with TYQ1 suspension; Mi, inoculated with nematodes; TYQ1 + Mi, co-inoculated with TYQ1 suspension and nematodes. (H) Fresh weight of cucumber plants. (I, J) Number of root galls per gram of root (I) and number of egg masses per gram of root (J). (K) Number of nematodes at different developmental stages within the roots 21 days after inoculation. (L) Size distribution of root gall diameters. (M) Chemotactic migration of nematodes toward roots. Mock, root treated with 10 mM MgSO4 buffer; E. coli, root inoculated with Escherichia coli suspension (negative control); TYQ1, root inoculated with TYQ1 suspension. (N, O) Lethality of TYQ1 metabolites toward nematodes. R2A, R2A medium only (no microbial metabolites added); E. coli, metabolites of E. coli (negative control); TYQ1, metabolites of TYQ. (P) Inhibitory effect of TYQ1 metabolites on nematode egg hatching. For all panels, data represent mean ± SEM. For (B), (D), (F), (O), and (P), different letters indicate statistically significant differences as determined by one-way ANOVA followed by Tukey’s post hoc test (P < .05). In (A) and (H–M), statistical significance was assessed using Student’s t-test. *P < .05, **P < .01, **P < .001. The number of biological replicates (n) is as follows: (A), (F), (O), (P), n = 4; (B), n = 3; (D), (L), n = 6; (H–J), n = 20; (K), n = 9; (M), n ≥ 4.
With the aim of clarifying the regulatory functions of TYQ1 on plant growth and stress resistance, we conducted a series of in vitro and in vivo experiments. Promoting growth characteristics tests indicated that TYQ1 has the potential to solubilize inorganic phosphate and secrete indole-3-acetic acid (Fig. S7). Inoculation with TYQ1 significantly enhanced plant growth and suppressed nematode infection, with plant biomass increasing by 38.4% under non-stress conditions and 19.8% under stress conditions, whereas the number of galls and egg masses per gram root reduced by 33.7% and 20.6% under nematode stress, respectively (Fig. 2G–L, Fig. S8). Gel migration assays further verified that TYQ1 inoculation reduced the migration rate of M. incognita to the roots (Fig. 2M). Moreover, the overall metabolites of TYQ1 exhibited an in vitro mortality rate and egg hatching inhibition rate of 44.7% and 73.7% against M. incognita, respectively (Fig. 2N–P). Further non-targeted metabolomic analysis of the TYQ1 metabolites revealed that among the top 50 metabolites (Fig. S9A, Supplementary Data 1), trans-cinnamic acid, myristic acid, and lutin at a concentration of 100 μM all demonstrated high mortality rates against M. incognita (Fig. S9B, Table S2).
The universality of TYQ1 in combating M. incognita was verified by inoculating the strain into the roots of cucumber seedlings grown in the three aforementioned soil types under either sterilized or unsterilized soil conditions (Fig. S10). The results showed that although TYQ1 could reduce the number of galls and egg masses to varying extents in all three soil types, the inhibitory effect was more stable and pronounced in unsterilized soils (Fig. S10E).
TYQ1 restructures the indigenous bacterial community in the rhizosphere
In an effort to investigate TYQ1’s interactions with indigenous microorganisms, we analyzed the rhizosphere bacterial community at 7, 21, and 35 days post–M. incognita inoculation (dai) (Fig. 3A–B, Fig. S11A–D). TYQ1-treated groups (TYQ1 and TYQ1 + Mi) were significantly distinct from the non-inoculated controls (Mock and Mi), indicating TYQ1’s sustained role in reshaping rhizomicrobiota. Specifically, TYQ1 altered the relative abundances of the phyla Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi, as well as their affiliated genera (Fig. 3B, Fig. S11D–E). The dynamics of microbial diversity indicated that TYQ1 temporarily inhibits microbial diversity by strengthening community dominance, whereas continuous nematode stress drives the rhizosphere micro-ecosystem to evolve toward diversity recovery (Fig. S11F–G). Based on this, we focused on the reconfiguration characteristics of the rhizosphere microbiota in the late stage of infection (35 dai). Specifically, TYQ1 inoculation resulted in a significant enrichment of the phylum Proteobacteria (Fig. S12), with its relative abundance increasing by 22.9% under non-nematode stress and 88.2% under nematode stress, within which the Sphingomonadaceae and Comamonadaceae families were identified as core response groups (Fig. 3C). Moreover, 15 genera exhibited a significantly increased relative abundance following TYQ1 inoculation (Fig. 3E). Among these, Sphingomonas and Acidovorax, which are the dominant genera within the Sphingomonadaceae and Comamonadaceae families, respectively (accounting for 60.6% and 46.9%; Fig. S13), exhibited a relatively high abundance (>1%) in the rhizosphere following the inoculation of TYQ1 (Fig. 3E). Specifically, the relative abundance of Sphingomonas was elevated by 35.1% under non-nematode stress and 103.6% under nematode stress, while that of Acidovorax increased by 218.8% under non-nematode stress and 129.7% under nematode stress. Furthermore, through sequence alignment, we found that only the sequence of OTU1981 had 100% homology with that of TYQ1, and OTU1981 was mainly present in the rhizosphere of cucumber plants inoculated with TYQ1 (Fig. 3D). By applying OLS regression modeling, we found that the relative abundances of Sphingomonas and Acidovorax were significantly positively correlated with the abundance of OTU1981 (Fig. 3F–G). Together, these results confirmed that inoculating TYQ1 induces the enrichment of Sphingomonas and Acidovorax in the rhizosphere.
TYQ1 inoculation reshaped the bacterial community in the cucumber rhizosphere. (A) Principal coordinate analysis (PCoA) of bacterial communities based on Bray–Curtis dissimilarity metrics (OTU level). Statistical analysis was performed using analysis of similarities (ANOSIM). Four biological replicates are shown. (B) Relative abundance (%) of the top 10 most abundant taxa (phylum level) in the rhizosphere soil at different time points after root-knot nematode inoculation. (C) Dot plot (left) displaying bacterial families with increased or decreased abundance in TYQ1-inoculated versus non-inoculated rhizosphere soil. Bar plots (right) illustrate the relative abundance of each family under different treatments. Data represent mean ± SEM. (D) Heatmap of OTUs belonging to the genus Rhizobium across samples. The central circle displays the phylogenetic tree of these OTUs and the TYQ1 strain. (E) Venn diagram showing the number of bacterial genera significantly increased (P < .05) by TYQ1 inoculation under both stressed and non-stressed conditions (top). The stacked bar chart shows the relative abundance of the commonly enriched genera (bottom). (F, G) Ordinary least squares (OLS) linear regression analysis between the abundance of Sphingomonas (F) and Acidovorax (G) and the abundance of OTU1981 (n = 8). The solid line represents the OLS regression fit, and the shaded area indicates the 95% confidence interval of the fitted values. Statistical significance was assessed using an F-test. (H, I) Volcano plots of OTUs with differential abundance (fold-change >2, P < .05) in response to TYQ1 inoculation under non-stressed and stressed conditions. Right points represent significantly upregulated OTUs, left points represent significantly downregulated OTUs, and gray points indicate non-significant changes. (J) Neighbor-joining tree of OTUs within the genus Sphingomonas (top 25 in abundance) and OTUs within the genus Acidovorax, along with a heatmap of their relative abundances under different treatments. “” indicates significant changes (P < .05) in relative abundance induced by TYQ1 inoculation. Major OTUs (OTU2477, OTU1716, OTU2167, and OTU2469) are highlighted. (K–Q) Ordinary least squares (OLS) linear regression analysis between the abundance of seven enriched OTUs and the abundance of OTU1918 (n = 8). The solid line represents the OLS regression fit, and the shaded area indicates the 95% confidence interval of the fitted values. Statistical significance was assessed using an F-test.*
For further identification of the core units of the microbial community reconfiguration induced by TYQ1, we focused on the response characteristics of OTUs within the Sphingomonas and Acidovorax genera (Fig. 3J). In the Sphingomonas genus, although multiple OTUs were significantly enriched in response to TYQ1 inoculation—with fold changes ranging from 1.25 to 5 times under non-nematode stress conditions and from 1.49 to 45 times under nematode stress conditions, only OTU2477 and OTU1716 maintained high abundance levels (>1%). Similarly, in the Acidovorax genus, only OTU2167 and OTU2649 showed both significant enrichment and high abundance under TYQ1 treatment. Subsequently, the screening of differentially abundant OTUs based on strict thresholds (|Fold-change| > 1.5, P < .05) revealed that 89 OTUs had significantly changed abundances under non-stress conditions (32 upregulated), whereas the number of responsive OTUs increased to 301 under nematode stress (78 upregulated). The volcano plot emphasized OTU2649, OTU613, OTU2715, OTU11267, OTU11234, and OTU3218 at the top of the significantly upregulated area (Fig. 3H–I). The OLS modeling demonstrated that the TYQ1 biomarker OTU1981 showed a significant and positive correlation with the abundances of most of the aforementioned characteristic OTUs (excluding OTU2649; Fig. 3K–Q, Fig. S14). In summary, the inoculation of TYQ1 restructured the rhizosphere bacterial community and led to the enrichment of certain specific groups.
Metabolic interaction between TYQ1 and the enriched strains promotes the colonization of TYQ1
To gain deeper insights into synergistic interactions between TYQ1 and the enriched strains, we isolated 310 culturable bacteria from TYQ1-inoculated rhizosphere soil, encompassing 29 genera across 5 phyla (Fig. S15). Sequence alignment (>97% similarity) identified seven isolates (designated SP, SX, AS, AF, NS, XA, and MA; Table S3) matching TYQ1-enriched OTUs (OTU2477, OTU1716, OTU2167, OTU2649, OTU613, OTU2715, and OTU11267). OTU11234 and OTU3218 were not isolated (rhizosphere relative abundance <0.05%). All seven isolated strains exhibited plant growth–promoting traits (Fig. S16). Given that these strains were recruited by TYQ1, we further evaluated their interactions with TYQ1 through plate confrontation experiments and biofilm formation ability tests. With the exception of SX, which did not display obvious attraction or repulsion toward TYQ1, all the other strains induced colony enlargement when co-cultured with TYQ1, indicating a significant attraction phenomenon (Fig. 4A). Moreover, no mutual inhibition was observed among the seven isolated strains (Fig. S17). Furthermore, all strains exhibited a synergistic effect with TYQ1 in biofilm formation (Fig. 4B), further verifying a positive interaction between TYQ1 and these enriched strains.
*Metabolic interactions between TYQ1 and the enriched strains. (A) Attraction between TYQ1 and enriched strains grown at increasing proximity on TSA medium. TYQ1, Rhizobium pusense TYQ1 (OTU1981); SP, Sphingomonas panni (OTU2477); NS, Novosphingobium subterraneum (OTU613); XA, Xenophilus aerolatus (OTU2715); AS, Acidovorax soli (OTU2167); MA, Microbacterium arborescens (OTU11267); SX, Sphingomonas xanthus (OTU1716); AF, Acidovorax facilis (OTU2649). (B) Biofilm formation by individual strains or in co-culture with TYQ1. (C–I) Growth curve of enriched strains in pure TSB medium and in TSB medium supplemented with 10% TYQ1 supernatant. The maximum growth rate (r) and carrying capacity (K) were obtained by fitting a logistic growth model. (J, K) Comparison of the carrying capacity (K) and maximum growth rate (r) of each enriched strain cultured in M9 medium with or without TYQ1 supernatant. (L) Growth curve of the TYQ1 strain in M9-glucose medium and in M9-filtrate medium. (M) Metabolic network diagram between TYQ1 and the enriched strains. Growth parameters (carrying capacity) derived from logistic model–fitted growth curves were plotted as edges in a directed graph. Edge width and color represent the carrying capacity of the target node strain when cultured using byproducts secreted by the source node strain. (N) Colonization ability of TYQ1 inoculated alone or within a SynCom in the rhizosphere. For all panels, data represent mean ± SEM. In (B), (J), and (K), significance was assessed using Student’s t-test. *P < .05, **P < .01, **P < .001. In (N), different letters indicate statistically significant differences determined by one-way ANOVA followed by Tukey’s post hoc test (P < .05). The number of biological replicates (n) is as follows: (B), n = 4; (C–K), (L, N), n = 3.
Investigating whether metabolic promotion mediates the interaction between TYQ1 and the enriched strains, we carried out a TSB medium supplementation experiment (Fig. S18A). By fitting the growth curves with a logistic model, it was discovered that generally the maximum growth rate of the enriched strains increased significantly after adding the supernatant of TYQ1, whereas their environmental carrying capacity did not change (Fig. 4C–K). Under the same conditions, the supernatant of the enriched strains did not influence TYQ1growth (Fig. S18B–D). Further carbon source utilization spectrum analysis indicated that TYQ1 could utilize most of the 64 carbon sources, and there was a broad overlap in carbon source utilization between TYQ1 and the seven enriched strains, suggesting potential nutritional competition among them (Fig. S16C).
We conducted a series of metabolite feeding experiments to determine whether cross-feeding occurred between TYQ1 and the enriched strains (Fig. S19A). The experimental findings indicated that TYQ1 could utilize the metabolites secreted by all seven enriched strains for growth (Fig. 4L). Except for AS, which exhibited a relatively slow background growth in M9 basic medium, the other six strains could also grow using the metabolites of TYQ1 (Fig. S19B–H). Moreover, there were extensive cross-feeding relationships among the seven strains. Thus, a metabolic interaction network centered on TYQ1 was constructed (Fig. 4M, Table S4), suggesting that TYQ1 appears to act as a central node in community assembly. To assess the centrality of TYQ1, we performed a node-removal experiment in Gephi. The removal led to the complete interruption of most of high-capacity metabolic flow paths directed to TYQ1, resulting in the loss of >42% of the high-intensity metabolic interactions in the network (Fig. S20, Table S6). When TYQ1 and the seven strains were combined in equal proportions to form a SynCom and inoculated onto cucumber roots, the colonization of TYQ1 showed a transient significant increase within 1 week after nematode inoculation compared to the single inoculation of TYQ1 (Fig. 4N, Fig. S21). In summary, the recruitment of beneficial rhizobacteria by TYQ1 can likely be ascribed to its extensive metabolic interaction capabilities centered around itself. Although these interactions are founded on competition, they are predominantly characterized by mutualism and synergy, thus facilitating community stability and the realization of functions.
TYQ1-centered SynCom elicits plant defense responses to combat nematode infection
We evaluated the biocontrol efficacy of the TYQ1-centered SynCom by comparing its anti–M. incognita performance with that of individual strains. In vitro assays indicated that all single strains exhibited significant nematicidal activity (with TYQ1 being the most potent; Fig. 5A–B), whereas the SynCom showed a synergistic, enhanced biocontrol effect. Additionally, although only AF and TYQ1 could significantly inhibit M. incognita chemotaxis toward roots, the SynCom also showed a more pronounced inhibitory effect in this regard (Fig. 5C). Based on the previously identified metabolic interaction network centered on TYQ1 in the SynCom (Fig. 4M), it was hypothesized that TYQ1 could potentially assume a vital part in the synergistic suppression of RKNs by this community. To validate this hypothesis, we assembled a complete SynCom (All) consisting of all eight strains and eight defective SynComs, each lacking one strain (i.e. -SX, -XA, -MA, -NS, -SP, -AS, -AF, and -TYQ1) (Fig. 5D–E). In general, the All exerted the most substantial inhibitory effect on root galls and egg masses, whereas the defective SynComs showed a diminished inhibitory capacity (Fig. 5D–E, Fig. S22). The -TYQ1 not only lost its inhibitory function but even had the opposite effect, facilitating the formation of egg masses on the roots.
*Ability of the SynCom to synergistically resist root-knot nematode infection. (A, B) In vitro inhibitory activity of SynCom metabolites and those from individual members against root- knot nematodes. (C) Chemotactic migration of root-knot nematodes toward roots. Mock, root treated with 10 mM MgSO4 buffer. Significance was assessed using Student’s t-test. *P < .05; **P < .01; **P < .001. (D, E) Number of root galls per gram of root (D) and number of egg masses per gram of root (E) inoculated with various synthetic communities in one-strain knockout experiment. Mock, root treated with 10 mM MgSO4 buffer. (F, G) Root gall numbers (F) and egg mass numbers (G) in cucumber plants inoculated with synthetic communities of different diversity. Each point represents one synthetic community, showing the mean value of 6–8 plants. (H) Fresh weight of cucumber plants. Mock, treated with 10 mM MgSO4 buffer; Mi, inoculated with nematodes; TYQ1 or SynCom, inoculated with TYQ1 or SynCom suspension; TYQ1 + Mi or SynCom + Mi, co-inoculated with TYQ1 or SynCom suspension and nematodes. (I) Number of root galls per gram of root. (J) Number of egg masses per gram of root. (K) Principal component analysis of genes expressed in cucumber roots. (L) Venn diagram of differentially expressed genes (DEGs). (M) Heatmap of DEGs. Highlighted labels indicate DEGs related to plant defense responses. (N) Principal component analysis of metabolites in cucumber roots. (O) Venn diagram of differential metabolites (DMs). (P) Categories and relative abundance of DMs. (Q) Heatmap of DMs belonging to the shikimate and phenylpropanoid pathways. For all panels, data represent mean ± SEM. In (A), (B), (D), (E), and (H–J), different letters indicate statistically significant differences determined by one-way ANOVA followed by Tukey’s post hoc test (P < .05). The number of biological replicates (n) is as follows: (A), (B), n = 3; (C), n ≥ 5; (D, E), n ≥ 20; (H–J), n ≥ 14.
To elucidate the central role of TYQ1 in the synergistic resistance, we established SynComs with diverse diversity gradients (ranging from 0 to 8 species; a total of 85 community combinations) and systematically compared the impacts of including or excluding TYQ1 on the suppression of M. incognita infection (Fig. 5F–G). Overall, the inhibitory effects on the number of galls and egg masses increased with the rise in diversity. At the same diversity level, communities containing TYQ1 were superior to the corresponding combinations without TYQ1, suggesting that TYQ1 is an essential prerequisite for the SynCom to fully manifest its synergistic nematicidal function. Compared with the single inoculation of TYQ1, the inoculation of the TYQ1-centered SynCom had a more pronounced positive effect on cucumber plants (Fig. S23). Under nematode stress, the single-strain treatment with TYQ1 led to an 18.1% increase in cucumber biomass and a reduction in the number of galls and egg masses by 10.9% and 26.9%, respectively (Fig. 5H–J). In contrast, the SynCom treatment resulted in a 41.2% increase in biomass, along with a reduction in the number of galls and egg masses by 37.1% and 45.5%, respectively. These findings clearly demonstrate that the TYQ1-centered SynCom is significantly more effective than the single inoculation of TYQ1 in enhancing the plant’s stress resistance, exhibiting an obvious community synergy effect. The consistent results from pot experiments using 12 distinct soil types confirmed the broad-spectrum suppressive effect of SynCom inoculation against root-knot nematode infection (Fig. S24, Table S5).
Transcriptome profiling was performed to investigate cucumber root transcriptional response to TYQ1 and TYQ1-centered SynCom inoculation. Distinct separation was observed among the treatment groups (Fig. 5K). Under nematode stress, 1553 differentially expressed genes (DEGs) were identified between the TYQ1 and SynCom treatments, with 535 commonly induced DEGs enriched in defense and abscisic acid response pathways; under non-stress conditions, 238 common DEGs were enriched in the plasma membrane and plasmodesmata-related functions (Fig. 5L, Fig. S25A–C). KEGG enrichment analysis further indicated that DEGs were extensively involved in various stress response processes, including phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, the MAPK signaling pathway, and plant–pathogen interaction (Fig. S25D–E). We selected 65 key genes co-regulated by TYQ1 and the SynCom, which were distributed across the aforementioned metabolic pathways (Fig. 5M). Among them, 18 genes were closely associated with defense responses, including phenylalanine ammonia-lyase (PAL) gene (e.g. CsaV3_4G002330.1) that catalyze the rate-limiting step of phenylpropanoid biosynthesis, WRKY transcription factor gene (e.g. CsaV3_3G033350.1) that is a key regulator of plant immune signaling, and pathogenesis-related protein (PR) genes (e.g. CsaV3_6G050560.1) involved in systemic resistance activation. These genes play pivotal roles in reinforcing cell wall integrity, inducing antimicrobial compound synthesis, and triggering immune signaling cascades to counteract RKN infection [35–37]. q-PCR validation demonstrated that under nematode stress, the majority of genes were significantly upregulated in both the TYQ1 and SynCom treatments (Fig. S25). Moreover, the expression levels of 10 genes (including CsaV3_2G009070.1, CsaV3_4G002330.1, CsaV3_7G008380.1, CsaV3_5G005000.1, CsaV3_3G033350.1, CsaV3_3G012170.1, CsaV3_2G034810.1, CsaV3_6G007840.1, CsaV3_1G004720.1, and CsaV3_6G050560.1) were further increased after inoculation with the SynCom (Fig. S26, Table S7). Thus, we conclude that although single inoculation of TYQ1 can activate plant defense responses, the SynCom can further enhance this response on this foundation. Furthermore, metabolomic analysis indicated that the root metabolite profiles varied among different treatment groups (Fig. 5N). Under nematode stress, 61 differentially expressed metabolites (DEMs) were detected in both the TYQ1 and SynCom treatments, while under non-stress conditions, 53 were identified (Fig. 5O, Fig. S25F). Under nematode stress conditions, the DEMs were primarily shikimates/phenylpropanoids, terpenoids, and alkaloids (Fig. 5P). Specifically, the shikimate/phenylpropanoid category includes phenylpropanoid derivatives, phenolic acid, lignans, coumarins, and flavonoids—which have been reported to exert distinct anti-RKN functions: phenylpropanoids that induce plant systemic resistance, phenolic acids and coumarins with direct nematotoxic activity, lignans that reinforce root-cell-wall rigidity to block RKN penetration, and flavonoids that inhibit nematode motility and egg hatching [38–41]. Consistent with these anti-RKN roles, most DEMs in this pathway exhibited a stepwise increase from the Mi treatment to the TYQ1 + Mi treatment and then to the SynCom + Mi treatment (e.g. poliumoside, trifolin, and calycanthoside) (Fig. 5Q, Supplementary Data 2). In summary, compared with the single inoculation of TYQ1, the TYQ1-centered SynCom more effectively activates the expression of plant defense genes and the accumulation of metabolites, thereby enhancing plant resistance to nematode infection.
Discussion
Current knowledge regarding the interactions between microbial inoculants and indigenous microbiomes remains limited [17, 18]. This highlights the necessity for further exploration of SynComs based on functional and strain interaction principles [19]. Here, we developed a stress-induced recruitment of keystone species–based system for designing functionally stable SynComs (Fig. 6). This SynCom exhibited significant synergistic effects and enhanced plant resistance to RKN stress. Our methodology can serve as an approach for identifying elite microbial strains and developing SynComs that can help combat various biotic or abiotic stresses in agricultural production.
Mechanism by which stress-induced keystone species recruitment drives the assembly of functional microbes to suppress root-knot nematode infection. Under root-knot nematode stress, cucumber plants mediate the significant enrichment of a keystone species (KS) in the rhizosphere through root exudates. This KS effectively suppresses nematode infection and promotes plant growth. Inoculation with this KS effectively recruits functional microbes (“partners”) from the indigenous rhizobacterial community to colonize the rhizosphere. Based on the metabolic interaction network between the KS and its “partners,” a KS-centered synthetic microbial community (KS-centered SynCom) was constructed. Compared to inoculation with the KS alone, the KS-centered SynCom exhibits stronger suppression of root-knot nematode infection and greater promotion of plant growth.
Our research shows that RKN infection consistently results in the reorganization of the bacterial microbiome in the rhizosphere, regardless of the type of soil (Fig. 1B). This mechanism enables plants to recruit beneficial microorganisms capable of enhancing their stress resistance [5, 42], which is consistent with the cry for help strategy adopted by plants in response to various stresses [12, 14]. Rhizobium were significantly enriched in the rhizosphere following RKN infection (Fig. 1E–F). This is accordance with a recent discovery regarding tomato root endophytic microbiota, but the inhibitory effects of Rhizobium were not verified in this study [43]. We isolated a Rhizobium strain (TYQ1) from the rhizosphere of M. incognita–infected plants and verified its significant inhibitory effect on RKN infection (Fig. 2H–P). Rhizobium is conventionally recognized for forming symbiotic nitrogen fixation systems with leguminous plants, and its function typically relies on colonization within nodules [44]. However, this study reveals that Rhizobium can also perform anti-stress functions in non-host plants (such as cucumber), indicating the cross-host and ecological diversity of the plant-beneficial functions of Rhizobium. Additionally, TYQ1 demonstrated universal inhibitory effects on RKNs in various types of soil (Fig. S10), especially under unsterilized soil conditions. This phenomenon prompted us to hypothesize that there is a positive interaction between TYQ1 and indigenous microorganisms, thereby synergistically enhancing its disease-suppressive effect on plants.
The selection of R. pusense TYQ1 as the core research object was driven by three mutually reinforcing, evidence-based rationales. First, TYQ1 exhibited cross-soil conserved enrichment. As the representative of OTU2834, it was the only taxon significantly enriched across three distinct soil types following M. incognita infection (Fig. 1G). In contrast, other enriched OTUs were either unculturable (e.g. OTU856) or soil specific, limiting their generalizability (Fig. S4). Second, TYQ1 possessed dual functional validation. Its cell-free supernatants directly inhibited M. incognita J2 motility and egg hatching via key metabolites (Fig. 2N–P), whereas in planta assays demonstrated that they reduced root galls and egg masses under nematode stress, alongside enhancing plant biomass (Fig. 2G–L). Third, TYQ1 had keystone potential to restructure indigenous microbial communities. Its inoculation consistently enriched beneficial genera (e.g. Sphingomonas and Acidovorax) and established a central metabolic interaction network, distinguishing it from other single-functional strains and aligning with our study’s focus on community-level biocontrol (Figs. 3 and 4). Collectively, these traits validated TYQ1 as a representative keystone species to dissect stress-driven microbial community assembly.
Inoculation with TYQ1 led to a significant reassembly of the rhizosphere microbial community (Fig. 3A, Fig. S11). A similar community reorganization has been observed across diverse plant–inoculant strain systems [25, 28, 45], suggesting that interactions between indigenous plant microbiota and exogenously introduced strains play a key role in mediating plant-associated microbial community assembly. However, such interactions are inherently dynamic, context dependent, and strongly shaped by strain-specific traits—including fine-scale genetic differences between strains that drive distinct ecological behaviors and interaction patterns [46]. The influence of exogenous inoculants on the indigenous microbial microbiome exhibits dynamic characteristics (e.g. bacterial α-diversity and species dominance peak at the initial stage and then gradually decline; Fig. S11F–G). This can be ascribed to the fact that over time, owing to microenvironmental alterations, the early ecological niche advantage of TYQ1 in the community is gradually replaced by other species [47, 48]. Although the direct influence of TYQ1, regarded as a keystone species, wanes over time, a group of indigenous microbial taxa become significantly enriched as a result of their metabolic interactions with TYQ1 (Figs. 3 and 4). The enriched taxa are predominantly concentrated in the Proteobacteria phylum (Fig. S12). This phylum is renowned for its rapid response to resource fluctuations and high growth rate, and most of its members are typical copiotrophic bacteria [10, 49, 50]. Presumably, the nutrient-solubilizing function of TYQ1 can increase the available nutrient content, thereby promoting the reproduction and niche occupation of these nutrient-loving bacteria while competitively inhibiting oligotrophic ones [10, 51].
Stability constitutes a critical bottleneck for the transition of SynComs from laboratory settings to practical applications. Currently, research focus in this field is gradually shifting from “how to assemble” to “how to assemble stably” [52, 53]. Addressing whether nematode infection can elicit nematode-suppressive microbial shifts independent of TYQ1, our SynCom manipulation experiments (defective communities and diversity gradients) revealed two key findings: (i) Nematode infection does trigger basal enrichment of other beneficial microbes, as exemplified by strains AF and SP that exhibited significant in vitro nematicidal activity (Fig. 5A–B); (ii) TYQ1 is nonetheless indispensable for maximizing community synergism—defective SynComs lacking TYQ1 not only lost efficient nematode suppression but also promoted egg mass formation, whereas TYQ1-containing communities outperformed their TYQ1-free counterparts at the same diversity level (Fig. 5D–G). This indicates that although TYQ1 is not irreplaceable for basal microbial suppression, it acts as a central coordinator to organize scattered beneficial microbes into a coherent, high-efficacy network, which is essential for stable and robust biocontrol in complex soil environments.
Metabolite exchange, particularly cross-feeding interactions, is a well-documented mechanism underlying microbial mutualism and community stability [21, 44, 54]. In this study, we observed a close metabolic interaction between TYQ1 and its recruited strains, with both sides providing each other with essential growth substances (Fig. 4). Although cross-feeding also occurs among other members of the community, the entire network is clearly centered around TYQ1 (Fig. 4M), a feature attributable to the strong metabolic capacity of TYQ1 (Fig. S16D) that enables it to create ecological niches for other species and thereby establish the structural framework for community coexistence [55]. The irreplaceable role of TYQ1 is further supported by the finding that its absence not only drastically reduced the SynCom’s nematode suppression ability (despite the biocontrol potential of other members) but also impaired the overall colonization capacity of the community (Figs. 4N and 5)—a phenomenon consistent with the principle that loss of core species directly compromises the fitness of dependent community members [56]. In contrast, certain recruited strains (e.g. AF and AS) exhibit robust plant growth–promoting functions despite having relatively weak nematode resistance. The absence of these strains led to a notable decline in the community’s plant growth–promoting activity (Fig. S22). Additionally, they might support the rhizosphere colonization of TYQ1 through nutrient feedback mechanisms (Fig. 4M). Thus, if TYQ1 is considered the “core” for nematode resistance, its recruited strains play the role of “satellites.” This distinct division of labor and collaborative mechanism is crucial for improving the structural stability and functional diversity within the community [20].
As expected, the TYQ1-centered SynCom exhibited a functional synergistic effect. It not only inhibited the infection of RKN but also activated plant defense responses and promoted the accumulation of shikimates/phenylpropanoids (Fig. 5H–Q). These metabolites, including lignin, coumarins, flavonoids, and phenolic acids, are derived from the phenylpropanoid pathway and are widely involved in plant stress responses and environmental adaptation [57–60]. As a key end product of this pathway, lignin can enhance the mechanical strength of the cell wall through deposition and consequently hinder the penetration of nematode stylets and the establishment of feeding sites. Coumarins and flavonoids attract beneficial microorganisms to indirectly enhance plant health and are directly toxic to RKNs. These findings indicate that the SynCom may more effectively inhibit RKN infection by synergistically improving the plant defense capacity. Although this study centered on the “further” recruitment effect of core strains enriched under adversity on the indigenous probiotic bacterial community and attributed the recruitment of these enriched strains to inter-strain interactions, it mainly focused on bacterial interactions. However, the rhizosphere microecology encompasses not only bacteria but also fungi, archaea, and protozoa. Thus, if subsequent research integrates the investigation of multi-domain microbial interactions, it is anticipated to offer a more comprehensive perspective for the construction and application of SynComs.
In conclusion, this study utilized a strain, TYQ1, which was enriched under nematode stress conditions and could effectively inhibit RKN infection, as the core strain to explore its interaction with the indigenous bacterial community. The study found that there was a close metabolic network between TYQ1 and its recruited strains. Based on this, the TYQ1-centered SynCom further enhanced the control efficiency of RKNs. These findings highlight the vital role of microbial interactions in improving the stress tolerance of plants. They also provide a theoretical foundation for establishing stable and efficient functional microbial communities and are of great significance for promoting the application of microbial preparations in sustainable agriculture.
Supplementary Material
wrag022_Supplemental_Files
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