Three endophytic strains, SE16 (Pantoea sp., NCBI accession number PX642997), SE19 (Priestia sp., NCBI accession number PX642996), and SE47 (Peribacillus sp., NCBI accession number PX642995), with P-solubilizing, indoleacetic acid (IAA)--producing, and ACC deaminase-producing characteristics, were all screened from S. sudanense and stored in the Key Laboratory of Microbial Engineering of Henan (Henan, China). Previous antagonistic experiments showed that there were no antagonistic effects among the three strains. S. sudanense seeds were purchased from Zhengzhou Huiboyuan Horticulture Co., Ltd. (Henan, China).

Soil for the pot experiment was collected from the surface layer (0–20 cm) of a paddy field in Xinxiang, Henan province, China. The soil was air-dried, ground, and sieved through a 2-mm mesh. An aqueous solution of K₂Cr₂O₇ was prepared using autoclaved distilled water to achieve a contamination level of 300 mg Cr per kg of soil. The solution was applied to the soil and mixed thoroughly to ensure even distribution of the Cr. Subsequently, the soil was air-dried in shade and allowed to equilibrate for 2 months. One hundred and fifty S. sudanense seeds were sown in plastic pots containing 1 kg of Cr-contaminated soil. For endophytes inoculation, SE16, SE19, and SE47 suspensions were prepared by culturing these strains in Luria–Bertani (LB) liquid medium overnight at 37 °C to the exponential phase with continuous shaking. Following centrifugation to clear the medium, the endophyte inocula were prepared by suspending the cells in sterilized water to achieve an inoculum density of 10⁹ cfu/mL, respectively. Isochoric bacterial suspensions were prepared in a 1:1 or 1:1:1 ratio for inoculated treatments. Six treatment groups with three replicates were used. The specific design is shown in Table 1. For treatment groups inoculated with endophytes, the endophytes were gently inoculated into the Cr-contaminated soil before planting and after the emergence of S. sudanense with 50 mL of endophyte inoculum. For control without inoculation, 50 mL of sterile water was drenched. The pot experiment was conducted in an artificial climate chamber for 30 days under the following cultivation conditions: a photoperiod of a 16-h: 8-h light/dark cycle, a temperature of 25 ± 1 °C, and a relative humidity of 75%. Soil and plant samples were collected from each pot after 30 days of cultivation.

Each plant sample was subdivided into shoots and roots. The shoots and roots were separated, washed with deionized water, and weighed to measure their fresh weight. They were then heat-killed at 105 °C for 30 min and oven-dried at 75 °C for 48 h to estimate Cr accumulation in the plant. Part of the fresh shoots and roots were taken, washed with distilled water, immediately frozen in liquid nitrogen, and stored at −80 °C for the analysis of chlorophyll content, malondialdehyde (MDA) content, peroxidase (POD), and catalase (CAT) activity.

The chlorophyll content of the shoot was determined following the method of Lichtenthaler (1987). The MDA content was determined by homogenizing samples in 10% TCA, followed by centrifugation at 10,000 g for 10 min. Thiobarbituric acid (0.6%) and supernatant were mixed and then heated at 100 °C for 15 min, followed by cooling and centrifugation at 10,000 g for 15 min. The supernatant absorbance was recorded at 450, 532, and 660 nm (Chen et al., 2017). The activities of POD and CAT were measured using kits provided by Nanjing Jiancheng Bioengineering Institute, China. The Cr content of plants was determined by nitric acid–perchloric acid digestion–flame photometry.

The bioconcentration factor (BCF) and translocation factor (TF) were calculated according to the following Equations 1, 2:

Data are presented as the mean ± standard deviation (mean ± SD). Statistical analyses were performed using a one-way analysis of variance (ANOVA) followed by least significant difference (LSD) tests with SPSS software. Differences were considered significant at a p-value of ≤ 0.05.

Pot experiments demonstrated that inoculation with endophytes under Cr stress significantly promoted the growth of S. sudanense (Figure 1). Both single and combined inoculations significantly increased shoot length (plant height) and root length. Compared with the non-inoculated control, plant height increased by 26.4–49.2%, and root length increased by 63.5–122.8% after inoculation with endophytes. Except for treatment T3, shoot fresh weights increased significantly, reaching 2.01–3.08 times that of the non-inoculated control. Root fresh weights were also significantly increased by inoculation, except in treatments T3 and T4.

The Cr uptake by S. sudanense grown in artificially contaminated conditions is shown in Figure 1. With or without inoculation of endophytes, the roots exhibited a higher Cr concentration compared to the shoots. Endophyte inoculation led to a marked reduction of Cr concentration in the shoots and roots of S. sudanense. Specifically, shoot Cr concentration was 2.59 to 6.93 times higher in non-inoculated control plants than in inoculated plants, while root Cr concentration in most inoculated treatments (except for the combined inoculation T5) decreased by 25.8 to 53.7% relative to the control. Furthermore, both the BCF and TF for Cr significantly decreased in all inoculation treatments compared with the non-inoculated control.

As key indicators of soil fertility and remediation status, soil enzymes are strongly influenced by pH, OM, and microbial activity. Consistent with previous findings, endophyte inoculation promoted soil microbial activity and further improved soil enzyme activity and fertility (Babu et al., 2015; Liu et al., 2022; Wang et al., 2022). In our study, although soil pH remained unaffected across treatments, inoculation increased the soil OM under Cr stress. Moreover, the combined inoculation treatment T5 resulted in a significant increase in alkaline phosphatase activity relative to the non-inoculated control.

The bioavailability of HMs in soil, which in turn determines phytoextraction efficiency, is primarily governed by their chemical speciation. In this study, endophyte inoculation was found to reduce the fraction of exchangeable Cr, thereby decreasing its bioavailability. This shift in speciation implied that the endophytes facilitated the stabilization of Cr in the soil.

The composition of the soil microbial community is a key factor influencing the toxicity of HMs and plant tolerance during the remediation process (Zhang et al., 2015). Given this factor, soil microbial community structure is increasingly used as an indicator to assess the effectiveness of phytoremediation in contaminated soils (Gao et al., 2025; Li et al., 2022; Lin et al., 2025). Under HM stress, plant growth is strongly dependent on soil microorganisms, which facilitate nutrient acquisition and enhance metal tolerance through various growth-promoting mechanisms (Babu et al., 2013; Bacon and White, 2016; Chen et al., 2020; Yung et al., 2021).

Alpha diversity indices, such as the Shannon, Simpson, Ace, and Chao indices, are widely used to assess the diversity and richness of a microbial community. Previous studies have demonstrated that inoculation with endophytes (either bacterial or fungal, alone or in combination) under HM stress typically enhanced phytoremediation efficiency by increasing the diversity and richness of the soil microbial community (Gao et al., 2025; Wang L. et al., 2020; Wang et al., 2022). While our findings revealed that the endophyte inoculation led to a reduction in both soil bacterial diversity and richness, this discrepancy may be attributed to the competitive advantage of the introduced endophytes, which could have occupied ecological niches and consumed resources, thereby suppressing native microorganisms. Additionally, the inoculation might have intensified host selective pressure, further shaping the microbial community structure (Jiang R. et al., 2025; Lin et al., 2025). Plant root-driven changes in rhizosphere microbial communities have been well-documented (Bulgarelli et al., 2012; Edwards et al., 2015). The reduction in bacterial community diversity in the rhizosphere soil of certain plant systems has been suggested to result from a combined decline in both taxonomic richness and evenness (Li et al., 2012; Shi et al., 2015). Soil pH, the speciation of heavy metals, and certain physicochemical properties such as N and potassium (K) were major factors influencing the microbial community structure in rhizosphere soil (Wang et al., 2022). Our study indicated that inoculating endophytes altered the physicochemical properties of S. sudanense rhizosphere soil and changed the speciation of chromium, which inevitably modified the root environment of S. sudanense. Hou et al. (2018) suggested that plant roots may selectively influence surrounding microorganisms, altering species abundance and reducing the evenness of taxonomic distribution (enriching specific taxa or causing the disappearance of low-abundance taxa), thereby leading to a decline in taxon-based diversity indices. Our findings also confirmed this point. Although the inoculation of endophytes reduced soil microbial diversity and abundance, it promoted the enrichment of microorganisms associated with plant heavy metal resistance. Additionally, bacterial growth rate and biomass production are simultaneously influenced by metal ion concentrations (Deng et al., 2007; Hou et al., 2018). Certain sensitive taxa may be diminished due to heavy metal toxicity (Pishchik et al., 2016), which is also one of the reasons for the reduction in diversity.

The relative abundance analysis of soil bacterial phylum level showed that endophyte inoculation resulted in significant changes in their relative abundance, especially Pseudomonadota and Bacteroidota, in soil treated by single inoculation T1 and combined inoculation. Pseudomonadota, a highly diverse and abundant phylum, exhibited strong potential in the detoxification of Mn(II), Hg(II), As(III), and Cr(VI) into their less harmful forms (Belzile et al., 2006; Biełło et al., 2023; Campos et al., 2010; He et al., 2023; Naziębło and Dobrzyński, 2025; Yao et al., 2020). Bacteroidota possessed genes related to HM resistance, such as those encoding metal transport proteins, antioxidant enzymes, and other protective mechanisms, and could utilize various organic and inorganic substances as energy sources and enable themselves to survive in stressful environments (Jiang R. et al., 2025). Together, these microbes contribute to the alleviation of HM toxicity and improvement of environmental quality.

Endophyte inoculation significantly led to the enrichment of some bacterial genera, such as Delftia and Saccharimonadales. The genera Delftia and Saccharimonadales are known to play a significant role in the bioremediation of pollutants. They can alleviate HM stress on plants through multiple mechanisms, such as secreting phytohormones like IAA, transforming HMs into less toxic forms, and releasing specific compounds to enhance plant nutrient uptake (Adarme-Duran et al., 2025; Chandwani et al., 2025; Conlon et al., 2025; Doolotkeldieva et al., 2024; Long et al., 2024; Lyu et al., 2021; Zheng et al., 2024). These findings suggest that the inoculation of endophytic bacteria promoted the enrichment of Delftia and Saccharimonadales, which in turn support the growth of the plants and enhance the resistance of plants to Cr.

Endophytes enhance the phytoremediation efficiency by altering the HM activity, mitigating their toxicity and metal-induced stress on plants, promoting plant growth, and improving the resistance of plants to HMs (Badawy et al., 2022; Gao et al., 2025; Herpell et al., 2023; Lin et al., 2025; Liu et al., 2024; Ren et al., 2025; Wang et al., 2022; Ahsan et al., 2019; Xiang et al., 2024). Our results demonstrated that the endophyte inoculation increased the plant biomass, reduced the Cr concentration in the shoot and root of S. sudanense, enhanced plant photosynthetic capacity, and alleviated HM-induced oxidative stress, thereby promoting phytoremediation efficiency.

Our results showed that, although Peribacillus sp. SE47 possesses growth-promoting traits such as P solubilization, IAA production, and ACC deaminase activity, it did not enhance the biomass of S. sudanense in pot experiments. Peribacillus frigoritolerans was proven to stimulate plant growth under sterile conditions, but it failed to exhibit such effects in non-sterile environments (Świątczak et al., 2024). This may be due to the native rhizosphere microbial communities’ presence, resulting in the variation of beneficial effects of PGPB on plant development (Pacheco da Silva et al., 2022). Furthermore, the growth-promoting effect of the combined microbial community SE19 + 47 did not improve significantly, likely because complex interactions occurred among the strains after the consortium was constructed (Jiang W. et al., 2025), leading to the expression changes of functional genes in strain SE19, such as those involved in plant growth promotion, under the control of regulatory networks (Geesink et al., 2024).

Heavy metal stress will also lead to lipid peroxidation and potential depolarization of the cytoplasmic membrane, thereby affecting the composition, structure, and permeability of the cell membrane, resulting in intracellular electrolyte leakage (Ullah et al., 2019). MDA, the product of lipid peroxidation, serves as a key indicator of oxidative stress (Babu et al., 2015). In this study, MDA contents both in the shoot and root of S. sudanense inoculated with endophytes decreased under Cr stress. Heavy metal exposure induces the production of reactive oxygen species (ROS), resulting in oxidative damage to the plant, such as lipid peroxidation. To mitigate such damage, plants activate antioxidant defense systems, in which both antioxidant enzymes and non-enzymatic antioxidants play crucial roles (Ullah et al., 2019). While numerous studies have declared that endophytic bacteria can stimulate the synthesis of antioxidant enzymes in plants to alleviate oxidative stress (Bilal et al., 2019; Shahzad et al., 2019; Wang et al., 2023; Yue et al., 2021), our findings revealed a decrease in the activities of POD and CAT. This discrepancy may be attributed to the fact that endophyte-induced increases in plant biomass diluted the internal Cr concentration, thereby reducing HM toxicity and the corresponding demand for enzymatic detoxification (Khan et al., 2015). Furthermore, endophytic bacteria can mitigate the phytotoxicity of HMs, alleviating HM-induced oxidative stress and antioxidant responses in plants (Ma et al., 2016; Ullah et al., 2019; Wang et al., 2023).

Endophytic bacteria could promote the accumulation of HMs and root–shoot transfer in plants. However, the transfer would be influenced by factors such as HM bioavailability, physicochemical properties, soil HM composition, as well as the species of both the plant and the endophytic bacteria (Babu et al., 2015; Fan et al., 2018; Ma et al., 2011; Ma et al., 2016; Wang et al., 2023). In this study, endophyte inoculation significantly reduced Cr concentration in the shoots and roots of S. sudanense, with roots consistently showing higher Cr concentration than shoots. Plants with BCF > 1 and TF < 1 can be applied for phytostabilization (Babu et al., 2015), so our results demonstrated the potential of S. sudanense for Cr stabilization in plant roots.