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. 2025 Jul 31;36(2):229–252. doi: 10.21315/tlsr2025.36.2.11

Isolation of Bacteria from Lead-Contaminated Soil and Bacterial Interaction Test with Plant Growing on Lead-Amended Media

Dian Siswanto 1,*, Nurul Istiqomah 2, Azizuddin Muhammad Nashafi 1, Mukhaddam Muhammad 1, Fathul Mukaromah 3, Irfan Mustafa 1
PMCID: PMC12618092  PMID: 41244245

Abstract

The study investigated bacterial isolation from lead-contaminated soil, revealing the lower bacterial density compared to agricultural soil bacteria, indicating soil degradation. Among the isolated bacteria, three isolates with codes L03, L16 and L19 exhibited high tolerance to lead concentrations up to 1,500 mg/L. Selected isolates demonstrated the ability to produce Indole-3-Acetic Acid (IAA) hormone, with one strain notably producing the highest IAA concentration. Furthermore, three isolates exhibited significant lead bioaccumulation efficiency. Molecular identification revealed Lysinibacillus fusiformis as the highest IAA-producing strain and lead accumulator. Plant growth experiments analysed the bacteria’s potency to alleviate the heavy metal stress on Codiaeum variegatum, Dracaena reflexa and Jasminum humile. Additionally, bacterial addition decreased lead absorption only by D. reflexa, potentially through biosorption and bioaccumulation mechanisms. Integrating L. fusiformis into phytoremediation strategies could offer an effective and sustainable approach for remediating Pb-contaminated environments.

Keywords: Codiaeum variegatum, Dracaena reflexa, Jasminum humile, Lysinibacillus fusiformis, Plant Growth Promoting Bacteria

Highlights.

  • Twenty-sixth of Pb-tolerant bacterial isolates from Pb-contaminated soil were identified, with L03, L16 and L19 isolates demonstrating high tolerance to 1,500 mg/L Pb and significant bioaccumulation efficiencies (71.2%–81.1%).

  • Lysinibacillus fusiformis (L16 isolate) stood out for its ability to produce Indole-3-Acetic Acid (IAA), enhancing plant growth by increasing the fresh weight and root length of Dracaena reflexa and reducing Pb concentrations in Codiaeum variegatum.

  • Integrating IAA-producing Pb-tolerant bacteria, particularly L. fusiformis, into phytoremediation strategies was suggested to provide an effective and sustainable solution for remediating Pb-contaminated environments.

INTRODUCTION

The advent of global industrialisation has significantly exacerbated environmental pollution, particularly through the release of heavy metals into various ecosystems (Bosu et al. 2022). Heavy metal contamination, stemming from mining, industrial processes and agricultural activities utilising metal-based compounds, poses a grave threat to environmental and human health (Tangahu et al. 2011). Among the plethora of heavy metals, lead (Pb) stands out for its deleterious effects on living organisms, with no known biological or physiological functions and notable toxicity to humans, plants and microorganisms (Genchi et al. 2020). Pb, in particular, is associated with a myriad of adverse health effects upon chronic exposure, including high blood pressure, nervous system disorders, renal dysfunction, hyperactivity, anemia and infertility (Yahaghi et al. 2018). The accumulation of heavy metals in soil elevates the risk of these contaminants entering the food chain via plant uptake, ultimately posing significant health risks to animals and humans (Uddin et al. 2021).

Microbial immobilisation emerges as a promising remediation technique, offering environmental soundness, low production of hazardous materials and minimal energy consumption. Through various mechanisms such as extracellular adsorption, biomineralisation and redox reactions, heavy metal-immobilising bacteria demonstrate the capacity to stabilise toxic metals in soil, thereby mitigating their accumulation in plants (Etesami 2018). Notably, Agrobacterium tumefaciens and bacterial consortia, particularly those of Lysinibacillus , exhibit significant capabilities in immobilising Cd and Pb, thereby reducing their bioavailability in the soil (El-Meihy et al. 2019; Wang et al. 2014; Zhang et al. 2020b; 2021).

Bacteria contribute to enhancing plant resistance to metal toxicity and decreasing metal accumulation through various mechanisms such as siderophore secretion and modulation of metal availability (Guo et al. 2020; Cheng et al. 2020; Wang et al. 2018). Additionally, Indole-3-Acetic Acid (IAA) plays pivotal roles in plant-microbe interactions and metal stress adaptation. Bacterial IAA production promotes plant growth and enhances nutrient absorption, thereby mitigating metal stress in plants (Mishra et al. 2017; Etesami et al. 2015). Previous research has shown that the IAA begins to increase the level of protection against adverse external conditions by increasing the coordination of various cellular defense systems (Wahab et al. 2022). In general, bacterial IAA can reduce metal stress in plants by increasing plant growth in metal-contaminated soil and increasing nutrient absorption by increasing plant roots (Mishra et al. 2017). Bacterial IAA also facilitates adaptation and tolerance to metals in metal-stress plants by inducing physiological changes. This can be observed when IAA is involved in reducing heavy metal toxicity in plants by reducing the absorption and translocation of these heavy metals or stimulating antioxidant enzymes (Etesami et al. 2015). Although certain bacterial isolates have been reported to play a role in bioremediation and phytoremediation, exploration and isolation of bacteria from specific Pb-contaminated areas are still needed to develop indigenous bacteria-based mitigation technologies.

This study consists of four stages: (1) isolating bacteria from lead-contaminated soil, (2) testing the obtained bacterial isolates––including analysing the production of IAA hormones and their capacity to accumulate lead—and (3) molecular identification of bacteria. Because several previous studies only stopped at the stage of identifying bacterial isolates, our study sought to evaluate (4) the efficacy of bacterial inoculation on the growth and metal tolerance of Codiaeum variegatum, Dracaena reflexa and Jasminum humile grown in lead-amended media. C. variegatum is known for its ability to accumulate and tolerate heavy metals such as lead (Pb). (Herlina et al. 2020; Afzal et al. 2023). Similarly, D. reflexa is easy to grow and effectively accumulates Pb in its roots and stems when exposed to soil contaminated with lead and diesel fuel (Fathia et al. 2015; Dadrasnia & Pariatamby 2016; Conte et al. 2021). Jasminum sambac , commonly known as white jasmine, is another plant recognised for its ability to accumulate lead, with Pb found in its leaves, stems, roots and flowers. J. sambac is considered a lead hyperaccumulator (Perveen et al. 2011). Given the potential of J. sambac, its close relative, J. humile (yellow jasmine), presents an intriguing opportunity for further investigation as a potential lead phytoremediation agent. By isolating, selecting and identifying bacteria isolates and elucidating the role of bacteria and plant-microbe interactions in lead-amended media, this research endeavors to contribute to developing sustainable solutions for mitigating heavy metal pollution and thus enhancing food safety.

MATERIALS AND METHODS

Soil Sampling and The Soil Chemical Characteristic Measurements

Soil samples were taken from Pb-contaminated soil in Mojokerto Regency, East Java Province, Indonesia, at three different points, which were marked by the codes LKD1, LKD2 and LKD3 with coordinates of 7°22′34.05″ S, 112°27′36.32″ E, 7°22′34.22″ S, 112°27′35.79″ E, 7°22′34.63″S, 112°27′35.15″E, respectively. From each coordinate, a soil sample was taken with three repetitions and then composited. Soil samples were taken at a depth of 0 cm–15 cm from the soil surface using a soil corer (Zhang et al. 2020a). Further, the soil samples were put in a plastic bag and then placed in a cool box until they arrived at the laboratory. Soil pH values were measured by pH meter, Pb-soil contents were measured using the Atomic Absorption Spectrophotometer (AAS), and soil organic matter contents were determined using the Walkley and Black method. The basic principle behind the Walkley and Black method is the use of potassium dichromate (K2Cr2O2) as an oxidising agent, which reacts with organic matter (organic carbon) in the soil, converting it into carbon dioxide. The amount of potassium dichromate consumed during the reaction is then measured to estimate the organic carbon content. Since soil organic matter (SOM) is typically considered to contain 58% organic carbon, the organic carbon result is multiplied by a factor of 1.724 to convert from organic carbon to organic matter (Hossain et al. 2023).

Isolation of Bacteria

Bacteria were isolated from Pb-contaminated soil samples using nutrient agar (NA) medium supplemented with Pb. The medium underwent sterilisation at 120°C for 20 min, followed by the addition of filter-sterilised Pb(NO3)2 solution to achieve a final concentration of 100 mg Pb/L (Kurnia et al. 2015). The soil samples were then serially diluted with sterile saline solution (0.85% NaCl). Each 0.1 mL dilution series was inoculated on the media by the spread plate method and incubated at 30°C for four days. Bacterial colonies with different morphological characteristics were selected and purified. The purified bacterial isolates were re-cultured in test tubes with NA media and stored for further research.

Maximum Pb Concentration Tolerance Test of Bacteria Isolates

The maximum tolerance test was based on the method of De Guzman et al. (2016) with slight modification. This method was used to determine the maximum level of lead concentration that the isolates could tolerate. Each purified isolate was grown on the NA media with Pb addition which varies as 100, 300, 600, 1,000 and 1,500 mg Pb/L. The isolates were grown at room temperature for 48 h. Three isolates grown on media containing high concentrations of Pb were selected for use in the next test.

The Growth Curve of Pb-tolerant Bacteria

The bacteria growth observation was based on the modified Sulistyantini and Utami (2021) method. The starter culture was taken as much as 5 mL, and the optical density (OD) values were equalised between the selected isolates. Then, the culture was added to a sterile culture bottle containing 145 mL of NB medium with a total concentration of 200 mg Pb/L. The bacterial cultures in the bottles were incubated at room temperature on a rotary shaker at a speed of 120 rpm. Bacterial cultures were taken aseptically as much as 5 mL every 1 h for the first 6 , then every 2 h until 31 h, and once at 48 h of incubation. Cultures taken at a predetermined time were measured for absorbance values using a UV-Vis spectrophotometer at 600 nm. The absorbance value obtained was then converted into the number of cells using a linear equation from the standard curve of bacterial isolate cells.

Bacterial Indole 3-Acetic Acid (IAA) Production Test

Isolates of Pb-tolerant bacteria were cultured in bottles containing 25 mL of sterile nutrient broth (NB) media amended with 0.6 mg/mL L-tryptophan in a rotary shaker at 150 rpm, 30°C. After incubation for 24 h, 48 h and 96 h, 1 mL of the cell-free suspension was mixed with 2 mL of Salkowski’s reagent and allowed to stand at room temperature for 20 min (Yahaghi et al. 2018). The pink colour developed was then read at a wavelength of 530 nm. Spectrophotometric absorption values were converted to bacterial IAA concentrations using a pure IAA calibration curve.

Pb bioaccumulation test on bacteria isolates

The Pb bioaccumulation test was based on the method of Huang et al. (2018) and Shao et al. (2019) with modifications. The starter cultures of three selected bacterial isolates that were in the exponential phase were equalised for their absorbance values, then 1 mL was inoculated into a sterile culture bottle containing 30 mL of NB medium and 200 mg/L of Pb. Bacterial cultures were incubated at room temperature for 24 h in a rotary shaker at 150 rpm. Subsequently, it was centrifuged at 3,200 rpm for 10 min, and the supernatant was filtered using filter paper (Whatman No. 42). The Pb content in the supernatant was determined by AAS. Heavy metal bioaccumulation efficiency (R) is calculated as follows:

R=Co-CfCo×100%

where, R = Heavy metal bioaccumulation efficiency (%), Cf = Final heavy metal concentration (mg/L) and Co = Initial heavy metal concentration (mg/L).

Bacteria Identification Based on 16S rDNA

Chromosomal DNA of the most potential bacterium was extracted using the Zymo DNA Extraction Kit. The sequence of 16S rDNA was amplified using universal bacterial primers 27f (5′-AGA GTT TGA TCC TGG CTC AG-3′) and 1492r (5′-GGTTACCTTGTTACGACTT-3′). PCR amplification of 16S rDNA was carried out using GoTaq® Green Master Mix in Mastercycler Personal thermocycler (Eppendorf) subjected to initial denaturation at 94°C for 5 min, followed by 35 cycles consisting of denaturation at 94°C for 30 s, annealing at 55°C for 30 s and extension at 72°C for 1.5 min and a final extension of 72°C for 10 min (Rohmah et al. 2020). Amplicon of 16S rDNA was purified and sequenced in the 1st BASE, Malaysia. The 16S rDNA sequence of the isolate was aligned with reference strains from GenBank® and analysed using the MEGA 11 programme (Tamura et al. 2021). A phylogenetic tree was constructed and inferred with the neighbour-joining algorithm with the Tamura-Nei model using 1000 replicate bootstraps (Saitou & Nei 1987).

Interaction of Bacteria with Plant Growth on Pb-Amended Media

Preparation of the test plants

The test plants used for this study were C. variegatum , D. reflexa and J. humile obtained from the Bumiaji Residents’ Garden in the Bumiaji area, Batu City, East Java Province, Indonesia. The selected plants are plants with a height between 30 cm–45 cm. The planting medium used is a combination of fertile soil, manure, husks and coir pith (Cho-Ruk et al. 2006). The planting media were uniform for all treatments; therefore, their physical and chemical properties were not measured. Plants were acclimatised in the experimental garden for seven days before adding lead and bacteria solution. A 200 mL Pb solution containing 100 mg Pb/L was poured on the planting medium surface.

Inoculation of bacteria starter

The bacteria starter was prepared by inoculating one loop of bacterial culture on NB media and incubating it at room temperature until the exponential growth phase was reached. Subsequently, the starter was poured into the soil area around the plant (Mello et al. 2020). A 100 mL of starter contains 7.4 × 108 bacterial cells/mL.

The measurement of growth percentage (fresh weight, plant shoot, plant root), leaf IAA concentration and Pb absorption of plant

The fresh weight, shoot and root of plants were measured 14 days after adding 200 mL of the lead solution containing 100 mg Pb/L to the surface of the growing media, then the increasing percentages were calculated. Control plants grown on media without the addition of bacteria were compared to plants grown on growing media with the addition of bacteria. The level of heavy metal absorption was determined on the whole plant. Root sections were separated and washed extensively with one mM Ca(NO3)2 ·4H2O and then with distilled water to remove Pb ions that were adsorbed on the root surface. The weight of shoots and roots was recorded after drying in an oven at 75°C for 72 h. Oven-dried plant samples were digested in a mixture of concentrated HNO3-HCl (70%) and 2H2O (30%), and the concentration of Pb in the extract was determined using AAS (Tauqeer et al. 2016). Total Pb uptake by plants was calculated as the multiplication of plant dry weight and Pb concentration. In addition, the measurement of the IAA content of plant leaves was carried out using the Salkowski method (Etesami et al. 2015).

Data Analysis

The dataset, including bacterial counts, pH levels, soil organic matter content and Pb concentrations across various locations, was initially presented descriptively without statistical analysis. However, to delve deeper into its insights, statistical scrutiny was applied to two key aspects: bacterial IAA hormone production and the bioaccumulation of Pb by bacteria, which involved employing ANOVA followed by Tukey’s post-hoc analysis to discern significant differences. Furthermore, statistical evaluation was extended to other crucial metrics, including the percentage increases in fresh weight, shoot and root growth of plants, leaf IAA content and plant Pb concentration. Again, ANOVA, followed by Tukey’s post-hoc analysis, was used to identify significant variations across different conditions. In addition to these analyses, principal component analysis (PCA) was conducted to gain insights into the correlation between various parameters in the plant-bacteria interaction test.

RESULTS

Soil Bacteria and The Soil Chemical Characteristics

Isolation of bacteria from Pb-contaminated soil samples revealed an average bacterial cell count ranging from 1.1 × 104 CFU/g to 8.5 × 104 CFU/g on NA media with a total Pb concentration of 100 mg/L (Table 1). These bacteria were sourced from soil samples exhibiting pH values spanning from 6.86 to 7.74, organic matter content ranging from 1.06 g/kg to 1.27 g/kg, and Pb concentrations varying between 20.39 mg/kg to 131.01 mg/kg.

Table 1.

Details of sampling location and the bacteria cell number, pH value, organic matter and total Pb of soil in each location.

Sites Position code Latitude Longitude Bacteria cell number** (CFU/g) pH value** Organic matter* (%) Soil Pb* (mg/kg)
1 LKD1 7° 22′ 34.05″ S 112° 27′ 36.32″ E 1.1 ± 0.5 × 104 7/74 ± 0.29 1.06 131.01
2 LKD2 7° 22′ 34.22″ S 112° 27′ 35.79″ E 8.5 ± 0.3 × 104 6.89 ± 0.31 1.12 29.92
3 LKD3 7° 22′ 34.63″ S 112° 27′ 35.15″ E 8.5 ± 3.0 × 104 7.45 ± 0.18 1.27 20.39
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Note:

*

: n = 1,

**

: n = 2

Morphology Colony of Bacteria Isolates and Bacterial Tolerance to Maximum Pb Concentration

Bacteria isolation from soil samples yielded 26 distinct isolates based on their morphological characteristics (Table 2). Subsequently, a maximum concentration tolerance test revealed varying tolerance levels across all isolates. Notably, three isolates, namely L03, L16 and L19, demonstrated remarkable resilience, capable of thriving in Pb concentrations as high as 1,500 mg/L (Table 3).

Table 2.

Morphology colony of bacteria isolated from Pb-contaminated soil.

Position code Isolate code Morphology colony
Shape Margin Elevation Pigmentation Optical property Texture
LKD1 L01 Irregular Curled Pulvinate Yellow Shiny Contoured
LKD1 L02 Irregular Curled Pulvinate Non pigmented Shiny Rough
LKD1 L03 Irregular Entire Pulvinate Brown Shiny Rough
LKD1 L04 Irregular Entire Raised Yellow Shiny Contoured
LKD1 L05 Irregular Curled Convex Non pigmented Shiny Contoured
LKD1 L06 Irregular Erose Convex Yellow Iridescent Contoured
LKD2 L07 Rhizoid Lobate Flat Non pigmented Translucent Rough
LKD2 L08 Rhizoid Lobate Flat Non pigmented Shiny Rough
LKD2 L09 Filamentous Lobate Flat Non pigmented Translucent Contoured
LKD2 L10 Filamentous Lobate Flat Non pigmented Translucent Rough
LKD2 L11 Irregular Curled Convex Yellow Iridescent Concentric (single ring)
LKD2 L12 Irregular Curled Convex Yellow Shiny Contoured
LKD2 L13 Irregular Curled Raised Non pigmented Iridescent Contoured
LKD2 L14 Circular Entire Raised Yellow Shiny Concentric (single ring)
LKD2 L15 Circular Entire Pulvinate Non pigmented Shiny Rough
LKD2 L16 Circular Entire Pulvinate Non pigmented Iridescent Concentric (single ring)
LKD3 L17 Circular Entire Convex Non pigmented Shiny Concentric (single ring)
LKD3 L18 Rhizoid Lobate Flat Non pigmented Shiny Rough
LKD3 L19 Irregular Lobate Flat Non pigmented Shiny Rough
LKD3 L20 Circular Entire Convex Non pigmented Shiny Concentric (single ring)
LKD3 L21 Circular Entire Flat Non pigmented Shiny Concentric (single ring)
LKD3 L22 Filamentous Lobate Convex Non pigmented Iridescent Contoured
LKD3 L23 Irregular Entire Pulvinate Brown Shiny Rough
LKD3 L24 Circular Entire Umbonate Non pigmented Shiny Rough
LKD3 L25 Irregular Entire Convex Yellow Shiny Contoured
LKD3 L26 Irregular Entire Flat Non pigmented Shiny Rough
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Table 3.

Bacteria tolerance test to Pb concentration variations.

Position code Isolate code Pb concentration (mg/L)
100 300 600 1000 1500 2100
LKD1 L01 + + + − − −
LKD1 L02 + + − − − −
LKD1 L03 + + + + + −
LKD1 L04 + + + + − −
LKD1 L05 + + + + − −
LKD1 L06 + + + + − −
LKD2 L07 + + − − − −
LKD2 L08 + + + + − −
LKD2 L09 + + − − − −
LKD2 L10 + + − c − −
LKD2 L11 + + + + − −
LKD2 L12 + + + + − −
LKD2 L13 + + − − − −
LKD2 L14 + + + − − −
LKD2 L15 + + − − − −
LKD2 L16 + + + + + −
LKD3 L17 + + − − − −
LKD3 L18 + + − − − −
LKD3 L19 + + + + + −
LKD3 L20 + + + + − −
LKD3 L21 + + + + − −
LKD3 L22 + + − − − −
LKD3 L23 + + + + − −
LKD3 L24 + + − − − −
LKD3 L25 + + + + − −
LKD3 L26 + + − − − −
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Note: + = colony appeared, − = colony not appeared.

Bacterial Growth of Selected Isolates Without and Under Pb Addition

Bacterial growth was observed and presented as a growth curve to determine the growth phases of bacterial isolates and the effect of Pb on bacterial growth. The results were obtained from the growth characteristics of each different bacterial isolate.

Comparative analysis of growth curves for bacterial isolates in control media (Fig. 1) and media supplemented with Pb at 200 mg/L (Fig. 2) revealed a discernible influence of Pb on bacterial growth patterns.

Figure 1.

Figure 1

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Growth of three selected isolates growth in nutrient broth with 0 mg Pb/L.

Figure 2.

Figure 2

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Growth of three selected isolates growth in nutrient broth with 200 mg Pb/L.

Bacterial Indole Acetic Acid (IAA) Hormone

Various results were obtained based on the IAA production test on three selected isolates with the highest tolerance to Pb. The bacterial IAA hormone produced ranged from 4.42 mg/L to 7.68 mg/L (Fig. 3).

Figure 3.

Figure 3

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The concentration of IAA production by three selected isolates.

Note: Values shown by bars with the same letters are not significantly different (P > 0.05).

Among the tested isolates, L16 produced the highest concentration of IAA, reaching 7.78 ± 0.61 mg/L, a statistically significant difference compared to the other two isolates (Fig. 3). Conversely, L03 exhibited the lowest IAA concentration at 5.57 ± 0.47 mg/L, while L19 produced IAA at 4.42 ± 0.33 mg/L.

Bioaccumulation of Pb by Bacteria

Three isolates, specifically L03, L16 and L19, exhibited remarkable potential in accumulating Pb, as demonstrated in Fig. 4. Notably, isolate L03 displayed the Pb bioaccumulation efficiency of 71.2 ± 1.9%, statistically significantly lower than other isolates. The bacteria isolate L16 had a similar Pb bioaccumulation efficiency to the L19 isolate. Each type of bacteria can have a different potential to accumulate heavy metals.

Figure 4.

Figure 4

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Efficiency of Pb bioaccumulation by three selected isolates.

Note: Values shown by bars with the same letters are not significantly different (P > 0.05).

Molecular Identification of Selected Bacteria Isolate

A bacterial phylogeny tree was meticulously constructed for the L16 isolate, which was identified as the most promising bacteria based on the similarity of its 16S rDNA sequences. As depicted in Fig. 5, isolate L16 exhibited a striking 98% similarity to Lysinibacillus fusiformis .

Figure 5.

Figure 5

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Phylogenic trees of L16 isolate and reference isolates based on the similarity of 16S rDNA sequences with Neighbour-Joining algorithm.

Effect of Pb on Plant Growth

The impact of Pb addition to the growth media on plant development was assessed by measuring plants’ fresh weight, shoot length, and root length after 14 days of treatment, as summarised in Table 4. Notably, plants treated with bacteria tended to have significantly higher values of growth parameters than those without bacterial supplementation, which suggests a positive influence of IAA-producing bacteria addition to plant roots on plant growth, possibly attributable to mechanisms involving Pb immobilisation by bacteria, as evidenced by lower plant Pb and leaf IAA concentrations.

Table 4.

The effect of added bacteria on growth, leaf IAA concentrations, Pb concentration of plant growth on Pb amended-media.

No Plant species In addition to growth media Plant growth Leaf IAA concentration (μg/ml) Plant Pb concentration (mg/kg)
Fresh weight (%) Shoot height (%) Root length (%)
1 C. variegatum Pb 4.5 ± 1.5a 1.6 ± 0.0a 2.9 ± 0.1a 37.7 ± 0.6d 0.3 ± 0.1b
2 C. variegatum Pb + bacteria 7.5 ± 0.1a 4.8 ± 2.7a 11.4 ± 0.3b 21.7 ± 1.2c 0.2 ± 0.1ab
3 D. reflexa Pb 6.6 ± 1.9a 3.1 ± 1.5a 4.1 ± 0.1a 10.5 ± 3.0b 0.5 ± 0.0c
4 D. reflexa Pb + bacteria 19.8 ± 2.2c 6.1 ± 1.4a 16.4 ± 4.4c 7.5 ± 2.8ab 0.2 ± 0.0a
5 J. humile Pb 13.3 ± 3.0b 3.8 ± 1.2a 2.9 ± 0.1a 8.3 ± 1.8ab 0.1 ± 0.0a
6 J. humile Pb + bacteria 10.1 ± 0.9ab 4.5 ± 2.2a 11.4 ± 0.3b 5.5 ± 0.5a 0.2 ± 0.0a
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Notes: The data is presented as mean ± standard deviation of three individual experiments. Values in the same column with the same letters are not significantly different (P > 0.05).

In particular, the percentage increase in fresh weight and root length of Dracaena reflexa appeared to be influenced by bacterial-mediated Pb immobilisation, leading to lower plant Pb concentrations. Moreover, the IAA concentration in plant leaves exhibited a noteworthy trend, with plant growth in Pb-amended media (without bacteria addition) showing higher leaf IAA concentrations. This trend was particularly evident when comparing Codiaeum variegatum with and without bacterial supplementation.

Based on PC utilising five parameters—Leaf IAA, Plant Pb, percent FW, Percent PR, and Percent PS (depicted in Fig. 6)—the treatment involving the addition of bacteria to three distinct plant types under Pb conditions yielded four discernible response groups. Group 1 comprises D. reflexa + Pb; group 2 encompasses C. variegatum + Pb; group 3 includes C. variegatum + Pb + bacteria and J. humile + Pb; and finally, group 4 consists of J. humile + Pb + bacteria and D. reflexa + Pb + bacteria.

Figure 6.

Figure 6

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The correlation analysis of parameters by PCA.

DISCUSSION

It is noteworthy that bacterial density in agricultural soil typically falls within the range of 3.0 × 106 to 8.0 × 108 CFU/g (Bhowmik et al. 2019; Vieira & Nahas 2005). In contrast, the Pb-tolerant bacterial counts in the soil samples analysed were found to range from 1.1 × 104 to 8.5 × 104 CFU/g. Given that Pb-tolerant bacteria constitute approximately 24.5% of the total bacterial population (Marzan et al. 2017), the estimated total bacterial count in our samples would be a maximum of 3.5 × 105 CFU/g. This discrepancy is further underscored by the soil Pb concentration data, suggesting that the soil samples could be characterised as unhealthy soil.

Numerous prior studies have highlighted that bacteria sourced from heavy metal-contaminated soil exhibit heightened metal tolerance compared to those inhabiting regular soil environments (González Henao & Ghneim-Herrera 2021; Jin et al. 2018). This resilience is often attributed to the bacteria’s ability to sustain enzymatic activity, enabling growth and adaptation amidst heavy metal stress environments (Seneviratne et al. 2016).

According to Wang et al. (2015), bacterial growth characteristics are divided into several growth phases, namely the lag or adaptation phase, exponential, stationary and death. Notably, the growth trajectory on Pb-amended media diverged from that on the standard NB medium. Bacterial growth in Pb-containing media predominantly exhibited an adaptation phase during the initial stages. This finding aligns with Arifiyanto et al. (2017) assertion that lead toxicity hastens the onset of the death phase while curtailing the stationary phase. Furthermore, insights from Huang et al. (2018) underscore the pivotal role of initial heavy metal concentration in modulating microbial growth kinetics under metal-contaminated conditions. Elevated lead concentrations corresponded to heightened growth inhibition, consistent with Marzan et al.’s (2017) observations regarding the dose-dependent toxicity of lead. Among the bacterial strains tested, L16 exhibited noteworthy resilience, displaying a logarithmic growth phase from the 3rd to the 31 hour when cultured in NB medium supplemented with an additional 200 mg Pb/L. The phenomena highlights the differential responses of bacterial isolates to Pb-induced stress, emphasising the adaptive capacity of certain strains in hostile environmental conditions.

Under interaction with plants, bacteria utilised IAA to promote plant growth and mitigated abiotic stresses (Etesami & Glick 2024). Bacterial IAA significantly increases plant mineral absorption and nutrient uptake, thereby increasing plant lateral and adventitious root growth (Tirry et al. 2018). About 80% of IAA hormone-producing bacteria can generally be found in the soil around plant roots. Bacteria isolated from the soil around plant roots also have the potential to produce IAA hormones even in the presence of heavy metals (Ahemad 2015). The production of IAA by bacteria is subject to various influencing factors, including microbial species, temperature, tryptophan concentration, media pH, agitation and incubation duration (Jasim et al. 2014). Heavy metals exert a notable influence on bacterial IAA production. Siderophore-producing bacteria, such as Escherichia N16, Enterobacter N9 and Enterobacter K131, as well as non-siderophore-producing strains like Serratia K120 and Serratia Mc 119, have demonstrated heightened IAA production in the presence of metals like Cu, Pb, and As in growth media. Specifically, increased bacterial IAA production under Pb exposure is attributed to heightened siderophore production and ACC (1-aminocyclopropane 1-carboxylate) deaminase activity (Carlos et al. 2016), which underscores the pivotal role of bacterial phytohormone production, such as IAA, in mediating plant-bacteria interactions and promoting plant growth in heavy metal-contaminated soils, even under stressful conditions (Tirry et al. 2018).

Several factors influence the level of heavy metal accumulation by bacteria, including metal concentration, temperature, pH and initial inoculum size. Higher metal concentrations correspond to increased toxicity levels, impacting bacterial growth and accumulation rates. For instance, Bacillus cereus R-1 experienced decreased growth and Pb accumulation rates as the Pb concentration in the medium escalated from 10 mg/L to 100 mg/L (Huang et al. 2018). Aslam et al. (2020) further substantiated the correlation between heavy metal exposure concentration and accumulation levels. Klebsiella pneumoniae , Stenotrophomonas sp. MB339 and Staphylococcus sp. MB371 exhibited varying Pb accumulation percentages at different concentrations, indicating concentration-dependent effects. Despite this, our study’s isolates—L03, L16 and L19—outperformed them at 200 mg/L Pb, showcasing bioaccumulation efficiencies exceeding 70%.

Additionally, incubation temperature plays a crucial role in bacterial heavy metal accumulation. Optimal temperatures ranging from 23°C to 29°C were maintained in our study, facilitating efficient Pb accumulation. The pH of the growth medium also influences bioaccumulation levels, with neutral pH favouring optimal bacterial metabolism and ion transport processes. Notably, our study maintained a pH close to 7, aligning with optimal conditions for heavy metal accumulation. Moreover, the initial inoculum significantly impacts heavy metal accumulation, with higher inoculum sizes correlating with increased absorption areas and enhanced metal ion binding, underscoring bacterial biomass’s importance in facilitating efficient heavy metal uptake (Devika 2013; Shaaban Emara et al. 2023).

Based on previous report, the genus Lysinibacillus, especially Lysinibacillus sphaericus OT4b.31, exhibits notable tolerance to heavy metals, particularly chromium (Cr6+) and lead (Pb2+). Vegetative cells of this bacterium can withstand Pb2+ concentrations up to 1.5 mM, while spore formation occurs at higher concentrations, with spores showing resilience even at concentrations exceeding 20 mM. Notably, the inhibition caused lead is reversible, as the spores can revert to vegetative cells when the metal concentrations are reduced. In bioaccumulation assays, L. sphaericus OT4b.31 effectively removed Pb2+ from the medium. After 4 h of exposure, the Pb2+ concentration decreased by 41 mg/L. Interestingly, the presence of additional metal ions did not affect the bioaccumulation rate, suggesting that the bacterium employs distinct mechanisms to tolerate and resist metal toxicity (Shaw & Dussan 2018).

Further investigation revealed the presence of energy-dependent efflux pumps in L. sphaericus OT4b.31. Initially, metal ions such as Pb2+ accumulate inside the cells by a protein for divalent cation transport, followed by an active expulsion process to maintain intracellular metal levels below toxic thresholds. The bacterium demonstrated a more rapid response to Pb2+ compared to Cr6+, with more frequent oscillations in the efflux process when exposed to Pb2+. These findings suggest that the efflux pumps play a key role in regulating metal toxicity and maintaining cellular homeostasis, supporting the bacterium’s ability to bioaccumulate metals while simultaneously extruding excess ions (Shaw & Dussan 2018).

Passera et al. (2021) elucidated that L. fusiformis possesses specific plant growth-promoting attributes, including auxin production and phosphate solubilisation. Additionally, Trivedi et al. (2012) reported on the unique interaction profile of L. fusiformis, noting its affinity for healthy plants. Remarkably, they observed L. fusiformis exclusively in the roots of healthy citrus trees, contrasting with its absence in those afflicted by “Candidatus Liberibacter asiaticus ” infection. Generally, Pb exposure poses significant toxicity to plants, with low concentrations stimulating enzymatic activity in soil and microbial biomass, albeit with inhibitory effects observed at higher concentrations. Enzymatic activity, especially that of aryl sulfatase enzymes, tends to decrease with increasing Pb concentrations in plants. However, hyperaccumulator plants exhibit distinct responses to high soil Pb concentrations, demonstrating tolerance and the ability to absorb Pb at elevated levels without compromising metabolic function (Collin et al. 2022).

The process of heavy metal absorption by plants through their roots involves several intricate stages. Within the root organs, plants initiate pH adjustments and produce chelating substances known as phytosiderophores. These phytosiderophores bind to metals, facilitating their uptake via active transport mechanisms into root cells. Subsequently, metals are transported through the plant’s vascular system, including the xylem and phloem, to other plant parts such as stems and leaves. This translocation mechanism mitigates metal toxicity within plant cells, representing a crucial detoxification mechanism in plant organs (Banakar et al. 2017). The interaction between test plants and bacteria is vital in plant growth and tolerance to toxic compounds (Ma et al. 2015). Increased levels of heavy metals in the soil can interfere with phosphate absorption, but bacteria can help plants’ role in P solubilisation (Chen et al. 2014). Ma et al. (2011) showed that bacteria could affect metal mobility and metal availability by plants through several mechanisms, including soil acidification and phosphate dissolution. The mechanism happens due to the ability of bacteria to assist host plants in adapting to unfavorable environments, as well as to induce plant growth and increase plant metal-stress tolerance (Ma et al. 2016).

When considering Pb absorption by plants in the presence of bacteria, reduced absorption levels may result from the intricate interplay between bacteria and plants in the Pb absorption mechanism. Certain genera of soil bacteria are renowned for their capacity to bind heavy metals like Pb. This binding ability not only diminishes the availability of metals for plant uptake but also enhances metal mobility and availability in the soil through mechanisms such as the release of chelating agents, phosphate solubilisation and redox changes (Jing et al. 2007; Etesami & Glick 2024).

The selection of C. variegatum , D. reflexa and J. humile in this study was based on their characteristics of tolerance to heavy metals. The plants known as hyperaccumulators have evolved the ability to accumulate and tolerate very high concentrations of heavy metals in their tissues without suffering significant damage. C. variegatum was reported for its ability to accumulate and tolerate heavy metals like Pb and studied on its metal tolerance index (MTI), translocation factor (TF) and bioaccumulation factor (BAF), highlighting its potential for remediating lead-contaminated soil (Herlina et al. 2020; Afzal et al. 2023). Likewise, D. reflexa is a hardy plant that effectively accumulates Pb in its roots and stems when grown in Pb- and diesel-contaminated soil, and it can also absorb Pb from motor vehicle exhaust (Fathia et al. 2015; Dadrasnia & Pariatamby 2016; Conte et al. 2021). Another plant, Jasminum sambac (white jasmine), is known for accumulating Pb in its leaves, stems, roots and flowers and is categorised as a lead hyperaccumulator (Perveen et al. 2011). Building on the potential of J. sambac, its relative, J. humile (yellow jasmine), is an interesting candidate for a lead phytoremediation agent.

These heavy metal-tolerant plants possess mechanisms to mitigate the risk of metal poisoning by actively sequestering metals into sub-cellular compartments (Violante et al. 2010). Plants accumulate Pb intricately linked to microbial activity, which can alter the bioavailability of heavy metals and facilitate their translocation within plant tissues (Babu et al. 2013). Based on PCA, Group 1 correlates strongly with the Plant Pb parameter, while Group 4 exhibits a strong correlation with the percent FW parameter. Groups 2 and 3 also manifest variations in leaf parameters IAA, Percent PR and Percent PS. Integrating Tukey’s post hoc analysis and PCA results underscores D. reflexa’s notably most positive response to adding L. fusiformis.

CONCLUSION

This study found 26 Pb-tolerant bacterial isolates from Pb-contaminated soil, with three (L03, L16 and L19) demonstrating high tolerance and survival at 1,500 mg/L Pb. These isolates also showed significant bioaccumulation efficiencies (71.2%–81.1%) and IAA production, suggesting their potential for use in bioremediation. Among them, L. fusiformis (L16) emerged as the most promising, as it positively influenced plant growth, notably increasing the fresh weight and root length of D. reflexa and reducing Pb concentrations in C. variegatum . The results highlight the potential of IAA-producing bacteria in mitigating heavy metal stress, supporting their application in phytoremediation systems. The findings suggest that integrating Pb-tolerant bacteria, particularly L. fusiformis, into phytoremediation strategies could offer an effective and sustainable approach for remediating Pb-contaminated environments. Future research should explore the mechanisms underlying bacterial IAA production and its interaction with plants under metal stress to optimise bioremediation processes further. Additionally, using native bacterial communities in conjunction with hyperaccumulator plants could enhance heavy metal removal efficiency, providing a low-cost, eco-friendly alternative to conventional methods. This approach has significant implications for improving soil quality, mitigating industrial pollution and safeguarding human and environmental health.

ACKNOWLEDGEMENTS

The authors would like to thank the Universitas Brawijaya for the Grant of Research Programme for Professor and Doctor with contract number: 1624/UN10.F09/PN/2021.

Footnotes

AUTHOR CONTRIBUTIONS: Dian Siswanto: Conceptual idea, Methodology design, Writing and editing Nurul Istiqomah, Fathul Mukaromah and Irfan Mustafa: Methodology design Azizuddin Muhammad Nashafi and Mukhaddam Muhammad: Data collection, Data analysis and interpretation, Writing and editing

REFERENCES

  1. Afzal MR, Naz M, Wan J, Dai Z, Ullah R, Rehman Sur, Du D. Insights into the mechanisms involved in lead (Pb) tolerance in invasive plants: The current status of understanding. Plants. 2023;12(11):2084. doi: 10.3390/plants12112084. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ahemad M. Enhancing phytoremediation of chromium-stressed soils through plant-growth-promoting bacteria. Journal of Genetic Engineering and Biotechnology. 2015;13(1):51–58. doi: 10.1016/j.jgeb.2015.02.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arifiyanto A, Apriyanti FD, Purwaningsih P, Kalqutny SH, Agustina D, Surtiningsih T, Shovitri M, Zulaika E. Lead (Pb) bioaccumulation; Genera Bacillus isolate S1 and SS19 as a case study. AIP Conference Proceedings. 2017;1854:020003. doi: 10.1063/1.4985394. [DOI] [Google Scholar]
  4. Aslam F, Yasmin A, Sohail S. Bioaccumulation of lead, chromium, and nickel by bacteria from three different genera isolated from industrial effluent. International Microbiology. 2020;23(2):253–261. doi: 10.1007/s10123-019-00098-w. [DOI] [PubMed] [Google Scholar]
  5. Babu AG, Kim JD, Oh BT. Enhancement of heavy metal phytoremediation by Alnus firma with endophytic Bacillus thuringiensis GDB-1. Journal of Hazardous Materials. 2013;250–251:477–483. doi: 10.1016/j.jhazmat.2013.02.014. [DOI] [PubMed] [Google Scholar]
  6. Banakar R, Alvarez Fernández Á, Abadía J, Capell T, Christou P. The expression of heterologous Fe (III) phytosiderophore transporter HvYS1 in rice increases Fe uptake, translocation and seed loading and excludes heavy metals by selective Fe transport. Plant Biotechnology Journal. 2017;15(4):423–432. doi: 10.1111/pbi.12637. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bhowmik A, Kukal SS, Saha D, Sharma H, Kalia A, Sharma S. Potential indicators of soil health degradation in different land use-based ecosystems in the shiwaliks of northwestern India. Sustainability (Switzerland) 2019;11(14):3908. doi: 10.3390/su11143908. [DOI] [Google Scholar]
  8. Bosu S, Rajamohan N, Rajasimman M. Enhanced remediation of lead (II) and cadmium (II) ions from aqueous media using porous magnetic nanocomposites: A comprehensive review on applications and mechanism. Environmental Research. 2022;213:113720. doi: 10.1016/j.envres.2022.113720. [DOI] [PubMed] [Google Scholar]
  9. Carlos MHJ, Stefani PVY, Janette AM, Melani MSS, Gabriela PO. Assessing the effects of heavy metals in ACC deaminase and IAA production on plant growth-promoting bacteria. Microbiological Research. 2016;188–189:53–61. doi: 10.1016/j.micres.2016.05.001. [DOI] [PubMed] [Google Scholar]
  10. Chen L, Luo S, Li X, Wan Y, Chen J, Liu C. Interaction of Cd-hyperaccumulator Solanum nigrum L. and functional endophyte Pseudomonas sp. Lk9 on soil heavy metals uptake. Soil Biology and Biochemistry. 2014;68:300–308. doi: 10.1016/j.soilbio.2013.10.021. [DOI] [Google Scholar]
  11. Cheng C, Han H, Wang Y, He L, Sheng X. Metal-immobilizing and urease-producing bacteria increase the biomass and reduce metal accumulation in potato tubers under field conditions. Ecotoxicology and Environmental Safety. 2020;203:111017. doi: 10.1016/j.ecoenv.2020.111017. [DOI] [PubMed] [Google Scholar]
  12. Cho-Ruk K, Kurukote J, Supprung P, Vetayasuporn S. Perennial plants in the phytoremediation of lead-contaminated soils. Biotechnology. 2006;5:1–4. doi: 10.3923/biotech.2006.1.4. [DOI] [Google Scholar]
  13. Collin S, Baskar A, Geevarghese DM, Ali MNVS, Bahubali P, Choudhary R, Lvov V, Tovar GI, Senatov F, Koppala S, Swamiappan S. Bioaccumulation of lead (Pb) and its effects in plants: A review. Journal of Hazardous Materials Letters. 2022;3:100064. doi: 10.1016/j.hazl.2022.100064. [DOI] [Google Scholar]
  14. Conte A, Chiaberge S, Pedron F, Barbafieri M, Petruzzelli G, Vocciante M, Franchi E, Pietrini I. Dealing with complex contamination: A novel approach with a combined bio-phytoremediation strategy and effective analytical techniques. Journal of Environmental Management. 2021;288(February):112381. doi: 10.1016/j.jenvman.2021.112381. [DOI] [PubMed] [Google Scholar]
  15. Dadrasnia A, Pariatamby A. Phyto-enhanced remediation of soil co-contaminated with lead and diesel fuel using biowaste and Dracaena reflexa: A laboratory study. Waste Management and Research. 2016;34(3):246–253. doi: 10.1177/0734242X15621375. [DOI] [PubMed] [Google Scholar]
  16. De Guzman MLC, Arcega KSG, Cabigao JNR, Su GLS. Isolation and identification of heavy metal-tolerant bacteria from an industrial site as a possible source for bioremediation of Cadmium, Lead and Nickel. Advances in Environmental Biology. 2016;10(1):10–15. [Google Scholar]
  17. Devika L, Rajaram R, Mathivanan K. Multiple heavy metal and antibiotic tolerance bacteria isolated from Equatorial Indian Ocean. International Journal of Microbiological Research. 2013;4:212–218. [Google Scholar]
  18. El-Meihy RM, Abou-Aly HE, Youssef AM, Tewfike TA, El-Alkshar EA. Efficiency of heavy metals-tolerant plant growth promoting bacteria for alleviating heavy metals toxicity on sorghum. Environmental and Experimental Botany. 2019;162:295–301. doi: 10.1016/j.envexpbot.2019.03.005. [DOI] [Google Scholar]
  19. Etesami H, Glick BR. Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience. Microbiological Research. 2024;281(November 2023):127602. doi: 10.1016/j.micres.2024.127602. [DOI] [PubMed] [Google Scholar]
  20. Etesami H, Alikhani HA, Hosseini HM. Indole-3-acetic acid (IAA) production trait, a useful screening to select endophytic and rhizosphere competent bacteria for rice growth promoting agents. MethodsX. 2015;2:72–78. doi: 10.1016/j.mex.2015.02.008. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Etesami H. Bacterial mediated alleviation of heavy metal stress and decreased accumulation of metals in plant tissues: Mechanisms and future prospects. Ecotoxicology and Environmental Safety. 2018;147:175–191. doi: 10.1016/j.ecoenv.2017.08.032. [DOI] [PubMed] [Google Scholar]
  22. Fathia LAN, Baskara M, Sitawati Analisis kemampuan tanaman semak di median jalan dalam menyerap logam berat Pb. [Capability analysis of shrub plant to absorb Pb in median roadside]. Jurnal Produksi Tanaman. 2015;3(7):528–534. [Google Scholar]
  23. Genchi G, Sinicropi MS, Lauria G, Carocci A, Catalano A. The effects of cadmium toxicity. International Journal of Environmental Research and Public Health. 2020;17(11):3782. doi: 10.3390/ijerph17113782. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. González Henao S, Ghneim-Herrera T. Heavy metals in soils and the remediation potential of bacteria associated with the plant microbiome. Frontiers in Environmental Science. 2021;9:604216. doi: 10.3389/fenvs.2021.604216. [DOI] [Google Scholar]
  25. Guo JK, Muhammad H, Lv X, Wei T, Ren XH, Jia HL, Atif S, Hua L. Prospects and applications of plant growth promoting rhizobacteria to mitigate soil metal contamination: A review. Chemosphere. 2020;246:125823. doi: 10.1016/j.chemosphere.2020.125823. [DOI] [PubMed] [Google Scholar]
  26. Herlina L, Purnaweni H, Sudarno S, Widianarko, Sunoko HR. Phytoremediation of lead-contaminated soil by ornament plant Codiaeum variegatum. Journal of Physics: Conference Series. 2020;1567(3):032043. doi: 10.1088/1742-6596/1567/3/032043. [DOI] [Google Scholar]
  27. Hossain SA, Mazrin M, Habib MH. Determination of organic carbon of soil by the Walkley & Black method. Method. 2023 doi: 10.13140/RG.2.2.32699.80162/1. [DOI] [Google Scholar]
  28. Huang F, Wang ZH, Cai YX, Chen SH, Tian JH, Cai KZ. Heavy metal bioaccumulation and cation release by growing Bacillus cereus RC-1 under culture conditions. Ecotoxicology and Environmental Safety. 2018;157:216–226. doi: 10.1016/j.ecoenv.2018.03.077. [DOI] [PubMed] [Google Scholar]
  29. Jasim B, Jimtha John C, Shimil V, Jyothis M, Radhakrishnan EK. Studies on the factors modulating indole-3-acetic acid production in endophytic bacterial isolates from Piper nigrum and molecular analysis of ipdc gene. Journal of Applied Microbiology. 2014;117(3):786–799. doi: 10.1111/jam.12569. [DOI] [PubMed] [Google Scholar]
  30. Jin Y, Luan Y, Ning Y, Wang L. Effects and mechanisms of microbial remediation of heavy metals in soil: A critical review. Applied Sciences (Switzerland) 2018;8(8):1336. doi: 10.3390/app8081336. [DOI] [Google Scholar]
  31. Jing Yd, He Zl, Yang Xe. Role of soil rhizobacteria in phytoremediation of heavy metal contaminated soils. Journal of Zhejiang University Science B. 2007;8(3):192–207. doi: 10.1631/jzus.2007.B0192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kurnia K, Sadi NH, Jumianto S. Isolation and characterization of Pb resistant bacteria from Cilalay Lake, Indonesia. Aceh International Journal of Science and Technology. 2015;4(3):83–87. doi: 10.13170/aijst.4.3.3016. [DOI] [Google Scholar]
  33. Ma Y, Oliveira RS, Nai F, Rajkumar M, Luo Y, Rocha I, Freitas H. The hyperaccumulator Sedum plumbizincicola harbors metal-resistant endophytic bacteria that improve its phytoextraction capacity in multi-metal contaminated soil. Journal of Environmental Management. 2015;156:62–69. doi: 10.1016/j.jenvman.2015.03.024. [DOI] [PubMed] [Google Scholar]
  34. Ma Y, Rajkumar M, Luo YM, Freitas H. Inoculation of endophytic bacteria on host and non-host plants: Effects on plant growth and Ni uptake. Journal of Hazardous Materials. 2011;195:230–237. doi: 10.1016/j.jhazmat.2011.08.034. [DOI] [PubMed] [Google Scholar]
  35. Ma Y, Rajkumar M, Zhang C, Freitas H. Beneficial role of bacterial endophytes in heavy metal phytoremediation. Journal of Environmental Management. 2016;174:14–25. doi: 10.1016/j.jenvman.2016.02.047. [DOI] [PubMed] [Google Scholar]
  36. Marzan LW, Hossain M, Mina SA, Akter Y, Chowdhury AMMA. Isolation and biochemical characterization of heavy-metal resistant bacteria from tannery effluent in Chittagong city, Bangladesh: Bioremediation viewpoint. Egyptian Journal of Aquatic Research. 2017;43(1):65–74. doi: 10.1016/j.ejar.2016.11.002. [DOI] [Google Scholar]
  37. Mello IS, Targanski S, Pietro-Souza W, Frutuoso Stachack FF, Terezo AJ, Soares MA. Endophytic bacteria stimulate mercury phytoremediation by modulating its bioaccumulation and volatilization. Ecotoxicology and Environmental Safety. 2020;202:110818. doi: 10.1016/j.ecoenv.2020.110818. [DOI] [PubMed] [Google Scholar]
  38. Mishra J, Singh R, Arora NK. Alleviation of heavy metal stress in plants and remediation of soil by rhizosphere microorganisms. Frontiers in Microbiology. 2017;8:1706. doi: 10.3389/fmicb.2017.01706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Passera A, Rossato M, Oliver JS, Battelli G, Shahzad GIR, Cosentino E, Sage JM, Toffolatti SL, Lopatriello G, Davis JR, Kaiser MD, Delledonne M, Casati P. Characterization of Lysinibacillus fusiformis strain S4C11: In vitro, in planta , and in silico analyses reveal a plant-beneficial microbe. Microbiological Research. 2021;244:126665. doi: 10.1016/j.micres.2020.126665. [DOI] [PubMed] [Google Scholar]
  40. Perveen N, Hanif MA, Noureen S, Ansari TM, Bhatti HN. Phytoremediation of Pb(II) by Jasminum sambac. Journal of the Chemical Society of Pakistan. 2011;33(4):592–597. [Google Scholar]
  41. Rohmah NS, Suharjono, Jatmiko YD, Siswanto D, Mustafa I. The potency of endophytic bacteria isolated from ficus septica as phytoremediation promoting agent of Cr (VI) contaminated soil. Biodiversitas. 2020;21(5):1920–1927. doi: 10.13057/biodiv/d210519. [DOI] [Google Scholar]
  42. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 1987;4(4):406–425. doi: 10.1093/oxfordjournals.molbev.a040454. [DOI] [PubMed] [Google Scholar]
  43. Seneviratne M, Gunaratne S, Bandara T, Weerasundara L, Rajakaruna N, Seneviratne G, Vithanage M. Plant growth promotion by Bradyrhizobium japonicum under heavy metal stress. South African Journal of Botany. 2016;105:19–24. doi: 10.1016/j.sajb.2016.02.206. [DOI] [Google Scholar]
  44. Shaaban Emara N, Elwakil BH, Zakaria M, Olama ZA. Mechanistic action of lead removal by the native isolate Bacillus amyloliquefaciens ON261680.1. Arabian Journal of Chemistry. 2023;16(8):104962. doi: 10.1016/j.arabjc.2023.104962. [DOI] [Google Scholar]
  45. Shao W, Li M, Teng Z, Qiu B, Huo Y, Zhang K. Effects of Pb(II) and Cr(VI) stress on phosphate-solubilizing bacteria (Bacillus sp. strain MRP-3): Oxidative stress and bioaccumulation potential. International Journal of Environmental Research and Public Health. 2019;16(12):2172. doi: 10.3390/ijerph16122172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Shaw DR, Dussan J. Transcriptional analysis and molecular dynamics simulations reveal the mechanism of toxic metals removal and efflux pumps in Lysinibacillus sphaericus OT4b.31. International Biodeterioration and Biodegradation. 2018;127:46–61. doi: 10.1016/j.ibiod.2017.11.016. [DOI] [Google Scholar]
  47. Sulistyantini C, Utami U. The effect of addition Mn2+ metal ions and incubation time to Bacillus cereus cellulase enzyme activity from endophytic bacteria of Curcuma rhizome (Curcuma zanthorrizha Roxb.) El-Hayah. 2021;8(2):62–69. doi: 10.18860/elha.v8i2.12463. [DOI] [Google Scholar]
  48. Tamura K, Stecher G, Kumar S. MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution. 2021;38(7):3022–3027. doi: 10.1093/molbev/msab120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Tangahu BV, Sheikh Abdullah SR, Basri H, Idris M, Anuar N, Mukhlisin M. A review on heavy metals (As, Pb, and Hg) uptake by plants through phytoremediation. International Journal of Chemical Engineering. 20112011:939161. doi: 10.1155/2011/939161. [DOI] [Google Scholar]
  50. Tauqeer MH, Ali S, Rizwan M, Ali Q, Saeed R, Iftikhar U, Ahmad R, Farid M, Abbasi GH. Phytoremediation of heavy metals by Alternanthera bettzickiana : Growth and physiological response. Ecotoxicology and Environmental Safety. 2016;126:138–146. doi: 10.1016/j.ecoenv.2015.12.031. [DOI] [PubMed] [Google Scholar]
  51. Tirry N, Tahri Joutey N, Sayel H, Kouchou A, Bahafid W, Asri M, El Ghachtouli N. Screening of plant growth promoting traits in heavy metals resistant bacteria: Prospects in phytoremediation. Journal of Genetic Engineering and Biotechnology. 2018;16(2):613–619. doi: 10.1016/j.jgeb.2018.06.004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Trivedi P, He Z, Van Nostrand JD, Albrigo G, Zhou J, Wang N. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere. ISME Journal. 2012;6(2):363–383. doi: 10.1038/ismej.2011.100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Uddin MM, Zakeel MCM, Zavahir JS, Marikar FMMT, Jahan I. Heavy metal accumulation in rice and aquatic plants used as human food: A general review. Toxics. 2021;9(2):360. doi: 10.3390/toxics9120360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Vieira FCS, Nahas E. Comparison of microbial numbers in soils by using various culture media and temperatures. Microbiological Research. 2005;160(2):197–202. doi: 10.1016/j.micres.2005.01.004. [DOI] [PubMed] [Google Scholar]
  55. Violante A, Cozzolino V, Perelomov L, Caporale A, Pigna M. Mobility and biovailability of heavy metal and metalloids in the soil environments. Journal of Soil Science and Plant Nutrition. 2010;10(3):268–292. doi: 10.4067/S0718-95162010000100005. [DOI] [Google Scholar]
  56. Wahab A, Abdi G, Saleem MH, Ali B, Ullah S, Shah W, Mumtaz S, Yasin G, Muresan CC, Marc RA. Plants’ physio-biochemical and phyto-hormonal responses to alleviate the adverse effects of drought stress: A comprehensive review. Plants. 2022;11(13):1620. doi: 10.3390/plants11131620. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Wang J, Li Q, Li MM, Chen TH, Zhou YF, Yue ZB. Competitive adsorption of heavy metal by extracellular polymeric substances (EPS) extracted from sulfate reducing bacteria. Bioresource Technology. 2014;163:374–376. doi: 10.1016/j.biortech.2014.04.073. [DOI] [PubMed] [Google Scholar]
  58. Wang L, Fan D, Chen W, Terentjev EM. Bacterial growth, detachment and cell size control on polyethylene terephthalate surfaces. Scientific Reports. 2015;5:15159. doi: 10.1038/srep15159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Wang XH, Luo WW, Wang Q, He LY, Sheng XF. Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil. Environmental Pollution. 2018;241:529–539. doi: 10.1016/j.envpol.2018.05.088. [DOI] [PubMed] [Google Scholar]
  60. Yahaghi Z, Shirvani M, Nourbakhsh F, de la Peña TC, Pueyo JJ, Talebi M. Isolation and characterization of Pb-solubilizing bacteria and their effects on Pb uptake by Brassica juncea : Implications for microbe-assisted phytoremediation. Journal of Microbiology and Biotechnology. 2018;28(7):1156–1167. doi: 10.4014/jmb.1712.12038. [DOI] [PubMed] [Google Scholar]
  61. Zhang H, Gao Z, Shi M, Fang S. Soil bacterial diversity and its relationship with soil co2 and mineral composition: A case study of the laiwu experimental site. International Journal of Environmental Research and Public Health. 2020;17(16):1–20. doi: 10.3390/ijerph17165699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Zhang K, Xue Y, Zhang J, Hu X. Removal of lead from acidic wastewater by bio-mineralized bacteria with pH self-regulation. Chemosphere. 2020;241:125041. doi: 10.1016/j.chemosphere.2019.125041. [DOI] [PubMed] [Google Scholar]
  63. Zhang K, Zhang D, Wu X, Xue Y. Continuous and efficient immobilization of heavy metals by phosphate-mineralized bacterial consortium. Journal of Hazardous Materials. 2021;416:125800. doi: 10.1016/j.jhazmat.2021.125800. [DOI] [PubMed] [Google Scholar]

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