Introduction

The essential elements of life, such as air, water, and land, are contaminated constantly with different pollutants (Chhikara and Dhankhar 2008). The main group of inorganic pollutants is heavy metals which can accumulate in soils, plants, animals, aquatic organisms, and humans at toxic levels (Muduli et al. 2012). Therefore, the biomagnification of heavy metals in the environment is a serious threat to human health (Hooda 2007; Yigit and Altindag 2006).

Heavy metals like mercury (Hg), lead (Pb), arsenic (As), and cadmium (Cd) have no beneficial effect on organisms and are even toxic to human(s) and other living systems (Adriano 2001). Metal toxicity occurs when essential elements are replaced from their native binding sites, and the structure of DNA and proteins is changing, and by interference in enzymatic ATP formation and osmoregulation (Poole and Gadd 1989). Pb and Cd which are major pollutants found in the environment cause damage to cell membranes, changes in the particularity of enzymes, and carcinogenesis (Olaniran et al. 2013). Chronic toxicity of Cd results in proteinuria and lung emphysema, and its acute toxicity causes headaches, nausea, and diarrhea. Toxicity of Pb also creates various symptoms in the hematopoietic, hepatic, and renal system even in the nervous system, and chronic toxicity with blood concentrations of about 400–600 mg L−1 can lead to persistent vomiting, lethargy, delirium, convulsions, and coma if not attended timely (Flora et al. 2012).

Utilization of bacteria possessing metal-detoxifying traits and plant growth-promoting attributes is an efficient and environmentally friendly treatment approach and when these bacteria are used as bioinoculants and biofertilizers in heavy metal-polluted soils significantly improve the growth of plants and enhance the phytoremediation process (Khan et al. 2009; Pilon-Smits 2005). These bacteria increase metal mobility and bioavailability in soils and thus increase uptake of metals by plants. So, growth and metal accumulation are stimulated via reducing soil pH, producing indole acetic acid (IAA), monocyclopropane-1-carboxylate (ACC) deaminase, siderophores (metal-chelating compounds), and organic acids (Ahemad and Kibret 2014; Rajkumar et al. 2010). It has been reported that under conditions of heavy metal stress, the growth of plants is enhanced by auxin and gibberellin which are synthesized by rhizobacteria and are called plant growth-promoting hormones (Sharp et al. 2011). Heavy metal remediation is performed by microorganisms via different methods, including biosorption, intracellular accumulation, enzyme-catalyzed transformation, bioleaching (the extraction of metals through the use of living organisms), biomineralization (minerals formed by living organisms), and redox reactions (Lloyd et al. 2002). Furthermore, rhizobacteria augment plant tolerance to metals by inducing thiol compounds, superoxide dismutase, or metallothionein (Khalid et al. 2017). (Ahmad et al. 2016; Nath et al. 2012)

Conventional remediation approaches for heavy metal-polluted soils and water are generally physical, chemical, and biological techniques, which can be used in association with each other. Compared to physical-chemical methods, biological techniques show the great advantage with respect to economical, eco-friendly, less disruptive, field-scale application, high public acceptability, low time of remediation, and cost involved (Khalid et al. 2017). One of the most promising methods of bioremediation is microbial remediation that makes use of microorganisms to promote absorption, precipitation, oxidation, and reduction of heavy metals in the soil.

In this research, ornamental cabbage was selected due to its ability to tolerate and absorb high concentrations of heavy metals (Boyd and Barbour 1986). This cabbage variety is usually planted in autumn and winter, the seasons that are not suitable for growth of most plants used in the phytoremediation process. Thus, in cool seasons, this plant could be a good choice for the phytoremediation of heavy metal-polluted sites in urban areas and around smelter plants, where the soils are contaminated with high levels of Cd and Pb. Inoculation of plants with heavy metal-resistant plant growth-promoting rhizobacteria (PGPR) has been found as an interesting option to improve plant performance under stressed conditions. The aims of this study were to separate, identify, and describe the features of Cd- and Pb-resistant bacteria from heavy metal-polluted soils to acquire strains that might be suitable for inoculation of Pb- and Zn-contaminated soils under unfavorable ecological conditions. These strains also could be utilized for immobilization and detoxification of heavy metals in contaminated soils and for intensification of the phytoremediation process.

Material and methods

Study area and sample collection

Nearly 30 soil samples were collected from six different sites nearby a lead-zinc factory located in Dandi city, Zanjan province (between 36° 32′ and 36° 35′ N and 47° 36′ and 47° 40′ E), Northwest of Iran. The collected samples in labeled pre-sterilized bottles were moved to the lab and kept at 4 °C during experiments.

Measurement of physicochemical parameters of soil samples

The physicochemical parameters of soil samples, including available concentrations of Pb and Cd (Lindsay and Norvell 1978), total concentrations of Pb and Cd (Hseu 2004), available concentrations of potassium and phosphorus (Helmke and Spark 1996; Olsen 1954), and pH (Thomas 1996), were measured.

Isolation of bacterial strains

For isolation of bacterial strains, 1 g of each soil sample was added to 9 ml of sterile water to prepare a suspension. Then, a serial dilution (10−1 to 10−6) was prepared from the suspension with sterile nutrient broth (NB) medium and incubated at 36–37 °C for 24 h. Then, 100 μl of each dilution was spread on nutrient agar (NA) medium and incubated at 37 °C for 24 h. Depending on differences in color, morphology, and shape, each microbial colony was selected and separately streaked on NA medium and incubated overnight at 37 °C. Then, pure strains grown in this medium were stored in nutrient broth medium containing 25% (v/v) glycerol at − 20 °C or − 80 °C for further studies (Jamaluddin et al. 2012).

Determination of minimum inhibitory concentration

The minimum inhibitory concentrations (MICs) of Pb and Cd for isolated strains were determined by agar dilution technique (Chen et al. 2006a). NB media with different concentrations of Cd and Pb were prepared. The concentrations of Pb were 50, 250, 500, 1000, 1250, 1500, 2000, 2500, 3000, and 3500 μg ml−1, and the concentrations of Cd were 5, 10, 20, 25, 35, 50, 75, 100, and 150 μg ml−1 using lead nitrate [Pb(NO3)2] and cadmium sulfate [3Cd(SO4) × 8H2O] as the sources, respectively.

Heavy metal accumulation assay

Bacterial strains were transferred to LB medium and cultivated for 1 h at 37 °C with shaking at 150 rpm to the optical density (OD600 nm) of 0.6. Then, 2 ml of sterilized Pb or Cd solution with a concentration of 100 ppm was added separately to each culture flask and again incubated for 24 h, at the same condition. After incubation, the whole bacterial cells were removed by centrifugation at 5000 rpm for 15 min using a mini spin rotor and supernatants were mixed with two volumes of concentrated HNO3 (70%). The HNO3-treated samples were heated on a hotplate stirrer (IKA, RTC basic) to 100 °C until the sample volumes reduced to initial supernatant volume for acid digestion. The extract was clarified by removing insoluble material using filter paper (Whatman 42). This extract was analyzed by atomic absorption spectrophotometer (Varian Specter. AA20) for the concentration of heavy metals, and the results were compared with control to calculate the reduction in the heavy metal concentration and thus, accumulation capacity (%) as follows (Marzan et al. 2017):

$$ {\displaystyle \begin{array}{c}\mathrm{Heavy}\ \mathrm{metal}\ \mathrm{accumulation}\ \mathrm{capacity}\ \left(\%\right)=\frac{\mathrm{Heavy}\ \mathrm{metal}\ \mathrm{utilized}\ \left(\mathrm{ppm}\right)\ \mathrm{by}\ \mathrm{a}\ \mathrm{microbial}\ \mathrm{strain}}{\mathrm{Heavy}\ \mathrm{metal}\ \mathrm{added}\ \mathrm{to}\ \mathrm{the}\ \mathrm{LB}\ \mathrm{medium}\ \left(\mathrm{ppm}\right)}\times 100\\ {}\mathrm{Heavy}\ \mathrm{metal}\ \mathrm{utilized}\ \left(\mathrm{ppm}\right)\ \mathrm{by}\ \mathrm{a}\ \mathrm{microbial}\ \mathrm{strain}=\mathrm{Heavy}\ \mathrm{metal}\ \mathrm{added}\ \mathrm{to}\ \mathrm{the}\ \mathrm{LB}\ \mathrm{medium}\ \left(\mathrm{ppm}\right)\hbox{--} \mathrm{Heavy}\ \mathrm{metal}\ \mathrm{a}\mathrm{t}\ \mathrm{t}\mathrm{he}\ \mathrm{end}\ \mathrm{of}\ \mathrm{culture}\ \left(\mathrm{ppm}\right)\end{array}} $$
(1)

Identification of phenotypic and biochemical traits of bacterial strains

The cultural and biochemical traits were used to identify the bacterial strains, including Gram reaction, potato soft rot, oxidation/fermentation of glucose, oxidase and catalase reactions, production of fluorescent pigment on King’s medium B, levan production, and hypersensitive reaction (HR) on tobacco plants (Schaad et al. 2001).

Resistance to antibiotics was determined on Mueller Hinton agar plates (MHA) by disk diffusion method (Oyetibo et al. 2010). Tests were conducted in triplicate with (Raja et al. 2009) the following antibiotics: ampicillin (100 μg ml−1), amoxicillin (50 μg ml−1), tetracycline (20 μg ml−1), kanamycin (30 μg ml−1), erythromycin (50 μg ml−1), and nalidixic acid (10 μg ml−1).

The Pikovskaya medium was used to determine the qualitative activity of a selected strain for mineral phosphate solubilization (Subba Rao 2016). The colony and halo zone diameters were determined and used to calculate the index of solubilization by the following formula (Premono et al. 1996):

$$ \mathrm{SI}=\frac{\mathrm{colony}\ \mathrm{diameter}+\mathrm{halo}\ \mathrm{zone}\ \mathrm{diameter}}{\mathrm{colony}\ \mathrm{diameter}} $$
(2)

Quantitative analysis of mineral phosphate solubilization, in Pikovskaya broth medium containing tricalcium phosphate (5 g L−1), was performed as described by Subba Rao (2016). A standard curve was prepared using KH2PO4 and the amount of soluble phosphate was measured from the standard curve (Olsen and Sommers 1982). The method of Aleksandrov medium (Jones Jr 2001) was used to determine potassium solubilization, the method of Patten and Glick (2002) to determine IAA production, and the method of Alstrom and Burns (Alström and Burns 1989) to determine HCN production..(Alström and Burns 1989; Patten and Glick 2002; Subba Rao 2016).

DNA extraction

The following method was used to extract DNA from heavy metal-resistant bacteria:

Bacterial strains were grown in 3 ml of LB medium at 28 °C for 48 h, and then, the bacterial suspension was centrifuged at 3000 rpm for 3 min and the supernatant was removed and the pellet was washed twice in 400 μl of sterile-deionized H2O and solved in 200 μl of sterile-deionized H2O. After adding 400 μl of 2X buffer (SDS 1%, 25 mM EDTA, 50 mM Tris-HCl, pH = 8) and 2 μl of proteinase K (10 μg ml−1; Sigma), the bacterial suspension was further incubated at 55 °C for 3 h. After lacing the cell walls of the bacteria, 400 μl of 7.5 M ammonium acetate was added and mixed gently but completely, and the mixture was centrifuged (Hettich Mikro 220R) at 12,500 rpm for 20 min at 4 °C. The aqueous phase was transferred to a clean polypropylene tube and 750 μl of cool isopropanol was added and kept overnight at − 20 °C. In the next step, tubes were centrifuged (Hettich Mikro 220R) at 12,500 rpm for 30 min at 4 °C. Then, pellet was rinsed twice with 70% ethanol, and finally, the DNA dissolved in 20 μl of sterile-deionized H2O and kept at − 20 °C.

Molecular identification

The polymerase chain reaction (PCR) was used to amplify the 16S rRNA gene of the extracted DNA using a universal primer pair 63f (5′-CAG GCC TAA CAC ATG CAA GTC-3′) and 1387r (5′-GGG CGG WGT GTA CAA GGC-3′) in 30 μl of a reaction mixture possessing 4 μl of DNA template, 1.5 μl of each primer at a concentration of 5 mM, and 16 μl of master mix at a concentration of 10 mM. To perform PCR, a thermocycler (Astec PC320, JAPAN) with the following program was used. The first denaturation was carried out at 95 °C for 5 min followed by 40 cycles of denaturation at 94 °C for 30 s; annealing was carried out at 55 °C for 30 s followed by the first extension at 72 °C for 1.5 min and the final extension at 72 °C for 10 min. The PCR product was sequenced bi-directionally by Bioneer company (Daejeon, South Korea). The obtained nucleotide sequences (1018–1470 bp) were edited and compared with other relevant sequences available in the GenBank database using the BLAST homology search program. Also, phylogenetic analyses were conducted with MEGA 6 software (Molecular Evolutionary Genetics Analysis, version 6.0) (Tamura et al. 2013) and the phylogenetic trees were constructed using the neighbor-joining method with 1000 bootstrap replications.

Pot trial

The effects of soil inoculation with five selected strains on the growth and accumulation ability of heavy metal of Pb and Cd of the ornamental cabbage plant were evaluated in pot trial. A soil with medium pollution for heavy metals (lead and cadmium) was used for the pot experiment and each pot was filled with 4 kg of this soil (X = 737,500, Y = 4,048,000 (UTM), total concentrations of Pb = 560 mg kg−1, available concentrations of Pb = 54 mg kg−1, total concentrations of Cd = 7 mg kg−1, available concentrations of Cd = 0.62 mg kg−1, pH = 7.69, available phosphorus = 12.5 mg kg−1, available potassium = 422 mg kg−1), and then, three seedlings of ornamental cabbage (Brassica oleracea var. acephala L. Pigeon Victoria F1) were planted in each pot. The rhizosphere soils of ornamental cabbage were inoculated in triplicate with 2 ml of bacterial suspension from each strain with 107–108 cfu ml−1 and the plants were placed in an experimental greenhouse with a photoperiod of 12 h and night and a day temperature of 15 °C and 20 °C, respectively. A control treatment containing uninoculated rhizosphere soil was also used. Three months after sowing, fresh and dry weights of plant biomass, dry weights of root and shoot, concentrations of Pb and Cd in the root and shoot as well as plant uptakes of Pb and Cd were measured. Thus, plants were harvested and then the harvested plant materials divided into root and aerial parts and washed with tap and distilled water, respectively. The plant samples were oven-dried at 60 °C for 72 h before determination of dry matter (DM). Samples of the root and aerial parts were digested by three-acid mixture [H2SO4 (65%), HClO4 (65%), and HNO3 (70%)] at the ratio of 1:1:5 (Allen et al. 1986), and then, the concentrations of Pb and Cd were measured in the extract of digestion using Atomic Absorption Spectrometer (Varian Spectra. AA20).

The bioaccumulation factor (BAF) determines the rate of transfer of lead and cadmium contaminants from soil to plant and is calculated by dividing the concentration (mg kg−1) of an element in the root to the total concentration (mg kg−1) of the same element in the soil. The translocation factor (TF) determines the mobility and distribution of heavy metals in plants and is calculated by dividing the concentration (mg kg−1) of an element in the shoot to the concentration (mg kg−1) of the same element in the root (Li et al. 2007).

Statistical analysis

For assessment of microbial traits, all tests were carried out in triplicate and the means of replicates analyzed statistically and where significant differences observed between the means, standard deviation, and student test were used to differentiate the means. To study the effects of microbial strains on plant growth, the analysis of variance (ANOVA) of data was carried out by SAS software (version 9.4), and Duncan’s multiple range test at 1 and 5% probability levels was used for mean comparison.

Results

Isolation of bacteria from soils

In the current study, 83 bacterial single colonies with differences in apparent characteristics and shape of colony were isolated from six soil samples. From the bacterial strains isolated, only 24 strains could tolerate Cd and Pb in nutrient agar (NA) with the concentrations of 5 and 50 μg ml−1, respectively.

MIC each metal

MIC for Pb ranged from 50 to 3500 μg ml−1 and for Cd from 5 to 150 μg ml−1, respectively. In this experiment, the number of resistant strains decreased with an increase in the heavy metal concentration of media. As summarized in Table 1, 12 strains were resistant to a wide range of concentrations of Pb and Cd. According to the results, five strains (52, 56, 57, 59, and 60) which showed good tolerance capacity against Pb and Cd were selected (Table 1). These five strains showed better tolerance to Pb so that the strains 52 and 56 were able to tolerate 3000 μg Pb/ml and 50 μg Cd/ml, and the strains 57, 59, and 60 were able to tolerate 3500 μg Pb/ml and 100 μg Cd/ml. These five potential strains (52, 56, 57, 59, and 60) were also selected for conducting further bioremediation tests.

Table 1 Minimum inhibitory concentration (MIC) and accumulation capacity of bacterial strains to heavy metals of Pb and Cd
Full size table

Assessment of heavy metal accumulation capacity of bacterial strains

Heavy metal accumulation capacity was measured by analyzing the heavy metal concentration of the treated samples by atomic absorption spectrophotometer (Varian Specter. AA20) and comparing it with that of control. Strain 57 showed the highest Pb accumulation ability and strains 52 and 60 stood in second and third places. Strain 57 was able to reduce 60% of Pb and 40% of Cd at 24 h (Table 1).

Phenotypic and molecular identification of selected strains

Several attributes (cultural, morphological, and biochemical) of five potential heavy metal degrading strains were measured based on Schaad et al. (2001) methods and the results are shown in Table 2. (Schaad et al. 2001).

Table 2 Characteristics of the five strains of heavy metal-resistant bacteria
Full size table

The sensitivity of selected bacterial strains to six antibiotics was determined. Those strains were considered susceptible to antibiotics when the inhibition zone was 12 mm or more in diameter. In the present study, the strain 52 exhibited a high resistance pattern towards all antibiotics used. All strains were resistant to the nalidixic acid antibiotic (Table 2) and the strains 57 and 60 had a very high sensitivity to erythromycin antibiotic. The strain 59 also showed a medium sensitivity to ampicillin, amoxicillin, erythromycin, and kanamycin.

The results of this study showed that strains 57, 59, and 60 were able to solubilize tricalcium phosphate (Ca3(PO4)2 in broth medium and the highest solubilizing ability belonged to strain 59 with 145.83 μg ml−1. In general, the pH of culture medium was regarded as an index for phosphate availability and the phosphate availability increased as the pH of the culture medium decreased. Since strain 59 decreased the pH value of the culture medium from 7.7 to 4.7, it was regarded as the most effective strain in this way (Table 2). Equation 3 which shows P solubilization from tricalcium phosphate as a result of the decrease in pH is given as follows (Bolan et al. 2003):

$$ {2\mathrm{Ca}}_3{\left({\mathrm{PO}}_4\right)}_2+8\ {\mathrm{H}}^{+}\to {3\mathrm{Ca}}^{2+}+{4\mathrm{H}}_2{{\mathrm{PO}}_4}^{-} $$

The results showed that strains 57 and 59 were capable of solubilizing potassium in broth medium containing 2 g L−1 muscovite mineral. The highest solubilizing ability belonged to strain 59 with 55.33 μg ml−1, and strain 57 with 42.67 μg ml−1 stood in second place (Table 2).

Development of pink color in flasks indicated IAA production by strains 52, 56, and 59. The amounts of IAA produced by these strains ranged from 3.77 to 31.94 μg ml−1 and the best IAA producer was strain 52 (Table 2).

The bacterial strains possessing HCN production ability were classified into four groups with very high, high, medium, and low ability. The results showed that strains 57, 59, and 60 were capable to produce HCN. Also, it was observed that HCN production ability in strains 57 and 60 was weak and in strain 59 was high and the color of filter paper changed to light brown (Table 2).

Molecular identification and phylogenetic analysis

Nucleotide BLAST search in the GenBank database with the partial sequences of 16S rRNA gene and phylogenetic analysis showed that the strains 56, 57, and 59 had a homology of 100% with Enterobacter kobei DSM 13645T, clone 3 (Accession No. LT547822.1), Bacillus cereus isolate BCsn (Accession No. HE660034.1), and Rhizobium pusense strain: Naga 0113 (Accession No. LC208007.1), respectively. Also, the strains 52 and 60 clustered phylogenetically with Enterobacter cloacae isolate L2 (Accession No. LK391629.1) and Agrobacterium tumefaciens strain A78 (Accession No. KC196487.1) with 99.66% and 98.54% sequence similarity, respectively. Figure 1 shows the phylogenetic relationship between strains. The sequences acquired in this study were stored in the GenBank database under the accession numbers of MH327251, MH327252, MH327253, MH327254, and MK123361, respectively.

Fig. 1
figure 1

The phylogenetic tree constructed using neighbor-joining method based on partial 16S rRNA gene sequences of the strains obtained in this study and selected relevant strains from GenBank. The numbers next to nodes are confidence values of bootstrap (1000 replicates). The scale at the bottom represents genetic distance in nucleotide substitutions per site

Full size image

Pot trial

According to the analyses of variance of data, the effects of soil inoculation with bacterial species on fresh and dry weights of plant biomass, dry weights of root and shoot, Pb accumulation in the root, Cd accumulation in the root and shoot, as well as Pb and Cd uptake of the plant, were significant at the probability level of 1% (p < 0.01) (Table 3).

Table 3 The ANOVA results, indicating the effects of soil inoculation with bacterial species on fresh-dry biomass weight, root and shoot dry weight, concentrations of Pb and Cd in the root and shoot, and uptake performances in ornamental cabbage
Full size table

Inoculation of the soil by bacterial species caused fresh and dry weights of the biomass of ornamental cabbage and dry weights of root and shoot to increase significantly when compared with control treatment (Fig. 2). The largest increase in fresh and dry weights of plant biomass and dry weights of root and shoot was observed when the rhizosphere soils were inoculated by R. pusense (strain 59) and E. cloacae (strain 52), respectively (Fig. 2).

Fig. 2
figure 2

The effect of soil inoculation with bacterial species on fresh and dry weights of biomass (a) and dry weights of root and shoot of ornamental cabbage (b) after 3 months of transplanting in soil with medium pollution of lead and cadmium

Full size image

Inoculation of rhizosphere soils with the bacterial species significantly increased Pb accumulation in the root and Cd accumulation in the root and shoot compared with uninoculated plants or control treatments (Fig. 3). The highest concentration of Pb in the root and the highest concentrations of Cd in the root and shoot were measured for treatments inoculated with A. tumefaciens (strain 60). But significant differences in Pb concentrations of shoots were not observed when inoculated treatments were compared to control treatment (Fig. 3).

Fig. 3
figure 3

The effect of soil inoculation with bacterial species on concentrations of Pb (a) and Cd (b) in the root and shoot in ornamental cabbage after 3 months of transplanting in soil with medium pollution for lead and cadmium

Full size image

The highest uptake performances of Pb and Cd in biomass of ornamental cabbage were measured in treatments inoculated with A. tumefaciens (strain 60) and R. pusense (strain 59) (Fig. 4). When A. tumefaciens (strain 60) used as a soil inoculant, the uptake performances of Pb and Cd in biomass of ornamental cabbage increased by 3 and 6 times, respectively, and by using R. pusense (strain 59), the uptake performances of Pb and Cd increased by 3 and 5 times, respectively (Fig. 4).

Fig. 4
figure 4

The effect of bacterial species on uptake performances of the Pb and Cd in ornamental cabbage after 3 months of transplanting in soil with medium pollution for lead and cadmium

Full size image

Inoculation of ornamental cabbage with the bacterial species significantly increased the bioaccumulation factors of Pb and Cd. In all treatments, the calculated bioaccumulation factor of Pb was less than one, but that of the Cd was more than one (Fig. 5a). Also, the calculated translocation factors of Pb and Cd were less than one, suggesting the immobilization of Pb and Cd in the root (Fig. 5b).

Fig. 5
figure 5

The effect of bacterial species on the bioaccumulation factor (a) and the translocation factor (b) of the Pb and Cd in ornamental cabbage plant

Full size image

Discussion

The five bacterial species identified in this study showed a high resistance pattern against Pb and Cd. MICs of Pb and Cd for E. cloacae (strain 52) and E. kobei (strain 56) were 3000 μg Pb/ml and 50 μg Cd/ml, respectively. Also, B. cereus (strain 57), R. pusense (strain 59), and A. tumefaciens (strain 60) showed simultaneous resistance to Pb and Cd with MICs of 3500 μg Pb/ml and 100 μg Cd/ml (Table 1). Sevim and Sevim (2015) isolated 15 Bacillus strains from soil samples and one of them, which belonged to the B. cereus, was resistant to heavy metals. The MICs of heavy metals for this strain were 2500 μg ml−1 for Pb and 250 μg ml−1 for Cd. Rohini and Jayalakshmi (2015) isolated a B. cereus strain from the copper-polluted area and the strain was considered as a highly potential strain for bacterial bioremediation of contaminated area since it had a maximum tolerable capacity of 600 ppm which was significantly higher than most reported tolerance level. A bacterium was separated from disposing yard of municipal solid waste and characterized by Khatun et al. (2012). According to biochemical and 16S rDNA sequence profile, it was identified as B. cereus. The tolerance of this bacterium against heavy metals like Cd2+ (1.25 mg ml−1) and Pb2+ (0.75 mg ml−1) was observed and it was noted that the bacterium had the most resistance to Cd2+ compared to other metals. Naik et al. (2012) separated a lead-resistant bacterium from industrial effluent and it was recognized as E. cloacae based on its morphological and biochemical traits and 16S rDNA sequence data. This bacterium resisted lead nitrate up to 1.6 mM. Singh et al. (2010) reported that the B. cereus (SIU1) indicated a high level of resistance to elevated concentration of lead (600 μg ml−1). A potent heavy metal accumulating microbial strain was isolated from a polluted soil by Banerjee et al. (2015) and characterized as E. cloacae. The MICs of lead and cadmium for this strain were 1100 and 900 ppm, respectively. This bacterial strain had a high potential for the lead bioaccumulation (95.25%) and followed by cadmium (64.17%). (Banerjee et al. 2015; Khatun et al. 2012; Naik et al. 2012; Rohini and Jayalakshmi 2015; Sevim and Sevim 2015; Singh et al. 2010; Yang et al. 2007).

Other researchers have also reported Pb- and Cd-resistant species, including Pseudomonas aeruginosa (BC2), Pseudomonas aeruginosa (BC5) (Raja et al. 2009), Pseudomonas sp., Bacillus sp. (Nath et al. 2012), Enterobacter sp. (EG16) (Chen et al. 2016), Rhizobium halophytocola (RT7) (Gupta et al. 2016), Pseudomonas (RS-1), Bacillus (RS-2), Bacillus (RS-3) (Kumar et al. 2016), Bacillus (CIK-517), Bacillus (CIK-519), and Enterobacter (CIK-521R) (Ahmad et al. 2016).

In accordance with the results of this study, B. cereus (strain 57) had the highest accumulation capacity for Pb and Cd which was 60% and 40%, respectively. Similarly, E. cloacae (strain 52) and R. pusense (strain 59) species showed, respectively, an accumulation capacity of 45% and 50% for Pb and 30% for Cd (Table 1). The B. cereus (S5 strain) was considered as a biological adsorbent for remediation of severe and trace cadmium pollution by Wu et al. (2016) since this bacterium was able to eliminate a high quantity (72.1–83.1%) of Cd2+ (mg l−1) from the medium. Syed and Chinthala (2015) reported that B. cereus (NSPA8) showed a remarkable level of lead biosorption with a maximum of 87–90%. Three bacterial strains, two of Klebsiella sp. and one E. cloacae, were separated from wastewaters of chemical and textile industries. These strains showed high efficiency in removing cadmium from the medium, and when 100 μg ml−1 of Cd was added to the medium, the strains namely CMBL-Cd1, CMBL-Cd2, and CMBL-Cd3, respectively, removed or accumulated 86%, 87%, and 85% of Cd from the medium within 24 h (Haq et al. 1999). Kumar et al. (2015) reported that Bacillus thuringiensis (strain Simi) had an accumulation capacity of 54% for Pb.

In this study, all microbial species were tested for their response to several widely used antibiotics. The antibiotic resistance patterns of the strains were different and only E. cloacae (strain52) species showed resistance to all antibiotics (Table 2). Kim and Wei (2007) showed that E. cloacae were resistant to ampicillin, cephalothin, and amoxicillin antibiotics. Singh et al. (2010) reported that the B. cereus (SIU1) was resistant to antibiotics such as penicillin, lincomycin, cloxacillin, and pefloxacin. Sevim and Sevim (2015) isolated B. cereus from soil samples that were resistant to some antibiotics (ampicillin, methicillin, cephalothin, trimethoprim/sulfamethoxazole, and oxacillin). Pramanik et al. (2018b) reported that E. kobei was resistant to some antibiotics such as erythromycin, cephalexin, ampicillin, and lincomycin. From resistance to antibiotics that were observed in strains that had not been exposed to antibiotics so far, it can be concluded that in the lack of direct pressure, concurrent resistance to multiple antibiotics can happen in bacteria. A relationship between bacterial tolerances to heavy metals and antibiotics has been indicated in many studies (Verma et al. 2001). Tolerances to antibiotics and heavy metals may help bacteria to adapt themselves to conditions of heavy metal stress faster by the expansion of resistant factors than by mutation and natural selection (Silver and Misra 1988). (Kim and Wei 2007; Pramanik et al. 2018b).

A large portion of soil P is not available for plants and phosphate solubilizing bacterial (PSB) can convert it to available forms (Zaidi et al. 2009). Several studies have reported Pseudomonas, Bacillus, and Rhizobium genera as potent mineral phosphate solubilizers (Gandhi et al. 2014; Karpagam and Nagalakshmi 2014; Susilowati and Syekhfani 2014; Tripti 2012). Their study showed that Pseudomonas had the highest P-solubilizing ability which was 12.23 mg P/l from tricalcium phosphate. The highest amounts of P solubilized from tricalcium phosphate by Bacillus and Rhizobium were 0.32 mg l−1 and 0.28 mg l−1, respectively. Other bacteria which mineralize and solubilize poorly available phosphorus included Flavobacterium, Achromobacter, Agrobacterium spp., Aerobacter, Micrococcus, Pseudomonas spp., Rhizobium spp. (Babalola and Glick 2012; Rodriguez and Fraga 1999), Azotobacter (Kumar et al. 2014), Burkholderia (Istina et al. 2015; Mamta et al. 2010; Rodriguez and Fraga 1999; Zhao et al. 2014), Enterobacter and Erwinia (Chakraborty et al. 2009; Rodriguez and Fraga 1999), and Bacillus spp. (Babalola and Glick 2012; Jahan et al. 2013; Raj et al. 2014). Among the studied strains, R. pusense (strain 59) (145.83 μg ml−1) and A. tumefaciens (strain 60) (136.83 μg ml−1) showed the highest P-solubilizing ability when compared to other strains (Table 2). Dhull et al. (2018) isolated several microbial strains from the root nodules of cluster bean that their efficiency for P solubilization varied from 36 to 79%. (Dhull et al. 2018).

Since a powerful correlation was established between the quantity of phosphorus solubilized and the pH of culture media, it is concluded that the main mechanism of phosphate solubilization is acidification of culture media (Chen et al. 2006b). A highly significant correlation was found between the amount of phosphate solubilized and the pH of the culture media. This observation strongly suggests that the main mechanism of phosphate solubilization is medium acidification (Castagno et al. 2011). The phosphate-solubilizing strains reduce the pH of the culture medium by the production of organic acids and R. pusense (strain 59) and A. tumefaciens (strain 60) reduced it from 7.7 to 4.7 and 5.3, respectively (Table 2).

The results of this study also showed that B. cereus (strain 57) and R. pusense (strain 59) species were capable of solubilizing potassium (42.67 and 55.33 μg ml−1, respectively) (Table 2). Species such as B. cereus IARI-J-6 and B. mycoides have already been introduced as potassium solubilizer with a value of 72.8 and 66.4 mg K/l, respectively (Rajawat et al. 2014). Meena et al. (2015) studied the release of potassium from waste mica (muscovite and biotite) and found that A. tumefaciens and R. pusense were potassium-solubilizing rhizobacteria. Also, R. pusense strain KRB-2 (MF135560) could release 7.05 mg K/l from mica (muscovite) after 6 weeks of incubation (Hauka et al. 2017). (Meena et al. 2015).

Researchers have shown that the majority of microorganisms (80%) isolated from the rhizosphere of different crops has the ability to synthesize and release auxins as secondary metabolites (Loper and Schroth 1986). It has been shown that from different PGPR strains, genera Azospirillum, Pseudomonas, Xanthomonas, and Rhizobium together with Agrobacterium, Alcaligenes, Enterobacter, Acetobacter, and Bradyrhizobium have the ability to synthesize auxins which increase plant growth (Egamberdieva et al. 2008; Khan et al. 2014; Kumar et al. 2008; Poonguzhali et al. 2008; Wani et al. 2007). Indole-3-acetic acid (IAA) is one of those important hormones provided by microbe to plant that enhances the growth of root and stem and thus the length of the plant (Aloni et al. 2006). Comparatively, some strains used in this study presented IAA production, including, E. cloacae strain 52, R. pusense strain 59, and E. kobei strain 56 (31.94, 26.78, and 24.11 μg ml−1, respectively) (Table 2). The E. cloacae UW5, a plant growth-promoting rhizobacterium, was able to produce high levels of IAA through the indolepyruvate pathway (Ryu and Patten 2008) by utilizing indole-3-pyruvate decarboxylase enzyme (Koga et al. 1994). Strains of Enterobacter sp. separated from the rhizosphere of sugar cane produced about 2.21 μg IAA/ml in vitro (Mantelin and Touraine 2004). IAA production by PGPR could be varied among different strains and is also affected by culture and medium conditions, growth stage, and substrate availability (Kumar et al. 2012). Goswamia et al. (Goswami et al. 2013) reported strains of Pseudomonas spp. that had the ability to produce IAA (29 mg ml−1) and solubilize phosphorus (34 mg ml−1). Pramanik et al. (2018b), after screening rhizosphere soil of rice supplemented with Cd, isolated E. kobei which grew profusely in high concentration (1000 mg l−1) of Cd and had PGP traits (P solubilization, IAA production, NH3 production, HCN activity, etc) which were essential for plant growth promotion. The production of IAA also increases root growth, which is needed for obtaining nutrients under Cd stress conditions (Mitra et al. 2018a; Mitra et al. 2018b; Pramanik et al. 2018a; Pramanik et al. 2017). (Goswami et al. 2013; Pramanik et al. 2018b).

To obtain a higher crop yield and for phytoremediation of heavy metal-polluted soils, rhizobacteria possessing PGP traits can be used (Kumar et al. 2016). The association of heavy metal-tolerant plants and useful rhizospheric microorganisms is one of the most important steps in developing an effective phytoremediation system with the use of microorganisms. In this research, ornamental cabbage was selected due to the ability to tolerate and absorb high concentrations of heavy metals (Boyd and Barbour 1986). Our investigation clearly demonstrated that five selected Pb- and Cd-resistant bacterial species promoted fresh and dry weights of plant biomass and also, dry weights of root and shoot in the contaminated soil significantly (Fig. 2). Under abiotic stress conditions, beneficial rhizospheric soil-borne microbes may enhance plant growth by different mechanisms, including optimization of growth by the supply of nutrients, synthesis of phytohormones such as IAA and 1-aminocyclopropane-1-carboxylate (ACC) deaminase, phosphate solubilization, and bioaccumulation or leaching of metals (Yang et al. 2009).

The bacterial strains separated in this study had the ability to produce IAA and solubilize phosphate. The principal consequence of IAA production is the growth stimulation of lateral and adventitious roots which enhances the uptake of nutrients (Golubev et al. 2011). When the ornamental cabbage was inoculated by the bacterial species, significant increases in Pb concentration of root, Cd concentrations of root and shoot, and uptake performances of Pb and Cd in plant biomass were observed (Figs. 3 and 4). Phosphate solubilization, potassium solubilization, IAA and HCN production, and pH reduction traits of the isolated strains lead to mobilization of metals in the soil and increases in concentrations of Pb and Cd in the root and shoot and uptake performances of Pb and Cd in plant biomass. Uptake and translocation of heavy metals may differ significantly and rely upon bacterial species and kind of heavy metals. Different metals to varying degrees show different mobility rates and the mobilization rate of a particular metal could be higher than the other metals within a plant. Previous findings indicate that different groups of rhizospheric microorganisms can increase the Cd uptake of plants (Kartik et al. 2016; Prapagdee and Khonsue 2015; Sangthong et al. 2016; Sheng and Xia 2006; Wu et al. 2006) which was attributed to increased Cd bioavailability in soils and the protection of plants against the inhibitory effects of Cd (Kartik et al. 2016; Sangthong et al. 2016). A similar result was indicated that A. tumefaciens CCNWGS0286, plant growth-promoting bacterium, separated from the nodules of Robinia pseudoacacia growing in zinc-lead mine tailings in Gansu province, China, displayed high resistance to heavy metals and enhanced significantly the dry weight of Robinia plant stems by 14.63%, 23.56%, and 28.07% in the presence of 0, 300, and 600 mg kg−1 zinc, respectively, compared with uninoculated plants (Hao et al. 2012). Enhancement of the root length, shoot length, and root shoot biomass was also shown by Romam-Ponce et al. (Roman-Ponce et al. 2017) while experimenting with the effect of seven rhizobacterial strains (as members of Alcaligenes, Bacillus, Curtobacterium, and Microbacterium) on Brassica nigra seedling growth (Roman-Ponce et al. 2017). A similar type of PGP study was also performed by Lal et al. (2019) working on two rhizobacterial strains Pantoea agglomerance (PC1) and Pseudomonas aeruginosa (SA) and its effect on Zea mays L. that showed a significant increase in seed germination in the presence of Cd2+ and Pb2+ ions (Lal et al. 2019). Wang et al. (2020) reported that Enterobacter TJ6 had a high ability to reduce Cd and Pb uptake of lettuce and concentrations of water-soluble Cd and Pb in soil solution. This bacterium protected lettuce against Cd and Pb toxicity by extracellular adsorption, Cd and Pb immobilization, and increased pH. The effects of heavy metal immobilization by the strain of Enterobacter TJ6 can guarantee vegetable safety in situ for the bioremediation of heavy metal-polluted farmland. Sharma et al. (2020) reported that inoculation of Cajanus cajan plant by Enterobacter sp. C1D reduced the adverse effect of Cd, and various plant growth parameters were significantly increased by bacterial treatment. Al Azad et al. (2020) reported that B. cereus had phenomenal bioaccumulation and metal-tolerant properties and it can clearly be manipulated regarding bioremediation purposes. Jan et al. (2019) reported that inoculation of rice by B. cereus under Cd2+ treatments enhanced plant growth, biomass production, and uptake of micronutrients. They said that B. cereus has the ability to alleviate Cd toxicity and increased phytoremediation efficiency of rice seedling under Cd stress. Li et al. (2019) reported that Rhizobium pusense KG2 had a minimal lethal concentration of 120 mg L−1 for Cd2+. In pot soils containing 50 and 100 mg kg−1 of Cd2+, strain KG2 caused a 45.9 and 35.3% decrease in soybean root Cd content, respectively. Meanwhile, KG2 improved the root and shoot length, nitrogen content, and biomass of soybean plants. Thus, it is concluded that plant inoculation by bacterial species can promote the effectiveness and efficiency of phytoremediation through growth enhancement and protection of plants against heavy metals.

In all treatments, the bioaccumulation factor of Pb was less than one, but that of the Cd was more than one (Fig. 5a). The translocation factors of Pb and Cd were also less than one (Fig. 5b). Ndeda and Manohar (2014) and Balabanova et al. (2015) reported that cadmium has the highest bioaccumulation factor among heavy metals. Similar results for translocation factors of Cd and Pb in cabbage grown in contaminated soils have been reported by other researchers (Hara and Sonoda 1979; Pandey and Sharma 2002; Xian 1989). It has been shown that the concentration of Cd in plants generally decreases in the order: root > leaves > fruits > seeds (Sarma et al. 2006), indicating more accumulation of this metal in the root than in the aerial parts. TF, also called shoot-root quotient, explains the ability of a plant species to translocate heavy metals from roots to shoots and leaves and plants with the TF values > 1 are considered suitable for phytoextraction whereas those with the TF values < 1 are appropriate for the phytostabilization programs (Shi et al. 2011; Wu et al. 2011). Based on the results of this study, the translocation factor of Cd in ornamental cabbage was less than one, but the bioaccumulation factor of Cd was more than one. Considering the higher concentration of the Cd in the roots than in the aerial parts, this plant can be classified as cadmium excluder plant. (Al Azad et al. 2020; Balabanova et al. 2015; Jan et al. 2019; Li et al. 2019; Ndeda and Manohar 2014; Sharma et al. 2020; Wang et al. 2020)

Conclusions

In heavy metal-polluted soils, microbial species have developed different resistance mechanisms to adapt themselves to the stress conditions caused by these metals. According to the results of this study, the long-term effects of pollutants have led to the emergence of resistant bacteria to heavy metals (Pb and Cd) in the study areas. Regarding the results of this study, very distinct behaviors were observed among microbial strains isolated from heavy metal-contaminated soils. Heavy metal-resistant microbial strains which produce IAA and HCN and solubilize phosphate and potassium could be utilized for immobilization and detoxification of heavy metals in contaminated soils and to intensify the phytoremediation process. On the other hand, ornamental cabbage is usually planted from early autumn until late winter. Since most of the plants used for phytoremediation cannot be grown during this time, ornamental cabbage could be as new plant hyperaccumulator and has potential for phytoremediation and utilized during autumn and winter in urban areas, especially around the factories with high levels of Pb and Cd.