1 Introduction

Accumulation of heavy metals in the aquatic ecosystem poses a serious risk to aquatic flora and fauna [31]. The subsequent enrichment via food chains further puts human health at risk [18]. Heavy metals also affect the microbial diversity, growth, morphology by disrupting the cell membrane integrity and denaturation of the cellular proteins, thereby disturbing the aquatic processes mediated by the microbes [22, 42]. Human exposure to heavy metals is associated with diseases such as cancer, damage to the organs, and death [16]. The aquatic environment, along with sediments and soil, plays a major role in biogeochemical cycles, and its pollution leads to disturbance of the ecological balance [17].

The present study focusses on the River Yamuna. The Yamuna River is the most important source of water for the northern parts of India. The River stretch is 48 km in length [6]. Almost 95% of the River water is used as a source of irrigation, remaining is used in the industries and household [11]. Assessment of water quality of the River was done in the study conducted by Bhattacharya et al. [6]. High levels of hazardous metals were found and various drains that emerge into the Yamuna are the main source of pollution. The irrigation through this polluted water leads to heavy metals contamination in crops and soil. Metals such as Pb2+, Cu2+, Cr6+, Ni2+, Cd2+, and Zn2+ were above the permissible limits set by the Food and Agricultural Organisation (FAO). Heavy metals are frequently discharged into the environment via the use of fertilizers, textile industries, pesticides, and irrigation via contaminated water [2]. The River plays a vital role in the local chores of people living in nearby areas. The rapid surge in the population, accompanied by the industrialization has led to river pollution. Although the heavy metals act as enzyme cofactors, most of them are toxic at low concentrations [35].

Concerns over the contamination of the water bodies with heavy metals have led to the development of remediation strategies to reduce the toxicity of the metal in the environment. Physical and chemical methods of remediation produce a large amount of sludge and also are not cost-effective. Over the years, the bioremediation of HM has received considerable importance as the use of microorganisms is eco-friendly and cost-effective and provides a sustainable alternative over the physico-chemical treatments [3, 24]. Microbes have adapted to tolerate the metal stress either by the efflux of metals, complexation, and reduction of metals and use the metals in anaerobic respiration as an electron receptor [30, 32]. Microbial flocculant is used for the removal of Pb2+ ions from the aqueous solution, and the efficiency was reached up to 99.85% [29]. Pseudomonas sp. CH6 and Herbaspirillium sp. CH13 removed 78% of Hg2+ and 66% of Cd2+ from the solution. Alcaligenes faecalis is reported to detoxify Cd2+, Pb2+, and Hg2+. Cd2+ is removed from the supernatants and is accumulated in the pellets of the bacterial cell [13]. Microbes resistant to metals have been isolated from the contaminated sites and studies on the interactions between microbes and heavy metals focus on microbial transformation and conversion of the toxic metal into a less toxic form by reduction [13, 14].

The current scenario demands an effective and eco-friendly approach to tackling heavy metal pollution. In this context, the present study was aimed to isolate and characterize the multi-metal resistant bacterial strain, studying its bioaccumulation characteristics and the use of FTIR and SEM–EDX to reveal the possible biosorption mechanism of the bacterial strain. Briefly, a bacterium isolates having the potential for multiple metal removal has been discussed.

2 Materials and methods

2.1 Preparation of metal stock solution

Stock solutions of 1000 mg/L were prepared by dissolving respective metal salts cadmium nitrate [Cd (NO3)2], potassium dichromate [K2Cr2O7], copper nitrate [Cu (NO3)2], nickel nitrate [Ni(NO3)2], and zinc nitrate [Zn(NO3)2] in double distilled water, and diluted before experimental use. Deionized ultra-pure water (RIONS Ultra 370 series) was used. For all the standards, chemicals were obtained from Merck, Germany.

2.2 Heavy metal assessment in River Yamuna

Cu2+, Cd2+, Cr6+, Ni2+, and Zn2+ were analyzed in Yamuna River water sample (28° 40’ 5.53” N, 77° 15′ 0.35″ E) in post-monsoon (September 2017–December 2017), pre-monsoon (February 2018–June 2018), and monsoon (August 2018) after acid digestion with concentrated nitric acid (65%) in the ratio of 1:10 in a micro wave digester and then filtered through Whatman No. 1 filter paper [15]. Quantification of the samples was done by atomic absorption spectroscopy (AAS) (pg instruments UK).

2.3 Water sample collection and bacterial isolation

Water samples were collected from River Yamuna (28° 40′ 5.53″ N, 77° 15′ 0.35″ E) and stored at 4 °C till further use. The water samples were diluted to 10−10 times in 0.1% phosphate buffered saline (PBS, pH 7.4) and spread plating was done on Luria Broth (LB agar) plates amended with 100 mg/L of the multi-metal mixture containing 20 mg/L each of Cu2+, Cd2+, Cr6+, Ni2+, and Zn2+ and incubated at 28 °C for 48 h. Morphologically distinct colonies that could resist the multi-metal stress were picked up, and the bacterial colonies were purified by repeated streaking and re-streaking. Three distinct colonies were purified and named as MMA, MMA1, and MMA 2 were checked for the metal tolerance at increasing multi-metal concentration.

2.4 Metal tolerance index of the bacteria

The strains were grown in LB at different concentrations of heavy metals ranging from 25 to 300 mg/L along with the control. Metal containing media was inoculated with bacterial strains and was incubated at 28 °C at 150 rpm, and growth was monitored for 5 days after every 24 h. To determine the metal tolerating index of the bacteria, the bacteria were inoculated on the LB agar plates amended with an appropriate amount of 300 mg/L total Cr6+, Cu2+, Ni2+, Zn2+, and Cd2+. The plates were incubated for 3 days at 28 °C. The experiment was done in triplicates. Biotic control was used without metal, and the tolerance index was evaluated by measuring the radius of the colony (in cm) against the biotic control. The radius was calculated by the ratio of the radius of the metal-laden colonies to the radius of untreated colony, i.e., Ti = Rm/Rc, where Ti = tolerance index; Rm = radius of the metal treated colony; Rc = radius of the control colony [10].

2.5 Identification of the isolated strain

2.5.1 Biochemical tests

The biochemical characterization was done using KB003 Hi-Media kit Hi25 for phenotypic characterization of the bacterial strain. 50 μL inoculums of 18- 24 h culture of the bacteria were added and incubated for 24 h. The color change which was observed after 24 h of incubation was accounted for positive or negative result. Bergey’s manual of determinative bacteriology 1989 was used to check the compatibility of the biochemical test and morphological tests with the BLAST results and closest phylogenetic neighbor [23].

2.5.2 Molecular characterization of the strain using 16S rRNA gene sequencing

The universal primers of bacteria 27F (5′-AGAGTTTGATCMTGGCTCAG-3′) and 1492R (5′-TACGGCTACCTTGTTACGACTT-3′) [36] were used for amplification in a thermocycler (Bio-Rad, India). The reaction mixture of 25 μL contained 7 μL of template (50–100 ng), 27F & 1492R 2.5 μL each (0.4 μM), 2 μL dNTPs (200 μM each), 2.5 μL reaction buffer (1X), 0.5 μL Taq polymerase (0.06 μL−1) and the volume was adjusted to 25 μL by nuclease-free water. The PCR protocol followed included initial denaturation at 94 °C for 5 min which is followed by 35 cycles at 94 °C for 30 s, 50 °C for 30 s, 72 °C for 90 s, final extension at 72 °C for 7 min and infinite hold at 4 °C. 1% agarose gel was used to run amplified PCR product and the band of 1.5 Kb was eluted, purified, and sent for commercial sequencing. EZ taxon database was used to know the similarity of the bacterial strains [44], the sequences were aligned using MUSCLE in MEGA X, the tree was constructed by Neighbor-Joining method [34] using Maximum Likelihood model [38] and tree topology was estimated using the Bootstrap value of 1000.

2.6 Bioaccumulation of heavy metals by the bacterial strain

Bioaccumulation studies were performed in 100 mL LB medium inoculated with Alcaligenes sp. MMA incubated at 28 °C at 150 rpm. The medium was amended with 20 mg/L of individual metal. The bioaccumulation experiments were performed according to the permissible metal limits set by the FAO, as well as their occurrence in the river. Each 10 mL sample was aseptically taken from the flask at 24, 48, and 72 h and centrifuged at 9000 rpm for 10 min. The supernatant and pellet were separated, and the supernatant was subjected to digestion 160 ± 4 °C for 20 min analyzed for metal ions via AAS. Abiotic control and biotic controls were also run in parallel. The dry weight of the biomass was measured using the gravimetric method. The mass of pellets was estimated, and contents were filtered on Whatman No. 1 filter paper which was dried before filtration and then weighed followed by drying overnight at 65 °C. The experiment was performed in triplicates. The amount of metal accumulation by the bacterial strain was calculated using the difference between the initial concentration and the concentration remaining in the supernatant. The specific uptake capacity (qm) and uptake yield (%) were calculated.

$${\text{Uptake yield }}\,\left( \% \right)\,{\text{ or}}\, \, \% \,{\text{ metal }}\,{\text{removal}} = \left( {{\text{Total }}\,{\text{metal}}\,{\text{ ion}}\,{\text{ concentration }}{-}{\text{ residual }}\,{\text{metal}}\,{\text{ ion}}\,{\text{ concentration}}} \right)/{\text{Total }}\,{\text{metal}}\,{\text{ ion }}\,{\text{concentration }} \times 100$$
$${\text{Specific }}\,{\text{uptake }}\,{\text{capacity}}\, \, \left( {q_{m} } \right) = {\text{Heavy }}\,{\text{metal}}\,{\text{ removed}}\,{\text{ after }}\,{\text{days }}\left( {{\text{mg}}/{\text{L}}} \right) \, /{\text{ Dried}}\,{\text{ biomass }}\left( {{\text{g}}/{\text{L}}} \right)$$

2.7 Morphological analysis

2.7.1 Scanning electron microscopy energy-dispersive X-ray spectroscopy (SEM–EDX)

To check the alteration in the morphology on the bacterial cell surface after heavy metal stress, cells are grown in the 20 mg/L of Cu2+, Cd2+, Cr6+, Ni2+, and Zn2+ along with abiotic control. After 24 h, the cultures were centrifuged at 10,000 rpm for 5 min and the pellet was washed with PBS (0.1 M) to remove the heavy metal from the suspension. The pellet was fixed with 2.5% glutaraldehyde overnight and then washed three times with PBS (pH 7.2) followed by serial dilution with 30%, 50%, 70%, 90%, and 100% ethanol (Merck) and then given in USIC, Delhi University for SEM analysis. SEM was performed via ZEISS to observe the cell morphology alteration due to the binding of metal ions. The metal ion’s presence on the bacteria was observed via EDX.

2.7.2 Fourier transform infrared spectroscopy (FTIR)

The functional groups responsible for metal uptake were analyzed by FTIR (Thermo Scientific Nikon I 50). Heavy metal concentration 20 mg/L (individual metal and multi-metal) and as well as biotic control were taken into consideration for FTIR. FTIR was done in the range of 650–4000 cm−1. Overnight bacterial cultures amended with individual metals were centrifuged and the pellet was lyophilized, 1 mg of the bacterial pellet was mixed with 100 mg KBr powder, and analyzed using FTIR.

3 Results

3.1 Heavy metal assessment of River Yamuna

The heavy metal assessment was done and the amount of heavy was estimated using AAS in all the three seasons for the year 2017–2018. Table 1 and Fig. 1 show the concentration of metals along with the permissible limit as set by FAO. Ni2+ remains undetected in all three seasons. Cu2+ and Zn2+ were not detected in post-monsoon, whereas it is found within the permissible limit in pre-monsoon and monsoon. Cd2+ was above the permissible limit in all three seasons, Cr6+ except for the post-monsoon was above the permissible limit in pre-monsoon and monsoon. The concentration of Cu2+ was below the permissible limit in the pre-monsoon and monsoon. Zn2+ was also detected under the permissible limits. Cu2+ is not detected post-monsoon which might be due to the dilution of the river water. The major source of Cu2+ is the electroplating industries at Wazirabad near the banks of the river. Cd2+ is above the permissible limit (0.01 ppm) in all the three seasons. Cd2+ contamination is contributed mainly by the industrial processes which use Cd2+ for metal coating and making of batteries of Cd–Ni [6]. Cr6+ was detected in all the three seasons and post-monsoon the concentration was lesser which might be due to the dilution of the river after the monsoon. Cr6+ contamination is attributed mainly to the electroplating industries. In our study, Ni2+ remains undetected in all the seasons in the year 2018, but according to the reports of Bhattacharya et al. [6], the Ni2+ was detected at this in the year 2013. Zn2+ was also detected under the permissible limits, sewage effluents mainly contribute to the presence of Zn2+ in water bodies.

Table 1 Heavy metal assessment of River Yamuna
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Fig. 1
figure 1

Concentration (mg L−1) of HMs in pre monsoon, monsoon and post monsoon in the year (2018)

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3.2 Isolation and maximum tolerance index (TI) of the bacterial isolates

Using the shake flask enrichment method, the bacteria were isolated from the River Yamuna. Initially three bacteria were isolated and named as MMA, MMA1, and MMA2. The maximum tolerance index of the bacterial strains was studied at 300 mg/L concentration of individual metals in the LB agar plates (Fig. 2). The tolerance index was calculated and it was found only bacterial strain MMA was able to grow in the plates amended with 300 mg/L of copper and zinc showed growth and the TI was found to be Cu2+ (0.83 ± 0.025) and Zn2+ (0.67 ± 0.015). The strain showed the lowest toxicity to the Cu2+, followed by Zn2+ and Cd2+, Cr6+, and Ni2+ is extremely toxic to the strain at 300 mg/L, whereas the bacterial strains (MMA1, MMA2) were unable to tolerate the high metal stress (Fig. 1S).

Fig. 2
figure 2

Metal tolerance index of the Alcaligenes sp. MMA

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3.3 Identification of the bacterial isolates

Based on the maximum tolerance index, strain MMA was able to tolerate and survive 300 mg/L concentration of Cu2+ and Zn2+ and was characterized as Alcaligenes sp. MMA using biochemical test and 16S rRNA gene sequencing.

3.3.1 Biochemical test results

For the biochemical tests, the KB003 kits were used, the result is summarized in Table 2.

Table 2 Biochemical test of strain MMA ‘+’ indicates positive (more than 90%), ‘‘indicates negative (more than 90%), ‘V’ indicates (11–89% positive)
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3.3.2 16S rRNA gene sequencing and phylogenetic analysis

Based on 16S rRNA gene sequencing, the strain MMA showed 99.93% similarity with Alcaligenes faecalis strain J481.The phylogenetic tree for Alcaligenes sp. MMA is shown in Fig. 3. GenBank accession numbers for the strains were obtained as MH 973170. The neighbor-Joining Method was used to infer the evolutionary history [34]. Maximum Likelihood Method was used as a model for tree construction. Evolutionary analyses were conducted in MEGA X [38].

Fig. 3
figure 3

Neighbor joining method was used to infer the evolutionary history [34]. Maximum Likelihood Method was used as a model. Evolutionary analyses were conducted in MEGA X [38]

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3.4 Bioaccumulation of heavy metal and effect of heavy metal on the metal uptake by Alcaligenes sp. MMA

Figure 4 shows the metal removal by the Alcaligenes sp. MMA. The maximum metal removal was observed at 20 mg/L for Cu2+(88.45%) followed by Ni2+(82.45%), Zn2+ (69.99%), Cd2+ (63.04%) and least for Cr6+ (48.93%), whereas the biomass trend was not the same as followed by the metal removal, the maximum biomass at the end of 72 h was observed for Ni2+ (4.0 g/L) followed by Cu2+ (2.6 g/L), Cr6+ (0.4 g/L) and Zn2+(0.4 g/L), and least for Cd2+(0.2 g/L), whereas in the biotic control it was 4.6 g/L. The previous studies by Gola et al. [20, 21], also showed that the heavy metal removal by fungi is not directly correlated with biomass production. The biomass was highest in the case of Ni2+ and Cu2+ stress when compared to the biotic control, Cu2+ is less toxic than other heavy metals for the bacterial strain, which is supported by significant metal removal, Cr6+ removal is the least in 72 h. In Cr6+ polluted environment, microbes adapt themselves to have effective systems to neutralize the toxic effects of chromate [28], although it was not observed in the case of Alcaligenes sp. MMA. Biomass produced in the case of Cd2+ is the least, which means Cd2+ is the most toxic out of the five metal for the bacterial strain but the metal removal was least in the case of Cr6+. pH at the end of 72 h was also measured and was found to be 6.5, 6.2, 6.0,5.5, and 5.2, for Cu2+, Ni2+, Zn2+, Cd2+, and Cr6+, respectively. The pH of the growth medium can influence the metal removal, pH controls the metal ion solubility in the medium, along with the functional group speciation present on the cell wall of the bacteria. It can be noted that pH is in the optimum range for the Cu2+ and Ni2+, hence maximum removal is observed. In the case of Cd2+, the pH is low which means more H + ions in the solution which might saturate the bacterial cell wall and generating a positive charge on the cell wall of the bacteria, so there is a repulsive force for the metal cations which are present in the medium, hence low removal can be observed.

Fig. 4
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Metal removal by Alcaligenes sp. MMA in 72 h

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There is no universal trend followed between the growth of bacterial cells in terms of biomass and the removal of metals. This is mainly due to the affinity of the metals to the bacterial biomass which influences the uptake by the bacterial cell. In the biotic control, in the absence of any metal stress, the lag phase was limited to only 2 h and was very short as compared to the 6–8 h in heavy metal stress (Fig. 5). Table 3 shows the biomass, metal removal, and the specific uptake capacity (qm) (mg/g) of the Alcaligenes sp. MMA. Most of the heavy metal removal is seen in the exponential phase. No significant metal removal was observed after 48 h. The specific uptake capacity was also calculated for the strain for different metals. An extended lag phase is observed in the case of Cd2+ and Cr6+stress. The increase in the lag phase is due to the bacterial adaptation to the stress conditions. Cr6+ and Cd2+ being extremely toxic to the bacteria have an extended lag phase of 6–8 h. The lag phase supports the formation of metabolic enzymes to support the growth of the bacteria and its adaptation to the stress medium. The lag phase depends on the morphology of the bacteria, the composition of the media, and the amount of inoculum. The low production of biomass in the case of Cd2+ is due to the slower metabolic activities of the bacteria in the stressed conditions. Cd2+ and Cr6+ are extremely toxic to the bacteria at 20 mg/L.

Fig. 5
figure 5

Growth curve of Alcaligenes sp. MMA in Biotic control and metal stress

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Table 3 Biomass, metal removal, and specific uptake capacity of Alcaligenes sp. MMA in heavy metals stress
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The specific uptake capacity (qm) at 20 mg/L was highest in the case of Cd2+ and least for Cr6+. The uptake of metals can be both on the surface of the bacterial cell or in the solution. It could be either extracellular accumulation/precipitation, intracellular accumulation, and cell surface sorption/precipitation. In the case of bioaccumulation experiments, the supernatant and pellets are separated, the supernatant is subjected to digestion, then followed by AAS, whereas the pellet is subjected to gravimetric analysis [1]. Further, this is dependent on the bacterial cell metabolism if the bacterial cell in the presence of heavy metals stress produces certain compounds which favor the precipitation reaction. Biosorption is used extensively in recent years for heavy metals removal. Bacteria and algae have been used as biosorbents. In the case of multi-metals, adsorption of different metals on the surface of the adsorbent takes place simultaneously. In the environment and industries, heavy metals co-exist in the same place, therefore the microbes can survive and tolerate the different metal mixture [9]. The removal of multi-metal by single species biomass depends on the concentration and number of metals competing for binding to the active site [7]. Biosorption technology can be used in a pilot scale. At the industrial level, various bioreactors have been designed for the removal of heavy metals. The packed bed column was used to treat the wastewater using the olive tree pruning. This is effective in the treatment of heavy metals at a low cost. Packed bed column was used with an increased flow rate, decreased breakthrough time, exhaustion time, and the removal efficiency of nearly 99% was achieved [27, 33]. Biosorption can also be used for the recovery and recycling of heavy metals. Prior to the recovery of heavy metals from aqueous solution, the individual metal ions must get separated from the solution. Zoogloea ramigera, a bacterium found mainly in activated sludge can be used as a biosorbent for elution of metals. Ni2+ and Cd2+ can be adsorbed using HCl and citrate solution [41]. Tang et al. [39] showed the recovery of Pb2+ from wastewater using precipitation and biosorption. Modified sugarcane bagasse is used for the selective adsorption of Pb2+ from a mixture of solution containing Zn2+, Ca2+, Pb2+, Cd2+, Na+, and K+. For the desorption of Pb2+, HNO3 was used with 98% recovery, and Na3PO4 was used as a most efficient precipitant [39]. Ali et al. [4], reviewed the magnetotactic bacteria efficiency to bind metals. The nanosized magnetosomes (magnetite crystals) aids in biosorption by providing them with the ability to move along the externally applied magnetic field. The sorption is reversible and fast [4]. Vishan et al. [40] showed that the dried biomass of Bacillus badius AK can be used as a biosorbent for the recovery and removal of Cd2+ from aqueous solutions under optimum conditions. In this study, the desorption of the metal was carried out, regeneration of the biosorbent was done by washing with distilled water, followed by another cycle of biosorption. Different desorbents such as HCl, CH3COOH, EDTA, and H2SO4 can be used. The biosrorbent becomes loaded with metal, and the attached metal can be recovered for re-using the biomass [25, 40]. Nanoparticles that are synthesized from the plants and microbes aids in metal removal by the process of bioremediation via adsorption, redox reaction, and photo-catalysis. Dendrimers, metal nanoparticles, carbon nanotube (CNT) can be employed as nanoparticles for the remediation of wastewater [37].

3.5 Morphological results

3.5.1 SEM–EDX

The SEM images showed a change in the morphology of metal-laden cells as compared to the control. The bacterial cells in control appeared uniform in shape, clear, and loosely packed having smooth outer surfaces but after biosorption of Cd2+ and Cr6+, there is a clear deformation in the bacterial cell wall, were densely packed with a lot of aggregation and roughness (Fig. 6). The possible reason for the roughness and wrinkling of the cells could be due to sequestration and precipitation of the functional groups [12]. The shape of the Alcaligenes in Zn2+ laden cells was preserved. In Cu2+ stress, the bacterial cell shows the accumulation of the heavy metal at the periphery, whereas in Ni2+ stress the accumulation was seen along with the deformation of the bacterial cell wall [43]. The SEM images show that metal ions induce a severe change in the morphology of the bacterial cell along with the toxicity. Similar results were obtained for Burkholderia sp. by Wei-Hua et al., 2009. In control, the integrity of the bacterial cell wall is maintained; however, a clear deformation is observed in the bacterial cell in stress conditions. The aggregation of the bacterial cells might be in response to heavy metal stress. Reports by Chakravarty and Banerjee [8] also showed the irregular electron-dense area and overlapping of the bacterial cells. Zn2+ has lesser or almost no effect on bacterial cell morphology which is also supported by the reports of Chakravarty and Banerjee. Zn2+ laden cell shows lesser aggregation and the cell shape was preserved, however, in the Cu2+ stress, there is heavy metal accumulation at the periphery whereas in Ni2+ stress, the deformation of the bacterial cell wall is seen along with the accumulation at the periphery,, [43]. The aggregation of the bacterial cells is due to the bacterial stress response, to decrease the surface area for the accumulation of the metals. The entomopathogenic fungi Beauveria bassiana showed the aggregation and shortening of hyphae in Pb2+laden cells [21]. EDX graph of bacterial biomass further confirms the presence of the metals on the bacterial cell surface (Fig. 7). The alkali earth metals peaks were also observed along with the metal peaks (Cu2+, Cd2+, Cr6+, Ni2+, and Zn2+). The significant peaks of Cu2+, Cd2+, Cr6+, Ni2+, and Zn2+are shown in Fig. 7.

Fig. 6
figure 6

Scanning electron micrographs of Alcaligenes sp. MMA in a metal absence (biotic control). b–f at 20 mg L−1 of Cu (II), Cd (II), Cr(VI), Ni (II) and Zn (II). Scale 1 μm

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Fig. 7
figure 7figure 7

EDX micrograph confirming the presence of the metals

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3.5.2 FTIR

The FTIR spectra both in the control as well as in the presence of heavy metal were obtained in the range of 500–4000 cm−1. FTIR spectra identify the functional groups present on the surface of bacteria and their interaction with the heavy metals (Fig. 8). The spectra of control biomass and metal-laden cells show a prominent peak at 3407 cm−1 pertaining to COOH and OH group, amines and amides, At 2924.7 cm−1, the intensities of the peak of Cd2+ and Cr6+ is low, this might be due to the low concentration of the active bond, i.e,. the functional group present, and the different vibrations of the functional groups in the molecule give rise to bands of differing intensity. The peak corresponds to CAH stretching. As compared to control, in the metal-laden cells especially in the Cd2+ and Cr6+ laden cells, shifting of the peaks was observed. A new peak is observed in the range of 2100–2200 cm−1, corresponding to C=N in Cr6+ laden cells. The shift in the peak corresponding to the S–C bond around 500–700 cm−1 is observed in metal-laden cells. The presence of new peaks was observed along with shifting and masking of functional groups ,i.e., amines, alkanes alkyl halides. Studies performed by Bahari et al. [5], Giri et al. [19] for Bacillus cereus cells when treated with arsenite and Escherichia coli cells exposed to Cd2+, Cr6+, Ni2+, and Fe3+ also showed -OH group complexation with the metal ions [26]. The result indicates that the hydroxyl, carboxyl, and amide are the dominant groups which are involved in biosorption.

Fig. 8
figure 8

FT-IR spectra showing the absorbance of the bacterial biomass in the absence of metal and in metal laden cells (20 mg L−1)

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4 Conclusion

Increased industrialization has contributed mainly to the pollution of metals. The recalcitrance of these compounds leads to their accumulation in the environment. The industrial discharge of the heavy metals directly into the water bodies results in their entry into the food chain. The use of this water directly for irrigational purposes leads to the contamination of the crops with heavy metals. The present study aimed to investigate the multi-metal resistant bacterial strain, present in the Yamuna River, its characterization and to study the bioaccumulation potential of the bacterial strain. SEM and FTIR studies were done for studying the morphological changes induced upon metal stress. This study establishes multiple heavy metals removal by Alcaligenes sp. The bioaccumulation of the heavy metals by the bacterial strain was seen and the metal removal was in the range of (44–88%). The effect of heavy metal was seen on the metal uptake by Alcaligenes sp. MMA. FTIR and SEM investigations further reveal the morphological changes induced by heavy metals. Cr6+ induces severe toxicity to the Alcaligenes sp. MMA and is also removed the least by the bacterial strain MMA. Along with Cr6+, Cd2+ also exerts toxicity to the Alcaligenes sp. the morphology of the bacterial cell is not uniform and the cell wall disruption is seen clearly, similarly in Cd2+ and Cr6+ laden cells a depression in the amide peak was seen in FTIR. The assessment of the River Yamuna was carried out which shows the Cd2+ and Cr6+ is present above the permissible limit as laid down by FAO, whereas the Cu2+ and Zn2+ were detected within the permissible limits and Ni2+ remains undetected in the three seasons. Further study should focus on the whole-cell protein extraction of bacterial cells for studying the differential expression of genes under metal stress. Pilot-scale applications of biosorption are already under consideration for heavy metal removal. Emerging technologies such as the use of biologically synthesized nanomaterials for heavy metal removal should be considered. Biosorption is a sustainable and promising technology, which makes the reuse of heavy metal feasible.