Isolation and molecular characterization of the indigenous Staphylococcus aureus strain K1 with the ability to reduce hexavalent chromium for its application in bioremediation of metal-contaminated sites

Introduction

Chromium is of great economic importance for its uses in different industries for various applications such as textile dyeing, wood preservation, pulp and paper manufacturing, tanning and chrome plating (Viti & Giovannetti, 2007). However, it is also becoming a major pollutant due to its untreated and uncontrolled discharge in industrial effluent in developed as well as in developing countries like Pakistan (Velma, Vutukuru & Tchounwou, 2009; Khan et al., 2015; Fatima & Ahmed, 2018). According to estimates, more than 170 thousand tons per annum of chromium waste are being discharged globally into environments due to various anthropogenic activities, thus causing severe environmental pollution and human health problems. In aquatic environment, chromium is found either chromium (III) or chromium (VI) (Kaur, Kumar & Kaur, 2014). Trivalent chromium (Cr⁺³) is least toxic as it got precipitated whereas chromate (Cr⁺⁶) is the most toxic form of chromium being released into environment by industrial effluents because of its strong oxidizing power and higher membrane transport (Viti et al., 2014). Chromate is actively transported across cell membranes both in prokaryotes and eukaryotes (Cervantes et al., 2001). Sulfate uptake pathways were reported to be involved in transport of chromate across biological membranes (Ramírez-Díaz et al., 2008) in bacteria such as Salmonella typhimurium, Escherichia coli, Pseudomonas fluorescens and Alcaligenes eutrophus (Cervantes et al., 2001). This is due to the fact that chromate is mainly found in the oxyanion form (i.e., CrO₂Q) and, thus cannot be trapped by the anionic components of cell membrane (Volesky & Holan, 1995). Once it enters the cell, it may cause asthma, cancer, allergic reactions, nervous and cardiovascular disorders and organ failure (Gupta & Kumar, 2012). According to different environmental protection agencies, removal of chromium from industrial discharge is pre-requisite before its final dispersal to surface water bodies (Viti et al., 2014).

The proper treatment of wastewater effluent not only fulfills the demands for agricultural irrigation but also minimizes the environmental pollution and protects the public health (Al-Jasser, 2011). However, industrial wastewater treatment is a well-developed engineering science requiring several techniques and processes to efficiently treat the wastewater (Asano & Levine, 1996). Like other developing countries, hardly a few percent (<8%) of wastewater is effectively treated in Pakistan (Martin et al., 2006), while rest is directly discharged into surface water bodies without undergoing any sort of treatment (Reinsch & Pearce, 2005).

In developed countries, various physiochemical processes such as filtration, electrochemical application, ion exchange, evaporation, chemical precipitation, oxidation, reduction, and reverse osmosis, have been used for removal of toxic metals from environment (Hassan et al., 2017). These methods are not only expensive but also release other harmful byproducts leading to environment pollution (Ahluwalia & Goyal, 2007). On the other hand, bioremediation is gaining attention as an alternative remediation technique due to its inexpensive and environment friendly nature (Kothe, Bergmann & Büchel, 2005), and, also save the extra cost of secondary pollution removal.

Bioremediation of wastewater using metal resistant bacteria could be considered as cost-effective and environmentally benign approach. This is due to the premise that these bacteria are in continuous contact with wastewater containing toxic metals since years; therefore, they have already adapted these extreme environmental conditions. Additionally, these extreme environments could provide novel bacteria that could be resistant to elevated concentrations of toxic metals. These bacteria could be used for bioremediation of contaminated wastewater being discharged into surface water bodies. Therefore, this study was carried out to investigate the presence of chromium tolerant bacteria in industrial effluent for its subsequent applications in environmental remediation practices.

Materials & Methods

Collection of wastewater samples

Wastewater samples (n = 6) were collected from discharge points of different industries located in industrial state of Kala Shah Kaku (KSK) near Lahore city, Pakistan (Fig. 1). Sampling bottles (250 ml) were washed with dilute nitric acid, rinsed with de-ionized water and again washed three times with the wastewater as described previously (Zhang et al., 2013). These samples were stored in icebox (at 4 °C) and transported to laboratory for further analyses.

Results

Biochemical, physiological and molecular identification of isolate K1

The isolate appeared to be coccus shaped (≈1 μm), gram-positive, catalase positive, oxidase and coagulase negative (Table 1). To further clarify the relationship between isolate K1 and S. aureus, BioMériux VITEK®2 system (GP card) was used for identification of isolate K1. Data obtained suggested that isolate K1 shared 37 out of 43 carbon sources with that of type strain Staphylococcus aureus ATCC 6538 whereas it differs in 6 carbon sources. Among them, bacterial isolate K1 used beta-galactosidase and lactose during growth, which were not used by Staphylococcus aureus ATCC 6538. On the other hand, Staphylococcus aureus ATCC 6538 assimilated α-glucosidase, D-maltose, and methyl-β-D-glucopyranoside as carbon sources for its growth that were not used by isolate K1. These results emphasized that bacterium K1, even after exhibiting significant differences from known strains, was closely related to Staphylococcus aureus and thus identified as Staphylococcus aureus strain K1. The BLASTn analysis applied to 16S rDNA gene sequence of Staphylococcus aureus K1 revealed that it was closely related (99% similarity) to Staphylococcus aureus strain NBRC 100910 and Staphylococcus aureus strain ATCC 12600. Phylogenetic analysis of 16S rDNA sequences that were retrieved from GenBank confirmed that isolate Staphylococcus aureus K1 appeared to be closely related to Staphylococcus aureus (Fig. 2).

Table 1:

Comparative morphological and biochemical characteristics of Staphylococcus aureus strain K1 and Staphylococcus aureus ATCC strain 6538 using VITEK-2 Systems.

Characters	Mnemonic	Staphylococcus aureus K1	Staphylococcus aureus ATCC 6538
		Morphological characteristics
Morphology		Round, Convex	Round, Convex
Color		Golden yellow	Golden yellow
Gram-reaction		Positive	Positive
Catalase		Positive	Positive
Coagulase plasma reaction		Negative	Positive
		Biochemical characteristics
D-Amygdalin	AMY	−	−
Phosphatidylinositol phospholipase C	PIPLC	−	−
D-xylose	dXYL	−	−
Arginine dihydrolase I	ADH 1	+	+
Beta-Galactosidase	BGAL	+	−
Alpha-Glucosidase	AGLU	−	+
Ala-Phe-Pro Arylamidase	APPA	−	−
Cyclodextrin	CDEX	−	−
L-Aspartate Arylamidase	AspA	−	−
Beta-Galactopyranosidase	BGAR	−	−
Alpha-Mannosidase	AMAN	−	−
Phosphatase	PHOS	+	+
Leucine ARYLAMIDASE	LeuA	+	+
L-Proline ARYLAMIDASE	ProA	−	−
BETA GLUCURONIDASE	BGURr	−	−
ALPHA-GALACTOSIDASE	AGAL	−	−
L-Pyrrolidonyl-ARYLAMIDASE	PyrA	+	+
BETA-GLUCURONIDASE	BGUR	−	−
Alanine ARYLAMIDASE	AlaA	−	−
Tyrosine ARYLAMIDASE	TyrA	−	−
D-SORBITOL	dSOR	−	−
UREASE	URE	−	−
POLYMIXIN B RESISTANCE	POLYB	+	+
D-GALACTOSE	dGAL	+	+
D-RIBOSE	dRIB	−	−
L-LACTATE alkalinization	ILATk	+	+
LACTOSE	LAC	+	−
N-ACETYL-D-GLUCOSAMINE	NAG	+	+
D-MALTOSE	dMAL	−	+
BACITRACIN RESISTANCE	BACI	+	+
NOVOBIOCIN RESISTANCE	NOVO	−	+
GROWTH IN 6.5% Nacl	NC6.5	+	+
D-MANNITOL	dMAN	+	+
D-MANNOSE	dMNE	+	+
METHYL-B-D-GLUCOPYRANOSIDE	MBdG	−	+
PULLULAN	PUL	−	−
D-RAFFINOSE	dRAF	−	−
O/129 RESISTANCE (comp.vibrio)	O129R	+	+
SALICIN	SAL	−	−
SACCHAROSE/SUCROSE	SAC	+	+
D-TREHALOSE	dTRE	+	+
ARGININE DIHYDrolase 2	ADH2s	+	+
OPTOCHIN RESISTANCE	OPTO	+	+

DOI: 10.7717/peerj.7726/table-1

Determination of minimum inhibitory concentration for hexavalent chromium

Although the growth of bacterium K1 seemed to be uninhibited by presence of chromium, but it exhibited much slower growth rate in the presence of metal (Cr⁶⁺) as reported in Fig. 3. Additionally, in the absence of metal (Cr⁶⁺), exponential growth of bacterium lasted for about 8 h whereas no such growth was observed when chromium was present in culture medium (Fig. 3). Furthermore, Staphylococcus aureus K1 showed visible growth in Tryptic Soy Broth (TSB) medium containing chromium (hexavalent) with no significant inhibition (although growth rate was reduced) in bacterial growth up to maximum 22 mM Cr⁶⁺ as depicted in Fig. 4. Moreover, minimum inhibitory concentration of other metals such as lead, copper, zinc, manganese, cobalt, mercury and silver against S. aureus K1 was in following order i.e., Co²⁺: 18 mM; Zn²⁺: 15 mM; Pb²⁺: 10 mM; Mn²⁺: 8 mM; Ag²⁺: 5 mM; Cu²⁺: 3 mM; Hg²⁺: 1 mM.

Effect of contact time (hours) on reduction of chromium (Cr⁶⁺) by Staphylococcus aureus strain K1

The most important factors that can affect the various physiological processes of growing bacterium include temperature, pH, and salt concentration (0.5% NaCl). Optimum values for these factors were also evaluated for S. aureus strain K1. It was observed that S. aureus strain K1 exhibited maximum growth at 35 °C and pH 8. Under optimum growth conditions, biosorption (metal removal) capacity of strain K1 in the presence of chromium (hexavalent) increased with increasing the contact period (Fig. 5). It was observed that Staphylococcus aureus K1 removed about 26%, 45%, 71%, 80% and 99% Cr⁶⁺ (1 mM) from the medium after 2, 4, 8, 16 and 24 h, respectively (Fig. 5).

FTIR analysis of bacterium S. aureus strain K1

Significant differences were observed in the overall infrared spectrum of cells with and without chromium treatment. IR spectrum of S. aureus K1 cells with chromium (1 mM) and without chromium were studied in the range of 500–4,000 cm⁻¹ that reflected the different absorption and stretching peaks validating the complex interactive nature of cellular surface (Fig. 6). In addition, the functional groups, involved in chromium sorption, were ionizable including carboxyl, hydroxyl groups and amino groups (Fig. 6).

Discussion

From the results, it was evident that metal tolerant bacteria can be isolated from metal polluted sites. As in this study, we have isolated and characterized an indigenous Staphylococcus aureus strain K1 from metal polluted environment that can tolerate up to 22 mM of Cr⁶⁺. Several studies had reported the similar results in which metal tolerant bacteria were isolated from metal contaminated habitats (Shakoori, Makhdoom & Haq, 2000; Camargo et al., 2003; Viti, Pace & Giovannetti, 2003; Thacker et al., 2006; Wang et al., 2010; Alam & Ahmad, 2011; Zhang et al., 2013; Khan et al., 2015; Oaikhena et al., 2016). Our results also corroborated the findings of Mustapha & Halimoon (2015) who isolated 21 bacteria from electroplating industry and reported only five of them to be chromium tolerant (up to 50 mg/L). However the growth rate of bacterial isolates in the presence of toxic metal was slow as already reported in various studies around the globe (Basu, Bhattacharya & Paul, 1997; Shakoori, Makhdoom & Haq, 2000; Zhang et al., 2013; Ahemad, 2014). The reason for much slower growth rate in our case could be attributed to elevated chromium concentrations (22 mM) whereas other researcher had used lower levels (2 mM) of Cr⁶⁺ (Zhang et al., 2013). Similarly, use of nutrient rich medium for bacterial growth could also undermine the toxic effects of metal(s) on bacterial growth. For example, Thacker & Madamwar (2005) evaluated the effect of various concentrations of metal on bacterial growth using nutrient rich culture media having tryptone and yeast extract. Under such conditions, chromium (Cr⁶⁺) could form complex with organic compounds (present in nutrient medium), which in result could undermine the toxic effects of chromium, becoming less effective against microbial metabolism (Caravelli, Giannuzzi & Zaritzky, 2008).

Although, degree of tolerance to different metals (Cr, Co, Zn, Pb, Mn, Ag, Cu, Hg) might vary according to bacterial genotype, type of metal; nature of metal and pH of culture media (Zhang et al., 2013). Such resistance to toxic metals might be attributed to other possible mechanisms such as ion exclusion, bioaccumulation of metal by microbes and production of low molecular weight binding proteins (Nies, 1999; Das, Dash & Chakraborty, 2016).

As far as resistance to antibiotics was concerned, it was found that the isolate K1 was sensitive to majority of antibiotics tested. These findings corroborated the results of other researchers who reported that non-pathogenic but metal tolerant bacterial isolates belonging to Serratia species were more susceptible to antibiotics (Ajithkumar, 2003; Jafarzade et al., 2012). Similarly, Shakoori et al. (2010) stated that arsenic-resistant Bacillus anthracis and Citrobacter freundii were found sensitive to tetracycline, kanamycin, erythromycin and nalidixic acid while Klebsiella oxytoca was found resistant to all of these antibiotics. Others observed that Bacillus species exhibited sensitivity to streptomycin, tetracycline, chloramphenicol, norfloxacin, neomycin, rifampicin, nalidixic acid and cotrimoxazole, while being resistant to kanamycin, ampicillin and methicillin (Samanta et al., 2017). These results were also in line with reports from Abakiliki (Ikeagwu, Amadi & Iroha, 2008) suggesting that Staphylococcus aureus was sensitive to ofloxacin and gentamicin. Although Staphylococcus aureus K1 was resistant to ceftazidime, aztreonam and nalidixic acid that could be related to occurrence of genes responsible for heavy metal and antibiotic resistance together (Silver, 1988).

Staphylococcus aureus strain K1 was an efficient reducer of hexavalent chromium as depicted in Fig. 5. The removal percentage of chromium (Cr⁶⁺) was much more higher than previously reported values for Cr⁶⁺ removal by other Staphylococcus species (Shakoori et al., 2010; Zhang et al., 2013) and other bacteria (Li & Krumholz, 2009). Microbial reduction of chromium ion can be either extracellular or intracellular (Campos, Martinez-Pacheco & Cervantes, 1995; Ackerley et al., 2004; Li & Krumholz, 2009) that could undergo through biotransformation (in which Cr⁶⁺ is reduced to Cr³⁺ through microbial enzymatic processes) and/or by biosorption (metallic ions get adsorbed on cellular surfaces) (Cheung & Gu, 2003; Desjardin et al., 2003). These processes can be employed not only for the physical removal of metal (chromium) as precipitate (Cr(OH)₃) but also can be helpful for decreasing the toxic effects of such metallic ions (Cheung & Gu, 2003). Hence Staphylococcus aureus K1 was an excellent reducer of chromium ion, it could be a potential candidate for bioremediation of chromium in that area as it could reduce nearly all of chromium present in medium after 24 h.

This rapid reduction of hexavalent chromium could be ascribed to surface binding due to the presence of different functional groups on cell wall and interior penetration (bioaccumulation) as reported previously (Rehman, Shakoori & Shakoori, 2006; Khan et al., 2015; Bingöl, Özmal & Akın, 2017; Long et al., 2017; Zhenggang et al., 2018). It was observed that the peaks attributed for amide linkages appearing at 1,620 and 1,526 cm⁻¹were shifted respectively to 1,625 and 1,521 cm⁻¹ on adsorption of chromium (Mungasavalli, Viraraghavan & Jin, 2007; Park, Yun & Park, 2005). The suppression and shift in peak intensity ranging 1,000–1,320 cm⁻¹, denoting the presence of phosphorous and carbon containing oxygen atoms, indicated their interaction with Cr⁺⁶ (Das & Guha, 2007). It seems that the bacterial cells have undergone the oxidation during biosorption of chromium that has resulted into changes in overall IR spectrum (Park, Yun & Park, 2005; Long et al., 2017). These functional groups have previously been reported to interact with metal ions (cations) (Bueno et al., 2008). In fact, metal ion could form coordination bonding with peptide bond with either of amino or carboxyl groups, or nitrogen and/ or oxygen (Pandi, Shashirekha & Swamy, 2009). In current study, shift in wavenumber from 3,271 to 3,267 cm⁻¹ of secondary amide was because of stretching of N-H group in the secondary-amide proteins representing the participation of membrane proteins in chromium binding (Abhay, Rawat & Singh, 2016). Our results reaffirmed the findings of (Mungasavalli, Viraraghavan & Jin, 2007), who assumed that amino groups could have leading role in chromium binding with cell membrane, as they were main constituents of protein, carbohydrates and hexosamines present in cell membrane. Furthermore, similar altered FTIR spectra was also observed for chromium-treated cyanobacteria, suggesting that formation of chromium complex with membrane protein (Pandi, Shashirekha & Swamy, 2009). These changes in FTIR spectrum of S. aureus strain K1 were indicative of the metal bonding processes that had taken place on bacterial surface with different functional groups (Bueno et al., 2008).

Conclusions

According to biochemical and molecular characterization, this bacterium belongs to genus Staphylococcus and sub-species aureus strain K1. It was able to grow in metal concentration up to 22 mM of Cr⁶⁺ and could remove 99% chromium (1 mM Cr⁶⁺) after 24 h under optimum growth conditions. On the basis of FTIR spectra, it can be deduced that carboxyl, amino and phosphate groups were involved in complexation with chromium. In addition, Staphylococcus aureus K1 was sensitive to different antibiotics and therefore can be used for bioremediation of contaminated wastewater and soils. Furthermore, this bacterium K1 could likely have competitive advantage over autochthonous or exogenous strains if utilized for bioremediation and could play a significant part in the bioremediation of chromium-contaminated environments.

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